PATENT ABSTRACT
The invention relates to the polynucleotide sequence of a nontypeable strain of  Haemophilus influenza  (NTHi) and polypeptides encoded by the polynucleotides and uses thereof. The invention also relates to NTHi genes which are upregulated during or in response to NTHi infection of the middle ear and/or the nasopharynx.

PATENT DESCRIPTION
[0001]    This application claims priority to U.S. Provisional Application No. 60/691,214, filed Jun. 16, 2005 and U.S. patent application Ser. No. 10/795,159 filed Mar. 5, 2004, which claims priority to U.S. Provisional Application No. 60/453,134 filed Mar. 6, 2003, all of which are incorporated by reference herein in its entirety. 
     
    
     FIELD OF INVENTION 
       [0002]    The invention relates to the polynucleotide sequence of a nontypeable strain of  Haemophilus influenzae  (NTHi) genome, NTHi genes contained within the genome and polyp eptides encoded by the polynucleotides. The invention also relates to uses of these NTHi polynucleotides and NTHi polypeptides including vaccines and methods of treating and preventing NTHi related disorders. The invention also relates to NTHi genes which are upregulated during or in response to NTHi infection of the middle ear or nasopharynx. 
       BACKGROUND 
       [0003]    Otitis media (OM) is a highly prevalent pediatric disease worldwide and is the primary cause for emergency room visits by children (Infante-Rivand and Fernandez,  Epidemiol. Rev.,  15: 444-465, 1993). Recent statistics indicate that 24.5 million physician office visits were made for OM in 1990, representing a greater than 200% increase over those reported in the 1980&#39;s. While rarely associated with mortality any longer, the morbidity associated with OM is significant. Hearing loss is a common problem associated with this disease, often times affecting a child&#39;s behavior, education and development of language skills (Baldwin,  Am. J. Otol.,  14: 601-604, 1993; Hunter et al.,  Ann. Otol. Rhinol. Laryngol. Suppl.,  163: 59-61, 1994; Teele et al.,  J. Infect. Dis.,  162: 685-694, 1990). The socioeconomic impact of OM is also great, with direct and indirect costs of diagnosing and managing OM exceeding $5 billion annually in the U.S. alone (Kaplan et al.,  Pediatr. Infect. Dis.  16: S9-11, 1997). 
         [0004]    Whereas antibiotic therapy is common and the surgical placement of tympanostomy tubes has been successful in terms of draining effusions, clearing infection and relieving pain associated with the accumulation of fluids in the middle ear, the emergence of multiple antibiotic-resistant bacteria and the invasive nature associated with tube placement, has illuminated the need for more effective and accepted approaches to the management and preferably, the prevention of OM. Surgical management of chronic OM involves the insertion of tympanostomy tubes through the tympanic membrane while a child is under general anesthesia. While this procedure is commonplace (prevalence rates are ˜13%; Bright et al.,  Am. J. Public Health,  83(7): 1026-8, 1993) and is highly effective in terms of relieving painful symptoms by draining the middle ear of accumulated fluids, it too has met with criticism due to the invasive nature of the procedure and its incumbent risks (Berman et al.,  Pediatrics,  93(3):353-63, 1994; Bright et al., supra.; Cimons,  ASM News,  60: 527-528; Paap,  Ann. Pharmacother.,  30(11): 1291-7, 1996). 
         [0005]    Progress in vaccine development is most advanced for  Streptococcus pneumoniae , the primary causative agent of acute OM (AOM), as evidenced by the recent approval and release of a seven-valent capsular-conjugate vaccine, PREVNAR® (Eskola and Kilpi,  Pedriatr. Infect. Dis. J.  16: S72-78, 2000). While PREVNAR® has been highly efficacious for invasive pneumococcal disease, coverage for OM has been disappointing (6-8%) with reports of an increased number of OM cases due to serotypes not included in the vaccine (Black et al.,  Pedriatr. Infect. Dis.,  19: 187-195; Eskola et al.,  Pedriatr. Infect. Dis  1, 19: S72-78, 2000; Eskola et al.,  N. Engl. J. Med.  344: 403-409, 2001; Snow et al.,  Otol. Neurotol.,  23: 1-2, 2002). Less progress has been made for non-typeable  Haemophilus influenzae  (NTHi), the gram-negative pathogen that predominates in chronic OM with effusion (Klein,  Pedriatr. Infect. Dis J.,  16: S5-8, 1997; Spinola et al.,  J. Infect. Dis.,  154: 100-109, 1986). Hampering development of effective vaccines against NTHi, is the currently incomplete understanding of the pathogenesis of NTHi-induced middle ear disease. Contributing to this delay is a lack of understanding of the dynamic interplay between microbe-expressed virulence factors and the host&#39;s immune response as the disease progresses from one of host immunological tolerance of a benign nasopharyngeal commensal, to that of an active defensive reaction to an opportunistic invader of the normally sterile middle ear space. 
         [0006]    Although strain Rd is the exemplar organism for the current small genome sequencing rationale, and an important model organism for studying  H. influenzae  biology, strain Rd is a poor model for the study of pathogenicity caused by members of the genus  Haemophilus . Serotype b strains of  H. influenzae  cause invasive diseases, for example meningitis, and nontypeable  H. influenzae  (NTHi) strains principally have a role in localized respiratory disease, particularly in otitis media (OM), acute sinusitis, community acquired pneumonia and have important consequences in patients with chronic obstructive pulmonary disease or cystic fibrosis (Kilpi et al.,  Pediatr Infect Dis J  20:654-62, 2001; Murphy,  Curr Opin Infect Dis  16:129-34, 2003; Roman et al.,  J Clin Microbial  42:1450-9, 2004; Sethi, Clin Microbiol Rev 14:336-63, 2001; St Geme,  Vaccine  19 Suppl 1:S41-50, 2000). Strain Rd, however, is a derivative of a serotype d strain. Serotype d strains are rarely associated with disease (Daines et at, J Med Microbiol 52:277-82 2003; Heath et al., Pediatr Infect Dis J 20:300-5, 2001; Rodriguez et al., Infect Immun 71:1635-42, 2003, Skoczynska et al., J Clin Microbiol 43:938-41, 2005). Because one of the most useful sets of data in the study of an organism&#39;s biology is its genomic sequence, a number of investigations have identified and characterized genes found in  H. influenzae  type b strains,  H. influenzae  Biogroup  Aegyptius  strains or in nontypeable strains that are not present in strain Rd (Bergman et al., Infect Immun 71:1098-108, 2003; Chang et al., Infect Immun 68:2630-7, 2000; Erdos et al., Int J Pediatr Otorhinolaryngol 67:749-55. 2003; Li et al., Mol Microbiol 47:1101-11, 2003; McMichael &amp; Green, Curr Opin Investig Drugs 4:953-8, 2003; Pomposiello &amp; Demple, 2001; Smoot et al., Infect Immun 70:2694-9, 2002). 
         [0007]    Currently there is a poor understanding of how NTHi causes OM in children. The identification of putative virulence factors necessary for induction of OM will contribute significantly to the understanding of the host-pathogen interaction and ultimately, the identification of potential vaccine candidates and targets of chemotherapy. There is a tremendous need to develop more effective and accepted approaches to the management and preferably, the prevention of otitis media. Vaccine development is a very promising and cost effective method to accomplish this goal (Giebank,  Pedriatr. Infect. Dis J.,  13(11): 1064-8, 1994: Karma et al.,  Int. J. Pedritr. Otorhinolaryngol.,  32(Suppl.): S127-34, 1995). 
       SUMMARY OF INVENTION 
       [0008]    The present invention provides for the identification and characterization of the genomic sequence of NTHi  H. influenzae  strain 86-028NP and the polypeptide sequences encoded thereby. The 3-fold analysis of the NTHi genomic sequence is set out in a series of contig sequences denoted as SEQ ID NO: 1-576, and the subsequent 8-fold analysis of the genomic sequence is set out in a series of 11 contig sequences denoted as SEQ ID NOS: 675-685. These contigs are raw data and one of skill in the art may assemble these contigs by comparing overlapping sequences to construct the complete genome of the NTHi stain 86-028NP using routine methods. 
         [0009]    The complete and annotated genome of NTHi strain 86-028NP is set out as SEQ ID NO: 772. The open reading frames are set in Table 6 as SEQ ID NOS: 773-2593. The amino acid sequence of the resulting gene products are set out as SEQ ID NOS: 2594-4414. The genome is approximately 1.91 kb in size, slightly larger than the strain Rd genome. A number of regions of gross genome rearrangement relative to the strain Rd genome have been identified as well as a number of genes unique to strain 86-028NP. 
         [0010]    The present invention also provides for antibodies specific for the NTHi polypeptides of the invention. Methods of detecting NTHi bacteria in a human or in sample, such as serum, sputum, ear fluid, blood, urine, lymphatic fluid and cerebrospinal fluid are contemplated. These methods include detecting NTHi polynucleotides with specific polynucleotide probes or detecting NTHi polypeptides with specific antibodies. The invention also contemplates diagnostic kits which utilize these methods of detecting NTHi bacteria. 
         [0011]    The present invention also contemplates methods of eliciting an immune response by administering a NTHi polypeptide of the invention or a NTHi peptide thereof. These methods include administering the NTHi polypeptide or NTHi peptide as a vaccine for treatment and/or prevention of diseases caused by NTHi infection, such as OM. The following NTHi genes are upregulated during or in response to middle ear and/or nasopharynx infections; and the polypeptides encoded by these genes and peptides thereof are contemplated as possible OM vaccine candidates and/or target of chemotherapy: hisB, lppB, sapA, lolA, rbsC, purE, ribB, arcB, uxuA, dsbB, ureH, licC, HI1647, ispZ, radC, mukF, glpR, ihfB, argR, cspD, HI0094, HI1163, HI1063, HI0665, HI1292, HI1064. NTHi hisB gene is set out as nucleotide sequence SEQ ID NO: 615 and encodes the amino acid sequence set out as SEQ ID NO: 616. NTHi sapA gene is set out as nucleotide sequence SEQ ID NO: 617 and encodes the amino acid sequence set out as SEQ ID NO: 618. NTHi rbsC gene is set out as nucleotide sequence SEQ ID NO: 619 and encodes the amino acid sequence set out as SEQ ID NO: 620. NTHi purE gene is set out as nucleotide sequence SEQ ID NO: 621 and encodes the amino acid sequence set out as SEQ ID NO: 622. NTHi ribB gene is set out as nucleotide sequence SEQ ID NO: 623 and encodes the amino acid sequence set out as SEQ ID NO: 624. NTHi arcB gene is set out as nucleotide sequence SEQ ID NO: 625 and encodes the amino acid sequence set out as SEQ ID NO: 626. NTHi uxuA gene is set out as nucleotide sequence SEQ ID NO: 627 and encodes the amino acid sequence set out as SEQ ID NO: 628. NTHi dsbB gene is set out as nucleotide sequence SEQ ID NO: 629 and encodes the amino acid sequence set out as SEQ ID NO: 630. NTHi ureH gene is set out as nucleotide sequence SEQ ID NO: 631 and encodes the amino acid sequence set out as SEQ ID NO: 632. NTHi licC gene is set out as nucleotide sequence SEQ ID NO: 633 and encodes the amino acid sequence set out as SEQ ID NO: 634. NTHi HI1647 gene is set out as nucleotide sequence SEQ ID NO: 635 and encodes the amino acid sequence set out as SEQ ID NO: 636. NTHi ispZ gene is set out as nucleotide sequence SEQ ID NO: 637 and encodes the amino acid sequence set out as SEQ ID NO: 638. NTHi radC gene is set out as nucleotide sequence SEQ ID NO: 639 and encodes the amino acid sequence set out as SEQ ID NO: 640. NTHi mukF gene is set out as nucleotide sequence SEQ ID NO: 641 and encodes the amino acid sequence set out as SEQ ID NO: 642. NTHi glpR gene is set out as nucleotide sequence SEQ ID NO: 643 and encodes the amino acid sequence set out as SEQ ID NO: 644. NTHi ihfB gene is set out as nucleotide sequence SEQ ID NO: 645 and encodes the amino acid sequence set out as SEQ ID NO: 646. NTHi argR gene is set out as nucleotide sequence SEQ ID NO: 647 and encodes the amino acid sequence set out as SEQ ID NO: 648. NTHi cspD gene is set out as nucleotide sequence SEQ ID NO: 649 and encodes the amino acid sequence set out as SEQ ID NO: 650. NTHi HI1163 gene is set out as nucleotide sequence SEQ ID NO: 651 and encodes the amino acid sequence set out as SEQ ID NO: 652. NTHi HD 063 gene is set out as nucleotide sequence SEQ ID NO: 653 and encodes the amino acid sequence set out as SEQ ID NO: 654. NTHi HI0665 gene is set out as nucleotide sequence SEQ ID NO: 655 and encodes the amino acid sequence set out as SEQ ID NO: 656. NTHi HI1292 gene is set out as nucleotide sequence SEQ ID NO: 657 and encodes the amino acid sequence set out as SEQ ID NO: 658. 
         [0012]    The novel NTHi genes included in the polynucleotide sequences presented as SEQ ID NOS: 1-576, SEQ ID NOS: 675-685 and the nucleotide sequences set out in Tables 4 and 4B are also up-regulated during infection of the middle ear and/or the nasopharynx, and therefore are contemplated to encode OM vaccine candidates and/or targets of chemotherapy. In addition, the following NTHi genes are contemplated to be virulence-associated genes and therefore are contemplated to encode possible OM vaccine candidates and/or targets of chemotherapy: HI1386, HI1462, HI1369, lav, HI1598. NTHi HI1386 gene sequence is set out as SEQ ID NO: 659 and encodes the amino acid sequence set out as SEQ ID NO: 660. NTHi HI1462 gene sequence is set out as SEQ ID NO: 661 and encodes the amino acid sequence set out as SEQ ID NO: 662. NTHi HI1369 gene sequence is set out as SEQ ID NO: 665 and encodes the amino acid sequence set out as SEQ ID NO: 666. NTHi lav gene sequence is set out as SEQ ID NO: 663 and encodes the amino acid sequence set out as SEQ ID NO: 664. NTHi HI1598 gene sequence is set out as SEQ ID NO: 669 and SEQ ID NO: 671 and encodes the amino acid sequence set out as SEQ ID NO: 670 and SEQ ID NO: 672. Additional NTHi genes associated with virulence include the polynucleotide sequences presented as SEQ ID NO: 667 and SEQ ID NO: 673. 
         [0013]    As a method of treating or preventing NTHi infection, the present invention contemplates administering a molecule that inhibits expression or the activity of the NTHi polypeptides, which are upregulated or active during infection. In particular, the invention contemplates methods of treating or preventing NTHi infection comprising modulating NTHi protein expression by administering an antisense oligonucleotide that specifically binds to NTHi genes that are upregulated during NTHi infections, such genes include hisB, lppB, sapA, lolA, rbsC, purE, ribB, arcB, uxuA, dsbB, ureH, licC, HI1647, ispZ, radC, mukF, glpR, ihfB, argR, cspD, HI0094, HI1163, HI1063, HI0665, HI1292, HI1064. The invention also contemplates methods of treating or preventing NTHi infection comprising administering antibodies or small molecules that modulate the activity of the proteins encoded by theses genes. The novel NTHi genes included in the polynucleotide sequences presented as SEQ ID NOS: 1-576, SEQ ID NOS: 675-685 and the nucleotide sequences set out in Tables 4 and 4B are also up-regulated during infection of the middle ear and/or the nasopharynx and therefore antisense oligonucleotides that specifically bind these polynucleotide sequences are also contemplated. 
       Polynucleotides and Polypeptides of the Invention 
       [0014]    The present invention provides for the sequences of the NTHi strain 86-028NP genome. The 3-fold analysis of the genomic sequence is presented as a series of contig sequences denoted herein as “contigs 1-576”. Each contig is assigned a sequence identification number that correlates with its “contig number”. Therefore, the contigs of the present invention as set out as SEQ ID NOS: 1-576. These contig polynucleotide sequences may be assembled into the complete genome sequence of the NTHi strain 86-028NP using routine methods. Upon completion of 8-fold sequence analysis of the NTHi strain 82-028NP genome, the genomic sequence was assembled into 11 contigs which are denoted herein as SEQ ID NOS: 675-685. Finally, the complete genome is presented as one nucleic acid sequence denoted herein as SEQ ID NO: 772. 
         [0015]    The present invention provides for the NTHi polynucleotide sequences and open reading frames contained within the contigs of SEQ ID NOS: 1-576, SEQ ID NOS: 675-685, SEQ ID NOS: 773-2593, and the nucleotide sequences set out in Table 3B, Table 4B and Table 5. The present invention also provides for the polypeptide sequences encoded by the NTHi polynucleotides of the present invention such as the amino acid sequences set out in SEQ ID NOS: 2594-4414, Table 3B, Table 4B and Table 5. The invention provides for polynucleotides that hybridize under stringent conditions to (a) the complement of the nucleotides sequence of SEQ ID NOS: 1-576; SEQ ID NOS: 675-685, SEQ ID NOS: 773-2593 and the nucleotide sequences set out in Table 3B, Table 4B and Table 5 herein (b) a polynucleotide which is an allelic variant of any polynucleotides recited above; (c) a polynucleotide which encodes a species homolog of any of the proteins recited above; or (d) a polynucleotide that encodes a polypeptide comprising a specific domain or truncation of the NTHi polypeptides of the present invention. 
         [0016]    The NTHi polynucleotides of the invention also include nucleotide sequences that are substantially equivalent to the polynucleotides recited above. Polynucleotides according to the invention can have, e.g., at least 65%, at least 70%, at least 75%, at least 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, or 89%, more typically at least 90%, 91%, 92%, 93%, or 94% and even more typically at least 95%, 96%, 97%, 98% or 99% sequence identity to the NTHi polynucleotides recited above. 
         [0017]    Included within the scope of the nucleic acid sequences of the invention are nucleic acid sequence fragments that hybridize under stringent conditions to the NTHi nucleotide sequences of SEQ ID NOS: 1-576, SEQ ID NOS: 675-685, SEQ ID NOS: 773-2593, and the nucleotide sequences set out in Table 3B, Table 4B and Table 5 herein, or compliments thereof, which fragment is greater than about 5 nucleotides, preferably 7 nucleotides, more preferably greater than 9 nucleotides and most preferably greater than 17 nucleotides. Fragments of, e.g., 15, 17, or 20 nucleotides or more that are selective for (i.e., specifically hybridize to any one of the polynucleotides of the invention) are contemplated. Probes capable of specifically hybridizing to a polynucleotide can differentiate NTHi polynucleotide sequences of the invention from other polynucleotide sequences in the same family of genes or can differentiate NTHi genes from other bacterial genes, and are preferably based on unique nucleotide sequences. 
         [0018]    The term “stringent” is used to refer to conditions that are commonly understood in the art as stringent. Hybridization stringency is principally determined by temperature, ionic strength, and the concentration of denaturing agents such as formamide. Examples of stringent conditions for hybridization and washing are 0.015 M sodium chloride, 0.0015 M sodium citrate at 65-68° C. or 0.015 M sodium chloride, 0.0015M sodium citrate, and 50% formamide at 42° C. See Sambrook et al.,  Molecular Cloning: A Laboratory Manual,  2 nd  Ed., Cold Spring Harbor Laboratory, (Cold Spring Harbor, N.Y. 1989). More stringent conditions (such as higher temperature, lower ionic strength, higher formamide, or other denaturing agent) may also be used, however, the rate of hybridization will be affected. In instances wherein hybridization of deoxyoligonucleotides is concerned, additional exemplary stringent hybridization conditions include washing in 6×SSC 0.05% sodium pyrophosphate at 37° C. (for 14-base oligos), 48° C. (for 17-base oligos), 55° C. (for 20-base oligos), and 60° C. (for 23-base oligos). 
         [0019]    Other agents may be included in the hybridization and washing buffers for the purpose of reducing non-specific and/or background hybridization. Examples are 0.1% bovine serum albumin, 0.1% polyvinyl-pyrrolidone, 0.1% sodium pyrophosphate, 0.1% sodium dodecylsulfate, NaDodSO 4 , (SDS), ficoll, Denhardt&#39;s solution, sonicated salmon sperm DNA (or other non-complementary DNA), and dextran sulfate, although other suitable agents can also be used. The concentration and types of these additives can be changed without substantially affecting the stringency of the hybridization conditions. Hybridization experiments are usually carried out at pH 6.8-7.4, however, at typical ionic strength conditions, the rate of hybridization is nearly independent of pH. See Anderson et al.,  Nucleic Acid Hybridisation: A Practical Approach , Ch. 4, IRL Press Limited (Oxford, England). Hybridization conditions can be adjusted by one skilled in the art in order to accommodate these variables and allow DNAs of different sequence relatedness to form hybrids. 
         [0020]    The sequences falling within the scope of the present invention are not limited to these specific sequences, but also include allelic and species variations thereof. Allelic and species variations can be routinely determined by comparing the sequence provided in SEQ ID NOS: 1-576, SEQ ID NOS: 675-685, SEQ ID NOS: 773-2593, and nucleotide sequences out in Table 3B, Table 4B and Table 5 herein, preferably the open reading frames therein, a representative fragment thereof, or a nucleotide sequence at least 90% identical, preferably 95% identical, to the open reading frames within SEQ ID NOS: 1-576, SEQ ID NOS: 675-685, SEQ ID NOS: 773-2593, and the nucleotide sequences set out in Table 3B, Table 4B and Table 5 with a sequence from another isolate of the same species. Preferred computer program methods to determine identity and similarity between two sequences include, but are not limited to, the GCG program package, including GAP (Devereux et al.,  Nucl. Acid. Res.,  12: 387, 1984; Genetics Computer Group, University of Wisconsin, Madison, Wis.), BLASTP, BLASTN, and FASTA (Altschul et al.,  J. Mol. Biol.,  215: 403-410, 1990). The BLASTX program is publicly available from the National Center for Biotechnology Information (NCBI) and other sources ( BLAST Manual , Altschul et al. NCB/NLM/NIH Bethesda, Md. 20894; Altschul et al., supra). The well known Smith Waterman algorithm may also be used to determine identity. 
         [0021]    Furthermore, to accommodate codon variability, the invention includes nucleic acid molecules coding for the same amino acid sequences as do the specific open reading frames (ORF) disclosed herein. In other words, in the coding region of an ORF, substitution of one codon for another codon that encodes the same amino acid is expressly contemplated. 
         [0022]    The isolated polypeptides of the invention include, but are not limited to, a polypeptide comprising: the amino acid sequences encoded by the nucleotide sequences included within the polynucleotide sequences set out as SEQ ID NOS: 1-576, SEQ ID NOS: 675-685, SEQ ID NOS: 773-2593, and the nucleotide sequences set out in Table 3B, Table 4B and Table 5, or the corresponding full length or mature protein. The polypeptides of the invention include the amino acid sequences of SEQ ID NO: 616, SEQ ID NO: 618, SEQ ID NO: 620, SEQ ID NO: 622, SEQ ID NO: 624, SEQ ID NO: 626, SEQ ID NO: 628, SEQ ID NO: 628, SEQ ID NO: 630, SEQ ID NO: 632, SEQ ID NO: 634, SEQ ID NO: 636, SEQ ID NO: 638, SEQ ID NO: 640, SEQ ID NO: 642, SEQ ID NO: 644, SEQ ID NO: 646, SEQ ID NO: 648, SEQ ID NO: 650, SEQ ID NO: 652, SEQ ID NO: 654, SEQ ID NO: 656, SEQ ID NO: 658, SEQ ID NO: 660, SEQ ID NO: 662, SEQ ID NO: 664, SEQ ID NO: 666, SEQ ID NO: 668, SEQ ID NO: 670, SEQ ID NO: 672, SEQ ID NO: 674, SEQ ID NO: 687, SEQ ID NO: 689, SEQ ID NO: 691, SEQ ID NO: 693, SEQ ID NO: 695, SEQ ID NO: 697, SEQ ID NO: 699, SEQ ID NO: 701, SEQ ID NO: 703, SEQ ID NO: 705, SEQ ID NO: 707, SEQ ID NO: 709, SEQ ID NO: 711, SEQ ID NO: 713, SEQ ID NO:715, SEQ ID NO: 717, SEQ ID NO: 719, SEQ ID NO: 721, SEQ ID NO:723, SEQ ID NO:725, SEQ ID NO:727, SEQ ID NO:729, SEQ ID NO: 731, SEQ ID NO: 733, SEQ ID NO: 735, SEQ ID NO: 737, SEQ ID NO: 739, SEQ ID NO: 741, SEQ ID NO: 743, SEQ ID NO: 745, SEQ ID NO: 747, SEQ ID NO: 749, SEQ ID NO: 751, SEQ ID NO: 753, SEQ ID NO: 755, SEQ ID NO: 757, SEQ ID NO: 759, SEQ ID NO: 761, 763, SEQ ID NO: 765, SEQ ID NO: 767, SEQ ID NO: 769 or SEQ ID NO: 771, SEQ ID NOS: 2594-4414 which are set out in Table 3B, Table 4B and Table 5 herein. 
         [0023]    Polypeptides of the invention also include polypeptides preferably with biological or immunogenic activity that are encoded by: (a) an open reading frame contained within the nucleotide sequences set forth as SEQ ID NOS: 1-576, SEQ ID NOS: 675-685, SEQ ID NOS: 773-2593, and the nucleotide sequences set out in Table 3B, Table 4B and Table 5, or (b) polynucleotides that hybridize to the complement of the polynucleotides of (a) under stringent hybridization conditions. 
         [0024]    The invention also provides biologically active or immunologically active variants of the amino acid sequences of the present invention; and “substantial equivalents” thereof (e.g., with at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, 86%, 87%, 88%, 89%, at least about 90%, 91%, 92%, 93%, 94%, typically at least about 95%, 96%, 97%, more typically at least about 98%, or most typically at least about 99% amino acid identity) that retain biological and/or immunogenic activity. Polypeptides encoded by allelic variants may have a similar, increased, or decreased activity compared to polypeptides encoded by the polynucleotides included within the nucleotide sequences presented in SEQ ID NOS: 1-576, SEQ ID NOS: 675-685, SEQ ID NOS: 773-2593, and the nucleotide sequences encoding the amino acid sequences set out as SEQ ID NOS: 2594-4414 and in Table 3B, Table 4B and Table 5 herein, and the polypeptides having an amino acid sequence set out in SEQ ID NOS: 2594-4414, Table 3B, Table 4B and Table 5 herein. 
         [0025]    NTHi peptides refer to fragments of the NTHi polypeptides encoded by the nucleotide sequences presented in SEQ ID NOS: 1-576, SEQ ID NOS: 675-685, SEQ ID NOS: 773-2593, or the nucleotide sequences set out in Table 3B, Table 4B and Table 5 herein, and the polypeptides having the amino acid sequences set out in SEQ ID NOS: 2594-4414 Table 3B, Table 4B and Table 5 herein. The preferred NTHi peptides are biologically and/or immunologically active. 
         [0026]    The present invention further provides isolated NTHi polypeptides or NTHi peptides encoded by the NTHi nucleic acid fragments of the present invention or by degenerate variants of the nucleic acid fragments of the present invention. The term “degenerate variant” refers to nucleotide fragments which differ from a nucleic acid fragment of the present invention (e.g., an ORF) by nucleotide sequence but, due to the degeneracy of the genetic code, encode an identical NTHi polypeptide sequence. Preferred nucleic acid fragments of the present invention are the ORFs that encode proteins. 
         [0027]    The invention also provides for NTHi polypeptides with one or more conservative amino acid substitutions that do not affect the biological and/or immunogenic activity of the polypeptide. Alternatively, the NTHi polypeptides of the invention are contemplated to have conservative amino acids substitutions which may or may not alter biological activity. The term “conservative amino acid substitution” refers to a substitution of a native amino acid residue with a nonnative residue, including naturally occurring and nonnaturally occurring amino acids, such that there is little or no effect on the polarity or charge of the amino acid residue at that position. For example, a conservative substitution results from the replacement of a non-polar residue in a polypeptide with any other non-polar residue. Further, any native residue in the polypeptide may also be substituted with alanine, according to the methods of “alanine scanning mutagenesis”. Naturally occurring amino acids are characterized based on their side chains as follows: basic: arginine, lysine, histidine; acidic: glutamic acid, aspartic acid; uncharged polar: glutamine, asparagine, serine, threonine, tyrosine; and non-polar: phenylalanine, tryptophan, cysteine, glycine, alanine, valine, proline, methionine, leucine, norleucine, isoleucine General rules for amino acid substitutions are set forth in Table 1 below. 
         [0000]    
       
         
               
               
               
             
           
               
                 TABLE 1 
               
               
                   
               
               
                   
                 Amino Acid Substitutions 
                   
               
               
                 Original Residues 
                 Exemplary Substitutions 
                 Preferred Substitutions 
               
               
                   
               
             
             
               
                 Ala 
                 Val, Leu, Ile 
                 Val 
               
               
                 Arg 
                 Lys, Gln, Asn 
                 Lys 
               
               
                 Asn 
                 Gln 
                 Gln 
               
               
                 Asp 
                 Glu 
                 Glu 
               
               
                 Cys 
                 Ser, Ala 
                 Ser 
               
               
                 Gln 
                 Asn 
                 Asn 
               
               
                 Glu 
                 Asp 
                 Asn 
               
               
                 Gly 
                 Pro, Ala 
                 Ala 
               
               
                 His 
                 Asn, Gln, Lys, Arg 
                 Arg 
               
               
                 Ile 
                 Leu, Val, Met, Ala, Phe, 
                 Leu 
               
               
                 Leu 
                 Norleucine, Ile, Val, Met, 
                 Leu 
               
               
                 Lys 
                 Arg, 1,4 Diaminobutyric 
                 Arg 
               
               
                 Met 
                 Leu, Phe, Ile 
                 Leu 
               
               
                 Phe 
                 Leu, Val, Ile, Ala, Tyr 
                 Arg 
               
               
                 Pro 
                 Ala 
                 Gly 
               
               
                 Ser 
                 Thr, Ala, Cys 
                 Thr 
               
               
                 Thr 
                 Ser 
                 Ser 
               
               
                 Trp 
                 Tyr, Phe 
                 Tyr 
               
               
                 Tyr 
                 Trp, Phe, Thr, Ser 
                 Phe 
               
               
                 Val 
                 Ile, Met, Leu, Phe, Ala, 
                 Leu 
               
               
                   
               
             
          
         
       
     
         [0028]    Antisense polynucleotides complementary to the polynucleotides encoding the NTHi polypeptides are also provided. 
         [0029]    The invention contemplates that polynucleotides of the invention may be inserted in a vector for amplification or expression. For expression, the polynucleotides are operatively linked to appropriate expression control sequence such as a promoter and polyadenylation signal sequences. Further provided are cells comprising polynucleotides of the invention. Exemplary prokaryotic hosts include bacteria such as  E. coli, Bacillus, Streptomyces, Pseudomonas, Salmonella  and  Serratia.    
         [0030]    The term “isolated” refers to a substance removed from, and essentially free of, the other components of the environment in which it naturally exists. For example, a polypeptide is separated from other cellular proteins or a DNA is separated from other DNA flanking it in a genome in which it naturally occurs. 
       Antibodies and Methods for Eliciting an Immune Response 
       [0031]    The invention provides antibodies which bind to antigenic epitopes unique to (Le., are specific for) NTHi polypeptides. Also provided are antibodies which bind to antigenic epitopes common among multiple  H. influenzae  subtypes but unique with respect to any other antigenic epitopes. The antibodies may be polyclonal antibodies, monoclonal antibodies, antibody fragments which retain their ability to bind their unique epitope (e.g., Fv, Fab and F(ab)2 fragments), single chain antibodies and human or humanized antibodies. Antibodies may be generated by techniques standard in the art. 
         [0032]    It is known in the art that antigens that mimic the capsular polysaccharide of  H. influenzae  will generate antibodies that exhibit the ability to kill bacteria in in vitro assays. These antibodies are also known to protect against challenge with  H. influenzae  in animal model systems. These studies indicate antibody to the capsular polysaccharrides are likely to elicit a protective immune response in humans. The present invention provides for antibodies specific for the NTHi polypeptides of the present invention and fragments thereof, which exhibit the ability to kill both  H. influenzae  bacteria and to protect humans from NTHi infection. The present invention also provides for antibodies specific for the NTHi polypeptides of the invention which reduce the virulence, inhibit adherence, inhibit cell division, and/or inhibit penetration into the epithelium of  H. influenzae  bacteria or enhance phagocytosis of the  H. influenzae  bacteria. 
         [0033]    In vitro complement mediated bactericidal assay systems (Musher et al.,  Infect. Immun.  39: 297-304, 1983; Anderson et al.,  J. Clin. Invest.  51: 31-38, 1972) may be used to measure the bactericidal activity of anti-NTHi antibodies. Further data on the ability of NTHi polypeptides and NTHi peptides to elicit a protective antibody response may be generated by using animal models of infection such as the chinchilla model system described herein. 
         [0034]    It is also possible to confer short-term protection to a host by passive immunotherapy via the administration of pre-formed antibody against an epitope of NTHi, such as antibodies against NTHi OMP, LOS or noncapsular proteins. Thus, the contemplated vaccine formulations can be used to produce antibodies for use in passive immunotherapy. Human immunoglobulin is preferred in human medicine because a heterologous immunoglobulin may provoke an immune response to its foreign immunogenic components. Such passive immunization could be used on an emergency basis for immediate protection of unimmunized individuals exposed to special risks. Alternatively, these antibodies can be used in the production of anti-idiotypic antibody, which in turn can be used as an antigen to stimulate an immune response against NTHi epitopes. 
         [0035]    The invention contemplates methods of eliciting an immune response to NTHi in an individual. These methods elicit immune responses which include one or more of killing NTHi bacteria, blocking NTHi attachment to cells and/or slowing NTHi replication. An “immunogenic dose” of a composition of the invention is one that generates, after administration, a detectable humoral and/or cellular immune response in comparison to the immune response detectable before administration or in comparison to a standard immune response before administration. The invention contemplates that the immune response resulting from the methods may be protective and/or therapeutic. In one embodiment, the methods comprise a step of administering an immunogenic dose of a composition comprising a NTHi protein or NTHi peptide of the invention. A NTHi protein or an antigenic peptide thereof may be fused with co-protein which may not by itself produce antibodies, but is capable of stabilizing the first protein and producing a fused protein which will have immunogenic and protective properties. Thus fused recombinant protein, preferably further comprises an antigenic co-protein, such as Glutathione-S-transferase (GST) or beta-galactosidase, relatively large co-proteins which solubilize the protein and facilitate production and purification thereof. Moreover, the co-protein may act as an adjuvant in the sense of providing a generalized stimulation of the immune system. The co-protein may be attached to either the amino or carboxy terminus of the first protein. Provided by this invention are compositions, particularly vaccine compositions, and methods comprising the NTHi polypeptides encoded by the polynucleotide of the invention or antigenic peptides thereof. 
         [0036]    The invention also contemplates methods of eliciting an immune response to multiple  H. influenzae  subtypes in an individual. These methods elicit immune responses which include one or more of killing the  H. influenzae  bacteria, blocking  H. influenzae  attachment to cells and/or slowing  H. influenzae  replication. These methods comprise a step of administering an immunogenic dose of a composition comprising a NTHi protein or NTHi peptide of the invention which comprise an antigenic epitope that is common among multiple  H. influenzae  subtypes but unique with respect to any other antigenic epitopes. 
         [0037]    In another embodiment, the methods comprise administering an immunogenic dose of a composition comprising a cell expressing a NTHi protein or NTHi peptide of the invention. In yet another embodiment, the Methods comprise administering an immunogenic dose of a composition comprising a polynucleotide encoding a NTHi protein or NTHi peptide of the invention. The polynucleotide may be a naked polynucleotide not associated with any other nucleic acid or may be in a vector such as a plasmid or viral vector (e.g., adeno-associated virus vector or adenovirus vector). The compositions of the invention may comprise one or more NTHi proteins or NTHi peptides alone or in combination with other epitopes that elicit an immune response to NTHi bacteria. The compositions of the invention may also comprise one or more NTHi proteins or peptides in combination with epitopes that elicit an immune response to one or more  H. influenzae  subtypes. Administration of the compositions may be by routes standard in the art, for example, parenteral, intravenous, oral, buccal, nasal, pulmonary, rectal, or vaginal. The methods may be used in combination in a single individual. The methods may be used prior or subsequent to NTHi infection of an individual. 
         [0038]    Genes that are up-regulated in NTHi infection of the middle ear and/or the nasopharynx and genes that are associated with NTHi virulence are described herein. The polypeptides and peptides thereof which are encoded by these NTHi genes are contemplated to be useful for eliciting an immune response for treating or preventing disorders associated with NTHi infection, such as OM. Some of the polypeptides encoded by these genes include: histidine biosynthesis protein, lipoprotein B, peptide ABC transporter, periplasmic SapA precursor, outer membrane lipoproteins carrier protein precursor, ribose transport system permease protein, phosphoribosylaminoimidazole carboxylase catalytic subunit, PurE, Phosphoribosylaminoimidazole carboxylase catalytic subunit, ornithine carbamolytransferase, mannonate dehydratase, disulfide oxidoreductase, urease accessory protein, phospshocholine cytidylytransferase, putative pyridoxine biosynthesis protein, singlet oxygen resistance protein, intracellular septation protein, DNA repair protein, MukF protein, glycerol-3-phosphate regulon repressor, integration host factor beta subunit, arginine repressor, cold shock like protein, stress response protein, LicA, MukF, RadA and those hypothetical proteins encoded by HI0094, HI1163, HI0665, HI1292, HI1064 HI186, HI0352 genes. NTHi OMPs, LOS and noncapsular proteins are also contemplated to elicit an immune response for prevention and treatment of disorders associated with NTHi infection. 
         [0039]    The invention includes methods of blocking binding of NTHi bacteria to host cells in an individual. The methods comprise administering antibodies or polypeptides of the invention that block binding of NTHi cellular attachment. Alternatively, administration of one or more small molecules that block binding of NTHi cell attachment is contemplated. In vitro assays may be used to demonstrate the ability of an antibody, polypeptide or small molecule of the invention to block NTHi cell attachment. 
         [0040]    Pharmaceutical compositions comprising antibodies of the invention, polypeptides of the invention and/or small molecules of the invention that block NTHi cellular attachment are provided. The pharmaceutical compositions may consist of one of the foregoing active ingredients alone, may comprise combinations of the foregoing active ingredients or may comprise additional active ingredients used to treat bacterial infections. The pharmaceutical compositions may comprise one or more additional ingredients such as pharmaceutically effective carriers. Dosage and frequency of the administration of the pharmaceutical compositions are determined by standard techniques and depend, for example, on the weight and age of the individual, the route of administration, and the severity of symptoms. Administration of the pharmaceutical compositions may be by routes standard in the art, for example, parenteral, intravenous, oral, buccal, nasal, pulmonary, rectal, or vaginal. 
         [0041]    Also provided by the invention are methods for detecting NTHi infection in an individual. In one embodiment, the methods comprise detecting NTHi polynucleotides of the invention in a sample using primers or probes that specifically bind to the polynucleotides. Detection of the polynucleotide may be accomplished by numerous techniques routine in the art involving, for example, hybridization and PCR. 
         [0042]    The antibodies of the present invention may also be used to provide reagents for use in diagnostic assays for the detection of NTHi antigens (NTHi polypeptides and peptides thereof) in various body fluids of individuals suspected of  H. influenzae  infection. In another embodiment, the NTHi proteins and peptides of the present invention may be used as antigens in immunoassays for the detection of NTHi in various patient tissues and body fluids including, but not limited to: blood, serum, ear fluid, spinal fluid, sputum, urine, lymphatic fluid and cerebrospinal fluid. The antigens of the present invention may be used in any immunoassay system known in the art including, but not limited to: radioimmunoassays, ELISA assays, sandwich assays, precipitin reactions, gel diffusion precipitin reactions, immunodiffusion assays, agglutination assays, fluorescent immunoassays, protein A immunoassays and immunoelectrophoresis assays. 
       Vaccines and Chemotherapeutic Targets 
       [0043]    An aspect of the invention relates to a method for inducing an immunological response in an individual, particularly a mammal which comprises inoculating the individual with a NTHi antigen protein or an antigenic peptide thereof. 
         [0044]    The present invention also provides for vaccine formulations which comprise an immunogenic recombinant NTHi protein or NTHi peptide of the invention together with a suitable carrier. The NTHi polypeptides and peptides thereof contemplated as vaccine candidates and/or targets of chemotherapy include, but are not limited to, histidine biosynthesis protein, lipoprotein B, peptide ABC transporter, periplasmic SapA precursor, outer membrane lipoproteins carrier protein precursor, ribose transport system permease protein, phosphoribosylaminoimidazole carboxylase catalytic subunit, PurE, 3,4-dihydroxt-2-butone 4-phosphate synthase, ornithine carbamolytransferase, marmonate dehydratase, disulfide oxidoreductase, urease accessory protein, phospshocholine cytidylytransferase, putative pyridoxine biosynthesis protein, singlet oxygen resistance protein, intracellular septation protein, DNA repair protein, MUKF protein, glycerol-3-phosphate regulon repressor, integration host factor beta subunit, arginine repressor, cold shock like protein, stress response protein, LicA, RadA and those hypothetical proteins encoded by HI0094, HI1163, HI0665, HI1292, HI1064 HI1386, HI0352 genes, NTHi OMPs, NTHi LOS and NTHi noncapsular proteins and polypeptides encoded by the novel NTHi polynucleotide sequences present in the nucleotide sequences set out as SEQ ID NOS: 1-576, SEQ ID NOS: 675-685, SEQ ID NOS: 773-2593, and the nucleotide sequences set out in Table 3B, Table 4B and Table 5 herein, and the polypeptides having the amino acid sequences set out in SEQ ID NOS: 2594-4414, Table 3B, Table 4B and Table 5 herein. 
         [0045]    Since the protein may be broken down in the stomach, it is preferably administered parenterally, including, for example, administration that is subcutaneous, intramuscular, intravenous, or intradermal. Formulations suitable for parenteral administration include aqueous and non-aqueous sterile injection solutions which may contain anti-oxidants, buffers, bacteriostats and solutes which render the formulation isotonic with the bodily fluid, preferably the blood, of the individual; and aqueous and non-aqueous sterile suspensions which may include suspending agents or thickening agents. The formulations may be presented in unit-dose or multi-dose containers, for example, sealed ampules and vials and may be stored in a freeze-dried condition requiring only the addition of the sterile liquid carrier immediately prior to use. The vaccine formulation may also include adjuvant systems for enhancing the immunogenicity of the formulation, such as oil-in water systems and other systems known in the art. The dosage will depend on the specific activity of the vaccine and can be readily determined by routine experimentation. 
         [0046]    A. Peptide Vaccines 
         [0047]    Peptide therapeutic agents, such as peptide vaccines, are well known in the art and are of increasing use in the pharmaceutical arts. Consistent drawbacks to the parenteral administration of such peptide compounds have been the rapidity of breakdown or denaturation. Infusion pumps, as well as wax or oil implants, have been employed for chronic administration of therapeutic agents in an effort to both prolong the presence of peptide-like therapeutic agents and preserve the integrity of such agents. Furthermore, the peptide-like agent should (with particular reference to each epitope of the peptide-like agent) ideally maintain native state configuration for an extended period of time and additionally be presented in a fashion suitable for triggering an immunogenic response in the challenged animal or immunized human. 
         [0048]    The NTHi antigenic peptides of the invention can be prepared in a number of conventional ways. The short peptides sequences can be prepared by chemical synthesis using standard means. Particularly convenient are solid phase techniques (see, e.g., Erikson et al.,  The Proteins  (1976) v. 2, Academic Press, New York, p. 255). Automated solid phase synthesizers are commercially available. In addition, modifications in the sequence are easily made by substitution, addition or omission of appropriate residues. For example, a cysteine residue may be added at the carboxy terminus to provide a sulfhydryl group for convenient linkage to a carrier protein, or spacer elements, such as an additional glycine residue, may be incorporated into the sequence between the linking amino acid at the C-terminus and the remainder of the peptide. The short NTHi peptides can also be produced by recombinant techniques. The coding sequence for peptides of this length can easily be synthesized by chemical techniques, e.g., the phosphotriester method described in Matteucci et al.,  J Am Chem Soc.,  103: 3185 (1981). 
         [0049]    Some of the NTHi peptide sequences contemplated herein may be considered too small to be immunogenic, they may be linked to carrier substances in order to, confer this property upon them. Any method of creating such linkages known in the art may be used. Linkages can be formed with heterobifunctional agents that generate a disulfide link at one functional group end and a peptide link at the other, such as a disulfide amide forming agent, e.g., N-succidimidyl-3-(2-pyridyldithio) proprionate (SPDP) (See, e.g., Jansen et al.,  Immun. Rev.  62:185, 1982) and bifunctional coupling agents that form a thioether rather than a disulfide linkage such as reactive esters of 6-maleimidocaproic acid, 2-bromoacetic acid, 2-iodoacetic acid, 4-(N-maleimido-methyl) cyclohexane-1-carboxylic acid and the like, and coupling agent which activate carboxyl groups by combining them with succinimide or 1-hydroxy-2-nitro-4-sulfonic acid, for sodium salt such as succinimmidyl 4-(N-maleimido-methyl) cyclohexane-1-carobxylate (SMCC). 
         [0050]    B. Vaccine Compositions and Administration 
         [0051]    A priming dose of the immunogen that is followed by one or more booster exposures to the immunogen may be necessary to be an effective vaccine (Kramp et al.,  Infect. Immun.,  25: 771-773, 1979; Davis et al.,  Immunology Letters,  14: 341-8 1986 1987). Examples of proteins or polypeptides that could beneficially enhance the immune response if co-administered include cytokines (e.g., IL-2, IL-12, GM-CSF), cytokine-inducing molecules (e.g. Leaf) or costimulatory molecules. Helper (HTL) epitopes could be joined to intracellular targeting signals and expressed separately from the CTL epitopes. This would allow direction of the HTL epitopes to a cell compartment different than the CTL epitopes. If required, this could facilitate more efficient entry of HTL epitopes into the MHC class II pathway, thereby improving CTL induction. In contrast to CTL induction, specifically decreasing the immune response by co-expression of immunosuppressive molecules (e.g. TGF-β) may be beneficial in certain diseases. 
         [0052]    Ideally, an immunogen will exhibit two properties; the capacity to stimulate the formation of the corresponding antibodies and the propensity to react specifically with these antibodies. Immunogens bear one or more epitopes which are the smallest part of an immunogen recognizable by the combing site of an antibody. In particular instances, immunogen, fractions of immunogens or conditions under which the immunogen is presented are inadequate to precipitate the desired immunological response resulting in insufficient immunity. This is often the case with peptides or other small molecules used as immunogens. Other substances such as immunomodulators (e.g., cytokines such as the interleukins) may be combined in vaccines as well. 
         [0053]    The vaccine art recognizes the use of certain substances called adjuvants to potentate an immune response when used in conjunction with an immunogen. Adjuvants are further used to elicit an immune response that is faster or greater than would be elicited without the use of the adjuvant. In addition, adjuvants may be used to create an immunological response using less immunogen than would be needed without the inclusion of adjuvant, to increase production of certain antibody subclasses that afford immunological protection or to enhance components of the immune response (e.g., humoral, cellular). Known adjuvants include emulsions such as Freund&#39;s Adjuvants and other oil emulsions,  Bordetella pertussis , MF59, purified saponin from  Quillaja saponaria  (QS21), aluminum salts such as hydroxide, phosphate and alum, calcium phosphate, (and other metal salts), gels such as aluminum hydroxide salts, mycobacterial products including muramyl dipeptides, solid materials, particles such as liposomes and virosomes. Examples of natural and bacterial products known to be used as adjuvants include monophosphoryl lipid A (MPL), RC-529 (synthetic MPL-like acylated monosaccharide), OM-174 which is a lipid A derivative from  E. coli , holotoxins such as cholera toxin (CT) or one of its derivatives, pertussis toxin (PT) and heat-labile toxin (LT) of  E. coli  or one of its derivatives, and CpG oligonucleotides. Adjuvant activity can be affected by a number of factors, such as carrier effect, depot formation, altered lymphocyte recirculation, stimulation of T-lymphocytes, direct stimulation of B-lymphocytes and stimulation of macrophages. 
         [0054]    Vaccines are typically prepared as injectables, either as liquid solutions or suspensions; solid forms suitable for solution in, or suspension in, liquid prior to injection may also be prepared. The preparation may also be emulsified. The active immunogenic ingredient is often mixed with excipients, which are pharmaceutically acceptable and compatible with the active ingredient. Suitable excipients are, e.g., water, saline, dextrose, glycerol, ethanol, or the like and combinations thereof. In addition, if desired, the vaccine may contain minor amounts of auxiliary substances such as wetting or emulsifying agents, pH buffering agents, or adjuvants, which enhance the effectiveness of the vaccine. The vaccines are conventionally administered parenterally, by injection, for example, either subcutaneously or intramuscularly. Additional formulations which are suitable for other modes of administration include suppositories and, in some cases, oral formulations. For suppositories, traditional binders and carriers may include, for example, polyalkalene glycols or triglycerides; such suppositories may be formed from mixtures containing the active ingredient in the range of 0.5% to 10%, preferably 1-2%. Oral formulations include such normally employed excipients as, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate and the like. These compositions take the form of solutions, suspensions, tablets, pills, capsules, sustained release formulations or powders and contain 10%-95% of active ingredient, preferably 25-70%. 
         [0055]    Vaccines may also be administered through transdermal routes utilizing jet injectors, microneedles, electroporation, sonoporation, microencapsulation, polymers or liposomes, transmucosal routes and intranasal routes using nebulizers, aerosols and nasal sprays. Microencapsulation using natural or synthetic polymers such as starch, alginate and chitosan, D-poly L-lactate (PLA), D-poly DL-lactic-coglycolic microspheres, polycaprolactones, polyorthoesters, polyanhydrides and polyphosphazenes polyphosphatazanes are useful for both transdermal and transmucosal administration. Polymeric complexes comprising synthetic poly-ornithate, poly-lysine and poly-arginine or amphipathic peptides are useful for transdermal delivery systems. In addition, due to their amphipathic nature, liposomes are contemplated for transdermal, transmucosal and intranasal vaccine delivery systems. Common lipids used for vaccine delivery include N-(1)2,3-(dioleyl-dihydroxypropyl)-N,N,N,-trimethylammonium-methyl sulfate (DOTAP), dioleyloxy-propyl-trimethylammonium chloride DOTMA, dimystyloxypropyl-3-dimethyl-hydroxyethyl ammonium (DMRIE), dimethyldioctadecyl ammonium bromide (DDAB) and 9N(N′,N-dimethylaminoethane) carbamoyl) cholesterol (DC-Chol). The combination of helper lipids and liposomes will enhance up-take of the liposomes through the skin. These helper lipids include, dioleoyl phosphatidylethanolamine (DOPE), dilauroylphosphatidylethanolamine (DLPE), dimyristoyl phosphatidylethanolamine (DMPE), dipalmitoylphosphatidylethanolamine (DPPE). In addition, triterpenoid glycosides or saponins derived from the Chilean soap tree bark ( Quillaja saponaria ) and chitosan (deacetylated chitan) have been contemplated as useful adjuvants for intranasal and transmucosal vaccine delivery. 
         [0056]    The proteins may be formulated into the vaccine as neutral or salt forms. Pharmaceutically acceptable salts, include the acid addition salts (formed with the free amino groups of the peptide) and which are formed with inorganic acids such as, e.g., hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric, mandelic. Salts formed with the free carboxyl groups may also be derived from inorganic bases such as, e.g., sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, 2-ethylamino ethanol, histidine, and procaine. 
         [0057]    The vaccines are administered in a manner compatible with the dosage formulation, and in such amount as will be therapeutically effective and immunogenic. The quantity to be administered depends on the subject to be treated, capacity of the subject&#39;s immune system to synthesize antibodies, and the degree of protection desired. Precise amounts of active ingredient required to be administered depend on the judgment of the practitioner and are peculiar to each individual. However, suitable dosage ranges are of the order of several hundred micrograms active ingredient per individual. Suitable regimes for initial administration and booster shots are also variable, but are typified by an initial administration followed in one or three month intervals by a subsequent injection or other administration. 
         [0058]    Upon immunization with a vaccine composition as described herein, the immune system of the host responds to the vaccine by producing large amounts of CTLs specific for the desired antigen, and the host becomes at least partially immune to later infection, or resistant to developing chronic infection. Vaccine compositions containing the NTHi polypeptide or NTHi peptides of the invention are administered to a patient susceptible to or otherwise at risk of bacterial infection to elicit an immune response against the antigen and thus enhance the patient&#39;s own immune response capabilities. In this use, the precise amounts again depend on the patient&#39;s state of health and weight, the mode of administration, the nature of the formulation, etc., but generally range from about 1.0 μg to about 5000 per 70 kilogram patient, more commonly from about 10 to about 500 mg per 70 kg of body weight. For therapeutic or immunization purposes, the NTHi polypeptide or NTHi peptides of the invention can also be expressed by attenuated viral hosts, such as vaccinia or fowlpox. This approach involves the use of vaccinia virus as a vector to express nucleotide sequences that encode the peptides of the invention. Upon introduction into an acutely or chronically infected host or into a noninfected host, the recombinant vaccinia virus expresses the immunogenic peptide, and thereby elicits a host CTL response. 
         [0059]    Humoral immune response may be measured by many well known methods, such as Single Radial Immunodiffussion Assay (SRID), Enzyme Immunoassay (EIA) and Hemagglutination Inhibition Assay (HAI). In particular, SRID utilizes a layer of a gel, such as agarose, containing the immunogen being tested. A well is cut in the gel and the serum being tested is placed in the well. Diffusion of the antibody out into the gel leads to the formation of a precipitation ring whose area is proportional to the concentration of the antibody in the serum being tested. EIA, also known as ELISA (Enzyme Linked Immunoassay), is used to determine total antibodies in the sample. The immunogen is adsorbed to the surface of a microtiter plate. The test serum is exposed to the plate followed by an enzyme linked immunoglobulin, such as IgG. The enzyme activity adherent to the plate is quantified by any convenient means such as spectrophotometry and is proportional to the concentration of antibody directed against the immunogen present in the test sample. HAI utilizes the capability of an immunogen such as viral proteins to agglutinate chicken red blood cells (or the like). The assay detects neutralizing antibodies, i.e., those antibodies able to inhibit hemagglutination. Dilution of the test serum are incubated with a standard concentration of immunogen, followed by the addition of the red blood cells. The presence of neutralizing antibodies will inhibit the agglutination of the red blood cells by the immunogen. Tests to measure cellular immune response include determination of delayed-type hypersensitivity or measuring the proliferative response of lymphocytes to target immunogen. 
         [0000]    Nontypeable  Haemophilus influenzae  (NTHi) 
         [0060]      H. influenzae  is a small, nonmotile gram negative bacterium. Unlike other  H. influenzae  strains, the nontypeable  H. influenzae  (NTHi) strains lack a polysaccharide capsule and are sometimes denoted as “nonencapsulated.” NTHi strains are genetically distinct from encapsulated strains and are more heterogenous than the type b  H. influenzae  isolates. NTHi presents a complex array of antigens to the human host. Possible antigens that may elicit protection include OMPs, lipopolysaccharides, lipoproteins, adhesion proteins and noncapsular proteins. 
         [0061]    Humans are the only host for  H. influenze . NTHi strains commonly reside in the upper respiratory tract including the nasopharynx and the posterior oropharynx, the lower respiratory tract and the female genital tract. NTHi causes a broad spectrum of diseases in humans, including but not limited to, otitis media, pneumonia, sinusitis, septicemia, endocarditis, epiglottitis, septic arthritis, meningitis, postpartum and neonatal infections, postpartum and neonatal sepsis, acute and chromic salpingitis, epiglottis, pericarditis, cellulitis, osteomyelitis, endocarditis, cholecystitis, intraabdominal infections, urinary tract infection, mastoiditis, aortic graft infection, conjunctitivitis, Brazilian purpuric fever, occult bacteremia and exacerbation of underlying lung diseases such as chronic bronchitis, bronchietasis and cystic fibrosis. 
         [0062]    Epidemiologic studies of NTHi have indicated that the strains are heterogeneous with respect to outer membrane protein profiles (Barenkamp et al.,  Infect. Immun.,  36: 535-40, 1982), enzyme allotypes (Musser et al.,  Infect. Immun.,  52: 183-191, 1986), and other commonly used epidemiologic tools. There have been several attempts to subtype NTHi, but none of the methodologies have been totally satisfactory. The outer-membrane protein composition of NTHi consists of approximately 20 proteins. All NTHi strains contains two common OMP&#39;s with molecular weights of 30,000 and 16,600 daltons. NTHi strains may be subtyped based on two OMP&#39;s within the 32,000-42,000 dalton range. The NTHi liposaccharide profile is fundamentally different than the enteric gram negative bacteria and separates into 1-4 distinct bands ranging from less than 20,000 daltons. 
         [0063]    A prototype NTHi isolate is the low passage isolate 86-028NP which was recovered from a child with chronic otitis media. This strain has been well characterized in vitro (Bakaletz et al.,  Infect. Immun.,  53: 331-5, 1988; Holmes et al.,  Microb. Pathog.,  23: 157-66, 1997) as well as in the chinchilla OM model (described herein) (Bakaletz et al.,  Vaccine,  15: 955-61, 1997; Suzuki et al.,  Infect. Imnzun.,  62: 1710-8, 1994; DeMaria et al.,  Infect. Inznzun.,  64: 5187-92, 1996). The 86-028NP strain was used, as described herein, to identify genes that are up-regulated in expression in the chinchilla model of otitis media and genes that are necessary for NTHi survival in the chinchilla middle ear. 
       DFI Strategy 
       [0064]    A differential fluorescence induction (DFI) strategy was used herein to identify NTHi genes induced during OM in a chinchilla animal model. Several methods have been developed to identify bacterial genes that contribute to the virulence of an organism during infection. Such methods include in vivo expression technology (WET) in which bacterial promoters regulate the expression of gene(s) required for synthesis of essential nutrients required for survival in the host; signature-tagged mutagenesis (STM) enabling tag-specific identification of genes that alter the virulence properties of a microorganism when mutated; DNA microarray technology to globally screen for transcriptionally active genes, and DFI which uses FACS analysis to select for transcriptionally active promoters (Chiang et al.,  Annu. Rev. Microbiol.,  53: 129-154, 1999). DFI is a high-throughput method that allows for the identification of differentially regulated genes regardless of the basal level of expression and does not exclude those that are essential for growth in vitro. 
         [0065]    DFI has been successfully utilized in many microorganisms. For example, a GFP reporter system and flow cytometry was used to study mycobacterial gene expression upon interaction with macrophages (Dhandayuthapani et al.,  Mol. Microbiol.,  17: 901-912, 1995). A promoter trap system was used to identify genes whose transcription was increased when Salmonellae were subjected to environments simulating in vivo growth and when internalized by cultured macrophage-like cells (Valdivia and Falkow,  Mol. Microbiol.,  22: 367-378, 1996; Valdivia and Falkow,  Science,  277: 2007-2011, 1997; Valdivia and Falkow,  Curr. Opin. Microbiol.,  1: 359-363, 1998). In addition, DFI has been used to identify promoters expressed in  S. pneumoniae  and  S. aureus  when grown under varied in vitro conditions simulating infection (Marra et al.,  Infect. Immun.,  148: 1483-1491, 2002; Schneider et al.,  Proc. Natl. Acad. Sci. U.S.A.,  97: 1671-1676, 2000). In addition, DFI has been utilized to study gene regulation in  Bacillus cereus  in response to environmental stimuli (Dunn and Handelsman, Gene, 226: 297-305, 1999), in  S. pneumoniae  in response to a competence stimulatory peptide (Bartilson et al.,  Mol. Microbiol.,  39: 126-135, 2001), and upon interaction with and invasion of host cells in  Bartonella henselae  Lee and Falkow,  Infect. Immun.,  66: 3964-3967, 1998),  Listeria monocytogenes  Wilson et al.,  Infect. Immun.,  69: 5016-5024, 2001),  Brucella abortus  (Eskra et al.,  Infect. Immun.,  69: 7736-7742, 2001), and  Escherichia coli  (Badger et al.,  Mol. Microbiol.,  36: 174-182, 2000). 
         [0066]    Whereas DFI has been successfully used to identify promoters active in cell culture models of infection or in vitro conditions designed to simulate an in vivo environment, few have applied DFI to identify promoters regulated in a specific biological niche within the whole animal. This is likely due to the numerous challenges associated with sorting from an in vivo environment. The host inflammatory response, dissemination and/or clearance of bacterial cells from the site of infection, as well as adherence of bacteria to epithelial cells, possibly via biofilm formation, can make bacteria inaccessible for retrieval from the living animal. These factors, among others, contribute to the complexity of the microenvironment and the heterogeneity of gene expression as the bacteria sense and respond to these changes. Recently, DFI has been used to identify promoters expressed in  S. pneumoniae  when the bacteria were screened in a mouse model of respiratory tract infection and a gerbil infection model of OM (Marra et al.,  Infect. Immun.  70: 1422-33, 2002; Marra et al.,  Microbiol.,  148: 1483-91, 2002). 
       Animal Model 
       [0067]    The chinchilla model is a widely accepted experimental model for OM. In particular, a chinchilla model of NTHi-induced OM has been well characterized (Bakaletz et al.,  J. Infect. Dis.,  168: 865-872, 1993; Bakaletz and Holmes,  Clin. Diagn. Lab. Immunol.,  4: 223-225, 1997; Suzuki and Bakaletz,  Infect. Immun.,  62: 1710-1718, 1994), and has been used to determine the protective efficacy of several NTHi outer membrane proteins, combinations of outer membrane proteins, chimeric synthetic peptide vaccine components, and adjuvant formulations as vaccinogens against OM (Bakaletz et al.,  Vaccine,  15: 955-961, 1997; Bakaletz et al.,  Infect. Immun.,  67: 2746-2762, 1999; Kennedy et al.,  Infect. Immun.,  68: 2756-2765, 2000). 
         [0068]    In particular, there is an unique in vivo model wherein adenovirus predisposes chinchillas to  H. influenzae -induced otitis media, which allowed for the establishment of relevant cell, tissue and organ culture systems for the biological assessment of NTHi (Bakaletz et al.,  J. Infect. Dis.,  168: 865-72, 1993; Suzuki et al.,  Infect. Immunity  62: 1710-8, 1994). Adenovirus infection alone has been used to assess for the transudation of induced serum antibodies into the tympanum (Bakaletz et al.,  Clin. Diagnostic Lab Immunol.,  4(2): 223-5, 1997) and has been used as a co-pathogen with NTHi, to determine the protective efficacy of several active and passive immunization regimens targeting various NTHi outer membrane proteins, combinations of OMPs, chimeric synthetic peptide vaccine components, and adjuvant formulations as vaccinogens against otitis media (Bakaletz et al.,  Infect Immunity,  67(6): 2746-62, 1999; Kennedy et al.,  Infect Immun.,  68(5): 2756-65, 2000; Novotny et al.,  Infect Immunity  68(4): 2119-28, 2000; Poolman et al., Vaccine 19 (Suppl. 1): S108-15, 2000). 
       Genes Unregulated In Vivo in Response to NTHi Infection of the Middle Ear 
       [0069]    In order to identify differentially regulated promoters in response to NTHi infection of the middle ear, a promoter trap library was constructed and sorting parameters defined. A portion of the promoter trap library was inoculated directly into the chinchilla middle ear and OM development was monitored by video otoscopy and tympanometry at 24 and 48 hours. In addition, the middle ear fluids were recovered 24 and 48 hours after infection. Two-color FACS analysis was used to isolated bacteria that were expressing GFP from other cells and debris associated with the effusion. Following isolation, DNA sequence of the  Haemophilus  inserts 5′ of the gfpmut3 gene were determined and analyzed. In this manner, we identified genes that are up-regulated as NTHi sense and respond to the environment of the chinchilla middle ear during AOM. The following genes were identified and due to their up-regulation during NTHi infection, they may play a role in NTHi infection and virulence. 
         [0070]    As described below in Example 7, following the DFI procedure described above and subsequent FACS analysis of gfp-expressing clones, 52 candidate clones containing potential in vivo-regulated promoters were isolated. The genes these clones control were categorized based upon general description and function within the cell and include general metabolic processes, environmental informational processing and membrane transport, membrane proteins and hypothetical proteins. Eight of these 52 clones contain sequences that are unique to NTHi strain 86-028NP. Importantly, 3 clones were isolated from independent screens in more than one animal thereby verifying the method of isolation. 
         [0071]    In order to independently confirm the FACS data, we determined the relative expression of candidate genes by quantitative RT-PCR. The parent strain 86-028NP, was used for these studies. Thus, wild-type gene expression without the influence of plasmid copy number on gene regulation was analyzed, allowing for the indication of false-positive clone identification by FACS. Of the 44 candidate clones containing sequence similar to that identified in  H. influenzae  strain Rd, quantitative comparison of gene expression in vitro and in vivo confirmed up-regulated gene expression for twenty-six genes (60%) when NTHi respond to environmental cues present in the chinchilla middle ear. This analysis identified in vivo-regulated promoters which drive expression of genes involved in membrane transport, environmental informational processing, cellular metabolism, gene regulation, as well as hypothetical proteins with unknown function. (See Table 4 in Example 6). 
         [0072]    Quantitative RT-PCR demonstrated a two-fold increase in lolA expression, enabling lipoprotein transport from the inner membrane to the outer membrane. Bacteria grow rapidly in the middle ear environment reaching 5.0×10 8  CFU NTHi ml middle ear fluid within 48 hours. The bacteria sense and respond to the environment, acquiring or synthesizing the necessary nutrients for growth and survival. The gene encoding the membrane component in ribose sugar transport, rbsC (SEQ ID NO: 619), showed a 5-fold increase in expression in vivo compared to cells growing in vitro. In addition, many genes involved in metabolic processes show a dramatic increase in gene expression in vivo compared to cells growing in vitro. These include a riboflavin synthesis gene, ribB (SEQ ID NO: 623), a purine nucleotide biosynthetic gene purE (SEQ ID NO: 621), ornithine carbamoyltransferase, arcB (SEQ ID NO: 625), involved in arginine degradation via the urea cycle and uxuA (SEQ ID NO: 627), encoding mannonate hydrolase, required for the uptake of D-glucuronate and transformation into glyceraldehyde 3-phosphate. In addition, but to a lesser degree, genes for histidine biosynthesis (hisB; SEQ ID NO: 615), DNA repair (radC; SEQ ID NO: 639) and a putative intracellular septation transmembrane protein (ispZ; SEQ ID NO: 637) were up-regulated. 
         [0073]    Disulfide bond formation is important for folding and assembly of many secreted proteins in bacteria. In prokaryotes, DsbA and DsbB make up the oxidative pathway responsible for the formation of disulfides. DsbB reoxidizes DsbA, which donates disulfide bonds directly to unfolded polypeptides, and DsbB has been demonstrated to generate disulfides de novo from oxidized quinones (Collet and Bardwell,  Mol. Microbiol.,  44: 1-8, 2002). In  H. influenzae  strain Rd, DsbA is required for competence for transformation (Tomb,  Proc. Natl. Acad. Sci. U.S.A.,  89: 10252-10256, 1992). Herein, an approximate 3-fold increase in dsbB gene (SEQ ID NO: 629) transcription was demonstrated, illuminating an important role for disulfide interchange for NTHi growing in the middle ear environment. 
         [0074]    Bacteria colonization of the middle ear, a normally sterile environment, results in a host inflammatory response and subsequent neutrophil infiltration. Bacteria have evolved numerous strategies to combat this host response. NTHi increase gene expression (4-fold) of ureH (SEQ ID NO:631), a homologue of a gene required for expression of active urease in  Helicobacter , shown to be involved in acid tolerance (Young et al.,  J. Bacterol.,  178: 6487-6495, 1996). Recently, it has been reported that urease activity may play a role in chronic  Actinobacillus pleuropneumoniae  infection by counteracting the decrease in pH occurring upon infection (Baltes et al.,  Infect. Immun.,  69: 472-478, 2000; Baltes et al.,  Infect. Immun.,  69: 472-478, 2001; Bosse and MacInnes,  Can. J. Vet. Res.,  64: 145-150). A biotype analysis on NTHi isolates from middle ear effusions demonstrated that 87% are urease positive (DeMaria et al.,  J. Clin. Microbiol.,  20: 1102-1104, 1984). However, the role of urease in NTHi virulence is unknown. Similarly, an increase in expression of a gene whose product demonstrates 88% sequence identity to a pyridoxine biosynthesis protein in  S. pneumoniae  and 60% homology to a putative singlet oxygen resistance protein that may function as an antioxidant. Phosphorylcholine (ChoP) has been implicated in the pathogenesis of NTHi (Weiser et al.,  Infect. Immun.,  65: 943-950, 1997). NTHi modulates ChoP expression by phase variation, decorating the LOS on the cell surface. ChoP may contribute to NTHi persistence in the respiratory tract via decreased susceptibility to antimicrobial peptides (Lysecko et al.,  Infect. Immun.,  68: 1664-1671, 2000) and alter the sensitivity to serum killing mediated by C-reactive protein (CRP) (Weiser et al.,  J. Exp. Med.,  187: 631-640, 1998). The microenvironment of the nasopharynx and middle ear cavity may select for the ChoP +  phenotype, as ChoP +  strains show greater colonization of the chinchilla nasopharynx (Tong et al.,  Infect. Immun.,  68: 4593-4597, 2000). Expression of the licC gene (SEQ ID NO: 633) was also increased. The licC gene encodes a phosphorylcholine cytidylyltransferase that plays a role in the biosynthesis of phosphorylcholine-derivatized LOS (Rock et al.,  J. Bacterol.,  183: 4927-4931, 2001). 
         [0075]    Also included among the in vivo-induced genes is a set whose products subsequently regulate gene expression or DNA replication. These genes include transcriptional regulation of glycerol metabolism by the glp repressor, glpR (SEQ ID NO: 643), the arginine repressor gene, argR (SEQ ID NO: 647), and the integration host factor (IHF) beta subunit, ihfB (SEQ ID NO: 645). IHF is a histone-like protein that binds DNA at specific sequences, an accessory factor involved in replication, site-specific recombination and transcription, altering the activity of a large number of operons (Goosen and van de Putte,  Mol. Microbiol.  16: 1-7, 1995). In addition, CspD inhibits DNA replication during stationary phase-induced stress response in  E. coli  (Yamanaka et al.,  Mol. Microbiol.,  39: 1572-1584, 2001) and the mukF (SEQ ID NO: 641) gene protein homologue contributes to a remodeling of the nucleiod structure into a more compact fog in prior to cell segregation (Sawitzke and Austin,  Proc. Natl. Acad. Sci. U.S.A.,  62: 1710-1718, 2000). The DFI strategy described herein also identified promoters induced in vivo for genes of unknown function. The hypothetical protein, HI0094, demonstrated an 8-fold increase in gene expression during early OM but its role remains unknown. HI1163 (SEQ ID NO: 651) showed 58% amino acid identity with the hypothetical YdiJ proteins, a putative oxidase, of  E. coli.    
         [0076]    A high-density transposon mutagenesis strategy was used to identify  H. influenzae  genes essential for growth on rich medium (Akerley et al.,  Proc. Natl. Acad. Sci. U.S.A.,  99: 966-971, 2002). Six genes were identified in the screen described herein that are included in essential gene set described in Akerley′ et al., supra. (hisB, lppB, lolA, ispZ, mukF and unknown HI0665). Recently genes of non-typeable  H. influenzae  that are expressed upon interaction with two human respiratory tract-derived epithelial cell lines have been identified. These genes included those involved in metabolic processes, stress responses, gene expression, cell envelope biosynthesis, DNA-related processes, cell division and ORF&#39;s encoding proteins of unknown function. (Ulsen et al.,  Mol. Microbiol.,  45: 485-500, 2002). Similarly the stress response gene, cspD (SEQ ID NO: 649), genes involved in purine and riboflavin biosynthesis, and a protein of unknown function, vapA was identified in the screen described herein. Expression of vapA was detected in vitro, yet vapA gene expression increased two-fold in vivo. These unique approaches identified known genes that are upregulated in NTHi-induced OM and therefore are likely to play a role in NTHi infection and virulence; and may be potential candidates for vaccines and antisense therapies and other therapeutic methods of treatment of NTHi related disorders. 
         [0077]    The DFI strategy resulted in the identification of promoters induced in vivo for genes of unknown function as well. The hypothetical protein, HI0094, demonstrated a 8-fold increase in gene expression during early OM but its role remains unknown. HI1163 (SEQ ID NO: 651) showed 58% amino acid identity with the hypothetical YdiJ proteins, a putative oxidase, of  E. coli . Therefore, these hypothetical genes are likely to play a role in OM induced by NTHi infection. 
     
    
     
       BRIEF DESCRIPTION OF FIGURES 
         [0078]      FIG. 1  depicts the LKP gene region in a panel of  Haemophilus  isolates. The strain 86-028NP sequence is identical in this region to the sequence in NTHi strain R3001. Both of these NTHi lack the hif gene cluster encoding the hemagglutinating pilus. 
           [0079]      FIG. 2  depicts the rfaD region in a panel of  Haemophilus  isolates. The gene arrangement in the rfaD region of the strain 86-028NP genome is similar to that of the strain Rd genome but different than the arrangement of these genes seen in the genome of most NTHi examined. 
           [0080]      FIGS. 3A-3M  set out the nucleotide sequences (SEQ ID NOS: 589-614) described in Table 4, which were identified to be upregulated during OM infection (see Example 6). The nucleotides (nt.) which correspond to known genes and those nt. which correspond to the contig sequences set out as SEQ ID NO: 1-576 are also presented. 
       
    
    
     DETAILED DESCRIPTION 
       [0081]    The following examples illustrate the invention wherein Example 1 describes the sequence of the NTHi genome, Example 2 describes the identified contigs and initial gene discovery, Example 3 describes construction of the NTHi promoter trap library, Example 4 describes the analyses of 86-028NP derivatives expressing GFP, Example 5 demonstrates direct labelling of bacteria from middle ear fluids, Example 6 describes identification of promoters induced in vivo in acute otitis media, Example 7 describes identification of virulence-associated genes, Example 8 describes identification of unique NTHi gene sequences, Example 9 described the analysis of the complete NTHi 86-028NP genome, and Example 10 compares the genomic DNA sequences of NTHi, strain 86-028NP and  H. influenzae  serotype d, strain kw20 
       Example 1 
     Sequence of a Non-Typeable  Haemophilus influenzae  Genome 
       [0082]    NTHi strain 86-028NP is a minimally passaged clinical isolate obtained from a pediatric patient who underwent tympanostomy and tube insertion for chronic OM at Columbus Children&#39;s Hospital. (Bakaletz et al.  Infection and Immunity,  56(2): 331-335, 1988) The 86-028NP strain was deposited with the American Type Tissue Collection (Manassas, Va. 20108 USA) on Oct. 16, 2002 and assigned accession no. PTA-4764. 
         [0083]    In an effort to more broadly approach the identification of the virulence determinants in NTHi, the genome of the NTHi 86-028NP strain was sequenced to 3-fold coverage. Chromosomal DNA was prepared from strain 86-028NP using the Puregene protocol and sheared to 2-4 kb in size with a Hydroshear instalment (Gene Machines). The sheared DNA was ethanol-precipitated, end-repaired using a mixture of Klenow enzyme and T4 DNA polymerase, and size-selected by agarose gel electrophoresis to obtain 2-4 kb fragments as described in Chissoe et al. ( Methods: a Companion to Methods of Enzymology  3: 55-65, 1991) and Sambrook et al. ( Molecular Cloning: a Laboratory Manual,  2 nd  Ed. Cold Springs Harbor, N Y, 1989). These fragments were cloned into vector pUC18 using the SmaI restriction site (phosphatase-treated) and transformed into  E. coli  XL-1 Blue, selecting for ampicillin resistance. Colonies that contain inserts were identified by blue/white screening on LB-Amp plates containing X-gal, and transferred into 96-deep well plates containing 1.5 ml of TB-Amp (TB=Terrific Broth) broth. The deep-well plate cultures were grown overnight (18-22 hours) at 37° C. Template preparation, sequencing and contig assembly were performed. 
         [0084]    Automated template preparation was performed on the Beckman Biomek 2000 automated robotics workstation as described in Chissoe et al., (supra.) Briefly, each 96-deep well plate, containing the clones prepared above, was centrifuged to pellet the cells, the supernatant decanted, and the cells frozen (if necessary) at −20° C. Four 96-deep well blocks were placed on the Biomek table, and the liquid handling robot was used to prepare the template using an automated version of a typical SDS-NaOH lysis protocol as described in Chissoe et al., (supra.). The final ethanol-precipitated templates were each dissolved in 50 μl ddH 2 O, and used for DNA sequencing. 
         [0085]    Sequencing reactions were run by re-arraying the templates (from 96-well plates) into 384-well plates, using the Robbins Hydra 96 robot. Cycle-sequencing reactions were run using PE Big-Dye™ terminators and universal primers (M13 forward and reverse), cleaned up over Sephadex G50 columns, and analyzed on a PE Biosystems 3700 capillary electrophoresis DNA sequencer according to the manufacturer&#39;s instructions. Sequencing reads (8219) were assembled into 576 contigs (SEQ ID NOS: 1-576 herein). The statistics for the 3-fold sequencing are shown in Table 2A. The total unique sequence in assembly 17 is 1.74 Mb. 
         [0000]    
       
         
               
               
               
               
             
               
               
               
               
             
           
               
                 TABLE 2A 
               
               
                   
               
               
                 Contig Size 
                 Total Number 
                 Total Length 
                 % of Cumulative 
               
               
                   
               
             
             
               
                   
               
             
          
           
               
                  0-1 kb 
                 65 
                 55961 
                  3.2% 
               
               
                  1-2 kb 
                 228 
                 333665 
                 19.2% 
               
               
                  2-3 kb 
                 101 
                 243059 
                 14.0% 
               
               
                  3-4 kb 
                 49 
                 172385 
                  9.9% 
               
               
                  4-5 kb 
                 45 
                 196699 
                 11.3% 
               
               
                  5-10 kb 
                 74 
                 515152 
                 29.6% 
               
               
                 10-20 kb 
                 11 
                 144591 
                  8.3% 
               
               
                 20-30 kb 
                 3 
                 77352 
                  4.4% 
               
               
                   
               
             
          
         
       
     
         [0086]    Subsequently, 8-fold sequencing analysis of the NTHi genome was carried out. The 8-fold sequencing assembled the NTHi genome into 11 contigs. Contigs 5, 8, 9, 10, 12-18 are denoted as SEQ ID NOS: 675-685 herein. The statistics for the 8-fold sequencing are shown in Table 2B. 
         [0000]    
       
         
               
               
               
               
             
               
               
               
               
             
           
               
                 TABLE 2B 
               
               
                   
               
               
                 Contig Size  
                 Total Number 
                 Total Length  
                 % of Cumulative 
               
               
                   
               
             
             
               
                   
               
             
          
           
               
                  0-1 kb 
                 5 
                 3950 
                  0.2% 
               
               
                  1-2 kb 
                 3 
                 4316 
                  0.2% 
               
               
                  2-3 kb 
                 0 
                 0 
                  0.0% 
               
               
                  3-4 kb 
                 1 
                 3964 
                  0.2% 
               
               
                  4-5 kb 
                 0 
                 0 
                  0.0% 
               
               
                  5-10 kb 
                 0 
                 0 
                  0.0% 
               
               
                 10-20 kb 
                 1 
                 15147 
                  0.8% 
               
               
                 20-30 kb 
                 2 
                 51888 
                  2.7% 
               
               
                 30-40 kb 
                 0 
                 0 
                  0.0% 
               
               
                 40-50 kb 
                 0 
                 0 
                  0.0% 
               
               
                 50-100 kb 
                 1 
                 85814 
                  4.5% 
               
               
                 &gt;100 kb 
                 5 
                 1760339 
                 91.4% 
               
               
                   
               
             
          
         
       
     
       Example 2 
     Contig Description and Initial Gene Discovery 
       [0087]    Seventy-five of the 88 contigs with length ≧5000 bp, identified with the 3-fold sequence analysis, show significant similarity via BLASTN to genes in  H. influenzae  strain Rd. To visualize the potential relationship between the gene order in  H. influenzae  strain 86-028NP and  H. influenzae  strain Rd, the 86-028NP three-fold contig set and the Rd gene set were bidirectionally compared using BLASTN. The results were plotted in gene-order verses contig space by sorting the contigs based on gene coordinates of the Rd genes hit, anchoring each contig at the smallest coordinate found as described in Ray et al., ( Bioinformatics  17: 1105-12, 2001). Compared in this fashion, an incomplete assembly of a genome with identical gene order to a completely known genome would display a monotonically increasing stair-stepped form. 
         [0088]    BLASTX was used to identify hits to sequences with homology to genes in the strain Rd genome as well as genes not found in  H. influenzae  strain Rd. Hits to strain Rd sequences were removed from the data set and the other hits summarized in Table 3A. The data are presented as follows: contig # (SEQ ID NO: #), column 1; E score for each hit, column 2; the name of the protein that had homology to a portion of the amino acid translation of the cited contig, column 3; the organism producing the homologue, column 4; and the Genbank protein identifier for each of the proteins cited in column 3, column 5; the corresponding nucleotides within the contig (referenced by SEQ ID NO:). In most instances, several homologues were identified but for clarity, the protein of greatest homology is cited in Table 3A. 
         [0089]    The sequences for some of the genes listed in Table 3A were identified within the 8-fold sequencing of the NTHi genome. Table 3B lists the location of these genes within the 11 contigs, the full length open reading frame sequence (identified by SEQ ID NO:), the derived amino acid sequence encoded by the open reading frame and the gene with high homology identified by BLASTX (as listed in Table 3A). 
         [0090]    To examine the relative short range gene arrangements in NTHi and the Rd strain, the gene order in two gene clusters that have been well-described were compared. First, the genes present in the hemagglutinating pilus (LKP) gene region were examined. (Mhlanga-Mutangadura et al.,  J Bacteria  180(17): 4693-703, 1998). The pilus gene cluster is located between the purE and pepN genes, only fragments of which are depicted in  FIG. 1 . The serotype b strain, Eagan, contains the hifABCDE gene cluster and produces hemagglutinating pili. Strain Rd lacks the hicAB genes as well as the hifABCDE gene cluster. In general, the nontypeable strains previously examined contained the hicAB genes but not the hif genes that encode the hemagglutinating pilus. The strain 86-028NP sequence (described herein) is identical in this region to the sequence in NTHi strain R3001 ( FIG. 1 ). The rfaD gene encodes an enzyme involved in the biosynthesis of endotoxin. In addition, the rfaD gene from NTHi strain 2019 has been characterized by Nichols et al. ( Infect Immunity  65(4): 1377-86, 1997). In strain 2019, the rfaD gene is immediately upstream of the rfaF gene that encodes another enzyme involved in endotoxin biosynthesis. The gene arrangement in strain Rd is different; the rfaD and rfaF genes are separated by approximately 11 kb of sequence. Most nontypeable strains examined contained the gene arrangement seen in strain 2019. In contrast, strain 86-028NP has a gene arrangement identical to that seen in strain Rd ( FIG. 2 ). 
         [0091]    A global analysis of the current assembly indicates that the gene content and order are similar to that in strain Rd. A more detailed analysis revealed that there are a substantial number of NTHi genes not previously seen in the Pasteurellaceae and some regions where the NTHi gene content and order is different than that seen in strain Rd. Thus, the current data suggest that the strain 86-028NP genome will contain a complex mosaic of Rd and non-Rd like features. 
         [0092]    The DFI strategy also identified novel NTHi sequences that had increased gene expression. A list of these novel contig sequences that contain genes or gene fragments that have homology to ORFs in other organisms (primarily gram-negative bacteria) is set out in Table 3A. For example, the nucleotide sequence of contig 442 (SEQ ID NO: 442), nucleotides 1498-1845 are highly homologous to the sequences encoding amino acids 1-116 of  H. influenzae  strain Rd lipoprotein B (LppB). The gene is positioned between the stationary phase survival gene, surE, and a gene encoding a 43 kD antigenic outer membrane lipoprotein that is highly homologous to the recently identified bacterial lipoprotein, LppB/NlpD, which has been associated with virulence (Padmalayam et al.,  Infect. Immun.,  68: 4972-4979, 2000). Recently, Zhang and coworkers demonstrated that nlpD and surE gene expression was induced during stationary phase of bacterial growth in  Thermotoga maritima  (Zhang et al.,  Structure  ( Camb ), 9: 1095-1106, 2001). Therefore, under stress-induced conditions in the middle ear, this NTHi lipoprotein may be expressed. 
         [0000]    
       
         
               
               
               
               
               
               
             
               
               
               
               
               
               
             
           
               
                 TABLE 3A 
               
               
                   
               
               
                   
                   
                   
                   
                 Genbank 
                   
               
               
                 Contig 
                 E score 
                 Hit Identity 
                 Organism 
                 Protein 
                 SEQ ID NO: 
               
               
                   
               
             
             
               
                   
               
             
          
           
               
                 104 
                 4.00E−59 
                 CpdB 
                 
                   Pasteurella 
                 
                 NP_246953.1 
                 nt. 204-659 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 104 
               
               
                 106 
                 9.00E−10 
                 hypothetical protein 
                 
                   Pyrococcus 
                 
                 G71244 
                 nt. 40-309 of 
               
               
                   
                   
                 PH0217 - 
                 
                   horikoshii 
                 
                   
                 SEQ ID NO: 106 
               
               
                 106 
                 1.00E−08 
                 unknown 
                 
                   Pasteurella 
                 
                 NP_246871.1 
                 nt. 605-694 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 106 
               
               
                 106 
                 2.00E−20 
                 Orf122 
                 
                   Chlorobium 
                 
                 AAG12204.1 
                 nt. 7-210 of 
               
               
                   
                   
                   
                 
                   tepidum 
                 
                   
                 SEQ ID NO: 106 
               
               
                 110 
                 3.00E−05 
                 ArdC antirestriction 
                 IncW plasmid pSa 
                 AAD52160.1 
                 compliment of 
               
               
                   
                   
                 protein 
                   
                   
                 nt. 959-1162 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 110 
               
               
                 110 
                 1.00E−33 
                 hypothetical protein 
                 
                   Salmonella 
                 
                 NP_458676.1 
                 compliment of 
               
               
                   
                   
                   
                   enterica  subsp. 
                   
                 nt. nt. 181-825 of 
               
               
                   
                   
                   
                   enterica  serovar 
                   
                 SEQ ID NO: 110 
               
               
                   
                   
                   
                 
                   Typhi 
                 
               
               
                 111 
                 5.00E−12 
                 putative membrane 
                 
                   Salmonella 
                 
                 NP_458664.1 
                 compliment of 
               
               
                   
                   
                 protein 
                   enterica  subsp. 
                   
                 nt. 45-287 of 
               
               
                   
                   
                   
                   enterica  serovar 
                   
                 SEQ ID NO: 111 
               
               
                   
                   
                   
                 
                   Typhi 
                 
               
               
                 111 
                 6.00E−41 
                 hypothetical protein 
                 
                   Salmonella 
                 
                 NP_458658.1 
                 compliment of 
               
               
                   
                   
                   
                   enterica  subsp. 
                   
                 nt. 1091-1480 of 
               
               
                   
                   
                   
                   enterica  serovar 
                   
                 SEQ ID NO: 111 
               
               
                   
                   
                   
                 
                   Typhi 
                 
               
               
                 114 
                 7.00E−80 
                 unknown 
                 
                   Pasteurella 
                 
                 NP_245828.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 nt. 118-696 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 114 
               
               
                 115 
                 2.00E−09 
                 A111R 
                 
                   Paramecium 
                 
                 NP_048459.1 
                 nt. 555-869 of 
               
               
                   
                   
                   
                   bursaria  Chlorella 
                   
                 SEQ ID NO: 115 
               
               
                   
                   
                   
                 virus 1 
               
               
                 118 
                 5.00E−45 
                 DNA methylase 
                 
                   Vibrio cholerae 
                 
                 NP_231404.1 
                 nt. 44-439 of 
               
               
                   
                   
                 HsdM, putative 
                   
                   
                 SEQ ID NO: 118 
               
               
                 122 
                 2.00E−18 
                 unknown 
                 
                   Pasteurella 
                 
                 NP_245314.1 
                 nt. 865-1302 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 122 
               
               
                 123 
                 4.00E−99 
                 RNA 
                 
                   Proteus mirabilis 
                 
                 P50509 
                 nt. 351-782 of 
               
               
                   
                   
                 POLYMERASE 
                   
                   
                 SEQ ID NO: 123 
               
               
                   
                   
                 SIGMA-32 
               
               
                   
                   
                 FACTOR 
               
               
                 124 
                 9.00E−58 
                 ACETOLACTATE 
                 
                   Spirulina platensis 
                 
                 P27868 
                 nt. 603-1025 of 
               
               
                   
                   
                 SYNTHASE 
                   
                   
                 SEQ ID NO: 124 
               
               
                   
                   
                 (ACETOHYDROXY- 
               
               
                   
                   
                 ACID SYNTHASE) 
               
               
                   
                   
                 (ALS) 
               
               
                 130 
                 0 
                 restriction 
                 
                   Neisseria 
                 
                 CAA09003.1 
                 nt. 495-1559 of 
               
               
                   
                   
                 modification 
                 
                   meningitidis 
                 
                   
                 SEQ ID NO: 130 
               
               
                   
                   
                 system-R protein 
               
               
                 131 
                 6.00E−91 
                 uronate isomerase 
                 
                   Salmonella 
                 
                 NP_457532.1 
                 compliment of 
               
               
                   
                   
                 (glucuronate 
                   enterica  subsp. 
                   
                 nt. 661-1380 of 
               
               
                   
                   
                 isomerase) 
                   enterica  serovar 
                   
                 SEQ ID NO: 131 
               
               
                   
                   
                   
                 
                   Typhi 
                 
               
               
                 133 
                 3.00E−30 
                 GyrA 
                 
                   Pasteurella 
                 
                 NP_245778.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 nt. 1447-1626 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 133 
               
               
                 133 
                 1.00E−27 
                 DNA GYRASE 
                 
                   Pectobacterium 
                 
                 P41513 
                 compliment of 
               
               
                   
                   
                 SUBUNIT A 
                 
                   carotovorum 
                 
                   
                 nt. 1302-1442 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 133 
               
               
                 138 
                 7.00E−06 
                 KicA 
                 
                   Pasteurella 
                 
                 NP_245545.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 nt. 92-157 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 138 
               
               
                 138 
                  1.00E−148 
                 TYPE II 
                 
                   Haemophilus 
                 
                 O30869 
                 compliment of 
               
               
                   
                   
                 RESTRICTION 
                 
                   aegyptius 
                 
                   
                 nt. 164-1045 of 
               
               
                   
                   
                 ENZYME HAEII 
                   
                   
                 SEQ ID NO: 138 
               
               
                   
                   
                 (ENDONUCLEASE 
               
               
                   
                   
                 HAEII) (R. HAEII) 
               
               
                 143 
                 4.00E−06 
                 Gifsy-1 prophage 
                 
                   Salmonella 
                 
                 NP_461555.1 
                 compliment of 
               
               
                   
                   
                 protein 
                   typhimurium  LT2 
                   
                 nt. 228-632 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 143 
               
               
                 143 
                 1.00E−14 
                 hypothetical protein 
                 Bacteriophage 
                 NP_050531.1 
                 compliment of 
               
               
                   
                   
                   
                 VT2-Sa 
                   
                 nt. 778-1248 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 143 
               
               
                 143 
                 5.00E−09 
                 hypothetical protein 
                 
                   Salmonella 
                 
                 CAD09979.1 
                 compliment of 
               
               
                   
                   
                   
                   enterica  subsp. 
                   
                 nt. 715-1026 of 
               
               
                   
                   
                   
                   enterica  serovar 
                   
                 SEQ ID NO: 143 
               
               
                   
                   
                   
                 
                   Typhi 
                 
               
               
                 143 
                 6.00E−10 
                 hypothetical 14.9 kd 
                 
                   Escherichia coli 
                 
                 NP_065324.1 
                 nt. 3-173 of 
               
               
                   
                   
                 protein 
                   
                   
                 SEQ ID NO: 143 
               
               
                 147 
                 1.00E−38 
                 GTP-binding 
                 
                   Escherichia coli 
                 
                 NP_289127.1 
                 compliment of 
               
               
                   
                   
                 elongation factor, 
                 O157:H7 EDL933 
                   
                 nt. 172-342 of 
               
               
                   
                   
                 may be inner 
                   
                   
                 SEQ ID NO: 147 
               
               
                   
                   
                 membrane protein 
               
               
                 147 
                 2.00E−14 
                 GTP-binding 
                 
                   Borrelia 
                 
                 NP_212222.1 
                 compliment of 
               
               
                   
                   
                 membrane protein 
                 
                   burgdorferi 
                 
                   
                 nt. 17-181 of 
               
               
                   
                   
                 (lepA) 
                   
                   
                 SEQ ID NO: 147 
               
               
                 148 
                 6.00E−17 
                 galactokinase 
                 
                   Homo sapiens 
                 
                 AAC35849.1 
                 compliment of 
               
               
                   
                   
                   
                   
                   
                 nt. 746-1246 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 148 
               
               
                 148 
                 7.00E−96 
                 GALACTOKINASE 
                 
                   Actinobacillus 
                 
                 P94169 
                 compliment of 
               
               
                   
                   
                 (GALACTOSE 
                 
                   pleuropneumoniae 
                 
                   
                 nt. 232-741 of 
               
               
                   
                   
                 KINASE) 
                   
                   
                 SEQ ID NO: 148 
               
               
                 149 
                 1.00E−92 
                 GTP-binding 
                   Buchnera  sp. 
                 NP_240245.1 
                 compliment of 
               
               
                   
                   
                 protein TypA/BipA 
                 APS 
                   
                 nt. 265-1077 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 149 
               
               
                 15 
                 2.00E−21 
                 ORF 1 
                 
                   Escherichia coli 
                 
                 CAA39631.1 
                 nt: 665-850 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 15 
               
               
                 150 
                 6.00E−17 
                 unknown 
                 
                   Pasteurella 
                 
                 NP_245919.1 
                 nt. 171-665 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 150 
               
               
                 153 
                 7.00E−07 
                 outer membrane 
                 
                   Rickettsia conorii 
                 
                 T30852 
                 nt. 51-623 of 
               
               
                   
                   
                 protein A 
                   
                   
                 SEQ ID NO: 153 
               
               
                 155 
                 7.00E−40 
                 cytochrome d 
                 
                   Vibrio cholerae 
                 
                 NP_233259.1 
                 nt. 583-1002 of 
               
               
                   
                   
                 ubiquinol oxidase, 
                   
                   
                 SEQ ID NO: 155 
               
               
                   
                   
                 subunit II 
               
               
                 157 
                 7.00E−13 
                 unknown 
                 
                   Pasteurella 
                 
                 NP_245490.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 nt. 1170-1367 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 157 
               
               
                 157 
                 2.00E−05 
                 glycosyl 
                 
                   Neisseria 
                 
                 AAA68012.1 
                 nt. 85-189 of 
               
               
                   
                   
                 transferase 
                 
                   gonorrhoeae 
                 
                   
                 SEQ ID NO: 157 
               
               
                 158 
                  1.00E−152 
                 MltC 
                 
                   Pasteurella 
                 
                 NP_246259.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 nt. 36-530 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 158 
               
               
                 161 
                 3.00E−25 
                 lipoprotein, putative 
                 
                   Vibrio cholerae 
                 
                 NP_230232.1 
                 nt. 870-1439 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 161 
               
               
                 163 
                 9.00E−53 
                 chorismate 
                 
                   Caulobacter 
                 
                 NP_421948.1 
                 nt. 1283-2029 of 
               
               
                   
                   
                 synthase 
                 
                   crescentus 
                 
                   
                 SEQ ID NO: 163 
               
               
                 168 
                 3.00E−13 
                 COPPER- 
                 
                   Mus musculus 
                 
                 Q64430 
                 nt. 66-995 of 
               
               
                   
                   
                 TRANSPORTING 
                   
                   
                 SEQ ID NO: 168 
               
               
                   
                   
                 ATPASE 1 
               
               
                   
                   
                 (COPPER PUMP 1) 
               
               
                 168 
                 2.00E−22 
                 Cu transporting 
                 
                   Homo sapiens 
                 
                 2001422A 
                 nt. 135-989 of 
               
               
                   
                   
                 ATPase P 
                   
                   
                 SEQ ID NO: 168 
               
               
                 174 
                 8.00E−48 
                 magnesium/cobalt 
                 
                   Mesorhizobium 
                 
                 NP_103977.1 
                 nt. 918-1205 of 
               
               
                   
                   
                 transport protein 
                 
                   loti 
                 
                   
                 SEQ ID NO: 174 
               
               
                 175 
                 5.00E−26 
                 vacB protein 
                   Buchnera  sp. 
                 NP_240369.1 
                 compliment of 
               
               
                   
                   
                   
                 APS 
                   
                 nt. 1-1587 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 175 
               
               
                 176 
                 3.00E−21 
                 putative ABC 
                 
                   Campylobacter 
                 
                 NP_282774.1 
                 compliment of 
               
               
                   
                   
                 transport system 
                 
                   jejuni 
                 
                   
                 nt. 259-1089 of 
               
               
                   
                   
                 permease protein [ 
                   
                   
                 SEQ ID NO: 176 
               
               
                 183 
                 5.00E−29 
                 PROBABLE ATP 
                 
                   Ralstonia 
                 
                 NP_521442.1 
                 compliment of 
               
               
                   
                   
                 SYNTHASE A 
                 
                   solanacearum 
                 
                   
                 nt. 42-677 of 
               
               
                   
                   
                 CHAIN 
                   
                   
                 SEQ ID NO: 183 
               
               
                   
                   
                 TRANSMEMBRANE 
               
               
                   
                   
                 PROTEIN 
               
               
                 185 
                 6.00E−85 
                 putative exported 
                 
                   Salmonella 
                 
                 NP_458655.1 
                 compliment of 
               
               
                   
                   
                 protein 
                   enterica  subsp. 
                   
                 nt. 162-1529 of 
               
               
                   
                   
                   
                   enterica  serovar 
                   
                 SEQ ID NO: 185 
               
               
                   
                   
                   
                 
                   Typhi 
                 
               
               
                 187 
                 2.00E−05 
                 transketolase 
                 
                   Homo sapiens 
                 
                 AAA61222.1 
                 nt. 709-819 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 187 
               
               
                 188 
                  1.00E−116 
                 ribonuclease E 
                 
                   Xylella fastidiosa 
                 
                 NP_299884.1 
                 compliment of 
               
               
                   
                   
                   
                 9a5c 
                   
                 nt. 280-1704 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 188 
               
               
                 192 
                 1.00E−38 
                 ImpA 
                 
                   Pasteurella 
                 
                 NP_245829.1 
                 nt. 35-448 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 192 
               
               
                 193 
                 3.00E−08 
                 Orf80 
                 Enterobacteria 
                 NP_052285.1 
                 nt. 1612-1818 of 
               
               
                   
                   
                   
                 phage 186 
                   
                 SEQ ID NO: 193 
               
               
                 193 
                 1.00E−06 
                 holin 
                 
                   Haemophilus 
                 
                 AAC45168.1 
                 nt. 370-576 of 
               
               
                   
                   
                   
                 
                   somnus 
                 
                   
                 SEQ ID NO: 193 
               
               
                 193 
                    0.007 
                 unknown 
                 Enterobacteria 
                 NP_052260.1 
                 nt. 1376-1609 of 
               
               
                   
                   
                   
                 phage 186 
                   
                 SEQ ID NO: 193 
               
               
                 193 
                 2.00E−48 
                 lysozyme 
                 
                   Haemophilus 
                 
                 AAC45169.1 
                 nt. 608-1093 of 
               
               
                   
                   
                   
                 
                   somnus 
                 
                   
                 SEQ ID NO: 193 
               
               
                 199 
                 4.00E−21 
                 unknown protein 
                 
                   Escherichia coli 
                 
                 NP_288675.1 
                 nt. 398-778 of 
               
               
                   
                   
                   
                 O157:H7 
                   
                 SEQ ID NO: 199 
               
               
                   
                   
                   
                 EDL933, 
               
               
                   
                   
                   
                 prophage CP- 
               
               
                   
                   
                   
                 933V 
               
               
                 199 
                 2.00E−49 
                 hypothetical protein 
                 Bacteriophage 
                 NP_049495.1 
                 compliment of 
               
               
                   
                   
                   
                 933W 
                   
                 nt. 1907-2392 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 199 
               
               
                 20 
                 1.00E−62 
                 RpL14 
                 
                   Pasteurella 
                 
                 NP_246344.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 nt. 233-601 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 20 
               
               
                 200 
                 2.00E−62 
                 hypothetical protein 
                 
                   Salmonella 
                 
                 NP_458658.1 
                 compliment of 
               
               
                   
                   
                   
                   enterica  subsp. 
                   
                 nt. 431-997 of 
               
               
                   
                   
                   
                   enterica  serovar 
                   
                 SEQ ID NO: 200 
               
               
                   
                   
                   
                 
                   Typhi 
                 
               
               
                 200 
                 3.00E−16 
                 hypothetical protein 
                 
                   Salmonella 
                 
                 NP_458657.1 
                 compliment of 
               
               
                   
                   
                   
                   enterica  subsp. 
                   
                 nt. 1028-1264 of 
               
               
                   
                   
                   
                   enterica  serovar 
                   
                 SEQ ID NO: 200 
               
               
                   
                   
                   
                 
                   Typhi 
                 
               
               
                 201 
                 2.00E−26 
                 TsaA 
                 
                   Pasteurella 
                 
                 NP_245732.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 nt. 1618-1809 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 201 
               
               
                 209 
                 6.00E−16 
                 TsaA 
                 
                   Pasteurella 
                 
                 NP_245732.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 nt. 2-136 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 209 
               
               
                 211 
                 2.00E−15 
                 unknown 
                 
                   Pasteurella 
                 
                 NP_245535.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 nt. 23-211 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 211 
               
               
                 211 
                 1.00E−70 
                 PUTATIVE 
                 
                   Ralstonia 
                 
                 NP_520082.1 
                 compliment of 
               
               
                   
                   
                 ATPASE PROTEIN 
                 
                   solanacearum 
                 
                   
                 nt. 475-915 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 211 
               
               
                 212 
                 3.00E−18 
                 hypothetical protein 
                 
                   Escherichia coli 
                 
                 NP_309775.1 
                 compliment of 
               
               
                   
                   
                   
                 O157:H7 
                   
                 nt. 895-1035 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 212 
               
               
                 216 
                  1.00E−173 
                 unknown 
                 
                   Pasteurella 
                 
                 NP_245069.1 
                 nt. 35-1543 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 216 
               
               
                 217 
                 9.00E−18 
                 diacylglycerol 
                 
                   Vibrio cholerae 
                 
                 NP_233101.1 
                 nt. 2083-2208 of 
               
               
                   
                   
                 kinase 
                   
                   
                 SEQ ID NO: 217 
               
               
                 221 
                 4.00E−34 
                 Tail-Specific 
                 
                   Chlamydia 
                 
                 NP_219953.1 
                 nt. 849-1421 of 
               
               
                   
                   
                 Protease 
                 
                   trachomatis 
                 
                   
                 SEQ ID NO: 221 
               
               
                 222 
                 4.00E−23 
                 AGR_C_3689p 
                 
                   Agrobacterium 
                 
                 NP_355005.1 
                 compliment of 
               
               
                   
                   
                   
                   tumefaciens  str. 
                   
                 nt. 940-1305 of 
               
               
                   
                   
                   
                 C58 (Cereon) 
                   
                 SEQ ID NO: 222 
               
               
                 224 
                 9.00E−19 
                 unknown 
                 
                   Pasteurella 
                 
                 NP_245536.1 
                 nt. 15-308 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 224 
               
               
                 225 
                 1.00E−89 
                 portal vector -like 
                 
                   Salmonella 
                 
                 NP_461651.1 
                 nt. 31-750 of of 
               
               
                   
                   
                 protein, in phage 
                 
                   typhimurium 
                 
                   
                 SEQ ID NO: 225 
               
               
                   
                   
                 P2 [ Salmonella   
                 LT2Fels-2 
               
               
                   
                   
                   typhimuriu m LT2] 
                 prophage 
               
               
                 229 
                 2.00E−25 
                 anaerobic 
                 
                   Salmonella 
                 
                 CAB62266.1 
                 nt. 1806-2108 of 
               
               
                   
                   
                 ribonucleotide 
                 
                   typhimurium 
                 
                   
                 SEQ ID NO: 229 
               
               
                   
                   
                 reductase 
               
               
                 234 
                 3.00E−08 
                 conserved 
                 
                   Xylella fastidiosa 
                 
                 NP_299850.1 
                 nt. 1680-2048 of 
               
               
                   
                   
                 hypothetical protein 
                 9a5c 
                   
                 SEQ ID NO: 234 
               
               
                 234 
                 1.00E−42 
                 Methionine 
                 
                   Clostridium 
                 
                 NP_348177.1 
                 compliment of 
               
               
                   
                   
                 sulfoxide reductase 
                 
                   acetobutylicum 
                 
                   
                 nt. 415-654 of 
               
               
                   
                   
                 C-terminal domain 
                   
                   
                 SEQ ID NO: 234 
               
               
                   
                   
                 related protein, 
               
               
                   
                   
                 YPPQ ortholog 
               
               
                 235 
                 4.00E−16 
                 phage-related tail 
                 Wolbachia 
                 AAK85310.1 
                 compliment of 
               
               
                   
                   
                 protein 
                 endosymbiont of 
                   
                 nt. 931-1929 of 
               
               
                   
                   
                   
                 
                   Drosophila 
                 
                   
                 SEQ ID NO: 235 
               
               
                   
                   
                   
                 
                   melanogaster 
                 
               
               
                 235 
                 6.00E−56 
                 similar to orfG 
                 
                   Salmonella 
                 
                 NP_461625.1 
                 compliment of 
               
               
                   
                   
                 protein in phage 
                   typhimurium  LT2, 
                   
                 nt. 313-1863 of 
               
               
                   
                   
                 186,  Salmonella   
                 Fels-2 prophage 
                   
                 SEQ ID NO: 235 
               
               
                   
                   
                   typhimurium  LT2 
               
               
                 236 
                 6.00E−20 
                 conserved 
                 
                   Pseudomonas 
                 
                 NP_252693.1 
                 nt. 1572-1916 of 
               
               
                   
                   
                 hypothetical protein 
                 
                   aeruginosa 
                 
                   
                 SEQ ID NO: 236 
               
               
                 240 
                 5.00E−27 
                 MODIFICATION 
                 
                   Brevibacterium 
                 
                 P10283 
                 compliment of 
               
               
                   
                   
                 METHYLASE BEPI 
                 
                   epidermidis 
                 
                   
                 nt. 922-1305 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 240 
               
               
                 241 
                 2.00E−15 
                 phage-related 
                 
                   Xylella fastidiosa 
                 
                 NP_299573.1 
                 compliment of 
               
               
                   
                   
                 protein 
                 9a5c 
                   
                 nt. 865-1305 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 241 
               
               
                 241 
                 4.00E−08 
                 hypothetical protein 
                 phage SPP1 
                 T42296 
                 nt. 73-636 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 241 
               
               
                 241 
                 4.00E−07 
                 hypothetical protein 
                 
                   Salmonella 
                 
                 NP_458686.1 
                 nt. 10-468 of 
               
               
                   
                   
                   
                   enterica  subsp. 
                   
                 SEQ ID NO: 241 
               
               
                   
                   
                   
                   enterica  serovar 
               
               
                   
                   
                   
                 
                   Typhi 
                 
               
               
                 242 
                 2.00E−29 
                 translation 
                 chloroplast - 
                 S35701 
                 compliment of 
               
               
                   
                   
                 elongation factor 
                 soybean 
                   
                 nt. 18-1085 of 
               
               
                   
                   
                 EF-G 
                   
                   
                 SEQ ID NO: 242 
               
               
                 247 
                 3.00E−23 
                 GTP 
                 
                   Synechococcus 
                 
                 Q54769 
                 compliment of 
               
               
                   
                   
                 CYCLOHYDROLASE 
                 sp. PCC 7942 
                   
                 nt. 1009-1257c of 
               
               
                   
                   
                 I (GTP-CH-I) 
                   
                   
                 SEQ ID NO: 247 
               
               
                 248 
                 6.00E−05 
                 phospho-N- 
                 
                   Aquifex aeolicus 
                 
                 NP_213025.1 
                 nt. 830-1747 of 
               
               
                   
                   
                 acetylmuramoyl- 
                   
                   
                 SEQ ID NO: 248 
               
               
                   
                   
                 pentapeptide- 
               
               
                   
                   
                 transferase 
               
               
                 25 
                 2.00E−86 
                 PROBABLE 
                 
                   Ralstonia 
                 
                 NP_522358.1 
                 compliment of 
               
               
                   
                   
                 TRANSPORT 
                 
                   solanacearum 
                 
                   
                 nt. 309-854 of 
               
               
                   
                   
                 TRANSMEMBRANE 
                   
                   
                 SEQ ID NO: 25 
               
               
                   
                   
                 PROTEIN 
               
               
                 25 
                 7.00E−06 
                 major facilitator 
                 
                   Caulobacter 
                 
                 NP_419155.1 
                 compliment of 
               
               
                   
                   
                 family transporter 
                 
                   crescentus 
                 
                   
                 nt. 134-283 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 25 
               
               
                 250 
                  1.00E−150 
                 CpdB 
                 
                   Pasteurella 
                 
                 NP_246953.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 nt. 36-1016 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 250 
               
               
                 252 
                 3.00E−57 
                 alanyl-tRNA 
                 
                   Vibrio cholerae 
                 
                 AAA99922.1 
                 compliment of 
               
               
                   
                   
                 synthetase 
                   
                   
                 nt. 1418-1951 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 252 
               
               
                 253 
                  1.00E−108 
                 similar to 
                 
                   Listeria 
                 
                 NP_464432.1 
                 compliment of 
               
               
                   
                   
                 glutathione 
                 
                   monocytogenes 
                 
                   
                 nt. 411-1358 of of 
               
               
                   
                   
                 Reductase 
                 EGD-e 
                   
                 SEQ ID NO: 253 
               
               
                 259 
                 3.00E−39 
                 hypothetical protein 
                 
                   Salmonella 
                 
                 NP_458654.1 
                 compliment of 
               
               
                   
                   
                   
                   enterica  subsp. 
                   
                 nt. 342-1037 of 
               
               
                   
                   
                   
                   enterica  serovar 
                   
                 SEQ ID NO: 259 
               
               
                   
                   
                   
                 
                   Typhi 
                 
               
               
                 259 
                 3.00E−17 
                 possible exported 
                 
                   Salmonella 
                 
                 NP_458653.1 
                 compliment of 
               
               
                   
                   
                 protein 
                   enterica  subsp. 
                   
                 nt. 1251-1607 of 
               
               
                   
                   
                   
                   enterica  serovar 
                   
                 SEQ ID NO: 259 
               
               
                   
                   
                   
                 
                   Typhi 
                 
               
               
                 261 
                 5.00E−74 
                 hypothetical protein 
                 
                   Haemophilus 
                 
                 S27582 
                 compliment of 
               
               
                   
                   
                 6 -  Haemophilus   
                 
                   influenzae 
                 
                   
                 nt. 3-422 of 
               
               
                   
                   
                 
                   influenzae 
                 
                   
                   
                 SEQ ID NO: 261 
               
               
                 263 
                 1.00E−94 
                 putative 
                 
                   Haemophilus 
                 
                 AAD01406.1 
                 nt. 2142-2672 of 
               
               
                   
                   
                 transposase 
                 
                   paragallinarum 
                 
                   
                 SEQ ID NO: 263 
               
               
                 264 
                  1.00E−126 
                 unknown 
                 
                   Actinobacillus 
                 
                 NP_067554.1 
                 nt. 40-714 of 
               
               
                   
                   
                   
                   actinomycetemco - 
                   
                 SEQ ID NO: 264 
               
               
                   
                   
                   
                 
                   mitans 
                 
               
               
                 264 
                  1.00E−103 
                 unknown 
                 
                   Actinobacillus 
                 
                 NP_067555.1 
                 nt. 695-1309 of 
               
               
                   
                   
                   
                   actinomycetemco - 
                   
                 SEQ ID NO: 264 
               
               
                   
                   
                   
                 
                   mitans 
                 
               
               
                 264 
                 2.00E−21 
                 unknown 
                 
                   Actinobacillus 
                 
                 NP_067556.1 
                 nt. 1302-1448 of 
               
               
                   
                   
                   
                   actinomycetemco - 
                   
                 SEQ ID NO: 264 
               
               
                   
                   
                   
                 
                   mitans 
                 
               
               
                 265 
                 6.00E−27 
                 Aminopeptidase 2 
                 chloroplast 
                 Q42876 
                 nt. 556-1539 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 265 
               
               
                 268 
                  1.00E−116 
                 MutY 
                 
                   Pasteurella 
                 
                 NP_246257.1 
                 nt. 1003-1581 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 268 
               
               
                 272 
                 1.00E−07 
                 hypothetical protein 
                 Bacteriophage 
                 NP_049495.1 
                 compliment of 
               
               
                   
                   
                   
                 933W 
                   
                 nt. 77-232 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 272 
               
               
                 274 
                 3.00E−13 
                 unknown 
                 
                   Pasteurella 
                 
                 NP_246952.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 nt. 1658-1975 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 274 
               
               
                 275 
                 3.00E−20 
                 CafA 
                 
                   Neisseria 
                 
                 AAG24267.1 
                 nt. 1299-1571 of 
               
               
                   
                   
                   
                 
                   gonorrhoeae 
                 
                   
                 SEQ ID NO: 275 
               
               
                 276 
                 1.00E−45 
                 mukE protein 
                 
                   Vibrio cholerae 
                 
                 NP_231351.1 
                 compliment of 
               
               
                   
                   
                   
                   
                   
                 nt. 650-1390 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 276 
               
               
                 276 
                 1.00E−69 
                 KicA 
                 
                   Pasteurella 
                 
                 NP_245545.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 nt. 647-1321 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 276 
               
               
                 278 
                 2.00E−56 
                 3-oxoacyl-[acyl- 
                 
                   Salmonella 
                 
                 NP_455686.1 
                 nt. 1366-1944 of 
               
               
                   
                   
                 carrier-protein] 
                   enterica  subsp. 
                   
                 SEQ ID NO: 278 
               
               
                   
                   
                 synthase III 
                   enterica  serovar 
               
               
                   
                   
                   
                 
                   Typhi 
                 
               
               
                 281 
                 5.00E−56 
                 unknown 
                 
                   Pasteurella 
                 
                 NP_246261.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 nt. 31-678 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 281 
               
               
                 282 
                 3.00E−09 
                 orf25; similar to T 
                 bacteriophage phi 
                 NP_490625.1 
                 compliment of 
               
               
                   
                   
                 gene of P2 
                 CTX 
                   
                 nt. 511-1032 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 282 
               
               
                 282 
                 1.00E−08 
                 orf11; similar to 
                 
                   Haemophilus 
                 
                 AAC45165.1 
                 compliment of 
               
               
                   
                   
                 phage P2 gene S- 
                 
                   somnus 
                 
                   
                 nt. 1450-1584 of 
               
               
                   
                   
                 like product, which 
                   
                   
                 SEQ ID NO: 282 
               
               
                   
                   
                 is involved in tail 
               
               
                   
                   
                 synthesis, 
               
               
                 282 
                 9.00E−27 
                 putative 
                 
                   Salmonella 
                 
                 NP_457167.1 
                 compliment of 
               
               
                   
                   
                 bacteriophage tail 
                   enterica  subsp. 
                   
                 nt. 3-509 of 
               
               
                   
                   
                 protein 
                   enterica  serovar 
                   
                 SEQ ID NO: 282 
               
               
                   
                   
                   
                 
                   Typhi 
                 
               
               
                 286 
                 5.00E−18 
                 plasmid-related 
                 
                   Listeria innocua 
                 
                 NP_471066.1 
                 compliment of 
               
               
                   
                   
                 protein 
                 plasmid 
                   
                 nt. 887-1501 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 286 
               
               
                 287 
                 8.00E−20 
                 GTP 
                 
                   Escherichia coli 
                 
                 NP_287920.1 
                 nt. 2-145 of 
               
               
                   
                   
                 cyclohydrolase II 
                 O157:H7 EDL933 
                   
                 SEQ ID NO: 287 
               
               
                 289 
                  1.00E−168 
                 MODIFICATION 
                 
                   Haemophilus 
                 
                 O30868 
                 compliment of 
               
               
                   
                   
                 METHYLASE 
                 
                   aegyptius 
                 
                   
                 nt. 138-1091 of 
               
               
                   
                   
                 HAEII 
                   
                   
                 SEQ ID NO: 289 
               
               
                 289 
                 5.00E−11 
                 TYPE II 
                 
                   Haemophilus 
                 
                 O30869 
                 compliment of 
               
               
                   
                   
                 RESTRICTION 
                 
                   aegyptius 
                 
                   
                 nt. 22-132 of 
               
               
                   
                   
                 ENZYME HAEII 
                   
                   
                 SEQ ID NO: 289 
               
               
                 289 
                 6.00E−47 
                 mukF homolog 
                 
                   Haemophilus 
                 
                 AAB70828.1 
                 compliment of 
               
               
                   
                   
                   
                   influenzae  biotype 
                   
                 nt. 1107-1385 of 
               
               
                   
                   
                   
                 
                   aegyptius 
                 
                   
                 SEQ ID NO: 289 
               
               
                 294 
                  1.00E−171 
                 LICA PROTEIN 
                 
                   Haemophilus 
                 
                 P14181 
                 compliment of 
               
               
                   
                   
                   
                 
                   influenzae 
                 
                   
                 nt. 677-1564 of 
               
               
                   
                   
                   
                 RM7004 
                   
                 SEQ ID NO: 294 
               
               
                 297 
                  1.00E−158 
                 DNA methylase 
                 
                   Vibrio cholerae 
                 
                 NP_231404.1 
                 compliment of 
               
               
                   
                   
                 HsdM, putative 
                   
                   
                 nt. 12-1136 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 297 
               
               
                 302 
                 0 
                 HEME-BINDING 
                 
                   Haemophilus 
                 
                 P33950 
                 nt. 3-1316 of 
               
               
                   
                   
                 PROTEIN A 
                   influenzae  DL42 
                   
                 SEQ ID NO: 302 
               
               
                 304 
                 6.00E−19 
                 hypothetical protein 
                 
                   Haemophilus 
                 
                 S27582 
                 nt. 121-267 of 
               
               
                   
                   
                 6 
                 
                   influenzae 
                 
                   
                 SEQ ID NO: 304 
               
               
                 305 
                 6.00E−40 
                 putative 
                 
                   Streptococcus 
                 
                 NP_269557.1 
                 nt. 65-805 of 
               
               
                   
                   
                 recombinase - 
                   pyogenes  M1 
                   
                 SEQ ID NO: 305 
               
               
                   
                   
                 phage associated 
                 GAS 
               
               
                 305 
                 7.00E−22 
                 single stranded 
                   Shewanella  sp. 
                 AAB57886.1 
                 nt. 1607-2014 of 
               
               
                   
                   
                 DNA-binding 
                 F1A 
                   
                 SEQ ID NO: 305 
               
               
                   
                   
                 protein 
               
               
                 305 
                 1.00E−43 
                 phage-related 
                 
                   Bacillus 
                 
                 NP_244410.1 
                 nt. 92-751 of 
               
               
                   
                   
                 protein 
                 
                   halodurans 
                 
                   
                 SEQ ID NO: 305 
               
               
                 312 
                 1.00E−28 
                 PUTATIVE 
                 
                   Ralstonia 
                 
                 NP_518994.1 
                 nt. 1819-2673 of 
               
               
                   
                   
                 BACTERIOPHAGE- 
                 
                   solanacearum 
                 
                   
                 SEQ ID NO: 312 
               
               
                   
                   
                 RELATED 
               
               
                   
                   
                 TRANSMEMBRANE 
               
               
                   
                   
                 PROTEIN 
               
               
                 312 
                 9.00E−25 
                 similar to 
                 
                   Homo sapiens 
                 
                 XP_068727.1 
                 nt. 27-1001 of 
               
               
                   
                   
                 BASEMENT 
                   
                   
                 SEQ ID NO: 312 
               
               
                   
                   
                 MEMBRANE- 
               
               
                   
                   
                 SPECIFIC 
               
               
                   
                   
                 HEPARAN 
               
               
                   
                   
                 SULFATE 
               
               
                   
                   
                 PROTEOGLYCAN 
               
               
                   
                   
                 CORE PROTEIN 
               
               
                   
                   
                 PRECURSOR 
               
               
                   
                   
                 (HSPG) 
               
               
                 315 
                 2.00E−45 
                 uracil permease 
                 
                   Deinococcus 
                 
                 NP_296001.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   radiodurans 
                 
                   
                 nt. 525-1592 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 315 
               
               
                 318 
                 7.00E−15 
                 CzcD 
                 
                   Pasteurella 
                 
                 NP_246276.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 nt. 3-227 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 318 
               
               
                 320 
                 2.00E−60 
                 orf3; similar to 
                 
                   Haemophilus 
                 
                 AAC45159.1 
                 compliment of 
               
               
                   
                   
                 endonuclease 
                 
                   somnus 
                 
                   
                 nt. 606-1241 of 
               
               
                   
                   
                 subunit of the 
                   
                   
                 SEQ ID NO: 320 
               
               
                   
                   
                 phage P2 
               
               
                   
                   
                 terminase (gene M) 
               
               
                 320 
                 2.00E−09 
                 orf4; similar to 
                 
                   Haemophilus 
                 
                 AAC45160.1 
                 compliment of 
               
               
                   
                   
                 head 
                 
                   somnus 
                 
                   
                 nt. 52-285 of 
               
               
                   
                   
                 completion/stabili- 
                   
                   
                 SEQ ID NO: 320 
               
               
                   
                   
                 zation protein (gene 
               
               
                   
                   
                 L) of phage P2 
               
               
                 320 
                 3.00E−35 
                 orf2; similar to 
                 
                   Haemophilus 
                 
                 AAC45158.1 
                 compliment of 
               
               
                   
                   
                 major capsid 
                 
                   somnus 
                 
                   
                 nt. 1271-1624 of 
               
               
                   
                   
                 protein precursor of 
                   
                   
                 SEQ ID NO: 320 
               
               
                   
                   
                 phage P2 (gene N) 
               
               
                 323 
                 4.00E−37 
                 dedC protein 
                 
                   Escherichia coli 
                 
                 AAA23966.1 
                 compliment of 
               
               
                   
                   
                   
                   
                   
                 nt. 74-463 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 323 
               
               
                 324 
                  1.00E−153 
                 conserved 
                 
                   Neisseria 
                 
                 NP_274972.1 
                 compliment of 
               
               
                   
                   
                 hypothetical protein 
                 
                   meningitidis 
                 
                   
                 nt. 930-1943 of 
               
               
                   
                   
                   
                 MC58 
                   
                 SEQ ID NO: 324 
               
               
                 326 
                 5.00E−52 
                 selenophosphate 
                 
                   Eubacterium 
                 
                 CAB53511.1 
                 compliment of 
               
               
                   
                   
                 synthetase 
                 
                   acidaminophilum 
                 
                   
                 nt. 1186-2292 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 326 
               
               
                 328 
                  1.00E−129 
                 secretion protein 
                 
                   Pseudomonas 
                 
                 NP_252510.1 
                 compliment of 
               
               
                   
                   
                 SecD 
                 
                   aeruginosa 
                 
                   
                 nt. 8-625 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 328 
               
               
                 333 
                 3.00E−08 
                 unknown 
                 
                   Pasteurella 
                 
                 NP_245489.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 nt. 5-418 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 333 
               
               
                 336 
                 6.00E−38 
                 probable methyl 
                 
                   Pseudomonas 
                 
                 NP_253353.1 
                 compliment of 
               
               
                   
                   
                 transferase 
                 
                   aeruginosa 
                 
                   
                 nt. 2547-2819 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 336 
               
               
                 338 
                 2.00E−98 
                 Pmi 
                 
                   Pasteurella 
                 
                 NP_245766.1 
                 nt. 144-842 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 338 
               
               
                 339 
                 2.00E−07 
                 tRNA 
                 
                   Escherichia coli 
                 
                 QQECPE 
                 nt. 2331-2540 of 
               
               
                   
                   
                 nucleotidyltransferase 
                   
                   
                 SEQ ID NO: 339 
               
               
                 340 
                 0 
                 DNA gyrase, 
                 
                   Salmonella 
                 
                 NP_461214.1 
                 compliment of 
               
               
                   
                   
                 subunit A, type II 
                   typhimurium  LT2 
                   
                 nt. 93-1799 of 
               
               
                   
                   
                 topoisomerase 
                   
                   
                 SEQ ID NO: 340 
               
               
                 342 
                 4.00E−12 
                 tolA protein 
                 
                   Haemophilus 
                 
                 JC5212 
                 nt. 980-1318 of 
               
               
                   
                   
                   
                 
                   influenzae 
                 
                   
                 SEQ ID NO: 342 
               
               
                 344 
                 1.00E−07 
                 MODIFICATION 
                 
                   Haemophilus 
                 
                 P50192 
                 compliment of 
               
               
                   
                   
                 METHYLASE 
                 
                   parahaemolyticus 
                 
                   
                 nt. 849-1034 of 
               
               
                   
                   
                 HPHIA 
                   
                   
                 SEQ ID NO: 344 
               
               
                 344 
                 8.00E−05 
                 ABC transporter 
                 
                   Leishmania major 
                 
                 AAF31030.1 
                 compliment of 
               
               
                   
                   
                 protein 1 
                   
                   
                 nt. 17-205 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 344 
               
               
                 349 
                 3.00E−44 
                 conserved 
                 
                   Neisseria 
                 
                 NP_273467.1 
                 compliment of 
               
               
                   
                   
                 hypothetical protein 
                 
                   meningitidis 
                 
                   
                 nt. 1397-1903 of 
               
               
                   
                   
                   
                 MC58 
                   
                 SEQ ID NO: 349 
               
               
                 349 
                 8.00E−09 
                 hypothetical protein 
                 
                   Pseudomonas 
                 
                 NP_252667.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   aeruginosa 
                 
                   
                 nt. 795-1121 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 349 
               
               
                 349 
                 9.00E−10 
                 conserved 
                 
                   Helicobacter 
                 
                 NP_207009.1 
                 compliment of 
               
               
                   
                   
                 hypothetical 
                   pylori  26695 
                   
                 nt. 1319-1816 of 
               
               
                   
                   
                 secreted protein 
                   
                   
                 SEQ ID NO: 349 
               
               
                 349 
                 2.00E−06 
                 putative TPR 
                 
                   Salmonella 
                 
                 NP_463149.1 
                 compliment of 
               
               
                   
                   
                 repeat protein 
                   typhimurium  LT2 
                   
                 nt. 2244-2558 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 349 
               
               
                 35 
                 1.00E−23 
                 type I restriction- 
                 
                   Xylella fastidiosa 
                 
                 NP_300003.1 
                 compliment of 
               
               
                   
                   
                 modification 
                 9a5c 
                   
                 nt. 29-388 of 
               
               
                   
                   
                 system specificity 
                   
                   
                 SEQ ID NO: 35 
               
               
                   
                   
                 determinant 
               
               
                 352 
                  1.00E−116 
                 putative peptidase 
                 
                   Escherichia coli 
                 
                 NP_416827.1 
                 compliment of 
               
               
                   
                   
                   
                 K12 
                   
                 nt. 951-1640 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 352 
               
               
                 352 
                 0 
                 unknown 
                 
                   Pasteurella 
                 
                 NP_245275.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 nt. 86-946 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 352 
               
               
                 354 
                 5.00E−86 
                 putative uronate 
                 
                   Salmonella 
                 
                 NP_462052.1 
                 compliment of 
               
               
                   
                   
                 isomerase 
                   typhimurium  LT2 
                   
                 nt. 168-914 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 354 
               
               
                 356 
                 1.00E−07 
                 isomerase-like 
                 
                   Escherichia coli 
                 
                 S57220 
                 nt. 5-73 of 
               
               
                   
                   
                 protein (DsbD) - 
                   
                   
                 SEQ ID NO: 356 
               
               
                 358 
                 1.00E−07 
                 USG protein 
                 
                   Pediococcus 
                 
                 CAC16793.1 
                 nt. 534-1307 of 
               
               
                   
                   
                   
                 
                   pentosaceus 
                 
                   
                 SEQ ID NO: 358 
               
               
                 358 
                    0.005 
                 HsdS protein 
                 
                   Escherichia coli 
                 
                 CAA10700.1 
                 nt. 26-205 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 358 
               
               
                 361 
                  1.00E−152 
                 maltodextrin 
                 
                   Escherichia coli 
                 
                 NP_289957.1 
                 compliment of 
               
               
                   
                   
                 phosphorylase 
                 O157:H7 EDL933 
                   
                 nt. 77-922 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 361 
               
               
                 363 
                 6.00E−06 
                 BH2505~unknown 
                 
                   Bacillus 
                 
                 NP_243371.1 
                 nt. 554-844 of 
               
               
                   
                   
                 conserved protein 
                 
                   halodurans 
                 
                   
                 SEQ ID NO: 363 
               
               
                 368 
                 1.00E−12 
                 H02F09.3.p 
                 
                   Caenorhabditis 
                 
                 NP_508295.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   elegans 
                 
                   
                 nt. 1069-1977 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 368 
               
               
                 368 
                 6.00E−27 
                 hypothetical 
                 
                   Mesorhizobium 
                 
                 NP_102360.1 
                 compliment of 
               
               
                   
                   
                 glycine-rich protein 
                 
                   loti 
                 
                   
                 nt. 1201-1986 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 368 
               
               
                 37 
                 6.00E−09 
                 putative ATP- 
                 
                   Escherichia coli 
                 
                 NP_415469.1 
                 compliment of 
               
               
                   
                   
                 binding component 
                 K12 
                   
                 nt. 455-691 of 
               
               
                   
                   
                 of a transport 
                   
                   
                 SEQ ID NO: 37 
               
               
                   
                   
                 system 
               
               
                 372 
                 7.00E−18 
                 conserved 
                 
                   Clostridium 
                 
                 BAB80319.1 
                 compliment of 
               
               
                   
                   
                 hypothetical protein 
                 
                   perfringens 
                 
                   
                 nt. 1763-1924 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 372 
               
               
                 376 
                 7.00E−24 
                 putative 
                 
                   Salmonella 
                 
                 NP_456379.1 
                 compliment of 
               
               
                   
                   
                 bacteriophage 
                   enterica  subsp. 
                   
                 nt. 158-808 of 
               
               
                   
                   
                 protein 
                   enterica  serovar 
                   
                 SEQ ID NO: 376 
               
               
                   
                   
                   
                 
                   Typhi 
                 
               
               
                 376 
                 8.00E−10 
                 hypothetical protein 
                 
                   Xylella fastidiosa 
                 
                 NP_298882.1 
                 compliment of 
               
               
                   
                   
                   
                 9a5c 
                   
                 nt. 1129-1671 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 376 
               
               
                 376 
                 9.00E−06 
                 Iin1713 
                 
                   Listeria innocua 
                 
                 NP_471049.1 
                 compliment of 
               
               
                   
                   
                   
                   
                   
                 nt. 913-1557 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 376 
               
               
                 377 
                 6.00E−05 
                 Vng1732c 
                   Halobacterium  sp. 
                 NP_260487.1 
                 nt. 2378-2587 of 
               
               
                   
                   
                   
                 NRC-1 
                   
                 SEQ ID NO: 377 
               
               
                 377 
                 1.00E−11 
                 INVASIN 
                 
                   Yersinia 
                 
                 P31489 
                 compliment of 
               
               
                   
                   
                 PRECURSOR 
                 
                   enterocolitica 
                 
                   
                 nt. 127-345 of 
               
               
                   
                   
                 (OUTER 
                   
                   
                 SEQ ID NO: 377 
               
               
                   
                   
                 MEMBRANE 
               
               
                   
                   
                 ADHESIN) 
               
               
                 382 
                 4.00E−16 
                 unknown 
                 
                   Pasteurella 
                 
                 NP_246871.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 nt. 967-1068 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 382 
               
               
                 383 
                 4.00E−36 
                 putative 
                 
                   Streptomyces 
                 
                 BAB69302.1 
                 nt. 488-1162 of 
               
               
                   
                   
                 transposase 
                 
                   avermitilis 
                 
                   
                 SEQ ID NO: 383 
               
               
                 383 
                 3.00E−58 
                 recombinase 
                 IncN plasmid R46 
                 NP_511241.1 
                 compliment of 
               
               
                   
                   
                   
                   
                   
                 nt. 1-393 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 383 
               
               
                 383 
                 4.00E−24 
                 transposase 
                 
                   Escherichia coli 
                 
                 I69674 
                 nt. 1294-1740 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 383 
               
               
                 383 
                 0 
                 tnpA 
                 
                   Yersinia 
                 
                 CAA73750.1 
                 nt. 1782-2834 of 
               
               
                   
                   
                   
                 
                   enterocolitica 
                 
                   
                 SEQ ID NO: 383 
               
               
                 385 
                 2.00E−31 
                 unknown 
                 
                   Pasteurella 
                 
                 NP_246065.1 
                 nt. 1515-1772 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 385 
               
               
                 386 
                 5.00E−65 
                 cydC [ 
                 
                   Escherichia coli 
                 
                 AAA66172.1 
                 compliment of 
               
               
                   
                   
                   
                   
                   
                 nt. 3438-4115 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 386 
               
               
                 386 
                 4.00E−33 
                 ABC transporter, 
                 
                   Mesorhizobium 
                 
                 NP_105463.1 
                 compliment of 
               
               
                   
                   
                 ATP-binding 
                 
                   loti 
                 
                   
                 nt. 2569-3390 of 
               
               
                   
                   
                 protein 
                   
                   
                 SEQ ID NO: 386 
               
               
                 388 
                 3.00E−45 
                 60 KDA INNER- 
                 
                   Coxiella burnetii 
                 
                 P45650 
                 compliment of 
               
               
                   
                   
                 MEMBRANE 
                   
                   
                 nt. 3211-3759 of 
               
               
                   
                   
                 PROTEIN 
                   
                   
                 SEQ ID NO: 388 
               
               
                   
                   
                 HOMOLOG 
               
               
                 390 
                 4.00E−25 
                 putative DNA- 
                 
                   Salmonella 
                 
                 NP_458175.1 
                 nt. 1051-1416 of 
               
               
                   
                   
                 binding protein 
                   enterica  subsp. 
                   
                 SEQ ID NO: 390 
               
               
                   
                   
                   
                   enterica  serovar 
               
               
                   
                   
                   
                 
                   Typhi 
                 
               
               
                 390 
                 3.00E−13 
                 transcriptional 
                 
                   Bacillus 
                 
                 NP_241773.1 
                 compliment of 
               
               
                   
                   
                 regulator 
                 
                   halodurans 
                 
                   
                 nt. 84-578 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 390 
               
               
                 390 
                 3.00E−06 
                 DNA translocase 
                 
                   Staphylocoecus 
                 
                 NP_372265.1 
                 compliment of 
               
               
                   
                   
                 stage III sporulation 
                   aureus  subsp. 
                   
                 nt. 620-871 of 
               
               
                   
                   
                 prot homolog 
                   aureus  Mu50 
                   
                 SEQ ID NO: 390 
               
               
                 395 
                 7.00E−31 
                 ATPase, Cu++ 
                 
                   Homo sapiens 
                 
                 NP_000044.1 
                 compliment of 
               
               
                   
                   
                 transporting, beta 
                   
                   
                 nt. 615-1406 of 
               
               
                   
                   
                 polypeptide 
                   
                   
                 SEQ ID NO: 395 
               
               
                 397 
                 3.00E−23 
                 terminase large 
                 Bacteriophage 
                 NP_112076.1 
                 compliment of 
               
               
                   
                   
                 subunit 
                 HK620 
                   
                 nt. 2363-2725 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 397 
               
               
                 397 
                 3.00E−16 
                 hypothetical protein 
                 
                   Xylella fastidiosa 
                 
                 NP_297824.1 
                 compliment of 
               
               
                   
                   
                   
                 9a5c 
                   
                 nt. 1517-1744 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 397 
               
               
                 398 
                 4.00E−67 
                 orf32 
                 
                   Haemophiius 
                 
                 NP_536839.1 
                 compliment of 
               
               
                   
                   
                   
                 phage HP2 
                   
                 nt. 1288-1866 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 398 
               
               
                 398 
                 8.00E−24 
                 putative 
                 
                   Salmonella 
                 
                 NP_463063.1 
                 compliment of 
               
               
                   
                   
                 cytoplasmic protein 
                   typhimurium  LT2 
                   
                 nt. 798-1220 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 398 
               
               
                 398 
                 2.00E−83 
                 orf31 
                 
                   Haemophilus 
                 
                 NP_043502.1 
                 compliment of 
               
               
                   
                   
                   
                 phage HP1 
                   
                 nt. 1881-2510 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 398 
               
               
                 399 
                 1.00E−94 
                 HEME/HEMOPEXIN- 
                 
                   Haemophilus 
                 
                 P45355 
                 nt. 88-774 of 
               
               
                   
                   
                 BINDING 
                   influenzae  N182 
                   
                 SEQ ID NO: 399 
               
               
                   
                   
                 PROTEIN 
               
               
                 401 
                 3.00E−63 
                 Sty SBLI 
                 
                   Salmonella 
                 
                 CAA68058.1 
                 nt. 1690-2742 of 
               
               
                   
                   
                   
                 
                   enterica 
                 
                   
                 SEQ ID NO: 401 
               
               
                 401 
                 3.00E−06 
                 RESTRICTION- 
                 
                   Mycoplasma 
                 
                 NP_325912.1 
                 nt. 79-489 of 
               
               
                   
                   
                 MODIFICATION 
                 
                   pulmonis 
                 
                   
                 SEQ ID NO: 401 
               
               
                   
                   
                 ENZYME 
               
               
                   
                   
                 SUBUNIT M3 
               
               
                 402 
                 2.00E−13 
                 OPACITY 
                 
                   Neisseria 
                 
                 Q05033 
                 compliment of 
               
               
                   
                   
                 PROTEIN OPA66 
                 
                   gonorrhoeae 
                 
                   
                 nt. 2634-2915 of 
               
               
                   
                   
                 PRECURSOR 
                   
                   
                 SEQ ID NO: 402 
               
               
                 406 
                 8.00E−13 
                 type I restriction 
                 
                   Neisseria 
                 
                 NP_273876.1 
                 nt. 281-520 of 
               
               
                   
                   
                 enzyme EcoR124IIR 
                 
                   meningitidis 
                 
                   
                 SEQ ID NO: 406 
               
               
                   
                   
                   
                 MC58 
               
               
                 407 
                 6.00E−65 
                 unknown 
                 
                   Pasteurella 
                 
                 NP_246237.1 
                 nt. 938-2450 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 407 
               
               
                 407 
                 5.00E−99 
                 PepE 
                 
                   Pasteurella 
                 
                 NP_245391.1 
                 nt. 1216-1917 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 407 
               
               
                 407 
                 1.00E−16 
                 Hemoglobin- 
                 
                   Haemophilus 
                 
                 Q48153 
                 nt. 1-141 of 
               
               
                   
                   
                 haptoglobin binding 
                   influenzae  Tn106 
                   
                 SEQ ID NO: 407 
               
               
                   
                   
                 protein A 
               
               
                 409 
                  1.00E−106 
                 hypothetical protein 
                 
                   Haemophilus 
                 
                 S27577 
                 compliment of 
               
               
                   
                   
                 1 
                 
                   influenzae 
                 
                   
                 nt. 2524-3159 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 409 
               
               
                 411 
                 4.00E−29 
                 heme-repressible 
                 
                   Haemophilus 
                 
                 AAB46794.1 
                 nt. 391-615 of 
               
               
                   
                   
                 hemoglobin-binding 
                   influenzae , type b, 
                   
                 SEQ ID NO: 411 
               
               
                   
                   
                 protein 
                 strain HI689 
               
               
                 411 
                 0 
                 Hemoglobin- 
                 
                   Haemophilus 
                 
                 Q48153 
                 nt. 651-3263 of 
               
               
                   
                   
                 haptoglobin binding 
                   influenzae  Tn106 
                   
                 SEQ ID NO: 411 
               
               
                   
                   
                 protein A 
               
               
                 412 
                 2.00E−07 
                 REGULATORY 
                 bacteriophage 
                 P03036 
                 compliment of 
               
               
                   
                   
                 PROTEIN CRO 
                 434 
                   
                 nt. 59-259 of 
               
               
                   
                   
                 (ANTIREPRESSOR) 
                   
                   
                 SEQ ID NO: 412 
               
               
                 412 
                 4.00E−06 
                 hypothetical protein 
                 Bacteriophage 
                 CAC83535.1 
                 nt. 1436-1654 of 
               
               
                   
                   
                   
                 P27 
                   
                 SEQ ID NO: 412 
               
               
                 413 
                 8.00E−07 
                 hypothetical protein 
                 
                   Deinococcus 
                 
                 NP_294301.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   radiodurans 
                 
                   
                 nt. 791-1012 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 413 
               
               
                 414 
                 9.00E−65 
                 conserved 
                 
                   Vibrio cholerae 
                 
                 NP_230092.1 
                 nt. 1696-2103 of 
               
               
                   
                   
                 hypothetical protein 
                   
                   
                 SEQ ID NO: 414 
               
               
                 414 
                 3.00E−93 
                 unknown 
                 
                   Pasteurella 
                 
                 NP_246834.1 
                 nt. 1777-2109 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 414 
               
               
                 416 
                 2.00E−17 
                 unknown 
                 
                   Pasteurella 
                 
                 NP_246629.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 nt. 2565-2831 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 416 
               
               
                 416 
                 4.00E−26 
                 hypothetical protein 
                 
                   Escherichia coli 
                 
                 S30728 
                 compliment of 
               
               
                   
                   
                 o154 
                   
                   
                 nt. 1928-2254 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 416 
               
               
                 416 
                 3.00E−37 
                 transport protein 
                 
                   Pseudomonas 
                 
                 NP_253757.1 
                 compliment of 
               
               
                   
                   
                 TatC 
                 
                   aeruginosa 
                 
                   
                 nt. 1494-2018 of of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 416 
               
               
                 417 
                 1.00E−66 
                 weakly similar to 
                 
                   Listeria innocua 
                 
                 NP_471073.1 
                 compliment of 
               
               
                   
                   
                 methyltransferases 
                   
                   
                 nt. 999-1928 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 417 
               
               
                 417 
                 5.00E−05 
                 DNA-BINDING 
                 
                   Pectobacterium 
                 
                 Q47587 
                 compliment of 
               
               
                   
                   
                 PROTEIN RDGA 
                 
                   carotovorum 
                 
                   
                 nt. 3526-4212 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 417 
               
               
                 417 
                 2.00E−29 
                 putative phage- 
                 
                   Yersinia pestis 
                 
                 NP_407132.1 
                 compliment of 
               
               
                   
                   
                 related protein 
                   
                   
                 nt. 2546-2938 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 417 
               
               
                 417 
                 3.00E−06 
                 Adenine-specific 
                 
                   Thermoplasma 
                 
                 NP_393798.1 
                 compliment of 
               
               
                   
                   
                 DNA methylase 
                 
                   acidophilum 
                 
                   
                 nt. 826-1020 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 417 
               
               
                 43 
                 9.00E−16 
                 PcnB 
                 
                   Pasteurella 
                 
                 NP_245801.1 
                 nt. 511-870 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 43 
               
               
                 434 
                 2.00E−97 
                 beta′ subunit of 
                 
                   Nephroselmis 
                 
                 NP_050840.1 
                 compliment of 
               
               
                   
                   
                 RNA polymerase 
                 
                   olivacea 
                 
                   
                 nt. 32-1534 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 434 
               
               
                 435 
                 4.00E−52 
                 MODIFICATION 
                 
                   Brevibacterium 
                 
                 P10283 
                 compliment of 
               
               
                   
                   
                 METHYLASE BEPI 
                 
                   epidermidis 
                 
                   
                 nt. 11-565 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 435 
               
               
                 435 
                 4.00E−57 
                 pentafunctional 
                 
                   Saccharomyces 
                 
                 NP_010412.1 
                 compliment of 
               
               
                   
                   
                 arom polypeptide 
                 
                   cerevisiae 
                 
                   
                 nt. 757-2064 of 
               
               
                   
                   
                 (contains: 3- 
                   
                   
                 SEQ ID NO: 435 
               
               
                   
                   
                 dehydroquinate 
               
               
                   
                   
                 synthase, 3- 
               
               
                   
                   
                 dehydroquinate, 
               
               
                   
                   
                 dehydratase (3- 
               
               
                   
                   
                 dehydroquinase), 
               
               
                   
                   
                 shikimate 5- 
               
               
                   
                   
                 dehydrogenase, 
               
               
                   
                   
                 shikimate kinase, 
               
               
                   
                   
                 and epsp synthase) 
               
               
                 437 
                 5.00E−70 
                 dihydrofolate 
                 
                   Haemophilus 
                 
                 S52336 
                 nt. 2393-2767 of 
               
               
                   
                   
                 reductase 
                 
                   influenzae 
                 
                   
                 SEQ ID NO: 437 
               
               
                   
                   
                   
                 (clinical isolate 
               
               
                   
                   
                   
                 R1042) 
               
               
                 438 
                  1.00E−106 
                 polyA polymerase 
                 
                   Vibrio cholerae 
                 
                 NP_230244.1 
                 nt. 3-1124 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 438 
               
               
                 439 
                 6.00E−60 
                 Porphyrin 
                 
                   Salmonella 
                 
                 NP_457816.1 
                 nt. 2343-2783 of 
               
               
                   
                   
                 biosynthetic protein 
                   enterica  subsp. 
                   
                 SEQ ID NO: 439 
               
               
                   
                   
                   
                   enterica  serovar 
               
               
                   
                   
                   
                 
                   Typhi 
                 
               
               
                 441 
                 5.00E−73 
                 RimM 
                 
                   Pasteurella 
                 
                 NP_246234.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 nt. 151-441 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 441 
               
               
                 442 
                 9.00E−31 
                 LIPOPROTEIN 
                 
                   Salmonella 
                 
                 P40827 
                 compliment of 
               
               
                   
                   
                 NLPD 
                 
                   typhimurium 
                 
                   
                 nt. 3362-3520 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 442 
               
               
                 444 
                 6.00E−24 
                 glycine betaine 
                 
                   Staphylococcus 
                 
                 NP_371872.1 
                 compliment of 
               
               
                   
                   
                 transporter 
                   aureus  subsp. 
                   
                 nt. 2242-2514 of 
               
               
                   
                   
                   
                   aureus  Mu50 
                   
                 SEQ ID NO: 444 
               
               
                 452 
                 6.00E−28 
                 unknown 
                 
                   Pasteurella 
                 
                 NP_245616.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 nt. 533-883 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 452 
               
               
                 452 
                 0 
                 Type I restriction 
                 
                   Escherichia coli 
                 
                 Q47163 
                 nt. 3291-4154 of 
               
               
                   
                   
                 enzyme Ecoprrl M 
                   
                   
                 SEQ ID NO: 452 
               
               
                   
                   
                 protein 
               
               
                 452 
                 2.00E−75 
                 type I restriction 
                 
                   Ureaplasma 
                 
                 NP_077929.1 
                 nt. 4156-4662 of 
               
               
                   
                   
                 enzyme M protein 
                 
                   urealyticum 
                 
                   
                 SEQ ID NO: 452 
               
               
                 455 
                 9.00E−56 
                 PROBABLE 
                 
                   Ralstonia 
                 
                 NP_520059.1 
                 nt. 2028-2774 of 
               
               
                   
                   
                 BACTERIOPHAGE 
                 
                   solanacearum 
                 
                   
                 SEQ ID NO: 455 
               
               
                   
                   
                 PROTEIN 
               
               
                 455 
                 2.00E−55 
                 orf2; similar to 
                 
                   Haemophilus 
                 
                 AAC45158.1 
                 nt. 2864-3490 of 
               
               
                   
                   
                 major capsid 
                 
                   somnus 
                 
                   
                 SEQ ID NO: 455 
               
               
                   
                   
                 protein precursor of 
               
               
                   
                   
                 phage P2 (gene N), 
               
               
                 455 
                  1.00E−175 
                 gpP 
                 Enterobacteria 
                 NP_046758.1 
                 compliment of 
               
               
                   
                   
                   
                 phage P2 
                   
                 nt. 127-1812 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 455 
               
               
                 456 
                 1.00E−38 
                 hypothetical protein 
                 
                   Pseudomonas 
                 
                 NP_542872.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   putida 
                 
                   
                 nt. 1010-1282 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 456 
               
               
                 456 
                  1.00E−172 
                 hypothetical protein 
                 
                   Pseudomonas 
                 
                 NP_542873.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   putida 
                 
                   
                 nt. 1443-2006 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 546 
               
               
                 457 
                  1.00E−116 
                 hypothetical protein 
                 
                   Haemophilus 
                 
                 S15287 
                 compliment of 
               
               
                   
                   
                 (galE 5′ region) - 
                 
                   influenzae 
                 
                   
                 nt. 62-961 of 
               
               
                   
                   
                 
                   Haemophilus 
                 
                   
                   
                 SEQ ID NO: 457 
               
               
                   
                   
                 
                   influenzae 
                 
               
               
                 457 
                  1.00E−134 
                 dTDPglucose 4,6- 
                 
                   Actinobacillus 
                 
                 T00102 
                 nt. 2637-3656 of 
               
               
                   
                   
                 dehydratase 
                   actinomycetemco - 
                   
                 SEQ ID NO: 457 
               
               
                   
                   
                   
                 
                   mitans 
                 
               
               
                 459 
                 2.00E−10 
                 RNA polymerase 
                   Synechocystis  sp. 
                 NP_441586.1 
                 nt. 25-117 of 
               
               
                   
                   
                 gamma-subunit 
                 PCC 6803 
                   
                 SEQ ID NO: 459 
               
               
                 461 
                 9.00E−51 
                 conserved 
                 
                   Staphylococcus 
                 
                 NP_370593.1 
                 nt. 4124-4624 of 
               
               
                   
                   
                 hypothetical protein 
                   aureus  subsp. 
                   
                 SEQ ID NO: 461 
               
               
                   
                   
                   
                   aureus  Mu50 
               
               
                 462 
                 9.00E−06 
                 NADH 
                 
                   Burkholderia 
                 
                 AAG01016.1 
                 nt. 703-828 of 
               
               
                   
                   
                 dehydrogenase 
                 
                   pseudomallei 
                 
                   
                 SEQ ID NO: 462 
               
               
                 465 
                 3.00E−41 
                 GTP-binding 
                   Synechocystis  sp. 
                 NP_441951.1 
                 compliment of 
               
               
                   
                   
                 protein Era 
                 PCC 6803 
                   
                 nt. 2470-2787 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 465 
               
               
                 466 
                 1.00E−15 
                 putative 
                 
                   Salmonella 
                 
                 NP_455548.1 
                 nt. 837-1478 of 
               
               
                   
                   
                 bacteriophage 
                   enterica  subsp. 
                   
                 SEQ ID NO: 466 
               
               
                   
                   
                 protein 
                   enterica  serovar 
               
               
                   
                   
                   
                 
                   Typhi 
                 
               
               
                 466 
                 1.00E−90 
                 orf31 
                 
                   Haemophilus 
                 
                 NP_043502.1 
                 nt. 2396-3199 of 
               
               
                   
                   
                   
                 phage HP1 
                   
                 SEQ ID NO: 466 
               
               
                 469 
                 0 
                 Hemoglobin and 
                 
                   Haemophilus 
                 
                 Q9X442 
                 compliment of 
               
               
                   
                   
                 hemoglobin- 
                   influenzae  HI689 
                   
                 nt. 427-3459 of 
               
               
                   
                   
                 haptoglobin binding 
                   
                   
                 SEQ ID NO: 469 
               
               
                   
                   
                 protein C precursor 
               
               
                 471 
                 8.00E−05 
                 transposase, 
                 
                   Neisseria 
                 
                 NP_274608.1 
                 nt. 2957-3217 of 
               
               
                   
                   
                 putative 
                 
                   meningitidis 
                 
                   
                 SEQ ID NO: 471 
               
               
                   
                   
                   
                 MC58 
               
               
                 472 
                 6.00E−08 
                 hypothetical protein 
                 
                   Salmonella 
                 
                 NP_458660.1 
                 compliment of 
               
               
                   
                   
                   
                   enterica  subsp. 
                   
                 nt. 2881-3270 of 
               
               
                   
                   
                   
                   enterica  serovar 
                   
                 SEQ ID NO: 472 
               
               
                   
                   
                   
                 
                   Typhi 
                 
               
               
                 472 
                 5.00E−23 
                 antirestriction 
                 
                   Mesorhizobium 
                 
                 NP_106707.1 
                 nt. 4908-5324 of 
               
               
                   
                   
                 protein 
                 
                   loti 
                 
                   
                 SEQ ID NO: 472 
               
               
                 472 
                 1.00E−75 
                 hypothetical protein 
                 
                   Salmonella 
                 
                 NP_458661.1 
                 compliment of 
               
               
                   
                   
                   
                   enterica  subsp. 
                   
                 nt. 1931-2776 of 
               
               
                   
                   
                   
                   enterica  serovar 
                   
                 SEQ ID NO: 472 
               
               
                   
                   
                   
                 
                   Typhi 
                 
               
               
                 472 
                 9.00E−72 
                 hypothetical protein 
                 
                   Salmonella 
                 
                 NP_458662.1 
                 compliment of 
               
               
                   
                   
                   
                   enterica  subsp. 
                   
                 nt. 544-1689 of 
               
               
                   
                   
                   
                   enterica  serovar 
                   
                 SEQ ID NO: 472 
               
               
                   
                   
                   
                 
                   Typhi 
                 
               
               
                 475 
                 3.00E−25 
                 unknown 
                 
                   Pasteurella 
                 
                 NP_244952.1 
                 nt. 3207-3626 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 475 
               
               
                 476 
                 8.00E−73 
                 putative DNA- 
                 
                   Salmonella 
                 
                 NP_458175.1 
                 compliment of 
               
               
                   
                   
                 binding protein 
                   enterica  subsp. 
                   
                 nt. 3339-4310 of 
               
               
                   
                   
                   
                   enterica  serovar 
                   
                 SEQ ID NO: 476 
               
               
                   
                   
                   
                 
                   Typhi 
                 
               
               
                 476 
                 6.00E−47 
                 anticodon nuclease 
                 
                   Neisseria 
                 
                 NP_273873.1| 
                 compliment of 
               
               
                   
                   
                   
                 
                   meningitidis 
                 
                   
                 nt. 4397-4885 of 
               
               
                   
                   
                   
                 MC58 
                   
                 SEQ ID NO: 476 
               
               
                 478 
                 3.00E−06 
                 methionin 
                 
                   Arabidopsis 
                 
                 CAB38313.1 
                 compliment of 
               
               
                   
                   
                 synthase-like 
                 
                   thaliana 
                 
                   
                 nt. 3554-3679 of 
               
               
                   
                   
                 enzyme 
                   
                   
                 SEQ ID NO: 478 
               
               
                 478 
                 3.00E−05 
                 unknown 
                 
                   Pasteurella 
                 
                 NP_245444.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 nt. 164-250 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 478 
               
               
                 479 
                 1.00E−18 
                 conserved 
                 
                   Xylella fastidiosa 
                 
                 NP_298841.1 
                 nt. 2302-2658 of 
               
               
                   
                   
                 hypothetical protein 
                 9a5c 
                   
                 SEQ ID NO: 479 
               
               
                 48 
                 3.00E−19 
                 Dca 
                 
                   Neisseria 
                 
                 AAF12796.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   gonorrhoeae 
                 
                   
                 nt. 225-746 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 48 
               
               
                 482 
                 1.00E−06 
                 hypothetical protein 
                 
                   Neisseria 
                 
                 NP_275122.1 
                 nt. 2055-2189 of 
               
               
                   
                   
                   
                 
                   meningitidis 
                 
                   
                 SEQ ID NO: 482 
               
               
                   
                   
                   
                 MC58 
               
               
                 482 
                 9.00E−28 
                 conserved 
                 
                   Neisseria 
                 
                 NP_274383.1 
                 nt. 1689-1898 of 
               
               
                   
                   
                 hypothetical protein 
                 
                   meningitidis 
                 
                   
                 SEQ ID NO: 482 
               
               
                   
                   
                   
                 MC58 
               
               
                 487 
                 5.00E−75 
                 conserved 
                 
                   Neisseria 
                 
                 NP_284304.1 
                 nt. 2541-2978 of 
               
               
                   
                   
                 hypothetical protein 
                 
                   meningitidis 
                 
                   
                 SEQ ID NO: 487 
               
               
                   
                   
                   
                 Z2491 
               
               
                 488 
                 2.00E−64 
                 unknown 
                 
                   Pasteurella 
                 
                 NP_246617.1 
                 nt. 2983-3540 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 488 
               
               
                 488 
                 8.00E−93 
                 1-deoxy-D-xylulose 
                 
                   Zymomonas 
                 
                 AAD29659.1 
                 nt. 1344-1880 of 
               
               
                   
                   
                 5-phosphate 
                 
                   mobilis 
                 
                   
                 SEQ ID NO: 488 
               
               
                   
                   
                 reductoisomerase 
               
               
                 491 
                 5.00E−51 
                 rubredoxin 
                 
                   Clostridium 
                 
                 AAB50346.1 
                 compliment of 
               
               
                   
                   
                 oxidoreductase 
                 
                   acetobutylicum 
                 
                   
                 nt. 1690-2439 of 
               
               
                   
                   
                 homolog 
                   
                   
                 SEQ ID NO: 491 
               
               
                 492 
                 1.00E−27 
                 phosphotransferase 
                 
                   Staphylococcus 
                 
                 AAK83253.1 
                 compliment of 
               
               
                   
                   
                 system enzyme 
                 
                   aureus 
                 
                   
                 nt. 755-970 of 
               
               
                   
                   
                 IIA-like protein 
                   
                   
                 SEQ ID NO: 492 
               
               
                 493 
                 2.00E−84 
                 unknown 
                 
                   Actinobacillus 
                 
                 AAC70895.1 
                 nt. 3333-3935 of 
               
               
                   
                   
                   
                   actinomycetemco - 
                   
                 SEQ ID NO: 493 
               
               
                   
                   
                   
                 
                   mitans 
                 
               
               
                 493 
                 4.00E−49 
                 unknown 
                 
                   Helicobacter 
                 
                 NP_223898.1 
                 nt. 3345-4010 of 
               
               
                   
                   
                   
                   pylori  J99 
                   
                 SEQ ID NO: 493 
               
               
                 493 
                 9.00E−31 
                 transcriptional 
                 
                   Acinetobacter 
                 
                 AAF20290.1 
                 nt. 1885-2793 of 
               
               
                   
                   
                 factor MdcH 
                 
                   calcoaceticus 
                 
                   
                 SEQ ID NO: 493 
               
               
                 493 
                 6.00E−30 
                 HimA 
                 
                   Pasteurella 
                 
                 NP_245565.1 
                 nt. 1129-1260 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 493 
               
               
                 494 
                 4.00E−85 
                 putative prophage 
                 
                   Yersinia pestis 
                 
                 NP_404712.1 
                 nt. 900-2099 of 
               
               
                   
                   
                 integrase 
                   
                   
                 SEQ ID NO: 494 
               
               
                 494 
                 4.00E−63 
                 DNA 
                 
                   Xylella fastidiosa 
                 
                 NP_299063.1 
                 compliment of 
               
               
                   
                   
                 methyltransferase 
                 9a5c 
                   
                 nt. 5544-6170 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 494 
               
               
                 494 
                 6.00E−19 
                 MODIFICATION 
                 
                   Lactococcus lactis 
                 
                 P34877 
                 compliment of 
               
               
                   
                   
                 METHYLASE 
                 subsp.  cremoris   
                   
                 nt. 5019-6113 of 
               
               
                   
                   
                 SCRFIA 
                   
                   
                 SEQ ID NO: 494 
               
               
                 497 
                 0 
                 transferrin-binding 
                 
                   Haemophilus 
                 
                 S70906 
                 nt. 3251-4999 of 
               
               
                   
                   
                 protein 1 
                   influenzae  (strain 
                   
                 SEQ ID NO: 497 
               
               
                   
                   
                   
                 PAK 12085) 
               
               
                 50 
                 5.00E−07 
                 AcpP 
                 
                   Pasteurella 
                 
                 NP_246856.1 
                 nt. 2-136 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 50 
               
               
                 501 
                 7.00E−50 
                 conserved 
                 
                   Vibrio cholerae 
                 
                 NP_231403.1 
                 compliment of 
               
               
                   
                   
                 hypothetical protein 
                   
                   
                 nt. 3649-4872 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 501 
               
               
                 501 
                 0 
                 type I restriction 
                 
                   Vibrio cholerae 
                 
                 NP_231400.1 
                 compliment of 
               
               
                   
                   
                 enzyme HsdR, 
                   
                   
                 nt. 1551-3440 of 
               
               
                   
                   
                 putative 
                   
                   
                 SEQ ID NO: 501 
               
               
                 501 
                 4.00E−13 
                 ATP-dependent 
                 
                   Deinococcus 
                 
                 NP_295921.1 
                 compliment of 
               
               
                   
                   
                 DNA helicase 
                 
                   radiodurans 
                 
                   
                 nt. 5317-5844 of 
               
               
                   
                   
                 RecG-related 
                   
                   
                 SEQ ID NO: 501 
               
               
                   
                   
                 protein 
               
               
                 501 
                 5.00E−11 
                 conserved 
                 
                   Ureaplasma 
                 
                 NP_077868.1 
                 compliment of 
               
               
                   
                   
                 hypothetical 
                 
                   urealyticum 
                 
                   
                 nt. 5098-5769 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 501 
               
               
                 504 
                 2.00E−44 
                 OUTER 
                 
                   Haemophilus 
                 
                 Q48218 
                 compliment of 
               
               
                   
                   
                 MEMBRANE 
                 
                   influenzae 
                 
                   
                 nt. 4681-5019 of 
               
               
                   
                   
                 PROTEIN P2 
                 AG30010 
                   
                 SEQ ID NO: 504 
               
               
                   
                   
                 PRECURSOR 
               
               
                   
                   
                 (OMP P2) 
               
               
                 507 
                 0 
                 SpoT 
                 
                   Pasteurella 
                 
                 NP_245857.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 nt. 3685-5316 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 507 
               
               
                 51 
                 6.00E−87 
                 glucosamine-- 
                 
                   Vibrio cholerae 
                 
                 NP_230141.1 
                 nt. 30-470 of 
               
               
                   
                   
                 fructose-6- 
                   
                   
                 SEQ ID NO: 51 
               
               
                   
                   
                 phosphate 
               
               
                   
                   
                 aminotransferase 
               
               
                   
                   
                 (isomerizing) 
               
               
                 512 
                 2.00E−28 
                 dipeptide transport 
                 
                   Yersinia pestis 
                 
                 NP_407439.1 
                 compliment of 
               
               
                   
                   
                 system permease 
                   
                   
                 nt. 1095-1580 of 
               
               
                   
                   
                 protein 
                   
                   
                 SEQ ID NO: 512 
               
               
                 512 
                 3.00E−82 
                 SapC 
                 
                   Pasteurella 
                 
                 NP_245850.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 nt. 730-1095 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 512 
               
               
                 514 
                 9.00E−06 
                 putative integral 
                 
                   Campylobacter 
                 
                 NP_281236.1 
                 compliment of 
               
               
                   
                   
                 membrane protein 
                 
                   jejuni 
                 
                   
                 nt. 577-684 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 514 
               
               
                 514 
                 3.00E−11 
                 orf, hypothetical 
                 
                   Escherichia coli 
                 
                 NP_286004.1 
                 compliment of 
               
               
                   
                   
                 protein 
                 O157:H7 EDL933 
                   
                 nt. 449-568 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 514 
               
               
                 518 
                 0 
                 putative inner 
                 
                   Neisseria 
                 
                 NP_284893.1 
                 nt. 92-1927 of 
               
               
                   
                   
                 membrane trans- 
                 
                   meningitidis 
                 
                   
                 SEQ ID NO: 518 
               
               
                   
                   
                 acylase protein 
                 Z2491 
               
               
                 519 
                 4.00E−30 
                 hypothetical protein 
                 
                   Mesorhizobium 
                 
                 NP_108196.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   loti 
                 
                   
                 nt. 2221-3159 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 519 
               
               
                 519 
                 2.00E−12 
                 conserved 
                 
                   Listeria innocua 
                 
                 NP_471067.1 
                 compliment of 
               
               
                   
                   
                 hypothetical protein 
                   
                   
                 nt. 3994-5241 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 519 
               
               
                 519 
                 6.00E−20 
                 hypothetical protein 
                 
                   Mesorhizobium 
                 
                 NP_108198.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   loti 
                 
                   
                 nt. 707-1552 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 519 
               
               
                 519 
                 4.00E−26 
                 putative 
                 
                   Salmonella 
                 
                 NP_455526.1 
                 compliment of 
               
               
                   
                   
                 bacteriophage 
                   enterica  subsp. 
                   
                 nt. 3982-5163 of 
               
               
                   
                   
                 protein 
                   enterica  serovar 
                   
                 SEQ ID NO: 519 
               
               
                   
                   
                   
                 
                   Typhi 
                 
               
               
                 52 
                 3.00E−94 
                 OUTER 
                 
                   Haemophilus 
                 
                 Q48218 
                 nt. 45-788 of 
               
               
                   
                   
                 MEMBRANE 
                 
                   influenzae 
                 
                   
                 SEQ ID NO: 52 
               
               
                   
                   
                 PROTEIN P2 
               
               
                   
                   
                 PRECURSOR 
               
               
                   
                   
                 (OMP P2) 
               
               
                 520 
                 0 
                 excision nuclease 
                 
                   Escherichia coli 
                 
                 NP_418482.1 
                 compliment of 
               
               
                   
                   
                 subunit A 
                 K12 
                   
                 nt. 6309-7745 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 520 
               
               
                 521 
                 5.00E−08 
                 zinc/manganese 
                 
                   Rickettsia conorii 
                 
                 NP_359651.1 
                 nt. 2236-2652 of 
               
               
                   
                   
                 ABC transporter 
                   
                   
                 SEQ ID NO: 521 
               
               
                   
                   
                 substrate binding 
               
               
                   
                   
                 protein 
               
               
                 521 
                  1.00E−140 
                 unknown 
                 
                   Pasteurella 
                 
                 NP_245865.1| 
                 nt. 338-1390 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 521 
               
               
                 521 
                 1.00E−86 
                 ORF_f432 
                 
                   Escherichia coli 
                 
                 AAB40463.1 
                 nt. 203-1390 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 521 
               
               
                 522 
                 3.00E−22 
                 unknown 
                 
                   Pasteurella 
                 
                 NP_246093.1 
                 nt. 670-885 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 522 
               
               
                 526 
                 5.00E−33 
                 exodeoxyribonuclease 
                 
                   Yersinia pestis 
                 
                 NP_404635.1 
                 nt. 5582-6202 of 
               
               
                   
                   
                 V alpha chain 
                   
                   
                 SEQ ID NO: 526 
               
               
                 526 
                 1.00E−62 
                 exodeoxyribonuclease 
                 
                   Vibrio cholerae 
                 
                 NP_231950.1 
                 nt. 5675-6193 of 
               
               
                   
                   
                 V, 67 kDa subunit 
                   
                   
                 SEQ ID NO: 526 
               
               
                 527 
                  1.00E−147 
                 unknown 
                 
                   Pasteurella 
                 
                 NP_245980.1 
                 nt. 4283-5203 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 527 
               
               
                 527 
                 0 
                 Mfd 
                 
                   Pasteurella 
                 
                 NP_245978.1 
                 nt. 7545-8759 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 527 
               
               
                 527 
                 0 
                 transcription-repair 
                 
                   Salmonella 
                 
                 NP_455708.1 
                 nt. 7611-8762 of 
               
               
                   
                   
                 coupling factor 
                   enterica  subsp. 
                   
                 SEQ ID NO: 527 
               
               
                   
                   
                 (TrcF) 
                   enterica  serovar 
               
               
                   
                   
                   
                 
                   Typhi 
                 
               
               
                 527 
                 0 
                 PROBABLE 
                 
                   Ralstonia 
                 
                 NP_519763.1 
                 nt. 7611-8870 of 
               
               
                   
                   
                 TRANSCRIPTION- 
                 
                   solanacearum 
                 
                   
                 SEQ ID NO: 527 
               
               
                   
                   
                 REPAIR 
               
               
                   
                   
                 COUPLING 
               
               
                   
                   
                 FACTOR 
               
               
                   
                   
                 PROTEIN 
               
               
                 528 
                 1.00E−48 
                 undecaprenyl 
                 
                   Chlamydia 
                 
                 NP_297109.1 
                 nt. 2918-3712 of 
               
               
                   
                   
                 pyrophosphate 
                 
                   muridarum 
                 
                   
                 SEQ ID NO: 528 
               
               
                   
                   
                 synthetase 
               
               
                 528 
                 0 
                 leucyl-tRNA 
                 
                   Vibrio cholerae 
                 
                 NP_230603.1 
                 compliment of 
               
               
                   
                   
                 synthetase 
                   
                   
                 nt. 180-2822 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 528 
               
               
                 529 
                  1.00E−104 
                 DNA PRIMASE 
                 
                   Legionella 
                 
                 P71481 
                 compliment of 
               
               
                   
                   
                   
                 
                   pneumophila 
                 
                   
                 nt. 3316-3960 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 529 
               
               
                 534 
                 9.00E−29 
                 putative integrase 
                 
                   Salmonella 
                 
                 NP_461690.1 
                 nt. 4668-5009 of 
               
               
                   
                   
                   
                   typhimurium  LT2 
                   
                 SEQ ID NO: 534 
               
               
                 534 
                 6.00E−18 
                 hypothetical protein 
                 
                   Neisseria 
                 
                 NP_283002.1 
                 compliment of 
               
               
                   
                   
                 NMA0153 
                 
                   meningitidis 
                 
                   
                 nt. 5933-6337 of 
               
               
                   
                   
                   
                 Z2491 
                   
                 SEQ ID NO: 534 
               
               
                 534 
                 2.00E−23 
                 hypothetical protein 
                 
                   Deinococcus 
                 
                 NP_294868.1 
                 nt. 6908-7654 of 
               
               
                   
                   
                   
                 
                   radiodurans 
                 
                   
                 SEQ ID NO: 534 
               
               
                 534 
                 1.00E−88 
                 prophage CP4-57 
                 
                   Escherichia coli 
                 
                 NP_417111.1 
                 nt. 5057-5875 of 
               
               
                   
                   
                 integrase 
                 K12 
                   
                 SEQ ID NO: 534 
               
               
                 535 
                  1.00E−115 
                 phosphate 
                   Buchnera  sp. 
                 NP_240007.1 
                 nt. 3385-4596 of 
               
               
                   
                   
                 acetyltransferase 
                 APS 
                   
                 SEQ ID NO: 535 
               
               
                 536 
                 3.00E−35 
                 cobalt membrane 
                 
                   Actinobacillus 
                 
                 AAD49727.1 
                 compliment of 
               
               
                   
                   
                 transport protein 
                 
                   pleuropneumoniae 
                 
                   
                 nt. 3531-4136 of 
               
               
                   
                   
                 CbiQ 
                   
                   
                 SEQ ID NO: 536 
               
               
                 536 
                 6.00E−37 
                 unknown 
                 
                   Pasteurella 
                 
                 NP_245305.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 nt. 6478-6921 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 536 
               
               
                 539 
                 2.00E−26 
                 Orf122 
                 
                   Chlorobium 
                 
                 AAG12204.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   tepidum 
                 
                   
                 nt. 1778-2008 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 539 
               
               
                 540 
                 1.00E−77 
                 heat shock protein 
                 
                   Neisseria 
                 
                 NP_273864.1 
                 compliment of 
               
               
                   
                   
                 HtpX 
                 
                   meningitidis 
                 
                   
                 nt. 2567-3481 of 
               
               
                   
                   
                   
                 MC58 
                   
                 SEQ ID NO: 540 
               
               
                 541 
                 0 
                 IleS 
                 
                   Pasteurella 
                 
                 NP_246601.1 
                 nt. 3167-4549 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 541 
               
               
                 545 
                 2.00E−09 
                 DNA-BINDING 
                 
                   Pectobacterium 
                 
                 Q47588 
                 nt. 3816-3977 of 
               
               
                   
                   
                 PROTEIN RDGB 
                 
                   carotovorum 
                 
                   
                 SEQ ID NO: 545 
               
               
                 545 
                 2.00E−11 
                 putative 
                 
                   Sinorhizobium 
                 
                 NP_437741.1 
                 compliment of 
               
               
                   
                   
                 transposase 
                 
                   meliloti 
                 
                   
                 nt. 2786-3019 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 544 
               
               
                 545 
                 2.00E−07 
                 Hypothetical 42.5 
                 
                   Escherichia coli 
                 
                 BAA77933.1 
                 compliment of 
               
               
                   
                   
                 kd protein in thrW- 
                   
                   
                 nt. 2614-2811 of 
               
               
                   
                   
                 argF intergenic 
                   
                   
                 SEQ ID NO: 545 
               
               
                   
                   
                 region 
               
               
                 545 
                 4.00E−18 
                 putative IS element 
                 
                   Salmonella 
                 
                 NP_454711.1 
                 nt. 1955-2230 of 
               
               
                   
                   
                 transposase 
                   enterica  subsp. 
                   
                 SEQ ID NO: 545 
               
               
                   
                   
                   
                   enterica  serovar 
               
               
                   
                   
                   
                 
                   Typhi 
                 
               
               
                 546 
                 0 
                 HEME/HEMOPEXIN- 
                 
                   Haemophilus 
                 
                 P45354 
                 nt. 5551-7809 of 
               
               
                   
                   
                 BINDING 
                 
                   influenzae 
                 
                   
                 SEQ ID NO: 546 
               
               
                   
                   
                 PROTEIN 
               
               
                 546 
                 0 
                 HEME/HEMOPEXIN 
                 
                   Haemophilus 
                 
                 P45356 
                 nt. 3842-5536 of 
               
               
                   
                   
                 UTILIZATION 
                 
                   influenzae 
                 
                   
                 SEQ ID NO: 546 
               
               
                   
                   
                 PROTEIN B 
               
               
                 546 
                 0 
                 HEME/HEMOPEXIN 
                 
                   Haemophilus 
                 
                 P45357 
                 nt. 1638-3176 of 
               
               
                   
                   
                 UTILIZATION 
                 
                   influenzae 
                 
                   
                 SEQ ID NO: 546 
               
               
                   
                   
                 PROTEIN C 
               
               
                 546 
                 2.00E−12 
                 HasR 
                 
                   Pasteurella 
                 
                 NP_246561.1 
                 nt. 3149-3763 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 546 
               
               
                 549 
                 0 
                 unknown 
                 
                   Pasteurella 
                 
                 NP_246821.1 
                 nt. 2526-3512 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 549 
               
               
                 549 
                  1.00E−121 
                 putative membrane 
                 
                   Yersinia pestis 
                 
                 NP_404859.1 
                 nt. 605-1108 of 
               
               
                   
                   
                 protein 
                   
                   
                 SEQ ID NO: 549 
               
               
                 549 
                 0 
                 unknown 
                 
                   Pasteurella 
                 
                 NP_246822.1 
                 nt. 1122-1664 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 549 
               
               
                 551 
                  1.00E−157 
                 type I restriction- 
                 
                   Xylella fastidiosa 
                 
                 NP_300016.1 
                 compliment of 
               
               
                   
                   
                 modification 
                 9a5c 
                   
                 nt. 7396-8322 of 
               
               
                   
                   
                 system 
                   
                   
                 SEQ ID NO: 551 
               
               
                   
                   
                 endonuclease 
               
               
                 552 
                  1.00E−100 
                 valyl-tRNA 
                 
                   Deinococcus 
                 
                 NP_293872.1 
                 compliment of 
               
               
                   
                   
                 synthetase 
                 
                   radiodurans 
                 
                   
                 nt. 6691-8688 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 552 
               
               
                 552 
                 0 
                 VALYL-TRNA 
                 
                   Haemophilus 
                 
                 P36432 
                 compliment of 
               
               
                   
                   
                 SYNTHETASE 
                 
                   parainfluenzae 
                 
                   
                 nt. 5850-6647 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 552 
               
               
                 553 
                 0 
                 DNA-directed RNA 
                 
                   Vibrio cholerae 
                 
                 NP_229982.1 
                 nt. 2668-6699 of 
               
               
                   
                   
                 polymerase, beta 
                   
                   
                 SEQ ID NO: 553 
               
               
                   
                   
                 subunit 
               
               
                 554 
                 0 
                 iron utilization 
                 
                   Haemophilus 
                 
                 T10887 
                 nt. 991-2508 of 
               
               
                   
                   
                 protein B 
                 
                   influenzae 
                 
                   
                 SEQ ID NO: 554 
               
               
                 559 
                  1.00E−100 
                 PREPROTEIN 
                 
                   Bacillus firmus 
                 
                 P96313 
                 nt. 3420-4472 of 
               
               
                   
                   
                 TRANSLOCASE 
                   
                   
                 SEQ ID NO: 559 
               
               
                   
                   
                 SECA SUBUNIT 
               
               
                 56 
                 2.00E−23 
                 RpL30 
                 
                   Pasteurella 
                 
                 NP_246336.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 nt. 656-832 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 56 
               
               
                 56 
                 9.00E−13 
                 RpS5 
                 
                   Pasteurella 
                 
                 NP_246337.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 nt. 843-1064 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 56 
               
               
                 560 
                  1.00E−157 
                 Na+/H+ antiporter 
                 
                   Vibrio cholerae 
                 
                 NP_231535.1 
                 2 compliment of 
               
               
                   
                   
                   
                   
                   
                 nt. 279-2989 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 560 
               
               
                 562 
                 1.00E−72 
                 putative biotin 
                 
                   Yersinia pestis 
                 
                 NP_404419.1 
                 nt. 7862-8878 of 
               
               
                   
                   
                 sulfoxide reductase 
                   
                   
                 SEQ ID NO: 562 
               
               
                   
                   
                 2 
               
               
                 562 
                  1.00E−125 
                 restriction 
                 
                   Neisseria 
                 
                 CAA09003.1 
                 nt. 2-985 of 
               
               
                   
                   
                 modification 
                 
                   meningitidis 
                 
                   
                 SEQ ID NO: 562 
               
               
                   
                   
                 system-R protein 
               
               
                 563 
                 0 
                 IMMUNOGLOBULIN 
                 
                   Haemophilus 
                 
                 P45384 
                 compliment of 
               
               
                   
                   
                 A1 PROTEASE 
                   influenzae  HK715 
                   
                 nt. 4127-9508 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 563 
               
               
                 563 
                 0 
                 3- 
                   Schizosaccharo - 
                 O14289 
                 nt. 1980-3983 of 
               
               
                   
                   
                 ISOPROPYLMALATE 
                 
                   myces pombe 
                 
                   
                 SEQ ID NO: 563 
               
               
                   
                   
                 DEHYDRATASE 
               
               
                   
                   
                 (IPMI) 
               
               
                 564 
                 2.00E−79 
                 orf32 
                 
                   Haemophilus 
                 
                 NP_536839.1 
                 nt. 6241-6831 of 
               
               
                   
                   
                   
                 phage HP2 
                   
                 SEQ ID NO: 564 
               
               
                 564 
                 7.00E−33 
                 probable variable 
                 
                   Salmonella 
                 
                 NP_457882.1 
                 nt. 3707-4177 of 
               
               
                   
                   
                 tail fibre protein 
                   enterica  subsp. 
                   
                 SEQ ID NO: 564 
               
               
                   
                   
                   
                   enterica  serovar 
               
               
                   
                   
                   
                 
                   Typhi 
                 
               
               
                 564 
                 2.00E−14 
                 M protein 
                 Enterobacteria 
                 NP_052264.1 
                 nt. 1905-2213 of 
               
               
                   
                   
                   
                 phage 186 
                   
                 SEQ ID NO: 564 
               
               
                 564 
                 4.00E−44 
                 similar to tail fiber 
                 
                   Salmonella 
                 
                 NP_461635.1 
                 nt. 3171-3692 of 
               
               
                   
                   
                 protein (gpH) in 
                   typhimurium  LT2, 
                   
                 SEQ ID NO: 564 
               
               
                   
                   
                 phage P2 
                 Fels-2 prophage 
               
               
                 564 
                 2.00E−85 
                 gpJ 
                 Enterobacteria 
                 NP_046773.1 
                 nt. 2267-3166 of 
               
               
                   
                   
                   
                 phage P2 
                   
                 SEQ ID NO: 564 
               
               
                 564 
                 1.00E−24 
                 hypothetical protein 
                 
                   Neisseria 
                 
                 NP_284534.1 
                 nt. 6852-7334 of 
               
               
                   
                   
                   
                 
                   meningitidis 
                 
                   
                 SEQ ID NO: 564 
               
               
                   
                   
                   
                 Z2491 
               
               
                 564 
                 4.00E−26 
                 gpV 
                 Enterobacteria 
                 NP_046771.1 
                 nt. 1337-1912 of 
               
               
                   
                   
                   
                 phage P2 
                   
                 SEQ ID NO: 564 
               
               
                 564 
                 2.00E−47 
                 similar to 
                 
                   Escherichia coli 
                 
                 BAA16182.1 
                 nt. 11383-11961 of 
               
               
                   
                   
                 [SwissProt P44255 
                   
                   
                 SEQ ID NO: 564 
               
               
                 564 
                 2.00E−51 
                 hypothetical protein 
                 
                   Neisseria 
                 
                 NP_284066.1 
                 nt. 10452-11180 of 
               
               
                   
                   
                 NMA1315 
                 
                   meningitidis 
                 
                   
                 SEQ ID NO: 564 
               
               
                   
                   
                   
                 Z2491 
               
               
                 564 
                 0 
                 orf31 
                 
                   Haemophilus 
                 
                 NP_043502.1 
                 nt. 4160-6226 of 
               
               
                   
                   
                   
                 phage HP1 
                   
                 SEQ ID NO: 564 
               
               
                 564 
                 2.00E−09 
                 rep 
                 
                   Haemophilus 
                 
                 NP_536816.1 
                 compliment of 
               
               
                   
                   
                   
                 phage HP2 
                   
                 nt. 9986-10234 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 564 
               
               
                 565 
                 2.00E−57 
                 resolvase/ 
                 
                   Haemophilus 
                 
                 AAL47097.1 
                 nt. 11885-12445 of 
               
               
                   
                   
                 integrase-like 
                   influenzae  biotype 
                   
                 SEQ ID NO: 565 
               
               
                   
                   
                 protein 
                 
                   aegyptius 
                 
               
               
                 565 
                 1.00E−93 
                 integrase 
                 
                   Actinobacillus 
                 
                 AAC70901.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   actinomycetemco- 
                 
                   
                 nt. 4118-4900 of 
               
               
                   
                   
                   
                 
                   mitans 
                 
                   
                 SEQ ID NO: 565 
               
               
                 565 
                 6.00E−35 
                 probable phage 
                 
                   Salmonella 
                 
                 NP_458745.1 
                 compliment of 
               
               
                   
                   
                 integrase 
                   enterica  subsp. 
                   
                 nt. 4148-4990 of 
               
               
                   
                   
                   
                   enterica  serovar 
                   
                 SEQ ID NO: 565 
               
               
                   
                   
                   
                 
                   Typhi 
                 
               
               
                 565 
                  1.00E−107 
                 hypothetical protein 
                 
                   Xylella fastidiosa 
                 
                 NP_299042.1 
                 compliment of 
               
               
                   
                   
                   
                 9a5c 
                   
                 nt. 5066-6817 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 565 
               
               
                 566 
                  1.00E−126 
                 hypothetical protein 
                 
                   Haemophilus 
                 
                 S15287 
                 compliment of 
               
               
                   
                   
                 (galE 5′ region) - 
                 
                   influenzae 
                 
                   
                 nt. 10726-11607 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 566 
               
               
                 567 
                 0 
                 unknown 
                 
                   Pasteurella 
                 
                 NP_246387.1 
                 nt. 5343-7688 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 567 
               
               
                 568 
                  1.00E−151 
                 multidrug 
                 
                   Escherichia coli 
                 
                 NP_311575.1 
                 nt. 6-1403 of 
               
               
                   
                   
                 resistance 
                 O157:H7 
                   
                 SEQ ID NO: 568 
               
               
                   
                   
                 membrane 
               
               
                   
                   
                 translocase 
               
               
                 568 
                  1.00E−141 
                 YhbX/YhjW/YijP/Yj 
                 
                   Neisseria 
                 
                 |NP_275002.1 
                 compliment of 
               
               
                   
                   
                 dB family protein 
                 
                   meningitidis 
                 
                   
                 nt. 11213-12634 of 
               
               
                   
                   
                   
                 MC58 
                   
                 SEQ ID NO: 568 
               
               
                 570 
                  1.00E−180 
                 hypothetical protein 
                 
                   Haemophilus 
                 
                 S71024 
                 compliment of 
               
               
                   
                   
                 3 (ksgA-lic2B 
                   influenzae  (strain 
                   
                 nt. 12845-13720 of 
               
               
                   
                   
                 intergenic region) 
                 RM7004) 
                   
                 SEQ ID NO: 570 
               
               
                 571 
                 0 
                 glycerophospho- 
                 
                   Haemophilus 
                 
                 A43576 
                 nt. 1656-2693 of 
               
               
                   
                   
                 diester 
                   influenzae  (isolate 
                   
                 SEQ ID NO: 571 
               
               
                   
                   
                 phosphodiesterase 
                 772) 
               
               
                 571 
                  1.00E−137 
                 outer membrane 
                 
                   Haemophilus 
                 
                 A43604 
                 nt. 6145-6909 of 
               
               
                   
                   
                 protein P4 
                 
                   influenzae 
                 
                   
                 SEQ ID NO: 571 
               
               
                   
                   
                 precursor - 
               
               
                   
                   
                 
                   Haemophilus 
                 
               
               
                   
                   
                 
                   influenzae 
                 
               
               
                 571 
                 2.00E−72 
                 CG8298 gene 
                 
                   Drosophila 
                 
                 AAF58597.1 
                 nt. 3813-5339 of 
               
               
                   
                   
                 product [alt 1] 
                 
                   melanogaster 
                 
                   
                 SEQ ID NO: 571 
               
               
                 572 
                 1.00E−40 
                 hypothetical protein 
                 
                   Chlamydia 
                 
                 G81737 
                 nt. 3734-4099 of 
               
               
                   
                   
                 TC0130 
                   muridarum  (strain 
                   
                 SEQ ID NO: 572 
               
               
                   
                   
                   
                 Nigg) 
               
               
                 572 
                 5.00E−10 
                 hypothetical protein 
                 
                   Pyrococcus 
                 
                 NP_142215.1 
                 nt. 4472-4888 of 
               
               
                   
                   
                   
                 
                   horikoshii 
                 
                   
                 SEQ ID NO: 572 
               
               
                 572 
                 3.00E−11 
                 109aa long 
                 
                   Sulfolobus 
                 
                 NP_377117.1 
                 nt. 7303-7470 of 
               
               
                   
                   
                 hypothetical protein 
                 
                   tokodaii 
                 
                   
                 SEQ ID NO: 572 
               
               
                 572 
                 8.00E−43 
                 hypothetical protein 
                 
                   Chlamydophila 
                 
                 NP_445524.1 
                 nt. 4289-4618 of 
               
               
                   
                   
                   
                 
                   pneumoniae 
                 
                   
                 SEQ ID NO: 572 
               
               
                   
                   
                   
                 AR39 
               
               
                 572 
                 9.00E−08 
                 CDH1-D 
                 
                   Gallus gallus 
                 
                 AAL31950.1 
                 nt. 7183-7521 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 572 
               
               
                 575 
                  1.00E−173 
                 topoisomerase B 
                 
                   Salmonella 
                 
                 NP_458624.1 
                 nt. 18980-20923 of 
               
               
                   
                   
                   
                   enterica  subsp. 
                   
                 SEQ ID NO: 575 
               
               
                   
                   
                   
                   enterica  serovar 
               
               
                   
                   
                   
                 
                   Typhi 
                 
               
               
                 575 
                  1.00E−100 
                 DNA helicase 
                 
                   Salmonella 
                 
                 NP_458617.1 
                 nt. 10399-11706 of 
               
               
                   
                   
                   
                   enterica  subsp. 
                   
                 SEQ ID NO: 575 
               
               
                   
                   
                   
                   enterica  serovar 
               
               
                   
                   
                   
                 
                   Typhi 
                 
               
               
                 65 
                 2.00E−53 
                 Sufl 
                 
                   Pasteurella 
                 
                 NP_245041.1 
                 nt. 3-821 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 65 
               
               
                 67 
                 4.00E−39 
                 putative MFS 
                 
                   Salmonella 
                 
                 NP_462786.1 
                 compliment of 
               
               
                   
                   
                 family tranport 
                   typhimurium  LT2 
                   
                 nt. 125-1033 of 
               
               
                   
                   
                 protein (1st mdule) 
                   
                   
                 SEQ ID NO: 67 
               
               
                 7 
                 4.00E−29 
                 putative membrane 
                 
                   Salmonella 
                 
                 NP_458664.1 
                 compliment of 
               
               
                   
                   
                 protein 
                   enterica  subsp. 
                   
                 nt. 2-559 of 
               
               
                   
                   
                   
                   enterica  serovar 
                   
                 SEQ ID NO: 7 
               
               
                   
                   
                   
                 
                   Typhi 
                 
               
               
                 72 
                 2.00E−51 
                 serine transporter 
                 
                   Vibrio cholerae 
                 
                 NP_230946.1 
                 nt. 18-803 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 72 
               
               
                 74 
                 3.00E−90 
                 hypothetical 21.8K 
                 
                   Haemophilus 
                 
                 JH0436 
                 compliment of 
               
               
                   
                   
                 protein (in locus 
                 
                   influenzae 
                 
                   
                 nt. 248-766 of 
               
               
                   
                   
                 involved in 
                   
                   
                 SEQ ID NO: 74 
               
               
                   
                   
                 transformation) - 
               
               
                 77 
                 2.00E−18 
                 RecX protein 
                 
                   Legionella 
                 
                 CAC33485.1 
                 nt. 480-920 of 
               
               
                   
                   
                   
                 
                   pneumophila 
                 
                   
                 SEQ ID NO: 77 
               
               
                 82 
                 4.00E−95 
                 unknown 
                 
                   Pasteurella 
                 
                 NP_246414.1 
                 nt. 128-955 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 82 
               
               
                 83 
                 2.00E−66 
                 unknown 
                 
                   Pasteurella 
                 
                 NP_246777.1 
                 nt. 5-556 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 83 
               
               
                 83 
                 6.00E−33 
                 CTP SYNTHASE 
                 
                   Helicobacter 
                 
                 NP_223042.1 
                 compliment of 
               
               
                   
                   
                   
                   pylori  J99 
                   
                 nt. 1027-1338 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 83. 
               
               
                 83 
                 4.00E−34 
                 CTP synthase 
                 
                   Campylobacter 
                 
                 NP_281249.1 
                 compliment of 
               
               
                   
                   
                   
                 
                   jejuni 
                 
                   
                 nt. 1024-1275 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 83 
               
               
                 84 
                 1.00E−16 
                 REPRESSOR 
                 Bacteriophage 
                 P14819 
                 nt. 823-1233 of 
               
               
                   
                   
                 PROTEIN CI 
                 phi-80 
                   
                 SEQ ID NO: 84 
               
               
                 84 
                 2.00E−05 
                 orf, hypothetical 
                 
                   Escherichia coli 
                 
                 NP_415875.1 
                 compliment of 
               
               
                   
                   
                 protein 
                 K12 
                   
                 nt. 533-700 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 84 
               
               
                 84 
                 4.00E−11 
                 orf33 
                 bacteriophage phi 
                 NP_490633.1 
                 compliment of 
               
               
                   
                   
                   
                 CTX 
                   
                 nt. 32-466 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO: 84 
               
               
                 85 
                 3.00E−42 
                 SpoT 
                 
                   Pasteurella 
                 
                 NP_245857.1 
                 nt. 899-1261 of 
               
               
                   
                   
                   
                 
                   multocida 
                 
                   
                 SEQ ID NO: 85 
               
               
                 90 
                  1.00E−103 
                 putative methylase 
                 Bacteriophage 
                 NP_108695.1 
                 compliment of 
               
               
                   
                   
                   
                 Tuc2009 
                   
                 nt. 478-1206 of 
               
               
                   
                   
                   
                   
                   
                 SEQ ID NO:90 
               
               
                 90 
                 4.00E−11 
                 probable adenine 
                 
                   Thermoplasma 
                 
                 NP_394624.1 
                 compliment of 
               
               
                   
                   
                 specific DNA 
                 
                   acidophilum 
                 
                   
                 nt. 397-1140 of 
               
               
                   
                   
                 methyltransferase 
                   
                   
                 SEQ ID NO: 90 
               
               
                   
               
             
          
         
       
     
         [0000]    
       
         
               
               
               
               
               
             
           
               
                 TABLE 3B 
               
               
                   
               
               
                   
                 Full Length 
                   
                   
                   
               
               
                   
                 Nucleotide 
                 Amino Acid 
                   
                 Homology to 
               
               
                 Hit Identity 
                 Sequence 
                 Sequence 
                 Location in Contig 
                 Genbank Protein 
               
               
                   
               
             
             
               
                 CpdB 
                 SEQ ID NO: 686 
                 SEQ ID NO: 687 
                 nt. 38041-36068 of 
                 NP_246953.1 
               
               
                   
                   
                   
                 SEQ ID NO: 681 
               
               
                   
                   
                   
                 (contig 14) 
               
               
                 putative membrane 
                 SEQ ID NO: 688 
                 SEQ ID NO: 689 
                 nt. 906601-908094 of 
                 NP_458664.1 
               
               
                 protein 
                   
                   
                 SEQ ID NO: 685 
               
               
                   
                   
                   
                 (contig 18) 
               
               
                 GTP-binding 
                 SEQ ID NO: 690 
                 SEQ ID NO: 691 
                 nt. 42557-40995 of 
                 NP_240245.1 
               
               
                 protein TypA/BipA 
                   
                   
                 SEQ ID NO: 683 
               
               
                   
                   
                   
                 (contig 16) 
               
               
                 outer membrane 
                 SEQ ID NO: 692 
                 SEQ ID NO: 693 
                 nt. 7000420-704187 of 
                 T30852 
               
               
                 protein A 
                   
                   
                 SEQ ID NO: 685 
               
               
                   
                   
                   
                 (contig 18) 
               
               
                 vacB protein 
                 SEQ ID NO: 694 
                 SEQ ID NO: 695 
                 nt. 39184-36836 of 
                 NP_240369.1 
               
               
                   
                   
                   
                 SEQ ID NO: 683 
               
               
                   
                   
                   
                 (contig 16) 
               
               
                 putative ABC 
                 SEQ ID NO: 696 
                 SEQ ID NO: 697 
                 nt. 59155-58370 of 
                 NP_282774.1 
               
               
                 transport system 
                   
                   
                 SEQ ID NO: 685 
               
               
                 permease protein [ 
                   
                   
                 (contig 18) 
               
               
                 putative exported 
                 SEQ ID NO: 698 
                 SEQ ID NO: 699 
                 nt. 901142-902542 of 
                 NP_458655.1 
               
               
                 protein 
                   
                   
                 SEQ ID NO: 685 
               
               
                   
                   
                   
                 (contig 18) 
               
               
                 ImpA 
                 SEQ ID NO: 700 
                 SEQ ID NO: 701 
                 nt. 348187-347747 of 
                 NP_245829.1 
               
               
                   
                   
                   
                 SEQ ID NO: 685 
               
               
                   
                   
                   
                 (contig 18) 
               
               
                 TsaA 
                 SEQ ID NO: 702 
                 SEQ ID NO: 703 
                 nt. 74941-75548 of 
                 NP_245732.1 
               
               
                   
                   
                   
                 SEQ ID NO: 684 
               
               
                   
                   
                   
                 (contig 17) 
               
               
                 PROBABLE 
                 SEQ ID NO: 704 
                 SEQ ID NO: 705 
                 nt. 74436-75176 of 
                 NP_522358.1 
               
               
                 TRANSPORT 
                 SEQ ID NO: 706 
                 SEQ ID NO: 707 
                 SEQ ID NO: 685 
               
               
                 TRANSMEMBRANE 
                   
                   
                 (contig 18) 
               
               
                 PROTEIN 
                   
                   
                 nt. 75160-75660 of 
               
               
                   
                   
                   
                 SEQ ID NO: 685 
               
               
                   
                   
                   
                 (contig 18) 
               
               
                 possible exported 
                 SEQ ID NO: 708 
                 SEQ ID NO: 709 
                 nt. 899618-900262 of 
                 NP_458653.1 
               
               
                 protein 
                   
                   
                 SEQ ID NO: 685 
               
               
                   
                   
                   
                 (contig 18) 
               
               
                 LICA PROTEIN 
                 SEQ ID NO: 710 
                 SEQ ID NO: 711 
                 nt. 356917-355958 of 
                 P14181 
               
               
                   
                   
                   
                 SEQ ID NO: 685 
               
               
                   
                   
                   
                 (contig 18) 
               
               
                 HEME-BINDING 
                 SEQ ID NO: 712 
                 SEQ ID NO: 713 
                 NT. 26114-27739 of 
                 P33950 
               
               
                 PROTEIN A 
                   
                   
                 SEQ ID NO: 683 
               
               
                   
                   
                   
                 (contig 16) 
               
               
                 similar to 
                 SEQ ID NO: 714 
                 SEQ ID NO: 715 
                 nt. 311610-312683 of 
                 XP_068727.1 
               
               
                 BASEMENT 
                   
                   
                 SEQ ID NO: 685 
               
               
                 MEMBRANE- 
                   
                   
                 (contig 18) 
               
               
                 SPECIFIC 
               
               
                 HEPARAN 
               
               
                 SULFATE 
               
               
                 PROTEOGLYCAN 
               
               
                 CORE PROTEIN 
               
               
                 PRECURSOR 
               
               
                 (HSPG) 
               
               
                 CzcD 
                 SEQ ID NO: 716 
                 SEQ ID NO: 717 
                 nt. 34865-35542 of 
                 NP_246276.1 
               
               
                   
                   
                   
                 SEQ ID NO: 681 
               
               
                   
                   
                   
                 (contig 14) 
               
               
                 conserved 
                 SEQ ID NO: 718 
                 SEQ ID NO: 719 
                 nt. 194993-193977 of 
                 NP_274972.1 
               
               
                 hypothetical protein 
                   
                   
                 SEQ ID NO: 685 
               
               
                   
                   
                   
                 (contig 18) 
               
               
                 secretion protein 
                 SEQ ID NO: 720 
                 SEQ ID NO: 721 
                 nt. 203707-201857 of 
                 NP_252510.1 
               
               
                 SecD 
                   
                   
                 SEQ ID NO: 683 
               
               
                   
                   
                   
                 (contig 17) 
               
               
                 ABC transporter 
                 SEQ ID NO: 722 
                 SEQ ID NO: 723 
                 nt. 3943-5859 of 
                 AAF31030.1 
               
               
                 protein 1 
                   
                   
                 SEQ ID NO: 681 
               
               
                   
                   
                   
                 (contig 14) 
               
               
                 conserved 
                 SEQ ID NO: 724 
                 SEQ ID NO: 725 
                 nt. 331090-331749 of 
                 NP_273467.1 
               
               
                 hypothetical protein 
                 SEQ ID NO: 726 
                 SEQ ID NO: 727 
                 SEQ ID NO: 685 
               
               
                   
                 SEQ ID NO: 728 
                 SEQ ID NO: 729 
                 (contig 18) 
               
               
                   
                   
                   
                 nt. 331938-332492 of 
               
               
                   
                   
                   
                 SEQ ID NO: 685 
               
               
                   
                   
                   
                 (contig 18) 
               
               
                   
                   
                   
                 nt. 332681-33232 of 
               
               
                   
                   
                   
                 SEQ ID NO: 685 
               
               
                   
                   
                   
                 (contig 18) 
               
               
                 INVASIN 
                 SEQ ID NO: 730 
                 SEQ ID NO: 731 
                 nt. 416757-417020 of 
                 P31489 
               
               
                 PRECURSOR 
                   
                   
                 SEQ ID NO: 685 
               
               
                 (OUTER 
                   
                   
                 (contig 18) 
               
               
                 MEMBRANE 
               
               
                 ADHESIN) 
               
               
                 HEME/HEMOPEXIN- 
                 SEQ ID NO: 732 
                 SEQ ID NO: 733 
                 nt. 229430-232195 of 
                 P45355 
               
               
                 BINDING 
                   
                   
                 SEQ ID NO: 384 
               
               
                 PROTEIN 
                   
                   
                 (contig 17) 
               
               
                 OPACITY 
                 SEQ ID NO: 734 
                 SEQ ID NO: 735 
                 nt. 375592-375879 of 
                 Q05033 
               
               
                 PROTEIN OPA66 
                   
                   
                 SEQ ID NO: 384 
               
               
                 PRECURSOR 
                   
                   
                 (contig 17) 
               
               
                 Hemoglobin- 
                 SEQ ID NO: 736 
                 SEQ ID NO: 737 
                 nt. 45709-42566 of 
                 Q48153 
               
               
                 haptoglobin 
                   
                   
                 SEQ ID NO: 681 
               
               
                 binding protein A 
                   
                   
                 (contig 14) 
               
               
                 transport protein 
                 SEQ ID NO: 738 
                 SEQ ID NO: 739 
                 nt. 134452-135222 of 
                 NP_253757.1 
               
               
                 TatC 
                   
                   
                 SEQ ID NO: 384 
               
               
                   
                   
                   
                 (contig 17) 
               
               
                 LIPOPROTEIN 
                 SEQ ID NO: 740 
                 SEQ ID NO: 741 
                 nt. 18895-20112 of 
                 P40827 
               
               
                 NLPD 
                   
                   
                 SEQ ID NO: 682 
               
               
                   
                   
                   
                 (contig 15) 
               
               
                 Hemoglobin and 
                 SEQ ID NO: 742 
                 SEQ ID NO: 743 
                 nt. 34181-31041 of 
                 Q9X442 
               
               
                 hemoglobin- 
                   
                   
                 SEQ ID NO: 682 
               
               
                 haptoglobin binding 
                   
                   
                 (contig 15) 
               
               
                 protein C precursor 
               
               
                 HimA 
                 SEQ ID NO: 744 
                 SEQ ID NO: 745 
                 nt. 382795-383085 of 
                 NP_245565.1 
               
               
                   
                   
                   
                 SEQ ID NO: 685 
               
               
                   
                   
                   
                 (contig 18) 
               
               
                 transferrin-binding 
                 SEQ ID NO: 746 
                 SEQ ID NO: 747 
                 nt. 178537-175799 of 
                 S70906 
               
               
                 protein 1 
                   
                   
                 SEQ ID NO: 683 
               
               
                   
                   
                   
                 (contig 16) 
               
               
                 SapC 
                 SEQ ID NO: 748 
                 SEQ ID NO: 749 
                 nt. 197754-196867 of 
                 NP_245850.1 
               
               
                   
                   
                   
                 SEQ ID NO: 685 
               
               
                   
                   
                   
                 (contig 18) 
               
               
                 heat shock protein 
                 SEQ ID NO: 750 
                 SEQ ID NO: 751 
                 nt. 40414-41265 of 
                 NP_273864.1 
               
               
                 HtpX 
                   
                   
                 SEQ ID NO: 682 
               
               
                   
                   
                   
                 (contig 15) 
               
               
                 HEME/HEMOPEXIN- 
                 SEQ ID NO: 752 
                 SEQ ID NO: 753 
                 nt. 229430-232195 of 
                 P45354 
               
               
                 BINDING 
                   
                   
                 SEQ ID NO: 684 
               
               
                 PROTEIN 
                   
                   
                 (contig 17) 
               
               
                 HEME/HEMOPEXIN 
                 SEQ ID NO: 754 
                 SEQ ID NO: 755 
                 nt. 227721-229418 of 
                 P45356 
               
               
                 UTILIZATION 
                   
                   
                 SEQ ID NO: 684 
               
               
                 PROTEIN B 
                   
                   
                 (contig 17) 
               
               
                 HEME/HEMOPEXIN 
                 SEQ ID NO: 756 
                 SEQ ID NO: 757 
                 nt 225516-227645 of 
                 P45357 
               
               
                 UTILIZATION 
                   
                   
                 SEQ ID NO: 684 
                 NP_246561.1 
               
               
                 PROTEIN C 
                   
                   
                 (contig 17) 
               
               
                 iron utilization 
                 SEQ ID NO: 758 
                 SEQ ID NO: 759 
                 nt. 32076-33611 of 
                 T10887 
               
               
                 protein B 
                   
                   
                 SEQ ID NO: 684 
               
               
                   
                   
                   
                 (contig 17) 
               
               
                 PREPROTEIN 
                 SEQ ID NO: 760 
                 SEQ ID NO: 761 
                 nt. 82314-84785 of 
                 P96313 
               
               
                 TRANSLOCASE 
                   
                   
                 SEQ ID NO: 683 
               
               
                 SECA SUBUNIT 
                   
                   
                 (contig 16) 
               
               
                 IMMUNOGLOBULIN 
                 SEQ ID NO: 762 
                 SEQ ID NO: 763 
                 nt. 171647-166263 of 
                 P45384 
               
               
                 A1 PROTEASE 
                   
                   
                 SEQ ID NO: 683 
               
               
                   
                   
                   
                 (contig 16) 
               
               
                 multidrug 
                 SEQ ID NO: 764 
                 SEQ ID NO: 765 
                 nt. 74524-72992 of 
                 NP_311575.1 
               
               
                 resistance 
                   
                   
                 SEQ ID NO: 683 
               
               
                 membrane 
                   
                   
                 (contig 16) 
               
               
                 translocase 
               
               
                 YhbX/YhjW/YijP/Yj 
                 SEQ ID NO: 766 
                 SEQ ID NO: 767 
                 nt. 61734-63200 of 
                 NP_275002.1 
               
               
                 dB family protein 
                   
                   
                 SEQ ID NO: 683 
               
               
                   
                   
                   
                 (contig 16) 
               
               
                 putative membrane 
                 SEQ ID NO: 768 
                 SEQ ID NO: 769 
                 nt. 906601-908094 of 
                 NP_458664.1 
               
               
                 protein 
                   
                   
                 SEQ ID NO: 685 
               
               
                   
                   
                   
                 (contig 18) 
               
               
                 putative membrane 
                 SEQ ID NO: 770 
                 SEQ ID NO: 771 
                 nt. 16185-17942 of 
                 NP_404859.1 
               
               
                 protein 
                   
                   
                 SEQ ID NO: 683 
               
               
                   
                   
                   
                 (contig) 
               
               
                   
               
             
          
         
       
     
       Example 3 
     Construction of the NTHi Promoter Trap Library 
       [0093]    To identify potential virulence determinants of NTHi, bacterial gene expression was monitored by differential fluorescence induction (DFI) during early disease progression in one specific anatomical niche of a chinchilla model of NTHi-induced otitis media (OM). Genomic DNA fragments from NTHi strain 86-028NP were cloned upstream of the promoterless gfpmut3 gene using a promoter trap library. Plasmid pGZRS39A, a derivative of pGZRS-1 isolated from  Actinobacillus pleuropneumoniae , is an  A. pleuropneumoniae - Escherichia coli  shuttle vector. This plasmid contains the origin of replication from  A. pleuropneumoniae , the lacZα gene from pUC19 and the kanamycin resistance gene from Tn903. (West et al.,  Genes,  160: 81-86, 1995). 
         [0094]    The promoter trap vector was constructed by cloning the GTP mutant gfpmut3 gene, as a BamHI to EcoRI fragment into pGZRS-39A to form pRSM2167. This mutant GTP gene contains two amino acid changes, S65G and S72A, that enhance fluorescence emission when excited at 488 nm. This mutant also has high solubility and fast kinetics of chromophore formation (Cormack et al.,  Gene,  173: 33-38, 1996). This plasmid was transformed by electroporation into NTHi strain 86-028NP, generating the parent-plasmid strain 86-028NP/pRSM2169. 
         [0095]    Random genomic DNA fragments (described in Example 1) were prepared for ligation into the promoter probe vector. Genomic DNA was isolated from strain 86-028NP using the Puregene DNA isolation kit (Gentra Systems, Minneapolis, Minn.) according to the manufacturer&#39;s protocol. Due to restriction barriers, it was necessary to isolate the plasmid DNA and use this for the library generation. The isolated DNA was partially digested with Sau3AI (NEB, Beverly, Mass.; 0.25 units/μg DNA) for 1 hour at 37° C., separated by gel electrophoresis and DNA fragments 0.5-1.5 kb in size were recovered using the Qiagen gel extraction kit. For vector preparation, pRSM2167 was isolated from an overnight culture using the Wizard Plus Maxiprep DNA purification system (Promega, Madison Wis.) according to the manufacturer&#39;s protocol. 
         [0096]    Plasmid DNA was linearized by BamHI digestion and 5′ phosphate groups removed by treatment with calf intestinal alkaline phosphatase (CIAP; GibcoBRL Life Technologies). Genomic DNA fragments were ligated with the linearized, phosphatase-treated vector and electroporated into competent NTHi strain 86-028NP prepared for electroporation according to a modified protocol (Mitchell et al.,  Nucleic Acids Res.,  19: 3625-3628, 1991). When plasmid DNA was electroporated back into NTHi strain 86-028NP, transformation efficiency was improved by one-thousand fold. Briefly, cells were grown to an OD 500 =0.3 in sBHI (brain heart infusion) broth at 37° C., 220 rpm. Cells were chilled on ice for 30 minutes and subsequently washed with an equal volume of 0.5×SG (1×SG: 15% glycerol, 272 mM sucrose) at 4° C. Washes were repeated a total of three times. Subsequently, the cells were diluted in 1×SG to a 100× concentrated volume. The cells were electroporated using the BioRad Gene Pulser II set at 200 ohms, 2.5 kV and 25 μF and then diluted in 1 ml prewarmed sBHI, incubated for 2 hours at 37° C., 5% CO 2  and plated on chocolate agar for overnight growth of transformants. 
         [0097]    Transformants were selected and frozen in pools of 1000 clones in skim milk containing 20% glycerol (vol/vol). A 68,000 member gfp promoter probe library was generated. Using the probability calculation of Clarke and Carbon (Cell, 9: 91-99, 1976), to achieve a 99% probability of having a given DNA sequence represented in a library of 300 bp fragments of strain 86-028NP DNA (1.8×10 6  bp/genome), a library of 27,629 clones was needed. Therefore the present library represents 2.5 fold coverage of the 86-028NP genome. 
         [0098]    In order to assess the quality of the library, fifty clones were selected at random, grown overnight on chocolate agar and the plasmids were isolated and insert DNA sequenced. A majority (64%) of the selected clones had insert sizes ranging between 200 and 500 bp while 32% exceeded 500 bp. The majority of inserts showed homology to unique  H. influenzae  strain Rd open reading frames (ORFs), and 15 clones had sequence unique to strain 86-028NP DNA. Of those clones with homology to strain Rd, 60% were in the correct orientation, 36% of which contained sequence upstream an ORF. Although a majority of clones had an insert size less than 500 bp, no correlation was found between small insert size and increased GFP expression. In fact four clones exhibited slight to moderate fluorescence in vitro, 3 of which had insert sizes between 200-500 base pairs and one had an insert that was greater than 700 base pairs. 
         [0099]    A fraction of the library (approximately 1000 clones) was grown on chocolate agar, harvested in PBS and analyzed by flow cytometry for GFP fluorescence. Compared to strain 86-028NP/pRSM2169 that contains the promoter trap vector without insert DNA, the pool of library clones displays an increased fluorescence intensity. Thus, the library contains clones with promoters at varying levels of activity. 
       Example 4 
     Analysis of 86-028NP Derivatives Expressing GFP 
       [0100]    In order to establish the FACS parameters necessary to identify and sort gfp-expressing bacteria, a panel of isolates demonstrating varying levels of gfp expression was utilized. Background fluorescence was assessed using strain 86-028NP/pRSM2169 (negative control), therefore any observed fluorescence would be due to the lacZ promoter driving gfp expression. However, this strain does not produce detectable levels of GFP and in fact, does not demonstrate increased fluorescence when compared to the parent strain 86-028NP. A high-level gfp-expressing isolate was generated by cloning a 500 bp fragment containing the strong promoter for outer membrane protein P2 expression into SalI-BamHI digested pRSM2167. This plasmid was transformed into 86-028NP by electroporation, generating the high-level gfp expressing strain 86-028NP/pRSM2211 (highly fluorescent control). This strain demonstrated an approximate 100 fold increase in GFP fluorescence compared to strain 86-028NP/pRSM2169. An intermediate fluorescent derivative clone, 86-028NP/pKMM4B5 (intermediate fluorescent control), was isolated by FACS analysis and used both in preliminary experiments and as a control for cell sorting. The DNA fragment containing a promoter driving gfp expression in vitro is unique to strain 86-028NP, having no known homology to DNA of other organisms. This clone exhibits an approximate 10 fold increase in fluorescence compared to strain 86-028NP/pRSM2169. 
         [0101]    The control strains were resuspended from growth on chocolate agar and labeled with cross-reactive Phycoprobe R-PE anti-human IgG (H+L) antibody (10 μg/ml in 100 μl PBS; Biomeda Corp) for 30 minutes at 4° C. Following three successive washes to remove unbound antibody, bacteria were resuspended in 300 μl DPBS for FACS analysis. These control preparations were used to set the appropriate size and fluorescence gates using a Coulter Epics Elite flow cytometer (Coulter Corp.) equipped with an argon laser emitting at 488 nm. Bacteria were gated for size based on log forward angle and side scatter detection and for sorting by FITC/PE labeling of bacteria. Sorted cells were collected into cold sBHI and plated on chocolate agar. After overnight growth, cells were collected for a secondary round of infection or were individually selected and grown overnight, screened by individual clone for fluorescence when grown in vitro, and frozen in skim milk containing 20% (vol/vol) glycerol prior to plasmid isolation and sequencing of insert DNA. Sorting efficiency of control strains was confirmed using a Coulter EPICS flow cytometer (Coulter Corp.). 
         [0102]    Many plasmids were segregated rapidly in vitro in the absence of antibiotic selection. Thus, in order to assess whether the promoter trap vector used here was prone to this event, a single colony of strain 86-028NP/pRSM2211 (highly fluorescent control) was isolated on chocolate agar and passaged 20 times in the absence of antibiotic selection. No significant decrease in fluorescence intensity was observed when compared to bacteria grown in the presence of antibiotic. In addition, the plasmid is maintained in the absence of antibiotic selection in vivo. Similar bacterial counts were observed when bacteria-containing middle ear fluids collected from a chinchilla were plated on chocolate agar with or without kanamycin. These data demonstrate that the promoter trap vector was stably maintained in the absence of antibiotic selection. 
         [0103]    In addition to problems with plasmid stability, early studies on the use of GFP as a reporter to study host-pathogen interactions demonstrated that GFP could be continuously synthesized as a cytoplasmic protein with low toxicity, having minimal effects on the bacterial cell-surface dynamics (Chalfie et al.,  Science,  263: 802-805, 1994). The construction of a high level gfp-expressing derivative allowed the assessment of the GFP toxicity on NTHi. Growth curves of both the wild-type strain (86-028NP) and the high GFP producing strain 86-028NP/pRSM2211 were compared when grown under similar conditions. The growth rates were similar, indicating that GFP expression was not toxic to the cells. 
         [0104]    The 86-028NP gfp-expressing derivatives were used to define the parameters for efficient cell sorting. Strain 86-028NP/pRSM2169 was mixed with the intermediate gfp-expressing derivative, strain 86-028NP/pKMM4B5, at a 100:1 ratio, simulating the in vivo environment that is expected to contain a small percentage of gfp-expressing clones relative to the total bacterial population. This mixture was subjected to FACS analysis, collecting the 1.8% most fluorescent population and the 52% least fluorescent population. Flow cytometric analysis of the sorted populations revealed an enrichment of strain 86-028NP/pKMM4B5 to 65% of the bacterial population, a phenomenon that was not observed when sorting on the negative population. Subsequent rounds of sorting would be expected to further enrich for this intermediate fluorescent population. The inability to decrease the amount of fluorescent bacteria in the negative sort was attributed to the size of the gate set for negative sorting. GFP-negative cells were enriched by gating on the 10% least fluorescent population. 
       Example 5 
     Direct Labeling of Bacteria from Middle Ear Fluids 
       [0105]    A similar strategy (as described in Example 5) was applied to sort fluorescent clones from effusions obtained from the chinchilla middle ear during AOM. Our ability to use differential fluorescence induction (DFI) in vivo was dependent upon our ability to sort gfp-expressing bacteria from non-fluorescent bacteria, fluorescent and non-fluorescent cellular debris, and eukaryotic cells. 
         [0106]    Healthy adult chinchillas ( Chinchilla lanigera ) with no evidence of middle ear infection by either otoscopy or tympanometry were used to screen the library for promoter activity in vivo. Two pools of the NTHi/pRSM2169 library (1000 clones each) were grown overnight on chocolate agar containing kanamycin. The library was combined and diluted in cold 10 mM sterile PBS to 3.3×10 6  CFU/ml and 300 μl (1.0×10 6  CFU; 500 CFU/clone) was used to inoculate the left and the right chinchilla transbullar cavity (2000 clones/ear). OM development was monitored by video otoscopy and tympanometry at 24 and 48 hours. The bacteria multiplied in the middle ear cavity, reaching a concentration 500 times the inoculum dose by 48 hours as expected (Bakaletz et al.,  Infect. Immunity  67: 2746-62, 1999). This bacterial adaptation to the host environment results in an inflammatory response, indicated by erythema, vessel dilation and bulging of the tympanic membrane, infiltration of polymorphonuclear cells (PMN&#39;s), and accumulation of fluid in the middle ear cavity as observed by otoscopy and microscopic examination of recovered effusions. Twenty-four and 48 hours later, middle ear fluids were retrieved by epitympanic tap, and prepared for FACS. 
         [0107]    It is important to note that this analysis was limited to those bacteria recoverable in the middle ear fluid. In some cases it was necessary to lavage the middle ear cavity to collect the bacteria for FACS analysis. Thus, this analysis includes genes up-regulated when NTHi are loosely adherent to mucosae. NTHi has been observed to form a biofilm in the middle ear cavity in a chinchilla model of OM (Erhlich et al.,  JAMA,  287: 1710-5, 2002). Since the protocols described herein select for clones recovered from the planktonic population, it is not expected to recover those clones in which genes are up-regulated when the bacteria are associated with mucosal biofilms. Homogenization of middle ear mucosae and subsequent bacterial cell isolation however, would enable us to recover these clones. It is also possible that some GFP-expressing clones were recovered in the effusion, yet were adherent to eukaryotic cells present in the effusion as exfoliated cells, or in aggregates. These bacteria are difficult to recover from the effusion without compromising the sorting efficiency. Therefore the middle ear fluids were treated with a mucolytic agent, then centrifuged to remove large aggregates and eukaryotic cells and prior to labeling. 
         [0108]    Chinchilla middle ear fluids were diluted, if necessary, to 250 μl with sterile saline. An equal volume of N-acetyl-L-cysteine (0.5%; w/v) in DPBS (pH 7.4) was added for 5 minutes at room temperature as a mucolytic agent (Miyamoto and Bakaletz,  Microb. Pathog.,  21: 343-356 1996). Fluids were centrifuged (300×g, 5 min) to remove cellular debris, red blood cells and inflammatory cells, and supernatants containing bacteria were transferred to a fresh tube. Bacteria were incubated with chinchilla antiserum (1:50 dilution) directed against a whole OMP preparation, derived from NTHi strain 86-028NP, for 45 minutes at 4° C., pelleted by centrifugation (2000×g, 5 min) and washed twice with cold DPBS containing 0.05% bovine serum albumin. Bacteria were subsequently labeled with cross-reactive phycoprobe R-PE anti-human IgG (H+L) antibody (10 μg/ml in 100 μl PBS; Biomeda Corp) for 30 minutes at 4° C. Following three successive washes to remove unbound antibody, cells were resuspended in 300 μl DPBS for FACS analysis. 
       Example 6 
     Identification of Promoters Induced In Vivo in Acute Otitis Media 
       [0109]      H. influenzae  86-028NP transformed with the promoter trap library was grown overnight on chocolate agar. To select against those clones containing promoters that expressed gfp in vitro, the library was subjected to one round of FACS analysis (as described in Example 6), collecting only those clones expressing low-level amounts of GFP. These clones were pooled and used to inoculate the chinchilla middle ear transbullarly. Following 24 and 48 hours of infection, bacteria-containing effusions were removed by epitympanic tap. Bacteria were indirectly labeled with R-PE-labeled antibody and subjected to FACS analysis by gating on fluorescently tagged bacteria but sorting for those that were also expressing. These clones were used to reinfect animals for further enrichment. Following the final round of sorting, single colony isolates were screened in vitro for lack of fluorescence. 
         [0110]    Those clones isolated by FACS analysis (positive for GFP fluorescence in vivo), which did not emit fluorescence in vitro were prepared for plasmid isolation and identification of insert DNA sequence. These clones were grown overnight on chocolate agar plates containing kanamycin and prepared for plasmid isolation using the Qiaprep Miniprep Kit (Qiagen) according to the manufacturer&#39;s protocol. Plasmid insert DNA was sequenced using the primer 5′-TGCCCATTAACATCACCATCTA-3′ (SEQ ID NO: 588) that is complementary to the gfpmut3 gene and downstream of the insert DNA. Sequencing reactions were performed using the ABI prism BigDye® terminator cycle sequencing ready reaction kit (Applied Biosystems) according to manufacturer&#39;s protocol using a GeneAmp PCR System 9700 (Applied Biosystems). The sequences were then purified by passage through sephadex G-50 in a 96-well multiscreen HV plate (Millipore) and subsequently analyzed on an ABI Prism 3100 DNA analyzer (Applied Biosystems). 
         [0111]    Insert sequences were compared to the complete annotated sequence of  H. influenzae  strain Rd. Those inserts with no nucleotide homology to strain Rd were subsequently analyzed using the BLASTN and BLASTX algorithms. Further sequence analysis was performed with DNASTAR (Madison, Wis.). Inserts in the correct orientation and containing sequence 5′ to a predicted ORF contained a putative promoter that was preferentially active when the NTHi bacteria were in the chinchilla middle ear. 
         [0112]    Fifty-two clones with putative promoters that were regulated in vivo were isolated. Of the 44 candidate clones containing sequence similar to that identified in  H. influenzae  strain Rd, quantitative comparison of gene expression in vitro and in vivo confirmed up-regulated gene expression for twenty-six genes (60%) when NTHi respond to environmental cues present in the chinchilla middle ear and these genes are summarized in Table 4A below. The in vivo-regulated promoters driving expression of genes are predicted to be involved in membrane transport, environmental informational processing, cellular metabolism, gene regulation, as well as hypothetical proteins with unknown function. 
         [0113]    In order to confirm the induction of putative promoter candidates in vivo, the relative amount of messenger RNA expression was compared when NTHi strain 86-028NP was grown in vitro to mid-log phase or in vivo for 48 hours. The RNA was isolated using TRIzol LS reagent (Gibco Life Technologies) according to the manufacturer&#39;s protocol. DNA was removed from the RNA preparation using DNA-free kit (Ambion) according to the manufacturer&#39;s protocol. DNase I treated RNA samples were purified by passage through a Qiagen RNeasy column. RNA purity and integrity was assessed by 260/280 nm spectrophotometer readings and on the Agilent 2100 Bioanalyzer (Agilent Technologies), respectively. 
         [0114]    In order to independently confirm the FACS data, we determined the relative expression of candidate genes by quantitative RT-PCR. The parent strain 86-028NP, was used for these studies. Real-time quantitative RT-PCR using the one-step QuantiTect SYBR Green RT-PCR kit (Qiagen) assessed transcription levels according to the manufacture&#39;s instructions. Briefly, using primers generated to an open reading frame downstream of the putative in vivo-induced promoters identified by FACS analysis, gene-specific mRNA was reverse transcribed and amplified by RT-PCR on the ABI Prism 7700 sequence detection system (Applied Biosystems). The amount of product was calculated using a standard curve generated to known amounts of bacterial genomic DNA (10 2 -10 7  genomic copies DNA) by amplifying a fragment of the gyrase (gyr) gene. Controls were analyzed in parallel to verify the absence of DNA in the RNA preparation (−RT control) as well as the absence of primer dimers in control samples lacking template RNA. In addition, RT-PCR products were analyzed by gel electrophoresis and, in all cases, a single product was observed at the appropriate base pair size. Amounts of bacterial RNA between samples were normalized relative to gyr expression, shown to be constitutively expressed under various growth conditions that we tested in vitro. Known amounts of bacterial genomic DNA (10 2 -10 7  genomic copies DNA) were used to generate a standard curve for RT-PCR quantitation by amplifying a fragment of the gyrase (gyr) gene. Gyrase is constitutively expressed in vitro under various growth conditions and was therefore used to normalize total bacterial RNA levels between samples. Relative gene expression in vivo was compared to that of gene expression in vitro and data expressed as fold-increase are summarized in Table 4A. 
         [0115]    The 8-fold sequencing of the NTHi genome identified the full length open reading frames for the majority of genes listed in Table 4A. Table 4B provides the full length nucleotide sequence within the NTHi genome and the corresponding amino acid sequence. The fold induction of the gene due to environmental cues present in the chinichilla middle ear and the product or function of the gene are repeated in Table 4B for convenience. 
         [0000]    
       
         
               
               
               
               
               
               
             
               
               
               
               
               
               
             
           
               
                 TABLE 4A 
               
               
                   
               
               
                   
                 Gene or 
                 SEQ 
                 GenBank 
                 Fold 
                   
               
               
                 Category 
                 ORF 
                 ID NO: 
                 Protein ID 
                 Induction 
                 Product or Function 
               
               
                   
               
             
             
               
                   
               
             
          
           
               
                 Amino acid metabolism 
                 hisB 
                 589 
                 NP_438632 
                 2.9 
                 Histidine biosynthesis 
               
               
                   
                   
                   
                   
                   
                 bifunctional protein 
               
               
                 Lipoprotein 
                 lppB 
                 590 
                 NP_438862.1 
                 2.6 
                 Lipoprotein B homologue 
               
               
                 Membrane transport 
                 sapA 
                 591 
                 NP_439780.1 
                 2.8 
                 Peptide ABC transporter; 
               
               
                   
                   
                   
                   
                   
                 periplasmic SapA precursor 
               
               
                   
                 lolA 
                 592 
                 NP_439736.1 
                 2.4 
                 Outer membrane lipoproteins 
               
               
                   
                   
                   
                   
                   
                 carrier protein precursor 
               
               
                   
                 rbsC 
                 593 
                 NP_438661.1 
                 5.1 
                 Ribose transport system 
               
               
                   
                   
                   
                   
                   
                 permease protein 
               
               
                 Purine synthesis 
                 purE 
                 594 
                 NP_439757.1 
                 51.7 
                 Phosphoribosylaminoimidazole 
               
               
                   
                   
                   
                   
                   
                 carboxylase catalytic 
               
               
                   
                   
                   
                   
                   
                 subunit; PurE 
               
               
                 Biosynthetic and 
                 ribB 
                 595 
                 NP_438923.1 
                 8.3 
                 3,4-dihydroxy-2-butanone 4- 
               
               
                 metabolic functions 
                   
                   
                   
                   
                 phosphate synthase; 
               
               
                   
                   
                   
                   
                   
                 riboflavin biosynthesis 
               
               
                   
                 arcB 
                 596 
                 NP_438753.1 
                 10 
                 Ornithine 
               
               
                   
                   
                   
                   
                   
                 carbamolytransferase; 
               
               
                   
                   
                   
                   
                   
                 arginine degradation 
               
               
                   
                 uxuA 
                 597 
                 NP_438228.1 
                 3.1 
                 Mannonate dehydratase; 
               
               
                   
                   
                   
                   
                   
                 production of glyceraldehyde 
               
               
                   
                   
                   
                   
                   
                 3-phosphate 
               
               
                   
                 dsbB 
                 598 
                 NP_438589.1 
                 2.6 
                 Disulfide oxidoreductase; 
               
               
                   
                   
                   
                   
                   
                 disulfide bond formation 
               
               
                   
                   
                   
                   
                   
                 protein B 
               
               
                   
                 ureH 
                 599 
                 NP_438693.1 
                 3.9 
                 Urease accessory protein 
               
               
                   
                 licC 
                 600 
                 NP_439688.1 
                 2.3 
                 Phosphocholine (ChoP) 
               
               
                   
                   
                   
                   
                   
                 cytidylyltransferase 
               
               
                   
                 HI1647 
                 601 
                 NP_439789.1 
                 2.0 
                 Putative pyridoxin 
               
               
                   
                   
                   
                   
                   
                 biosynthesis protein; singlet 
               
               
                   
                   
                   
                   
                   
                 oxygen resistance protein 
               
               
                 DNA replication, 
                 ispZ 
                 602 
                 P43810 
                 2.5 
                 Probable intracellular 
               
               
                 repair 
                   
                   
                   
                   
                 septation protein 
               
               
                   
                 radC 
                 603 
                 NP_439113.1 
                 2.1 
                 DNA repair protein 
               
               
                   
                 mukF 
                 604 
                 P45185 
                 2.0 
                 MukF protein homologue; 
               
               
                   
                   
                   
                   
                   
                 remodeling of nucleiod 
               
               
                   
                   
                   
                   
                   
                 structure 
               
               
                 Gene regulation 
                 glpR 
                 605 
                 NP_438777.1, 
                 2.8 
                 Glycerol-3-phosphate regulon 
               
               
                   
                   
                   
                 NP_439170.1 
                   
                 repressor 
               
               
                   
                 ihfB 
                 606 
                 P43724 
                 2.5 
                 Integration host factor beta 
               
               
                   
                   
                   
                   
                   
                 subunit 
               
               
                   
                 argR 
                 607 
                 NP_439365.1 
                 2.7 
                 Arginine repressor 
               
               
                   
                 cspD 
                 608 
                 NP_439584.1 
                 2.1 
                 Cold shock like protein; 
               
               
                   
                   
                   
                   
                   
                 stress response protein 
               
               
                 Hypothetical or 
                 HI0094 
                 609 
                 NP_438267.1 
                 8.3 
                 Hypothetical protein 
               
               
                 unknown proteins 
                 HI1163 
                 610 
                 NP_439321.1 
                 2.3 
                 Conserved hypothetical 
               
               
                   
                   
                   
                   
                   
                 protein; putative oxidase 
               
               
                   
                 HI1063 
                 611 
                 NP_439221.1 
                 2.7 
                 Hypothetical protein 
               
               
                   
                 HI0665 
                 612 
                 NP_438824.1 
                 2.8 
                 Hypothetical protein 
               
               
                   
                 HI1292 
                 613 
                 NP_439444.1 
                 2.6 
                 Hypothetical protein 
               
               
                   
                 HI1064 
                 614 
                 NP_439222.1 
                 2.6 
                 Hypothetical protein 
               
               
                   
               
             
          
         
       
     
         [0000]    
       
         
               
               
               
               
               
               
               
             
               
               
               
               
               
               
               
             
           
               
                 TABLE 4B 
               
               
                   
               
               
                   
                   
                 Full 
                   
                   
                   
                   
               
               
                   
                 Gene 
                 Length 
               
               
                   
                 or 
                 Nucleotide 
                 Amino Acid 
                   
                 Fold 
                 Product or 
               
               
                 Category 
                 ORF 
                 Sequence 
                 Sequence 
                 Location in Contig 
                 Induction 
                 Function 
               
               
                   
               
             
             
               
                   
               
             
          
           
               
                 Amino 
                 hisB 
                 SEQ ID NO: 
                 SEQ ID NO: 
                 nt. 68378-67290 
                 2.9 
                 Histidine 
               
               
                 acid 
                   
                 615 
                 616 
                 of SEQ ID NO: 
                   
                 biosynthesis 
               
               
                 metabolism 
                   
                   
                   
                 680 (contig 13) 
                   
                 bifunctional protein 
               
               
                 Membrane 
                 sapA 
                 SEQ ID NO: 
                 SEQ ID NO: 
                 nt. 200403-198709 
                 2.8 
                 Peptide ABC 
               
               
                 transport 
                   
                 617 
                 618 
                 of SEQ ID NO: 
                   
                 transporter; 
               
               
                   
                   
                   
                   
                 685 (contig 18) 
                   
                 periplasmic SapA 
               
               
                   
                   
                   
                   
                   
                   
                 precursor 
               
               
                   
                 rbsC 
                 SEQ ID NO: 
                 SEQ ID NO: 
                 nt. 42773-41802 
                 5.1 
                 Ribose transport 
               
               
                   
                   
                 619 
                 620 
                 of SEQ ID NO: 
                   
                 system permease 
               
               
                   
                   
                   
                   
                 680 (contig 13) 
                   
                 protein 
               
               
                 Purine 
                 purE 
                 SEQ ID NO: 
                 SEQ ID NO: 
                 nt. 219625-219131 
                 51.7 
                 Phosphoribosylamino- 
               
               
                 synthesis 
                   
                 621 
                 622 
                 of SEQ ID NO: 
                   
                 imidazole 
               
               
                   
                   
                   
                   
                 685 (contig 18) 
                   
                 carboxylase catalytic 
               
               
                   
                   
                   
                   
                   
                   
                 subunit; PurE 
               
               
                 Biosynthetic 
                 ribB 
                 SEQ ID NO: 
                 SEQ ID NO: 
                 nt. 131537-132184 
                 8.3 
                 3,4-dihydroxy-2- 
               
               
                 and 
                   
                 623 
                 624 
                 of SEQ ID NO: 
                   
                 butanone 4- 
               
               
                 metabolic 
                   
                   
                   
                 682 (contig 15) 
                   
                 phosphate synthase; 
               
               
                 functions 
                   
                   
                   
                   
                   
                 riboflavin 
               
               
                   
                   
                   
                   
                   
                   
                 biosynthesis 
               
               
                   
                 arcB 
                 SEQ ID NO: 
                 SEQ ID NO: 
                 nt. 49710-48706 
                 10 
                 Ornithine 
               
               
                   
                   
                 625 
                 626 
                 of SEQ ID NO: 
                   
                 carbamolytransferase; 
               
               
                   
                   
                   
                   
                 681 (contig 14) 
                   
                 arginine 
               
               
                   
                   
                   
                   
                   
                   
                 degradation 
               
               
                   
                 uxuA 
                 SEQ ID NO: 
                 SEQ ID NO: 
                 nt. 840671-841855 
                 3.1 
                 Mannonate 
               
               
                   
                   
                 627 
                 628 
                 of SEQ ID NO: 
                   
                 dehydratase; 
               
               
                   
                   
                   
                   
                 685 (contig 18) 
                   
                 production of 
               
               
                   
                   
                   
                   
                   
                   
                 glyceraldehyde 3- 
               
               
                   
                   
                   
                   
                   
                   
                 phosphate 
               
               
                   
                 dsbB 
                 SEQ ID NO: 
                 SEQ ID NO: 
                 nt. 388050-388583 
                 2.6 
                 Disulfide 
               
               
                   
                   
                 629 
                 630 
                 of SEQ ID NO: 
                   
                 oxidoreductase; 
               
               
                   
                   
                   
                   
                 384 (contig 17) 
                   
                 disulfide bond 
               
               
                   
                   
                   
                   
                   
                   
                 formation protein B 
               
               
                   
                 ureH 
                 SEQ ID NO: 
                 SEQ ID NO: 
                 nt. 4452-5267 
                 3.9 
                 Urease accessory 
               
               
                   
                   
                 631 
                 632 
                 of SEQ ID NO: 
                   
                 protein 
               
               
                   
                   
                   
                   
                 680 (contig 13) 
               
               
                   
                 licC 
                 SEQ ID NO: 
                 SEQ ID NO: 
                 nt. 355083-354382 
                 2.3 
                 Phosphocholine 
               
               
                   
                   
                 633 
                 634 
                 of SEQ ID NO: 
                   
                 (ChoP) 
               
               
                   
                   
                   
                   
                 385 (contig 18) 
                   
                 cytidylyltransferase 
               
               
                   
                 HI1647 
                 SEQ ID NO: 
                 SEQ ID NO: 
                 nt. 664017-664892 
                 2.0 
                 Putative pyridoxin 
               
               
                   
                   
                 635 
                 636 
                 of SEQ ID NO: 
                   
                 biosynthesis protein; 
               
               
                   
                   
                   
                   
                 685 (contig 18) 
                   
                 singlet oxygen 
               
               
                   
                   
                   
                   
                   
                   
                 resistance protein 
               
               
                 DNA 
                 ispZ 
                 SEQ ID NO: 
                 SEQ ID NO: 
                 nt. 4512-5069 
                 2.5 
                 Probable 
               
               
                 replication, 
                   
                 637 
                 638 
                 of SEQ ID NO: 
                   
                 intracellular 
               
               
                 repair 
                   
                   
                   
                 683 (contig 16) 
                   
                 septation protein 
               
               
                   
                 radC 
                 SEQ ID NO: 
                 SEQ ID NO: 
                 nt. 132695-132030 
                 2.1 
                 DNA repair protein 
               
               
                   
                   
                 639 
                 640 
                 of SEQ ID NO: 
               
               
                   
                   
                   
                   
                 683 (contig 16) 
               
               
                   
                 mukF 
                 SEQ ID NO: 
                 SEQ ID NO: 
                 nt. 504549-503215 
                 2.0 
                 MukF protein 
               
               
                   
                   
                 641 
                 642 
                 of SEQ ID NO: 
                   
                 homologue; 
               
               
                   
                   
                   
                   
                 685 (contig 18) 
                   
                 remodeling of 
               
               
                   
                   
                   
                   
                   
                   
                 nucleiod structure 
               
               
                 Gene 
                 glpR 
                 SEQ ID NO: 
                 SEQ ID NO: 
                 nt. 72716-73483 
                 2.8 
                 Glycerol-3- 
               
               
                 regulation 
                   
                 643 
                 644 
                 of SEQ ID NO: 
                   
                 phosphate regulon 
               
               
                   
                   
                   
                   
                 682 (contig 15) 
                   
                 repressor 
               
               
                   
                 ihfB 
                 SEQ ID NO: 
                 SEQ ID NO: 
                 nt. 661004-660720 
                 2.5 
                 Integration host 
               
               
                   
                   
                 645 
                 646 
                 of SEQ ID NO: 
                   
                 factor beta subunit 
               
               
                   
                   
                   
                   
                 685 (contig 18) 
               
               
                   
                 argR 
                 SEQ ID NO: 
                 SEQ ID NO: 
                 nt. 178540-178085 
                 2.7 
                 Arginine repressor 
               
               
                   
                   
                 647 
                 648 
                 of SEQ ID NO: 
               
               
                   
                   
                   
                   
                 685 (contig 18) 
               
               
                   
                 cspD 
                 SEQ ID NO: 
                 SEQ ID NO: 
                 nt. 435310-435528 
                 2.1 
                 Cold shock like 
               
               
                   
                   
                 649 
                 650 
                 of SEQ ID NO: 
                   
                 protein; stress 
               
               
                   
                   
                   
                   
                 685 (contig 18) 
                   
                 response protein 
               
               
                 Hypothetical 
                 HI1163 
                 SEQ ID NO: 
                 SEQ ID NO: 
                 nt. 137202-134119 
                 2.3 
                 Conserved 
               
               
                 or 
                   
                 651 
                 652 
                 of SEQ ID NO: 
                   
                 hypothetical protein; 
               
               
                 unknown 
                   
                   
                   
                 685 (contig 18) 
                   
                 putative oxidase 
               
               
                 proteins 
               
               
                   
                 HI1063 
                 SEQ ID NO: 
                 SEQ ID NO: 
                 nt. 35158-34937 
                 2.7 
                 Hypothetical protein 
               
               
                   
                   
                 653 
                 654 
                 of SEQ ID NO: 
               
               
                   
                   
                   
                   
                 685 (contig 18) 
               
               
                   
                 HI0665 
                 SEQ ID NO: 
                 SEQ ID NO: 
                 nt. 17949-18980 
                 2.8 
                 Hypothetical protein 
               
               
                   
                   
                 655 
                 656 
                 of SEQ ID NO: 
               
               
                   
                   
                   
                   
                 679 (contig 12) 
               
               
                   
                 HI1292 
                 SEQ ID NO: 
                 SEQ ID NO: 
                 nt. 555002-555799 
                 2.6 
                 Hypothetical protein 
               
               
                   
                   
                 657 
                 658 
                 of SEQ ID NO: 
               
               
                   
                   
                   
                   
                 685 (contig 18) 
               
               
                   
               
             
          
         
       
     
       Example 7 
     Identification of Virulence-Associated Genes 
       [0116]    In many bacterial species, a subset of virulence-associated genes is regulated by errors in replication of short repeats. These repeats may be 5′ to a gene or in the coding sequence, and their presence is an indication of controlled expression of the gene, which indicates association with virulence. Addition or deletion of a repeat results in the expression or of lack of expression of the particular virulence determinant. 
         [0117]    The NTHi  H. influenzae  strain 86-028NP contig set was queried for short oligonucleotide repeats. The region surrounding the repeats was analyzed to identify the gene(s) associated with the repeat. Table 5 lists the identified repeats and the ORF (identified by BLAST) associated with each repeat. 
         [0118]    Further sequence analysis has identified the full length nucleotide sequence of the virulence-associated genes and the corresponding amino acid sequences encoded by the ORF. The derived amino acid sequences are highly homologous to the listed Genbank sequence. 
         [0000]    
       
         
               
               
               
               
               
               
             
           
               
                 TABLE 5 
               
               
                   
               
               
                   
                 Location 
                 Location 
                 Full Length 
                   
                   
               
               
                   
                 in 3-fold 
                 in 8-fold 
                 Nucleotide 
                 Amino Acid 
                 Genebank 
               
               
                 Repeat 
                 Contigs 
                 Contigs 
                 Sequence 
                 Sequence 
                 Accession No. 
               
               
                   
               
             
             
               
                 SEQ ID NO: 581 
                 115 
                 nt. 484533-483643 of 
                 SEQ ID NO: 659 
                 SEQ ID NO: 660 
                 NP_439538.1 
               
               
                   
                 nt. 473-540 of 
                 SEQ ID NO: 685 
               
               
                   
                 SEQ ID NO: 115 
                 (contig 18) 
               
               
                 SEQ ID NO: 582 
                 377 
                 nt. 416274-414910 of 
                 SEQ ID NO: 661 
                 SEQ ID NO: 662 
                 P45217 
               
               
                   
                 nt. 546-597 of 
                 SEQ ID NO: 685 
               
               
                   
                 SEQ ID NO: 337 
                 (contig 18) 
               
               
                 SEQ ID NO: 583 
                 505 
                 nt. 414500-416614 of 
                 SEQ ID NO: 663 
                 SEQ ID NO: 664 
                 AAK76425 
               
               
                   
                 nt. 310-393 of 
                 SEQ ID NO: 684 
               
               
                   
                 SEQ ID NO: 505 
                 (contig 17) 
               
               
                 SEQ ID NO: 584 
                 508 
                 nt. 506516-507913 of 
                 SEQ ID NO: 665 
                 SEQ ID NO: 666 
                 NP_439520 
               
               
                   
                 nt. 2079-2120 of 
                 SEQ ID NO: 685 
               
               
                   
                 SEQ ID NO: 508 
                 (contig 18) 
               
               
                 SEQ ID NO: 585 
                 518 
                 nt. 354274-352406 of 
                 SEQ ID NO: 667 
                 SEQ ID NO: 668 
                 NP_284893 
               
               
                   
                 nt. 758-789 of 
                 SEQ ID NO: 684 
               
               
                   
                 SEQ ID NO: 518 
                 (contig 17) 
               
               
                 SEQ ID NO: 586 
                 543 
                 nt. 347864-243236 of 
                 SEQ ID NO: 669 
                 SEQ ID NO: 670 
                 AAA20524 
               
               
                   
                 nt. 1814-196 of 
                 SEQ ID NO: 685 
               
               
                   
                 SEQ ID NO: 543 
                 (contig 18) 
               
               
                 SEQ ID NO: 586 
                 543 
                 nt. 699709-704187 of 
                 SEQ ID NO: 671 
                 SEQ ID NO: 672 
                 AAD56660 
               
               
                   
                 nt. 1814-196 of 
                 SEQ ID NO: 685 
               
               
                   
                 SEQ ID NO: 543 
                 (contig 18) 
               
               
                 SEQ ID NO: 587 
                 567 
                 nt. 85546-84689 of 
                 SEQ ID NO: 673 
                 SEQ ID NO: 674 
                 ZP_00053190 
               
               
                   
                 nt. 13309-13320 of 
                 SEQ ID NO: 681 
               
               
                   
                 SEQ ID NO: 567 
                 (contig 14) 
               
               
                   
               
             
          
         
       
     
       Example 8 
     Identification of Unique NTHi Gene Sequences 
       [0119]    Genes associated with NTHi virulence were also identified by comparing the level of expression of the gene when the NTHi bacterium was infecting a tissue verses the level of expression of the same gene when the NTHi was grown on artificial laboratory media. These novel genes were identified using the promoter trap techniques described above in Examples 4-6, and subsequently comparisons with the known Rd genome demonstrated these genes are unique to NTHi strain 86-028NP. 
         [0120]    The DNA sequence identified using this screening procedure are set forth as SEQ ID NOS: 577-580. These sequences did not contain genes or gene fragments that have homologues in the  H. influenzae  Rd. genome sequence. Even though these are completely novel sequences, due to their expression level during NTHi infection in the chinchilla middle ear, it is likely that expression of these genes are involved in NTHi virulence. 
       Example 9 
     Complete Sequence Analysis of NTHi Strain 86-028NP 
       [0121]    Library Construction: 
         [0122]    Chromosomal DNA was prepared from strain 86-028NP using Puregene reagents (Gentra Systems, Minneapolis, Minn.). For the initial shotgun sequencing of the genome, 1 to 2 kb and 2 to 4 kb libraries of genomic DNA were constructed in pUC18 as previously described (Munson et al., Infect Immun 72:3002-10, 2004). For the scaffolding library, genomic DNA was manually sheared into a mean fragment size of 40 kb using a Hamilton syringe. After end repair, fragments were fractionated using a 0.7% low melting temperature agarose gel. Fragments larger than 30 kb were excised and an in-gel ligation to pEpiFOS-5 was performed. The ligation mixture recovered from the gel was packaged into Lambda phage, in vitro, and used to transfect EPI100 cells (Epicentre, Madison, Wis.). 
         [0123]    Sequencing: 
         [0124]    For the shotgun portion of the sequencing, cycle-sequencing reactions were run using PE Big-Dye™ terminators and universal primers (M13 forward and reverse) as previously described (Munson et al., Infect Immun 72:3002-10, 2004). To end-sequence the scaffolding library, plasmid was first purified using a R.E.A.L. Prep 96 Plasmid Kit (QIAGEN Inc., Valencia, Calif.), then amplified using a TempliPhi™ DNA Amplification Kit (Amersham Biosciences Corp., Piscataway, N.J.) before running reactions using PE Big-Dye™ terminators and pEpiFOS-5 forward and reverse sequencing primers (Epicentre, Madison, Wis.). The reactions for the clean-up portions of the project were run using PE Big-Dye™ terminators and custom primers (Integrated DNA Technologies, Coralville, Iowa). Excess dye terminators were removed with Sephadex G50 columns in 96-well format and sequence determined on either an ABI 3700 or an ABI 3100 capillary electrophoresis DNA sequencer (Applied Biosystems, Foster City, Calif.). 
         [0125]    Genome Closure: 
         [0126]    Paired end-sequences from the scaffolding library and PCR were used to order the contigs and to add sequence in areas of low sequence coverage. Paired custom primers (Integrated DNA Technologies, Coralville, Iowa) were designed to bind at the ends of each contig as well as regions flanking areas of low sequence coverage. The intervening regions were amplified with a standard PCR protocol as described in Sambrook et al., Molecular Cloning: A Laboratory Manual (Third Edition). Cold Spring Harbor Laboratory Press., 2001 using Taq polymerase (Roche Diagnostics, Indianapolis, Ind.) and sequenced on both strands. Ribosomal RNA operons and the HMW gene clusters were completely sequenced using clones from the scaffolding library as templates. 
         [0127]    Assembly: 
         [0128]    Phred/Phrap was used for data assembly, employing the default assembly parameters (Ewing et al.,  Genome Res  8:186-94, 1998; Ewing et al.,  Genome Res  8:175-85, 1988; Gordon et al.,  Genome Res  8:195-202, 1998) as described in Munson et al.,  Infect Immun  72:3002-10, 2004. Assemblies were checked using the paired-end sequence data from 507 clones using the Seqman II program from the DNASTAR suite. 
         [0129]    Data Analyses: 
         [0130]    Coding regions were identified using Glimmer2 (v2.13) trained on the set of 1178 longest ORFs identified by the Glimmer2 long-orfs program (Delcher et al.,  Nucleic Acids Res  27:4636-41, 1999). Automated annotation by similarity was done by searching the Glimmer ORF set against the strain Rd proteome, the SwissProt database, the NCBI COGs database, and the KEGG database. The strain Rd database was compared bi-directionally with the strain 86-028NP ORF set using tricross to determine high-confidence regions of similarity and to produce the dotplot comparison of genome organization Ray et al.,  Bioinformatics  17:1105-12, 2001). 
         [0131]    The automatically predicted annotation information was further manually curated using Artemis (Rodriguez et al.,  Infect Immun  71:1635-42, 2003) for visualization and demarcation of genomic regions of interest, and a custom FileMaker Pro database was generated which was then used to apply manual revisions and archive data related to the functional assignment. FASTA analyses were used for the primary automated comparisons. The strong synteny between the strain 80-028NP and strain Rd genomes allowed assignment of a function to the majority of the genes automatically, with similarity held to 90% or better at the amino acid level for matching. The near one-to-one mapping from the strain 86-028NP genome to the strain Rd genome was confirmed by assembly of the strain Rd ORFs onto the strain 86-028NP genome sequence, and the reverse assembly of the strain 86-028NP ORFs onto the Rd genome, using the SeqMan program with the assembly criteria of 80% identity at the nucleotide level. 
         [0132]    Manual BLAST analyses were used to explore the potential function of ORFs that did not show strong similarity to known genes. Manual curation of the automatic assignments was carried out to conform annotations to the current literature and repair the few places where the automated algorithm was easily led astray (notably the HMW gene clusters, the hemoglobin-binding proteins and the hsd gene clusters, whose high family similarity confounds automated assignment). 
         [0133]    The tRNA genes were identified by tRNAscan-SE v1.11 (Lowe et al.,  Nucleic Acids Res  25:955-64, 1997). The rRNA operons were identified based on 16, 23 and 5S rRNA similarity with strain Rd, and the CLUSTALW alignment of the neighborhoods containing these genes to determine the boundaries of the semi-conserved regions. 
         [0134]    The complete genomic DNA sequence of the  H. influenzae , strain 86-028NP, is set out as SEQ ID NO: 772. The open reading frames within the genomic DNA are set out as SEQ ID NOS: 773-2593 and are described in Table 6. The resulting gene products are set out as SEQ ID NOS: 2581-4414 and are described in Table 7. The “c” preceding the nucleotides of the open reading frames indicates the open reading frame is complementary to the 5′ to 3′ sequence set out as SEQ ID NO: 722. The unique NTHi genes are marked in Table 6. The genome sequence will be available from GenBank as Accession number CP000057, which is incorporated by reference herein in its entirety. 
         [0135]    The following open reading frames are defined as pseudogenes in Table 6 because these nucleotide sequences contain a frameshift or a stop codon within the sequence: SEQ ID NO: 822 (kdgK), SEQ ID NO: 928, SEQ ID NO: 994 (bolA), SEQ ID NO: 276 (adhC) SEQ ID NO: 1102 (dusC), SEQ ID NO: 1121 (merP), SEQ ID NO: 1135, SEQ ID NO:1236, SEQ ID NO: 1254, SEQ ID NO: 1376 (lic2C), SEQ ID NO: 1431 (hgpD), SEQ ID NO: 1502, SEQ ID NO:1505 (ppx), SEQ ID NO: 1523 (hgpC), SEQ ID NO: 1585 (lex2A), SEQ ID NO: 1637 SEQ ID NO: 1713, SEQ ID NO: 1856 (mod), SEQ ID NO: 1899, SEQ ID NO: 2006, SEQ ID NO: 2080, SEQ ID NO: 2155, SEQ ID NO: 2202, SEQ ID NO:2257, SEQ ID NO: 2331, SEQ ID NO:2345, SEQ ID NO: 2365, SEQ ID NO: 2555 (metE) and SEQ ID NO:2563 (pmi). The hgpD, hgpC, lex2A and NTHI1769 genes contain contingency repeats that cause the sequence to shift in and out of the reading frame and the resulting amino acid sequences (SEQ ID NOS: 3242, 3332 and 4142) are partial translation. These contingency repeats regulate gene expression in the  H. influenzae  and therefore the genes encoding these proteins will be correctly translated after insertion or deletion of 1 or more repeats 
         [0000]    
       
         
               
             
               
               
               
               
               
             
               
               
               
               
               
             
           
               
                 TABLE 6 
               
             
             
               
                   
               
               
                 NTHi Open Reading Frames and Gene Products 
               
             
          
           
               
                   
                   
                 Unique 
                   
                   
               
               
                   
                 Gene 
                 to NTHi 
               
               
                 CDS 
                 Name 
                 86-0268 
                 Product Name 
                 SEQ ID NO: 
               
               
                   
               
             
          
           
               
                   2-1021 
                 gapA 
                   
                 glyceraldehyde 3-phosphate dehydrogenase 
                 773 
               
               
                 1191-3014 
                 — 
                   
                 putative long-chain-fatty-acid--CoA ligase 
                 774 
               
               
                 C 3051-3839  
                 — 
                   
                 conserved hypothetical protein 
                 775 
               
               
                 C 3855-4319  
                 — 
                   
                 conserved hypothetical protein 
                 776 
               
               
                 C 4581-5393  
                 fdhD 
                   
                 FdhD protein homolog 
                 777 
               
               
                 5664-8750 
                 fdxG 
                   
                 formate dehydrogenase major subunit 
                 778 
               
               
                 8752-9690 
                 fdxH 
                   
                 formate dehydrogenase, iron-sulfur subunit 
                 779 
               
               
                  9683-10399 
                 fdxI 
                   
                 formate dehydrogenase, cytochrome B556 subunit 
                 780 
               
               
                 10469 . . . 11377 
                 fdhE 
                   
                 FdhE homolog 
                 781 
               
               
                 C 11421 . . . 11861      
                 rimI 
                   
                 ribosomal-protein-alanine acetyltransferase 
                 782 
               
               
                 C 11864 . . . 12268      
                 holD 
                   
                 DNA polymerase III, psi subunit 
                 783 
               
               
                 12374 . . . 13366 
                 rsmC 
                   
                 ribosomal RNA small subunit methyltransferase C 
                 784 
               
               
                 C 13434 . . . 14342      
                 era 
                   
                 GTP-binding protein era homolog 
                 785 
               
               
                 C 14339 . . . 15022      
                 rnc 
                   
                 ribonuclease III 
                 786 
               
               
                 C 15024 . . . 16073      
                 lepB 
                   
                 Signal peptidase I 
                 787 
               
               
                 C 16082 . . . 17878      
                 lepA 
                   
                 GTP-binding protein LepA 
                 788 
               
               
                 C 18047 . . . 18430      
                 — 
                   
                 conserved hypothetical acid-induced glycyl radical 
                 789 
               
               
                   
                   
                   
                 enzyme 
               
               
                 18688 . . . 19347 
                 ung 
                   
                 uracil-DNA glycosylase 
                 790 
               
               
                 C 19417 . . . 20841      
                 — 
                   
                 conserved hypothetical protein 
                 791 
               
               
                 C 21224 . . . 22663      
                 — 
                   
                 conserved hypothetical protein 
                 792 
               
               
                 C 22665 . . . 24062      
                 citG 
                   
                 CitXG 
                 793 
               
               
                 C 24243 . . . 25745      
                 citF 
                   
                 citrate lyase alpha chain 
                 794 
               
               
                 C 25760 . . . 26635      
                 citE 
                   
                 citrate lyase beta chain 
                 795 
               
               
                 C 26632 . . . 26919      
                 citD 
                   
                 citrate lyase acyl carrier protein 
                 796 
               
               
                 C 26957 . . . 27964      
                 citC 
                   
                 [citrate [pro-3S]-lyase] ligase 
                 797 
               
               
                 C 28215 . . . 29177      
                 lipA 
                   
                 Lipoic acid synthetase 
                 798 
               
               
                 C 29231 . . . 29869      
                 lipB 
                   
                 lipoate-protein ligase B 
                 799 
               
               
                 C 29871 . . . 30149      
                 — 
                   
                 conserved hypothetical protein 
                 800 
               
               
                 C 30205 . . . 31386      
                 dacA 
                   
                 penicillin-binding protein 5 precursor 
                 801 
               
               
                 C 31402 . . . 32265      
                 rlpA 
                   
                 RlpA-like protein 
                 802 
               
               
                 C 32318 . . . 33433      
                 mrdB 
                   
                 Rod shape-determining protein RodA 
                 803 
               
               
                 C 33423 . . . 35378      
                 mrdA 
                   
                 penicillin-binding protein 2 
                 804 
               
               
                 C 35400 . . . 35867      
                 — 
                   
                 conserved hypothetical protein 
                 805 
               
               
                 C 35921 . . . 36229      
                 — 
                   
                 conserved hypothetical protein 
                 806 
               
               
                 C 36354 . . . 38009      
                 — 
                   
                 conserved hypothetical membrane protein 
                 807 
               
               
                 38215 . . . 39993 
                 — 
                   
                 conserved hypothetical ABC transporter ATP- 
                 808 
               
               
                   
                   
                   
                 binding protein 
               
               
                 40042 . . . 41178 
                 mreB 
                   
                 rod shape-determining protein MreB 
                 809 
               
               
                 41258 . . . 42313 
                 mreC 
                   
                 rod shape-determining protein MreC 
                 810 
               
               
                 42313 . . . 42801 
                 mreD 
                   
                 rod shape-determining protein MreD 
                 811 
               
               
                 C 42852 . . . 43628      
                 — 
                   
                 conserved hypothetical protein 
                 812 
               
               
                 C 43638 . . . 44441      
                 xthA 
                   
                 exodeoxyribonuclease III 
                 813 
               
               
                 C 44489 . . . 45163      
                 rluA2 
                   
                 conserved hypothetical pseudouridine synthase 
                 814 
               
               
                 C 45163 . . . 46227      
                 — 
                   
                 conserved hypothetical membrane protein 
                 815 
               
               
                 C 46287 . . . 46949      
                 — 
                   
                 conserved hypothetical FtsH-interacting integral 
                 816 
               
               
                   
                   
                   
                 membrane protein 
               
               
                 C 47276 . . . 47830      
                 — 
                   
                 conserved hypothetical protein 
                 817 
               
               
                 47897 . . . 48259 
                 phnA 
                   
                 PhnA homolog 
                 818 
               
               
                 C 48312 . . . 48950      
                 eda 
                   
                 KHG/KDPG aldolase 
                 819 
               
               
                 C 48959 . . . 50362      
                 uxuC 
                 ✓ 
                 uronate isomerase 
                 820 
               
               
                 C 50372 . . . 51229      
                 — 
                   
                 putative oxidoreductase 
                 821 
               
               
                 C 51229 . . . 52172      
                 kdgK 
                   
                 pseudogene for 2-dehydro-3-deoxygluconokinase 
                 822 
               
               
                 C 52192 . . . 53463      
                 — 
                   
                 putative TRAP-type C4-dicarboxylate transport 
                 823 
               
               
                   
                   
                   
                 system, large permease component 
               
               
                 C 53473 . . . 53970      
                 — 
                   
                 putative TRAP-type C4-dicarboxylate transport 
                 824 
               
               
                   
                   
                   
                 system, small permease component 
               
               
                 C 54009 . . . 54995      
                 — 
                   
                 putative TRAP-type C4-dicarboxylate transport 
                 825 
               
               
                   
                   
                   
                 system, periplasmic component 
               
               
                 C 55022 . . . 56050      
                 — 
                   
                 conserved hypothetical zinc-type alcohol 
                 826 
               
               
                   
                   
                   
                 dehydrogenase-like protein 
               
               
                 56160 . . . 56960 
                 uxuR 
                   
                 Uxu operon regulator 
                 827 
               
               
                 56988 . . . 58172 
                 uxuA 
                   
                 mannonate dehydratase 
                 828 
               
               
                 C 58225 . . . 58938      
                 — 
                   
                 putative membrane protein TerC 
                 829 
               
               
                 C 59036 . . . 60865      
                 uvrC 
                   
                 UvrABC system protein C 
                 830 
               
               
                 C 60867 . . . 61631      
                 kdsB 
                   
                 3-deoxy-D-manno-octulosonic acid cytidylyl- 
                 831 
               
               
                   
                   
                   
                 transferase 
               
               
                 C 61702 . . . 62700      
                 lpxK 
                   
                 tetraacyldisaccharide 4′-kinase 
                 832 
               
               
                 C 62773 . . . 64536      
                 msbA 
                   
                 lipid A export ATP-binding protein MsbA 
                 833 
               
               
                 C 64577 . . . 66943      
                 rec2 
                   
                 recombination protein 2 
                 834 
               
               
                 67202 . . . 67639 
                 dksA 
                   
                 DnaK suppressor protein 
                 835 
               
               
                 67887 . . . 69245 
                 pcnB 
                   
                 probable poly polymerase 
                 836 
               
               
                 69254 . . . 69736 
                 folK 
                   
                 2-amino-4-hydroxy-6-hydroxymethyl- 
                 837 
               
               
                   
                   
                   
                 dihydropteridine pyrophosphokinase 
               
               
                 69812 . . . 70288 
                 — 
                   
                 conserved hypothetical protein 
                 838 
               
               
                 70296 . . . 71594 
                 amiB 
                   
                 probable N-acetylmuramoyl-L-alanine amidase 
                 839 
               
               
                   
                   
                   
                 AmiB precursor 
               
               
                 71595 . . . 73484 
                 mutL 
                   
                 DNA mismatch repair protein MutL 
                 840 
               
               
                 73492 . . . 74427 
                 miaA 
                   
                 tRNA delta-isopentenylpyrophosphate 
                 841 
               
               
                   
                   
                   
                 transferase 
               
               
                 74433 . . . 77378 
                 glnE 
                   
                 glutamate-ammonia-ligase adenylyltransferase 
                 842 
               
               
                 C 77463 . . . 79139      
                 recN 
                   
                 DNA repair protein RecN 
                 843 
               
               
                 C 79251 . . . 80069      
                 ppnK 
                   
                 probable inorganic polyphosphate/ATP-NAD 
                 844 
               
               
                   
                   
                   
                 kinase 
               
               
                 80133 . . . 80837 
                 grpE 
                   
                 grpE 
                 845 
               
               
                 C 80850 . . . 81194      
                 — 
                   
                 conserved hypothetical protein 
                 846 
               
               
                 C 81187 . . . 81627      
                 — 
                   
                 conserved hypothetical protein 
                 847 
               
               
                 81908 . . . 84031 
                 nrdD 
                   
                 anaerobic ribonucleoside-triphosphate 
                 848 
               
               
                   
                   
                   
                 reductase 
               
               
                 84150 . . . 85010 
                 tesB 
                   
                 Acyl-CoA thioesterase II 
                 849 
               
               
                 C 85171 . . . 86550      
                 cysS 
                   
                 cysteinyl-tRNA synthetase 
                 850 
               
               
                 86653 . . . 87162 
                 ppiB 
                   
                 peptidyl-prolyl cis-trans isomerase B 
                 851 
               
               
                 87166 . . . 87597 
                 — 
                   
                 conserved hypothetical protein 
                 852 
               
               
                 87739 . . . 88527 
                 — 
                   
                 putative deoxyribonuclease 
                 853 
               
               
                 88589 . . . 88846 
                 — 
                 ✓ 
                 hypothetical protein 
                 854 
               
               
                 88857 . . . 89132 
                 — 
                 ✓ 
                 hypothetical protein 
                 855 
               
               
                 C 89182 . . . 89505      
                 trxA 
                   
                 thioredoxin 
                 856 
               
               
                 C 89625 . . . 90620      
                 ddh 
                   
                 2-hydroxyacid dehydrogenase homolog 
                 857 
               
               
                 C 90633 . . . 91778      
                 metB 
                   
                 cystathionine gamma-synthase 
                 858 
               
               
                 92334 . . . 93170 
                 — 
                 ✓ 
                 predicted ATPase involved in chromosome 
                 859 
               
               
                   
                   
                   
                 partitioning 
               
               
                 93172 . . . 94527 
                 dnaB2 
                 ✓ 
                 replicative DNA helicase 
                 860 
               
               
                 94520 . . . 96220 
                 — 
                 ✓ 
                 conserved hypothetical protein 
                 861 
               
               
                 96220 . . . 96771 
                 — 
                 ✓ 
                 conserved hypothetical protein 
                 862 
               
               
                 96921 . . . 98144 
                 — 
                 ✓ 
                 conserved hypothetical protein 
                 863 
               
               
                 98441 . . . 99196 
                 — 
                 ✓ 
                 conserved hypothetical protein 
                 864 
               
               
                 99196 . . . 99684 
                 — 
                 ✓ 
                 conserved hypothetical protein 
                 865 
               
               
                  99930 . . . 100352 
                 ssb2 
                 ✓ 
                 Single-strand binding protein 
                 866 
               
               
                 100379 . . . 100897 
                 — 
                 ✓ 
                 conserved putative lipoprotein 
                 867 
               
               
                 C 101113 . . . 101670      
                 — 
                 ✓ 
                 1conserved hypothetical protein 
                 868 
               
               
                 101746 . . . 103806 
                 topB2 
                 ✓ 
                 DNA topoisomerase III 
                 869 
               
               
                 104691 . . . 105119 
                 — 
                 ✓ 
                 conserved hypothetical protein 
                 870 
               
               
                 105131 . . . 105223 
                 — 
                   
                 hypothetical protein 
                 871 
               
               
                 105234 . . . 105875 
                 — 
                 ✓ 
                 conserved hypothetical protein 
                 872 
               
               
                 105910 . . . 106317 
                 — 
                 ✓ 
                 hypothetical protein 
                 873 
               
               
                 106418 . . . 106888 
                 radC2 
                 ✓ 
                 putative DNA repair radC-like protein 
                 874 
               
               
                 106981 . . . 107577 
                 — 
                 ✓ 
                 conserved hypothetical protein 
                 875 
               
               
                 107635 . . . 108399 
                 — 
                 ✓ 
                 conserved hypothetical protein 
                 876 
               
               
                 108498 . . . 109127 
                 pilL 
                 ✓ 
                 conserved putative lipoprotein 
                 877 
               
               
                 109131 . . . 109871 
                 — 
                 ✓ 
                 conserved putative exported protein 
                 878 
               
               
                 109850 . . . 110608 
                 — 
                 ✓ 
                 conserved putative exported protein 
                 879 
               
               
                 110624 . . . 111130 
                 — 
                 ✓ 
                 conserved putative exported protein 
                 880 
               
               
                 111127 . . . 113376 
                 — 
                 ✓ 
                 conserved hypothetical protein 
                 881 
               
               
                 113695 . . . 114381 
                 — 
                 ✓ 
                 conserved putative membrane protein 
                 882 
               
               
                 114512 . . . 114862 
                 — 
                 ✓ 
                 conserved putative membrane protein 
                 883 
               
               
                 115131 . . . 115532 
                 — 
                 ✓ 
                 conserved putative membrane protein 
                 884 
               
               
                 115552 . . . 115923 
                 — 
                 ✓ 
                 conserved putative membrane protein 
                 885 
               
               
                 115935 . . . 116579 
                 — 
                 ✓ 
                 conserved putative exported protein 
                 886 
               
               
                 116579 . . . 117448 
                 — 
                 ✓ 
                 conserved hypothetical protein 
                 887 
               
               
                 117459 . . . 118859 
                 — 
                 ✓ 
                 conserved putative exported protein 
                 888 
               
               
                 118869 . . . 119276 
                 — 
                 ✓ 
                 conserved putative lipoprotein 
                 889 
               
               
                 119292 . . . 122162 
                 — 
                 ✓ 
                 conserved hypothetical protein 
                 890 
               
               
                 122170 . . . 122577 
                 — 
                 ✓ 
                 conserved hypothetical protein 
                 891 
               
               
                 122587 . . . 122910 
                 — 
                 ✓ 
                 conserved hypothetical membrane protein 
                 892 
               
               
                 122919 . . . 124412 
                 — 
                 ✓ 
                 conserved putative membrane protein 
                 893 
               
               
                 C 124468 . . . 124797      
                 — 
                 ✓ 
                 conserved hypothetical membrane protein 
                 894 
               
               
                 C 124955 . . . 127960      
                 tnpA 
                 ✓ 
                 transposon Tn3 transposase 
                 895 
               
               
                 126925 . . . 127041 
                 — 
                 ✓ 
                 hypothetical protein 
                 896 
               
               
                 128088 . . . 128726 
                 tnpR 
                 ✓ 
                 transposon Tn3 resolvase 
                 897 
               
               
                 128751 . . . 128930 
                 — 
                 ✓ 
                 hypothetical protein 
                 898 
               
               
                 C 128975 . . . 129382      
                 — 
                 ✓ 
                 hypothetical exported protein 
                 899 
               
               
                 C 129398 . . . 131398      
                 — 
                 ✓ 
                 conserved putative exported protein 
                 900 
               
               
                 C 131413 . . . 132354      
                 — 
                 ✓ 
                 conserved putative exported protein 
                 901 
               
               
                 C 132351 . . . 132794      
                 — 
                 ✓ 
                 conserved hypothetical protein 
                 902 
               
               
                 133106 . . . 133525 
                 — 
                 ✓ 
                 conserved hypothetical membrane protein 
                 903 
               
               
                 133610 . . . 133843 
                 — 
                 ✓ 
                 conserved hypothetical protein 
                 904 
               
               
                 133846 . . . 134094 
                 — 
                 ✓ 
                 hypothetical protein 
                 905 
               
               
                 134098 . . . 134256 
                 — 
                 ✓ 
                 hypothetical protein 
                 906 
               
               
                 134387 . . . 135340 
                 traC 
                 ✓ 
                 conserved putative antirestriction protein 
                 907 
               
               
                 135444 . . . 136205 
                 — 
                 ✓ 
                 possible type I restriction enzyme M subunit 
                 908 
               
               
                 136431 . . . 136997 
                 — 
                 ✓ 
                 hypothetical protein 
                 909 
               
               
                 137037 . . . 137411 
                 — 
                 ✓ 
                 conserved hypothetical protein 
                 910 
               
               
                 137401 . . . 138078 
                 — 
                 ✓ 
                 conserved hypothetical protein 
                 911 
               
               
                 138056 . . . 138673 
                 — 
                 ✓ 
                 conserved hypothetical protein 
                 912 
               
               
                 C 138937 . . . 139536      
                 — 
                 ✓ 
                 resolvase/integrase-like protein 
                 913 
               
               
                 C 139551 . . . 139742      
                 — 
                 ✓ 
                 hypothetical protein 
                 914 
               
               
                 C 140211 . . . 140465      
                 — 
                 ✓ 
                 hypothetical protein 
                 915 
               
               
                 141656 . . . 142369 
                 — 
                 ✓ 
                 conserved hypothetical protein 
                 916 
               
               
                 143089 . . . 144342 
                 — 
                 ✓ 
                 hypothetical protein 
                 917 
               
               
                 144485 . . . 146401 
                 — 
                 ✓ 
                 conserved hypothetical protein 
                 918 
               
               
                 146462 . . . 147304 
                 — 
                 ✓ 
                 putative site-specific recombinase 
                 919 
               
               
                 C 147954 . . . 149231      
                 thrC 
                   
                 threonine synthase 
                 920 
               
               
                 C 149274 . . . 150218      
                 thrB 
                   
                 homoserine kinase 
                 921 
               
               
                 C 150231 . . . 152678      
                 thrA 
                   
                 aspartokinase/homoserine dehydrogenase 
                 922 
               
               
                 153002 . . . 153715 
                 — 
                   
                 conserved hypothetical protein 
                 923 
               
               
                 153755 . . . 154891 
                 grk 
                   
                 glycerate kinase 
                 924 
               
               
                 C 154900 . . . 156159      
                 — 
                   
                 conserved hypothetical protein 
                 925 
               
               
                 C 156281 . . . 157387      
                 — 
                   
                 conserved hypothetical protein 
                 926 
               
               
                 C 157589 . . . 157909      
                 — 
                   
                 conserved hypothetical protein 
                 927 
               
               
                 157962 . . . 158171 
                 — 
                   
                 pseudogene for glycerol-3-phosphate regulon 
                 928 
               
               
                   
                   
                   
                 repressor 
               
               
                 C 158260 . . . 159015      
                 — 
                   
                 conserved hypothetical protein 
                 929 
               
               
                 159216 . . . 159497 
                 — 
                   
                 conserved hypothetical protein 
                 930 
               
               
                 159649 . . . 160647 
                 hitA 
                   
                 iron-utilization periplasmic protein hFbpA 
                 931 
               
               
                 160765 . . . 162285 
                 hitB 
                   
                 iron(III)-transport system permease protein 
                 932 
               
               
                   
                   
                   
                 hFbpB 
               
               
                 162287 . . . 163342 
                 hitC 
                   
                 iron-utilization ATP-binding protein hFbpC 
                 933 
               
               
                 C 163377 . . . 164057      
                 — 
                   
                 putative D-alanyl-D-alanine carboxypeptidase 
                 934 
               
               
                 C 164059 . . . 165192      
                 dapE 
                   
                 succinyl-diaminopimelate desuccinylase 
                 935 
               
               
                 C 165220 . . . 165564      
                 — 
                   
                 conserved hypothetical protein 
                 936 
               
               
                 C 165643 . . . 167538      
                 — 
                   
                 chaperone protein HtpG 
                 937 
               
               
                 167750 . . . 168589 
                 — 
                   
                 conserved hypothetical NIF3-like protein 
                 938 
               
               
                 168763 . . . 171135 
                 hsdM1 
                 ✓ 
                 putative type I restriction-modification system, 
                 939 
               
               
                   
                   
                   
                 methyltransferase subunit 
               
               
                 171318 . . . 172727 
                 — 
                 ✓ 
                 predicted transcriptional regulator containing 
                 940 
               
               
                   
                   
                   
                 an HTH domain 
               
               
                 172899 . . . 174149 
                 hsdS1 
                 ✓ 
                 putative type I site-specific restriction- 
                 941 
               
               
                   
                   
                   
                 modification system, S subunit 
               
               
                 174249 . . . 177275 
                 hsdR1 
                 ✓ 
                 putative type I site-specific restriction- 
                 942 
               
               
                   
                   
                   
                 modification system, R subunit 
               
               
                 C 177500 . . . 178879      
                 ffh 
                   
                 Signal recognition particle protein 
                 943 
               
               
                 179130 . . . 180422 
                 corB 
                   
                 putative Mg2+ and Co2+ transporter 
                 944 
               
               
                 180443 . . . 181321 
                 — 
                   
                 conserved hypothetical protein 
                 945 
               
               
                 181323 . . . 181802 
                 — 
                 ✓ 
                 conserved hypothetical protein 
                 946 
               
               
                 181892 . . . 182233 
                 — 
                   
                 conserved hypothetical protein 
                 947 
               
               
                 182400 . . . 183689 
                 serS 
                   
                 Seryl-tRNA synthetase 
                 948 
               
               
                 184024 . . . 184653 
                 gst 
                   
                 glutathione S-transferase 
                 949 
               
               
                 C 184665 . . . 184961      
                 — 
                   
                 conserved hypothetical protein 
                 950 
               
               
                 185014 . . . 187251 
                 hemR 
                   
                 hemin receptor 
                 951 
               
               
                 C 194299 . . . 196434      
                 — 
                   
                 possible SAM-dependent methyltransferase 
                 952 
               
               
                 196827 . . . 197936 
                 mltA 
                   
                 membrane-bound lytic murein transglycosylase 
                 953 
               
               
                   
                   
                   
                 A precursor 
               
               
                 197936 . . . 198706 
                 — 
                   
                 conserved hypothetical protein 
                 954 
               
               
                 198884 . . . 199885 
                 znuA 
                   
                 high-affinity zinc uptake system protein ZnuA 
                 955 
               
               
                 199935 . . . 200441 
                 — 
                   
                 conserved hypothetical protein 
                 956 
               
               
                 C 200554 . . . 201912      
                 mpl 
                   
                 UDP-N-acetylmuramate:L-alanyl-gamma-D- 
                 957 
               
               
                   
                   
                   
                 glutamyl-meso-diaminopimelate ligase 
               
               
                 C 202297 . . . 203484      
                 metC 
                   
                 cystathionine beta-lyase 
                 958 
               
               
                 203615 . . . 204223 
                 tsaA 
                 ✓ 
                 probable peroxiredoxin 
                 959 
               
               
                 204324 . . . 204881 
                 pgsA 
                   
                 CDP-diacylglycerol--glycerol-3-phosphate 3- 
                 960 
               
               
                   
                   
                   
                 phosphatidyltransferase 
               
               
                 C 205445 . . . 205975      
                 ppa 
                   
                 inorganic pyrophosphatase 
                 961 
               
               
                 206209 . . . 207525 
                 — 
                   
                 conserved hypothetical protein 
                 962 
               
               
                 207748 . . . 208389 
                 udk 
                   
                 uridine kinase 
                 963 
               
               
                 208398 . . . 208985 
                 dcd 
                   
                 deoxycytidine triphosphate deaminase 
                 964 
               
               
                 208989 . . . 210164 
                 — 
                   
                 conserved hypothetical protein 
                 965 
               
               
                 210164 . . . 211372 
                 — 
                   
                 probable sugar efflux transporter 
                 966 
               
               
                 C 211433 . . . 212947      
                 engA 
                   
                 GTP-binding protein EngA 
                 967 
               
               
                 C 213629 . . . 214396      
                 dnaQ 
                   
                 DNA polymerase III, epsilon chain 
                 968 
               
               
                 214457 . . . 214921 
                 rnhA 
                   
                 ribonuclease HI 
                 969 
               
               
                 215187 . . . 216284 
                 omP2 
                   
                 Outer membrane protein P2 precursor 
                 970 
               
               
                 C 216481 . . . 217626      
                 nagA 
                   
                 N-acetylglucosamine-6-phosphate deacetylase 
                 971 
               
               
                 C 217763 . . . 218575      
                 nagB 
                   
                 glucosamine-6-phosphate deaminase 
                 972 
               
               
                 C 218911 . . . 219792      
                 nanA 
                   
                 N-acetylneuraminate lyase 
                 973 
               
               
                 C 219803 . . . 220669      
                 — 
                   
                 putative HTH-type transcriptional regulator 
                 974 
               
               
                 C 220662 . . . 221564      
                 nanK 
                   
                 putative N-acetylmannosamine kinase 
                 975 
               
               
                 C 221609 . . . 222295      
                 nanE 
                   
                 putative N-acetylmannosamine-6-phosphate 
                 976 
               
               
                   
                   
                   
                 2-epimerase 
               
               
                 222645 . . . 223634 
                 — 
                   
                 putative sialic acid transporter, TRAP-type 
                 977 
               
               
                   
                   
                   
                 C4-dicarboxylate transport system, periplasmic 
               
               
                   
                   
                   
                 component 
               
               
                 223699 . . . 225549 
                 siaT 
                   
                 putative sialic acid transporter, TRAP-type 
                 978 
               
               
                   
                   
                   
                 C4-dicarboxylate transport system, large 
               
               
                   
                   
                   
                 permease component 
               
               
                 225713 . . . 226852 
                 — 
                   
                 conserved hypothetical protein 
                 979 
               
               
                 227014 . . . 227448 
                 — 
                   
                 putative protein-S-isoprenylcysteine 
                 980 
               
               
                   
                   
                   
                 methyltransferase 
               
               
                 C 227490 . . . 228377      
                 hflC 
                   
                 HflC 
                 981 
               
               
                 C 228377 . . . 229609      
                 hflK 
                   
                 HhflK 
                 982 
               
               
                 C 229719 . . . 230426      
                 — 
                   
                 putative 4′-phosphopantetheinyl transferase 
                 983 
               
               
                 C 230486 . . . 231817      
                 dcuB2 
                   
                 anaerobic C4-dicarboxylate transporter DcuB 
                 984 
               
               
                 C 232021 . . . 232251      
                 acpP 
                   
                 acyl carrier protein 
                 985 
               
               
                 C 232511 . . . 233239      
                 fabG 
                   
                 3-oxoacyl-[acyl-carrier protein] reductase 
                 986 
               
               
                 C 233256 . . . 234194      
                 fabD 
                   
                 malonyl CoA-acyl carrier protein transacylase 
                 987 
               
               
                 C 234694 . . . 235644      
                 fabH 
                   
                 3-oxoacyl-[acyl-carrier-protein] synthase III 
                 988 
               
               
                 C 235830 . . . 236000      
                 rpmF 
                   
                 50S ribosomal protein L32 
                 989 
               
               
                 C 236023 . . . 236547      
                 — 
                   
                 conserved hypothetical protein 
                 990 
               
               
                 236704 . . . 237576 
                 psd 
                   
                 phosphatidylserine decarboxylase proenzyme 
                 991 
               
               
                 C 237685 . . . 239055      
                 gor 
                   
                 glutathione reductase 
                 992 
               
               
                 C 239271 . . . 239870      
                 — 
                   
                 conserved hypothetical lipoprotein 
                 993 
               
               
                 239964 . . . 240275 
                 bolA 
                   
                 Pseudogene for BolA homolog 
                 994 
               
               
                 240566 . . . 241909 
                 nqrA 
                   
                 Na(+)-translocating NADH-quinone reductase 
                 995 
               
               
                   
                   
                   
                 subunit A 
               
               
                 241912 . . . 243147 
                 nqrB 
                   
                 Na(+)-translocating NADH-quinone reductase 
                 996 
               
               
                   
                   
                   
                 subunit B 
               
               
                 243140 . . . 243874 
                 nqrC 
                   
                 Na(+)-translocating NADH-quinone reductase 
                 997 
               
               
                   
                   
                   
                 subunit C 
               
               
                 243874 . . . 244500 
                 nqrD 
                   
                 Na(+)-translocating NADH-quinone reductase 
                 998 
               
               
                   
                   
                   
                 subunit D 
               
               
                 244504 . . . 245100 
                 nqrE 
                   
                 Na(+)-translocating NADH-quinone reductase 
                 999 
               
               
                   
                   
                   
                 subunit E 
               
               
                 245113 . . . 246348 
                 nqrF 
                   
                 Na(+)-translocating NADH-quinone reductase 
                 1000 
               
               
                   
                   
                   
                 subunit F 
               
               
                 246492 . . . 247532 
                 apbE 
                   
                 thiamine biosynthesis lipoprotein ApbE 
                 1001 
               
               
                 247535 . . . 247795 
                 — 
                   
                 conserved hypothetical protein 
                 1002 
               
               
                 247870 . . . 249063 
                 trmU 
                   
                 probable tRNA (5-methylaminomethyl-2- 
                 1003 
               
               
                   
                   
                   
                 thiouridylate)-methyltransferase 
               
               
                 C 249107 . . . 249841      
                 — 
                   
                 conserved hypothetical protein 
                 1004 
               
               
                 C 249843 . . . 250817      
                 rluD 
                   
                 ribosomal large subunit pseudouridine synthase D 
                 1005 
               
               
                 250925 . . . 251713 
                 — 
                   
                 conserved hypothetical lipoprotein 
                 1006 
               
               
                 C 251792 . . . 252274      
                 — 
                   
                 conserved hypothetical protein 
                 1007 
               
               
                 C 252306 . . . 253046      
                 pflA 
                   
                 pyruvate formate-lyase 1 activating enzyme 
                 1008 
               
               
                 253171 . . . 255489 
                 pflB 
                   
                 formate acetyltransferase 
                 1009 
               
               
                 C 255521 . . . 256375      
                 focA 
                   
                 probable formate transporter 
                 1010 
               
               
                 256880 . . . 257794 
                 — 
                   
                 conserved hypothetical protein 
                 1011 
               
               
                 257973 . . . 259418 
                 — 
                   
                 putative Na+/alanine symporter 
                 1012 
               
               
                 C 259603 . . . 260430      
                 — 
                   
                 conserved hypothetical protein 
                 1013 
               
               
                 C 260439 . . . 261575      
                 adhC 
                   
                 pseudogene for putative alcohol dehydrogenase 
                 1014 
               
               
                   
                   
                   
                 class III 
               
               
                 261698 . . . 262105 
                 — 
                   
                 putative HTH-type transcriptional regulator 
                 1015 
               
               
                 262263 . . . 262550 
                 tatA 
                   
                 Sec-independent protein translocase protein 
                 1016 
               
               
                   
                   
                   
                 TatA/E 
               
               
                 262554 . . . 263114 
                 tatB 
                   
                 Sec-independent protein translocase protein 
                 1017 
               
               
                   
                   
                   
                 TatB 
               
               
                 263124 . . . 263894 
                 tatC 
                   
                 Sec-independent protein translocase protein 
                 1018 
               
               
                   
                   
                   
                 TatC 
               
               
                 264255 . . . 265604 
                 gdhA 
                   
                 NADP-specific glutamate dehydrogenase 
                 1019 
               
               
                 C 265712 . . . 266152      
                 fur 
                   
                 Ferric uptake regulation protein 
                 1020 
               
               
                 C 266181 . . . 266705      
                 fldA 
                   
                 flavodoxin 
                 1021 
               
               
                 C 267655 . . . 268260      
                 seqA 
                   
                 seqA 
                 1022 
               
               
                 266802 . . . 267665 
                 — 
                   
                 putative esterase/lipase 
                 1023 
               
               
                 268263 . . . 269621 
                 menE 
                   
                 O-succinylbenzoate--CoA ligase 
                 1024 
               
               
                 269649 . . . 272987 
                 — 
                   
                 putative small-conductance mechanosensitive 
                 1025 
               
               
                   
                   
                   
                 channel 
               
               
                 272997 . . . 274070 
                 aroC 
                   
                 chorismate synthase 
                 1026 
               
               
                 274243 . . . 275103 
                 mepA 
                   
                 penicillin-insensitive murein endopeptidase 
                 1027 
               
               
                 275121 . . . 275888 
                 — 
                   
                 conserved hypothetical protein 
                 1028 
               
               
                 275935 . . . 276891 
                 msbB 
                   
                 lipid A biosynthesis (KDO)2-(lauroyl)-lipid 
                 1029 
               
               
                   
                   
                   
                 IVA acyltransferase 
               
               
                 277018 . . . 277989 
                 selD 
                   
                 selenide, water dikinase 
                 1030 
               
               
                 C 278098 . . . 278448      
                 rplsS 
                   
                 50S ribosomal protein L19 
                 1031 
               
               
                 C 278485 . . . 279225      
                 trmD 
                   
                 tRNA (guanine-N(1)-)-methyltransferase 
                 1032 
               
               
                 C 279263 . . . 279790      
                 rimM 
                   
                 16S rRNA processing protein RimM 
                 1033 
               
               
                 C 279835 . . . 280083      
                 rspP 
                   
                 30S ribosomal protein S16 
                 1034 
               
               
                 280363 . . . 281148 
                 — 
                   
                 conserved hypothetical protein 
                 1035 
               
               
                 281171 . . . 282982 
                 nadN 
                   
                 NAD nucleotidase 
                 1036 
               
               
                 283267 . . . 283809 
                 aroK 
                   
                 shikimate kinase 
                 1037 
               
               
                 283829 . . . 284917 
                 aroB 
                   
                 3-dehydroquinate synthase 
                 1038 
               
               
                 284919 . . . 285779 
                 dam 
                   
                 DNA adenine methylase 
                 1039 
               
               
                 286744 . . . 286851 
                 — 
                   
                 conserved hypothetical protein 
                 1040 
               
               
                 C 286870 . . . 287595      
                 pgpB 
                   
                 phosphatidylglycerophosphatase B 
                 1041 
               
               
                 287641 . . . 288315 
                 ribA 
                   
                 GTP cyclohydrolase II 
                 1042 
               
               
                 C 288631 . . . 290175      
                 — 
                   
                 putative ABC-type oligopeptide transport 
                 1043 
               
               
                   
                   
                   
                 system, periplasmic component 
               
               
                 C 290168 . . . 290530      
                 — 
                   
                 conserved hypothetical protein 
                 1044 
               
               
                 290649 . . . 292694 
                 prlc 
                   
                 oligopeptidase A 
                 1045 
               
               
                 292926 . . . 294470 
                 Hsdm2 
                   
                 putative type I restriction-modification system 
                 1046 
               
               
                   
                   
                   
                 methyltransferase subunit 
               
               
                 294555 . . . 295727 
                 Hsds2 
                   
                 putative type I restriction-modification system 
                 1047 
               
               
                   
                   
                   
                 specificity protein 
               
               
                 295729 . . . 296883 
                 prrC 
                 ✓ 
                 putative anticodon nuclease 
                 1048 
               
               
                 296886 . . . 297884 
                 — 
                 ✓ 
                 conserved hypothetical DNA binding protein 
                 1049 
               
               
                 297895 . . . 300978 
                 Hsdr2 
                   
                 putative type I restriction-modification system 
                 1050 
               
               
                 C 301125 . . . 301754      
                 — 
                   
                 conserved hypothetical protein 
                 1051 
               
               
                 C 301968 . . . 303809      
                 arcb 
                   
                 aerobic respiration control sensor protein ArcB 
                 1052 
               
               
                 C 303878 . . . 304522      
                 — 
                   
                 predicted uracil-DNA glycosylase 
                 1053 
               
               
                 C 310574 . . . 311482      
                 bira 
                   
                 BirA bifunctional protein 
                 1054 
               
               
                 311609 . . . 313075 
                 guab 
                   
                 inosine-5′-monophosphate dehydrogenase 
                 1055 
               
               
                 313185 . . . 314756 
                 guaa 
                   
                 glutamine-hydrolyzing GMP synthase 
                 1056 
               
               
                 C 314818 . . . 315720      
                 — 
                   
                 conserved hypothetical protein 
                 1057 
               
               
                 315783 . . . 316289 
                 — 
                   
                 putative transcriptional regulator 
                 1058 
               
               
                 316328 . . . 317530 
                 nhaa 
                   
                 Na(+)/H(+) antiporter 1 
                 1059 
               
               
                 317718 . . . 319028 
                 bmq 
                   
                 branched-chain amino acid transport system 
                 1060 
               
               
                   
                   
                   
                 carrier protein 
               
               
                 C 319136 . . . 319603      
                 — 
                   
                 conserved hypothetical protein 
                 1061 
               
               
                 C 319630 . . . 320076      
                 — 
                   
                 conserved hypothetical protein 
                 1062 
               
               
                 320349 . . . 322478 
                 pnp 
                   
                 polyribonucleotide nucleotidyltransferase 
                 1063 
               
               
                 322560 . . . 323504 
                 nlpL 
                   
                 lipoprotein NlpI 
                 1064 
               
               
                 323624 . . . 325465 
                 deaD 
                   
                 Cold-shock DEAD-box protein A homolog 
                 1065 
               
               
                 325643 . . . 327031 
                 — 
                   
                 predicted soluble lytic transglycosylase fused 
                 1066 
               
               
                   
                   
                   
                 to an ABC-type amino acid-binding protein 
               
               
                 327036 . . . 327188 
                 — 
                   
                 conserved hypothetical protein 
                 1067 
               
               
                 C 327322 . . . 327618      
                 — 
                   
                 conserved hypothetical protein 
                 1068 
               
               
                 C 327675 . . . 327884      
                 — 
                   
                 conserved hypothetical protein 
                 1069 
               
               
                 C 327952 . . . 328302      
                 arsC 
                   
                 putative arsenate reductase 
                 1070 
               
               
                 328381 . . . 329430 
                 perM 
                   
                 putative permease PerM homolog 
                 1071 
               
               
                 C 329544 . . . 330521      
                 secF 
                   
                 protein-export membrane protein SecF 
                 1072 
               
               
                 C 330529 . . . 332379      
                 secD 
                   
                 protein-export membrane protein SecD 
                 1073 
               
               
                 C 332449 . . . 332742      
                 — 
                   
                 conserved hypothetical preprotein translocase 
                 1074 
               
               
                   
                   
                   
                 subunit YajC 
               
               
                 C 332850 . . . 333071      
                 — 
                   
                 predicted redox protein, regulator of disulfide 
                 1075 
               
               
                   
                   
                   
                 bond formation 
               
               
                 C 333068 . . . 333586      
                 — 
                   
                 conserved hypothetical protein 
                 1076 
               
               
                 C 333651 . . . 334799      
                 tgt 
                   
                 queuine tRNA-ribosyltransferase 
                 1077 
               
               
                 C 335144 . . . 336235      
                 quea 
                   
                 S-adenosylmethionine:tRNA ribosyltransferase- 
                 1078 
               
               
                   
                   
                   
                 isomerase 
               
               
                 C 336359 . . . 336805      
                 — 
                   
                 conserved hypothetical protein 
                 1079 
               
               
                 C 336948 . . . 341126      
                 hap 
                 ✓ 
                 adhesion and penetration protein Hap 
                 1080 
               
               
                 C 341444 . . . 344275      
                 uvra 
                   
                 UvrABC system protein A 
                 1081 
               
               
                 344428 . . . 344934 
                 ssb 
                   
                 Single-strand binding protein 
                 1082 
               
               
                 C 345112 . . . 345906      
                 tonb 
                   
                 TonB 
                 1083 
               
               
                 345916 . . . 346359 
                 exbD 
                   
                 transport protein ExbD 
                 1084 
               
               
                 346363 . . . 346815 
                 exbB 
                   
                 transport protein ExbB 
                 1085 
               
               
                 346984 . . . 347451 
                 bcp 
                   
                 bacterioferritin comigratory protein 
                 1086 
               
               
                 347552 . . . 348448 
                 dapA 
                   
                 dihydrodipicolinate synthase 
                 1087 
               
               
                 348559 . . . 349188 
                 — 
                   
                 conserved hypothetical lipoprotein 
                 1088 
               
               
                 349378 . . . 349701 
                 — 
                   
                 conserved hypothetical protein 
                 1089 
               
               
                 C 350415 . . . 351353      
                 lgtC 
                   
                 UDP-galactose--lipooligosaccharide 
                 1090 
               
               
                   
                   
                   
                 galactosyltransferase 
               
               
                 C 351421 . . . 352008      
                 orfM 
                   
                 predicted xanthosine triphosphate 
                 1091 
               
               
                   
                   
                   
                 pyrophosphatase 
               
               
                 C 352020 . . . 352745      
                 kdkA 
                   
                 3-deoxy-D-manno-octulosonic acid kinase 
                 1092 
               
               
                 352822 . . . 353865 
                 opsX 
                   
                 ADP-heptose-lipooligosaccharide 
                 1093 
               
               
                   
                   
                   
                 heptosyltransferase I 
               
               
                 354187 . . . 356316 
                 hxuC 
                   
                 heme/hemopexin-binding protein C 
                 1094 
               
               
                 356392 . . . 358089 
                 hxuB 
                   
                 heme/hemopexin-binding protein B 
                 1095 
               
               
                 358101 . . . 360866 
                 hxuA 
                   
                 heme/hemopexin-binding protein A 
                 1096 
               
               
                 C 360962 . . . 361318      
                 folB 
                   
                 dihydroneopterin aldolase 
                 1097 
               
               
                 361401 . . . 362000 
                 — 
                   
                 conserved hypothetical protein 
                 1098 
               
               
                 362042 . . . 363745 
                 narQ 
                   
                 sensor protein NarQ 
                 1099 
               
               
                 363755 . . . 364780 
                 murB 
                   
                 UDP-N-acetylenolpyruvoylglucosamine 
                 1100 
               
               
                   
                   
                   
                 reductase 
               
               
                 364906 . . . 365751 
                 rpoH 
                   
                 RNA polymerase sigma-32 factor 
                 1101 
               
               
                 C 365791 . . . 366218      
                 dusC 
                 ✓ 
                 pseudogene for tRNA-dihydrouridine synthase C - 
                 1102 
               
               
                 C 366218 . . . 367084      
                 djlA 
                   
                 DnaJ-like protein DjlA 
                 1103 
               
               
                 C 367163 . . . 367804      
                 pyrE 
                   
                 orotate phosphoribosyltransferase 
                 1104 
               
               
                 C 367828 . . . 368544      
                 rph 
                   
                 ribonuclease PH 
                 1105 
               
               
                 C 368845 . . . 370287      
                 gltX 
                   
                 glutamyl-tRNA synthetase 
                 1106 
               
               
                 371037 . . . 372692 
                 Lpt6 
                   
                 PE-tn-6--lipooligosaccharide phosphoryl- 
                 1107 
               
               
                   
                   
                   
                 ethanolamine transferase 
               
               
                 C 372710 . . . 373519      
                 rbn 
                   
                 tRNA processing ribonuclease BN 
                 1108 
               
               
                 C 373516 . . . 374001      
                 — 
                   
                 conserved hypothetical protein 
                 1109 
               
               
                 C 374004 . . . 374666      
                 — 
                   
                 conserved hypothetical protein 
                 1110 
               
               
                 374881 . . . 375660 
                 udp 
                   
                 uridine phosphorylase 
                 1111 
               
               
                 C 375886 . . . 377202      
                 — 
                   
                 conserved hypothetical metabolite transport 
                 1112 
               
               
                   
                   
                   
                 protein 
               
               
                 C 377258 . . . 378001      
                 — 
                   
                 conserved hypothetical protein 
                 1113 
               
               
                 C 378062 . . . 379768      
                 mend 
                   
                 menaquinone biosynthesis protein MenD 
                 1114 
               
               
                 C 379784 . . . 381055      
                 menf 
                   
                 menaquinone-specific isochorismate synthase 
                 1115 
               
               
                 381212 . . . 382426 
                 Aspc3 
                   
                 probable aspartate aminotransferase 
                 1116 
               
               
                 382543 . . . 383799 
                 mtr 
                   
                 tryptophan-specific transport protein 
                 1117 
               
               
                 383908 . . . 385275 
                 sdaa 
                   
                 L-serine dehydratase 
                 1118 
               
               
                 C 385310 . . . 386548      
                 sdac 
                   
                 Serine transporter 
                 1119 
               
               
                 C 386771 . . . 388939      
                 — 
                   
                 probable cation-transporting ATPase 
                 1120 
               
               
                 C 388914 . . . 389702      
                 merP 
                   
                 pseudogene for probable inorganic ion transport 
                 1121 
               
               
                   
                   
                   
                 protein 
               
               
                 389779 . . . 390165 
                 — 
                 ✓ 
                 probable heavy metal dependent transcriptional 
                 1122 
               
               
                   
                   
                   
                 regulator 
               
               
                 C 390179 . . . 390496      
                 metJ 
                   
                 Met repressor 
                 1123 
               
               
                 390740 . . . 392002 
                 rho 
                   
                 transcription termination factor rho 
                 1124 
               
               
                 C 392056 . . . 392748      
                 pilD 
                   
                 putative type 4 prepilin-like protein specific 
                 1125 
               
               
                   
                   
                   
                 leader peptidase 
               
               
                 C 392745 . . . 393965      
                 pilC 
                   
                 putative type IV pilin secretion protein 
                 1126 
               
               
                 C 393962 . . . 395356      
                 pilB 
                   
                 putative type IV pilin secretion protein 
                 1127 
               
               
                 C 395353 . . . 395802      
                 pilA 
                   
                 Type IV pilin subunit protein 
                 1128 
               
               
                 395917 . . . 396477 
                 ampD 
                   
                 ampD 
                 1129 
               
               
                 397099 . . . 397998 
                 corC 
                   
                 magnesium and cobalt efflux protein CorC 
                 1130 
               
               
                 397982 . . . 399550 
                 cutE 
                   
                 apolipoprotein N-acyltransferase 
                 1131 
               
               
                 399600 . . . 400337 
                 — 
                   
                 conserved hypothetical RNA methyltransferase 
                 1132 
               
               
                 400334 . . . 400894 
                 — 
                   
                 conserved hypothetical protein 
                 1133 
               
               
                 400894 . . . 401313 
                 ruvX 
                   
                 putative holliday junction resolvase 
                 1134 
               
               
                 C 401363 . . . 402288      
                 — 
                   
                 pseudogene for recombination associated 
                 1135 
               
               
                   
                   
                   
                 protein RdgC, 
               
               
                 402483 . . . 403694 
                 — 
                 ✓ 
                 prophage CP4-57-like integrase 
                 1136 
               
               
                 403731 . . . 404165 
                 — 
                 ✓ 
                 hypothetical protein 
                 1137 
               
               
                 404278 . . . 404700 
                 — 
                 ✓ 
                 hypothetical protein 
                 1138 
               
               
                 404709 . . . 405482 
                 — 
                 ✓ 
                 hypothetical protein 
                 1139 
               
               
                 406017 . . . 406208 
                 — 
                 ✓ 
                 hypothetical protein 
                 1140 
               
               
                 406257 . . . 406409 
                 — 
                 ✓ 
                 hypothetical protein 
                 1141 
               
               
                 C 406576 . . . 407466      
                 — 
                 ✓ 
                 hypothetical protein 
                 1142 
               
               
                 408127 . . . 408942 
                 proC 
                   
                 pyrroline-5-carboxylate reductase 
                 1143 
               
               
                 408942 . . . 410108 
                 hcaT 
                   
                 probable 3-phenylpropionic acid transporter 
                 1144 
               
               
                 410139 . . . 411032 
                 xerD 
                   
                 Site-specific recombinase XerD 
                 1145 
               
               
                 411205 . . . 411492 
                 — 
                   
                 conserved hypothetical protein 
                 1146 
               
               
                 C 411544 . . . 412551      
                 ruvB 
                   
                 holliday junction DNA helicase RuvB 
                 1147 
               
               
                 C 412559-413173  
                 ruvA 
                   
                 holliday junction DNA helicase RuvA 
                 1148 
               
               
                 C 413236-413808  
                 ruvC 
                   
                 holliday junction DNA helicase RuvC 
                 1149 
               
               
                 C 413885-414595  
                 — 
                   
                 conserved hypothetical protein 
                 1150 
               
               
                 C 414607-415080  
                 ntpA 
                   
                 dATP pyrophosphohydrolase 
                 1151 
               
               
                 C 415102-416868  
                 aspS 
                   
                 Aspartyl-tRNA synthetase 
                 1152 
               
               
                 417087-417605 
                 — 
                   
                 conserved hypothetical protein 
                 1153 
               
               
                 417658-418383 
                 — 
                   
                 conserved hypothetical protein 
                 1154 
               
               
                 418476-418712 
                 — 
                   
                 conserved hypothetical protein 
                 1155 
               
               
                 418709-419113 
                 — 
                   
                 Predicted nucleic acid-binding domain, 
                 1156 
               
               
                   
                   
                   
                 containsPIN domain 
               
               
                 419180-419587 
                 gloA 
                   
                 Lactoylglutathione lyase 
                 1157 
               
               
                 419661-420350 
                 Rnt 
                   
                 Ribonuclease T 
                 1158 
               
               
                 420664-422016 
                 — 
                   
                 conserved hypothetical protein 
                 1159 
               
               
                 422049-422636 
                 — 
                   
                 Predicted primosomal replication protein N 
                 1160 
               
               
                 C 422987-423553  
                 Efp 
                   
                 Elongation factor P 
                 1161 
               
               
                 423591-424607 
                 — 
                   
                 Predicted lysine 2,3-aminomutase 
                 1162 
               
               
                 424706-426001 
                 oapA 
                   
                 Opacity associated protein OapA 
                 1163 
               
               
                 426060-426464 
                 oapB 
                   
                 Opacity associated protein OapB 
                 1164 
               
               
                 426467-427177 
                 recO 
                   
                 DNA repair protein RecO 
                 1165 
               
               
                 427177-428493 
                 rumA 
                   
                 23S rRNA (uracil-5--)methyltransferase RumA 
                 1166 
               
               
                 428571-430802 
                 relA 
                   
                 GTP pyrophosphokinase 
                 1167 
               
               
                 430817-431173 
                 dgkA 
                   
                 Diacylglycerol kinase 
                 1168 
               
               
                 431256-431849 
                 Mog 
                   
                 Molybdopterin biosynthesis mog protein 
                 1169 
               
               
                 431851-432189 
                 glnB 
                   
                 Nitrogen regulatory protein P-II 
                 1170 
               
               
                 432189-433235 
                 — 
                   
                 conserved hypothetical protein 
                 1171 
               
               
                 C 433277-435469  
                 priA 
                   
                 Prismosomal protein N 
                 1172 
               
               
                 435554-436294 
                 trmB 
                   
                 tRNA (guanine-N(7)-)-methyltransferase 
                 1173 
               
               
                 436379-436723 
                 — 
                   
                 conserved hypothetical protein 
                 1174 
               
               
                 436929-437459 
                 napF 
                   
                 Ferredoxin-type protein NapF 
                 1175 
               
               
                 437452-437733 
                 napD 
                   
                 NapD 
                 1176 
               
               
                 437755-440253 
                 napA 
                   
                 Periplasmic nitrate reductase 
                 1177 
               
               
                 440307-441146 
                 napG 
                   
                 Ferredoxin-type protein NapG 
                 1178 
               
               
                 441146-442009 
                 napH 
                   
                 Ferredoxin-type protein NapH 
                 1179 
               
               
                 442006-442458 
                 napB 
                   
                 Diheme cytochrome C NapB 
                 1180 
               
               
                 442473-443075 
                 napC 
                   
                 Cytochrome C-type protein NapC 
                 1181 
               
               
                 C 443235-443879  
                 Adk 
                   
                 Adenylate kinase 
                 1182 
               
               
                 C 443964-445241  
                 Lic3c 
                   
                 Putative integral membrane signal transducer 
                 1183 
               
               
                   
                   
                   
                 protein 
               
               
                 C 445383-446399  
                 galE 
                   
                 UDP-glucose 4-epimerase 
                 1184 
               
               
                 C 446572-447534  
                 Lic3A 
                   
                 CMP-Neu5Ac--lipooligosaccharide alpha 
                 1185 
               
               
                   
                   
                   
                 2-3 sialytransferase 
               
               
                 447933-448655 
                 — 
                   
                 Putative ABC-type nitrate/sulfonate/bicarbonate 
                 1186 
               
               
                   
                   
                   
                 transport system, ATPase component 
               
               
                 448652-449389 
                 — 
                   
                 Putative ABC-type nitrate/sulfonate/bicarbonate 
                 1187 
               
               
                   
                   
                   
                 transport system, permease component 
               
               
                 449411-450355 
                 — 
                   
                 Putative ABC-type nitrate/sulfonate/bicarbonate 
                 1188 
               
               
                   
                   
                   
                 transport system, periplasmic component 
               
               
                 450365-451012 
                 — 
                   
                 Putative transcription activator 
                 1189 
               
               
                 C 451107-451922  
                 hfeD 
                   
                 Putative ABC-type chelated iron transport 
                 1190 
               
               
                   
                   
                   
                 system, permease component 
               
               
                 C 451915-452763  
                 hfeC 
                   
                 Putative ABC-type chelated iron transport 
                 1191 
               
               
                   
                   
                   
                 system, permease component 
               
               
                 C 452767-453687  
                 hfeB 
                   
                 Putative ABC-type chelated iron transport 
                 1192 
               
               
                   
                   
                   
                 system, ATPase component 
               
               
                 C 453687-454568  
                 hfeA 
                   
                 Putative periplasmic chelated iron binding 
                 1193 
               
               
                   
                   
                   
                 protein 
               
               
                 454874-455338 
                 — 
                 ✓ 
                 Hypothetical protein 
                 1194 
               
               
                 C 455430-456308  
                 pbpG 
                   
                 Penicillin-binding protein 7 homolog precursos 
                 1195 
               
               
                 456533-457705 
                 — 
                   
                 Predicted Fe—S-cluster redox enzyme 
                 1196 
               
               
                 457805-458344 
                 — 
                   
                 Conserved hypothetical protein 
                 1197 
               
               
                 458416-459327 
                 — 
                   
                 Conserved hypothetical transcriptional regulator 
                 1198 
               
               
                   
                   
                   
                 with an N-terminal xre-type HTH domain 
               
               
                 459336-460442 
                 gcpE 
                   
                 4-hydroxy-2-methyl-2-(E)-butenyl 4- 
                 1199 
               
               
                   
                   
                   
                 diphosphate synthase 
               
               
                 460452-461723 
                 hisS 
                   
                 Histidyl-tRNA synthetase 
                 1200 
               
               
                 461741-462355 
                 — 
                   
                 Conserved hypothetical protein 
                 1201 
               
               
                 C 462406 . . . 462600      
                 — 
                   
                 conserved hypothetical protein 
                 1202 
               
               
                 C 462600-462941  
                 Fdx 
                   
                 Feerdoxin, 2Fe—S 
                 1203 
               
               
                 C 462981-464840  
                 hscA 
                   
                 Chaperone protein HscA 
                 1204 
               
               
                 C 464859-465545  
                 — 
                   
                 Conserved hypothetical protein 
                 1205 
               
               
                 C 465596-466120  
                 hscB 
                   
                 Co-chaperone protein HscB 
                 1206 
               
               
                 C 466133-466456  
                 — 
                   
                 Conserved hypothetical protein 
                 1207 
               
               
                 C 466514-466894  
                 nifU 
                   
                 NifU-like protein 
                 1208 
               
               
                 C 466954-468174  
                 nifS2 
                   
                 Cysteine sedulferase 
                 1209 
               
               
                 C 468235-468687  
                 — 
                   
                 Predicted transcriptional regulator 
                 1210 
               
               
                 C 468740-469465  
                 — 
                   
                 Hypothetical tRNA/rRNA methyltransferase 
                 1211 
               
               
                 C 469905-470366  
                 Pal 
                   
                 Outer membrane protein P6 precursor 
                 1212 
               
               
                 C 470390-471673  
                 tolB 
                   
                 TolB 
                 1213 
               
               
                 C 471715-472941  
                 tolA 
                   
                 TolA 
                 1214 
               
               
                 C 472957-473376  
                 tolR 
                   
                 TolR 
                 1215 
               
               
                 C 473447-474133  
                 tolQ 
                   
                 TolQ 
                 1216 
               
               
                 C 474150-474560  
                 — 
                   
                 Predicted thioestererase 
                 1217 
               
               
                 474885-476807 
                 dinG 
                   
                 Probable ATP-dependent helicase 
                 1218 
               
               
                 476820-477530 
                 — 
                   
                 Possible inactive homolog of metal-dependent 
                 1219 
               
               
                   
                   
                   
                 proteases, putative molecular chaperone 
               
               
                 477555 . . . 478106 
                 — 
                   
                 possible starvation-inducible outer membrane 
                 1220 
               
               
                   
                   
                   
                 lipoprotein 
               
               
                 478148-479836 
                 lcfA 
                   
                 Long chain fatty acid CoA ligase 
                 1221 
               
               
                 479892-481034 
                 rnD 
                   
                 Ribonuclease D 
                 1222 
               
               
                 C 481077-482945  
                 — 
                 ✓ 
                 Conserved hypothetical acyltransferase 
                 1223 
               
               
                 C 483019-484110  
                 — 
                   
                 Predicted GTPase, probable translation factor 
                 1224 
               
               
                 C 484158-484742  
                 Pth 
                   
                 Peptidyl-tRNA hydrolase 
                 1225 
               
               
                 484925-485233 
                 — 
                   
                 Conserved hypothetical protein 
                 1226 
               
               
                 485236-486450 
                 — 
                   
                 Conserved hypothetical cupin superfamily 
                 1227 
               
               
                   
                   
                   
                 metalloenzyme 
               
               
                 486452-487771 
                 xseA 
                   
                 Exodeoxyribonuclease VII large subunit 
                 1228 
               
               
                 487948-488601 
                 adpP 
                   
                 ADP-ribose pyrophoaphatase 
                 1229 
               
               
                 488611-489435 
                 Icc 
                   
                 Predicted phosphohydrolase 
                 1230 
               
               
                 C 489533-489820  
                 — 
                   
                 Conserved hypothetical protein 
                 1231 
               
               
                 490017-491393 
                 ompP1 
                   
                 Outer membrane protein P1 precursor 
                 1232 
               
               
                 491439-492008 
                 Ogt 
                   
                 Methylated-DNA-protein-cysteine 
                 1233 
               
               
                 492005-492676 
                 mutH 
                   
                 DNA mismatch repair protein MutH 
                 1234 
               
               
                 C 492684-493976  
                 mesJ 
                   
                 Putative cell cycle protein MesJ 
                 1235 
               
               
                 C 493976-494080  
                 — 
                   
                 Pseudogene for pyridoxamine kinase 
                 1236 
               
               
                 C 494153-495100  
                 accA 
                   
                 Acetyl-coenzyme A carboxylase carboxyl 
                 1237 
               
               
                   
                   
                   
                 transferase subunit alpha 
               
               
                 C 495189-495974  
                 znuB 
                   
                 High affinity zinc uptake system membrane 
                 1238 
               
               
                   
                   
                   
                 protein ZnuB 
               
               
                 C 495974-496780  
                 znuC 
                   
                 High-affinity zinc uptake system ATP binding 
                 1239 
               
               
                   
                   
                   
                 protein AnuC 
               
               
                 495652-498379 
                 — 
                   
                 Conserved hypothetical metalloprotease 
                 1240 
               
               
                 498494-499450 
                 tyrR 
                   
                 Transcriptional regulatory protein TyrR 
                 1241 
               
               
                 C 499546-499821  
                 hfq 
                   
                 host factor-I protein Hfq 
                 1242 
               
               
                 C 499912-500907  
                 rluC 
                   
                 ribosomal large subunit pseudouridine synthase C 
                 1243 
               
               
                 501253-504108 
                 rne 
                   
                 ribonuclease E 
                 1244 
               
               
                 504340-504552 
                 — 
                   
                 Conserved hypothetical protein 
                 1245 
               
               
                 504876-505673 
                 thiM 
                   
                 hydroxyethylthiazole kinase 
                 1246 
               
               
                 505666-506475 
                 thiD 
                   
                 phosphomethylpyrimidine kinase 
                 1247 
               
               
                 506486-507166 
                 thiE 
                   
                 thiamine-phosphate pyrophosphorylase 
                 1248 
               
               
                 507150-508454 
                 — 
                   
                 Conserved hypothetical metabolite transport 
                 1249 
               
               
                 C 508466-508567  
                 — 
                   
                 hypothetical protein 
                 1250 
               
               
                 508623-510002 
                 — 
                   
                 putative protease 
                 1251 
               
               
                 C 510036-511355  
                 srmB 
                   
                 ATP-dependent RNA helicase SrmB 
                 1252 
               
               
                 511401-512123 
                 — 
                   
                 predicted O-methyltransferase 
                 1253 
               
               
                 C 512154-512759  
                 — 
                   
                 pseudogene for conserved hypothetical 
                 1254 
               
               
                   
                   
                   
                 tRNA/rRNA methyltransferase 
               
               
                 512906-514273 
                 pssA 
                   
                 CDP-diacylglycerol -- serine O-phosphatidyl- 
                 1255 
               
               
                   
                   
                   
                 transferase 
               
               
                 C 514319-515044  
                 fadR 
                   
                 fatty acid metabolism regulator protein 
                 1256 
               
               
                 515145-516713 
                 nhaB 
                   
                 Na(+)/H(+) antiporter 2 
                 1257 
               
               
                 516723-517256 
                 dsbB 
                   
                 disulfide bond formation protein B 
                 1258 
               
               
                 C 517311-519143  
                 glmS 
                   
                 glucosamine--fructose-6-phosphate amino- 
                 1259 
               
               
                   
                   
                   
                 transferase 
               
               
                 C 519256-519666  
                 hupA 
                   
                 DNA-binding protein HU 
                 1260 
               
               
                 C 519668-520258  
                 — 
                   
                 conserved hypothetical protein 
                 1261 
               
               
                 C 520294-521088  
                 nudC 
                   
                 NADH pyrophosphatase 
                 1262 
               
               
                 C 521155-521751  
                 orfG 
                   
                 conserved hypothetical 21.9 KD protein in 
                 1263 
               
               
                   
                   
                   
                 locus involved in transformation 
               
               
                 C 521827-522513  
                 comF 
                   
                 competence protein F 
                 1264 
               
               
                 C 522526-523863  
                 comE 
                   
                 competence protein E 
                 1265 
               
               
                 C 523873-524283  
                 comD 
                   
                 competence protein D 
                 1266 
               
               
                 C 524283-524804  
                 comC 
                   
                 competence protein C 
                 1267 
               
               
                 C 524801-525307  
                 comB 
                   
                 competence protein B 
                 1268 
               
               
                 C 525308-526105  
                 comA 
                   
                 competence protein A 
                 1269 
               
               
                 526204-528798 
                 mrcA 
                   
                 penicillin-binding protein 1A 
                 1270 
               
               
                 528871-529716 
                 — 
                   
                 conserved hypothetical protein 
                 1271 
               
               
                 529849-530214 
                 — 
                   
                 conserved hypothetical protein 
                 1272 
               
               
                 530345-530947 
                 recR 
                   
                 recombination protein RecR 
                 1273 
               
               
                 530963-532918 
                 topB 
                   
                 DNa topoisomerase III 
                 1274 
               
               
                 533027-533368 
                 secG 
                   
                 protein-export membrane protein SecG 
                 1275 
               
               
                 C 533913-535583  
                 fruA 
                   
                 PTS system, fructose-specific IIBC component 
                 1276 
               
               
                 C 535585-536526  
                 fruK 
                   
                 1-phosphofructokinase 
                 1277 
               
               
                 C 536528-538027  
                 fruB 
                   
                 PTS system, fructose-specific IIA/FPr 
                 1278 
               
               
                   
                   
                   
                 component 
               
               
                 C 538099-538635  
                 — 
                   
                 conserved hypothetical protein 
                 1279 
               
               
                 C 538722-539000  
                 vapD 
                   
                 virulence-associated protein D 
                 1280 
               
               
                 C 539009-539200  
                 vapX 
                   
                 VapX 
                 1281 
               
               
                 C 539272-540570  
                 — 
                   
                 conserved hypothetical protein 
                 1282 
               
               
                 C 540621-541145  
                 — 
                   
                 conserved-hypothetical protein 
                 1283 
               
               
                 C 541172-541954  
                 — 
                   
                 putative deoxyribonuclase 
                 1284 
               
               
                 C 542009-542992  
                 holB 
                   
                 DNA polymerase III, delta subunit 
                 1285 
               
               
                 C 542989-543117  
                 — 
                 ✓ 
                 hypothetical protein 
                 1286 
               
               
                 543192-545315 
                 lav 
                 ✓ 
                 autotransported protein Lav 
                 1287 
               
               
                 C 546221-546880  
                 tmk 
                   
                 thymidylate kinase 
                 1288 
               
               
                 C 546870-547913  
                 — 
                   
                 predicted periplasmic solute-binding protein 
                 1289 
               
               
                 C 547983-548924  
                 surA 
                   
                 survival protein SurA homolog 
                 1290 
               
               
                 C 548994-549533  
                 pyrR 
                   
                 PyrR bifunctional protein 
                 1291 
               
               
                 549665-550456 
                 mazG 
                   
                 predicted pyrophosphatase MazG 
                 1292 
               
               
                 C 550506-551381  
                 — 
                   
                 conserved hypothetical protein 
                 1293 
               
               
                 551574-553985 
                 lon 
                   
                 ATP-dependent protease La 
                 1294 
               
               
                 554102-555253 
                 — 
                   
                 predicted Fe—S oxidoreductase 
                 1295 
               
               
                 555387-556046 
                 rpiA 
                   
                 ribose 5-phosphate isomerase A 
                 1296 
               
               
                 556076-557308 
                 serA 
                   
                 D-3-phosphoglycerate dehydrogenase 
                 1297 
               
               
                 C 557351-558193  
                 — 
                   
                 predicted aminomethyltransferase related to 
                 1298 
               
               
                   
                   
                   
                 GcvT 
               
               
                 C 558203-559066  
                 — 
                   
                 conserved hypothetical stress-induced protein 
                 1299 
               
               
                 559515-560426 
                 hisG 
                   
                 ATP phosphoribosyltransferase 
                 1300 
               
               
                 560519-561802 
                 hisD 
                   
                 histidinol dehydrogenase 
                 1301 
               
               
                 561871-562974 
                 hisC 
                   
                 hisitidinol-phosphate aminotransferase 1 
                 1302 
               
               
                 563086-564174 
                 hisB 
                   
                 histidine biosynthesis bifunctional protein HisB 
                 1303 
               
               
                 564240-564839 
                 hisH 
                   
                 imidazole glycerol phosphate synthase subunit 
                 1304 
               
               
                   
                   
                   
                 HisH 
               
               
                 564875-565624 
                 hisA 
                   
                 1-5-[methylideneamino] imidazole-4- 
                 1305 
               
               
                   
                   
                   
                 carboxamine isomerase 
               
               
                 565606-566382 
                 hisF 
                   
                 imidazole glycerol phosphate synthase subunit 
                 1306 
               
               
                   
                   
                   
                 HisF 
               
               
                 566382-567047 
                 hisI 
                   
                 histidine biosynthesis bifunctional protein hisIE 
                 1307 
               
               
                 567129-567281 
                 — 
                   
                 conserved hypothetical protein 
                 1308 
               
               
                 567311-568513 
                 tyrP 
                   
                 tyrosine-specific transportprotein 1 
                 1309 
               
               
                 C 568699-569127  
                 atpC 
                   
                 ATP synthase epsilon chain 
                 1310 
               
               
                 C 569157-570530  
                 atpD 
                   
                 ATP synthase beta chain 
                 1311 
               
               
                 C 570547-571416  
                 atpG 
                   
                 ATP synthase gamma chain 
                 1312 
               
               
                 C 571432-572973  
                 atpA 
                   
                 ATP synthase alpha chain 
                 1313 
               
               
                 C 572986-573519  
                 atpH 
                   
                 ATP synthase delta chain 
                 1314 
               
               
                 C 573532-574002  
                 atpF 
                   
                 ATP synthase B chain 
                 1315 
               
               
                 C 574052-574306  
                 atpE 
                   
                 ATP cynthase C chain 
                 1316 
               
               
                 C 574362-575150  
                 atpB 
                   
                 ATP synthase A chain 
                 1317 
               
               
                 C 575187-575561  
                 — 
                   
                 predicted F0F1-type ATP synthase subunit I 
                 1318 
               
               
                 C 575687-576298  
                 gidB 
                   
                 methyltransferase GidB 
                 1319 
               
               
                 C 576438-576815  
                 — 
                   
                 conserved hypothetical protein 
                 1320 
               
               
                 576931-577533 
                 — 
                   
                 predicted phosphatase/phosphohexomutase 
                 1321 
               
               
                 577533-578006 
                 — 
                   
                 predicted membrane protein 
                 1322 
               
               
                 578191-578694 
                 luxS 
                   
                 S-ribosylhomocysteinase 
                 1323 
               
               
                 C 579638-580345  
                 aphA 
                   
                 Class B acid phosphatase 
                 1324 
               
               
                 580565-581092 
                 hslV 
                   
                 ATP-dependent protease HslV 
                 1325 
               
               
                 581103-582437 
                 hslU 
                   
                 HslU, ATP-dependent chaperone of the HslUV 
                 1326 
               
               
                   
                   
                   
                 protease 
               
               
                 C 582507-583559  
                 ptoD2 
                   
                 spermidine/putrescine-binding periplasmic 
                 1327 
               
               
                   
                   
                   
                 protein 2 precursor 
               
               
                 583699-584664 
                 ordL 
                   
                 probable oxidoereductase OrdL 
                 1328 
               
               
                 585158-586600 
                 rmuC 
                   
                 DNA recombination protein RmuC 
                 1329 
               
               
                 586764-587183 
                 rbsD 
                   
                 ribose transport permease protein 
                 1330 
               
               
                 587197-588678 
                 rbsA 
                   
                 ribose transport ATP-binding protein 
                 1331 
               
               
                 588691-589662 
                 rbsC 
                   
                 ribose transport permease protein 
                 1332 
               
               
                 589682-590560 
                 rbsB 
                   
                 ribose-binding periplasmic protein 
                 1333 
               
               
                 590658-591578 
                 rbsK 
                   
                 ribokinase 
                 1334 
               
               
                 591606-592604 
                 rbsR 
                   
                 ribose operon repressor 
                 1335 
               
               
                 592710-893261 
                 — 
                   
                 predicted membrane protein 
                 1336 
               
               
                 C 593401-593889  
                 menG 
                   
                 S-adenosylmethionine:2-demtyhylmenaquinone 
                 1337 
               
               
                   
                   
                   
                 methyltransferase 
               
               
                 C 593491-594873  
                 menA 
                   
                 1,4-dihydroxy-2-naphthoate octaprenyl- 
                 1338 
               
               
                   
                   
                   
                 transferase 
               
               
                 594920-595639 
                 — 
                   
                 conserved hypothetical protein 
                 1339 
               
               
                 C 595692-596678  
                 tehA 
                   
                 tellurite resistance protein 
                 1340 
               
               
                 C 596830-601080  
                 rpoC 
                   
                 DNA-directed RNA polymerase beta′ chain 
                 1341 
               
               
                 C 601287-605318  
                 rpoB 
                   
                 DNA-directed RNA polymerase beta chain 
                 1342 
               
               
                 C 605702-606391  
                 rpla 
                   
                 50S ribosomal protein L1 
                 1343 
               
               
                 C 606396-606824  
                 rplk 
                   
                 50S ribosomal protein L11 
                 1344 
               
               
                 C 606997-607713  
                 deoD 
                   
                 purine nucleoside phosphorylase 
                 1345 
               
               
                 C 607797-609050  
                 — 
                   
                 predicted nucleoside permease 
                 1346 
               
               
                 C 609149-609937  
                 — 
                   
                 predicted pyruvate-formate lyase-activating enzyme 
                 1347 
               
               
                 C 609946-611490  
                 — 
                   
                 conserved hypothetical glycyl radical protein 
                 1348 
               
               
                 611703-612359 
                 — 
                   
                 predicted membrane protein 
                 1349 
               
               
                 C 612315-613385  
                 waaQ 
                   
                 ADP-heptose--lipooligosaccharide 
                 1350 
               
               
                   
                   
                   
                 heptosyltransferase III 
               
               
                 C 613423-614502  
                 fba 
                   
                 frustose-biphosphate aldolase 
                 1351 
               
               
                 C 614613-615773  
                 pgk 
                   
                 phosphoglycerate kinase 
                 1352 
               
               
                 C 615869-616663  
                 — 
                   
                 probable rubonuclease I 
                 1353 
               
               
                 616741-617001 
                 — 
                   
                 putative ferredoxin-like protein 
                 1354 
               
               
                 C 617135-618355  
                 tyrQ 
                   
                 tyrosine-specific transport protein 2 
                 1355 
               
               
                 C 618392-618973  
                 tdk 
                   
                 thymidine kinase 
                 1356 
               
               
                 C 618982-620010  
                 gcp 
                   
                 probable O-sialoglycoprotein endopeptidase 
                 1357 
               
               
                 620242-620457 
                 rpsU 
                   
                 30S ribosomal protein 521 
                 1358 
               
               
                 620591-622372 
                 — 
                   
                 DNA primase 
                 1359 
               
               
                 622443-624314 
                 rpoD 
                   
                 DNA polymerase sigma factor RpoD 
                 1360 
               
               
                 C 624624-626051  
                 aspA 
                   
                 aspartate ammonia-lyase 
                 1361 
               
               
                 C 626198-627013  
                 ureH 
                   
                 urease accessory protein UreH 
                 1362 
               
               
                 C 627088-627765  
                 ureG 
                   
                 urease accessory protein UreG 
                 1363 
               
               
                 C 627868-628578  
                 ureF 
                   
                 urease accessory protein UreF 
                 1364 
               
               
                 C 628560-629117  
                 ureE 
                   
                 urease accessory protein UreE 
                 1365 
               
               
                 C 629245-630963  
                 ureC 
                   
                 urease alpha subunit 
                 1366 
               
               
                 C 630975-631280  
                 ureB 
                   
                 urease beta subunit 
                 1367 
               
               
                 C 631357-631659  
                 ureA 
                   
                 urease gamma subunit 
                 1368 
               
               
                 631822-632112 
                 groES 
                   
                 10 kDa chaperonin 
                 1369 
               
               
                 632135-633772 
                 groEL 
                   
                 60 kDa chaperonin 
                 1370 
               
               
                 C 633946-634395  
                 rplI 
                   
                 50S ribosomal protein L9 
                 1371 
               
               
                 C 634412-634639  
                 rpsR 
                   
                 30S ribosomal protein S18 
                 1372 
               
               
                 C 634652-634798  
                 priB 
                   
                 primsomal replication protein N 
                 1373 
               
               
                 C 634965-635342  
                 rpsF 
                   
                 308 ribosomal protein S6 
                 1374 
               
               
                 C 635534-635788  
                 infA 
                   
                 translation initiation factor IF-1 
                 1375 
               
               
                 635963-637037 
                 lic2C 
                 ✓ 
                 pseudogene for UFDP-glucose-- 
                 1376 
               
               
                   
                   
                   
                 lipoligosaccharide glucosyltransferase 
               
               
                 637121-637987 
                 ksgA 
                   
                 dimethyladenosine transferase 
                 1377 
               
               
                 C 638024-638962  
                 lic2A 
                   
                 UDP-Gal--lipooligosaccharide 
                 1378 
               
               
                   
                   
                   
                 galactosyltransferase 
               
               
                 639015-639842 
                 apaH 
                   
                 bis-tetraphosphatase, symmetrical 
                 1379 
               
               
                 639852-640475 
                 — 
                   
                 conserved hypothetical protein 
                 1380 
               
               
                 C 640601-642055  
                 gnd 
                   
                 6-phosphogluconate dehydrogenase 
                 1381 
               
               
                   
                   
                   
                 decarboxylating 
               
               
                 C 642171-642713  
                 — 
                   
                 conserved hypothetical protein 
                 1382 
               
               
                 C 642796-642984  
                 — 
                   
                 conserved hypothetical protein 
                 1383 
               
               
                 C 643054-643791  
                 devB 
                   
                 6-phosphgluconolactonase 
                 1384 
               
               
                 C 643895-645379  
                 zwf 
                   
                 glucose-6-phosphate 1-dehydrogenase 
                 1385 
               
               
                 C 645455-646264  
                 cysQ 
                   
                 cysQ 
                 1386 
               
               
                 C 646269-646685  
                 — 
                   
                 conserved hypothetical protein 
                 1387 
               
               
                 C 646742-648724  
                 — 
                   
                 predicted membrane protein 
                 1388 
               
               
                 648953-649348 
                 hslR 
                   
                 heat shock protein 15 homolog 
                 1389 
               
               
                 C 649374-649826  
                 asnC 
                   
                 regulator protein AsnC 
                 1390 
               
               
                 649980-650972 
                 asnA 
                   
                 aspartate --ammonia ligase 
                 1391 
               
               
                 651035-651388 
                 — 
                 ✓ 
                 conserved hypothetical transposase-like protein 
                 1392 
               
               
                 652001-652858 
                 — 
                 ✓ 
                 hypothetical protein 
                 1393 
               
               
                 C 653015-653131  
                 — 
                 ✓ 
                 hypothetical protein 
                 1394 
               
               
                 653423-653563 
                 — 
                 ✓ 
                 hypothetical protein 
                 1395 
               
               
                 C 653743-654417  
                 gph 
                   
                 phosphoglycolate phosphatase 
                 1396 
               
               
                 C 654463-655267  
                 rpe 
                   
                 ribulose-phosphate 3-epimerase 
                 1397 
               
               
                 C 655289-657709  
                 gyrB 
                   
                 DNA gyrase subunit B 
                 1398 
               
               
                 C 657835-660147  
                 — 
                   
                 predicted transcriptional accessory protein 
                 1399 
               
               
                 660243-660719 
                 greB 
                   
                 transcription elongation factor GreB 
                 1400 
               
               
                 C 660789-661406  
                 — 
                   
                 conserved hypothetical transcriptional regulator 
                 1401 
               
               
                 C 661406-662311  
                 oxyR 
                   
                 hydrogen peroxide-indncible genes activator 
                 1402 
               
               
                 662434-663159 
                 pdgC 
                   
                 peroxiredoxin•glutaredoxin 
                 1403 
               
               
                 C 663251-663472  
                 slyX 
                   
                 slyX 
                 1404 
               
               
                 663570-664295 
                 fkby 
                   
                 probably FKBP-type peptidyl-proyl cis-trans 
                 1405 
               
               
                   
                   
                   
                 isomerase 
               
               
                 664385-665050 
                 — 
                   
                 conserved hypothetical protein 
                 1406 
               
               
                 665050-665430 
                 — 
                   
                 uncharacterized conserved protein involved in 
                 1407 
               
               
                   
                   
                   
                 intracellular sulfur reduction 
               
               
                 665427-665786 
                 — 
                   
                 uncharacterized conserved protein involved in 
                 1408 
               
               
                   
                   
                   
                 oxidation of intracellular sulfur 
               
               
                 66579S-666082 
                 — 
                   
                 uncharacterized conserved protein involved in 
                 1409 
               
               
                   
                   
                   
                 oxidation of intracellular sulfur 
               
               
                 C 666213-667397  
                 tufB 
                   
                 elongation factor Tu 
                 1410 
               
               
                 668103-669026 
                 coaA 
                   
                 pantothenate kinase 
                 1411 
               
               
                 C 669117-670064  
                 rseB 
                   
                 sigma-E factor regulatory protein RseB 
                 1412 
               
               
                 C 670144-670719  
                 rseA 
                   
                 sigma-B factor negative regulator protein 
                 1413 
               
               
                   
                   
                   
                 homolog 
               
               
                 C 670744-671313  
                 rpoE 
                   
                 RNA polymerase sigma-E factor 
                 1414 
               
               
                 C 671422-671679  
                 — 
                   
                 conserved hypothetical protein 
                 1415 
               
               
                 C 671769-672155  
                 mscL 
                   
                 large-conductance mechanosensitive channel 
                 1416 
               
               
                 C 672229-673604  
                 trkA 
                   
                 Trk system potassium uptake protein TrkA 
                 1417 
               
               
                 C 673617-674969  
                 sun 
                   
                 SUN protein 
                 1418 
               
               
                 C 674969-675925  
                 fmt 
                   
                 methionyl-tRNA formyltransferase 
                 1419 
               
               
                 C 676026-676535  
                 def 
                   
                 peptide deformylase 
                 1420 
               
               
                 676725-677162 
                 — 
                 ✓ 
                 hypothetical protein 
                 1421 
               
               
                 677140 . . . 677325 
                 — 
                 ✓ 
                 hypothetical protein 
                 1422 
               
               
                 C 683606-684259  
                 sxy 
                   
                 DNA transformation protein TfoX 
                 1423 
               
               
                 684631-685695 
                 recA 
                   
                 RecA 
                 1424 
               
               
                 685774-686232 
                 recX 
                   
                 regulatory protein RecX 
                 1425 
               
               
                 C 686229-686615  
                 crcB 
                   
                 CrcB 
                 1426 
               
               
                 C 686615-687433  
                 — 
                   
                 predicted hydrolase of the HAD superfamily 
                 1427 
               
               
                 687836-688840 
                 argF 
                   
                 ornithine carbamoyltransferase, catabolic 
                 1428 
               
               
                 688850-689782 
                 arcC 
                   
                 carbamate kinase 
                 1429 
               
               
                 689887-691416 
                 — 
                   
                 predicted membrane protein 
                 1430 
               
               
                 C 691826-694980  
                 hgpD 
                 ✓ 
                 pseudogene for hemoglobin-haptoglobin 
                 1431 
               
               
                   
                   
                   
                 binding protein D 
               
               
                 696052-696756 
                 pepE 
                   
                 peptidase E 
                 1432 
               
               
                 696774-698069 
                 — 
                   
                 predicted C4-dicarboxylate transporter 
                 1433 
               
               
                 698141-699412 
                 abgA 
                   
                 aminobenzoyl glutamate utilization protein A 
                 1434 
               
               
                 699505-701478 
                 cpdB 
                   
                 2′,3′-cyclic-nucleotide 2′-phosphodiesterase 
                 1435 
               
               
                 C 701587-701994  
                 — 
                 ✓ 
                 HTH-type transcriptional regulator 
                 1436 
               
               
                 C 702004-702681  
                 — 
                 ✓ 
                 zinc transported ZitB 
                 1437 
               
               
                 703189-705078 
                 gidA 
                   
                 glucose inhibited division protein A 
                 1438 
               
               
                 705260-705634 
                 rpsL 
                   
                 30S ribosoomal protein S12 
                 1439 
               
               
                 705791-706261 
                 rpsG 
                   
                 30S ribosomal protein S7 
                 1440 
               
               
                 706345-708447 
                 fusA 
                   
                 elongation factor G 
                 1441 
               
               
                 708512-709696 
                 tufB2 
                   
                 elongation factor Tu 
                 1442 
               
               
                 710156-710500 
                 — 
                 ✓ 
                 predicted chloride channel protein 
                 1443 
               
               
                 710491-710673 
                 — 
                   
                 predicted chloride channel protein 
                 1444 
               
               
                 710676-711659 
                 dusA 
                   
                 tRNA-dihydrouridine synthase A 
                 1445 
               
               
                 C 711707-711997  
                 — 
                   
                 conserved hypothetical protein 
                 1446 
               
               
                 C 712020-713030  
                 trpS 
                   
                 tryptophanyl-tRNA synthetase 
                 1447 
               
               
                 713153-713770 
                 — 
                   
                 predicted protein involved in purine metabolism 
                 1448 
               
               
                 713793-715163 
                 purB 
                   
                 adenylosuccinate lyase 
                 1449 
               
               
                 715435-715926 
                 rplJ 
                   
                 50S ribosomal protein L10 
                 1450 
               
               
                 715981-716532 
                 rplL 
                   
                 50S nbosomal protein L7/L12 
                 1451 
               
               
                 716511-717881 
                 glmU 
                   
                 bifunctional GlmU protein 
                 1452 
               
               
                 C 717916-718227  
                 — 
                   
                 hypothetical protein 
                 1453 
               
               
                 C 718766-719701  
                 pldB 
                   
                 probable lysophospholipase L2 
                 1454 
               
               
                 C 719755-720820  
                 asd 
                   
                 aspartate-semialdehyde dehydrogenase 
                 1455 
               
               
                 C 721036-721752  
                 — 
                   
                 conserved hypothetical protein 
                 1456 
               
               
                 721944-722600 
                 — 
                 ✓ 
                 predicted 2-methylthioadenine synthetase 
                 1457 
               
               
                 C 722664-723242  
                 mdaB 
                   
                 putative NADPH-quinone reductase, modulator 
                 1458 
               
               
                   
                   
                   
                 of drug activity B 
               
               
                 723521-725533 
                 rep 
                   
                 ATP-dependent DNA helicase rep 
                 1459 
               
               
                 C 725539-725751  
                 — 
                   
                 predicted periplasmic lipoprotein 
                 1460 
               
               
                 C 725748-726218  
                 kdtB 
                   
                 phosphopantetheine adenylyltransferase 
                 1461 
               
               
                 C 726215-727498  
                 kdtA 
                   
                 3-deoxy-D-manno-octulosonic acid transferase 
                 1462 
               
               
                 727561-728325 
                 lgtF 
                   
                 UDP-glucose--lipooligosaccharide 
                 1463 
               
               
                   
                   
                   
                 glucosyltransferase 
               
               
                 C 728322-728885  
                 tag 
                   
                 DNA-3-methyladenine glycolase 
                 1464 
               
               
                 C 729000-729752  
                 — 
                 ✓ 
                 hypothetical protein 
                 1465 
               
               
                 C 729764-730570  
                 aroE 
                   
                 shikimate 5-dehydrogenase 
                 1466 
               
               
                 C 730574-731125  
                   
                   
                 predicted translation factor SUA5 
                 1467 
               
               
                 C 731141-731677  
                 — 
                   
                 Zn-finger domain associated with 
                 1468 
               
               
                   
                   
                   
                 topoisomerase typr I 
               
               
                 C 731687-733603  
                 — 
                   
                 probable ABC transporter, ATP binding protein 
                 1469 
               
               
                 C 733788-734084  
                 — 
                   
                 putative HTH-type transcriptional regulator 
                 1470 
               
               
                 C 734077-734259  
                 — 
                 ✓ 
                 conserved hypothetical protein 
                 1471 
               
               
                 C 734529-737507  
                 hgpB 
                 ✓ 
                 hemoglobin-haptoglobin binding protein B 
                 1472 
               
               
                 738238-739983 
                 — 
                   
                 hypothetical ABC transporter, ATP-binding 
                 1473 
               
               
                   
                   
                   
                 protein 
               
               
                 739976-741634 
                 — 
                   
                 probable ABC transporter, ATP binding protein 
                 1474 
               
               
                 C 741718-742749  
                 — 
                   
                 conserved hypothetical protein 
                 1475 
               
               
                 C 742746-743066  
                 — 
                   
                 conserved hypothetical protein 
                 1476 
               
               
                 C 743054-743362  
                 — 
                   
                 putative HTH-type transcriptional regulator 
                 1477 
               
               
                 C 743567-744568  
                 glpX 
                   
                 fructose-1,6-bisphosphatase class II GlpX 
                 1478 
               
               
                 744730-744948 
                 — 
                   
                 conserved hypothetical protein 
                 1479 
               
               
                 745047-745487 
                 mioC 
                   
                 MioC 
                 1480 
               
               
                 745484-745918 
                 dtd 
                   
                 D-tyrosyl-tRNA (Tyr) deacylase 
                 1481 
               
               
                 C 746225-746701  
                 ispF 
                   
                 3-C-methyl-D-erythritol 2,4-cyclodiphosphate 
                 1482 
               
               
                   
                   
                   
                 synthase 
               
               
                 C 746698-747375  
                 ispD 
                   
                 2-C-methyl-D-erythritol 4-phosphate 
                 1483 
               
               
                   
                   
                   
                 cytidylyltransferase 
               
               
                 C 747375-747653  
                 ftsB 
                   
                 cell division protein FtcB 
                 1484 
               
               
                 C 747776-748243  
                 gpt 
                   
                 xanthine-guanine phosphoribosyltransferase 
                 1485 
               
               
                 748354-749808 
                 pepD 
                   
                 aminoacyl-histidine dipeptidase 
                 1486 
               
               
                 C 749861-750748  
                 xerC 
                   
                 site-specific recombinase XerC 
                 1487 
               
               
                 C 750742-751182  
                 — 
                   
                 conserved hypothetical protein 
                 1488 
               
               
                 751348-752138 
                 tpiA 
                   
                 triosephosphate isomerase 
                 1489 
               
               
                 C 752221-752538  
                 glpE 
                   
                 thiosulfate sulfurtransferase GlpE 
                 1490 
               
               
                 C 752539-753417  
                 — 
                   
                 conserved hypothetical protein 
                 1491 
               
               
                 C 753449-754327  
                 ilvY 
                   
                 HTH-type transcriptional activator IlvY 
                 1492 
               
               
                 755011-756489 
                 ilvC 
                   
                 ketol-acid reductoisomerase 
                 1493 
               
               
                 C 756600-757880  
                 glpC 
                   
                 anaerobic glycerol-3-phosphate dehydrogenase 
                 1494 
               
               
                   
                   
                   
                 subunit C 
               
               
                 C 757891-759189  
                 glpB 
                   
                 anaerobic glycerol-3-phosphate dehydrogenase 
                 1495 
               
               
                   
                   
                   
                 subunit B 
               
               
                 C 759179-760870  
                 glpA 
                   
                 anaerobic glycerol-3-phosphate dehydrogenase 
                 1496 
               
               
                   
                   
                   
                 subunit A 
               
               
                 761163-762605 
                 glpT 
                   
                 glycerol-3-phosphate transporter 
                 1497 
               
               
                 762709-763803 
                 glpQ 
                   
                 glycerophosphoryl diester phosphodiesterase 
                 1498 
               
               
                   
                   
                   
                 precursor 
               
               
                 764033-764827 
                 glpF 
                   
                 glycerol uptake facilitator protein 
                 1499 
               
               
                 764848-766359 
                 glpK 
                   
                 glycerol kinase 
                 1500 
               
               
                 C 766443-766910  
                 gpt2 
                   
                 xanthine-guanine phosphoribosyltransferase 
                 1501 
               
               
                 766932-767069 
                 — 
                   
                 pseudogene for glycerophosphoryl diester 
                 1502 
               
               
                   
                   
                   
                 phosphodiesterase precursor 
               
               
                 767195-768019 
                 hel 
                   
                 outer membrane protein P4, NADP phosphatase 
                 1503 
               
               
                 768186-768869 
                 rluE 
                   
                 ribosomal large subunit pseudouridine synthase E 
                 1504 
               
               
                 C 768998-770002  
                 ppx 
                   
                 pseudogene for putative exopolyphosphatase 
                 1505 
               
               
                 C 769974-773858  
                 — 
                   
                 conserved hypothetical protein 
                 1506 
               
               
                 C 773868-775604  
                 — 
                   
                 conserved hypothetical protein 
                 1507 
               
               
                 C 775755-776327  
                 slyD 
                   
                 FKBP-type peptidyl-prolyl cis-trans isomerase 
                 1508 
               
               
                   
                   
                   
                 SlyD 
               
               
                 C 776405-776827  
                 — 
                   
                 conserved hypothetical protein 
                 1509 
               
               
                 776936-777955 
                 truD 
                   
                 tRNA pseudouridine synthase D 
                 1510 
               
               
                 777965-778714 
                 surE 
                   
                 acid phosphatase surE 
                 1511 
               
               
                 778723-779301 
                 — 
                   
                 conserved hypothetical protein 
                 1512 
               
               
                 779310-779495 
                 — 
                   
                 conserved hypothetical protein 
                 1513 
               
               
                 779530-780747 
                 lppB 
                   
                 outer membrane antigenic lipoprotein B 
                 1514 
               
               
                 781115-782533 
                 tnaA 
                 ✓ 
                 tryptophanase 
                 1515 
               
               
                 782617-783849 
                 tnaB 
                 ✓ 
                 tryptophan-specific transport protein 
                 1516 
               
               
                 783990-786575 
                 mutS 
                   
                 DNA mismatch repair protein MutS 
                 1517 
               
               
                 786781-788166 
                 selA 
                   
                 L-seryl-tRNA selenium transferase 
                 1518 
               
               
                 788163-790022 
                 selB 
                   
                 selenocysteine-specific elongation factor 
                 1519 
               
               
                 790041-790895 
                 — 
                 ✓ 
                 hypothetical protein 
                 1520 
               
               
                 791015-791311 
                 — 
                   
                 conserved hypothetical protein 
                 1521 
               
               
                 791311 . . . 791619 
                 — 
                   
                 conserved hypothetical protein 
                 1522 
               
               
                 C 791676-794868  
                 hgpC 
                 ✓ 
                 pseudogene for hemoglobin-haptoglobin 
                 1523 
               
               
                   
                   
                   
                 utilization protein C 
               
               
                 795165-796463 
                 tig 
                   
                 trigger factor 
                 1524 
               
               
                 796586-797167 
                 clpP 
                   
                 ATP-dependent clp protease proteolytic subunit 
                 1525 
               
               
                 797177-798412 
                 clpX 
                   
                 ATP-dependent Clp protease ATP-binding 
                 1526 
               
               
                   
                   
                   
                 subunit ClpX 
               
               
                 798557-798973 
                 secE 
                   
                 preprotein translocase SecE 
                 1527 
               
               
                 798975-799532 
                 nusG 
                   
                 transcription antitermination protein NusG 
                 1528 
               
               
                 799683-800435 
                 vacJ 
                   
                 VacJ lipoprotein 
                 1529 
               
               
                 800489-800881 
                 — 
                   
                 putative translation initiation inhibitor YjgF 
                 1530 
               
               
                   
                   
                   
                 family 
               
               
                 801049-801900 
                 htpX 
                   
                 probable protease HtpX 
                 1531 
               
               
                 C 801942-802223  
                 sirA 
                   
                 SirA 
                 1532 
               
               
                 802297-802917 
                 — 
                   
                 conserved hypothetical protein 
                 1533 
               
               
                 802290-804383 
                 trkH 
                   
                 Trk system potassium uptake protein TrkH 
                 1534 
               
               
                 810818-811237 
                 psiE 
                   
                 PsiE 
                 1535 
               
               
                 C 811301-812587  
                 hemY 
                   
                 HemY 
                 1536 
               
               
                 C 812598-813809  
                 hemX 
                   
                 putative uroporphyrin-III C-methyltransferase 
                 1537 
               
               
                 814115-816646 
                 cya 
                   
                 adenylate cyclase 
                 1538 
               
               
                 816720-717727 
                 gpsA 
                   
                 glycerol-3-phosphate dehydrogenase 
                 1539 
               
               
                 817744-818547 
                 cysE 
                   
                 serine acetyltransferase 
                 1540 
               
               
                 818557-819372 
                 — 
                   
                 conserved hypothetical shikimate 5- 
                 1541 
               
               
                   
                   
                   
                 dehydrogenase-like protein 
               
               
                 819510-820895 
                 — 
                   
                 possible di- and tricarboxylate transporter 
                 1542 
               
               
                 C 821033-821881  
                 folD 
                   
                 FolD bifunctional protein 
                 1543 
               
               
                 C 822409-823695  
                 fucP 
                   
                 L-fucose permease 
                 1544 
               
               
                 C 823734-824384  
                 fucA 
                   
                 L-fuculose phosphate aldolase 
                 1545 
               
               
                 C 824404-824838  
                 fucU 
                   
                 fucose operon protein FucU 
                 1546 
               
               
                 C 824852-826264  
                 fucK 
                   
                 L-fuculokinase 
                 1547 
               
               
                 C 826337-828151  
                 fucI 
                   
                 L-fucose isomerase 
                 1548 
               
               
                 C 828336-829085  
                 fucR 
                   
                 L-fucose operon activator 
                 1549 
               
               
                 829284-832055 
                 hepA 
                   
                 RNA polymerase associated protein homolog 
                 1550 
               
               
                 832058-832717 
                 rluA 
                   
                 ribosomal large subunit pseudouridine synthase A 
                 1551 
               
               
                 832744-833322 
                 glpG 
                   
                 GlpG 
                 1552 
               
               
                 833352-834119 
                 glpR 
                   
                 glycerol-3-phosphate regulon repressor 
                 1553 
               
               
                 C 834421-835242  
                 metQ 
                   
                 probable D-methionine-binding lipoprotein 
                 1554 
               
               
                   
                   
                   
                 MetQ 
               
               
                 C 835281-835970  
                 metI 
                   
                 probable D-methionine transport system 
                 1555 
               
               
                   
                   
                   
                 permease protein 
               
               
                 C 835960-836997  
                 metN 
                   
                 probable D-methionine transport ATP-binding 
                 1556 
               
               
                   
                   
                   
                 protein 
               
               
                 837173-837727 
                 — 
                   
                 conserved hypothetical protein 
                 1557 
               
               
                 843979-844539 
                 — 
                   
                 conserved hypothetical protein 
                 1558 
               
               
                 844543-844983 
                 — 
                   
                 conserved hypothetical protein 
                 1559 
               
               
                 C 845045-845671  
                 narP 
                   
                 nitrate/nitrite response regulator protein 
                 1560 
               
               
                 C 845877-847124  
                 lysA 
                   
                 diaminopimelate decarboxylase 
                 1561 
               
               
                 C 847172-847303  
                 — 
                   
                 hypothetical protein 
                 1562 
               
               
                 847386-847691 
                 cyaY 
                   
                 CyaY 
                 1563 
               
               
                 847693-849552 
                 recQ 
                   
                 ATP-dependent DNA helicase RecQ 
                 1564 
               
               
                 849637-851355 
                 proS 
                   
                 prolyl-tRNA synthetase 
                 1565 
               
               
                 C 851443-853791  
                 ostA 
                   
                 organic solvent tolerance protein 
                 1566 
               
               
                 C 853914-855323  
                 sufI 
                   
                 SufI 
                 1567 
               
               
                 C 855325-856047  
                 plsC 
                   
                 1-acyl-sn-glycerol-3-phosphate acyltransferase 
                 1568 
               
               
                 856133-856846 
                 lpxH 
                   
                 UDP-2,3-diacylglucosamine hydrolase 
                 1569 
               
               
                 C 857076-858602  
                 — 
                   
                 conserved hypothetical sodium dependent transporter 
                 1570 
               
               
                 858849-859475 
                 ilvG 
                   
                 acetolactate synthase isozyme II large subunit 
                 1571 
               
               
                 859517-861355 
                 ilvD 
                   
                 dihydroxy-acid dehydratase 
                 1572 
               
               
                 861435-862976 
                 thd1 
                   
                 threonine dehydratase biosynthetic 
                 1573 
               
               
                 863014-866493 
                 dnaE 
                   
                 DNA polymerase III alpha subunit 
                 1574 
               
               
                 866732-868375 
                 pgmB 
                   
                 phosphoglucomutase 
                 1575 
               
               
                 C 868542-869051  
                 secB 
                   
                 protein-export protein SecB 
                 1576 
               
               
                 C 869065-869511  
                 — 
                   
                 predicted rhodanese-related sulfurtransferase 
                 1577 
               
               
                 869759-871081 
                 dcuB 
                   
                 anaerobic C4-dicarboxylate transporter DcuB 
                 1578 
               
               
                 871285-872619 
                 ndhA 
                   
                 NADH dehydrogenase 
                 1579 
               
               
                 C 872699-875131  
                 plsB 
                   
                 glycerol-3-phosphate acyltransferase 
                 1580 
               
               
                 875380-876006 
                 lexA 
                   
                 LexA repressor 
                 1581 
               
               
                 876152-876976 
                 dapF 
                   
                 diaminopimelate epimerase 
                 1582 
               
               
                 877196-877693 
                 tpx 
                   
                 probable thiol peroxidase 
                 1583 
               
               
                 878256-882218 
                 purL 
                   
                 phosphoribosylformylglycinamidine synthase 
                 1584 
               
               
                 882414-882652 
                 lex2A 
                 ✓ 
                 pseudogene for Lex2A homolog 
                 1585 
               
               
                 882724-883467 
                 lex2B 
                 ✓ 
                 UDP-glucose--lipooligosaccharide 
                 1586 
               
               
                   
                   
                   
                 glucosyltransferase 
               
               
                 C 883528-884370  
                 — 
                   
                 conserved hypothetical protein 
                 1587 
               
               
                 C 884370-885602  
                 — 
                   
                 predicted membrane-bound metallopeptidase 
                 1588 
               
               
                 885778-886461 
                 gpmA 
                   
                 2,3-bisphosphoglycerate-dependent 
                 1589 
               
               
                   
                   
                   
                 phsphoglycerate mutase 
               
               
                 C 886539-886751  
                 rpL31 
                   
                 50S ribosomal protein L31 
                 1590 
               
               
                 886928-888064 
                 mutY 
                   
                 A/G-specific adenine glycosylase 
                 1591 
               
               
                 888042-888314 
                 — 
                   
                 conserved hypothetical protein 
                 1592 
               
               
                 888329-889402 
                 mltC 
                   
                 membrane-bound lytic murein transglycolase 
                 1593 
               
               
                   
                   
                   
                 C precursor 
               
               
                 C 890013-890693  
                 — 
                   
                 predicted diadenosine tetraphosphatase and 
                 1594 
               
               
                   
                   
                   
                 related serine/threonine protein phosphatase 
               
               
                 C 890690-891955  
                 nadR 
                   
                 bifunctional protein NadR 
                 1595 
               
               
                 892174-892821 
                 ribB 
                   
                 3,4-dihydroxy-2-butanone 4-phosphate synthase 
                 1596 
               
               
                 892836-892684 
                 lpsA 
                   
                 lipooligosaccharide glycosyl transferase 
                 1597 
               
               
                 C 893733-894215  
                 — 
                   
                 conserved hypothetical tRNA/rRNA 
                 1598 
               
               
                   
                   
                   
                 methyltransferase 
               
               
                 C 894225-894806  
                 — 
                   
                 predicted N6-adenine-specific methylase 
                 1599 
               
               
                 894861-896105 
                 FtsY 
                   
                 cell division protein FtsY 
                 1600 
               
               
                 896124-896780 
                 ftsE 
                   
                 cell division ATP-binding protein EtsE 
                 1601 
               
               
                 896790-897722 
                 ftsx 
                   
                 cell division protein ftsx 
                 1602 
               
               
                 C 897817-898998  
                 atoB 
                   
                 acetyl-CoA acetyltransferase 
                 1603 
               
               
                 C 899013-900356  
                 atoE 
                   
                 short chain fatty acids transporter 
                 1604 
               
               
                 C 900359-901024  
                 atoA 
                   
                 acetate CoA-transferase beta subunit 
                 1605 
               
               
                 C 901035-901688  
                 atoD 
                   
                 acetate CoA-transferase alpha subunit 
                 1606 
               
               
                 901894-902841 
                 — 
                   
                 putative HTH-type transcriptional regulator 
                 1607 
               
               
                 903078-903389 
                 rpsJ 
                   
                 30S ribosomal protein S10 
                 1608 
               
               
                 903406-904032 
                 rplC 
                   
                 50S ribosomal protein L3 
                 1609 
               
               
                 904048-904650 
                 rplD 
                   
                 50S ribosomal protein L4 
                 1610 
               
               
                 904647-904946 
                 rplW 
                   
                 50S ribosomal protein L23 
                 1611 
               
               
                 904964-905785 
                 rplB 
                   
                 50 S ribosomal protein L2 
                 1612 
               
               
                 905811-906086 
                 rpsS 
                   
                 30S ribosomal protein S19 
                 1613 
               
               
                 906098-906430 
                 rplV 
                   
                 50S ribosomal protein L22 
                 1614 
               
               
                 906448-907155 
                 rpsC 
                   
                 30S ribosomal protein S3 
                 1615 
               
               
                 607169-907579 
                 rplP 
                   
                 50S ribosomal protein L16 
                 1616 
               
               
                 907579-907770 
                 rpmC 
                   
                 50S ribosomal protein L29 
                 1617 
               
               
                 907770-908027 
                 rpsQ 
                   
                 30S ribosomal protein S17 
                 1618 
               
               
                 908417-909040 
                 — 
                   
                 conserved hypothetical protein 
                 1619 
               
               
                 909321-909692 
                 rplN 
                   
                 50S ribosomal protein L14 
                 1620 
               
               
                 909703-910014 
                 rplX 
                   
                 50S ribosomal protein L24 
                 1621 
               
               
                 910032-910571 
                 rplE 
                   
                 50S ribosomal protein L5 
                 1622 
               
               
                 910583-910888 
                 rpsN 
                   
                 30S ribosomal protein S14 
                 1623 
               
               
                 910925-911317 
                 rpsH 
                   
                 30S ribosomal protein S8 
                 1624 
               
               
                 911333-911866 
                 rplF 
                   
                 50S ribosomal protein L6 
                 1625 
               
               
                 911880-912233 
                 rplR 
                   
                 50S ribosomal protein L18 
                 1626 
               
               
                 912248-912748 
                 rpsE 
                   
                 30S ribosomal protein S5 
                 1627 
               
               
                 912755-912934 
                 rpmD 
                   
                 50S ribosomal protein L30 
                 1628 
               
               
                 912938-913372 
                 rplO 
                   
                 50S ribosomal protein L15 
                 1629 
               
               
                 913380-914705 
                 secY 
                   
                 preprotein translocase SecY subunit 
                 1630 
               
               
                 914987-915343 
                 rpsM 
                   
                 30S ribosomal protein S13 
                 1631 
               
               
                 915359-915748 
                 rpsK 
                   
                 30S ribosomal protein S11 
                 1632 
               
               
                 915776-916396 
                 rpsD 
                   
                 30S ribosomal protein S4 
                 1633 
               
               
                 916428-917414 
                 rpoA 
                   
                 DNA-directed RNA polymerase alpha chain 
                 1634 
               
               
                 917455-917841 
                 rplQ 
                   
                 50S ribosomal protein L17 
                 1635 
               
               
                 C 917968-918564  
                 — 
                   
                 predicted cAMP-binding protein - catabolite 
                 1636 
               
               
                   
                   
                   
                 gene activator and regulatory subunit of cAMP- 
               
               
                   
                   
                   
                 dependent protein kinase 
               
               
                 C 918683-919383  
                 — 
                   
                 pseudogene for conserved hypothetical protein, 
                 1637 
               
               
                   
                   
                   
                 predicted arylsulfatase regulator, Fe—S 
               
               
                   
                   
                   
                 oxidoreductase 
               
               
                 919587-920326 
                 — 
                   
                 predicted permease 
                 1638 
               
               
                 C 920358-921551  
                 dxr 
                   
                 1-deoxy-D-xylulose 5′phosphate reductoisomerase 
                 1639 
               
               
                 C 921661-922218  
                 frr 
                   
                 ribosome recycling factor 
                 1640 
               
               
                 C 922370-923986  
                 pckA 
                   
                 phosphoenolpyruvate carboxykinase 
                 1641 
               
               
                 C 924159-925040  
                 hslO 
                   
                 33 kDa chaperonin 
                 1642 
               
               
                 C 925185-926558  
                 argH 
                   
                 argininosuccinate lyase 
                 1643 
               
               
                 C 926693-927580  
                 galU 
                   
                 UTP-glucose-1-phosphate uridylyltransferase 
                 1644 
               
               
                 C 927602-927793  
                 csrA 
                   
                 carbon storage regulator homolog 
                 1645 
               
               
                 C 927871-930495  
                 alaS 
                   
                 alanyl-tRNA synthetase 
                 1646 
               
               
                 C 930682-931107  
                 uspA 
                   
                 universal stress protein A 
                 1647 
               
               
                 C 931209-932501  
                 pepP 
                   
                 Xaa-Pro aminopeptidase 
                 1648 
               
               
                 C 932513-933061  
                 — 
                   
                 conserved hypothetical protein 
                 1649 
               
               
                 C 933232-934257  
                 galM 
                   
                 aldose 1-epimerase 
                 1650 
               
               
                 C 934264-935460  
                 galK 
                   
                 glactokinase 
                 1651 
               
               
                 C 935495-936544  
                 galT 
                   
                 galactose-1-phosphate uridylyltransferase 
                 1652 
               
               
                 936752-937750 
                 galR 
                   
                 HTH-type transcriptional regulator GalR 
                 1653 
               
               
                 937841-938890 
                 mglB 
                   
                 D-galactose-binding periplasmic protein 
                 1654 
               
               
                   
                   
                   
                 precursos 
               
               
                 938956-940476 
                 mglA 
                   
                 galactoside transport ATP-binding protein 
                 1655 
               
               
                   
                   
                   
                 MglA 
               
               
                 940493-941503 
                 mglC 
                   
                 galactoside transport system permease protein 
                 1656 
               
               
                   
                   
                   
                 MglC 
               
               
                 941649-942383 
                 — 
                   
                 conserved hypothetical protein 
                 1657 
               
               
                 942389-942946 
                 ispZ 
                   
                 probable intracellular septation protein A 
                 1658 
               
               
                 942946-943410 
                 — 
                   
                 putative acyl-CoA thioester hydrolase 
                 1659 
               
               
                 943427-943723 
                 — 
                   
                 conserved hypothetical protein 
                 1660 
               
               
                 943739-945520 
                 slt 
                   
                 putative soluble lytic murein transglycosylase 
                 1661 
               
               
                 945558-945863 
                 trpR 
                   
                 Trp operon repressor 
                 1662 
               
               
                 946006-946590 
                 mtgA 
                   
                 monofuctional biosynthetic peptidoglycan 
                 1663 
               
               
                   
                   
                   
                 transglycolase 
               
               
                 C 946696-947040  
                 frdD 
                   
                 fumarate reductase subunit D 
                 1664 
               
               
                 C 947053-947463  
                 frdC 
                   
                 fumarate reductase subunit C 
                 1665 
               
               
                 C 947474-948244  
                 frdB 
                   
                 fumarate reductase iron-sulfur protein 
                 1666 
               
               
                 C 948327-950036  
                 frdA 
                   
                 fumarate reductase flavoprotein subunit 
                 1667 
               
               
                 950217-951218 
                 genX 
                   
                 putative lysyl-tRNA synthetase 
                 1668 
               
               
                 C 951484-952167  
                 cpxR 
                   
                 transcriptional regulatory protein CpxR 
                 1669 
               
               
                 C 952221-952634  
                 smpA 
                   
                 small protein A 
                 1670 
               
               
                 C 952700-953725  
                 ndpA 
                   
                 nucleosid-associated protein NdpA 
                 1671 
               
               
                 953842-954060 
                 — 
                   
                 conserved hypothetical protein 
                 1672 
               
               
                 954062-955819 
                 — 
                   
                 predicted hydrolase of alkaline phosphatase 
                 1673 
               
               
                   
                   
                   
                 superfamily 
               
               
                 956017-957009 
                 — 
                   
                 conserved hypothetical protein 
                 1674 
               
               
                 C 957148-957726  
                 mobA 
                   
                 probable molybdopterin-guanine dinucleotide 
                 1675 
               
               
                   
                   
                   
                 biosyntheses protein A 
               
               
                 957791-958057 
                 — 
                   
                 conserved hypothetical protein 
                 1676 
               
               
                 958068-958685 
                 dsbA 
                   
                 thiol:disulfide interchange protein DsbA 
                 1677 
               
               
                 958747-959085 
                 — 
                   
                 conserved hypothetical protein 
                 1678 
               
               
                 959226-960317 
                 trmA 
                   
                 tRNA (Uracil-5)-methyltransferase 
                 1679 
               
               
                 960506-961072 
                 — 
                   
                 conserved hypothetical protein 
                 1680 
               
               
                 961066-961500 
                 — 
                   
                 predicted positive regulator of Sigma E 
                 1681 
               
               
                 961901-962437 
                 mobB 
                   
                 molybdopterin-guanine dinucleotide 
                 1682 
               
               
                   
                   
                   
                 biosynthesis protein B 
               
               
                 962434-963825 
                 — 
                   
                 conserved hypothetical protein 
                 1683 
               
               
                 963966-965615 
                 hbpA 
                   
                 heme-binding protein A 
                 1684 
               
               
                 965791-966552 
                 — 
                   
                 putative heme iron utilization protein 
                 1685 
               
               
                 C 966689-967036  
                 — 
                   
                 conserved hypothetical protein 
                 1686 
               
               
                 C 967051-969843  
                 polA 
                   
                 DNA polymerase I 
                 1687 
               
               
                 969992-970294 
                 — 
                   
                 conserved hypothetical protein 
                 1688 
               
               
                 970617-971180 
                 — 
                   
                 predicted 5-formyltetrahydrofolate cyclo-ligase 
                 1689 
               
               
                 971308-973878 
                 clpB 
                   
                 ClpB 
                 1690 
               
               
                 C 973916-974656  
                 — 
                   
                 probable tRNA/rRNA methyltransferase 
                 1691 
               
               
                 C 974712-977060  
                 vacB 
                   
                 ribonuclease R 
                 1692 
               
               
                 C 977252-977959  
                 — 
                   
                 conserved hypothetical protein 
                 1693 
               
               
                 978095-978784 
                 pdxH 
                   
                 pyridoxamine 5′-phosphate oxidase 
                 1694 
               
               
                 C 978871-980721  
                 typA 
                   
                 GTP-binding protein TypA/BipA 
                 1695 
               
               
                 C 980848-981828  
                 lic3A2 
                   
                 CMP-neu5Ac--lipooligosaccharide alpha 2-3 
                 1696 
               
               
                   
                   
                   
                 sialyltransferase 
               
               
                 981985-983397 
                 glnA 
                   
                 glutamine synthetase 
                 1697 
               
               
                 983484-984527 
                 rmlB 
                 ✓ 
                 dTDP-glucose 4,6-dehydratase 
                 1698 
               
               
                 984604-985908 
                 pepB 
                   
                 peptidase B 
                 1699 
               
               
                 985915-986340 
                 ndk 
                   
                 nucleoside diphosphate kinase 
                 1700 
               
               
                 C 986410-987582  
                 — 
                   
                 conserved hypothetical GTP-binding protein 
                 1701 
               
               
                 C 987610-988530  
                 — 
                   
                 conserved hypothetical transport protein 
                 1702 
               
               
                 C 988610-988867  
                 rpmA 
                   
                 50S ribosomal protein L27 
                 1703 
               
               
                 C 988888-989199  
                 rplU 
                   
                 50S ribosomal protein L21 
                 1704 
               
               
                 989412-990401 
                 ispB 
                   
                 octaprenyl-diphosphate synthase 
                 1705 
               
               
                 990452-991189 
                 — 
                   
                 conserved hypothetical protein 
                 1706 
               
               
                 C 991249-992619  
                 — 
                   
                 predicted Na+/alanine symporter 
                 1707 
               
               
                 C 993019-993729  
                 arcA 
                   
                 aerobic respiration control protein ArcA 
                 1708 
               
               
                 993921-995660 
                 dsbD 
                   
                 thiol:disulfide interchange protein DsbD 
                 1709 
               
               
                 995777-996181 
                 — 
                   
                 predicted membrane protein 
                 1710 
               
               
                 996370-997968 
                 purH 
                   
                 bifunctional purine biosynthesis protein PurH 
                 1711 
               
               
                 998064-999353 
                 purD 
                   
                 phosphonbosylamine--glycine ligase 
                 1712 
               
               
                  999509-1001076 
                 — 
                 ✓ 
                 pseudogene for predicted membrane-associated, 
                 1713 
               
               
                   
                   
                   
                 metal-dependent hydrolase 
               
               
                 1001199-1002464 
                 glyA 
                   
                 serine hydroxymethyltransferase 
                 1714 
               
               
                 1002523-1003155 
                 coaE 
                   
                 dephospho-CoA kinase 
                 1715 
               
               
                 1003148-1003354 
                 — 
                   
                 conserved hypothetical zinc-binding protein 
                 1716 
               
               
                 1003463-1004719 
                 rh1B 
                   
                 ATP-dependent RNA helicase Rh1B 
                 1717 
               
               
                 1004961-1005524 
                 — 
                   
                 hypothetical transcriptional regulator 
                 1718 
               
               
                 1005556-1006752 
                 — 
                   
                 predicted membrane-fusion protein 
                 1719 
               
               
                 1006752-1009850 
                 — 
                   
                 predicted cation/multidrug efflux pump 
                 1720 
               
               
                 1010385-1010855 
                 — 
                   
                 predicted cell division protein 
                 1721 
               
               
                 C 1010868-1012400  
                 emrB 
                   
                 multidrug resistance protein 
                 1722 
               
               
                 C 1012410-1013582  
                 emrA 
                   
                 multidrug resistance protein A 
                 1723 
               
               
                 C 1013755-1014237  
                 folA 
                   
                 dihydrofolate reductase 
                 1724 
               
               
                 1014339-1015445 
                 proB 
                   
                 glutamate 5-kinase 
                 1725 
               
               
                 1015526-1016116 
                 nudH 
                   
                 probable nucleoside polyphosphate hydrolase 
                 1726 
               
               
                 1016116-1016910 
                 — 
                   
                 predicted permease 
                 1727 
               
               
                 1016919-1017725 
                 lgt 
                   
                 prolipoprotein diacylglyceryl transferase 
                 1728 
               
               
                 1017735-1018586 
                 thyA 
                   
                 thymidylate synthase 
                 1729 
               
               
                 1018586-1019107 
                 — 
                   
                 conserved hypothetical protein 
                 1730 
               
               
                 C 1019135-1019449  
                 — 
                   
                 conserved hypothetical protein 
                 1731 
               
               
                 1019520-1019831 
                 — 
                   
                 conserved hypothetical protein 
                 1732 
               
               
                 1019956-1022661 
                 secA 
                   
                 preprotein translocase SecA subunit 
                 1733 
               
               
                 1022726-1023136 
                 mutT 
                   
                 mutator protein MutT 
                 1734 
               
               
                 1023245-1025101 
                 kefB 
                   
                 glutathione-regulated potassium-efflux system 
                 1735 
               
               
                   
                   
                   
                 protein 
               
               
                 1025202-1025966 
                 — 
                   
                 conserved hypothetical SAM-dependent 
                 1736 
               
               
                   
                   
                   
                 methtransferase 
               
               
                 1026111-1026866 
                 rpsB 
                   
                 30S ribosomal protein S2 
                 1737 
               
               
                 1027000-1027851 
                 tsf 
                   
                 elongation factor Ts 
                 1738 
               
               
                 C 1028031-1029056  
                 lpxD 
                   
                 UDP-3-O-[3-hydroxymyristoyl] glucosamine 
                 1739 
               
               
                   
                   
                   
                 N-acyltransferase 
               
               
                 C 1029069-1029662  
                 omp26 
                   
                 outer membrane protein 26 
                 1740 
               
               
                 C 1029770-1032172  
                 — 
                   
                 protective surface antigen D15 
                 1741 
               
               
                 C 1032192-1033523  
                 — 
                   
                 predicted membrane bound zinc 
                 1742 
               
               
                   
                   
                   
                 matalloprotease with PDZ domain 
               
               
                 C 1033533-1034399  
                 cdsA 
                   
                 phosphaatidate cytidylyltransferase 
                 1743 
               
               
                 C 1034417-1035136  
                 uppS 
                   
                 undecaprenyl pyrophosphate synthetase 
                 1744 
               
               
                 1035385-1037970 
                 leuS 
                   
                 leucyl-tRNA synthetase 
                 1745 
               
               
                 1038020-1038568 
                 — 
                   
                 conserved predicted lipoprotein 
                 1746 
               
               
                 1038568-1039602 
                 holA 
                   
                 DNA polymerase III, delta subunit 
                 1747 
               
               
                 C 1039836-1042004  
                 glyS 
                   
                 glycyl-tRNA synthetase beta chain 
                 1748 
               
               
                 C 1042050-1042466  
                 — 
                 ✓ 
                 hypothetical protein 
                 1749 
               
               
                 C 1042606-1042971  
                 — 
                   
                 conserved hypothetical protein 
                 1750 
               
               
                 C 1043001-1043261  
                 — 
                   
                 glutaredoxin-related protein 
                 1751 
               
               
                 C 1043320-1044228  
                 glyQ 
                   
                 glycyl-tRNA synthetase alpha chain 
                 1752 
               
               
                 1044491-1046017 
                 hktE 
                   
                 catalase 
                 1753 
               
               
                 C 1046249-1047430  
                 — 
                   
                 predicted glutathionylspermidine synthase 
                 1754 
               
               
                 C 1047431-1048012  
                 — 
                   
                 conserved hypothetical protein 
                 1755 
               
               
                 C 1048025-1048477  
                 — 
                   
                 conserved hypothetical protein 
                 1756 
               
               
                 C 1048528-1049838  
                 eno 
                   
                 enolase 
                 1757 
               
               
                 C 1049959-1051164  
                 — 
                   
                 conserved hypothetical protein 
                 1758 
               
               
                 C 1051161-1052303  
                 nrfF 
                   
                 formate-dependent nitrite reductase complex 
                 1759 
               
               
                   
                   
                   
                 nrfFG subunit 
               
               
                 C 1052300-1052830  
                 dsbE2 
                   
                 probable thiol:disulfide interchange protein 
                 1760 
               
               
                   
                   
                   
                 DsbE 
               
               
                 C 1052830-1054737  
                 nrfE 
                   
                 cytochrome c-type biogenesis protein NrfE 
                 1761 
               
               
                 C 1054846-1055658  
                 suhB 
                   
                 inositol-1-monophosphatase 
                 1762 
               
               
                 1055858-1056370 
                 — 
                   
                 conserved hypothetical protein 
                 1763 
               
               
                 1056370-1057089 
                 — 
                   
                 predicted Type II secretory pathway, PulJ- 
                 1764 
               
               
                   
                   
                   
                 like protein 
               
               
                 1057086-1057769 
                 — 
                   
                 conserved hypothetical protein 
                 1765 
               
               
                 1057774-1058049 
                 — 
                   
                 conserved hypothetical protein 
                 1766 
               
               
                 1058095-1061460 
                 — 
                   
                 exodeoxyribonuclease V gamma chain 
                 1767 
               
               
                 1061515-1061964 
                 — 
                   
                 predicted transcriptional regulator 
                 1768 
               
               
                 1061967-1063085 
                 ribD 
                   
                 riboflavin biosynthesis protein RibD 
                 1769 
               
               
                 11063086-1064108  
                 degS 
                   
                 protease DegS 
                 1770 
               
               
                 C 1064182-1064997  
                 mutM 
                   
                 formamidopyrimidine-DNA glycosylase 
                 1771 
               
               
                 C 1065229-1066764  
                 ddc 
                   
                 L-2,4-diaminobutyrate decarboxylase 
                 1772 
               
               
                 C 1066784-1067182  
                 — 
                   
                 predicted nucleic acid-binding protein, contains 
                 1773 
               
               
                   
                   
                   
                 PIN domain 
               
               
                 C 1067182-1067415  
                 — 
                   
                 conserved hypothetical protein 
                 1774 
               
               
                 C 1067562-1068926  
                 dat 
                   
                 diaminobutyrate--2-oxoglutarate 
                 1775 
               
               
                   
                   
                   
                 aminotransferase 
               
               
                 C 1069273-1069443  
                 rpmG 
                   
                 50S ribosomal protein L33 
                 1776 
               
               
                 C 1069455-1069691  
                 rpmB 
                   
                 50S ribosomal protein L28 
                 1777 
               
               
                 C 1069905-1070609  
                 radC 
                   
                 DNA repair protein Radc homolog 
                 1778 
               
               
                 1070733-1071935 
                 dfp 
                   
                 phosphopantothenoylcysteine synthetase/ 
                 1779 
               
               
                   
                   
                   
                 decarboxylase 
               
               
                 1071983-1072438 
                 dut 
                   
                 deoxyuridine 5′triphosphate 
                 1780 
               
               
                   
                   
                   
                 nucleotidohydrolase 
               
               
                 1072442-1073098 
                 ttk 
                   
                 ttk 
                 1781 
               
               
                 1073120-1073371 
                 — 
                   
                 hypothetical protein 
                 1782 
               
               
                 1073356-1074030 
                 crp 
                   
                 catabolite gene activator 
                 1783 
               
               
                 C 1074395-1075573  
                 — 
                   
                 hypothetical RNA methyltransferase 
                 1784 
               
               
                 C 1075566-1076621  
                 nagZ 
                   
                 beta-hexosaminidase 
                 1785 
               
               
                 C 1076625-1076975  
                 — 
                   
                 predicted periplasmic lipoprotein 
                 1786 
               
               
                 C 1076975-1077367  
                 — 
                   
                 HIT-like protein 
                 1787 
               
               
                 C 1077442-1080267  
                 ileS 
                   
                 isoleucyl-tRNA synthetase 
                 1788 
               
               
                 C 1080296-1081234  
                 ribF 
                   
                 riboflavin biosynthesis protein RibF 
                 1789 
               
               
                 C 1081269-1082801  
                 mviN 
                   
                 putative virulence factor MviN 
                 1790 
               
               
                 1083104-1083373 
                 rpsT 
                   
                 30S ribosomal protein S20 
                 1791 
               
               
                 C 1083445-1084011  
                 — 
                   
                 conserved hypothetical protein 
                 1792 
               
               
                 1084157-1085014 
                 menB 
                   
                 naphthoate synthase 
                 1793 
               
               
                 1085184-1086173 
                 menC 
                   
                 O-succinylbenzoate synthase 
                 1794 
               
               
                 1086230-1086679 
                 aroQ 
                   
                 3-dehydroquinate dehydratase 
                 1795 
               
               
                 1086833-1087300 
                 accB 
                   
                 biotin carboxyl carrier protein of acetyl-CoA 
                 1796 
               
               
                   
                   
                   
                 carboxylase 
               
               
                 1087477-1088823 
                 accC 
                   
                 biotin carboxylase 
                 1797 
               
               
                 1089028-1089285 
                 — 
                   
                 conserved hypothetical membrane protein 
                 1798 
               
               
                 1089282-1090736 
                 panF 
                   
                 sodium/pantothenase symporter 
                 1799 
               
               
                 1090857-1091729 
                 — 
                   
                 conserved hypothetical protein 
                 1800 
               
               
                 1091764-1092651 
                 prmA 
                   
                 ribosomal protein L11 methyltransferase 
                 1801 
               
               
                 1092798-1093778 
                 dusB 
                   
                 tRNA-dihydrouridine synthase B 
                 1802 
               
               
                 1093772-1094071 
                 fis 
                   
                 DNA-binding protein fis 
                 1803 
               
               
                 C 1094172-1094657  
                 smpB 
                   
                 SsrA-binding protein 
                 1804 
               
               
                 C 1094896-1095861  
                 pfkA 
                   
                 6-phosphfructokinase 
                 1805 
               
               
                 C 1095957-1096538  
                 — 
                   
                 conserved hypothetical protein 
                 1806 
               
               
                 C 1096531-1097382  
                 — 
                   
                 conserved hypothetical protein 
                 1807 
               
               
                 C 1097360-1098481  
                 smf 
                   
                 smf 
                 1808 
               
               
                 1099025-1100572 
                 leuA 
                   
                 2-isopropylmalate synthase 
                 1809 
               
               
                 1100735-1101811 
                 leuB 
                   
                 3-isopropylmalate dehydrogenase 
                 1810 
               
               
                 1101988-1103397 
                 leuC 
                   
                 3-isopropylmalate dehydratase large subunit 
                 1811 
               
               
                 1103422-1104024 
                 leuD 
                   
                 3-isopropylmalate dehydratase small subunit 
                 1812 
               
               
                 C 1104138-1109522  
                 Iga1 
                 ✓ 
                 IgA-specific serine endopeptidase 
                 1813 
               
               
                 C 1109749-1110828  
                 recF 
                   
                 DNA replication and repair protein RecF 
                 1814 
               
               
                 C 1110830-1111930  
                 dnaN 
                   
                 DNA polymerase III, beta chain 
                 1815 
               
               
                 C 1112123-1113487  
                 dnaA 
                   
                 chromosomal replication initiator protein DnaA 
                 1816 
               
               
                 C 1113674-1116412  
                 tbp1 
                   
                 transferrin-binding protein 1 
                 1817 
               
               
                 C 1116457-1118349  
                 tbp2 
                   
                 transferrin-binding protein 2 
                 1818 
               
               
                 1118446-1119906 
                 — 
                   
                 conserved hypothetical protein 
                 1819 
               
               
                 1120082-1120216 
                 rpmH 
                   
                 50S ribosomal protain L34 
                 1820 
               
               
                 1120229-1120588 
                 rnpA 
                   
                 ribonuclease P protein component 
                 1821 
               
               
                 1120552-1120812 
                 — 
                   
                 conserved hypothetical protein 
                 1822 
               
               
                 1120812-1122437 
                 yidC 
                   
                 proprotein translocase subunit YidC 
                 1823 
               
               
                 1123308-1124666 
                 trmE 
                   
                 probable tRNA moficiation GTPase TrmE 
                 1824 
               
               
                 1124855-1126723 
                 ppiD 
                   
                 peptidyl-prolyl cis-trans isomerase D 
                 1825 
               
               
                 1126811-1128370 
                 — 
                   
                 predicted PR--lipooligosaccharide 
                 1826 
               
               
                   
                   
                   
                 phosphorylethanolamine transferase 
               
               
                 1128440-1128955 
                 lspA 
                   
                 lipoprotein signal peptidase 
                 1827 
               
               
                 1128952-1129896 
                 ispH 
                   
                 4-hydroxy-3-methylbut-2-enyl diphosphate 
                 1828 
               
               
                   
                   
                   
                 reductase 
               
               
                 1130065-1130412 
                 — 
                   
                 conserved hypothetical protein 
                 1829 
               
               
                 1130659-1131657 
                 tbpA 
                   
                 thiamine-binding periplasmic protein 
                 1830 
               
               
                 1131662-1133278 
                 thiP 
                   
                 thiamine transport system permease protein 
                 1831 
               
               
                 1133256-1133909 
                 thiQ 
                   
                 thiamine transport ATP-binding protein 
                 1832 
               
               
                 1134022-1135023 
                 bioB 
                   
                 biotin synthase 
                 1833 
               
               
                 C 1135148-1137145  
                 tktA 
                   
                 transketolase 
                 1834 
               
               
                 1137526-1138470 
                 serB 
                   
                 phosphoserine phosphatase 
                 1835 
               
               
                 1138488-1138979 
                 — 
                   
                 conserved hypothetical protein 
                 1836 
               
               
                 1139275-1140222 
                 corA 
                   
                 magnesium and cobalt transport protein CorA 
                 1837 
               
               
                 1140213-1140767 
                 — 
                   
                 predicted integral membrane protein 
                 1838 
               
               
                 C 1140947-1141831  
                 — 
                   
                 predicted glutamine amidotransferase 
                 1839 
               
               
                 C 1141988-1142515  
                 — 
                 ✓ 
                 hypothetical protein 
                 1840 
               
               
                 1142645-1143847 
                 — 
                   
                 predicted ATPase 
                 1841 
               
               
                 C 1144037-1145386  
                 — 
                 ✓ 
                 hypothetical protein 
                 1842 
               
               
                 C 1145854-1146354  
                 — 
                   
                 predicted ferredoxin 
                 1843 
               
               
                 C 1146354-1146964  
                 — 
                   
                 conserved hypothetical protein 
                 1844 
               
               
                 C 1147077-1147916  
                 dmsC 
                   
                 anaerobic dimethyl sulfoxide reductase chain C 
                 1845 
               
               
                 C 1147918-1148535  
                 dmsB 
                   
                 anaerobic dimenthyl sulfoxide reductase chain B 
                 1846 
               
               
                 C 1148546-1150966  
                 dmaA 
                   
                 anaerobic dimethyl sulfoxide reductase chain A 
                 1847 
               
               
                 1151219-1152328 
                 — 
                   
                 conserved hypothetical protein 
                 1848 
               
               
                 1152372-1152665 
                 — 
                   
                 putative mercuric transport MerT homolog 
                 1849 
               
               
                 1152674-1152952 
                 — 
                   
                 predicted copper chaperone MerP homolog 
                 1850 
               
               
                 C 1153077-1154921  
                 — 
                   
                 conserved hypothetical ABC transporter 
                 1851 
               
               
                 C 1155000-1155896  
                 — 
                   
                 conserved hypothetical transcriptional regulator 
                 1852 
               
               
                 1156008-1156349 
                 — 
                   
                 conserved putative gamma-carboxy- 
                 1853 
               
               
                   
                   
                   
                 muconolactone decarboxylase subunit 
               
               
                 C 1156460-1157056  
                 — 
                   
                 conserved hypothetical protein 
                 1854 
               
               
                 C 1157062-1159227  
                 res 
                   
                 putative type III restriction-modification sustem 
                 1855 
               
               
                   
                   
                   
                 HindVIP enzyme res 
               
               
                 C 1159217-1161318  
                 mod 
                 ✓ 
                 pseudogene for putative type III restriction- 
                 1856 
               
               
                   
                   
                   
                 modification system HibdVIP enzyme mod 
               
               
                 C 1161534-1162127  
                 rnhB 
                   
                 ribonuclease HII 
                 1857 
               
               
                 C 1162120-1163292  
                 lpxB 
                   
                 lipid-A-disaccharide synthase 
                 1858 
               
               
                 C 1163359-1164147  
                 lpxA 
                   
                 acyl0[acyl-carrier-protein]--UDP-N- 
                 1859 
               
               
                   
                   
                   
                 acetylglucosamine O-Acyltransferase 
               
               
                 C 1164161-1164607  
                 fabZ 
                   
                 (3R)-hydroxymyristoyl-[acyl carrier protein] 
                 1860 
               
               
                   
                   
                   
                 dehydratase 
               
               
                 C 1164683-1166290  
                 — 
                   
                 predicted PR--lipooligosaccharide 
                 1861 
               
               
                   
                   
                   
                 phosphorylethanolamine transferase 
               
               
                 1166383-1167096 
                 pyrH 
                   
                 uridylate kinase 
                 1862 
               
               
                 C 1167335-1168300  
                 nrfD 
                   
                 NrfD, formate-dependent nitrite reductase, 
                 1863 
               
               
                   
                   
                   
                 membrane component 
               
               
                 C 1168297-1168974  
                 nrfC 
                   
                 NrfC, Fe—S-cluster-containing hydrogenase 
                 1864 
               
               
                   
                   
                   
                 component 1 
               
               
                 1168971-1169654 
                 nrfB 
                   
                 NrfB, cytochrome C-type protein 
                 1865 
               
               
                 C 1169698-1171314  
                 nrfA 
                   
                 cytochrome c552 
                 1866 
               
               
                 C 1171476-1175384  
                 hrpA 
                   
                 ATP-dependent helicase HrpA homolog 
                 1867 
               
               
                 C 1175381-1175755  
                 — 
                   
                 conserved putative small membrane protein 
                 1868 
               
               
                 C 1175756-1176208  
                 — 
                   
                 conserved putative membrane protein 
                 1869 
               
               
                 C 1176474-1177610  
                 cyoB 
                   
                 probable cyrochrome oxidase subunit II 
                 1870 
               
               
                 C 1177625-1179190  
                 cyoA 
                   
                 probable cytochrome oxidase dubunit I 
                 1871 
               
               
                 1179843-1181480 
                 pyrG 
                   
                 CTP synthase 
                 1872 
               
               
                 C 1181625-1182305  
                 pnuC 
                   
                 nictinamide riboside transporter 
                 1873 
               
               
                 C 1182487-1183260  
                 — 
                   
                 probable amino-acid ABC transporter 
                 1874 
               
               
                   
                   
                   
                 ATP-binding protein 
               
               
                 C 1183264-1183941  
                 — 
                   
                 probable amino-acid ABC transporter 
                 1875 
               
               
                   
                   
                   
                 permease protein 
               
               
                 C 1183964-1184737  
                 — 
                   
                 probable amino-acid ABC transporter 
                 1876 
               
               
                   
                   
                   
                 binding protein 
               
               
                 C 1185038-1186312  
                 murA 
                   
                 UDP-N-acetylglucosamine a-carboxy- 
                 1877 
               
               
                   
                   
                   
                 vinyltransferase 
               
               
                 C 1186323-1186580  
                 — 
                   
                 predicted transcriptional regulator, BolA 
                 1878 
               
               
                   
                   
                   
                 superfamily 
               
               
                 C 1186601-1186918  
                 — 
                   
                 predicted NTP binding protein, contains 
                 1879 
               
               
                   
                   
                   
                 STAS domain 
               
               
                 C 1186929-1187573  
                 — 
                   
                 conserved ABC-type transport system protein 
                 1880 
               
               
                 C 1187606-1188106  
                 — 
                   
                 conserved ABC-type transport system protein, 
                 1881 
               
               
                   
                   
                   
                 periplasmic component 
               
               
                 C 1188116-1188901  
                 — 
                   
                 conserved ABC-type transport system protein, 
                 1882 
               
               
                   
                   
                   
                 permease component 
               
               
                 C 1188898-1189692  
                 — 
                   
                 conserved ABC-type transport system protein, 
                 1883 
               
               
                   
                   
                   
                 ATPase component 
               
               
                 C 1190098-1190745  
                 sodA 
                   
                 superoxide dismutase [Mn] 
                 1884 
               
               
                 1190994-1191632 
                 ccmA 
                   
                 heme exporter protein A 
                 1885 
               
               
                 1191637-1192302 
                 ccmB 
                   
                 heme exporter protein B 
                 1886 
               
               
                 1192363-1193103 
                 ccmC 
                   
                 heme exporter protein C 
                 1887 
               
               
                 1193146-1193349 
                 ccmD 
                   
                 heme exporter protein D 
                 1888 
               
               
                 1193346-1193867 
                 ccmE 
                   
                 cytochrome c-type biogenesis protein CcmE 
                 1889 
               
               
                 1193864-1195813 
                 ccmF 
                   
                 cytochrome c-type biogenesis protein CcmF 
                 1890 
               
               
                 1195953-1196498 
                 dsbE 
                   
                 thiol:disulfide interchange protein DsbE 
                 1891 
               
               
                 1196498-1197877 
                 ccmH 
                   
                 pseudogene for cytochrome c-type biogenesis 
                 1892 
               
               
                   
                   
                   
                 protein CcmH precursor 
               
               
                 1197998-1198489 
                 — 
                   
                 hypothetical protein 
                 1893 
               
               
                 1198491-1198799 
                 — 
                   
                 conserved hypothetical protein 
                 1894 
               
               
                 C 1198804-1200843  
                 ligN 
                   
                 DNA ligase 
                 1895 
               
               
                 C 1200928-1201914  
                 zipA 
                   
                 cell division protein ZipA 
                 1896 
               
               
                 1202067-1202885 
                 cysZ 
                   
                 CysZ 
                 1897 
               
               
                 1202894-1203934 
                 cysK 
                   
                 cysteine synthase 
                 1898 
               
               
                 1204182-1205406 
                 — 
                   
                 pseudogene for conserved hypothetical 
                 1899 
               
               
                   
                   
                   
                 metabolite transport protein 
               
               
                 C 1205515-1206555  
                 rfaF 
                   
                 ADP-heptose--lipooligosaccharide 
                 1900 
               
               
                   
                   
                   
                 heptosyltransferase II 
               
               
                 C 1206631-1207794  
                 xylR 
                   
                 xylose operon refulatory protein 
                 1901 
               
               
                 C 1207906-1209312  
                 — 
                   
                 conserved hypothetical Na(+)/H(+) antiporter 
                 1902 
               
               
                 C 1209314-1210486  
                 aspC2 
                   
                 putative aspartate aminotransferase 
                 1903 
               
               
                 1210699-1212018 
                 xylA 
                   
                 xylose isomerase 
                 1904 
               
               
                 1212021-1213556 
                 xylB 
                   
                 xylulose kinase 
                 1905 
               
               
                 C 1213607-1214533  
                 rfaD 
                   
                 ADP-L-glycero-D-manno-heptose-6-epimerase 
                 1906 
               
               
                 C 1214586-1215089  
                 — 
                   
                 thioredoxin-like protein 
                 1907 
               
               
                 1215200-1215871 
                 deoC 
                   
                 deoxyribose-phosphate aldolase 
                 1908 
               
               
                 C 1215905-1217434  
                 comM 
                   
                 competence protein ComM 
                 1909 
               
               
                 C 1217549-1218166  
                 engB 
                   
                 Probable GTP-binding protein EngB 
                 1910 
               
               
                 1218259-1219137 
                 — 
                   
                 D-xylose transport permease protein 
                 1911 
               
               
                 C 1219177-1220175  
                 oppF 
                   
                 oligopeptide transport ATP-binsing protein 
                 1912 
               
               
                 C 1220172-1221143  
                 oppD 
                   
                 oligopeptide transport ATP-binding protein 
                 1913 
               
               
                 C 1221153-1222088  
                 oppC 
                   
                 oligopeptide transport system permease protein 
                 1914 
               
               
                 C 1222098-1223018  
                 oppB 
                   
                 oligopeptide transport system permease protein 
                 1915 
               
               
                 C 1223099-1224724  
                 oppA 
                   
                 periplasmic oligopeptide-binding protein 
                 1916 
               
               
                 1225019-1225972 
                 talB 
                   
                 Transaldolase 
                 1917 
               
               
                 1227033-1228634 
                 — 
                   
                 carbon starvation protein, predicted membrane 
                 1918 
               
               
                   
                   
                   
                 protein 
               
               
                 1228836-1229291 
                 mraZ 
                   
                 MraZ 
                 1919 
               
               
                 1229322-1230287 
                 mraW 
                   
                 predicted S-adenosylmethionine-dependent 
                 1920 
               
               
                   
                   
                   
                 methyltransferase involved in cell envelope 
               
               
                   
                   
                   
                 biogenesis 
               
               
                 1230290-1230613 
                 ftsL 
                   
                 cell division protein FtsL 
                 1921 
               
               
                 1230626-1232458 
                 ftsI 
                   
                 peptidoglycan synthetase FtsI 
                 1922 
               
               
                 1232468-1233934 
                 murE 
                   
                 UDP-N-acetylmuramoylalanyl-D-glutamate-- 
                 1923 
               
               
                   
                   
                   
                 2,6-diaminopimelate ligase 
               
               
                 1233948-1235321 
                 murF 
                   
                 UDP-N-acetylmuramoyl-tripeptide--D-alanyl- 
                 1924 
               
               
                   
                   
                   
                 D-alanine ligase 
               
               
                 1235315-1236397 
                 mraY 
                   
                 phospho-N-acetylmuramoyl-pentapeptide- 
                 1925 
               
               
                   
                   
                   
                 transferase 
               
               
                 1236509-1237822 
                 murD 
                   
                 UDP-N-acetylmuramoylaalanine--D-glutamate 
                 1926 
               
               
                   
                   
                   
                 ligase 
               
               
                 1237845-1239029 
                 ftsW 
                   
                 cell division protein FtsW 
                 1927 
               
               
                 1239041-1240096 
                 murG 
                   
                 UDP-N-acetylglucosamine--N- 
                 1928 
               
               
                   
                   
                   
                 acetylmuramylpyrophosphoryl-undecaprenol 
               
               
                   
                   
                   
                 N-acetylglucosamine transferase 
               
               
                 1240234-1241661 
                 murC 
                   
                 UDP-N-acetylmuramate--L-alanine ligase 
                 1929 
               
               
                 1241730-1242650 
                 ddlB 
                   
                 D-alanine--D-alanine ligase 
                 1930 
               
               
                 1242650-1243414 
                 ftsQ 
                   
                 cell division protein FtsQ 
                 1931 
               
               
                 1243433-1244710 
                 ftsA 
                   
                 cell division protein FtsA 
                 1932 
               
               
                 1244794-1246059 
                 ftsZ 
                   
                 cell division protein FtsZ 
                 1933 
               
               
                 1246098-1247015 
                 lpxC 
                   
                 UDP-3-O-[3-hydroxymyristoyl] N- 
                 1934 
               
               
                   
                   
                   
                 acetylglucosamine deacetylase 
               
               
                 1247142-1248299 
                 pheA 
                   
                 P-protein 
                 1935 
               
               
                 C 1248344-1249201  
                 — 
                   
                 predicted P-loop-containing kinase 
                 1936 
               
               
                 C 1249219-1249713  
                 ptsN 
                   
                 nitrogen regulatory IIA protein 
                 1937 
               
               
                 C 1249716-1250441  
                 — 
                   
                 probable ABC transporter ATP-binding protein 
                 1938 
               
               
                 C 1250445-1250963  
                 — 
                   
                 conserved hypothetical protein 
                 1939 
               
               
                 C 1250944-1251552  
                 — 
                   
                 conserved hypothetical protein 
                 1940 
               
               
                 C 1251602-1252138  
                 — 
                   
                 conserved hypothetical protein 
                 1941 
               
               
                 1252227-1253582 
                 pmbA 
                   
                 pmbA 
                 1942 
               
               
                 1253957-1254496 
                 hpt 
                   
                 hypoxanthine phosphoribosyltransferase 
                 1943 
               
               
                 1254802-1256124 
                 — 
                   
                 predicted Na+/dicarboxylate symporter 
                 1944 
               
               
                 C 1256224-1256691  
                 nrdG 
                   
                 anaerobic ribonucleoside-triphosphate 
                 1945 
               
               
                   
                   
                   
                 reductase activating protein 
               
               
                 C 1256939-1258669  
                 cydC 
                   
                 transport ATP-binding protein CydC 
                 1946 
               
               
                 C 1258669-1260429  
                 cydD 
                   
                 transport ATP binding protein CydD 
                 1947 
               
               
                 C 1260501-1261457  
                 trxB 
                   
                 thioredoxin reductase 
                 1948 
               
               
                 C 1261531-1262388  
                 — 
                   
                 thioredoxin domain-containing protein 
                 1949 
               
               
                 C 1262467-1263438  
                 hemH 
                   
                 ferrochelatase 
                 1950 
               
               
                 C 1263435-1263851  
                 — 
                   
                 conserved hypothetical protein 
                 1951 
               
               
                 C 1263865-1266948  
                 — 
                   
                 conserved FAD/FMN-containing 
                 1952 
               
               
                   
                   
                   
                 dehydrogenase 
               
               
                 1267323-1268402 
                 ompP5 
                   
                 outer membrane protein P5 
                 1953 
               
               
                 1268514-1268876 
                 — 
                   
                 conserved glutaredoxin-related protein 
                 1954 
               
               
                 C 1268953-1270053  
                 — 
                   
                 histidinol-phosphate aminotransferase 2 
                 1955 
               
               
                 C 1270141-1271229  
                 serC 
                   
                 phosphoserine aminotransferase 
                 1956 
               
               
                 1271420-1271764 
                 — 
                   
                 conserved hypothetical protein 
                 1957 
               
               
                 C 1271804-1272370  
                 — 
                   
                 conserved hypothetical protein 
                 1958 
               
               
                 C 1272370-1273356  
                 — 
                   
                 conserved hypothetical protein 
                 1959 
               
               
                 1273398-1273979 
                 trpG2 
                   
                 putative anthranilate synthase component II 
                 1960 
               
               
                 1274064-1275218 
                 metK 
                   
                 S-adenosylmethionine synthetase 
                 1961 
               
               
                 1275513-1276028 
                 sprT 
                   
                 SprT 
                 1962 
               
               
                 1276079-1276591 
                 opa 
                   
                 opacity protein 
                 1963 
               
               
                 C 1276627-1276932  
                 — 
                   
                 conserved hypothetical protein 
                 1964 
               
               
                 C 1277139-1277822  
                 artM 
                   
                 arginine transport system permease protein 
                 1965 
               
               
                 C 1277822-1278487  
                 artQ 
                   
                 arginine transport system permease protein 
                 1966 
               
               
                 C 1278491-1279210  
                 artI 
                   
                 arginine-binding periplasmic protein 
                 1967 
               
               
                 C 1279228-1279959  
                 artP 
                   
                 arginine transport ATP-binding protein 
                 1968 
               
               
                 C 1280085-1280069  
                 gmhA 
                   
                 phosphoheptose isomerase 
                 1969 
               
               
                 1280769-1281683 
                 ligA 
                   
                 DNA ligase 
                 1970 
               
               
                 C 1281712-1282695  
                 dppF 
                   
                 dipeptide transport ATP binding protein 
                 1971 
               
               
                 C 1282698-1283690  
                 dppD 
                   
                 dipeptide transport ATP binding protein 
                 1972 
               
               
                 C 1283700-1284587  
                 dppC 
                   
                 dipeptide transport system permease protein 
                 1973 
               
               
                 C 1284602-1285603  
                 dppB 
                   
                 dipeptide transport system permease protein 
                 1974 
               
               
                 C 1285693-1287876  
                 uvrD 
                   
                 DNA helicase II 
                 1975 
               
               
                 C 1288483-1289118  
                 — 
                   
                 predicted organic radical activating enzyme 
                 1976 
               
               
                 C 1289119-1289544  
                 — 
                   
                 predicted 6-pyruval-tetrahydropterin synthase 
                 1977 
               
               
                 C 1289537-1290220  
                 — 
                   
                 predicted PP-loop superfamily ATPase 
                 1978 
               
               
                 1290376-1290519 
                 — 
                   
                 conserved hypothetical protein 
                 1979 
               
               
                 C 1290570-1291601  
                 ilvE 
                   
                 branched chain amino acid amino transferase 
                 1980 
               
               
                 1292076-1292969 
                 gcvA 
                   
                 glycine cleavage system transcriptional 
                 1981 
               
               
                   
                   
                   
                 activator 
               
               
                 1292962-1294053 
                 — 
                   
                 predicted SAM-dependent methyltransferase 
                 1982 
               
               
                 1294089-1295258 
                 sucC 
                   
                 succinyl-CoA synthetase beta chain 
                 1983 
               
               
                 1295258-1296139 
                 sucD 
                   
                 succinyl-CoA synthetase alpha chain 
                 1984 
               
               
                 1296260-1296883 
                 — 
                   
                 putative translation factor, Sua5 
                 1985 
               
               
                 1296931-1289004 
                 rluB 
                   
                 ribosomal large subunit pseudouridine synthase B 
                 1986 
               
               
                 1298015-1298986 
                 cysB 
                   
                 HTH-type transcriptional regulator CysB 
                 1987 
               
               
                 C 1299045-1299989  
                 — 
                   
                 conserved hypothetical adenine-specific 
                 1988 
               
               
                   
                   
                   
                 methylase 
               
               
                 1300120-1300623 
                 — 
                   
                 conserved hypothetical protein 
                 1989 
               
               
                 C 1300701-1302836  
                 pta 
                   
                 phosphate acetyltransferase 
                 1990 
               
               
                 C 1302904-1304109  
                 ackA 
                   
                 acetate kinase 
                 1991 
               
               
                 1304326-1304769 
                 — 
                   
                 conserved hypothetical protein 
                 1992 
               
               
                 1304856-1305347 
                 cvpA 
                   
                 colicin C production protein 
                 1993 
               
               
                 1305358-1306875 
                 — 
                   
                 amidophosphoribosyltransferase 
                 1994 
               
               
                 C 1306940-1307830  
                 sulA 
                   
                 cell division inhibitor SulA 
                 1995 
               
               
                 C 1307830-1308285  
                 argR 
                   
                 argininr repressor 
                 1996 
               
               
                 1308492-1309427 
                 mdh 
                   
                 malate dehydrogenase 
                 1997 
               
               
                 C 1309514-1311022  
                 lysS 
                   
                 lysyl-tRNA synthetase 
                 1998 
               
               
                 C 1311134-1311985  
                 prfB 
                   
                 peptide chain release factor 2 
                 1999 
               
               
                 1312365-1313054 
                 dsbC 
                   
                 thiol:disulfide interchange protein DsbC 
                 2000 
               
               
                 1313342-1315069 
                 recJ 
                   
                 single stranded DNA specific exonuclease RecJ 
                 2001 
               
               
                 1315062-1315769 
                 — 
                   
                 conserved hypothetical protein 
                 2002 
               
               
                 1315766-1316458 
                 mtnA 
                   
                 MTA/SAH nucleosidase 
                 2003 
               
               
                 C 1316532-1319279  
                 hup 
                   
                 heme utilization protein 
                 2004 
               
               
                 C 1319579-1321177  
                 — 
                   
                 putative L-Lactate permease 
                 2005 
               
               
                 1321367-1321546 
                 — 
                   
                 pseudogene for ctidylate kinase 
                 2006 
               
               
                 C 1321581-1322585  
                 fbp 
                   
                 frustose-1,6-bisphosphatase 
                 2007 
               
               
                 1322820-1323629 
                 truA 
                   
                 tRNA pseudouridine synthase A 
                 2008 
               
               
                 C 1323722-1324738  
                 sapZ 
                   
                 Predicted membrane protein 
                 2009 
               
               
                 C 1324750-1325559  
                 sapF 
                   
                 ABC-type transport system, ATPase component 
                 2010 
               
               
                   
                   
                   
                 involved in antimicrobial peptide resistance 
               
               
                 C 1325559-1326608  
                 sapD 
                   
                 ABC-type transport system, ATP binding 
                 2011 
               
               
                   
                   
                   
                 component, involved in antimicrobial peptide 
               
               
                   
                   
                   
                 resistance 
               
               
                 C 1326612-1327499  
                 sapC 
                   
                 ABC-type transport system, permease protein, 
                 2012 
               
               
                   
                   
                   
                 involved in antimicrobial peptide resistance 
               
               
                 C 1327489-1328454  
                 sapB 
                   
                 ABC-type transport system, permease protein, 
                 2013 
               
               
                   
                   
                   
                 involved in antimicrobial peptide resistance 
               
               
                 C 1328454-1330148  
                 sapA 
                   
                 ABC-type transport system, periplasmic 
                 2014 
               
               
                   
                   
                   
                 component, involved in antimicrobial peptide 
               
               
                   
                   
                   
                 resistance 
               
               
                 1330218-1331630 
                 — 
                   
                 Predicted ATPase 
                 2015 
               
               
                 C 1331667-1334306  
                 Ppc 
                   
                 Phosphoenolpyruvate carboxylase 
                 2016 
               
               
                 C 1334489-1335499  
                 purR 
                   
                 HTH-type transcriptional repressor PurR 
                 2017 
               
               
                 1335796-1336689 
                 dapD 
                   
                 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate 
                 2018 
               
               
                   
                   
                   
                 N-succinyltransferase 
               
               
                 C 1336746-1338044  
                 PurA 
                   
                 adenylosuccinate synthetase 
                 2019 
               
               
                 C 1338173-1338538  
                 — 
                   
                 predicted aspartokinase 
                 2020 
               
               
                 C 1339386-1339673  
                 rplY 
                   
                 50S ribosomal protein L25 
                 2021 
               
               
                 1339841-1340497 
                 — 
                   
                 uncharacterized membrane-associate protein 
                 2022 
               
               
                 C 1340544-1340960  
                 — 
                   
                 conserved hypothetical protein 
                 2023 
               
               
                 C 1340991-1341341  
                 — 
                   
                 putative translation initiation inhibitor, YjgF 
                 2024 
               
               
                   
                   
                   
                 family 
               
               
                 1341453-1342169 
                 — 
                   
                 conserved hypothetical protein 
                 2025 
               
               
                 1342170-1342712 
                 — 
                   
                 conserved hypothetical protein 
                 2026 
               
               
                 C 1342727-1343185  
                 — 
                   
                 HTH-type trancriptional regulator 
                 2027 
               
               
                 1343224-1343907 
                 — 
                   
                 putative ABC-type Co2+ transport system, 
                 2028 
               
               
                   
                   
                   
                 periplasmic component 
               
               
                 1343920-1344408 
                 — 
                   
                 conserved hypothetical protein 
                 2029 
               
               
                 1344408-1345028 
                 cbiM 
                   
                 predicted ABC-type cobalt transport system, 
                 2030 
               
               
                   
                   
                   
                 permease component 
               
               
                 1345028-1345660 
                 — 
                   
                 predicted cobalt transport protein 
                 2031 
               
               
                 1345662-1346288 
                 cbiO 
                   
                 predicted ABC-type cobalt transport system, 
                 2032 
               
               
                   
                   
                   
                 ATPase component 
               
               
                 C 1346395-1347585  
                 aspC 
                   
                 aspartate aminotransferase 
                 2033 
               
               
                 1347725-1348813 
                 purK 
                   
                 phosphoribosylaminoimidazole carboxylase 
                 2034 
               
               
                   
                   
                   
                 ATPase subunit 
               
               
                 C 1348883-1349377  
                 purE 
                   
                 phosphoribosylaminoimidazole carboxylase 
                 2035 
               
               
                   
                   
                   
                 catalytic subunit 
               
               
                 1349548-1349796 
                 hicA 
                 ✓ 
                 HicA 
                 2036 
               
               
                 1349793-1350137 
                 hicB 
                 ✓ 
                 HicB 
                 2037 
               
               
                 1350181-1352790 
                 pepN 
                   
                 aminopeptidase N 
                 2038 
               
               
                 C 1352862-1353476  
                 ribE 
                   
                 riboflavin synthase alpha chain 
                 2039 
               
               
                 1353520-1354914 
                 norM 
                   
                 probable multidrug resistance protein NorM 
                 2040 
               
               
                 1354923-1355639 
                 sfsA 
                   
                 sugar fermentation stimulation protein 
                 2041 
               
               
                 1355839-1357026 
                 tyrS 
                   
                 tyrosyl-tRNA synthase 
                 2042 
               
               
                 C 1357090-1358037  
                 prsA 
                   
                 ribose phosphate pyrophosphokinase 
                 2043 
               
               
                 C 1358039-1358992  
                 ispE 
                   
                 4-diphosphocytidyl-2-C-methyl-D-erythritol 
                 2044 
               
               
                   
                   
                   
                 kinase 
               
               
                 C 1358992-1359621  
                 lolB 
                   
                 outer-membrane lipoprotein LolB 
                 2045 
               
               
                 C 1359684-1360934  
                 cca 
                   
                 tRNA nucleotidyltransferase 
                 2046 
               
               
                 C 1360941-1361552  
                 — 
                   
                 conserved hypothetical protein 
                 2047 
               
               
                 C 1361618-1362880  
                 — 
                   
                 putative phosphate permease 
                 2048 
               
               
                 C 1362905-1363585  
                 — 
                   
                 conserved hypothetical phosphate transport 
                 2049 
               
               
                   
                   
                   
                 regulator 
               
               
                 1363793-1364248 
                 — 
                   
                 predicted membrane protein 
                 2050 
               
               
                 1364287-1364574 
                 — 
                   
                 conserved hypothetical protein 
                 2051 
               
               
                 1364604-1365557 
                 — 
                   
                 conserved hypothetical protein 
                 2052 
               
               
                 1365547-1366263 
                 — 
                   
                 conserved hypothetical protein 
                 2053 
               
               
                 1367371-1367538 
                 — 
                 ✓ 
                 hypothetical protein 
                 2054 
               
               
                 1367936-1368052 
                 — 
                 ✓ 
                 hypothetical protein 
                 2055 
               
               
                 1368502 . . . 1368666 
                 — 
                 ✓ 
                 hypothetical protein 
                 2056 
               
               
                 C 1368856-1370808  
                 hmw2C 
                 ✓ 
                 HMW2C, putative glycosyltransferase involved 
                 2057 
               
               
                   
                   
                   
                 in glycosylation of HMW1A and HMW2A 
               
               
                 C 1371200-1372837  
                 hmw2B 
                 ✓ 
                 HMW2B, OMP-85-like protein required for 
                 2058 
               
               
                   
                   
                   
                 HMW1A and HMW2A secretion 
               
               
                 C 1372988-1377616  
                 — 
                 ✓ 
                 HMW2A, high molecular weight adhesin 2 
                 2059 
               
               
                   
                 hmw2A 
               
               
                 1378041-1379087 
                 — 
                   
                 conserved hypothetical protein 
                 2060 
               
               
                 1379320-1380696 
                 radA 
                   
                 DNA repair protein RadA homolog 
                 2061 
               
               
                 1380755-1381255 
                 lrp 
                   
                 leucine-responsive regulatory protein 
                 2062 
               
               
                 1381257-1384013 
                 ftsk 
                   
                 DNa translocase FtsK 
                 2063 
               
               
                 1384031-1384648 
                 lolA 
                   
                 outer-membrane lipoproteins carrier protein 
                 2064 
               
               
                   
                   
                   
                 precursor 
               
               
                 1384709-1386049 
                 — 
                   
                 predicted ATPase related to the helicase subunit 
                 2065 
               
               
                   
                   
                   
                 of the holliday junction resolvase 
               
               
                 C 1386137 . . . 1387279      
                 — 
                 ✓ 
                 hypothetical protein 
                 2066 
               
               
                 C 1387289-1388512  
                 — 
                 ✓ 
                 modification methylase BepI-like 
                 2067 
               
               
                 C 1388767-1390065  
                 aroA 
                   
                 3-phosphoshikimate 1-carboxyvinyltransferase 
                 2068 
               
               
                 C 1390065-1390901  
                 purU 
                   
                 formyltetrahydrofolate deformylase 
                 2069 
               
               
                 C 1390971-1391375  
                 hns 
                   
                 DNA-binding protein H-NS homolog 
                 2070 
               
               
                 1391779-1393338 
                 — 
                   
                 predicted Na+/H+ antiporter 
                 2071 
               
               
                 1393406-1393555 
                 — 
                   
                 hypothetical protein 
                 2072 
               
               
                 1393605-1395326 
                 ilvI 
                   
                 acetolactate synthase large subunit 
                 2073 
               
               
                 1395326-1395817 
                 ilvH 
                   
                 acetolactate synthase small subunit 
                 2074 
               
               
                 C 1396111-1397844  
                 argS 
                   
                 arginyl-tRNA synthetase 
                 2075 
               
               
                 1397924-1398493 
                 — 
                   
                 conserved hypothetical protein 
                 2076 
               
               
                 1398572-1398793 
                 — 
                   
                 hypothetical lipoprotein 
                 2077 
               
               
                 1399816-1399280 
                 pcp 
                   
                 outer-membrane lipoprotein PCP precursor 
                 2078 
               
               
                 C 1399464-1400435  
                 lgtD 
                   
                 UDP-0glcNAc-lipooligosaccharide N- 
                 2079 
               
               
                   
                   
                   
                 acetylglucosamine glycosyltransferase 
               
               
                 1400502 . . . 1400999 
                 — 
                   
                 pseudogene for IS1016-V6 protein homolog, 
                 2080 
               
               
                   
                   
                   
                 degenerate 
               
               
                 C 1401073-1402764  
                 pgi 
                   
                 glucose-6-phosphate isomerase 
                 2081 
               
               
                 C 1402819-1403901  
                 alr 
                   
                 alanine racemase 
                 2082 
               
               
                 C 1403911-1405425  
                 dnaB 
                   
                 replicative DNA helicase 
                 2083 
               
               
                 C 1405459-1406895  
                 pykA 
                   
                 pyruvate kinase 
                 2084 
               
               
                 1407432-1408691 
                 — 
                 ✓ 
                 prophage CP4-57-like integrase 
                 2085 
               
               
                 C 1409305-1409574  
                 — 
                 ✓ 
                 hypothetical protein 
                 2086 
               
               
                 C 1409679-1409849  
                 — 
                 ✓ 
                 hypothetical protein 
                 2087 
               
               
                 C 1409839-1410372  
                 — 
                 ✓ 
                 hypothetical protein 
                 2088 
               
               
                 C 1410444-1410860  
                 — 
                 ✓ 
                 hypothetical protein 
                 2089 
               
               
                 C 1410864-1411541  
                 — 
                 ✓ 
                 hypothetical protein 
                 2090 
               
               
                 C 1411560-1412723  
                 — 
                 ✓ 
                 modification methylase Bsp6I-like 
                 2091 
               
               
                 C 1413329-1414225  
                 rdgC 
                 ✓ 
                 recombination associated protein 
                 2092 
               
               
                 C 1414350-1415696  
                 — 
                 ✓ 
                 hypothetical protein 
                 2093 
               
               
                 C 1415758-1416192  
                 ssb3 
                 ✓ 
                 single strand binding protein 
                 2094 
               
               
                 C 1416192-1416836  
                 — 
                 ✓ 
                 hypothetical protein 
                 2095 
               
               
                 C 1416817-1417737  
                 — 
                 ✓ 
                 predicted recombinational DNA repair protein, 
                 2096 
               
               
                   
                   
                   
                 RecE pathway 
               
               
                 C 1417750-1418043  
                 — 
                 ✓ 
                 hypothetical protein 
                 2097 
               
               
                 C 1418040-1418384  
                 — 
                 ✓ 
                 hypothetical protein 
                 2098 
               
               
                 C 1418398-1419135  
                 — 
                 ✓ 
                 modification methylase DpnIIB-like 
                 2099 
               
               
                 C 1419226-1420257  
                 — 
                 ✓ 
                 hypothetical protein 
                 2100 
               
               
                 C 1420247-1420498  
                 — 
                 ✓ 
                 hypothetical protein 
                 2101 
               
               
                 C 1420617-1420928  
                 — 
                 ✓ 
                 hypothetical protein 
                 2102 
               
               
                 C 1421314-1421499  
                 — 
                 ✓ 
                 hypothetical protein 
                 2103 
               
               
                 C 1421660-1422808  
                 — 
                 ✓ 
                 hypothetical protein 
                 2104 
               
               
                 C 1422819-1423679  
                 — 
                 ✓ 
                 hypothetical protein 
                 2105 
               
               
                 C 1423742-1424107  
                 — 
                 ✓ 
                 hypothetical protein 
                 2106 
               
               
                 C 1424109-1424696  
                 — 
                 ✓ 
                 hypothetical protein 
                 2107 
               
               
                 1424852-1425037 
                 — 
                 ✓ 
                 hypothetical protein 
                 2108 
               
               
                 1425068-1425496 
                 — 
                 ✓ 
                 hypothetical protein 
                 2109 
               
               
                 C 1425497-1426006  
                 — 
                 ✓ 
                 hypothetical protein 
                 2110 
               
               
                 C 1426011-1426601  
                 — 
                 ✓ 
                 hypothetical protein 
                 2111 
               
               
                 C 1426598-1427233  
                 — 
                 ✓ 
                 hypothetical protein 
                 2112 
               
               
                 C 1427218-1428000  
                 — 
                 ✓ 
                 hypothetical protein 
                 2113 
               
               
                 C 1428002-1428235  
                 — 
                 ✓ 
                 hypothetical protein 
                 2114 
               
               
                 C 1428281-1428733  
                 — 
                 ✓ 
                 hypothetical protein 
                 2115 
               
               
                 C 1428777-1428983  
                 — 
                 ✓ 
                 hypothetical protein 
                 2116 
               
               
                 1429117-1430085 
                 — 
                 ✓ 
                 hypothetical protein 
                 2117 
               
               
                 1430279-1430605 
                 — 
                 ✓ 
                 hypothetical protein 
                 2118 
               
               
                 1430592-1430996 
                 — 
                 ✓ 
                 hypothetical protein 
                 2119 
               
               
                 1430993-1431382 
                 — 
                 ✓ 
                 hypothetical protein 
                 2120 
               
               
                 1431357-1431587 
                 — 
                 ✓ 
                 hypothetical protein 
                 2121 
               
               
                 1431596-1432555 
                 — 
                 ✓ 
                 hypothetical protein 
                 2122 
               
               
                 1432534-1432953 
                 — 
                 ✓ 
                 predicted DNA modification methylase 
                 2123 
               
               
                 C 1432950-1433171  
                 — 
                 ✓ 
                 hypothetical protein 
                 2124 
               
               
                 1433229-1433597 
                 — 
                 ✓ 
                 hypothetical protein 
                 2125 
               
               
                 1433611-1434927 
                 — 
                 ✓ 
                 predicted phage terminase large subunit 
                 2126 
               
               
                 1434929-1436245 
                 — 
                 ✓ 
                 hypothetical protein 
                 2127 
               
               
                 1436175-1436987 
                 — 
                   
                 uncharacterized protein, homolog of phage Mu 
                 2128 
               
               
                   
                   
                   
                 protein gp30 
               
               
                 1436993-1438066 
                 — 
                 ✓ 
                 hypothetical protein 
                 2129 
               
               
                 1438080-1438499 
                 — 
                 ✓ 
                 hypothetical protein 
                 2130 
               
               
                 1438507-1439508 
                 — 
                 ✓ 
                 hypothetical protein 
                 2131 
               
               
                 1439511-1439699 
                 — 
                 ✓ 
                 hypothetical protein 
                 2132 
               
               
                 1439703-1440053 
                 — 
                 ✓ 
                 hypothetical protein 
                 2133 
               
               
                 1440046-1440504 
                 — 
                 ✓ 
                 hypothetical protein 
                 2134 
               
               
                 1440504-1440863 
                 — 
                 ✓ 
                 hypothetical protein 
                 2135 
               
               
                 1440865-1441374 
                 — 
                 ✓ 
                 hypothetical protein 
                 2136 
               
               
                 1441361-1442434 
                 — 
                 ✓ 
                 hypothetical protein 
                 2137 
               
               
                 1442480-1442905 
                 — 
                 ✓ 
                 hypothetical protein 
                 2138 
               
               
                 1442905-1443387 
                 — 
                 ✓ 
                 hypothetical protein 
                 2139 
               
               
                 1443423-1443575 
                 — 
                 ✓ 
                 hypothetical protein 
                 2140 
               
               
                 1443572-1445989 
                 — 
                 ✓ 
                 predicted phage-related minor tail protein 
                 2141 
               
               
                 C 1446064-1446636  
                 — 
                 ✓ 
                 hypothetical protein 
                 2142 
               
               
                 1446944-1447525 
                 — 
                 ✓ 
                 hypothetical protein 
                 2143 
               
               
                 1447522-1447836 
                 — 
                 ✓ 
                 hypothetical protein 
                 2144 
               
               
                 1447833-1448789 
                 — 
                 ✓ 
                 hypothetical protein 
                 2145 
               
               
                 1448792-1449463 
                 — 
                 ✓ 
                 hypothetical protein 
                 2146 
               
               
                 1449460-1449825 
                 — 
                 ✓ 
                 hypothetical protein 
                 2147 
               
               
                 1449818-1451254 
                 — 
                 ✓ 
                 hypothetical protein 
                 2148 
               
               
                 1451263-1451877 
                 — 
                 ✓ 
                 hypothetical protein 
                 2149 
               
               
                 1451887-1454235 
                 — 
                 ✓ 
                 probable tail fiber protein 
                 2150 
               
               
                 1454247-1454849 
                 — 
                 ✓ 
                 hypothetical protein 
                 2151 
               
               
                 1454846-1455346 
                 — 
                 ✓ 
                 hypothetical protein 
                 2152 
               
               
                 1455412-1455861 
                 — 
                 ✓ 
                 conserved hypothetical protein 
                 2153 
               
               
                 C 1455900-1456163  
                 — 
                 ✓ 
                 hypothetical protein 
                 2154 
               
               
                 1456754-1457884 
                 — 
                   
                 pseudogene for putative integrase/recombinase, 
                 2155 
               
               
                   
                   
                   
                 degenerate 
               
               
                 C 1457947-1458228  
                 — 
                   
                 hypothetical protein 
                 2156 
               
               
                 1458276-1458461 
                 — 
                   
                 mu-like prophage protein gp29 
                 2157 
               
               
                 1458521-1459189 
                 — 
                   
                 conserved hypothetical protein 
                 2158 
               
               
                 1459291-1459437 
                 — 
                   
                 hypothetical protein 
                 2159 
               
               
                 1459470-1460006 
                 — 
                   
                 conserved hypothetical protein 
                 2160 
               
               
                 1460207-1460653 
                 — 
                 ✓ 
                 hypothetical protein 
                 2161 
               
               
                 1460653-1460829 
                 — 
                 ✓ 
                 hypothetical protein 
                 2162 
               
               
                 1430841-1461500 
                 — 
                 ✓ 
                 hypothetical protein 
                 2163 
               
               
                 1461500-1461676 
                 — 
                 ✓ 
                 hypothetical protein 
                 2164 
               
               
                 1461689-1462246 
                 — 
                 ✓ 
                 hypothetical protein 
                 2165 
               
               
                 1462243-1462419 
                 — 
                 ✓ 
                 hypothetical protein 
                 2166 
               
               
                 1462432-1462983 
                 — 
                 ✓ 
                 hypothetical protein 
                 2167 
               
               
                 1463259-1464344 
                 prfA 
                   
                 peptide chain release factor 1 
                 2168 
               
               
                 1464367-1464837 
                 — 
                   
                 conserved hypothetical protein 
                 2169 
               
               
                 1464837-1465715 
                 hemK 
                   
                 HemK 
                 2170 
               
               
                 1465715-1466518 
                 — 
                   
                 conserved hypothetical protein 
                 2171 
               
               
                 1466533-1467387 
                 kdsA 
                   
                 2-dehyrdro-3-deoxyphosphooctonate aldolase 
                 2172 
               
               
                 1467447-1468394 
                 — 
                   
                 putative 2-hydroxyacid dehydrogenase 
                 2173 
               
               
                 1468394-1469575 
                 lolC 
                   
                 lipoprotein releasing system transmembrane 
                 2174 
               
               
                   
                   
                   
                 protein 
               
               
                 1469587-1470879 
                 bioA 
                   
                 adenosylmethionine-8-amino-7-oxononanoate 
                 2175 
               
               
                   
                   
                   
                 aminotransferase 
               
               
                 1470888-1472027 
                 bioF 
                   
                 8-amino-7-oxononanoate synthase 
                 2176 
               
               
                 1472037-1472684 
                 — 
                   
                 conserved hypothetical protein 
                 2177 
               
               
                 1472672-1473454 
                 bioC 
                   
                 putative biotin synthesis protein BioC 
                 2178 
               
               
                 1473464-1474105 
                 bioD-B 
                   
                 probable dethiobiotin synthetase 2 
                 2179 
               
               
                 1474187-1474870 
                 lolD 
                   
                 lipoprotein releasing system ATP-binding 
                 2180 
               
               
                   
                   
                   
                 protein LolD 
               
               
                 1474870-1476120 
                 lolE 
                   
                 ABC-type transport system, involved in 
                 2181 
               
               
                   
                   
                   
                 lipoprotein release, permease component 
               
               
                 1476339-1477427 
                 aroG 
                   
                 phospho-2-dehyrdro-3-deoxyheptonate aldolase 
                 2182 
               
               
                 C 1477497-1477937  
                 impA 
                   
                 impA 
                 2183 
               
               
                 1478222-1479466 
                 — 
                   
                 predicted Na+/serine symporter 
                 2184 
               
               
                 1479588-1480196 
                 — 
                   
                 putative NAD(P)H oxidoreductase 
                 2185 
               
               
                 1480196-1480750 
                 — 
                   
                 predicted component of anaerobic 
                 2186 
               
               
                   
                   
                   
                 dehydrogenases 
               
               
                 C 1480797-1481351  
                 — 
                   
                 predicted nitroreductase 
                 2187 
               
               
                 1481449-1483296 
                 sppA 
                   
                 protease IV 
                 2188 
               
               
                 C 1483334-1484131  
                 licD 
                   
                 phosphorylcholine transferase 
                 2189 
               
               
                 C 1484131-1484832  
                 licC 
                   
                 LicC 
                 2190 
               
               
                 C 1484829-1485707  
                 licB 
                   
                 LicB 
                 2191 
               
               
                 C 1485707-1486666  
                 licA 
                   
                 LicA 
                 2192 
               
               
                 C 1486754-1488766  
                 — 
                   
                 predicted glycine/D-amino acid oxidases, 
                 2193 
               
               
                   
                   
                   
                 deaminating 
               
               
                 1488913-1490133 
                 fabB 
                   
                 3-oxacyl-[acyl-carrier-protein] synthase I 
                 2194 
               
               
                 C 1490196-1490459  
                 rrxA 
                   
                 glutaredoxin 
                 2195 
               
               
                 1490576-1491484 
                 rimK 
                   
                 probable ribosomal protein S6 modification 
                 2196 
               
               
                   
                   
                   
                 protein 
               
               
                 C 1495122-1492736  
                 gltS 
                   
                 sodium/glutamate symport carrier protein 
                 2197 
               
               
                 C 1492778-1495021  
                 parC 
                   
                 topoisomerase IV subunit A 
                 2198 
               
               
                 C 1495088-1496986  
                 parE 
                   
                 topoisomerase IV subunit B 
                 2199 
               
               
                 C 1497060-1497995  
                 htrB 
                   
                 lipid A biosynthesis lauroyl acyltransferase 
                 2200 
               
               
                 1498092-1499522 
                 rfaE 
                   
                 ADP-heptose synthase 
                 2201 
               
               
                 C 1499886-1499981  
                 — 
                   
                 pseudogene for Type I restriction enzyme 
                 2202 
               
               
                   
                   
                   
                 R protein 
               
               
                 C 1500193-1500549  
                 — 
                 ✓ 
                 hypothetical protein 
                 2203 
               
               
                 1500660-1501064 
                 uupA2 
                   
                 ABC transporter ATP-binding protein 
                 2204 
               
               
                 1501061-1501621 
                 uppB 
                   
                 ABC transporter ATP-binding protein 
                 2205 
               
               
                 C 1501649-1502338  
                 — 
                   
                 putative carbonic anhydrase 
                 2206 
               
               
                 C 1502414-1503922  
                 asnS 
                   
                 asparaginyl-tRNA synthetase 
                 2207 
               
               
                 1504044-1504517 
                 ribH 
                   
                 6,7-dimethyl-8-ribityllumazine synthase 
                 2208 
               
               
                 1504521-1504955 
                 nusB 
                   
                 N utilization substance protein B 
                 2209 
               
               
                 1505022-1506008 
                 thiL 
                   
                 thiamine-monophosphate kinase 
                 2210 
               
               
                 1506005-1506496 
                 pgpA 
                   
                 phosphatidylglycerophosphatase A 
                 2211 
               
               
                 1506496-1507125 
                 — 
                   
                 predicted threonine efflux protein 
                 2212 
               
               
                 1507142-1507954 
                 dapB 
                   
                 dihydrodipicolinate reductase 
                 2213 
               
               
                 C 1507949-1508197  
                 — 
                   
                 conserved hypothetical ferredoxin-like protein 
                 2214 
               
               
                 1508243-1508983 
                 — 
                   
                 conserved-hypothetical protein 
                 2215 
               
               
                 1509132-1510121 
                 pheS 
                   
                 ohenylalanyl-tRNA synthetase alpha chain 
                 2216 
               
               
                 1510155-1512542 
                 pheT 
                   
                 ohenylalanyl-tRNA synthetase beta chain 
                 2217 
               
               
                 1512544-1512834 
                 himA 
                   
                 integration host factor alpha-subunit 
                 2218 
               
               
                 1512887-1513372 
                 — 
                   
                 conserved hypothetical lipoprotein 
                 2219 
               
               
                 1513381-1514391 
                 — 
                 ✓ 
                 hypothetical protein 
                 2220 
               
               
                 1514450-1514905 
                 — 
                 ✓ 
                 putative 5′(3′)-deoxyribonucleotidase 
                 2221 
               
               
                 1514889-1515599 
                 — 
                 ✓ 
                 NAD-dependent deacetylase 
                 2222 
               
               
                 C 1515648-1516670  
                 — 
                 ✓ 
                 hypothetical protein 
                 2223 
               
               
                 1516865-1517065 
                 ftsK2 
                 ✓ 
                 DNA translocase ftsK 
                 2224 
               
               
                 1517062-1517907 
                 — 
                 ✓ 
                 NAD-dependent deacetylase sirtuin 5 
                 2225 
               
               
                 1517907-1518668 
                 — 
                 ✓ 
                 hypothetical protein 
                 2226 
               
               
                 1518746-1519720 
                 — 
                 ✓ 
                 hypothetical protein 
                 2227 
               
               
                 1519797-1519964 
                 — 
                 ✓ 
                 hypothetical protein 
                 2228 
               
               
                 1520134-1521849 
                 — 
                 ✓ 
                 predicted serine/threonine protein phosphatase 
                 2229 
               
               
                   
                   
                   
                 family protein 
               
               
                 1521869-1522306 
                 — 
                   
                 predicted arylsulfatase A-like enzyme 
                 2230 
               
               
                 1522388-1523200 
                 — 
                   
                 predicted enzyme related to aldose 1-epimerase 
                 2231 
               
               
                 1523468-1523875 
                 infC 
                   
                 translation initiation factor IF-3 
                 2232 
               
               
                 1524014-1524283 
                 rpmI 
                   
                 50S ribosomal protein L35 
                 2233 
               
               
                 1524349-1524702 
                 rplT 
                   
                 50S ribosomal protein L20 
                 2234 
               
               
                 1524815-1528450 
                 recB 
                   
                 exodeoxyribonuclease V beta chain 
                 2235 
               
               
                 1528450-1530372 
                 recD 
                   
                 exodeoxyribonuclease V alpha chain 
                 2236 
               
               
                 C 1530441-1530887  
                 — 
                   
                 conserved hypothetical protein 
                 2237 
               
               
                 1530984-1532789 
                 lonB 
                   
                 putative protease Lahomolog, predicted ATP- 
                 2238 
               
               
                   
                   
                   
                 dependent protease 
               
               
                 1532958-1533491 
                 fabA 
                   
                 3-hydroxydecanoyl-[acyl-carrier-protein] 
                 2239 
               
               
                   
                   
                   
                 dehydratase 
               
               
                 1533727-1534455 
                 — 
                   
                 conserved hypothetical protein 
                 2240 
               
               
                 1534452-1534589 
                 — 
                   
                 conserved hypothetical protein 
                 2241 
               
               
                 1534725-1534994 
                 rpsO 
                   
                 30S ribosomal protein S15 
                 2242 
               
               
                 C 1535066-1535437  
                 — 
                   
                 conserved hypothetical transposase-like protein 
                 2243 
               
               
                 C 1535434-1535550  
                 — 
                   
                 conserved hypothetical protein 
                 2244 
               
               
                 C 1535766-1537205  
                 dacB 
                   
                 penicillin-binding protein 4 precursor 
                 2245 
               
               
                 1537369-1537845 
                 greA 
                   
                 transcription elongation factor GreA 
                 2246 
               
               
                 C 1537884-1538183  
                 — 
                   
                 predicted RNA-binding protein containing KH 
                 2247 
               
               
                   
                   
                   
                 domain, possible ribosomal protein 
               
               
                 1538310-1538939 
                 ftsJ 
                   
                 ribosomal RNA large subunit methyltransferase J 
                 2248 
               
               
                 1539030-1540937 
                 FTSh 
                   
                 cell division protein FtsH homolog 1 
                 2249 
               
               
                 1541049-1541879 
                 folP 
                   
                 dihydropteroate synthase 
                 2250 
               
               
                 1541912-1543249 
                 mrsA 
                   
                 predicted phosphomannomutase 
                 2251 
               
               
                 1543308-1543802 
                 sixA 
                   
                 phosphohistidine phosphatase SixA homolog 
                 2252 
               
               
                 1544004-1544579 
                 — 
                 ✓ 
                 conserved hypothetical protein 
                 2253 
               
               
                 C 1544657-1546021  
                 — 
                   
                 conserved hypothetical protein 
                 2254 
               
               
                 1546248-1546388 
                 — 
                   
                 hypothetical protein 
                 2255 
               
               
                 1546382-1546534 
                 — 
                   
                 hypothetical protein 
                 2256 
               
               
                 1546609-1546767 
                 — 
                   
                 pseudogene for surface protein autotransporter 
                 2257 
               
               
                   
                   
                   
                 domain 
               
               
                 1546843-1547439 
                 — 
                   
                 possible RNA polymerase sigma factor 24 
                 2258 
               
               
                 1547449-1547622 
                 — 
                   
                 hypothetical protein 
                 2259 
               
               
                 C 1547717-1548619  
                 — 
                 ✓ 
                 hypothetical protein 
                 2260 
               
               
                 1548755-1549816 
                 msaB 
                   
                 peptide methionine sulfoxide reductase 
                 2261 
               
               
                   
                   
                   
                 MsrA/MsrB 
               
               
                 1549828-1550469 
                 — 
                   
                 conserved hypothetical cytochrome c-type 
                 2262 
               
               
                   
                   
                   
                 biogenesis protein 
               
               
                 1550514-1550984 
                 — 
                   
                 conserved hypothetical protein 
                 2263 
               
               
                 C 1551166-1551489  
                 — 
                   
                 conserved hypothetical protein 
                 2264 
               
               
                 C 1551556-1552287  
                 moeB 
                   
                 molybdopterin biosynthesis protein MoeB 
                 2265 
               
               
                 C 1552291-1553505  
                 moeA 
                   
                 molybdopterin biosynthesis protein MoeA 
                 2266 
               
               
                 1553643-1554299 
                 folE 
                   
                 GTP cyclohydrolase I 
                 2267 
               
               
                 1554303-1554626 
                 — 
                   
                 conserved hypothetical protein 
                 2268 
               
               
                 1554729-1555457 
                 bioD-A 
                   
                 probable dethiobiotin synthetase 1 
                 2269 
               
               
                 C 1555546-1556424  
                 metF 
                   
                 5,10-methylenetetrahydrofolate reductase 
                 2270 
               
               
                 1556887-1557315 
                 rplM 
                   
                 50S ribosomal protein L13 
                 2271 
               
               
                 1557332-1557724 
                 rpsI 
                   
                 30S ribosomal protein S9 
                 2272 
               
               
                 1557905-1558543 
                 sspA 
                   
                 stringent starvation protein A 
                 2273 
               
               
                 1558543-1558995 
                 sspB 
                   
                 stringent starvation protein B 
                 2274 
               
               
                 C 1559031-1560908  
                 dxs 
                   
                 1-deoxy-D-xylulose 5-phosphate synthase 
                 2275 
               
               
                 C 1560950-1561840  
                 ispA 
                   
                 geranyltranstransferase 
                 2276 
               
               
                 C 1561840-1562094  
                 xseB 
                   
                 exodeoxyribonuclease VII small subunit 
                 2277 
               
               
                 1562253-1563710 
                 thiI 
                   
                 predicted thiamine biosynthesis ATP 
                 2278 
               
               
                   
                   
                   
                 pyrophosphatase 
               
               
                 1563725-1564045 
                 — 
                   
                 conserved hypothetical protein 
                 2279 
               
               
                 1564039-1454758 
                 truC 
                   
                 tRNA pseudouridine synthase C 
                 2280 
               
               
                 1564751-1564909 
                 — 
                   
                 conserved hypothetical protein 
                 2281 
               
               
                 1565058-1565276 
                 cspD 
                   
                 cold shock-like protein CspD 
                 2282 
               
               
                 C 1565415-1565891  
                 — 
                   
                 conserved hypothetical protein 
                 2283 
               
               
                 1565950-1566903 
                 usg 
                   
                 predicted aspartate-semialdehyde 
                 2284 
               
               
                   
                   
                   
                 dehydrogenase 
               
               
                 C 1567047-1567853  
                 trpA 
                   
                 tryptophan synthase alpha chain 
                 2285 
               
               
                 C 1567853-1569046  
                 trpB 
                   
                 tryptophan synthase beta chain 
                 2286 
               
               
                 C 1569063-1569821  
                 — 
                   
                 conserved hypothetical oxidoreductase 
                 2287 
               
               
                 1570001-1571035 
                 purM 
                   
                 phosphoribosylformylglycinamidine cyclo- 
                 2288 
               
               
                   
                   
                   
                 ligase 
               
               
                 1571090-1571728 
                 purN 
                   
                 phosphoribosylglycinamide formyltransferase 
                 2289 
               
               
                 C 1571812-1572648  
                 — 
                   
                 predicted ABC-type transport system protein, 
                 2290 
               
               
                   
                   
                   
                 periplasmic component 
               
               
                 C 1572846-1573868  
                 uspE 
                   
                 universal stress protein E 
                 2291 
               
               
                 C 1573897 . . . 1574670      
                 fnr 
                   
                 fumarate and nitrate reduction regulatory 
                 2292 
               
               
                   
                   
                   
                 protein 
               
               
                 1575288-1575644 
                 — 
                   
                 putative integrase/recombinase 
                 2293 
               
               
                 C 1575529-1575918  
                 — 
                   
                 conserved hypothetical protein 
                 2294 
               
               
                 C 1576223-1576474  
                 — 
                   
                 predicted phage anti-repressor protein 
                 2295 
               
               
                 C 1576812-1578083  
                 — 
                 ✓ 
                 hypothetical protein 
                 2296 
               
               
                 1578684-1578887 
                 — 
                 ✓ 
                 hypothetical protein 
                 2297 
               
               
                 C 1578865-1579023  
                 — 
                 ✓ 
                 hypothetical protein 
                 2298 
               
               
                 C 1579351-1579572  
                 — 
                 ✓ 
                 hypothetical protein 
                 2299 
               
               
                 C 1580499-1580834  
                 — 
                 ✓ 
                 hypothetical protein 
                 2300 
               
               
                 C 1580837-1581916  
                 — 
                 ✓ 
                 hypothetical protein 
                 2301 
               
               
                 C 1581968-1582666  
                 — 
                 ✓ 
                 predicted transcriptional regulator 
                 2302 
               
               
                 1582777-1582965 
                 — 
                 ✓ 
                 hypothetical protein 
                 2303 
               
               
                 1583014-1583454 
                 — 
                 ✓ 
                 hypothetical protein 
                 2304 
               
               
                 1583503-1584177 
                 — 
                 ✓ 
                 hypothetical protein 
                 2305 
               
               
                 1584174-1584932 
                 — 
                 ✓ 
                 hypothetical protein 
                 2306 
               
               
                 1584917-1585558 
                 — 
                 ✓ 
                 hypothetical protein 
                 2307 
               
               
                 1585555-1585779 
                 — 
                 ✓ 
                 hypothetical protein 
                 2308 
               
               
                 1585816-1586232 
                 ninB 
                 ✓ 
                 Putative recombination protein NinB 
                 2309 
               
               
                 1586500-1586889 
                 ninG 
                   
                 putative recombination protein NinG homolog 
                 2310 
               
               
                 1586909-1587538 
                 — 
                 ✓ 
                 hypothetical protein 
                 2311 
               
               
                 1587662-1587940 
                 — 
                   
                 conserved hypothetical protein 
                 2312 
               
               
                 C 1587990-1588967  
                 — 
                 ✓ 
                 hypothetical protein 
                 2313 
               
               
                 1589196-1589981 
                 — 
                   
                 conserved hypothetical protein 
                 2314 
               
               
                 1590012-1590194 
                 — 
                   
                 hypothetical protein 
                 2315 
               
               
                 1590318-1590674 
                 — 
                   
                 conserved hypothetical protein 
                 2316 
               
               
                 1590754-1591245 
                 — 
                   
                 conserved hypothetical protein 
                 2317 
               
               
                 1591238-1591561 
                 — 
                   
                 hypothetical protein 
                 2318 
               
               
                 1591473-1591754 
                 — 
                   
                 conserved hypothetical protein 
                 2319 
               
               
                 C 1591756-1592034  
                 — 
                 ✓ 
                 hypothetical protein 
                 2320 
               
               
                 1592079-1592591 
                 — 
                   
                 conserved hypothetical protein 
                 2321 
               
               
                 1592578-1593921 
                 — 
                   
                 predicted phage terminase large subunit 
                 2322 
               
               
                 1593923-1595257 
                 — 
                   
                 conserved hypothetical protein 
                 2323 
               
               
                 1595286-1596467 
                 — 
                 ✓ 
                 uncharacterized protein, homolog of phage Mu 
                 2324 
               
               
                   
                   
                   
                 protein gp30 
               
               
                 1596613-1596789 
                 — 
                   
                 conserved hypothetical protein 
                 2325 
               
               
                 1596953-1597972 
                 pyrD 
                   
                 dihyrdoorotate dehydrogenase 
                 2326 
               
               
                 1597972-1598796 
                 trpH 
                   
                 TrpH 
                 2327 
               
               
                 C 1598895-1599503  
                 — 
                   
                 conserved hypothetical protein 
                 2328 
               
               
                 C 1599631-1601025  
                 fumC 
                   
                 fumurate hydratase class II 
                 2329 
               
               
                 C 1601175-1602113  
                 — 
                 ✓ 
                 putative glycosyl transferase, glycosyl 
                 2330 
               
               
                   
                   
                   
                 transferase family 8 protein 
               
               
                 1602322-1602666 
                 — 
                   
                 pseudogene for usg protein homolog 
                 2331 
               
               
                 1602769-1603203 
                 holC 
                   
                 DNA polymerase III, chi subunit 
                 2332 
               
               
                 1603288-1603458 
                 — 
                   
                 conserved hypothetical protein 
                 2333 
               
               
                 1603471-1603845 
                 — 
                   
                 conserved hypothetical protein 
                 2334 
               
               
                 1603873-1604040 
                 — 
                   
                 hypothetical protein 
                 2335 
               
               
                 1604067-1604381 
                 — 
                   
                 conserved hypothetical protein 
                 2336 
               
               
                 1604425-1604826 
                 — 
                 ✓ 
                 hypothetical protein 
                 2337 
               
               
                 1604878-1607742 
                 valS 
                   
                 valyl-tRNA synthetase 
                 2338 
               
               
                 C 1607777-1607884  
                 — 
                   
                 hypothetical protein 
                 2339 
               
               
                 C 1608172-1609605  
                 trpC 
                   
                 tryptophan biosynthesis protein trpCF 
                 2340 
               
               
                 C 1609643-1610644  
                 trpD 
                   
                 anthranilate phosphoribosyltransferase 
                 2341 
               
               
                 C 1610697-1611083  
                 — 
                   
                 conserved hypothetical protein 
                 2342 
               
               
                 C 1611132-1611719  
                 trpG 
                   
                 anthranilate synthase component II 
                 2343 
               
               
                 C 1611732-1613288  
                 trpE 
                   
                 anthranilate synthase component I 
                 2344 
               
               
                 C 1613390-1614300  
                 — 
                 ✓ 
                 pseudogene for conserved hypothetical 
                 2345 
               
               
                   
                   
                   
                 glycosyltransferase 
               
               
                 C 1614423-1614920  
                 ftnB 
                   
                 ferritin-like protein 2 
                 2346 
               
               
                 C 1614936-1615484  
                 ftnA 
                   
                 ferritin-like protein 1 
                 2347 
               
               
                 1615927-1616946 
                 pstS 
                   
                 phosphate-binding periplasmic protein 
                 2348 
               
               
                   
                   
                   
                 precursor PstS 
               
               
                 1617038-1617985 
                 pstC 
                   
                 phosphate transport system permease 
                 2349 
               
               
                   
                   
                   
                 protein PstC 
               
               
                 1617987-1618835 
                 pstA 
                   
                 phoaphate transport system permease 
                 2350 
               
               
                   
                   
                   
                 proteain PstA 
               
               
                 1618845-1619612 
                 pstB 
                   
                 phosphate import ATP-binding protein PstB 
                 2351 
               
               
                 1619709-1620404 
                 phoB 
                   
                 phosphate regulon transcriptional regulatory 
                 2352 
               
               
                   
                   
                   
                 protein PhoB 
               
               
                 1620401-1621678 
                 phoR 
                   
                 phosphate regulon sensor protein PhoR 
                 2353 
               
               
                 C 1622370-1623791  
                 sbcB 
                   
                 exodeoxyribonuclease I 
                 2354 
               
               
                 C 1623804-1624679  
                 — 
                   
                 conserved hypothetical protein 
                 2355 
               
               
                 C 1624683-1625591  
                 — 
                   
                 conserved hypothetical protein 
                 2356 
               
               
                 C 1625661-1630193  
                 — 
                   
                 cell division protein MukB 
                 2357 
               
               
                 C 1630193-1630927  
                 — 
                   
                 cell division protein MukE 
                 2358 
               
               
                 C 1630931-1631989  
                 haeIIR 
                 ✓ 
                 type II restriction exzyme HaeII 
                 2359 
               
               
                 C 1631992-1632948  
                 haeIIM 
                 ✓ 
                 modification methylase HaeII 
                 2360 
               
               
                 C 1632961-1634388  
                 mukF 
                   
                 MukF homolog 
                 2361 
               
               
                 1634445-1635377 
                 — 
                   
                 predicted ATPase of the PP-loop superfamily 
                 2362 
               
               
                   
                   
                   
                 implicated in cell cycle control 
               
               
                 1635379-1635708 
                 — 
                   
                 predicted dissimilatory sulfite reductase, 
                 2363 
               
               
                   
                   
                   
                 desulfoviridin, gamma subunit 
               
               
                 1635816-1636025 
                 mop 
                   
                 probable molybdenum-pterin binding protein 
                 2364 
               
               
                 1636209-1638621 
                 — 
                   
                 pseudogene for conserved hypothetical protein, 
                 2365 
               
               
                   
                   
                   
                 denegerate 
               
               
                 1638725-1641505 
                 pqqL 
                   
                 probable zinc protease 
                 2366 
               
               
                 C 1641628-1643559  
                 thrS 
                   
                 threonyl-tRNA synthetase 
                 2367 
               
               
                 1643843-1644427 
                 acpD 
                   
                 probable acyl carrier protein phosphodiesterase 
                 2368 
               
               
                 C 1644504-1647110  
                 topA 
                   
                 DNA topoisomerase I 
                 2369 
               
               
                 1647206-1648123 
                 — 
                   
                 putative HTH-type transcriptional regulator 
                 2370 
               
               
                 C 1648187-1649611  
                 pntB 
                   
                 NAD(P) transhydrogenase subunit beta 
                 2371 
               
               
                 C 1649622 . . . 1651160      
                 pntA 
                   
                 NAD(P) transhydrogenase subunit alpha 
                 2372 
               
               
                 C 1651421-1653886  
                 glgP 
                   
                 glycogen phosphorylase 
                 2373 
               
               
                 C 1654133-1655563  
                 glgA 
                   
                 glycogen synthase 
                 2374 
               
               
                 C 1655671-1657005  
                 glgC 
                   
                 glucose-1-phosphate adenylyltransferase 
                 2375 
               
               
                 C 1656955-1658971  
                 glgX 
                   
                 glycogen operon protein GlgX 
                 2376 
               
               
                 C 1659070-1661262  
                 glgB 
                   
                 1,4-alpha-glucan branching enzyme 
                 2377 
               
               
                 C 1661272-1663371  
                 malQ 
                   
                 4-alpha-glucanotransferase 
                 2378 
               
               
                 C 1663433-1663897  
                 — 
                   
                 conserved hypothetical protein 
                 2379 
               
               
                 C 1663963-1665636  
                 glnS 
                   
                 glutaminyl-tRNA synthetase 
                 2380 
               
               
                 C 1666056-1667531  
                 cafA 
                   
                 ribonuclease G 
                 2381 
               
               
                 1667647-1669161 
                 putP 
                   
                 sodium/proline symporter 
                 2382 
               
               
                 1669158-1670123 
                 — 
                   
                 conserved hypothetical protein 
                 2383 
               
               
                 C 1670166-1671044  
                 cdd 
                   
                 cytiding deaminase 
                 2384 
               
               
                 1671318-1671800 
                 — 
                   
                 conserved hypothetical DNA-binding ferritin- 
                 2385 
               
               
                   
                   
                   
                 like protein 
               
               
                 C 1672372-1673610  
                 pepT 
                   
                 peptidase T 
                 2386 
               
               
                 1673880-1675025 
                 potA 
                   
                 spermidine/putrescine transport ATP-binding 
                 2387 
               
               
                   
                   
                   
                 protein 
               
               
                 1675009-1675869 
                 potB 
                   
                 spermidine/putrescine transport permease 
                 2388 
               
               
                   
                   
                   
                 protein 
               
               
                 1675869-1676639 
                 potC 
                   
                 spermidine/putrescine transport system 
                 2389 
               
               
                   
                   
                   
                 permease protein 
               
               
                 1676686-1677852 
                 potD1 
                   
                 spermidine/putrescine-binding periplasmic 
                 2390 
               
               
                   
                   
                   
                 protein 1 precursor 
               
               
                 C 1677933-1679876  
                 uupA 
                   
                 ABC transporter ATP-binding protein 
                 2391 
               
               
                 C 1679970-1681355  
                 — 
                   
                 deoxyguanosinetriphosphate 
                 2392 
               
               
                   
                   
                   
                 triphosphohydrolase-like protein 
               
               
                 C 1681448-1682143  
                 — 
                   
                 putative effector of murein hydrolase 
                 2393 
               
               
                 C 1682162-1682584  
                 — 
                   
                 putative effector of murein hydrolase 
                 2394 
               
               
                 1682699-1683181 
                 — 
                   
                 predicted micrococcal nuclease-like protein 
                 2395 
               
               
                 1683183-1684382 
                 nifS 
                   
                 predicted selenocysteine lyase 
                 2396 
               
               
                 1684379-1684759 
                 — 
                   
                 predicted SufE protein probably involved in 
                 2397 
               
               
                   
                   
                   
                 Fe—S center assembly 
               
               
                 1684750-1685547 
                 — 
                   
                 Zn-ribbon-containing, possible nucleic-acid 
                 2398 
               
               
                   
                   
                   
                 binding protein 
               
               
                 1685591-1686430 
                 — 
                   
                 predicted enzyme related to GTP 
                 2399 
               
               
                   
                   
                   
                 cyclohydrolase I 
               
               
                 C 1686463-1687587  
                 tyrA 
                   
                 T-protein 
                 2400 
               
               
                 C 1687677-1688597  
                 truB 
                   
                 tRNA pseudouridine synthase B 
                 2401 
               
               
                 C 1688597-1688983  
                 rbfA 
                   
                 ribosome-binding factor A 
                 2402 
               
               
                 1689148-1690818 
                 hsdM3 
                   
                 putative type I restriction enzyme HindVIIP 
                 2403 
               
               
                   
                   
                   
                 M protein 
               
               
                 1690811-1692076 
                 hsdS3 
                 ✓ 
                 putative type I restriction enzyme HindVIIP 
                 2404 
               
               
                   
                   
                   
                 specificity protein 
               
               
                 1692069-1693115 
                 — 
                 ✓ 
                 hypothetical protein 
                 2405 
               
               
                 1693117-1696284 
                 hsdR3 
                   
                 putative type I restriction enzyme HindVIIP 
                 2406 
               
               
                   
                   
                   
                 R protein 
               
               
                 C 1696363-1698897  
                 infB 
                   
                 translation initiation factor IF-2 
                 2407 
               
               
                 C 1698909-1700396  
                 nusA 
                   
                 transcriptional elongation protein NusA 
                 2408 
               
               
                 C 1700413-1700868  
                 — 
                   
                 conserved hypothetical protein 
                 2409 
               
               
                 C 1702529-1703293  
                 — 
                 ✓ 
                 hypothetical protein 
                 2410 
               
               
                 C 1703297-1703824  
                 — 
                 ✓ 
                 hypothetical protein 
                 2411 
               
               
                 C 1703834-1704973  
                 — 
                 ✓ 
                 hypothetical protein 
                 2412 
               
               
                 C 1704990-1705358  
                 — 
                 ✓ 
                 hypothetical protein 
                 2413 
               
               
                 C 1705372-1706193  
                 — 
                 ✓ 
                 hypothetical protein 
                 2414 
               
               
                 C 1706250-1706753  
                 — 
                 ✓ 
                 hypothetical protein 
                 2415 
               
               
                 C 1706750-1707352  
                 — 
                 ✓ 
                 hypothetical protein 
                 2416 
               
               
                 C 1707364-1709886  
                 — 
                 ✓ 
                 probable tail fiber protein 
                 2417 
               
               
                 C 1709895-1710431  
                 — 
                 ✓ 
                 predicted bacteriophage P2-related tail 
                 2418 
               
               
                   
                   
                   
                 formation protein gpI 
               
               
                 C 1710421-1711335  
                 — 
                 ✓ 
                 predicted phage-related baseplate assembly 
                 2419 
               
               
                   
                   
                   
                 protein 
               
               
                 C 1711332-1711670  
                 — 
                 ✓ 
                 predicted baseplate assembly protein W 
                 2420 
               
               
                 C 1711672-1712271  
                 — 
                 ✓ 
                 predicted phage P2-like baseplate assembly 
                 2421 
               
               
                   
                   
                   
                 protein 
               
               
                 C 1712375-1712803  
                 — 
                 ✓ 
                 hypothetical protein 
                 2422 
               
               
                 C 1712812-1713369  
                 — 
                 ✓ 
                 hypothetical protein 
                 2423 
               
               
                 C 1713467-1713919  
                 — 
                 ✓ 
                 hypothetical protein 
                 2424 
               
               
                 C 1713897-1714097  
                 — 
                 ✓ 
                 hypothetical protein 
                 2425 
               
               
                 C 1714141-1716105  
                 — 
                 ✓ 
                 predicted phage-related tail protein 
                 2426 
               
               
                 C 1716148-1716915  
                 — 
                 ✓ 
                 hypothetical protein 
                 2427 
               
               
                 1716960-1717298 
                 — 
                 ✓ 
                 hypothetical protein 
                 2428 
               
               
                 C 1717309-1717491  
                 — 
                 ✓ 
                 hypothetical protein 
                 2429 
               
               
                 1717595-1717942 
                 — 
                 ✓ 
                 hypothetical protein 
                 2430 
               
               
                 C 1717943-1718404  
                 — 
                 ✓ 
                 probable bacteriophage tail completion protein 
                 2431 
               
               
                   
                   
                   
                 gpS homolog 
               
               
                 C 1718404-1718790  
                 — 
                 ✓ 
                 probable bacteriophage tail completion protein 
                 2432 
               
               
                   
                   
                   
                 gpR homolog 
               
               
                 C 1718840-1718947  
                 — 
                 ✓ 
                 hypothetical protein 
                 2433 
               
               
                 C 1718980-1719102  
                 — 
                 ✓ 
                 hypothetical protein 
                 2434 
               
               
                 C 1719099-1719314  
                 — 
                 ✓ 
                 DnaK suppressor protein, bacteriophage PSP3 
                 2435 
               
               
                   
                   
                   
                 gp34 homolog 
               
               
                 C 1719489-1719839  
                 — 
                 ✓ 
                 hypothetical protein 
                 2436 
               
               
                 C 1719824-1720342  
                 — 
                 ✓ 
                 predicted phage-related lysozyme 
                 2437 
               
               
                 1720335 . . . 1720556 
                 — 
                 ✓ 
                 hypothetical protein 
                 2438 
               
               
                 C 1720558-1720767  
                 — 
                 ✓ 
                 hypothetical protein 
                 2439 
               
               
                 C 1720767-1721273  
                 — 
                 ✓ 
                 hypothetical protein 
                 2440 
               
               
                 C 1721567-1722217  
                 — 
                 ✓ 
                 predicted terminase, endonuclease subunit 
                 2441 
               
               
                 C 1722229-1723278  
                 — 
                 ✓ 
                 predicted major capsid protein 
                 2442 
               
               
                 C 1723299-1724114  
                 — 
                 ✓ 
                 predicted capsid scaffolding protein 
                 2443 
               
               
                 1724279-1726060 
                 — 
                 ✓ 
                 terminase, ATPase subunit 
                 2444 
               
               
                 1726070-1727080 
                 — 
                 ✓ 
                 predicted portal vertex protein 
                 2445 
               
               
                 C 1727788-1728462  
                 siaB 
                   
                 acylneuraminate cytidylyltransferase 
                 2446 
               
               
                 1728576-1729238 
                 — 
                   
                 putative NAD(P)H nitroreductase 
                 2447 
               
               
                 C 1729285-1730445  
                 mrp 
                   
                 Mrp 
                 2448 
               
               
                 1730548-1732596 
                 metG 
                   
                 methionyl-tRNA synthetase 
                 2449 
               
               
                 1732707-1733567 
                 tehB 
                   
                 tellurite resistance protein 
                 2450 
               
               
                 C 1733611-1734312  
                 gloB 
                   
                 probable hydroxyacylglutathione hydrolase 
                 2451 
               
               
                 C 1734364-1735170  
                 — 
                   
                 conserved hypothetical protein 
                 2452 
               
               
                 1735406-1735882 
                 — 
                   
                 conserved hypothetical protein 
                 2453 
               
               
                 1736019-1737782 
                 — 
                   
                 conserved hypothetical protein 
                 2454 
               
               
                 1738382-1741024 
                 gyrA 
                   
                 DNA gyrase subunt A 
                 2455 
               
               
                 C 1741079-1742155  
                 metX 
                   
                 homoserine O-acetyltransferase 
                 2456 
               
               
                 1742259-1742993 
                 sanA 
                   
                 SanA 
                 2457 
               
               
                 C 1743281-1744594  
                 folC 
                   
                 folypolyglutamate synthase 
                 2458 
               
               
                 C 1744587-1745477  
                 accD 
                   
                 acethy-coenzyme A carboxylase carboxyl 
                 2459 
               
               
                   
                   
                   
                 transferase subunit beta 
               
               
                 1745671-1747062 
                 htoA 
                   
                 probable periplasmic serine protease do/ 
                 2460 
               
               
                   
                   
                   
                 HhoA-like precursor 
               
               
                 C 1747115-1750555  
                 mfd 
                   
                 transcription-repair coupling factor 
                 2461 
               
               
                 C 1750657-1750830  
                 — 
                   
                 conserved hypothetical protein 
                 2462 
               
               
                 C 1750827-1752797  
                 — 
                   
                 predicted P-loop ATPase fused to an 
                 2463 
               
               
                   
                   
                   
                 acetyltransferase 
               
               
                 C 1752802-1753143  
                 — 
                   
                 conserved hypothetical protein 
                 2464 
               
               
                 C 1753205-1754875  
                 — 
                   
                 ABC transported ATP-binding protein 
                 2465 
               
               
                 C 1755038-1755361  
                 — 
                   
                 predicted plasmid maintenance system 
                 2466 
               
               
                   
                   
                   
                 antidote protein 
               
               
                 C 1755372-1755677  
                 — 
                   
                 predicted plasmid maintenance system 
                 2467 
               
               
                   
                   
                   
                 killer protein 
               
               
                 1756002-1756622 
                 — 
                   
                 predicted ABC-type transport system, 
                 2468 
               
               
                   
                   
                   
                 periplasmic component 
               
               
                 1756625-1757593 
                 — 
                   
                 predicted ABC-type transport system, 
                 2469 
               
               
                   
                   
                   
                 permease component 
               
               
                 C 1758207-1760246  
                 uvrB 
                   
                 UvrABC system protein B 
                 2470 
               
               
                 C 1760276-1762201  
                 — 
                   
                 predicted phosphoglycerol transferase- 
                 2471 
               
               
                   
                   
                   
                 like protein 
               
               
                 C 1762442-1764712  
                 mao2 
                   
                 NADP-dependent malic enzyme 
                 2472 
               
               
                 1764910-1765530 
                 — 
                   
                 possible polysaccharide biosynthesis protein 
                 2473 
               
               
                 1765621-1766319 
                 rsuA 
                   
                 ribosomal small subunit pseodouridine synthase A 
                 2474 
               
               
                 1766321-1767517 
                 bcr 
                   
                 bicyclomycin resistance protein 
                 2475 
               
               
                 C 1767549-1768349  
                 — 
                   
                 conserved hypothetical protein 
                 2476 
               
               
                 1768447-1769109 
                 — 
                   
                 predicted membrane protein 
                 2477 
               
               
                 1769130-1770383 
                 proA 
                   
                 gamma-glutamyl phosphate reductase 
                 2478 
               
               
                 C 1770462-1771607  
                 dnaJ 
                   
                 chaperone protein DnaJ 
                 2479 
               
               
                 C 1771694-1773601  
                 dnaK 
                   
                 chaperone protein DnaK 
                 2480 
               
               
                 1773868-1775310 
                 — 
                   
                 conserved hypothetical protein 
                 2481 
               
               
                 C 1775467-1775925  
                 mgsA 
                   
                 methylglyoxal synthase 
                 2482 
               
               
                 1776225-1778885 
                 aceE 
                   
                 pyruvate dehydrogenase E1 component 
                 2483 
               
               
                 1778948-1780645 
                 aceF 
                   
                 dihydrolipoamide acetyltransferase component 
                 2484 
               
               
                   
                   
                   
                 of pyruvate dehydrogenase complex 
               
               
                 1780759-1782183 
                 lpdA 
                   
                 dihydrolipoamide dehudrogenase 
                 2485 
               
               
                 C 1782230-1782337  
                 — 
                   
                 hypothetical protein 
                 2486 
               
               
                 1782343-1782885 
                 apt 
                   
                 adenine phosphoribosyltransferase 
                 2487 
               
               
                 1782897-1784963 
                 dnzX 
                   
                 DNA polymerase III subunit gamma/tau 
                 2488 
               
               
                 1785103-1785729 
                 upp 
                   
                 uracil phosphoribosyltransferase 
                 2489 
               
               
                 1785833-1787077 
                 uraA 
                   
                 probable uracil permease 
                 2490 
               
               
                 1787143-1787838 
                 — 
                   
                 predicted ATPase involved in DNA replication 
                 2491 
               
               
                   
                   
                   
                 initiation 
               
               
                 C 1787905-1788186  
                 — 
                   
                 predicted translation initiation factor 1-like 
                 2492 
               
               
                   
                   
                   
                 proterin 
               
               
                 C 1788193-1788885  
                 pyrF 
                   
                 orotidine 5′-phosphate decarboxylase 
                 2493 
               
               
                 C 1788909-1790099  
                 — 
                   
                 predicted N-acetylglucosaminyl transferase 
                 2494 
               
               
                 C 1790099-1790392  
                 — 
                   
                 predicted membrane protein 
                 2495 
               
               
                 C 1790467-1790751  
                 ihfB 
                   
                 integration host factor beta subunit 
                 2496 
               
               
                 C 1790874-1792523  
                 rpsA 
                   
                 30S ribosomal protein S1 
                 2497 
               
               
                 C 1792626-1793420  
                 cmk 
                   
                 ctidylate kinase 
                 2498 
               
               
                 1793766-1794641 
                 — 
                   
                 conserved hypothetical pyridoxine biosynthesis 
                 2499 
               
               
                   
                   
                   
                 enzyme 
               
               
                 1794642-1795220 
                 — 
                   
                 predicted glutamine amidotransferase involved 
                 2500 
               
               
                   
                   
                   
                 in pyridoxine biosynthesis 
               
               
                 C 1795769-1797463  
                 dld 
                   
                 D-lactate dehydrogenase 
                 2501 
               
               
                 1797723-1797833 
                 — 
                   
                 conserved hypothetical protein 
                 2502 
               
               
                 C 1798368-1798919  
                 nlpC 
                   
                 probable lipoprotein NlpC 
                 2503 
               
               
                 C 1799032-1800480  
                 tldD 
                   
                 TldD 
                 2504 
               
               
                 C 1800582-1801433  
                 — 
                   
                 predicted methyltransferase 
                 2505 
               
               
                 1801505-1803232 
                 — 
                   
                 putative lipoprotein 
                 2506 
               
               
                 1803232-1803591 
                 — 
                   
                 predicted endonuclease distantly related to 
                 2507 
               
               
                   
                   
                   
                 archael holliday junction resolvase 
               
               
                 1803604-1804188 
                 — 
                   
                 predicted phosphoheptose isomerase 
                 2508 
               
               
                 1804245-1804826 
                 — 
                   
                 predicted periplasmic or secreted lipoprotein 
                 2509 
               
               
                 1805081-1807351 
                 nrdA 
                   
                 ribonucleoside-diphosphate reductase 
                 2510 
               
               
                   
                   
                   
                 alpha chain 
               
               
                 1807493-1808623 
                 nrdB 
                   
                 ribonucleoside-diphosphate reductase 
                 2511 
               
               
                   
                   
                   
                 beta chain 
               
               
                 C 1808739-1809968  
                 sucB 
                   
                 dihydrolipoamide succinyltransferase 
                 2512 
               
               
                   
                   
                   
                 component of 2-oxoglutarate dehydrogenase 
               
               
                   
                   
                   
                 complex 
               
               
                 C 1810071-1812923  
                 sucA 
                   
                 2-oxoglutarate dehydrogenase E1 component 
                 2513 
               
               
                 C 1813081-1813719  
                 — 
                   
                 predicted Zn-dependent hydrolase-like protein, 
                 2514 
               
               
                   
                   
                   
                 including glyoxylases 
               
               
                 C 1813729-1814484  
                 — 
                   
                 conserved putative deoxyribonuclease 
                 2515 
               
               
                 C 1814536-1815096  
                 — 
                   
                 conserved hypothetical protein 
                 2516 
               
               
                 C 1815112-1816581  
                 — 
                   
                 conserved hypothetical protein 
                 2517 
               
               
                 C 1816655-1818742  
                 prc 
                   
                 tail-specific protease precursor 
                 2518 
               
               
                 C 1818764-1819402  
                 proQ 
                   
                 predicted activator of osmoprotectant 
                 2519 
               
               
                   
                   
                   
                 transporter PropP 
               
               
                 1819587-1820837 
                 — 
                   
                 paraquat-inducible protein A-like protein 
                 2520 
               
               
                 1820821-1823466 
                 — 
                   
                 paraquat-inducible protein B-like protein 
                 2521 
               
               
                 C 1823521-1823973  
                 moaE 
                   
                 molybdopterin converting factor subunit 2 
                 2522 
               
               
                 C 1823974-1824219  
                 moaD 
                   
                 molybdopterin converting factor subunit 1 
                 2523 
               
               
                 C 1824221-1824703  
                 moac 
                   
                 molybdenum cofactor biosynthesis protein C 
                 2524 
               
               
                 C 1824795-1825808  
                 moaA 
                   
                 molybdenum cofactor biosynthesis protein A 
                 2525 
               
               
                 1826253-1826726 
                 — 
                   
                 predicted regulator of cell morphogenesis and 
                 2526 
               
               
                   
                   
                   
                 NO signaling 
               
               
                 1826726-1826923 
                   
                   
                 predicted regulator of cell morphogenesis and 
                 2527 
               
               
                   
                   
                   
                 NO signaling 
               
               
                 1827460-1728473 
                 — 
                   
                 probable phosphosugar isomerase Hi1678 
                 2528 
               
               
                 1828483-1829025 
                 yrbI 
                   
                 3-deoxy-D-manno-octulosonate 8-phosphate 
                 2529 
               
               
                   
                   
                   
                 phosphatase 
               
               
                 1829456-1833934 
                 hmw1A 
                 ✓ 
                 HMW1A, high molecular weight adhesin 1 
                 2530 
               
               
                 1834085-1835722 
                 hmw1B 
                 ✓ 
                 HAM1B, OMP-85-like protein required for 
                 2531 
               
               
                   
                   
                   
                 secretion of HMW1A and HMW2A 
               
               
                 1835916-1837868 
                 hmw1C 
                 ✓ 
                 HMW1C, putative glycosyltransferase involved 
                 2532 
               
               
                   
                   
                   
                 in glycosylation of HMW1A and HWM2A 
               
               
                 C 1837945-1840101  
                 — 
                   
                 predicted membrane protein 
                 2533 
               
               
                 C 1840169-1840834  
                 — 
                   
                 conserved hypothetical protein 
                 2534 
               
               
                 1841032-1842093 
                 sohB 
                   
                 possible protease SohB 
                 2535 
               
               
                 1842377-1842955 
                 rnfA 
                   
                 predicted NADH:ubiquinone oxidoreductase, 
                 2536 
               
               
                   
                   
                   
                 subunit RnfA 
               
               
                 1843043-1843624 
                 rnfB 
                   
                 predicted NADH:ubiquinone oxidoreductase, 
                 2537 
               
               
                   
                   
                   
                 subunit RnfB 
               
               
                 1843625-1845622 
                 rnfC 
                   
                 predicted NADH:ubiquinone oxidoreductase, 
                 2538 
               
               
                   
                   
                   
                 subunit RnfC 
               
               
                 1845752-1846828 
                 rnfD 
                   
                 predicted NADH:ubiquinone oxidoreductase, 
                 2539 
               
               
                   
                   
                   
                 subunit RnfD 
               
               
                 1846828-1847451 
                 rnfG 
                   
                 predicted NADH:ubiquinone oxidoreductase, 
                 2540 
               
               
                   
                   
                   
                 subunit RnfG 
               
               
                 1847453-1848160 
                 — 
                   
                 predicted NADH:ubiquinone oxidoreductase, 
                 2541 
               
               
                   
                   
                   
                 subunit RnfE 
               
               
                 1848282-1848917 
                 nth 
                   
                 endonuclease III 
                 2542 
               
               
                 1848976-1850349 
                 — 
                   
                 predicted Na+-dependent transporters 
                 2543 
               
               
                   
                   
                   
                 of the SNF family 
               
               
                 C 1850373-1851428  
                 modC 
                   
                 molybdenum import ATP-binding protein 
                 2544 
               
               
                 C 1851415-1852104  
                 modB 
                   
                 molybdenum transport system permease protein 
                 2545 
               
               
                 C 1852278-1853042  
                 modA 
                   
                 molybdate-binding periplasmic protein 
                 2546 
               
               
                 1853180-1853947 
                 mode 
                   
                 Transcriptional regulator ModE 
                 2547 
               
               
                 1854057-1854860 
                 lsgF 
                   
                 Putative UDP-galactose-lipooligosaccharide 
                 2548 
               
               
                   
                   
                   
                 galactosyltransferase 
               
               
                 C 1854862-1855746  
                 lsgE 
                   
                 Putative UDP-galactose-lipooligosaccharide 
                 2549 
               
               
                   
                   
                   
                 galactosyltransferase 
               
               
                 C 1855758-1856531  
                 lsgD 
                   
                 Putative UDP-glcNAc-lipooligosaccharide 
                 2550 
               
               
                   
                   
                   
                 N-acetylglucosaminyl glycosyltransferase 
               
               
                 C 1856543-1857604  
                 lsgC 
                   
                 Putative UDP-galactose--lipooligosaccharide 
                 2551 
               
               
                   
                   
                   
                 galactosyltransferase 
               
               
                 C 1857606-1858520  
                 lsgB 
                   
                 CMP-N-acetylneuraminate-beta-galactosamide- 
                 2552 
               
               
                   
                   
                   
                 alpha-2,3-sialytransferase 
               
               
                 C 1858517-1859722  
                 lsgA 
                   
                 putative lipooligosaccharide flippase 
                 2553 
               
               
                 1859857-1860600 
                 — 
                   
                 conserved hypothetical protein 
                 2554 
               
               
                 C 1860823-1863092  
                 metE 
                   
                 pseudogene for 5- 
                 2555 
               
               
                   
                   
                   
                 nethyltetrahydropteroytrigultamate - 
               
               
                   
                   
                   
                 homocysteine methyltransferase 
               
               
                 C 1863286-1864362  
                 — 
                   
                 predicted permease 
                 2556 
               
               
                 C 1864359-1865462  
                 — 
                   
                 predicted permease 
                 2557 
               
               
                 1865570-1867045 
                 pepA 
                   
                 cytosol aminopeptidase 
                 2558 
               
               
                 C 1867081-1869090  
                 — 
                   
                 predicted choline-glycine betaine transporter 
                 2559 
               
               
                 C 1869385-1870740  
                 qseC 
                   
                 sensor protein QseC 
                 2560 
               
               
                 C 1870737-1871402  
                 qseB 
                   
                 transcriptional regulatory protein QseB 
                 2561 
               
               
                 C 1871466-1871831  
                 — 
                   
                 conserved hypothetical protein 
                 2562 
               
               
                 C 1871946-1872966  
                 pmi 
                 ✓ 
                 pseudogene for mannose-6-phosphate 
                 2563 
               
               
                   
                   
                   
                 isomerase 
               
               
                 C 1873336-1873836  
                 crr 
                   
                 PTS system, glucose-specific IIA component 
                 2564 
               
               
                 C 1873896-1875623  
                 ptsI 
                   
                 Phosphoenolpyruvate-protein 
                 2565 
               
               
                   
                   
                   
                 phosphotransferase 
               
               
                 C 1875703-1875960  
                 ptsH 
                   
                 Phosphocarrier protein HPr 
                 2566 
               
               
                 C 1876119-1877159  
                 — 
                   
                 probable GTPase 
                 2567 
               
               
                 1877230-1877778 
                 orn 
                   
                 oligoribonuclease 
                 2568 
               
               
                 C 1878178-1879245  
                 wecA 
                   
                 undecaprenyl phosphate 
                 2569 
               
               
                 C 1879320-1881911  
                 glnD 
                   
                 [protein-PII] uridylyltransferase 
                 2570 
               
               
                 C 1882005-1882811  
                 map 
                   
                 methionine aminopeptidase 
                 2571 
               
               
                 1882947-1883291 
                 — 
                   
                 conserved hypothetical protein 
                 2572 
               
               
                 1883293-1883646 
                 — 
                   
                 conserved hypothetical protein 
                 2573 
               
               
                 1883653-1885998 
                 mrcB 
                   
                 penicillin-binding protein 1B 
                 2574 
               
               
                 1886123-1887043 
                 purC 
                   
                 phosphoribosylaminoimidazole- 
                 2575 
               
               
                   
                   
                   
                 succinocarboxamine synthase 
               
               
                 1887199-1888533 
                 argG 
                   
                 argininosuccinate synthase 
                 2576 
               
               
                 C 1888604-1889797  
                 — 
                   
                 Mn2+ and Fe2+ transporter of the NRAMP 
                 2577 
               
               
                   
                   
                   
                 family 
               
               
                 C 1889841-1890578  
                 — 
                   
                 conserved hypothetical protein 
                 2578 
               
               
                 C 1890565-1891494  
                 — 
                   
                 predicted allophanate hydrolase subunit 2 
                 2579 
               
               
                 C 1891491-1892132  
                 — 
                   
                 predicted allophanate hydrolase subunit 1 
                 2580 
               
               
                 C 1892394-1894373  
                 rnb 
                   
                 exoribonuclease II 
                 2581 
               
               
                 C 1894471-1895358  
                 fabI 
                   
                 enoyl-[acyl-carrier-protein] reductase [NADH] 
                 2582 
               
               
                 1895438-1897021 
                 prfC 
                   
                 peptide chain release factor 3 
                 2583 
               
               
                 C 1897097-1897330  
                 — 
                   
                 conserved hypothetical protein 
                 2584 
               
               
                 C 1897433-1897762  
                 — 
                   
                 predicted branched chain amino acid permease 
                 2585 
               
               
                 C 1897759-1898493  
                 — 
                   
                 predicted branched chain amino acid permease 
                 2586 
               
               
                 C 1898503-1899432  
                 metR 
                   
                 HTH-type transcriptional regulator MetR 
                 2587 
               
               
                 C 1905763-1906908  
                 lldD 
                   
                 L-lactate dehydrogenase 
                 2588 
               
               
                 C 1907120-1907929  
                 murI 
                   
                 glutamate racemase 
                 2589 
               
               
                 C 1907959-1910040  
                 recG 
                   
                 ATP-dependent DNA helicase 
                 2590 
               
               
                 C 1910037-1912151  
                 spoT 
                   
                 guanosine-3′,5′-bis 3′pyrophosphohydrolase 
                 2591 
               
               
                 C 1912224-1912490  
                 rpoZ 
                   
                 DNA directed RNA polymerase omega chain 
                 2592 
               
               
                 C 1912553-1913179  
                 gmk 
                   
                 guanylate kinase 
                 2593 
               
               
                   
               
             
          
         
       
     
         [0000]    
       
         
               
             
               
               
               
             
           
               
                 TABLE 7 
               
             
             
               
                   
               
               
                 Gene Products of the NTHi Genome 
               
             
          
           
               
                 Gene 
                   
                 SEQ ID 
               
               
                 Name 
                 Product Name 
                 NO: 
               
               
                   
               
               
                 gapA 
                 glyceraldehyde 3-phosphate dehydrogenase 
                 2594 
               
               
                 — 
                 putative long-chain-fatty-acid--CoA ligase 
                 2595 
               
               
                 — 
                 conserved hypothetical protein 
                 2596 
               
               
                 — 
                 conserved hypothetical protein 
                 2597 
               
               
                 fdhD 
                 FdhD protein homolog 
                 2598 
               
               
                 fdxG 
                 formate dehydrogenase major subunit 
                 2599 
               
               
                 fdxH 
                 formate dehydrogenase, iron-sulfur subunit 
                 2600 
               
               
                 fdxI 
                 formate dehydrogenase, cytochrome B556 subunit 
                 2601 
               
               
                 fdhE 
                 FdhE homolog 
                 2602 
               
               
                 rimI 
                 ribosomal-protein-alanine acetyltransferase 
                 2603 
               
               
                 holD 
                 DNA polymerase III, psi subunit 
                 2604 
               
               
                 rsmC 
                 ribosomal RNA small subunit methyltransferase C 
                 2605 
               
               
                 era 
                 GTP-binding protein era homolog 
                 2606 
               
               
                 rnc 
                 ribonuclease III 
                 2607 
               
               
                 lepB 
                 Signal peptidase I 
                 2608 
               
               
                 lepA 
                 GTP-binding protein LepA 
                 2609 
               
               
                 — 
                 conserved hypothetical acid-induced glycyl 
                 2610 
               
               
                   
                 radical enzyme  
                   
               
               
                 ung 
                 uracil-DNA glycosylase 
                 2611 
               
               
                 — 
                 conserved hypothetical protein 
                 2612 
               
               
                 — 
                 conserved hypothetical protein 
                 2613 
               
               
                 citG 
                 CitXG 
                 2614 
               
               
                 citF 
                 citrate lyase alpha chain 
                 2615 
               
               
                 citE 
                 citrate lyase beta chain 
                 2616 
               
               
                 citD 
                 citrate lyase acyl carrier protein 
                 2617 
               
               
                 citC 
                 [citrate [pro-3S]-lyase] ligase 
                 2618 
               
               
                 lipA 
                 Lipoic acid synthetase 
                 2619 
               
               
                 lipB 
                 lipoate-protein ligase B 
                 2620 
               
               
                 — 
                 conserved hypothetical protein 
                 2621 
               
               
                 dacA 
                 penicillin-binding protein 5 precursor 
                 2622 
               
               
                 rlpA 
                 RlpA-like protein 
                 2623 
               
               
                 mrdB 
                 Rod shape-determining protein RodA 
                 2624 
               
               
                 mrdA 
                 penicillin-binding protein 2 
                 2625 
               
               
                 — 
                 conserved hypothetical protein 
                 2626 
               
               
                 — 
                 conserved hypothetical protein 
                 2627 
               
               
                 — 
                 conserved hypothetical membrane protein 
                 2628 
               
               
                 — 
                 conserved hypothetical ABC transporter ATP-binding 
                 2629 
               
               
                   
                 protein 
                   
               
               
                 mreB 
                 rod shape-determining protein MreB 
                 2630 
               
               
                 mreC 
                 rod shape-determining protein MreC 
                 2631 
               
               
                 mreD 
                 rod shape-determining protein MreD 
                 2632 
               
               
                 — 
                 conserved hypothetical protein 
                 2633 
               
               
                 xthA 
                 exodeoxyribonuclease III 
                 2634 
               
               
                 rluA2 
                 conserved hypothetical pseudouridine synthase 
                 2635 
               
               
                 — 
                 conserved hypothetical membrane protein 
                 2636 
               
               
                 — 
                 conserved hypothetical FtsH-interacting integral 
                 2637 
               
               
                   
                 membrane protein 
                   
               
               
                 — 
                 conserved hypothetical protein 
                 2638 
               
               
                 phnA 
                 PhuA homolog 
                 2639 
               
               
                 eda 
                 KHG/KDPG aldolase 
                 2640 
               
               
                 uxuC 
                 uronate isomerase 
                 2641 
               
               
                 — 
                 putative oxidoreductase 
                 2642 
               
               
                 — 
                 putative TRAP-type C4-dicarboxylate transport 
                 2643 
               
               
                   
                 system, large permease component 
                   
               
               
                 — 
                 putative TRAP-type C4-dicarboxylate transport 
                 2644 
               
               
                   
                 system, small permease component 
                   
               
               
                 — 
                 putative TRAP-type C4-dicarboxylate transport 
                 2645 
               
               
                   
                 system, periplasmic component 
                   
               
               
                 — 
                 conserved hypothetical zinc-type alcohol 
                 2646 
               
               
                   
                 dehydrogenase-like protein 
                   
               
               
                 uxuR 
                 Uxu operon regulator 
                 2647 
               
               
                 uxuA 
                 mannonate dehydratase 
                 2648 
               
               
                 — 
                 putative membrane protein TerC 
                 2649 
               
               
                 uvrC 
                 UvrABC system protein C 
                 2650 
               
               
                 kdsB 
                 3-deoxy-D-manno-octulosonic acid 
                 2651 
               
               
                   
                 cytidylyltransferase 
                   
               
               
                 lpxK 
                 tetraacyldisaccharide 4′-kinase 
                 2652 
               
               
                 msbA 
                 lipid A export ATP-binding protein MsbA 
                 2653 
               
               
                 rec2 
                 recombination protein 2 
                 2654 
               
               
                 dksA 
                 DnaK suppressor protein 
                 2655 
               
               
                 pcnB 
                 probable poly polymerase 
                 2656 
               
               
                 folK 
                 2-amino-4-hydroxy-6-hydroxymethyl- 
                 2657 
               
               
                   
                 dihydropteridine pyrophosphokinase 
                   
               
               
                 — 
                 conserved hypothetical protein 
                 2658 
               
               
                 amiB 
                 probable N-acetylmuramoyl-L-alanine amidase AmiB 
                 2659 
               
               
                   
                 precursor 
                   
               
               
                 mutL 
                 DNA mismatch repair protein MutL 
                 2660 
               
               
                 miaA 
                 tRNA delta-isopentenylpyrophosphate transferase 
                 2661 
               
               
                 glnE 
                 glutamate-ammonia-ligase adenylyltransferase 
                 2662 
               
               
                 recN 
                 DNA repair protein RecN 
                 2663 
               
               
                 ppnK 
                 probable inorganic polyphosphate/ATP-NAD kinase 
                 2664 
               
               
                 grpE 
                 grpE 
                 2665 
               
               
                 — 
                 conserved hypothetical protein 
                 2666 
               
               
                 — 
                 conserved hypothetical protein 
                 2667 
               
               
                 nrdD 
                 anaerobic ribonucleoside-triphosphate reductase 
                 2668 
               
               
                 tesB 
                 Acyl-CoA thioesterase II 
                 2669 
               
               
                 cysS 
                 cysteinyl-tRNA synthetase 
                 2670 
               
               
                 ppiB 
                 peptidyl-prolyl cis-trans isomerase B 
                 2671 
               
               
                 — 
                 conserved hypothetical protein 
                 2672 
               
               
                 — 
                 putative deoxyribonuclease 
                 2673 
               
               
                 — 
                 hypothetical protein 
                 2674 
               
               
                 — 
                 hypothetical protein 
                 2675 
               
               
                 trxA 
                 thioredoxin 
                 2676 
               
               
                 ddh 
                 2-hydroxyacid dehydrogenase homolog 
                 2677 
               
               
                 metB 
                 cystathionine gamma-synthase 
                 2678 
               
               
                 — 
                 predicted ATPase involved in chromosome 
                 2679 
               
               
                   
                 partitioning 
                   
               
               
                 dnaB2 
                 replicative DNA helicase 
                 2680 
               
               
                 — 
                 conserved hypothetical protein 
                 2681 
               
               
                 — 
                 conserved hypothetical protein 
                 2682 
               
               
                 — 
                 conserved hypothetical protein 
                 2683 
               
               
                 — 
                 conserved hypothetical protein 
                 2684 
               
               
                 — 
                 conserved hypothetical protein 
                 2685 
               
               
                 ssb2 
                 Single-strand binding protein 
                 2686 
               
               
                 — 
                 conserved putative lipoprotein 
                 2687 
               
               
                 — 
                 1conserved hypothetical protein 
                 2688 
               
               
                 topB2 
                 DNA topoisomerase III 
                 2689 
               
               
                 — 
                 conserved hypothetical protein 
                 2690 
               
               
                 — 
                 hypothetical protein 
                 2691 
               
               
                 — 
                 conserved hypothetical protein 
                 2692 
               
               
                 — 
                 hypothetical protein 
                 2693 
               
               
                 radC2 
                 putative DNA repair radC-like protein 
                 2694 
               
               
                 — 
                 conserved hypothetical protein 
                 2695 
               
               
                 — 
                 conserved hypothetical protein 
                 2696 
               
               
                 pilL 
                 conserved putative lipoprotein 
                 2697 
               
               
                 — 
                 conserved putative exported protein 
                 2698 
               
               
                 — 
                 conserved putative exported protein 
                 2699 
               
               
                 — 
                 conserved putative exported protein 
                 2700 
               
               
                 — 
                 conserved hypothetical protein 
                 2701 
               
               
                 — 
                 conserved putative membrane protein 
                 2702 
               
               
                 — 
                 conserved putative membrane protein 
                 2703 
               
               
                 — 
                 conserved putative membrane protein 
                 2704 
               
               
                 — 
                 conserved putative membrane protein 
                 2705 
               
               
                 — 
                 conserved putative exported protein 
                 2706 
               
               
                 — 
                 conserved hypothetical protein 
                 2707 
               
               
                 — 
                 conserved putative exported protein 
                 2708 
               
               
                 — 
                 conserved putative lipoprotein 
                 2709 
               
               
                 — 
                 conserved hypothetical protein 
                 2710 
               
               
                 — 
                 conserved hypothetical protein 
                 2711 
               
               
                 — 
                 conserved hypothetical membrane protein 
                 2712 
               
               
                 — 
                 conserved putative membrane protein 
                 2713 
               
               
                 — 
                 conserved hypothetical membrane protein 
                 2714 
               
               
                 tnpA 
                 transposon Tn3 transposase 
                 2715 
               
               
                 — 
                 hypothetical protein 
                 2716 
               
               
                 tnpR 
                 transposon Tn3 resolvase 
                 2717 
               
               
                 — 
                 hypothetical protein 
                 2718 
               
               
                 — 
                 hypothetical exported protein 
                 2719 
               
               
                 — 
                 conserved putative exported protein 
                 2720 
               
               
                 — 
                 conserved putative exported protein 
                 2721 
               
               
                 — 
                 conserved hypothetical protein 
                 2722 
               
               
                 — 
                 conserved hypothetical membrane protein 
                 2723 
               
               
                 — 
                 conserved hypothetical protein 
                 2724 
               
               
                 — 
                 hypothetical protein 
                 2725 
               
               
                 — 
                 hypothetical protein 
                 2726 
               
               
                 traC 
                 conserved putative antirestriction protein 
                 2727 
               
               
                 — 
                 possible type I restriction enzyme M subunit 
                 2728 
               
               
                 — 
                 hypothetical protein 
                 2729 
               
               
                 — 
                 conserved hypothetical protein 
                 2730 
               
               
                 — 
                 conserved hypothetical protein 
                 2731 
               
               
                 — 
                 conserved hypothetical protein 
                 2732 
               
               
                 — 
                 resolvase/integrase-like protein 
                 2733 
               
               
                 — 
                 hypothetical protein 
                 2734 
               
               
                 — 
                 hypothetical protein 
                 2735 
               
               
                 — 
                 conserved hypothetical protein 
                 2736 
               
               
                 — 
                 hypothetical protein 
                 2737 
               
               
                 — 
                 conserved hypothetical protein 
                 2738 
               
               
                 — 
                 putative site-specific recombinase 
                 2739 
               
               
                 thrC 
                 threonine synthase 
                 2740 
               
               
                 thrB 
                 homoserine kinase 
                 2741 
               
               
                 thrA 
                 aspartokinase/homoserine dehydrogenase 
                 2742 
               
               
                 — 
                 conserved hypothetical protein 
                 2743 
               
               
                 grk 
                 glycerate kinase 
                 2744 
               
               
                 — 
                 conserved hypothetical protein 
                 2745 
               
               
                 — 
                 conserved hypothetical protein 
                 2746 
               
               
                 — 
                 conserved hypothetical protein 
                 2747 
               
               
                 — 
                 conserved hypothetical protein 
                 2748 
               
               
                 — 
                 conserved hypothetical protein 
                 2749 
               
               
                 hitA 
                 iron-utilization periplasmic protein hFbpA 
                 2750 
               
               
                 hitB 
                 iron(III)-transport system permease protein 
                 2751 
               
               
                   
                 hFbpB 
                   
               
               
                 hitC 
                 iron-utilization ATP-binding protein hFbpC 
                 2752 
               
               
                 — 
                 putative D-alanyl-D-alanine carboxypeptidase 
                 2753 
               
               
                 dapE 
                 succinyl-diaminopimelate desuccinylase 
                 2754 
               
               
                 — 
                 conserved hypothetical protein 
                 2755 
               
               
                 — 
                 chaperone protein HtpG 
                 2756 
               
               
                 — 
                 conserved hypothetical NIF3-like protein 
                 2757 
               
               
                 hsdM1 
                 putative type I restriction-modification system, 
                 2758 
               
               
                   
                 methyltransferase subunit 
                   
               
               
                 — 
                 predicted transcriptional regulator containing 
                 2759 
               
               
                   
                 an HTH domain 
                   
               
               
                 hsdS1 
                 putative type I site-specific restriction-modification 
                 2760 
               
               
                   
                 system, S subunit 
                   
               
               
                 hsdR1 
                 putative type I site-specific restriction-modification 
                 2761 
               
               
                   
                 system, R subunit 
                   
               
               
                 ffh 
                 Signal recognition particle protein 
                 2762 
               
               
                 corB 
                 putative Mg2+ and Co2+ transporter 
                 2763 
               
               
                 — 
                 conserved hypothetical protein 
                 2764 
               
               
                 — 
                 conserved hypothetical protein 
                 2765 
               
               
                 — 
                 conserved hypothetical protein 
                 2766 
               
               
                 serS 
                 Seryl-tRNA synthetase 
                 2767 
               
               
                 gst 
                 glutathione S-transferase 
                 2768 
               
               
                 — 
                 conserved hypothetical protein 
                 2769 
               
               
                 hemR 
                 heroin receptor 
                 2770 
               
               
                 — 
                 possible SAM-dependent methyltransferase 
                 2771 
               
               
                 mltA 
                 membrane-bound lytic murein transglycosylase A 
                 2772 
               
               
                   
                 precursor 
                   
               
               
                 — 
                 conserved hypothetical protein 
                 2773 
               
               
                 znuA 
                 high-affinity zinc uptake system protein ZnuA 
                 2774 
               
               
                 — 
                 conserved hypothetical protein 
                 2775 
               
               
                 mpl 
                 UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl- 
                 2776 
               
               
                   
                 meso-diaminopimelate ligase 
                   
               
               
                 metC 
                 cystathionine beta-lyase 
                 2777 
               
               
                 tsaA 
                 probable peroxiredoxin 
                 2778 
               
               
                 pgsA 
                 CDP-diacylglycerol--glycerol-3-phosphate 3- 
                 2779 
               
               
                   
                 phosphatidyltransferase 
                   
               
               
                 ppa 
                 inorganic pyrophosphatase 
                 2780 
               
               
                 — 
                 conserved hypothetical protein 
                 2781 
               
               
                 udk 
                 uridine kinase 
                 2782 
               
               
                 dcd 
                 deoxycytidine triphosphate deaminase 
                 2783 
               
               
                 — 
                 conserved hypothetical protein 
                 2784 
               
               
                 — 
                 probable sugar efflux transporter 
                 2785 
               
               
                 engA 
                 GTP-binding protein EngA 
                 2786 
               
               
                 dnaQ 
                 DNA polymerase III, epsilon chain 
                 2787 
               
               
                 rnhA 
                 ribonuclease HI 
                 2788 
               
               
                 omP2 
                 Outer membrane protein P2 precursor 
                 2789 
               
               
                 nagA 
                 N-acetylglucosamine-6-phosphate deacetylase 
                 2790 
               
               
                 nagB 
                 glucosamine-6-phosphate deaminase 
                 2791 
               
               
                 nanA 
                 N-acetylneuraminate lyase 
                 2792 
               
               
                 — 
                 putative HTH-type transcriptional regulator 
                 2793 
               
               
                 nanK 
                 putative N-acetylmannosamine kinase 
                 2794 
               
               
                 nanE 
                 putative N-acetylmannosamine-6-phosphate 
                 2795 
               
               
                   
                 2-epimerase 
                   
               
               
                 — 
                 putative sialic acid transporter, TRAP-type 
                 2796 
               
               
                   
                 C4-dicarboxylate transport system, periplasmic 
                   
               
               
                   
                 component 
                   
               
               
                 siaT 
                 putative sialic acid transporter, TRAP-type 
                 2797 
               
               
                   
                 C4-dicarboxylate transport system, large permease 
                   
               
               
                   
                 component 
                   
               
               
                 — 
                 conserved hypothetical protein 
                 2798 
               
               
                 — 
                 putative protein-S-isoprenylcysteine 
                 2799 
               
               
                   
                 methyltransferase 
                   
               
               
                 hflC 
                 HflC 
                 2800 
               
               
                 hflK 
                 HhflK 
                 2801 
               
               
                 — 
                 putative 4′-phosphopantetheinyl transferase 
                 2802 
               
               
                 dcuB2 
                 anaerobic C4-dicarboxylate transporter DcuB 
                 2803 
               
               
                 acpP 
                 acyl carrier protein 
                 2804 
               
               
                 fabG 
                 3-oxoacyl-[acyl-carrier protein] reductase 
                 2805 
               
               
                 fabD 
                 malonyl CoA-acyl carrier protein transacylase 
                 2806 
               
               
                 fabH 
                 3-oxoacyl-[acyl-carrier-protein] synthase III 
                 2807 
               
               
                 rpmF 
                 50S ribosomal protein L32 
                 2808 
               
               
                 — 
                 conserved hypothetical protein 
                 2809 
               
               
                 psd 
                 phosphatidylserine decarboxylase proenzyme 
                 2810 
               
               
                 gor 
                 glutathione reductase 
                 2811 
               
               
                 — 
                 conserved hypothetical lipoprotein 
                 2812 
               
               
                 nqrA 
                 Na(+)-translocating NADH-quinone reductase 
                 2813 
               
               
                   
                 subunit A 
                   
               
               
                 nqrB 
                 Na(+)-translocating NADH-quinone reductase 
                 2814 
               
               
                   
                 subunit B 
                   
               
               
                 nqrC 
                 Na(+)-translocating NADH-quinone reductase 
                 2815 
               
               
                   
                 subunit C 
                   
               
               
                 nqrD 
                 Na(+)-translocating NADH-quinone reductase 
                 2816 
               
               
                   
                 subunit D 
                   
               
               
                 nqrE 
                 Na(+)-translocating NADH-quinone reductase 
                 2817 
               
               
                   
                 subunit E 
                   
               
               
                 nqrF 
                 Na(+)-translocating NADH-quinone reductase 
                 2818 
               
               
                   
                 subunit F 
                   
               
               
                 apbE 
                 thiamine biosynthesis lipoprotein ApbE 
                 2819 
               
               
                 — 
                 conserved hypothetical protein 
                 2820 
               
               
                 trmU 
                 probable tRNA (5-methylaminomethyl-2- 
                 2821 
               
               
                   
                 thiouridylate)-methyltransferase 
                   
               
               
                 — 
                 conserved hypothetical protein 
                 2822 
               
               
                 rluD 
                 ribosomal large subunit pseudouridine synthase 
                 2823 
               
               
                   
                 D 
                   
               
               
                 — 
                 conserved hypothetical lipoprotein 
                 2824 
               
               
                 — 
                 conserved hypothetical protein 
                 2825 
               
               
                 pflA 
                 pyruvate formate-lyase 1 activating enzyme 
                 2826 
               
               
                 pflB 
                 formate acetyltransferase 
                 2827 
               
               
                 focA 
                 probable formate transporter 
                 2828 
               
               
                 — 
                 conserved hypothetical protein 
                 2829 
               
               
                 — 
                 putative Na+/alanine symporter 
                 2830 
               
               
                 — 
                 conserved hypothetical protein 
                 2831 
               
               
                 — 
                 putative HTH-type transcriptional regulator 
                 2832 
               
               
                 tatA 
                 Sec-independent protein translocase protein 
                 2833 
               
               
                   
                 TatA/E 
                   
               
               
                 tatB 
                 Sec-independent protein translocase protein 
                 2834 
               
               
                   
                 TatB 
                   
               
               
                 tatC 
                 Sec-independent protein translocase protein 
                 2835 
               
               
                   
                 TatC 
                   
               
               
                 gdhA 
                 NADP-specific glutamate dehydrogenase 
                 2836 
               
               
                 fur 
                 Ferric uptake regulation protein 
                 2837 
               
               
                 fldA 
                 flavodoxin 
                 2838 
               
               
                 seqA 
                 seqA 
                 2839 
               
               
                 — 
                 putative esterase/lipase 
                 2840 
               
               
                 menE 
                 O-succinylbenzoate--CoA ligase 
                 2841 
               
               
                 — 
                 putative small-conductance mechanosensitive 
                 2842 
               
               
                   
                 channel 
                   
               
               
                 aroC 
                 chorismate synthase 
                 2843 
               
               
                 mepA 
                 penicillin-insensitive murein endopeptidase 
                 2844 
               
               
                 — 
                 conserved hypothetical protein 
                 2845 
               
               
                 msbB 
                 lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA 
                 2846 
               
               
                   
                 acyltransferase 
                   
               
               
                 selD 
                 selenide, water dikinase 
                 2847 
               
               
                 rplsS 
                 50S ribosomal protein L19 
                 2848 
               
               
                 trmD 
                 tRNA (guanine-N(1)-)-methyltransferase 
                 2849 
               
               
                 rimM 
                 16S rRNA processing protein RimM 
                 2850 
               
               
                 rspP 
                 30S ribosomal protein S16 
                 2851 
               
               
                 — 
                 conserved hypothetical protein 
                 2852 
               
               
                 nadN 
                 NAD nucleotidase 
                 2853 
               
               
                 aroK 
                 shikimate kinase 
                 2854 
               
               
                 aroB 
                 3-dehydroquinate synthase 
                 2855 
               
               
                 dam 
                 DNA adenine methylase 
                 2856 
               
               
                 — 
                 conserved hypothetical protein 
                 2857 
               
               
                 pgpB 
                 phosphatidylglycerophosphatase B 
                 2858 
               
               
                 ribA 
                 GTP cyclohydrolase II 
                 2859 
               
               
                 — 
                 putative ABC-type oligopeptide transport system, 
                 2860 
               
               
                   
                 periplasmic component 
                   
               
               
                 — 
                 conserved hypothetical protein 
                 2861 
               
               
                 prlc 
                 oligopeptidase A 
                 2862 
               
               
                 Hsdm2 
                 putative type I restriction-modification system 
                 2863 
               
               
                   
                 methyltransferase subunit 
                   
               
               
                 Hsds2 
                 putative type I restriction-modification system 
                 2864 
               
               
                   
                 specificity protein 
                   
               
               
                 prrC 
                 putative anticodon nuclease 
                 2865 
               
               
                 — 
                 conserved hypothetical DNA binding protein 
                 2866 
               
               
                 Hsdr2 
                 putative type I restriction-modification system 
                 2867 
               
               
                 — 
                 conserved hypothetical protein 
                 2868 
               
               
                 arcb 
                 aerobic respiration control sensor protein ArcB 
                 2869 
               
               
                 — 
                 predicted uracil-DNA glycosylase 
                 2870 
               
               
                 bira 
                 BirA bifunctional protein 
                 2871 
               
               
                 guab 
                 inosine-5′-monophosphate dehydrogenase 
                 2872 
               
               
                 guaa 
                 glutamine-hydrolyzing GMP synthase 
                 2873 
               
               
                 — 
                 conserved hypothetical protein 
                 2874 
               
               
                 — 
                 putative transcriptional regulator 
                 2875 
               
               
                 nhaa 
                 Na(+)/H(+) antiporter 1 
                 2876 
               
               
                 brnq 
                 branched-chain amino acid transport system 
                 2877 
               
               
                   
                 carrier protein 
                   
               
               
                 — 
                 conserved hypothetical protein 
                 2878 
               
               
                 — 
                 conserved hypothetical protein 
                 2879 
               
               
                 pnp 
                 polyribonucleotide nucleotidyltransferase 
                 2880 
               
               
                 n1pL 
                 lipoprotein N1pI 
                 2881 
               
               
                 dead 
                 Cold-shock DEAD-box protein A homolog 
                 2882 
               
               
                 — 
                 predicted soluble lytic transglycosylase fused 
                 2883 
               
               
                   
                 to an ABC-type amino acid-binding protein 
                   
               
               
                 — 
                 conserved hypothetical protein 
                 2884 
               
               
                 — 
                 conserved hypothetical protein 
                 2885 
               
               
                 — 
                 conserved hypothetical protein 
                 2886 
               
               
                 arsc 
                 putative arsenate reductase 
                 2887 
               
               
                 perm 
                 putative permease PerM homolog 
                 2888 
               
               
                 secf 
                 protein-export membrane protein SecF 
                 2889 
               
               
                 secd 
                 protein-export membrane protein SecD 
                 2890 
               
               
                 — 
                 conserved hypothetical preprotein translocase 
                 2891 
               
               
                   
                 subunit YajC 
                   
               
               
                 — 
                 predicted redox protein, regulator of disulfide 
                 2892 
               
               
                   
                 bond formation 
                   
               
               
                 — 
                 conserved hypothetical protein 
                 2893 
               
               
                 tgt 
                 queuine tRNA-ribosyltransferase 
                 2894 
               
               
                 quea 
                 S-adenosylmethionine:tRNA ribosyltransferase- 
                 2895 
               
               
                   
                 isomerase 
                   
               
               
                 — 
                 conserved hypothetical protein 
                 2896 
               
               
                 hap 
                 adhesion and penetration protein Hap 
                 2897 
               
               
                 uvra 
                 UvrABC system protein A 
                 2898 
               
               
                 ssb 
                 Single-strand binding protein 
                 2899 
               
               
                 tonb 
                 TonB 
                 2900 
               
               
                 exbd 
                 transport protein ExbD 
                 2901 
               
               
                 exbb 
                 transport protein ExbB 
                 2902 
               
               
                 bcp 
                 bacterioferritin comigratory protein 
                 2903 
               
               
                 dapa 
                 dihydrodipicolinate synthase 
                 2904 
               
               
                 — 
                 conserved hypothetical lipoprotein 
                 2905 
               
               
                 — 
                 conserved hypothetical protein 
                 2906 
               
               
                 lgtC 
                 UDP-galactose--lipooligosaccharide 
                 2907 
               
               
                   
                 galactosyltransferase 
                   
               
               
                 orfM 
                 predicted xanthosine triphosphate pyrophosphatase 
                 2908 
               
               
                 kdkA 
                 3-deoxy-D-manno-octulosonic acid kinase 
                 2909 
               
               
                 opsX 
                 ADP-heptose--lipooligosaccharide 
                 2910 
               
               
                   
                 heptosyltransferase I 
                   
               
               
                 hxuC 
                 heme/hemopexin-binding protein C 
                 2911 
               
               
                 hxuB 
                 heme/hemopexin-binding protein B 
                 2912 
               
               
                 hxuA 
                 heme/hemopexin-binding protein A 
                 2913 
               
               
                 folB 
                 dihydroneopterin aldolase 
                 2914 
               
               
                 — 
                 conserved hypothetical protein 
                 2915 
               
               
                 narQ 
                 sensor protein NarQ 
                 2916 
               
               
                 murB 
                 UDP-N-acetylenolpyruvoylglucosamine reductase 
                 2917 
               
               
                 rpoH 
                 RNA polymerase sigma-32 factor 
                 2918 
               
               
                 dj1A 
                 DnaJ-like protein Dj1A 
                 2919 
               
               
                 pyrE 
                 orotate phosphoribosyltransferase 
                 2920 
               
               
                 rph 
                 ribonuclease PH 
                 2921 
               
               
                 gltX 
                 glutamyl-tRNA synthetase 
                 2922 
               
               
                 Lpt6 
                 PE-tn-6--lipooligosaccharide 
                 2923 
               
               
                   
                 phosphorylethanolamine transferase 
                   
               
               
                 rbn 
                 tRNA processing ribonuclease BN 
                 2924 
               
               
                 — 
                 conserved hypothetical protein 
                 2925 
               
               
                 — 
                 conserved hypothetical protein 
                 2926 
               
               
                 udp 
                 uridine phosphorylase 
                 2927 
               
               
                 — 
                 conserved hypothetical metabolite transport 
                 2928 
               
               
                   
                 protein 
                   
               
               
                 — 
                 conserved hypothetical protein 
                 2929 
               
               
                 mend 
                 menaquinone biosynthesis protein MenD 
                 2930 
               
               
                 menf 
                 menaquinone-specific isochorismate synthase 
                 2931 
               
               
                 Aspc3 
                 probable aspartate aminotransferase 
                 2932 
               
               
                 mtr 
                 tryptophan-specific transport protein 
                 2933 
               
               
                 sdaa 
                 L-serine dehydratase 
                 2934 
               
               
                 sdac 
                 Serine transporter 
                 2935 
               
               
                 — 
                 probable cation-transporting ATPase 
                 2936 
               
               
                 — 
                 probable heavy metal dependent transcriptional 
                 2937 
               
               
                   
                 regulator 
                   
               
               
                 metJ 
                 Met repressor 
                 2938 
               
               
                 rho 
                 transcription termination factor rho 
                 2939 
               
               
                 pilD 
                 putative type 4 prepilin-like protein specific 
                 2940 
               
               
                   
                 leader peptidase 
                   
               
               
                 pilC 
                 putative type IV pilin secretiotrprotein 
                 2941 
               
               
                 pilB 
                 putative type IV pilin secretion protein 
                 2942 
               
               
                 pilA 
                 Type IV pilin subunit protein 
                 2943 
               
               
                 ampD 
                 ampD 
                 2944 
               
               
                 corC 
                 magnesium and cobalt efflux protein CorC 
                 2945 
               
               
                 cutE 
                 apolipoprotein N-acyltransferase 
                 2946 
               
               
                 — 
                 conserved hypothetical RNA methyltransferase 
                 2947 
               
               
                 — 
                 conserved hypothetical protein 
                 2948 
               
               
                 ruvX 
                 putative holliday junction resolvase 
                 2949 
               
               
                 — 
                 prophage CP4-57-like integrase 
                 2950 
               
               
                 — 
                 hypothetical protein 
                 2951 
               
               
                 — 
                 hypothetical protein 
                 2952 
               
               
                 — 
                 hypothetical protein 
                 2953 
               
               
                 — 
                 hypothetical protein 
                 2954 
               
               
                 — 
                 hypothetical protein 
                 2955 
               
               
                 — 
                 hypothetical protein 
                 2956 
               
               
                 proC 
                 pyrroline-5-carboxylate reductase 
                 2957 
               
               
                 hcaT 
                 probable 3-phenylpropionic acid transporter 
                 2958 
               
               
                 xerD 
                 Site-specific recombinase XerD 
                 2959 
               
               
                 — 
                 conserved hypothetical protein 
                 2960 
               
               
                 ruvB 
                 holliday junction DNA helicase RuvB 
                 2961 
               
               
                 ruvA 
                 holliday junction DNA helicase RuvA 
                 2962 
               
               
                 ruvC 
                 holliday junction DNA helicase RuvC 
                 2963 
               
               
                 — 
                 conserved hypothetical protein 
                 2964 
               
               
                 ntpA 
                 dATP pyrophosphohydrolase 
                 2965 
               
               
                 aspS 
                 Aspartyl-tRNA synthetase 
                 2966 
               
               
                 — 
                 conserved hypothetical protein 
                 2967 
               
               
                 — 
                 conserved hypothetical protein 
                 2968 
               
               
                 — 
                 conserved hypothetical protein 
                 2969 
               
               
                 — 
                 Predicted nucleic acid-binding domain, containsPIN 
                 2970 
               
               
                   
                 domain 
                   
               
               
                 gloA 
                 Lactoylglutathione lyase 
                 2971 
               
               
                 Rnt 
                 Ribonuclease T 
                 2972 
               
               
                 — 
                 conserved hypothetical protein 
                 2973 
               
               
                 — 
                 Predicted primosomal replication protein N 
                 2974 
               
               
                 Efp 
                 Elongation factor P 
                 2975 
               
               
                 — 
                 Predicted lysine 2,3-aminomutase 
                 2976 
               
               
                 oapA 
                 Opacity associated protein OapA 
                 2977 
               
               
                 oapB 
                 Opacity associated protein OapB 
                 2978 
               
               
                 recO 
                 DNA repair protein RecO 
                 2979 
               
               
                 rumA 
                 23S rRNA (uracil-5--)methyltransferase RumA 
                 2980 
               
               
                 relA 
                 GTP pyrophosphokinase 
                 2981 
               
               
                 dgkA 
                 Diacylglycerol kinase 
                 2982 
               
               
                 Mog 
                 Molybdopterin biosynthesis mog protein 
                 2983 
               
               
                 glnB 
                 Nitrogen regulatory protein P-II 
                 2984 
               
               
                 — 
                 conserved hypothetical protein 
                 2985 
               
               
                 priA 
                 Prismosomal protein N 
                 2986 
               
               
                 trmB 
                 tRNA (guanine-N(7)-)-methyltransferase 
                 2987 
               
               
                 — 
                 conserved hypothetical protein 
                 2988 
               
               
                 napF 
                 Ferredoxin-type protein NapF 
                 2989 
               
               
                 napD 
                 NapD 
                 2990 
               
               
                 napA 
                 Periplasmic nitrate reductase 
                 2991 
               
               
                 napG 
                 Ferredoxin-type protein NapG 
                 2992 
               
               
                 napH 
                 Ferredoxin-type protein NapH 
                 2993 
               
               
                 napB 
                 Diheme cytochrome C NapB 
                 2994 
               
               
                 napC 
                 Cytochrome C-type protein NapC 
                 2995 
               
               
                 Adk 
                 Adenylate kinase 
                 2996 
               
               
                 Lic3c 
                 Putative integral membrane signal transducer protein 
                 2997 
               
               
                 galE 
                 UDP-glucose 4-epimerase 
                 2998 
               
               
                 Lic3A 
                 CMP-Neu5Ac--lipooligosaccharide alpha 2-3 
                 2999 
               
               
                   
                 sialytransferase 
                   
               
               
                 — 
                 Putative ABC-type nitrate/sulfonate/bicarbonate 
                 3000 
               
               
                   
                 transport system, ATPase component 
                   
               
               
                 — 
                 Putative ABC-type nitrate/sulfonate/bicarbonate 
                 3001 
               
               
                   
                 transport system, permease component 
                   
               
               
                 — 
                 Putative ABC-type nitrate/sulfonate/bicarbonate 
                 3002 
               
               
                   
                 transport system, periplasmic component 
                   
               
               
                 — 
                 Putative transcription activator 
                 3003 
               
               
                 hfeD 
                 Putative ABC-type chelated iron transport system, 
                 3004 
               
               
                   
                 permease component 
                   
               
               
                 hfeC 
                 Putative ABC-type chelated iron transport system, 
                 3005 
               
               
                   
                 permease component 
                   
               
               
                 hfeB 
                 Putative ABC-type chelated iron transport system, 
                 3006 
               
               
                   
                 ATPase component 
                   
               
               
                 hfeA 
                 Putative periplasmic chelated iron binding protein 
                 3007 
               
               
                 — 
                 Hypothetical protein 
                 3008 
               
               
                 pbpG 
                 Penicillin-binding protein 7 homolog precursos 
                 3009 
               
               
                 — 
                 Predicted Fe-S-cluster redox enzyme 
                 3010 
               
               
                 — 
                 Conserved hypothetical protein 
                 3011 
               
               
                 — 
                 Conserved hypothetical transcriptional regulator with 
                 3012 
               
               
                   
                 an N-terminal xre-type HTH domain 
                   
               
               
                 gcpE 
                 4-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate 
                 3013 
               
               
                   
                 synthase 
                   
               
               
                 hisS 
                 Histidyl-tRNA synthetase 
                 3014 
               
               
                 — 
                 Conserved hypothetical protein 
                 3015 
               
               
                 — 
                 conserved hypothetical protein 
                 3016 
               
               
                 Fdx 
                 Feerdoxin, 2Fe-S 
                 3017 
               
               
                 hscA 
                 Chaperone protein HscA 
                 3018 
               
               
                 — 
                 Conserved hypothetical protein 
                 3019 
               
               
                 hscB 
                 Co-chaperone protein HscB 
                 3020 
               
               
                 — 
                 Conserved hypothetical protein 
                 3021 
               
               
                 nifU 
                 NifU-like protein 
                 3022 
               
               
                 nifS2 
                 Cysteine sedulferase 
                 3023 
               
               
                 — 
                 Predicted transcriptional regulator 
                 3024 
               
               
                 — 
                 Hypothetical tRNA/rRNA methyltransferase 
                 3025 
               
               
                 Pa1 
                 Outer membrane protein P6 precursor 
                 3026 
               
               
                 to1B 
                 To1B 
                 3027 
               
               
                 to1A 
                 To1A 
                 3028 
               
               
                 to1R 
                 To1R 
                 3029 
               
               
                 to1Q 
                 To1Q 
                 3030 
               
               
                 — 
                 Predicted thioestererase 
                 3031 
               
               
                 dinG 
                 Probable ATP-dependent helicase 
                 3032 
               
               
                 — 
                 Possible inactive homolog of metal-dependent 
                 3033 
               
               
                   
                 proteases, putative molecular chaperone 
                   
               
               
                 — 
                 possible starvation-inducible outer membrane 
                 3034 
               
               
                   
                 lipoprotein 
                   
               
               
                 lcfA 
                 Long chain fatty acid CoA ligase 
                 3035 
               
               
                 mD 
                 Ribonuclease D 
                 3036 
               
               
                 — 
                 Conserved hypothetical acyltransferase 
                 3037 
               
               
                 — 
                 Predicted GTPase, probable translation factor 
                 3038 
               
               
                 Pth 
                 Peptidyl-tRNA hydrolase 
                 3039 
               
               
                 — 
                 Conserved hypothetical protein 
                 3040 
               
               
                 — 
                 Conserved hypothetical cupin superfamily 
                 3041 
               
               
                   
                 metalloenzyme 
                   
               
               
                 xseA 
                 Exodeoxyribonuclease VII large subunit 
                 3042 
               
               
                 adpP 
                 ADP-ribose pyrophoaphatase 
                 3043 
               
               
                 Icc 
                 Predicted phosphohydrolase 
                 3044 
               
               
                 — 
                 Conserved hypothetical protein 
                 3045 
               
               
                 ompP1 
                 Outer membrane protein P1 precursor 
                 3046 
               
               
                 Ogt 
                 Methylated-DNA-protein-cysteine 
                 3047 
               
               
                 mutH 
                 DNA mismatch repair protein MutH 
                 3048 
               
               
                 mesJ 
                 Putative cell cycle protein MesJ 
                 3049 
               
               
                 accA 
                 Acetyl-coenzyme A carboxylase carboxyl transferase 
                 3050 
               
               
                   
                 subunit alpha 
                   
               
               
                 znuB 
                 High affinity zinc uptake system membrane protein 
                 3051 
               
               
                   
                 ZnuB 
                   
               
               
                 znuC 
                 High-affinity zinc uptake system ATP binding protein 
                 3052 
               
               
                   
                 AnuC 
                   
               
               
                 — 
                 Conserved hypothetical metalloprotease 
                 3053 
               
               
                 tyrR 
                 Transcriptional regulatory protein TyrR 
                 3054 
               
               
                 hfq 
                 host factor-I protein Hfq 
                 3055 
               
               
                 rluC 
                 ribosomal large subunit pseudouridine synthase C 
                 3056 
               
               
                 rne 
                 ribonuclease E 
                 3057 
               
               
                 — 
                 Conserved hypothetical protein 
                 3058 
               
               
                 thiM 
                 hydroxyethylthiazole kinase 
                 3059 
               
               
                 thiD 
                 phosphomethylpyrimidine kinase 
                 3060 
               
               
                 thiE 
                 thiamine-phosphate pyrophosphorylase 
                 3061  
               
               
                 — 
                 Conserved hypothetical metabolite transport 
                 3062 
               
               
                 — 
                 hypothetical protein 
                 3063 
               
               
                 — 
                 putative protease 
                 3064 
               
               
                 srmB 
                 ATP-dependent RNA helicase SrmB 
                 3065 
               
               
                 — 
                 predicted O-methyltransferase 
                 3066 
               
               
                 pssA 
                 CDP-diacylglycerol--serine O- 
                 3067 
               
               
                   
                 phosphatidyltransferase 
                   
               
               
                 fadR 
                 fatty acid metabolism regulator protein 
                 3068 
               
               
                 nhaB 
                 Na(+)/H(+) antiporter 2 
                 3069 
               
               
                 dsbB 
                 disulfide bond formation protein B 
                 3070 
               
               
                 glmS 
                 glucosamine--fructose-6-phosphate aminotransferase 
                 3071 
               
               
                 hupA 
                 DNA-binding protein HU 
                 3072 
               
               
                 — 
                 conserved hypothetical protein 
                 3073 
               
               
                 nudC 
                 NADH pyrophosphatase 
                 3074 
               
               
                 orfG 
                 conserved hypothetical 21.9 KD protein in locus 
                 3075 
               
               
                   
                 involved in transformation 
                   
               
               
                 comF 
                 competence protein F 
                 3076 
               
               
                 comE 
                 competence protein E 
                 3077 
               
               
                 comD 
                 competence protein D 
                 3078 
               
               
                 comC 
                 competence protein C 
                 3079 
               
               
                 comB 
                 competence protein B 
                 3080 
               
               
                 comA 
                 competence protein A 
                 3081 
               
               
                 mrcA 
                 penicillin-binding protein 1A 
                 3082 
               
               
                 — 
                 conserved hypothetical protein 
                 3083 
               
               
                 — 
                 conserved hypothetical protein 
                 3084 
               
               
                 recR 
                 recombination protein RecR 
                 3085 
               
               
                 topB 
                 DNa topoisomerase III 
                 3086 
               
               
                 secG 
                 protein-export membrane protein SecG 
                 3087 
               
               
                 fruA 
                 PTS system, fructose-specific IIBC component 
                 3088 
               
               
                 fruK 
                 1-phosphofructokinase 
                 3089 
               
               
                 fruB 
                 PTS system, fructose-specific IIA/FPr component 
                 3090 
               
               
                 — 
                 conserved hypothetical protein 
                 3091 
               
               
                 vapD 
                 virulence-associated protein D 
                 3092 
               
               
                 vapX 
                 VapX 
                 3093 
               
               
                 — 
                 conserved hypothetical protein 
                 3094 
               
               
                 — 
                 conserved hypothetical protein 
                 3095 
               
               
                 — 
                 putative deoxyribonuclase 
                 3096 
               
               
                 holB 
                 DNA polymerase III, delta subunit 
                 3097 
               
               
                 — 
                 hypothetical protein 
                 3098 
               
               
                 lav 
                 autotransported protein Lav 
                 3099 
               
               
                 tmk 
                 thymidylate kinase 
                 3100 
               
               
                 — 
                 predicted periplasmic solute-binding protein 
                 3101 
               
               
                 surA 
                 survival protein SurA homolog 
                 3102 
               
               
                 pyrR 
                 PyrR bifunctional protein 
                 3103 
               
               
                 mazG 
                 predicted pyrophosphatase MazG 
                 3104 
               
               
                 — 
                 conserved hypothetical protein 
                 3105 
               
               
                 lon 
                 ATP-dependent protease La 
                 3106 
               
               
                 — 
                 predicted Fe-S oxidoreductase 
                 3107 
               
               
                 rpiA 
                 ribose 5-phosphate isomerase A 
                 3108 
               
               
                 serA 
                 D-3-phosphoglycerate dehydrogenase 
                 3109 
               
               
                 — 
                 predicted aminomethyltransferase related to GcvT 
                 3110 
               
               
                 — 
                 conserved hypothetical stress-induced protein 
                 3111 
               
               
                 hisG 
                 ATP phosphoribosyltransferase 
                 3112 
               
               
                 hisD 
                 histidinol dehydrogenase 
                 3113 
               
               
                 hisC 
                 hisitidinol-phosphate aminotransferase 1 
                 3114 
               
               
                 hisB 
                 histidine biosynthesis bifunctional protein HisB 
                 3115 
               
               
                 hisH 
                 imidazole glycerol phosphate synthase subunit HisH 
                 3116 
               
               
                 hisA 
                 1-5-[methylideneamino] imidazole-4-carboxamine 
                 3117 
               
               
                   
                 isomerase 
                   
               
               
                 hisF 
                 imidazole glycerol phosphate synthase subunit HisF 
                 3118 
               
               
                 hisI 
                 histidine biosynthesis bifunctional protein hisIE 
                 3119 
               
               
                 — 
                 conserved hypothetical protein 
                 3120 
               
               
                 tyrP 
                 tyrosine-specific transportprotein 1 
                 3121 
               
               
                 atpC 
                 ATP synthase epsilon chain 
                 3122 
               
               
                 atpD 
                 ATP synthase beta chain 
                 3123 
               
               
                 atpG 
                 ATP synthase gamma chain 
                 3124 
               
               
                 atpA 
                 ATP synthase alpha chain 
                 3125 
               
               
                 atpH 
                 ATP synthase delta chain 
                 3126 
               
               
                 atpF 
                 ATP synthase B chain 
                 3127 
               
               
                 atpE 
                 ATP cynthase C chain 
                 3128 
               
               
                 atpB 
                 ATP synthase A chain 
                 3129 
               
               
                 — 
                 predicted F0F1-type ATP synthase subunit I 
                 3130 
               
               
                 gidB 
                 methyltransferase GidB 
                 3131 
               
               
                 — 
                 conserved hypothetical protein 
                 3132 
               
               
                 — 
                 predicted phosphatase/phosphohexomutase 
                 3133 
               
               
                 — 
                 predicted membrane protein 
                 3134 
               
               
                 luxS 
                 S-ribosylhomocysteinase 
                 3135 
               
               
                 aphA 
                 Class B acid phosphatase 
                 3136 
               
               
                 hs1V 
                 ATP-dependent protease Hs1V 
                 3137 
               
               
                 hs1U 
                 Hs1U, ATP-dependent chaperone of the Hs1UV 
                 3138 
               
               
                   
                 protease 
                   
               
               
                 ptoD2 
                 spelluidine/putrescine-binding periplasmic protein 2 
                 3139 
               
               
                   
                 precursor 
                   
               
               
                 ordL 
                 probable oxidoereductase OrdL 
                 3140 
               
               
                 rmuC 
                 DNA recombination protein RmuC 
                 3141 
               
               
                 rbsD 
                 ribose transport permease protein 
                 3142 
               
               
                 rbsA 
                 ribose transport ATP-binding protein 
                 3143 
               
               
                 rbsC 
                 ribose transport permease protein 
                 3144 
               
               
                 rbsB 
                 ribose-binding periplasmic protein 
                 3145 
               
               
                 rbsK 
                 ribokinase 
                 3146 
               
               
                 rbsR 
                 ribose operon repressor 
                 3147 
               
               
                 — 
                 predicted membrane protein 
                 3148 
               
               
                 menG 
                 S-adenosylmethionine:2-demtyhylmenaquinone 
                 3149 
               
               
                   
                 methyltransferase 
                   
               
               
                 menA 
                 1,4-dihydroxy-2-naphthoate octaprenyltransferase 
                 3150 
               
               
                 — 
                 conserved hypothetical protein 
                 3151 
               
               
                 tehA 
                 tellurite resistance protein 
                 3152 
               
               
                 rpoC 
                 DNA-directed RNA polymerase beta′ chain 
                 3153 
               
               
                 rpoB 
                 DNA-directed RNA polymerase beta chain 
                 3154 
               
               
                 rplA 
                 50S ribosomal protein L1 
                 3155 
               
               
                 rplK 
                 50S ribosomal protein L11 
                 3156 
               
               
                 deoD 
                 purine nucleoside phosphorylase 
                 3157 
               
               
                 — 
                 predicted nucleoside permease 
                 3158 
               
               
                 — 
                 predicted pyruvate-formate lyase-activating enzyme 
                 3159 
               
               
                 — 
                 conserved hypothetical glycyl radical protein 
                 3160 
               
               
                 — 
                 predicted membrane protein 
                 3161 
               
               
                 waaQ 
                 ADP-heptose--lipooligosaccharide heptosyltransferase 
                 3162 
               
               
                   
                 III 
                   
               
               
                 fba 
                 frustose-biphosphate aldolase 
                 3163 
               
               
                 pgk 
                 phosphoglycerate kinase 
                 3164 
               
               
                 — 
                 probable rubonuclease I 
                 3165 
               
               
                 — 
                 putative ferredoxin-like protein 
                 3166 
               
               
                 tyrQ 
                 tyrosine-specific transport protein 2 
                 3167 
               
               
                 tdk 
                 thymidine kinase 
                 3168 
               
               
                 gcp 
                 probable O-sialoglycoprotein endopeptidase 
                 3169 
               
               
                 rpsU 
                 30S ribosomal protein S21 
                 3170 
               
               
                 — 
                 DNA primase 
                 3171 
               
               
                 rpoD 
                 DNA polymerase sigma factor RpoD 
                 3172 
               
               
                 aspA 
                 aspartate ammonia-lyase 
                 3173 
               
               
                 ureH 
                 urease accessory protein UreH 
                 3174 
               
               
                 ureG 
                 urease accessory protein UreG 
                 3175 
               
               
                 ureF 
                 urease accessory protein UreF 
                 3176 
               
               
                 ureE  
                 urease accessory protein UreE 
                 3177 
               
               
                 ureC 
                 urease alpha subunit 
                 3178 
               
               
                 ureB 
                 urease beta subunit 
                 3179 
               
               
                 ureA 
                 urease gamma subunit 
                 3180 
               
               
                 groES 
                 10 kDa chaperonin 
                 3181 
               
               
                 groEL 
                 60 kDa chaperonin 
                 3182 
               
               
                 rplI 
                 50S ribosomal protein L9 
                 3183 
               
               
                 rpsR 
                 30S ribosomal protein S18 
                 3184 
               
               
                 priB 
                 primsomal replication protein N 
                 3185 
               
               
                 rpsF 
                 30S ribosomal protein S6 
                 3186 
               
               
                 infA 
                 translation initiation factor IF-1 
                 3187 
               
               
                 ksgA 
                 dimethyladenosine transferase 
                 3188 
               
               
                 lic2A 
                 UDP-Gal--lipooligosaccharide galactosyltransferase 
                 3189 
               
               
                 apaH 
                 bis-tetraphosphatase, symmetrical 
                 3190 
               
               
                 — 
                 conserved hypothetical protein 
                 3191 
               
               
                 gnd 
                 6-phosphogluconate dehydrogenase decarboxylating 
                 3192 
               
               
                 — 
                 conserved hypothetical protein 
                 3193 
               
               
                 — 
                 conserved hypothetical protein 
                 3194 
               
               
                 devB 
                 6-phosphgluconolactonase 
                 3195 
               
               
                 zwf 
                 glucose-6-phosphate 1-dehydrogenase 
                 3196 
               
               
                 cysQ 
                 cysQ 
                 3197 
               
               
                 — 
                 conserved hypothetical protein 
                 3198 
               
               
                 — 
                 predicted membrane protein 
                 3199 
               
               
                 hslR 
                 heat shock protein 15 homolog 
                 3200 
               
               
                 asnC 
                 regulatory protein AsnC 
                 3201 
               
               
                 asnA 
                 aspartate--ammonia ligase 
                 3202 
               
               
                 — 
                 conserved hypothetical transposase-like protein 
                 3203 
               
               
                 — 
                 hypothetical protein 
                 3204 
               
               
                 — 
                 hypothetical protein 
                 3205 
               
               
                 — 
                 hypothetical protein 
                 3206 
               
               
                 gph 
                 phosphoglycolate phosphatase 
                 3207 
               
               
                 rpe 
                 ribulose-phosphate 3-epimerase 
                 3208 
               
               
                 gyrB 
                 DNA gyrase subunit B 
                 3209 
               
               
                 — 
                 predicted transcriptional accessory protein 
                 3210 
               
               
                 greB 
                 transcription elongation factor GreB 
                 3211 
               
               
                 — 
                 conserved hypothetical transcriptional regulator  
                 3212 
               
               
                 oxyR 
                 hydrogen peroxide-inducible genes activator 
                 3213 
               
               
                 pdgC 
                 peroxiredoxin.glutaredoxin 
                 3214 
               
               
                 slyX 
                 slyX 
                 3215 
               
               
                 fkby 
                 probably FKBP-type peptidyl-proyl cis-trans 
                 3216 
               
               
                   
                 isomerase 
                   
               
               
                 — 
                 conserved hypothetical protein 
                 3217 
               
               
                 — 
                 uncharacterized conserved protein involved in 
                 3218 
               
               
                   
                 intracellular sulfur reduction 
                   
               
               
                 — 
                 uncharacterized conserved protein involved in 
                 3219 
               
               
                   
                 oxidation of intracellular sulfur 
                   
               
               
                 — 
                 uncharacterized conserved protein involved in 
                 3220 
               
               
                   
                 oxidation of intracellular sulfur 
                   
               
               
                 tufB 
                 elongation factor Tu 
                 3221 
               
               
                 coaA 
                 pantothenate kinase 
                 3222 
               
               
                 rseB 
                 sigma-E factor regulatory protein RseB 
                 3223 
               
               
                 rseA 
                 sigma-E factor negative regulator protein homolog 
                 3224 
               
               
                 rpoE 
                 RNA polymerase sigma-E factor 
                 3225 
               
               
                 — 
                 conserved hypothetical protein 
                 3226 
               
               
                 mscL 
                 large-conductance mechanosensitive channel 
                 3227 
               
               
                 trkA 
                 Trk system potassium uptake protein TrkA 
                 3228 
               
               
                 sun 
                 SUN protein 
                 3229 
               
               
                 fmt 
                 methionyl-tRNA formyltransferase 
                 3230 
               
               
                 def 
                 peptide deformylase 
                 3231 
               
               
                 — 
                 hypothetical protein 
                 3232 
               
               
                 — 
                 hypothetical protein 
                 3233 
               
               
                 sxy 
                 DNA transformation protein TfoX 
                 3234 
               
               
                 recA 
                 RecA 
                 3235 
               
               
                 recX 
                 regulatory protein RecX 
                 3236 
               
               
                 crcB 
                 CrcB 
                 3237 
               
               
                 — 
                 predicted hydrolase of the HAD superfamily 
                 3238 
               
               
                 argF 
                 ornithine carbamoyltransferase, catabolic 
                 3239 
               
               
                 arcC 
                 carbamate kinase 
                 3240 
               
               
                 — 
                 predicted membrane protein 
                 3241 
               
               
                 hgpD 
                 pseudogene for hemoglobin-haptoglobin binding 
                 3242 
               
               
                   
                 protein D 
                   
               
               
                 pepE 
                 peptidase E 
                 3243 
               
               
                 — 
                 predicted C4-dicarboxylate transporter 
                 3244 
               
               
                 abgA 
                 aminobenzoyl-glutamate utilization protein A 
                 3245 
               
               
                 cpdB 
                 2′,3′-cyclic-nucleotide 2′-phosphodiesterase 
                 3246 
               
               
                 — 
                 HTH-type transcriptional regulator 
                 3247 
               
               
                 — 
                 zinc transported ZitB 
                 3248 
               
               
                 gidA 
                 glucose inhibited division protein A 
                 3249 
               
               
                 rpsL 
                 30S ribosoomal protein S12 
                 3250 
               
               
                 rpsG 
                 30S ribosomal protein S7 
                 3251 
               
               
                 fusA 
                 elongation factor G 
                 3252 
               
               
                 tufB2 
                 elongation factor Tu 
                 3253 
               
               
                 — 
                 predicted chloride channel protein 
                 3254 
               
               
                 — 
                 predicted chloride channel protein 
                 3255 
               
               
                 dusA 
                 tRNA-dihydrouridine synthase A 
                 3256 
               
               
                 — 
                 conserved hypothetical protein 
                 3257 
               
               
                 trpS 
                 tryptophanyl-tRNA synthetase 
                 3258 
               
               
                 — 
                 predicted protein involved in purine metabolism 
                 3259 
               
               
                 purB 
                 adenylosuccinate lyase 
                 3260 
               
               
                 rplJ 
                 50S ribosomal protein L10 
                 3261 
               
               
                 rplL 
                 50S ribosomal protein L7/L12 
                 3262 
               
               
                 glmU 
                 bifunctional GlmU protein 
                 3263 
               
               
                 — 
                 hypothetical protein 
                 3264 
               
               
                 pldB 
                 probable lysophospholipase L2 
                 3265 
               
               
                 asd 
                 aspartate-semialdehyde dehydrogenase 
                 3266 
               
               
                 — 
                 conserved hypothetical protein 
                 3267 
               
               
                 — 
                 predicted 2-methylthioadenine synthetase 
                 3268 
               
               
                 mdaB 
                 putative NADPH-quinone reductase, modulator of 
                 3269 
               
               
                   
                 drug activity B 
                   
               
               
                 rep 
                 ATP-dependent DNA helicase rep 
                 3270 
               
               
                 — 
                 predicted periplasmic lipoprotein 
                 3271 
               
               
                 kdtB 
                 phosphopantetheine adenylyltransferase 
                 3272 
               
               
                 kdtA 
                 3-deoxy-D-manno-octulosonic acid transferase 
                 3273 
               
               
                 lgtF 
                 UDP-glucose--lipooligosaccharide glucosyltransferase 
                 3274 
               
               
                 tag 
                 DNA-3-methyladenine glycolase 
                 3275 
               
               
                 — 
                 hypothetical protein 
                 3276 
               
               
                 aroE 
                 shikimate 5-dehydrogenase 
                 3277 
               
               
                   
                 predicted translation factor SUA5 
                 3278 
               
               
                 — 
                 Zn-finger domain associated with topoisomerase typr  
                 3279 
               
               
                   
                 I 
                   
               
               
                 — 
                 probable ABC transporter, ATP binding protein 
                 3280 
               
               
                 — 
                 putative HTH-type transcriptional regulator 
                 3281 
               
               
                 — 
                 conserved hypothetical protein 
                 3282 
               
               
                 hgpB 
                 hemoglobin-haptoglobin binding protein B 
                 3283 
               
               
                 — 
                 hypothetical ABC transporter, ATP-binding protein 
                 3284 
               
               
                 — 
                 probable ABC transporter, ATP binding protein 
                 3285 
               
               
                 — 
                 conserved hypothetical protein 
                 3286 
               
               
                 — 
                 conserved hypothetical protein 
                 3287 
               
               
                 — 
                 putative HTH-type transcriptional regulator 
                 3288 
               
               
                 glpX 
                 fructose-1,6-bisphosphatase class II GlpX 
                 3289 
               
               
                 — 
                 conserved hypothetical protein 
                 3290 
               
               
                 mioC 
                 MioC 
                 3291 
               
               
                 dtd 
                 D-tyrosyl-tRNA (Tyr) deacylase 
                 3292 
               
               
                 ispF 
                 3-C-methyl-D-erythritol 2,4-cyclodiphosphate 
                 3293 
               
               
                   
                 synthase 
                   
               
               
                 ispD 
                 2-C-methyl-D-erythritol 4-phosphate 
                 3294 
               
               
                   
                 cytidylyltransferase 
                   
               
               
                 ftsB 
                 cell division protein FtcB 
                 3295 
               
               
                 gpt 
                 xanthine-guanine phosphoribosyltransferase 
                 3296 
               
               
                 pepD 
                 aminoacyl-histidine dipeptidase 
                 3297 
               
               
                 xerC 
                 site-specific recombinase XerC 
                 3298 
               
               
                 — 
                 conserved hypothetical protein 
                 3299 
               
               
                 tpiA 
                 triosephosphate isomerase 
                 3300 
               
               
                 glpE 
                 thiosulfate sulfurtransferase GlpE 
                 3301 
               
               
                 — 
                 conserved hypothetical protein 
                 3302 
               
               
                 ilvY 
                 HTH-type transcriptional activator IlvY 
                 3303 
               
               
                 iIvC 
                 ketol-acid reductoisomerase 
                 3304 
               
               
                 glpC 
                 anaerobic glycerol-3-phosphate dehydrogenase 
                 3305 
               
               
                   
                 subunit C 
                   
               
               
                 glpB 
                 anaerobic glycerol-3-phosphate dehydrogenase 
                 3306 
               
               
                   
                 subunit B 
                   
               
               
                 glpA 
                 anaerobic glycerol-3-phosphate dehydrogenase 
                 3307 
               
               
                   
                 subunit A 
                   
               
               
                 glpT 
                 glycerol-3-phosphate transporter 
                 3308 
               
               
                 glpQ 
                 glycerophosphoryl diester phosphodiesterase  
                 3309 
               
               
                   
                 precursor 
                   
               
               
                 glpF 
                 glycerol uptake facilitator protein 
                 3310 
               
               
                 glpK 
                 glycerol kinase 
                 3311 
               
               
                 gpt2 
                 xanthine-guanine phosphoribosyltransferase 
                 3312 
               
               
                 hel 
                 outer membrane protein P4, NADP phosphatase 
                 3313 
               
               
                 rluE 
                 ribosomal large subunit pseudouridine synthase E 
                 3314 
               
               
                 — 
                 conserved hypothetical protein 
                 3315 
               
               
                 — 
                 conserved hypothetical protein 
                 3316 
               
               
                 slyD 
                 FKBP-type peptidyl-prolyl cis-trans isomerase SlyD 
                 3317 
               
               
                 — 
                 conserved hypothetical protein 
                 3318 
               
               
                 truD 
                 tRNA pseudouridine synthase D 
                 3319 
               
               
                 surE 
                 acid phosphatase surE 
                 3320 
               
               
                 — 
                 conserved hypothetical protein 
                 3321 
               
               
                 — 
                 conserved hypothetical protein 
                 3322 
               
               
                 lppB 
                 outer membrane antigenic lipoprotein B 
                 3323 
               
               
                 tnaA 
                 tryptophanase 
                 3324 
               
               
                 tnaB 
                 tryptophan-specific transport protein 
                 3325 
               
               
                 mutS 
                 DNA mismatch repair protein MutS 
                 3326 
               
               
                 selA 
                 L-seryl-tRNA selenium transferase 
                 3327 
               
               
                 selB 
                 selenocysteine-specific elongation factor 
                 3328 
               
               
                 — 
                 hypothetical protein 
                 3329 
               
               
                 — 
                 conserved hypothetical protein 
                 3330 
               
               
                 — 
                 conserved hypothetical protein 
                 3331 
               
               
                 hgpC 
                 pseudogene for hemoglobin-haptoglobin utilization 
                 3332 
               
               
                   
                 protein C 
                   
               
               
                 tig 
                 trigger factor 
                 3333 
               
               
                 clpP 
                 ATP-dependent clp protease proteolytic subunit 
                 3334 
               
               
                 clpX 
                 ATP-dependent Clp protease ATP-binding subunit 
                 3335 
               
               
                   
                 ClpX 
                   
               
               
                 secE 
                 preprotein translocase SecE 
                 3336 
               
               
                 nusG 
                 transcription antitermination protein NusG 
                 3337 
               
               
                 vacJ 
                 VacJ lipoprotein 
                 3338 
               
               
                 — 
                 putative translation initiation inhibitor YjgF family 
                 3339 
               
               
                 htpX 
                 probable protease HtpX 
                 3340 
               
               
                 sirA 
                 SirA 
                 3341 
               
               
                 — 
                 conserved hypothetical protein 
                 3342 
               
               
                 trkH 
                 Trk system potassium uptake protein TrkH 
                 3343 
               
               
                 psiE 
                 PsiE 
                 3344 
               
               
                 hemY 
                 HemY 
                 3345 
               
               
                 hemX 
                 putative uroporphyrin-III C-methyltransferase 
                 3346 
               
               
                 cya 
                 adenylate cyclase 
                 3347 
               
               
                 gpsA 
                 glycerol-3-phosphate dehydrogenase 
                 3348 
               
               
                 cysE 
                 serine acetyltransferase 
                 3349 
               
               
                 — 
                 conserved hypothetical shikimate 5-dehydrogenase- 
                 3350 
               
               
                   
                 like protein 
                   
               
               
                 — 
                 possible di-and tricarboxylate transporter 
                 3351 
               
               
                 folD 
                 FolD bifunctional protein 
                 3352 
               
               
                 fucP 
                 L-fucose permease 
                 3353 
               
               
                 fucA 
                 L-fuculose phosphate aldolase 
                 3354 
               
               
                 fucU 
                 fucose operon protein FucU 
                 3355 
               
               
                 fucK 
                 L-fuculokinase 
                 3356 
               
               
                 fucI 
                 L-fucose isomerase 
                 3357 
               
               
                 fucR 
                 L-fucose operon activator 
                 3358 
               
               
                 hepA 
                 RNA polymerase associated protein homolog 
                 3359 
               
               
                 rluA 
                 ribosomal large subunit pseudouridine synthase A 
                 3360 
               
               
                 glpG 
                 GlpG 
                 3361 
               
               
                 glpR 
                 glycerol-3-phosphate regulon repressor 
                 3362 
               
               
                 metQ 
                 probable D-methionine-binding lipoprotein MetQ 
                 3363 
               
               
                 metI 
                 probable D-methionine transport system permease 
                 3364 
               
               
                   
                 protein 
                   
               
               
                 metN 
                 probable D-methionine transport ATP-binding protein 
                 3365 
               
               
                 — 
                 conserved hypothetical protein 
                 3366 
               
               
                 — 
                 conserved hypothetical protein 
                 3367 
               
               
                 — 
                 conserved hypothetical protein 
                 3368 
               
               
                 narP 
                 nitrate/nitrite response regulator protein 
                 3369 
               
               
                 lysA 
                 diaminopimelate decarboxylase 
                 3370 
               
               
                 — 
                 hypothetical protein 
                 3371 
               
               
                 cyaY 
                 CyaY 
                 3372 
               
               
                 recQ 
                 ATP-dependent DNA helicase RecQ 
                 3373 
               
               
                 proS 
                 prolyl-tRNA synthetase 
                 3374 
               
               
                 ostA 
                 organic solvent tolerance protein 
                 3375 
               
               
                 sufI 
                 SufI 
                 3376 
               
               
                 plsC 
                 1-acyl-sn-glycerol-3-phosphate acyltransferase 
                 3377 
               
               
                 lpxH 
                 UDP-2,3-diacylglucosamine hydrolase 
                 3378 
               
               
                 — 
                 conserved hypothetical sodium dependent transporter 
                 3379 
               
               
                 ilvG 
                 acetolactate synthase isozyme II large subunit 
                 3380 
               
               
                 ilvD 
                 dihydroxy-acid dehydratase 
                 3381 
               
               
                 thdl 
                 threonine dehydratase biosynthetic 
                 3382 
               
               
                 dnaE 
                 DNA polymerase III alpha subunit 
                 3383 
               
               
                 pgmB 
                 phosphoglucomutase 
                 3384 
               
               
                 secB 
                 protein-export protein SecB 
                 3385 
               
               
                 — 
                 predicted rhodanese-related sulfurtransferase 
                 3386 
               
               
                 dcuB 
                 anaerobic C4-dicarboxylate transporter DcuB 
                 3387 
               
               
                 ndhA 
                 NADH dehydrogenase 
                 3388 
               
               
                 plsB 
                 glycerol-3-phosphate acyltransferase 
                 3389 
               
               
                 lexA 
                 LexA repressor 
                 3390 
               
               
                 dapF 
                 diaminopimelate epimerase 
                 3391 
               
               
                 tpx 
                 probable thiol peroxidase 
                 3392 
               
               
                 purL 
                 phosphoribosylformylglycinamidine synthase 
                 3393 
               
               
                 lex2B 
                 UDP-glucose--lipooligosaccharide glucosyltransferase 
                 3394 
               
               
                 — 
                 conserved hypothetical protein  
                 3395 
               
               
                 — 
                 predicted membrane-bound metallopeptidase 
                 3396 
               
               
                 gpmA 
                 2,3-bisphosphoglycerate-dependent phsphoglycerate 
                 3397 
               
               
                   
                 mutase 
                   
               
               
                 rpL31 
                 50S ribosomal protein L31 
                 3398 
               
               
                 mutY 
                 A/G-specific adenine glycosylase 
                 3399 
               
               
                 — 
                 conserved hypothetical protein 
                 3400 
               
               
                 mltC 
                 membrane-bound lytic murein transglycolase C 
                 3401 
               
               
                   
                 precursor 
                   
               
               
                 — 
                 predicted diadenosine tetraphosphatase and related 
                 3402 
               
               
                   
                 serine/threonine protein phosphatase 
                   
               
               
                 nadR 
                 bifunctional protein NadR 
                 3403 
               
               
                 ribB 
                 3,4-dihydroxy-2-butanone 4-phosphate synthase 
                 3404 
               
               
                 lpsA 
                 lipooligosaccharide glycosyl transferase 
                 3405 
               
               
                 — 
                 conserved hypothetical tRNA/rRNA  
                 3406 
               
               
                   
                 methyltransferase 
                   
               
               
                 — 
                 predicted N6-adenine-specific methylase 
                 3407 
               
               
                 FtsY 
                 cell division protein FtsY 
                 3408 
               
               
                 ftsE 
                 cell division ATP-binding protein EtsE 
                 3409 
               
               
                 ftsx 
                 cell division protein ftsx 
                 3410 
               
               
                 atoB 
                 acetyl-CoA acetyltransferase 
                 3411 
               
               
                 atoE 
                 short chain fatty acids transporter 
                 3412 
               
               
                 atoA 
                 acetate CoA-transferase beta subunit 
                 3413 
               
               
                 atoD 
                 acetate CoA-transferase alpha subunit 
                 3414 
               
               
                 — 
                 putative HTH-type transcriptional regulator 
                 3415 
               
               
                 rpsJ 
                 30S ribosomal protein S10 
                 3416 
               
               
                 rplC 
                 50S ribosomal protein L3 
                 3417 
               
               
                 rplD 
                 50S ribosomal protein L4 
                 3418 
               
               
                 rpIW 
                 50S ribosomal protein L23 
                 3419 
               
               
                 rplB 
                 50S ribosomal protein L2 
                 3420 
               
               
                 rpsS 
                 30S ribosomal protein S19 
                 3421 
               
               
                 rplV 
                 50S ribosomal protein L22 
                 3422 
               
               
                 rpsC 
                 30S ribosomal protein S3 
                 3423 
               
               
                 rplP 
                 50S ribosomal protein L16 
                 3424 
               
               
                 rpmC 
                 50S ribosomal protein L29 
                 3425 
               
               
                 rpsQ 
                 30S ribosomal protein S17 
                 3426 
               
               
                 — 
                 conserved hypothetical protein 
                 3427 
               
               
                 rplN 
                 50S ribosomal protein L14 
                 3428 
               
               
                 rplX 
                 50S ribosomal protein L24 
                 3429 
               
               
                 rplE 
                 50S ribosomal protein L5 
                 3430 
               
               
                 rpsN 
                 30S ribosomal protein S14 
                 3431 
               
               
                 rpsH 
                 30S ribosomal protein S8 
                 3432 
               
               
                 rplF 
                 50S ribosomal protein L6 
                 3433 
               
               
                 rplR 
                 50S ribosomal protein L18 
                 3434 
               
               
                 rpsE 
                 30S ribosomal protein S5 
                 3435 
               
               
                 rpmD 
                 50S ribosomal protein L30 
                 3436 
               
               
                 rplO 
                 50S ribosomal protein L15 
                 3437 
               
               
                 secY 
                 preprotein translocase SecY subunit 
                 3438 
               
               
                 rpsM 
                 30S ribosomal protein S13 
                 3439 
               
               
                 rpsK 
                 30S ribosomal protein S11 
                 3440 
               
               
                 rpsD 
                 30S ribosomal protein S4 
                 3441 
               
               
                 rpoA 
                 DNA-directed RNA polymerase alpha chain 
                 3442 
               
               
                 rplQ 
                 50S ribosomal protein L17 
                 3443 
               
               
                 — 
                 predicted cAMP-binding protein-catabolite gene 
                 3444 
               
               
                   
                 activator and regulatory subunit of cAMP-dependent 
                   
               
               
                   
                 protein kinase 
                   
               
               
                 — 
                 predicted permease 
                 3445 
               
               
                 dxr 
                 1-deoxy-D-xylulose 5′phosphate reductoisomerase 
                 3446 
               
               
                 frr 
                 ribosome recycling factor 
                 3447 
               
               
                 pckA 
                 phosphoenolpyruvate carboxykinase 
                 3448 
               
               
                 hslO 
                 33 kDa chaperonin 
                 3449 
               
               
                 argH 
                 argininosuccinate lyase 
                 3450 
               
               
                 galU 
                 UTP-glucose-1-phosphate uridylyltransferase 
                 3451 
               
               
                 csrA 
                 carbon storage regulator homolog 
                 3452 
               
               
                 alaS 
                 alanyl-tRNA synthetase 
                 3453 
               
               
                 uspA 
                 universal stress protein A 
                 3454 
               
               
                 pepP 
                 Xaa-Pro aminopeptidase 
                 3455 
               
               
                 — 
                 conserved hypothetical protein 
                 3456 
               
               
                 galM 
                 aldose 1-epimerase 
                 3457 
               
               
                 galK 
                 glactokinase 
                 3458 
               
               
                 galT 
                 galactose-1-phosphate uridylyltransferase 
                 3459 
               
               
                 galR 
                 HTH-type transcriptional regulator GalR 
                 3460 
               
               
                 mglB 
                 D-galactose-binding periplasmic protein precursos 
                 3461 
               
               
                 mglA 
                 galactoside transport ATP-binding protein MglA 
                 3462 
               
               
                 mglC 
                 galactoside transport system permease protein MglC 
                 3463 
               
               
                 — 
                 conserved hypothetical protein 
                 3464 
               
               
                 ispZ 
                 probable intracellular septation protein A 
                 3465 
               
               
                 — 
                 putative acyl-CoA thioester hydrolase 
                 3466 
               
               
                 — 
                 conserved hypothetical protein 
                 3467 
               
               
                 slt 
                 putative soluble lytic murein transglycosylase 
                 3468 
               
               
                 trpR 
                 Trp operon repressor 
                 3469 
               
               
                 mtgA 
                 monofuctional biosynthetic peptidoglycan 
                 3470 
               
               
                   
                 transglycolase 
                   
               
               
                 frdD 
                 fumarate reductase subunit D 
                 3471 
               
               
                 frdC 
                 fumarate reductase subunit C 
                 3472 
               
               
                 frdB 
                 fumarate reductase iron-sulfur protein 
                 3473 
               
               
                 frdA 
                 fumarate reductase flavoprotein subunit 
                 3474 
               
               
                 genX 
                 putative lysyl-tRNA synthetase 
                 3475 
               
               
                 cpxR 
                 transcriptional regulatory protein CpxR 
                 3476 
               
               
                 smpA 
                 small protein A 
                 3477 
               
               
                 ndpA 
                 nucleosid-associated protein NdpA 
                 3478 
               
               
                 — 
                 conserved hypothetical protein 
                 3479 
               
               
                 — 
                 predicted hydrolase of alkaline phosphatase 
                 3480 
               
               
                   
                 superfamily 
                   
               
               
                 — 
                 conserved hypothetical protein 
                 3481 
               
               
                 mobA 
                 probable molybdopterin-guanine dinucleotide 
                 3482 
               
               
                   
                 biosyntheses protein A 
                   
               
               
                 — 
                 conserved hypothetical protein 
                 3483 
               
               
                 dsbA 
                 thiol:disulfide interchange protein DsbA 
                 3484 
               
               
                 — 
                 conserved hypothetical protein 
                 3485 
               
               
                 trmA 
                 tRNA (Uracil-5)-methyltransferase 
                 3486 
               
               
                 — 
                 conserved hypothetical protein 
                 3487 
               
               
                 — 
                 predicted positive regulator of Sigma E 
                 3488 
               
               
                 mobB 
                 molybdopterin-guanine dinucleotide biosynthesis 
                 3489 
               
               
                   
                 protein B 
                   
               
               
                 — 
                 conserved hypothetical protein 
                 3490 
               
               
                 hbpA 
                 heme-binding protein A 
                 3491 
               
               
                 — 
                 putative heme iron utilization protein 
                 3492 
               
               
                 — 
                 conserved hypothetical protein 
                 3493 
               
               
                 polA 
                 DNA polymerase I 
                 3494 
               
               
                 — 
                 conserved hypothetical protein 
                 3495 
               
               
                 — 
                 predicted 5-formyltetrahydrofolate cyclo-ligase 
                 3496 
               
               
                 clpB 
                 ClpB 
                 3497 
               
               
                 — 
                 probable tRNA/rRNA methyltransferase 
                 3498 
               
               
                 vacB 
                 ribonuclease R 
                 3499 
               
               
                 — 
                 conserved hypothetical protein 
                 3500 
               
               
                 pdxH 
                 pyridoxamine 5′-phosphate oxidase 
                 3501 
               
               
                 typA 
                 GTP-binding protein TypA/BipA 
                 3502 
               
               
                 lic3A2 
                 CMP-neu5Ac--lipooligosaccharide alpha 2-3 
                 3503 
               
               
                   
                 sialyltransferase 
                   
               
               
                 glnA 
                 glutamine synthetase 
                 3504 
               
               
                 rmlB 
                 dTDP-glucose 4,6-dehydratase 
                 3505 
               
               
                 pepB 
                 peptidase B 
                 3506 
               
               
                 ndk 
                 nucleoside diphosphate kinase 
                 3507 
               
               
                 — 
                 conserved hypothetical GTP-binding protein 
                 3508 
               
               
                 — 
                 conserved hypothetical transport protein 
                 3509 
               
               
                 rpmA 
                 50S ribosomal protein L27 
                 3510 
               
               
                 rplU 
                 50S ribosomal protein L21 
                 3511 
               
               
                 ispB 
                 octaprenyl-diphosphate synthase 
                 3512 
               
               
                 — 
                 conserved hypothetical protein 
                 3513 
               
               
                 — 
                 predicted Na+/alanine symporter 
                 3514 
               
               
                 arcA 
                 aerobic respiration control protein ArcA 
                 3515 
               
               
                 dsbD 
                 thiol:disulfide interchange protein DsbD 
                 3516 
               
               
                 — 
                 predicted membrane protein 
                 3517 
               
               
                 purH 
                 bifunctional purine biosynthesis protein PurH 
                 3518 
               
               
                 purD 
                 phosphoribosylamine--glycine ligase 
                 3519 
               
               
                 glyA 
                 serine hydroxymethyltransferase 
                 3520 
               
               
                 coaE 
                 dephospho-CoA kinase 
                 3521 
               
               
                 — 
                 conserved hypothetical zinc-binding protein 
                 3522 
               
               
                 rh1B 
                 ATP-dependent RNA helicase Rh1B 
                 3523 
               
               
                 — 
                 hypothetical transcriptional regulator 
                 3524 
               
               
                 — 
                 predicted membrane-fusion protein 
                 3525 
               
               
                 — 
                 predicted cation/multidrug efflux pump 
                 3526 
               
               
                 — 
                 predicted cell division protein 
                 3527 
               
               
                 emrB 
                 multidrug resistance protein 
                 3528 
               
               
                 emrA 
                 multidrug resistance protein A 
                 3529 
               
               
                 folA 
                 dihydrofolate reductase 
                 3530 
               
               
                 proB 
                 glutamate 5-kinase 
                 3531 
               
               
                 nudH 
                 probable nucleoside polyphosphate hydrolase 
                 3532 
               
               
                 — 
                 predicted permease 
                 3533 
               
               
                 lgt 
                 prolipoprotein diacylglyceryl transferase 
                 3534 
               
               
                 thyA 
                 thymidylate synthase 
                 3535 
               
               
                 — 
                 conserved hypothetical protein 
                 3536 
               
               
                 — 
                 conserved hypothetical protein 
                 3537 
               
               
                 — 
                 conserved hypothetical protein 
                 3538 
               
               
                 secA 
                 preprotein translocase SecA subunit 
                 3539 
               
               
                 mutT 
                 mutator protein MutT 
                 3540 
               
               
                 kefB 
                 glutathione-regulated potassium-efflux system protein 
                 3541 
               
               
                 — 
                 conserved hypothetical SAM-dependent 
                 3542 
               
               
                   
                 methtransferase 
                   
               
               
                 rpsB 
                 30S ribosomal protein S2 
                 3543 
               
               
                 tsf 
                 elongation factor Ts 
                 3544 
               
               
                 lpxD 
                 UDP-3-O-[3-hydroxymyristoyl] glucosamine N- 
                 3545 
               
               
                   
                 acyltransferase 
                   
               
               
                 omp26 
                 outer membrane protein 26 
                 3546 
               
               
                 — 
                 protective surface antigen D15 
                 3547 
               
               
                 — 
                 predicted membrane bound zinc matalloprotease with 
                 3548 
               
               
                   
                 PDZ domain 
                   
               
               
                 cdsA 
                 phosphaatidate cytidylyltransferase 
                 3549 
               
               
                 uppS 
                 undecaprenyl pyrophosphate synthetase 
                 3550 
               
               
                 leuS 
                 leucyl-tRNA synthetase 
                 3551 
               
               
                 — 
                 conserved predicted lipoprotein 
                 3552 
               
               
                 holA 
                 DNA polymerase III, delta subunit 
                 3553 
               
               
                 glyS 
                 glycyl-tRNA synthetase beta chain 
                 3554 
               
               
                 — 
                 hypothetical protein 
                 3555 
               
               
                 — 
                 conserved hypothetical protein 
                 3556 
               
               
                 — 
                 glutaredoxin-related protein 
                 3557 
               
               
                 glyQ 
                 glycyl-tRNA synthetase alpha chain 
                 3558 
               
               
                 hktE 
                 catalase 
                 3559 
               
               
                 — 
                 predicted glutathionylspermidine synthase 
                 3560 
               
               
                 — 
                 conserved hypothetical protein 
                 3561 
               
               
                 — 
                 conserved hypothetical protein 
                 3562 
               
               
                 eno 
                 enolase 
                 3563 
               
               
                 — 
                 conserved hypothetical protein 
                 3564 
               
               
                 nrfF 
                 formate-dependent nitrite reductase complex nrfFG 
                 3565 
               
               
                   
                 subunit 
                   
               
               
                 dsbE2 
                 probable thiol:disulfide interchange protein DsbE 
                 3566 
               
               
                 nrfE 
                 cytochrome c-type biogenesis protein NrfE 
                 3567 
               
               
                 suhB 
                 inositol-1-monophosphatase 
                 3568 
               
               
                 — 
                 conserved hypothetical protein 
                 3569 
               
               
                 — 
                 predicted Type II secretory pathway, PulJ-like  
                 3570 
               
               
                   
                 protein  
                   
               
               
                 — 
                 conserved hypothetical protein 
                 3571 
               
               
                 — 
                 conserved hypothetical protein 
                 3572 
               
               
                 — 
                 exodeoxyribonuclease V gamma chain 
                 3573 
               
               
                 — 
                 predicted transcriptional regulator 
                 3574 
               
               
                 ribD 
                 riboflavin biosynthesis protein RibD 
                 3575 
               
               
                 degS 
                 protease DegS 
                 3576 
               
               
                 mutM 
                 formamidopyrimidine-DNA glycosylase 
                 3577 
               
               
                 ddc 
                 L-2,4-diaminobutyrate decarboxylase 
                 3578 
               
               
                 — 
                 predicted nucleic acid-binding protein, contains PIN 
                 3579 
               
               
                   
                 domain 
                   
               
               
                 — 
                 conserved hypothetical protein 
                 3580 
               
               
                 dat 
                 diaminobutyrate--2-oxoglutarate aminotransferase 
                 3581 
               
               
                 rpmG 
                 50S ribosomal protein L33 
                 3582 
               
               
                 rpmB 
                 50S ribosomal protein L28 
                 3583 
               
               
                 radC 
                 DNA repair protein Radc homolog 
                 3584 
               
               
                 dfp 
                 phosphopantothenoylcysteine 
                 3585 
               
               
                   
                 synthetase/decarboxylase 
                   
               
               
                 dut 
                 deoxyuridine 5′-triphosphate nucleotidohydrolase 
                 3586 
               
               
                 ttk 
                 ttk 
                 3587 
               
               
                 — 
                 hypothetical protein 
                 3588 
               
               
                 crp 
                 catabolite gene activator 
                 3589 
               
               
                 — 
                 hypothetical RNA methyltransferase 
                 3590 
               
               
                 nagZ 
                 beta-hexosaminidase 
                 3591 
               
               
                 — 
                 predicted periplasmic lipoprotein 
                 3592 
               
               
                 — 
                 HIT-like protein 
                 3593 
               
               
                 ileS 
                 isoleucyl-tRNA synthetase 
                 3594 
               
               
                 ribF 
                 riboflavin biosynthesis protein RibF 
                 3595 
               
               
                 mviN 
                 putative virulence factor MviN 
                 3596 
               
               
                 rpsT 
                 30S ribosomal protein S20 
                 3597 
               
               
                 — 
                 conserved hypothetical protein 
                 3598 
               
               
                 menB 
                 naphthoate synthase 
                 3599 
               
               
                 menC 
                 O-succinylbenzoate synthase 
                 3600 
               
               
                 aroQ 
                 3-dehydroquinate dehydratase 
                 3601 
               
               
                 accB 
                 biotin carboxyl carrier protein of acetyl-CoA 
                 3602 
               
               
                   
                 carboxylase 
                   
               
               
                 accC 
                 biotin carboxylase 
                 3603 
               
               
                 — 
                 conserved hypothetical membrane protein 
                 3604 
               
               
                 panF 
                 sodium/pantothenase symporter 
                 3605 
               
               
                 — 
                 conserved hypothetical protein 
                 3606 
               
               
                 prmA 
                 ribosomal protein L11 methyltransferase 
                 3607 
               
               
                 dusB 
                 tRNA-dihydrouridine synthase B 
                 3608 
               
               
                 fis 
                 DNA-binding protein fis 
                 3609 
               
               
                 smpB 
                 SsrA-binding protein 
                 3610 
               
               
                 pfkA 
                 6-phosphfructokinase 
                 3611 
               
               
                 — 
                 conserved hypothetical protein 
                 3612 
               
               
                 — 
                 conserved hypothetical protein 
                 3613 
               
               
                 smf 
                 smf 
                 3614 
               
               
                 leuA 
                 2-isopropylmalate synthase 
                 3615 
               
               
                 leuB 
                 3-isopropylmalate dehydrogenase 
                 3616 
               
               
                 leuC 
                 3-isopropylmalate dehydratase large subunit 
                 3617 
               
               
                 leuD 
                 3-isopropylmalate dehydratase small subunit 
                 3618 
               
               
                 igal 
                 IgA-specific serine endopeptidase 
                 3619 
               
               
                 recF 
                 DNA replication and repair protein RecF 
                 3620 
               
               
                 dnaN 
                 DNA polymerase III, beta chain 
                 3621 
               
               
                 dnaA 
                 chromosomal replication initiator protein DnaA 
                 3622 
               
               
                 tbp1 
                 transferrin-binding protein 1 
                 3623 
               
               
                 tbp2 
                 transferrin-bindingprotein 2 
                 3624 
               
               
                 — 
                 conserved hypothetical protein 
                 3625 
               
               
                 rpmH 
                 50S ribosomal protain L34 
                 3626 
               
               
                 rnpA 
                 ribonuclease P protein component 
                 3627 
               
               
                 — 
                 conserved hypothetical protein 
                 3628 
               
               
                 yidC 
                 proprotein translocase subunit YidC 
                 3629 
               
               
                 trmE 
                 probable tRNA moficiation GTPase TrmE 
                 3630 
               
               
                 ppiD 
                 peptidyl-prolyl cis-trans isomerase D 
                 3631 
               
               
                 — 
                 predicted PR--lipooligosaccharide 
                 3632 
               
               
                   
                 phosphorylethanolamine transferase 
                   
               
               
                 lspA 
                 lipoprotein signal peptidase 
                 3633 
               
               
                 ispH 
                 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 
                 3634 
               
               
                 — 
                 conserved hypothetical protein 
                 3635 
               
               
                 tbpA 
                 thiamine-binding periplasmic protein 
                 3636 
               
               
                 thiP 
                 thiamine transport system permease protein 
                 3637 
               
               
                 thiQ 
                 thiamine transport ATP-binding protein 
                 3638 
               
               
                 bioB 
                 biotin synthase 
                 3639 
               
               
                 tktA 
                 transketolase 
                 3640 
               
               
                 serB 
                 phosphoserine phosphatase 
                 3641 
               
               
                 — 
                 conserved hypothetical protein 
                 3642 
               
               
                 corA 
                 magnesium and cobalt transport protein CorA 
                 3643 
               
               
                 — 
                 predicted integral membrane protein 
                 3644 
               
               
                 — 
                 predicted glutamine amidotransferase 
                 3645 
               
               
                 — 
                 hypothetical protein 
                 3646 
               
               
                 — 
                 predicted ATPase 
                 3647 
               
               
                 — 
                 hypothetical protein 
                 3648 
               
               
                 — 
                 predicted ferredoxin 
                 3649 
               
               
                 — 
                 conserved hypothetical protein 
                 3650 
               
               
                 dmsC 
                 anaerobic dimethyl sulfoxide reductase chain C 
                 3651 
               
               
                 dmsB 
                 anaerobic dimenthyl sulfoxide reductase chain B 
                 3652 
               
               
                 dmaA 
                 anaerobic dimethyl sulfoxide reductase chain A 
                 3653 
               
               
                 — 
                 conserved hypothetical protein 
                 3654 
               
               
                 — 
                 putative mercuric transport MerT homolog 
                 3655 
               
               
                 — 
                 predicted copper chaperone MerP homolog 
                 3656 
               
               
                 — 
                 conserved hypothetical ABC transporter 
                 3657 
               
               
                 — 
                 conserved hypothetical transcriptional regulator 
                 3658 
               
               
                 — 
                 conserved putative gamma-carboxymuconolactone 
                 3659 
               
               
                   
                 decarboxylase subunit 
                   
               
               
                 — 
                 conserved hypothetical protein 
                 3660 
               
               
                 res 
                 putative type III restriction-modification sustem 
                 3661 
               
               
                   
                 HindVIP enzyme res 
                   
               
               
                 rnhB 
                 ribonuclease HII 
                 3662 
               
               
                 lpxB 
                 lipid-A-disaccharide synthase 
                 3663 
               
               
                 lpxA 
                 acyl0[acyl-carrier-protein]---UDP-N- 
                 3664 
               
               
                   
                 acetylglucosamine O-Acyltransferase 
                   
               
               
                 fabZ 
                 (3R)-hydroxymyristoyl-[acyl carrier protein] 
                 3665 
               
               
                   
                 dehydratase 
                   
               
               
                 — 
                 predicted PR--lipooligosaccharide 
                 3666 
               
               
                   
                 phosphorylethanolamine transferase 
                   
               
               
                 pyrH 
                 uridylate kinase 
                 3667 
               
               
                 nrfD 
                 NrfD, formate-dependent nitrite reductase, membrane 
                 3668 
               
               
                   
                 component 
                   
               
               
                 nrfC 
                 NrfC, Fe-S-cluster-containing hydrogenase  
                 3669 
               
               
                   
                 component 1 
                   
               
               
                 nrfB 
                 NrfB, cytochrome C-type protein 
                 3670 
               
               
                 nrfA 
                 cytochrome c552 
                 3671 
               
               
                 hrpA 
                 ATP-dependent helicase HrpA homolog 
                 3672 
               
               
                 — 
                 conserved putative small membrane protein 
                 3673 
               
               
                 — 
                 conserved putative membrane protein 
                 3674 
               
               
                 cyoB 
                 probable cyrochrome oxidase subunit II 
                 3675 
               
               
                 cyoA 
                 probable cytochrome oxidase dubunit I 
                 3676 
               
               
                 pyrG 
                 CTP synthase 
                 3677 
               
               
                 pnuC 
                 nictinamide riboside transporter 
                 3678 
               
               
                 — 
                 probable amino-acid ABC transporter ATP-binding 
                 3679 
               
               
                   
                 protein 
                   
               
               
                 — 
                 probable amino-acid ABC transporter permease 
                 3680 
               
               
                   
                 protein 
                   
               
               
                 — 
                 probable amino-acid ABC transporter binding protein 
                 3681 
               
               
                 murA 
                 UDP-N-acetylglucosamine a-carboxyvinyltransferase 
                 3682 
               
               
                 — 
                 predicted transcriptional regulator, BoIA superfamily 
                 3683 
               
               
                 — 
                 predicted NTP binding protein, contains STAS  
                 3684 
               
               
                   
                 domain 
                   
               
               
                 — 
                 conserved ABC-type transport system protein 
                 3685 
               
               
                 — 
                 conserved ABC-type transport system protein, 
                 3686 
               
               
                   
                 periplasmic component 
                   
               
               
                 — 
                 conserved ABC-type transport system protein, 
                 3687 
               
               
                   
                 permease component 
                   
               
               
                 — 
                 conserved ABC-type transport system protein,  
                 3688 
               
               
                   
                 ATPase component 
                   
               
               
                 sodA 
                 superoxide dismutase [Mn] 
                 3689 
               
               
                 ccmA 
                 heme exporter protein A 
                 3690 
               
               
                 ccmB 
                 heme exporter protein B 
                 3691 
               
               
                 ccmC 
                 heme exporter protein C 
                 3692 
               
               
                 ccmD 
                 heme exporter protein D 
                 3693 
               
               
                 ccmE 
                 cytochrome c-type biogenesis protein CcmE 
                 3694 
               
               
                 ccmF 
                 cytochrome c-type biogenesis protein CcmF 
                 3695 
               
               
                 dsbE 
                 thiol:disulfide interchange protein DsbE 
                 3696 
               
               
                 — 
                 hypothetical protein 
                 3697 
               
               
                 — 
                 conserved hypothetical protein 
                 3698 
               
               
                 ligN 
                 DNA ligase 
                 3699 
               
               
                 zipA 
                 cell division protein ZipA 
                 3700 
               
               
                 cysZ 
                 CysZ 
                 3701 
               
               
                 cysK 
                 cysteine synthase 
                 3702 
               
               
                 rfaF 
                 ADP-heptose--lipooligosaccharide heptosyltransferase  
                 3703 
               
               
                   
                 II 
                   
               
               
                 xylR 
                 xylose operon refulatory protein 
                 3704 
               
               
                 — 
                 conserved hypothetical Na(+)/H(+) antiporter 
                 3705 
               
               
                 aspC2 
                 putative aspartate aminotransferase 
                 3706 
               
               
                 xylA 
                 xylose isomerase 
                 3707 
               
               
                 xylB 
                 xylulose kinase 
                 3708 
               
               
                 rfaD 
                 ADP-L-glycero-D-manno-heptose-6-epimerase 
                 3709 
               
               
                 — 
                 thioredoxin-like protein 
                 3710 
               
               
                 deoC 
                 deoxyribose-phosphate aldolase 
                 3711 
               
               
                 comM 
                 competence protein ComM 
                 3712 
               
               
                 engB 
                 Probable GTP-binding protein EngB 
                 3713 
               
               
                 — 
                 D-xylose transport permease protein 
                 3714 
               
               
                 oppF 
                 oligopeptide transport ATP-binsing protein 
                 3715 
               
               
                 oppD 
                 oligopeptide transport ATP-binding protein 
                 3716 
               
               
                 oppC 
                 oligopeptide transport system permease protein 
                 3717 
               
               
                 oppB 
                 oligopeptide transport system permease protein 
                 3718 
               
               
                 oppA 
                 periplasmic oligopeptide-binding protein 
                 3719 
               
               
                 talB 
                 Transaldolase 
                 3720 
               
               
                 — 
                 carbon starvation protein, predicted membrane  
                 3721 
               
               
                   
                 protein 
                   
               
               
                 mraZ 
                 MraZ 
                 3722 
               
               
                 mraW 
                 predicted S-adenosylmethionine-dependent 
                 3723 
               
               
                   
                 methyltransferase involved in cell envelope  
                   
               
               
                   
                 biogenesis 
                   
               
               
                 ftsL 
                 cell division protein FtsL 
                 3724 
               
               
                 ftsI 
                 peptidoglycan synthetase FtsI 
                 3725 
               
               
                 murE 
                 UDP-N-acetylmuramoylalanyl-D-glutamate--2,6- 
                 3726 
               
               
                   
                 diaminopimelate ligase 
                   
               
               
                 murF 
                 UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D- 
                 3727 
               
               
                   
                 alanine ligase 
                   
               
               
                 mraY 
                 phospho-N-acetylmuramoyl-pentapeptide-transferase 
                 3728 
               
               
                 murD 
                 UDP-N-acetylmuramoylaalanine--D-glutamate ligase 
                 3729 
               
               
                 ftsW 
                 cell division protein FtsW 
                 3730 
               
               
                 murG 
                 UDP-N-acetylglucosamine--N- 
                 3731 
               
               
                   
                 acetylmuramylpyrophosphoryl-undecaprenol N- 
                   
               
               
                   
                 acetylglucosamine transferase 
                   
               
               
                 murC 
                 UDP-N-acetylmuramate--L-alanine ligase 
                 3732 
               
               
                 ddlB 
                 D-alanine--D-alanine ligase 
                 3733 
               
               
                 ftsQ 
                 cell division protein FtsQ 
                 3734 
               
               
                 ftsA 
                 cell division protein FtsA 
                 3735 
               
               
                 ftsZ 
                 cell division protein FtsZ 
                 3736 
               
               
                 lpxC 
                 UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine 
                 3737 
               
               
                   
                 deacetylase 
                   
               
               
                 pheA 
                 P-protein 
                 3738 
               
               
                 — 
                 predicted P-loop-containing kinase 
                 3739 
               
               
                 ptsN 
                 nitrogen regulatory IIA protein 
                 3740 
               
               
                 — 
                 probable ABC transporter ATP-binding protein 
                 3741 
               
               
                 — 
                 conserved hypothetical protein 
                 3742 
               
               
                 — 
                 conserved hypothetical protein 
                 3743 
               
               
                 — 
                 conserved hypothetical protein 
                 3744 
               
               
                 pmbA 
                 pmbA 
                 3745 
               
               
                 hpt 
                 hypoxanthine phosphoribosyltransferase 
                 3746 
               
               
                 — 
                 predicted Na+/dicarboxylate symporter 
                 3747 
               
               
                 nrdG 
                 anaerobic ribonucleoside-triphosphate reductase 
                 3748 
               
               
                   
                 activating protein 
                   
               
               
                 cydC 
                 transport ATP-binding protein CydC 
                 3749 
               
               
                 cydD 
                 transport ATP binding protein CydD 
                 3750 
               
               
                 trxB 
                 thioredoxin reductase 
                 3751 
               
               
                 — 
                 thioredoxin domain-containing protein 
                 3752 
               
               
                 hemH 
                 ferrochelatase 
                 3753 
               
               
                 — 
                 conserved hypothetical protein 
                 3754 
               
               
                 — 
                 conserved FAD/FMN-containing dehydrogenase 
                 3755 
               
               
                 ompP5 
                 outer membrane protein P5 
                 3756 
               
               
                 — 
                 conserved glutaredoxin-related protein 
                 3757 
               
               
                 — 
                 histidinol-phosphate aminotransferase 2 
                 3758 
               
               
                 serC 
                 phosphoserine aminotransferase 
                 3759 
               
               
                 — 
                 conserved hypothetical protein 
                 3760 
               
               
                 — 
                 conserved hypothetical protein 
                 3761 
               
               
                 — 
                 conserved hypothetical protein 
                 3762 
               
               
                 trpG2 
                 putative anthranilate synthase component II 
                 3763 
               
               
                 metK 
                 S-adenosylmethionine synthetase 
                 3764 
               
               
                 sprT 
                 SprT 
                 3765 
               
               
                 opa 
                 opacity protein 
                 3766 
               
               
                 — 
                 conserved hypothetical protein 
                 3767 
               
               
                 artM 
                 arginine transport system permease protein 
                 3768 
               
               
                 artQ 
                 arginine transport system permease protein 
                 3769 
               
               
                 artI 
                 arginine-binding periplasmic protein 
                 3770 
               
               
                 artP 
                 arginine transport ATP-binding protein 
                 3771 
               
               
                 gmhA 
                 phosphoheptose isomerase 
                 3772 
               
               
                 ligA 
                 DNA ligase 
                 3773 
               
               
                 dppF 
                 dipeptide transport ATP binding protein 
                 3774 
               
               
                 dppD 
                 dipeptide transport ATP binding protein 
                 3775 
               
               
                 dppC 
                 dipeptide transport system permease protein 
                 3776 
               
               
                 dppB 
                 dipeptide transport system permease protein 
                 3777 
               
               
                 uvrD 
                 DNA helicase II 
                 3778 
               
               
                 — 
                 predicted organic radical activating enzyme 
                 3779 
               
               
                 — 
                 predicted 6-pyruval-tetrahydropterin synthase 
                 3780 
               
               
                 — 
                 predicted PP-loop superfamily ATPase 
                 3781 
               
               
                 — 
                 conserved hypothetical protein 
                 3782 
               
               
                 ilvE 
                 branched chain amino acid amino transferase 
                 3783 
               
               
                 gcvA 
                 glycine cleavage system transcriptional activator 
                 3784 
               
               
                 — 
                 predicted SAM-dependent methyltransferase 
                 3785 
               
               
                 sucC 
                 succinyl-CoA synthetase beta chain 
                 3786 
               
               
                 sucD 
                 succinyl-CoA synthetase alpha chain 
                 3787 
               
               
                 — 
                 putative translation factor, Sua5 
                 3788 
               
               
                 rluB 
                 ribosomal large subunit pseudouridine synthase B 
                 3789 
               
               
                 cysB 
                 HTH-type transcriptional regulator CysB 
                 3790 
               
               
                 — 
                 conserved hypothetical adenine-specific methylase 
                 3791 
               
               
                 — 
                 conserved hypothetical protein 
                 3792 
               
               
                 pta 
                 phosphate acetyltransferase 
                 3793 
               
               
                 ackA 
                 acetate kinase 
                 3794 
               
               
                 — 
                 conserved hypothetical protein 
                 3795 
               
               
                 cvpA 
                 colicin C production protein 
                 3796 
               
               
                 — 
                 amidophosphoribosyltransferase 
                 3797 
               
               
                 sulA 
                 cell division inhibitor SulA 
                 3798 
               
               
                 argR 
                 argininr repressor 
                 3799 
               
               
                 mdh 
                 malate dehydrogenase 
                 3800 
               
               
                 lysS 
                 lysyl-tRNA synthetase 
                 3801 
               
               
                 prfB 
                 peptide chain release factor 2 
                 3802 
               
               
                 dsbC 
                 thiol:disulfide interchange protein DsbC 
                 3803 
               
               
                 recJ 
                 single stranded DNA specific exonuclease RecJ 
                 3804 
               
               
                 — 
                 conserved hypothetical protein 
                 3805 
               
               
                 mtnA 
                 MTA/SAH nucleosidase 
                 3806 
               
               
                 hup 
                 heme utilization protein 
                 3807 
               
               
                 — 
                 putative L-Lactate permease 
                 3808 
               
               
                 fbp 
                 frustose-1,6-bisphosphatase 
                 3809 
               
               
                 truA 
                 tRNA pseudouridine synthase A 
                 3810 
               
               
                 sapZ 
                 Predicted membrane protein 
                 3811 
               
               
                 sapF 
                 ABC-type transport system, ATPase component 
                 3812 
               
               
                   
                 involved in antimicrobial peptide resistance 
                   
               
               
                 sapD 
                 ABC-type transport system, ATP binding component, 
                 3813 
               
               
                   
                 involved in antimicrobial peptide resistance 
                   
               
               
                 sapC 
                 ABC-type transport system, permease protein, 
                 3814 
               
               
                   
                 involved in antimicrobial peptide resistance 
                   
               
               
                 sapB 
                 ABC-type transport system, permease protein, 
                 3815 
               
               
                   
                 involved in antimicrobial peptide resistance 
                   
               
               
                 sapA 
                 ABC-type transport system, periplasmic component, 
                 3816 
               
               
                   
                 involved in antimicrobial peptide resistance 
                   
               
               
                 — 
                 Predicted ATPase 
                 3817 
               
               
                 Ppc 
                 Phosphoenolpyruvate carboxylase 
                 3818 
               
               
                 purR 
                 HTH-type transcriptional repressor PurR 
                 3819 
               
               
                 dapD 
                 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N- 
                 3820 
               
               
                   
                 succinyltransferase 
                   
               
               
                 PurA 
                 adenylosuccinate synthetase 
                 3821 
               
               
                 — 
                 predicted aspartokinase 
                 3822 
               
               
                 rplY 
                 50S ribosomal protein L25 
                 3823 
               
               
                 — 
                 uncharacterized membrane-associate protein 
                 3824 
               
               
                 — 
                 conserved hypothetical protein 
                 3825 
               
               
                 — 
                 putative translation initiation inhibitor, YjgF family 
                 3826 
               
               
                 — 
                 conserved hypothetical protein 
                 3827 
               
               
                 — 
                 conserved hypothetical protein 
                 3828 
               
               
                 — 
                 HTH-type trancriptional regulator 
                 3829 
               
               
                 — 
                 putative ABC-type Co2+ transport system, 
                 3830 
               
               
                   
                 periplasmic component 
                   
               
               
                 — 
                 conserved hypothetical protein 
                 3831 
               
               
                 cbiM 
                 predicted ABC-type cobalt transport system,  
                 3832 
               
               
                   
                 permease component 
                   
               
               
                 — 
                 predicted cobalt transport protein 
                 3833 
               
               
                 cbiO 
                 predicted ABC-type cobalt transport system, ATPase 
                 3834 
               
               
                   
                 component 
                   
               
               
                 aspC 
                 aspartate aminotransferase 
                 3835 
               
               
                 purK 
                 phosphoribosylaminoimidazole carboxylase ATPase 
                 3836 
               
               
                   
                 subunit 
                   
               
               
                 purE 
                 phosphoribosylaminoimidazole carboxylase catalytic 
                 3837 
               
               
                   
                 subunit 
                   
               
               
                 hicA 
                 HicA 
                 3838 
               
               
                 hicB 
                 HicB 
                 3839 
               
               
                 pepN 
                 aminopeptidase N 
                 3840 
               
               
                 ribE 
                 riboflavin synthase alpha chain 
                 3841 
               
               
                 norM 
                 probable multidrug resistance protein NorM 
                 3842 
               
               
                 sfsA 
                 sugar fermentation stimulation protein 
                 3843 
               
               
                 tyrS 
                 tyrosyl-tRNA synthase 
                 3844 
               
               
                 prsA 
                 ribose phosphate pyrophosphokinase 
                 3845 
               
               
                 ispE 
                 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase 
                 3846 
               
               
                 lolB 
                 outer-membrane lipoprotein LolB 
                 3847 
               
               
                 cca 
                 tRNA nucleotidyltransferase 
                 3848 
               
               
                 — 
                 conserved hypothetical protein 
                 3849 
               
               
                 — 
                 putative phosphate permease 
                 3850 
               
               
                 — 
                 conserved hypothetical phosphate transport regulator 
                 3851 
               
               
                 — 
                 predicted membrane protein 
                 3852 
               
               
                 — 
                 conserved hypothetical protein 
                 3853 
               
               
                 — 
                 conserved hypothetical protein 
                 3854 
               
               
                 — 
                 conserved hypothetical protein 
                 3855 
               
               
                 — 
                 hypothetical protein 
                 3856 
               
               
                 — 
                 hypothetical protein 
                 3857 
               
               
                 — 
                 hypothetical protein 
                 3858 
               
               
                 hmw2C 
                 HMW2C, putative glycosyltransferase involved in 
                 3859 
               
               
                   
                 glycosylation of HMW1A and HMW2A 
                   
               
               
                 hmw2B 
                 HMW2B, OMP-85-like protein required for  
                 3860 
               
               
                   
                 HMW1A and HMW2A secretion 
                   
               
               
                 -hmw2A 
                 HMW2A, high molecular weight adhesin 2 
                 3861 
               
               
                 — 
                 conserved hypothetical protein 
                 3862 
               
               
                 radA 
                 DNA repair protein RadA homolog 
                 3863 
               
               
                 lrp 
                 leucine-responsive regulatory protein 
                 3864 
               
               
                 ftsK 
                 DNa translocase FtsK 
                 3865 
               
               
                 lolA 
                 outer-membrane lipoproteins carrier protein precursor 
                 3866 
               
               
                 — 
                 predicted ATPase related to the helicase subunit of  
                 3867 
               
               
                   
                 the holliday junction resolvase 
                   
               
               
                 — 
                 hypothetical protein 
                 3868 
               
               
                 — 
                 modification methylase BepI-like 
                 3869 
               
               
                 aroA 
                 3-phosphoshikimate 1-carboxyvinyltransferase 
                 3870 
               
               
                 purU 
                 formyltetrahydrofolate deformylase 
                 3871 
               
               
                 hns 
                 DNA-binding protein H-NS homolog 
                 3872 
               
               
                 — 
                 predicted Na+/H+ antiporter 
                 3873 
               
               
                 — 
                 hypothetical protein 
                 3874 
               
               
                 ilvI 
                 acetolactate synthase large subunit 
                 3875 
               
               
                 ilvH 
                 acetolactate synthase small subunit 
                 3876 
               
               
                 argS 
                 arginyl-tRNA synthetase 
                 3877 
               
               
                 — 
                 conserved hypothetical protein 
                 3878 
               
               
                 — 
                 hypothetical lipoprotein 
                 3879 
               
               
                 pcp 
                 outer-membrane lipoprotein PCP precursor 
                 3880 
               
               
                 lgtD 
                 UDP-0glcNAc-lipooligosaccharide N- 
                 3881 
               
               
                   
                 acetylglucosamine glycosyltransferase 
                   
               
               
                 pgi 
                 glucose-6-phosphate isomerase 
                 3882 
               
               
                 alr 
                 alanine racemase 
                 3883 
               
               
                 dnaB 
                 replicative DNA helicase 
                 3884 
               
               
                 pykA 
                 pyruvate kinase 
                 3885 
               
               
                 — 
                 prophage CP4-57-like integrase 
                 3886 
               
               
                 — 
                 hypothetical protein 
                 3887 
               
               
                 — 
                 hypothetical protein 
                 3888 
               
               
                 — 
                 hypothetical protein 
                 3889 
               
               
                 — 
                 hypothetical protein 
                 3890 
               
               
                 — 
                 hypothetical protein 
                 3891 
               
               
                 — 
                 modification methylase Bsp6I-like 
                 3892 
               
               
                 rdgC 
                 recombination associated protein 
                 3893 
               
               
                 — 
                 hypothetical protein 
                 3894 
               
               
                 ssb3 
                 single strand binding protein 
                 3895 
               
               
                 — 
                 hypothetical protein 
                 3896 
               
               
                 — 
                 predicted recombinational DNA repair protein, RecE 
                 3897 
               
               
                   
                 pathway 
                   
               
               
                 — 
                 hypothetical protein 
                 3898 
               
               
                 — 
                 hypothetical protein 
                 3899 
               
               
                 — 
                 modification methylase DpnIIB-like 
                 3900 
               
               
                 — 
                 hypothetical protein 
                 3901 
               
               
                 — 
                 hypothetical protein 
                 3902 
               
               
                 — 
                 hypothetical protein 
                 3903 
               
               
                 — 
                 hypothetical protein 
                 3904 
               
               
                 — 
                 hypothetical protein 
                 3905 
               
               
                 — 
                 hypothetical protein 
                 3906 
               
               
                 — 
                 hypothetical protein 
                 3907 
               
               
                 — 
                 hypothetical protein 
                 3908 
               
               
                 — 
                 hypothetical protein 
                 3909 
               
               
                 — 
                 hypothetical protein 
                 3910 
               
               
                 — 
                 hypothetical protein 
                 3911 
               
               
                 — 
                 hypothetical protein 
                 3912 
               
               
                 — 
                 hypothetical protein 
                 3913 
               
               
                 — 
                 hypothetical protein 
                 3914 
               
               
                 — 
                 hypothetical protein 
                 3915 
               
               
                 — 
                 hypothetical protein 
                 3916 
               
               
                 — 
                 hypothetical protein 
                 3917 
               
               
                 — 
                 hypothetical protein 
                 3918 
               
               
                 — 
                 hypothetical protein 
                 3919 
               
               
                 — 
                 hypothetical protein 
                 3920 
               
               
                 — 
                 hypothetical protein 
                 3921 
               
               
                 — 
                 hypothetical protein 
                 3922 
               
               
                 — 
                 hypothetical protein 
                 3923 
               
               
                 — 
                 predicted DNA modification methylase 
                 3924 
               
               
                 — 
                 hypothetical protein 
                 3925 
               
               
                 — 
                 hypothetical protein 
                 3926 
               
               
                 — 
                 predicted phage terminase large subunit 
                 3927 
               
               
                 — 
                 hypothetical protein 
                 3928 
               
               
                 — 
                 uncharacterized protein, homolog of phage Mu  
                 3929 
               
               
                   
                 protein gp30 
                   
               
               
                 — 
                 hypothetical protein 
                 3930 
               
               
                 — 
                 hypothetical protein 
                 3931 
               
               
                 — 
                 hypothetical protein 
                 3932 
               
               
                 — 
                 hypothetical protein 
                 3933 
               
               
                 — 
                 hypothetical protein 
                 3934 
               
               
                 — 
                 hypothetical protein 
                 3935 
               
               
                 — 
                 hypothetical protein 
                 3936 
               
               
                 — 
                 hypothetical protein 
                 3937 
               
               
                 — 
                 hypothetical protein 
                 3938 
               
               
                 — 
                 hypothetical protein 
                 3939 
               
               
                 — 
                 hypothetical protein 
                 3940 
               
               
                 — 
                 hypothetical protein 
                 3941 
               
               
                 — 
                 predicted phage-related minor tail protein 
                 3942 
               
               
                 — 
                 hypothetical protein 
                 3943 
               
               
                 — 
                 hypothetical protein 
                 3944 
               
               
                 — 
                 hypothetical protein 
                 3945 
               
               
                 — 
                 hypothetical protein 
                 3946 
               
               
                 — 
                 hypothetical protein 
                 3947 
               
               
                 — 
                 hypothetical protein 
                 3948 
               
               
                 — 
                 hypothetical protein 
                 3949 
               
               
                 — 
                 hypothetical protein 
                 3950 
               
               
                 — 
                 probable tail fiber protein 
                 3951 
               
               
                 — 
                 hypothetical protein 
                 3952 
               
               
                 — 
                 hypothetical protein 
                 3953 
               
               
                 — 
                 conserved hypothetical protein 
                 3954 
               
               
                 — 
                 hypothetical protein 
                 3955 
               
               
                 — 
                 hypothetical protein 
                 3956 
               
               
                 — 
                 mu-like prophage protein gp29 
                 3957 
               
               
                 — 
                 conserved hypothetical protein 
                 3958 
               
               
                 — 
                 hypothetical protein 
                 3959 
               
               
                 — 
                 conserved hypothetical protein 
                 3960 
               
               
                 — 
                 hypothetical protein 
                 3961 
               
               
                 — 
                 hypothetical protein 
                 3962 
               
               
                 — 
                 hypothetical protein 
                 3963 
               
               
                 — 
                 hypothetical protein 
                 3964 
               
               
                 — 
                 hypothetical protein 
                 3965 
               
               
                 — 
                 hypothetical protein 
                 3966 
               
               
                 — 
                 hypothetical protein 
                 3967 
               
               
                 prfA 
                 peptide chain release factor 1 
                 3968 
               
               
                 — 
                 conserved hypothetical protein 
                 3969 
               
               
                 hemK 
                 HemK 
                 3970 
               
               
                 — 
                 conserved hypothetical protein 
                 3971 
               
               
                 kdsA 
                 2-dehyrdro-3-deoxyphosphooctonate aldolase 
                 3972 
               
               
                 — 
                 putative 2-hydroxyacid dehydrogenase 
                 3973 
               
               
                 lolC 
                 lipoprotein releasing system transmembrane protein 
                 3974 
               
               
                 bioA 
                 adenosylmethionine-8-amino-7-oxononanoate 
                 3975 
               
               
                   
                 aminotransferase 
                   
               
               
                 bioF 
                 8-amino-7-oxononanoate synthase 
                 3976 
               
               
                 — 
                 conserved hypothetical protein 
                 3977 
               
               
                 bioC 
                 putative biotin synthesis protein BioC 
                 3978 
               
               
                 bioD-B 
                 probable dethiobiotin synthetase 2 
                 3979 
               
               
                 lolD 
                 lipoprotein releasing system ATP-binding protein 
                 3980 
               
               
                   
                 LolD 
                   
               
               
                 lolE 
                 ABC-type transport system, involved in lipoprotein 
                 3981 
               
               
                   
                 release, permease component 
                   
               
               
                 aroG 
                 phospho-2-dehyrdro-3-deoxyheptonate aldolase 
                 3982 
               
               
                 impA 
                 impA 
                 3983 
               
               
                 — 
                 predicted Na+/serine symporter 
                 3984 
               
               
                 — 
                 putative NAD(P)H oxidoreductase 
                 3985 
               
               
                 — 
                 predicted component of anaerobic dehydrogenases 
                 3986 
               
               
                 — 
                 predicted nitroreductase 
                 3987 
               
               
                 sppA 
                 protease IV 
                 3988 
               
               
                 licD 
                 phosphorylcholine transferase 
                 3989 
               
               
                 licC 
                 LicC 
                 3990 
               
               
                 licB 
                 LicB 
                 3991 
               
               
                 licA 
                 LicA 
                 3992 
               
               
                 — 
                 predicted glycine/D-amino acid oxidases,  
                 3993 
               
               
                   
                 deaminating 
                   
               
               
                 fabB 
                 3-oxacyl-[acyl-carrier-protein] synthase I 
                 3994 
               
               
                 rrxA 
                 glutaredoxin 
                 3995 
               
               
                 rimK 
                 probable ribosomal protein S6 modification protein 
                 3996 
               
               
                 gltS 
                 sodium/glutamate symport carrier protein 
                 3997 
               
               
                 parC 
                 topoisomerase IV subunit A 
                 3998 
               
               
                 parE 
                 topoisomerase IV subunit B 
                 3999 
               
               
                 htrB 
                 lipid A biosynthesis lauroyl acyltransferase 
                 4000 
               
               
                 rfaE 
                 ADP-heptose synthase 
                 4001 
               
               
                 — 
                 hypothetical protein 
                 4002 
               
               
                 uupA2 
                 ABC transporter ATP-binding protein 
                 4003 
               
               
                 uppB 
                 ABC transporter ATP-binding protein 
                 4004 
               
               
                 — 
                 putative carbonic anhydrase 
                 4005 
               
               
                 asnS 
                 asparaginyl-tRNA synthetase 
                 4006 
               
               
                 ribH 
                 6,7-dimethyl-8-ribityllumazine synthase 
                 4007 
               
               
                 nusB 
                 N utilization substance protein B 
                 4008 
               
               
                 thiL 
                 thiamine-monophosphate kinase 
                 4009 
               
               
                 pgpA 
                 phosphatidylglycerophosphatase A 
                 4010 
               
               
                 — 
                 predicted threonine efflux protein 
                 4011 
               
               
                 dapB 
                 dihydrodipicolinate reductase 
                 4012 
               
               
                 — 
                 conserved hypothetical ferredoxin-like protein 
                 4013 
               
               
                 — 
                 conserved hypothetical protein 
                 4014 
               
               
                 pheS 
                 ohenylalanyl-tRNA synthetase alpha chain 
                 4015 
               
               
                 pheT 
                 ohenylalanyl-tRNA synthetase beta chain 
                 4016 
               
               
                 himA 
                 integration host factor alpha-subunit 
                 4017 
               
               
                 — 
                 conserved hypothetical lipoprotein 
                 4018 
               
               
                 — 
                 hypothetical protein 
                 4019 
               
               
                 — 
                 putative 5′(3′)-deoxyribonucleotidase 
                 4020 
               
               
                 — 
                 NAD-dependent deacetylase 
                 4021 
               
               
                 — 
                 hypothetical protein 
                 4022 
               
               
                 ftsK2 
                 DNA translocase ftsK 
                 4023 
               
               
                 — 
                 NAD-dependent deacetylase sirtuin 5 
                 4024 
               
               
                 — 
                 hypothetical protein 
                 4025 
               
               
                 — 
                 hypothetical protein 
                 4026 
               
               
                 — 
                 hypothetical protein 
                 4027 
               
               
                 — 
                 predicted serine/threonine protein phosphatase family 
                 4028 
               
               
                   
                 protein 
                   
               
               
                 — 
                 predicted arylsulfatase A-like enzyme 
                 4029 
               
               
                 — 
                 predicted enzyme related to aldose 1-epimerase 
                 4030 
               
               
                 infC 
                 translation initiation factor IF-3 
                 4031 
               
               
                 rpmI 
                 50S ribosomal protein L35 
                 4032 
               
               
                 rpT 
                 50S ribosomal protein L20 
                 4033 
               
               
                 recB 
                 exodeoxyribonuclease V beta chain 
                 4034 
               
               
                 recD 
                 exodeoxyribonuclease V alpha chain 
                 4035 
               
               
                 — 
                 conserved hypothetical protein 
                 4036 
               
               
                 lonB 
                 putative protease Lahomolog, predicted ATP- 
                 4037 
               
               
                   
                 dependent protease 
                   
               
               
                 fabA 
                 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase 
                 4038 
               
               
                 — 
                 conserved hypothetical protein 
                 4039 
               
               
                 — 
                 conserved hypothetical protein 
                 4040 
               
               
                 rpsO 
                 30S ribosomal protein S15 
                 4041 
               
               
                 — 
                 conserved hypothetical transposase-like protein 
                 4042 
               
               
                 — 
                 conserved hypothetical protein 
                 4043 
               
               
                 dacB 
                 penicillin-binding protein 4 precursor 
                 4044 
               
               
                 greA 
                 transcription elongation factor GreA 
                 4045 
               
               
                 — 
                 predicted RNA-binding protein containing KH 
                 4046 
               
               
                   
                 domain, possible ribosomal protein 
                   
               
               
                 ftsJ 
                 ribosomal RNA large subunit methyltransferase J 
                 4047 
               
               
                 FTSh 
                 cell division protein FtsH homolog 1 
                 4048 
               
               
                 folP 
                 dihydropteroate synthase 
                 4049 
               
               
                 mrsA 
                 predicted phosphomannomutase 
                 4050 
               
               
                 sixA 
                 phosphohistidine phosphatase SixA homolog 
                 4051 
               
               
                 — 
                 conserved hypothetical protein 
                 4052 
               
               
                 — 
                 conserved hypothetical protein 
                 4053 
               
               
                 — 
                 hypothetical protein 
                 4054 
               
               
                 — 
                 hypothetical protein 
                 4055 
               
               
                 — 
                 possible RNA polymerase sigma factor 24 
                 4056 
               
               
                 — 
                 hypothetical protein 
                 4057 
               
               
                 — 
                 hypothetical protein 
                 4058 
               
               
                 msaB 
                 peptide methionine sulfoxide reductase MsrA/MsrB 
                 4059 
               
               
                 — 
                 conserved hypothetical cytochrome c-type biogenesis 
                 4060 
               
               
                   
                 protein 
                   
               
               
                 — 
                 conserved hypothetical protein 
                 4061 
               
               
                 — 
                 conserved hypothetical protein 
                 4062 
               
               
                 moeB 
                 molybdopterin biosynthesis protein MoeB 
                 4063 
               
               
                 moeA 
                 molybdopterin biosynthesis protein MoeA 
                 4064 
               
               
                 folE 
                 GTP cyclohydrolase I 
                 4065 
               
               
                 — 
                 conserved hypothetical protein 
                 4066 
               
               
                 bioD-A 
                 probable dethiobiotin synthetase 1 
                 4067 
               
               
                 metF 
                 5, 10-methylenetetrahydrofolate reductase 
                 4068 
               
               
                 rplM 
                 50S ribosomal protein L13 
                 4069 
               
               
                 rpsI 
                 30S ribosomal protein S9 
                 4070 
               
               
                 sspA 
                 stringent starvation protein A 
                 4071 
               
               
                 sspB 
                 stringent starvation protein B 
                 4072 
               
               
                 dxs 
                 1-deoxy-D-xylulose 5-phosphate synthase 
                 4073 
               
               
                 ispA 
                 geranyltranstransferase 
                 4074 
               
               
                 xseB 
                 exodeoxyribonuclease VII small subunit 
                 4075 
               
               
                 thiI 
                 predicted thiamine biosynthesis ATP pyrophosphatase 
                 4076 
               
               
                 — 
                 conserved hypothetical protein 
                 4077 
               
               
                 truC 
                 tRNA pseudouridine synthase C 
                 4078 
               
               
                 — 
                 conserved hypothetical protein 
                 4079 
               
               
                 cspD 
                 cold shock-like protein CspD 
                 4080 
               
               
                 — 
                 conserved hypothetical protein 
                 4081 
               
               
                 usg 
                 predicted aspartate-semialdehyde dehydrogenase 
                 4082 
               
               
                 trpA 
                 tryptophan synthase alpha chain 
                 4083 
               
               
                 trpB 
                 tryptophan synthase beta chain 
                 4084 
               
               
                 — 
                 conserved hypothetical oxidoreductase 
                 4085 
               
               
                 purM 
                 phosphoribosylformylglycinamidine cyclo-ligase 
                 4086 
               
               
                 purN 
                 phosphoribosylglycinamide formyltransferase 
                 4087 
               
               
                 — 
                 predicted ABC-type transport system protein, 
                 4088 
               
               
                   
                 periplasmic component 
                   
               
               
                 uspE 
                 universal stress protein E 
                 4089 
               
               
                 fnr 
                 fumurate and nitrate reduction regulatory protein 
                 4090 
               
               
                 — 
                 putative integrase/recombinase 
                 4091 
               
               
                 — 
                 conserved hypothetical protein 
                 4092 
               
               
                 — 
                 predicted phage anti-repressor protein 
                 4093 
               
               
                 — 
                 hypothetical protein 
                 4094 
               
               
                 — 
                 hypothetical protein 
                 4095 
               
               
                 — 
                 hypothetical protein 
                 4096 
               
               
                 — 
                 hypothetical protein 
                 4097 
               
               
                 — 
                 hypothetical protein 
                 4098 
               
               
                 — 
                 hypothetical protein 
                 4099 
               
               
                 — 
                 predicted transcriptional regulator 
                 4100 
               
               
                 — 
                 hypothetical protein 
                 4101 
               
               
                 — 
                 hypothetical protein 
                 4102 
               
               
                 — 
                 hypothetical protein 
                 4103 
               
               
                 — 
                 hypothetical protein 
                 4104 
               
               
                 — 
                 hypothetical protein 
                 4105 
               
               
                 — 
                 hypothetical protein 
                 4106 
               
               
                 ninB 
                 putative recombination protein NinB 
                 4107 
               
               
                 ninG 
                 putative recombination protein NinG homolog 
                 4108 
               
               
                 — 
                 hypothetical protein 
                 4109 
               
               
                 — 
                 conserved hypothetical protein 
                 4110 
               
               
                 — 
                 hypothetical protein 
                 4111 
               
               
                 — 
                 conserved hypothetical protein 
                 4112 
               
               
                 — 
                 hypothetical protein 
                 4113 
               
               
                 — 
                 conserved hypothetical protein 
                 4114 
               
               
                 — 
                 conserved hypothetical protein 
                 4115 
               
               
                 — 
                 hypothetical protein 
                 4116 
               
               
                 — 
                 conserved hypothetical protein 
                 4117 
               
               
                 — 
                 hypothetical protein 
                 4118 
               
               
                 — 
                 conserved hypothetical protein 
                 4119 
               
               
                 — 
                 predicted phage terminase large subunit 
                 4120 
               
               
                 — 
                 conserved hypothetical protein 
                 4121 
               
               
                 — 
                 uncharacterized protein, homolog of phage Mu  
                 4122 
               
               
                   
                 protein gp30 
                   
               
               
                 — 
                 conserved hypothetical protein 
                 4123 
               
               
                 pyrD 
                 dihyrdoorotate dehydrogenase 
                 4124 
               
               
                 trpH 
                 TrpH 
                 4125 
               
               
                 — 
                 conserved hypothetical protein 
                 4126 
               
               
                 fumC 
                 fumurate hydratase class II 
                 4127 
               
               
                 — 
                 putative glycosyl transferase, glycosyl transferase 
                 4128 
               
               
                   
                 family 8 protein 
                   
               
               
                 holC 
                 DNA polymerase III, chi subunit 
                 4129 
               
               
                 — 
                 conserved hypothetical protein 
                 4130 
               
               
                 — 
                 conserved hypothetical protein 
                 4131 
               
               
                 — 
                 hypothetical protein 
                 4132 
               
               
                 — 
                 conserved hypothetical protein 
                 4133 
               
               
                 — 
                 hypothetical protein 
                 4134 
               
               
                 valS 
                 valyl-tRNA synthetase 
                 4135 
               
               
                 — 
                 hypothetical protein 
                 4136 
               
               
                 trpC 
                 tryptophan biosynthesis protein trpCF 
                 4137 
               
               
                 trpD 
                 anthranilate phosphoribosyltransferase 
                 4138 
               
               
                 — 
                 conserved hypothetical protein 
                 4139 
               
               
                 trpG 
                 anthranilate synthase component II 
                 4140 
               
               
                 trpE 
                 anthranilate synthase component I 
                 4141 
               
               
                 — 
                 pseudogene for conserved hypothetical 
                 4142 
               
               
                   
                 glycosyltransferase 
                   
               
               
                 ftnB 
                 ferritin-like protein 2 
                 4143 
               
               
                 ftnA 
                 ferritin-like protein 1 
                 4144 
               
               
                 pstS 
                 phosphate-binding periplasmic protein precursor PstS 
                 4145 
               
               
                 pstC 
                 phosphate transport system permease protein PstC 
                 4146 
               
               
                 pstA 
                 phoaphate transport system permease proteain PstA 
                 4147 
               
               
                 pstB 
                 phosphate import ATP-binding protein PstB 
                 4148 
               
               
                 phoB 
                 phosphate regulon transcriptional regulatory protein 
                 4149 
               
               
                   
                 PhoB 
                   
               
               
                 phoR 
                 phosphate regulon sensor protein PhoR 
                 4150 
               
               
                 sbcB 
                 exodeoxyribonuclease I 
                 4151 
               
               
                 — 
                 conserved hypothetical protein 
                 4152 
               
               
                 — 
                 conserved hypothetical protein 
                 4153 
               
               
                 — 
                 cell division protein MukB 
                 4154 
               
               
                 — 
                 cell division protein MukE 
                 4155 
               
               
                 haeIIR 
                 type II restriction exzyme HaeII 
                 4156 
               
               
                 haeIIM 
                 modification methylase HaeII 
                 4157 
               
               
                 mukF 
                 MukF homolog 
                 4158 
               
               
                 — 
                 predicted ATPase of the PP-loop superfamily 
                 4159 
               
               
                   
                 implicated in cell cycle control 
                   
               
               
                 — 
                 predicted dissimilatory sulfite reductase, 
                 4160 
               
               
                   
                 desulfoviridin, gamma subunit 
                   
               
               
                 mop 
                 probable molybdenum-pterin binding protein 
                 4161 
               
               
                 pqqL 
                 probable zinc protease 
                 4162 
               
               
                 thrS 
                 threonyl-tRNA synthetase 
                 4163 
               
               
                 acpD 
                 probable acyl carrier protein phosphodiesterase 
                 4164 
               
               
                 topA 
                 DNA topoisomerase I 
                 4165 
               
               
                 — 
                 putative HTH-type transcriptional regulator 
                 4166 
               
               
                 pntB 
                 NAD(P) transhydrogenase subunit beta 
                 4167 
               
               
                 pntA 
                 NAD(P) transhydrogenase subunit alpha 
                 4168 
               
               
                 glgP 
                 glycogen phosphorylase 
                 4169 
               
               
                 glgA 
                 glycogen synthase 
                 4170 
               
               
                 glgC 
                 glucose-1-phosphate adenylyltransferase 
                 4171 
               
               
                 glgX 
                 glycogen operon protein GlgX 
                 4172 
               
               
                 glgB 
                 1,4-alpha-glucan branching enzyme 
                 4173 
               
               
                 malQ 
                 4-alpha-glucanotransferase 
                 4174 
               
               
                 — 
                 conserved hypothetical protein 
                 4175 
               
               
                 glnS 
                 glutaminyl-tRNA synthetase 
                 4176 
               
               
                 cafA 
                 ribonuclease G 
                 4177 
               
               
                 putP 
                 sodium/proline symporter 
                 4178 
               
               
                 — 
                 conserved hypothetical protein 
                 4179 
               
               
                 cdd 
                 cytiding deaminase 
                 4180 
               
               
                 — 
                 conserved hypothetical DNA-binding ferritin-like 
                 4181 
               
               
                   
                 protein 
                   
               
               
                 pepT 
                 peptidase T 
                 4182 
               
               
                 potA 
                 spermidine/putrescine transport ATP-binding protein 
                 4183 
               
               
                 potB 
                 spermidine/putrescine transport permease protein 
                 4184 
               
               
                 potC 
                 spermidine/putrescine transport system permease 
                 4185 
               
               
                   
                 protein 
                   
               
               
                 potD1 
                 spermidine/putrescine-binding periplasmic protein 1 
                 4186 
               
               
                   
                 precursor 
                   
               
               
                 uupA 
                 ABC transporter ATP-binding protein 
                 4187 
               
               
                 — 
                 deoxyguanosinetriphosphate triphosphohydrolase-like 
                 4188 
               
               
                   
                 protein 
                   
               
               
                 — 
                 putative effector of murein hydrolase 
                 4189 
               
               
                 — 
                 putative effector of murein hydrolase 
                 4190 
               
               
                 — 
                 predicted micrococcal nuclease-like protein 
                 4191 
               
               
                 nifS 
                 predicted selenocysteine lyase 
                 4192 
               
               
                 — 
                 predicted SufE protein probably involved in Fe-S 
                 4193 
               
               
                   
                 center assembly 
                   
               
               
                 — 
                 Zn-ribbon-containing, possible nucleic-acid binding 
                 4194 
               
               
                   
                 protein 
                   
               
               
                 — 
                 predicted enzyme related to GTP cyclohydrolase I 
                 4195 
               
               
                 tyrA 
                 T-protein 
                 4196 
               
               
                 truB 
                 tRNA pseudouridine synthase B 
                 4197 
               
               
                 rbfA 
                 ribosome-binding factor A 
                 4198 
               
               
                 hsdM3 
                 putative type I restriction enzyme HindVIIP M  
                 4199 
               
               
                   
                 protein 
                   
               
               
                 hsdS3 
                 putative type I restriction enzyme HindVIIP 
                 4200 
               
               
                   
                 specificity protein 
                   
               
               
                 — 
                 hypothetical protein 
                 4201 
               
               
                 hsdR3 
                 putative type I restriction enzyme HindVIIP R  
                 4202 
               
               
                   
                 protein 
                   
               
               
                 infB 
                 translation initiation factor IF-2 
                 4203 
               
               
                 nusA 
                 transcriptional elongation protein NusA 
                 4204 
               
               
                 — 
                 conserved hypothetical protein 
                 4205 
               
               
                 — 
                 hypothetical protein 
                 4206 
               
               
                 — 
                 hypothetical protein 
                 4207 
               
               
                 — 
                 hypothetical protein 
                 4208 
               
               
                 — 
                 hypothetical protein 
                 4209 
               
               
                 — 
                 hypothetical protein 
                 4210 
               
               
                 — 
                 hypothetical protein 
                 4211 
               
               
                 — 
                 hypothetical protein 
                 4212 
               
               
                 — 
                 probable tail fiber protein 
                 4213 
               
               
                 — 
                 predicted bacteriophage P2-related tail formation 
                 4214 
               
               
                   
                 protein gpI 
                   
               
               
                 — 
                 predicted phage-related baseplate assembly protein 
                 4215 
               
               
                 — 
                 predicted baseplate assembly protein W 
                 4216 
               
               
                 — 
                 predicted phage P2-like baseplate assembly protein 
                 4217 
               
               
                 — 
                 hypothetical protein 
                 4218 
               
               
                 — 
                 hypothetical protein 
                 4219 
               
               
                 — 
                 hypothetical protein 
                 4220 
               
               
                 — 
                 hypothetical protein 
                 4221 
               
               
                 — 
                 predicted phage-related tail protein 
                 4222 
               
               
                 — 
                 hypothetical protein 
                 4223 
               
               
                 — 
                 hypothetical protein 
                 4224 
               
               
                 — 
                 hypothetical protein 
                 4225 
               
               
                 — 
                 hypothetical protein 
                 4226 
               
               
                 — 
                 probable bacteriophage tail completion protein gpS 
                 4227 
               
               
                   
                 homolog 
                   
               
               
                 — 
                 probable bacteriophage tail completion protein gpR 
                 4228 
               
               
                   
                 homolog 
                   
               
               
                 — 
                 hypothetical protein 
                 4229 
               
               
                 — 
                 hypothetical protein 
                 4230 
               
               
                 — 
                 DnaK suppressor protein, bacteriophage PSP3 gp34 
                 4231 
               
               
                   
                 homolog 
                   
               
               
                 — 
                 hypothetical protein 
                 4232 
               
               
                 — 
                 predicted phage-related lysozyme 
                 4233 
               
               
                 — 
                 hypothetical protein 
                 4234 
               
               
                 — 
                 hypothetical protein 
                 4235 
               
               
                 — 
                 hypothetical protein 
                 4236 
               
               
                 — 
                 predicted terminase, endonuclease subunit 
                 4237 
               
               
                 — 
                 predicted major capsid protein 
                 4238 
               
               
                 — 
                 predicted capsid scaffolding protein 
                 4239 
               
               
                 — 
                 terminase, ATPase subunit 
                 4240 
               
               
                 — 
                 predicted portal vertex protein 
                 4241 
               
               
                 siaB 
                 acylneuraminate cytidylyltransferase 
                 4242 
               
               
                 — 
                 putative NAD(P)H nitroreductase 
                 4243 
               
               
                 mrp 
                 Mrp 
                 4244 
               
               
                 metG 
                 methionyl-tRNA synthetase 
                 4245 
               
               
                 tehB 
                 tellurite resistance protein 
                 4246 
               
               
                 gloB 
                 probable hydroxyacylglutathione hydrolase 
                 4247 
               
               
                 — 
                 conserved hypothetical protein 
                 4248 
               
               
                 — 
                 conserved hypothetical protein 
                 4249 
               
               
                 — 
                 conserved hypothetical protein 
                 4250 
               
               
                 gyrA 
                 DNA gyrase subunt A 
                 4251 
               
               
                 metX 
                 homoserine O-acetyltransferase 
                 4252 
               
               
                 sanA 
                 SanA 
                 4253 
               
               
                 folC 
                 folypolyglutamate synthase 
                 4254 
               
               
                 accD 
                 acethy-coenzyme A carboxylase carboxyl transferase 
                 4255 
               
               
                   
                 subunit beta 
                   
               
               
                 htoA 
                 probable periplasmic serine protease do/HhoA-like 
                 4256 
               
               
                   
                 precursor 
                   
               
               
                 mfd 
                 transcription-repair coupling factor 
                 4257 
               
               
                 — 
                 conserved hypothetical protein 
                 4258 
               
               
                 — 
                 predicted P-loop ATPase fused to an acetyltransferase  
                 4259 
               
               
                 — 
                 conserved hypothetical protein 
                 4260 
               
               
                 — 
                 ABC transported ATP-binding protein 
                 4261 
               
               
                 — 
                 predicted plasmid maintenance system antidote  
                 4262 
               
               
                   
                 protein 
                   
               
               
                 — 
                 predicted plasmid maintenance system killer protein 
                 4263 
               
               
                 — 
                 predicted ABC-type transport system, periplasmic 
                 4264 
               
               
                   
                 component 
                   
               
               
                 — 
                 predicted ABC-type transport system, permease 
                 4265 
               
               
                   
                 component 
                   
               
               
                 uvrB 
                 UvrABC system protein B 
                 4266 
               
               
                 — 
                 predicted phosphoglycerol transferase-like protein 
                 4267 
               
               
                 mao2 
                 NADP-dependent malic enzyme 
                 4268 
               
               
                 — 
                 possible polysaccharide biosynthesis protein 
                 4269 
               
               
                 rsuA 
                 ribosomal small subunit pseodouridine synthase A 
                 4270 
               
               
                 bcr 
                 bicyclomycin resistance protein 
                 4271 
               
               
                 — 
                 conserved hypothetical protein 
                 4272 
               
               
                 — 
                 predicted membrane protein 
                 4273 
               
               
                 proA 
                 gamma-glutamyl phosphate reductase 
                 4274 
               
               
                 dnaJ 
                 chaperone protein DnaJ 
                 4275 
               
               
                 dnaK 
                 chaperone protein DnaK 
                 4276 
               
               
                 — 
                 conserved hypothetical protein 
                 4277 
               
               
                 mgsA 
                 methylglyoxal synthase 
                 4278 
               
               
                 aceE 
                 pyruvate dehydrogenase E1 component 
                 4279 
               
               
                 aceF 
                 dihydrolipoamide acetyltransferase component of 
                 4280 
               
               
                   
                 pyruvate dehydrogenase complex 
                   
               
               
                 lpdA 
                 dihydrolipoamide dehudrogenase 
                 4281 
               
               
                 — 
                 hypothetical protein 
                 4282 
               
               
                 apt 
                 adenine phosphoribosyltransferase 
                 4283 
               
               
                 dnzX 
                 DNA polymerase III subunit gamma/tau 
                 4284 
               
               
                 upp 
                 uracil phosphoribosyltransferase 
                 4285 
               
               
                 uraA 
                 probable uracil permease 
                 4286 
               
               
                 — 
                 predicted ATPase involved in DNA replication 
                 4287 
               
               
                   
                 initiation 
                   
               
               
                 — 
                 predicted translation initiation factor 1-like proterin 
                 4288 
               
               
                 pyrF 
                 orotidine 5′-phosphate decarboxylase 
                 4289 
               
               
                 — 
                 predicted N-acetylglucosaminyl transferase 
                 4290 
               
               
                 — 
                 predicted membrane protein 
                 4291 
               
               
                 ihfB 
                 integration host factor beta subunit 
                 4292 
               
               
                 rpsA 
                 30S ribosomal protein S1 
                 4293 
               
               
                 cmk 
                 ctidylate kinase 
                 4294 
               
               
                 — 
                 conserved hypothetical pyridoxine biosynthesis 
                 4295 
               
               
                   
                 enzyme 
                   
               
               
                 — 
                 predicted glutamine amidotransferase involved in 
                 4296 
               
               
                   
                 pyridoxine biosynthesis 
                   
               
               
                 dld 
                 D-lactate dehydrogenase 
                 4297 
               
               
                 — 
                 conserved hypothetical protein 
                 4298 
               
               
                 nlpC 
                 probable lipoprotein NlpC 
                 4299 
               
               
                 tldD 
                 T1dD 
                 4300 
               
               
                 — 
                 predicted methyltransferase 
                 4301 
               
               
                 — 
                 putative lipoprotein 
                 4302 
               
               
                 — 
                 predicted endonuclease distantly related to archael 
                 4303 
               
               
                   
                 holliday junction resolvase 
                   
               
               
                 — 
                 predicted phosphoheptose isomerase 
                 4304 
               
               
                 — 
                 predicted periplasmic or secreted lipoprotein 
                 4305 
               
               
                 nrdA 
                 ribonucleoside-diphosphate reductase alpha chain 
                 4306 
               
               
                 nrdB 
                 ribonucleoside-diphosphate reductase beta chain 
                 4307 
               
               
                 sucB 
                 dihydrolipoamide succinyltransferase component of 
                 4308 
               
               
                   
                 2-oxoglutarate dehydrogenase complex 
                   
               
               
                 sucA 
                 2-oxoglutarate dehydrogenase E1 component 
                 4309 
               
               
                 — 
                 predicted Zn-dependent hydrolase-like protein, 
                 4310 
               
               
                   
                 including glyoxylases 
                   
               
               
                 — 
                 conserved putative deoxyribonuclease 
                 4311 
               
               
                 — 
                 conserved hypothetical protein 
                 4312 
               
               
                 — 
                 conserved hypothetical protein 
                 4313 
               
               
                 prc 
                 tail-specific protease precursor 
                 4314 
               
               
                 proQ 
                 predicted activator of osmoprotectant transporter 
                 4315 
               
               
                   
                 PropP 
                   
               
               
                 — 
                 paraquat-inducible protein A-like protein 
                 4316 
               
               
                 — 
                 paraquat-inducible protein B-like protein 
                 4317 
               
               
                 moaE 
                 molybdopterin converting factor subunit 2 
                 4318 
               
               
                 moaD 
                 molybdopterin converting factor subunit 1 
                 4319 
               
               
                 moaC 
                 molybdenum cofactor biosynthesis protein C 
                 4320 
               
               
                 moaA 
                 molybdenum cofactor biosynthesis protein A 
                 4321 
               
               
                 — 
                 predicted regulator of cell morphogenesis and NO 
                 4322 
               
               
                   
                 signaling 
                   
               
               
                   
                 predicted regulator of cell morphogenesis and NO 
                 4323 
               
               
                   
                 signaling 
                   
               
               
                 — 
                 probable phosphosugar isomerase Hi1678 
                 4324 
               
               
                 yrbI 
                 3-deoxy-D-manno-octulosonate 8-phosphate 
                 4325 
               
               
                   
                 phosphatase 
                   
               
               
                 hmw1A 
                 HMW1A, high molecular weight adhesin 1 
                 4326 
               
               
                 hmw1B 
                 HMW1B, OMP-85-like protein required for  
                 4327 
               
               
                   
                 secretion of HMW1A and HMW2A 
                   
               
               
                 hmw1C 
                 HMW1C, putative glycosyltransferase involved in 
                 4328 
               
               
                   
                 glycosylation of HMW and HWM2A 
                   
               
               
                 — 
                 predicted membrane protein 
                 4329 
               
               
                 — 
                 conserved hypothetical protein 
                 4330 
               
               
                 sohB 
                 possible protease SohB 
                 4331 
               
               
                 rnfA 
                 predicted NADH:ubiquinone oxidoreductase, subunit 
                 4332 
               
               
                   
                 RnfA 
                   
               
               
                 rnfB 
                 predicted NADH:ubiquinone oxidoreductase, subunit 
                 4333 
               
               
                   
                 RnfB 
                   
               
               
                 rnfC 
                 predicted NADH:ubiquinone oxidoreductase, subunit 
                 4334 
               
               
                   
                 RnfC 
                   
               
               
                 mfD 
                 predicted NADH:ubiquinone oxidoreductase, subunit 
                 4335 
               
               
                   
                 RnfD 
                   
               
               
                 rnfG 
                 predicted NADH:ubiquinone oxidoreductase, subunit 
                 4336 
               
               
                   
                 RnfG 
                   
               
               
                 — 
                 predicted NADH:ubiquinone oxidoreductase, subunit 
                 4337 
               
               
                   
                 RnfE 
                   
               
               
                 nth 
                 endonuclease III 
                 4338 
               
               
                 — 
                 predicted Na+-dependent transporters of the SNF 
                 4339 
               
               
                   
                 family 
                   
               
               
                 modC 
                 molybdenum import ATP-binding protein 
                 4340 
               
               
                 modB 
                 molybdenum transport system permease protein 
                 4341 
               
               
                 modA 
                 molybdate-binding periplasmic protein 
                 4342 
               
               
                 mode 
                 Transcriptional regulator ModE 
                 4343 
               
               
                 lsgF 
                 Putative UDP-galactose-lipooligosaccharide 
                 4344 
               
               
                   
                 galactosyltransferase 
                   
               
               
                 lsgE 
                 Putative UDP-galactose-lipooligosaccharide 
                 4345 
               
               
                   
                 galactosyltransferase 
                   
               
               
                 lsgD 
                 Putative UDP-glcNAc-lipooligosaccharide N- 
                 4346 
               
               
                   
                 acetylglucosaminyl glycosyltransferase 
                   
               
               
                 lsgC 
                 Putative UDP-galactose--lipooligosaccharide 
                 4347 
               
               
                   
                 galactosyltransferase 
                   
               
               
                 lsgB 
                 CMP-N-acetylneuraminate-beta-galactosamide-alpha- 
                 4348 
               
               
                   
                 2,3-sialytransferase 
                   
               
               
                 lsgA 
                 putative lipooligosaccharide flippase 
                 4349 
               
               
                 — 
                 conserved hypothetical protein 
                 4350 
               
               
                 — 
                 predicted permease 
                 4351 
               
               
                 — 
                 predicted permease 
                 4352 
               
               
                 pepA 
                 cytosol aminopeptidase 
                 4353 
               
               
                 — 
                 predicted choline-glycine betaine transporter 
                 4354 
               
               
                 qseC 
                 sensor protein QseC 
                 4355 
               
               
                 qseB 
                 transcriptional regulatory protein QseB 
                 4356 
               
               
                 — 
                 conserved hypothetical protein 
                 4357 
               
               
                 crr 
                 PTS system, glucose-specific IIA component 
                 4358 
               
               
                 ptsI 
                 Phosphoenolpyruvate-protein phosphotransferase 
                 4359 
               
               
                 ptsH 
                 Phosphocarrier protein HPr 
                 4360 
               
               
                 — 
                 probable GTPase 
                 4361 
               
               
                 orn 
                 oligoribonuclease 
                 4362 
               
               
                 wecA 
                 undecaprenyl phosphate 
                 4363 
               
               
                 glnD 
                 [protein-PIT] uridylyltransferase 
                 4364 
               
               
                 map 
                 methionine aminopeptidase 
                 4365 
               
               
                 — 
                 conserved hypothetical protein 
                 4366 
               
               
                 — 
                 conserved hypothetical protein 
                 4367 
               
               
                 mrcB 
                 penicillin-binding protein 1B 
                 4368 
               
               
                 purC 
                 phosphoribosylaminoimidazole-succinocarboxamine 
                 4369 
               
               
                   
                 synthase 
                   
               
               
                 argG 
                 argininosuccinate synthase 
                 4370 
               
               
                 — 
                 Mn2+ and Fe2+ transporter of the NRAMP family 
                 4371 
               
               
                 — 
                 conserved hypothetical protein 
                 4372 
               
               
                 — 
                 predicted allophanate hydrolase subunit 2 
                 4373 
               
               
                 — 
                 predicted allophanate hydrolase subunit 1 
                 4374 
               
               
                 rnb 
                 exoribonuclease II 
                 4375 
               
               
                 fabI 
                 enoyl-[acyl-carrier-protein] reductase [NADH] 
                 4376 
               
               
                 prfC 
                 peptide chain release factor 3 
                 4377 
               
               
                 — 
                 conserved hypothetical protein 
                 4378 
               
               
                 — 
                 predicted branched chain amino acid permease 
                 4379 
               
               
                 — 
                 predicted branched chain amino acid permease 
                 4380 
               
               
                 metR 
                 HTH-type transcriptional regulator MetR 
                 4381 
               
               
                 lldD 
                 L-lactate dehydrogenase 
                 4382 
               
               
                 murI 
                 glutamate racemase 
                 4383 
               
               
                 recG 
                 ATP-dependent DNA helicase 
                 4384 
               
               
                 spoT 
                 guanosine-3′,5′-bis 3′ pyrophosphohydrolase 
                 4385 
               
               
                 rpoZ 
                 DNA directed RNA polymerase omega chain 
                 4386 
               
               
                 gmk 
                 guanylate kinase 
                 4387 
               
               
                   
               
             
          
         
       
     
       Example 10 
     Comparison of the Genomes of NTHi, Strain 86-028NP and  H. influenzae , Strain RD 
       [0136]    The genomic sequence of strain 86-028NP contains 1,913,428 bp. This is approximately 4 percent larger than the strain Rd genome (1,830,137 bp) (Fleischmann et al.,  Science  269:496-512, 1995). There are also a larger number of genes in strain 86-028NP: 1942 compared to 1743 in strain Rd. The gene complement was compared to that of strain Rd using the Seqman program in the DNASTAR suite. With 80% identity at the nucleotide level as a cutoff value, 285 ORFS were identified in the 86-028NP genome that were absent from the strain Rd genome and 167 ORFs were identified in the strain Rd genome that are absent from the strain 86-028NP genome. 
         [0137]    Strain 86-028NP, like strain Rd, has six ribosomal operons. Using tRNAscan-SE v1.11, 58 tRNA genes were identified in the strain 86-028NP genome, representing the 20 common amino acids. The tRNA-Glu, tRNA-Ala and tRNA-Ile genes were located in spacer regions between the 16S and 23S ribosomal RNA genes. A tRNA gene containing the UCA anticodon was also identified. This anticodon corresponds to an opal stop codon and is typically associated with an opal-suppressing tRNA that incorporates selenocysteine. The tRNA is adjacent to two genes encoding selB (NTHI0836), a Sec tRNA specific elongation factor, and selA (NTHI0835), the enzyme that converts serine to dehydroalanine preparatory to forming selenocysteine by incorporation of selenium (Forchhammer et al.,  Nature  342:453-6, 1989) The selD gene (NTHI0297), encoding selenophosphate synthetase was also identified. The importance of this selenocysteine system is evidenced by the coding sequence for the alpha subunit of formate dehydrogenase (NTHI0007) containing an inframe TGA stop codon that is presumably read as a selenocysteine codon. The inframe TGA stop codon was previously noted in the current annotation of the strain Rd formate dehydrogenase gene (GenPept Accession P46448). 
         [0138]    A gross comparison between the genomes involving analysis of the gene order of strain 86-028NP and that of strain Rd reveals a single major rearrangement in the form of a large inversion. This 471 kb inversion represents almost 25% of the strain 86-028NP genome and is bounded by NTHI1391, and NTHI1394 (homologues of HI1218 and HI1645 respectively) and by NTHI11949 and NTHI1950 (homologues of HI1219 and HI1647 respectively). HI1219 and HI1646 are partially duplicated genes in strain Rd annotated as cmkA and cmkB (cytidylate kinases). One cmk gene (NTHI1949) is present in strain 86-028NP with a small cmk-like fragment between NTHI1391 and NTHI1394. Several clones from the scaffolding library overlap each end of the inversion in the 86-028NP genome validating our assembly. Within this large inversion are several insertions, the largest of which are approximately 13 kb, 27 kb and 51 kb in size. These regions contain predominantly hypothetical and conserved hypothetical genes as well as a number of homologues of phage genes. For example, the 27 kb insertion contains remnants of HP1- and HP2-like phage genes. The largest insert is bounded by homologues of integrase genes. In strain Rd, a mu-like phage is localized to this region (Morgan et al.,  J Mol Biol  317:337-59, 2002) This phage is not present in the strain 86-028NP genome. Also within the large inverted region is a 21 kb inversion that restores synteny with the Rd genome. 
         [0139]    In addition to the large inversion, strain 86-028NP has other regions of divergence from co-linearity with the strain Rd genome. These include 9 regions greater than 5 kb, which contain sequences with no apparent homology to DNA that is present in strain Rd. Two of these regions contain the HMW adhesins that are discussed below. Hypothetical genes predominate in six of the unique regions. The ninth region is approximately 56 kb in size. It lies between NTHI0100 and NTHI0165. BLASTn analysis indicated that genes in this region, designated ICEHin86-028NP, have high homology to genes in the  H. influenzae  type b plasmid, ICEHin1056 (Mohd-Zain et al.,  J Bacteriol  186:8114-22, 2004). ICEHin1056 is a member of an extended family of genomic islands that are defined by a series of common core genes (Mohd-Zain et al.,  J Bacteriol  186:8114-22, 2004). ICEHin86-028NP possesses homologues of 45 ICEHin1056 ORFs. These include ORFs near the 5′ end of ICEHin86-028NP, including the defined core genes, that primarily encode proteins with putative roles in plasmid replication and conjugation and ORFs near the 3′ end that primarily encode conserved hypothetical proteins with motifs that suggest that they may be either membrane associated or exported. Notably, ICEHin86-028NP lacks the genes encoding proteins involved in tetracycline, chloramphenicol and β-lactam resistance found in ICEHin1056. Scattered within ICEHin86-028NP are a transposase, resolvases, and a putative integrase regulator suggesting that ICEHin86-028NP is a composite element derived from several mobile genetic elements. 
         [0140]    ICEHin1506 has a sequence designated as an attP site 5′ the first gene. In strain 86-028NP, a perfect copy of this attP site is present 5′ to NTHI0101 and a copy of this attP site, with a single nucleotide change, is present 3′ of NTHI0164. The attP sites are implicated in the incorporation of mobile genetic elements into bacterial chromosomes to form genomic islands, possibly suggesting a mechanism by which this large section of genetic material became integrated into the strain 86-028NP genome (Dimopoulou et al.,  Antimicrob Agents Chemother  46:1602-3, 2002). ICEHin86-028NP has a G+C content of 39%, lower than any of the other related genomic islands and close to strain 86-028NP&#39;s overall genome G+C content of 38%. This implies a long-term genomic association for this element. The presence of this element with its complement of genes homologous to those in ICEHin1506 (Dimopoulou et al.,  Antimicrob Agents Chemother  46:1602-3, 2002) which are thought to encode membrane-associated and secreted proteins may have important implications for the virulence of strain 86-028NP. 
         [0141]    Several members of the Pasteurellaceae including  Haemophilus ducreyi, Pasteurella multocida  and  Actinobacillus actinomycetemcomitans  produce well characterized protein toxins. In contrast,  H. influenzae  does not appear to produce protein toxins and genes encoding putative protein toxins were not identified in the strain 86-028NP genome. In  H. influenzae , the genes encoding glycosyltransferases responsible for endotoxin biosynthesis and genes encoding proteins that give the bacteria enhanced “fitness” during the process of infection have generally been considered virulence determinants. These genes include those that encode adhesins, the heme and haemoglobin binding proteins as well as the genes that encode proteins that protect against oxidative stress. 
       Contingency Genes 
       [0142]      H. influenzae  has a limited number of two-component regulatory systems and other global regulators. Moxon and co-workers have argued that loci termed “simple contingency loci” provide an alternative mechanism for regulating gene expression, thus increasing the fitness of an organism by contributing to that organism&#39;s ability to rapidly respond to changing environmental conditions. These loci contain short tandem sequence repeats either within, or 5′ to, a coding region. During DNA replication, addition or loss of a repeat within a reading frame results in an alteration in the reading frame. When localized 5′ to a coding region, addition or loss of a repeat results in a change in promoter activity (Bayliss et al.,  Clin Invest  107:657-62, 2001). Loci containing simple sequence repeats have been studied extensively in  H. influenzae , for example (Hood et al.,  Proc Natl Acad Sci USA  93:11121-5, 1996). Several of the loci described in the following sections as phase variable contain simple sequence repeats. 
       Adhesins 
       [0143]    Strain 86-028NP possesses a number of genes which encode products that primarily function in adherence to host cells (Table 8). One of these, the outer membrane protein P5, has previously been identified and its function carefully dissected (Jiang et al.,  Infect Immun  67:187-92, 1999; Kennedy et al.,  Infect Immun  68:2756-65, 2000; Novotny et al.,  J Immunol  171:1978-83, 2003; Novotny et al.,  Infect Immun  68:2119-28, 2000; Novotny et al.,  Vaccine  20:3590-7, 2002; Sirakova et al.,  Infect Immun  62:2002-20, 1994). Strain 86-028NP possesses a gene cluster containing four genes that are homologues of pilABCD from strain Rd,  Actinobacillus pleuropneumoniae  and  P. multocida  (Bakaletz et al.,  Infect Immun  73:1635-4, 2005; Doughty et al.,  Vet Microbiol  72:79-90, 2000; Ruffolo et al.,  Infect Immun  65:339-43, 1997 Stevenson et al.,  Vet Microbiol  92:121-34, 2003). These genes together with the comE gene and genes yet to be identified encode a type IV pilus that has a role in adherence of strain 86-028NP to nasopharyngeal tissues (Kennedy et al.,  Infect. Immun.,  68: 2756-2765, 2000). 
         [0144]    Strain 86-028NP possesses two high molecular weight (HMW) adhesin gene clusters that are absent in strain Rd. The high molecular weight adhesins were first characterized in NTHi, strain 12, which has two HMW gene clusters, each encoding three proteins (HMWA, HMWB and HMWC). HMWA is the structural component of the adhesin, HMWB has a role in trans-membrane translocation, while HMWC is required for glycosylation of HMWA (Barenkamp et al.,  Infect Immun  60:1302-13, 1992. Barenkamp et al.,  Infect Immun  62:3320-8; 1994; Grass et al.,  Mol Microbiol  48:737-51, 2003; St Geme et al.,  Mol Microbiol  27:617-30, 1998). Similarly, strain 86-028NP&#39;s two HMW gene clusters contain homologues of the hmwA, B and C genes in the same gene context as in strain 12 (Buscher et al.,  J Bacterial  186:4209-17, 2004). The HMW1A and HMW2A proteins from strain 86-028NP are 72% identical, with the major area of divergence, including a 41 amino acid insertion in HMW2A, toward the C-termini. The paired HMWB and HMWC proteins from strain 86-028NP are 99% identical, respectively. The sequence ATCTTTC is repeated 17 times upstream of hmw1A and 23 times upstream of hmw2A. In strain 12, 16 repeats of this sequence are found 5′ of each hmw gene cluster (Barenkamp et al.,  Infect Immun  60:1302-13, 1992). 
         [0145]    Hap is an autotransported protein with a domain homologous to the catalytic domain of IgA1 proteases. The NTHI0354 gene encodes a protein with 83% identity to Hap from the NTHi strain N187 (St Geme et al.,  Mol Microbiol  14:217-3, 1994). Strain 86-028NP, along with other NTHi strains that possess HMW1 and HMW2, lacks the gene encoding Hia, another  Haemophilus  adhesin (Barenkamp et al.,  Mol Microbiol  19:1215-23, 1996). Strain 86-028NP also lacks the hif gene cluster, encoding the hemagglutinating pilus as we previously reported (Munson et al.,  Infect Immun  72:3002-10, 2004). 
         [0000]    
       
         
               
             
               
               
               
               
               
               
             
               
               
               
               
               
               
             
               
               
               
               
               
             
               
               
               
               
               
               
             
           
               
                 TABLE 8 
               
             
             
               
                   
               
               
                 NTHi genes that encode proteins that primarily function in adherence to host cells 
               
             
          
           
               
                   
                   
                 Gene 
                 SEQ ID 
                   
                   
               
               
                 NTHI# 
                 HI# 
                 name  
                 NO: 
                 Function 
                 Contingency Repeats 
               
               
                   
               
             
          
           
               
                 354 
                   
                 hap 
                 1080 
                 Adhesion and penetration protein Hap 
                   
               
               
                 406  
                 296 
                 pilD  
                 1125 
                 Putative type 4 prepilin-like protein specific 
                   
               
               
                   
                   
                   
                   
                 leader peptidase (EC 3.4.23.43) 
                   
               
               
                 407  
                 297 
                 pilC 
                 1126 
                 Putative type IV pilin secretion protein 
                   
               
               
                 408  
                 298  
                 pilB 
                 1127 
                 Putative type IV pilin secretion protein 
                   
               
               
                 409  
                 299  
                 pilA 
                 1128  
                 Type IV pilin subunit protein 
                   
               
               
                 1332 
                 1164 
                 ompP5 
                 1953 
                 Outer membrane protein P5 (OMP P5- 
                   
               
               
                   
                   
                   
                   
                 homologous adhesin) 
                   
               
             
          
           
               
                 1448 
                   
                 hmw2C 
                 2057 
                 HMW2C, putative glycosyltransferase involved in glycosylation of 
               
               
                   
                   
                   
                   
                 HMW1A and HMW2A 
               
             
          
           
               
                 1449 
                   
                 hmw2B 
                 2058 
                 HMW2B, OMP-85-like protein required for 
                   
               
               
                   
                   
                   
                   
                 HMW1A and HMW2A secretion 
                   
               
               
                 1450 
                   
                 hmw2A 
                 2059 
                 HMW2A, high molecular weight  
                 ATCTTTC repeated 23 
               
               
                   
                   
                   
                   
                 adhesin 2 
                 times, 5′ of gene 
               
               
                 1983 
                   
                 hmw1A 
                 2530 
                 HMW1A, high molecular weight  
                 ATCTTTC repeated 17 
               
               
                   
                   
                   
                   
                 adhesin 1 
                 times, 5′ of gene 
               
               
                 1984 
                   
                 hmw1B 
                 2531 
                 HMW1B, OMP-85-like protein required for 
                   
               
               
                   
                   
                   
                   
                 secretion of HMW1A and HMW2A 
                   
               
               
                 1985 
                   
                 Hmw1C 
                 2532 
                 HMW1C, putative gylcosyltransferase 
                   
               
               
                   
                   
                   
                   
                 involved in glycosylation of HMW1A and 
                   
               
               
                   
                   
                   
                   
                 HMW1B 
               
               
                   
               
             
          
         
       
     
         [0146]    In Tables 8, 9 and 10, the “NTHI number” refers to the locus tag number within the NTHi, strain 86-028NP genome as indicated at the Microbial-Pathogenesis  H. influenzae  86028 NP web site and in Genbank Accession No. CP000057. The HI number” refers to the corresponding locus tag number in the TIGR (The Institute for genomic redearc 
       Lipooligosaccharide Synthesis [See [Page 13 of Original Application] 
       [0147]    The structure, biosynthesis and role in virulence of  H. influenzae  lipooligosaccharide (LOS) has been studied extensively. Table 9 contains a list of genes involved in lipooligosaccharide biosynthesis. Strain 86-028NP has the full complement of genes required to synthesize the heptose-Kdo-Lipid A portion of LOS. The lgtF and lpsA genes encode glycosyltransferases that add glucose, and glucose or galactose, to heptose residues 1 and 3, respectively. Both of these genes are present in the strain 86-028NP genome, therefore it is likely that carbohydrate chains can be extended from the heptose 1 and heptose 3 residues of the strain 86-028NP LOS (Hood et al.,  Microbiology  150:2089-97, 2004). In the serotype b strain RM153, the lic2C gene encodes a glucosyltransferase that adds glucose to heptose 2 (Hood et al.,  Microbiology  150:2089-97, 2004). In the strain 86-028NP genome, this gene contains a frame shift. The phase variable lic2A and licA genes, encoding a galactosyltranferase and choline kinase, respectively, are present in the strain 86-028NP genome (High et al.,  Mol Microbiol  9:1275-82, 1993; Hood et al.,  Glycobiology  11:957-67, 2001; Weiser et al.,  Infect Immun  65:943-50, 1997). The lex2B gene which encodes a glucosyltransferase in the serotype b strain DL42, as well as a number of other serotypeable strains, is present in the strain 86-028NP genome (Griffin et al.,  Microbiology  149:3165-75, 2003; Jarosik et al.,  Infect Immun  62:4861-7, 1994). Five-prime to the lex2B gene in strain DL42 is the short phase variable lex2A gene. In strain 86-028NP, this gene is out-of-frame compared to the DL42 sequence (Genbank Accession U05670), due to the loss of one tetranucleotide repeat and a 5 bp deletion. Recently, Hood and co-workers described a locus in strain Rd, designated hmg, that contains HI0866 through HI0874 (Hood et al.,  J Bacteriol  186:7429-39, 2004). With the exception of a homologue of rmlB, these genes are absent from the strain 86-028NP genome. This includes the siaA gene which encodes a sialyltransferase recently shown to be important in biofilm formation in NTHI strain 2019 (Greiner et al.,  Infect Immun  72:4249-60, 2004; Jones et al.,  J Biol Chem  277:14598-611, 2002). Two copies of a homologue of the lic3A gene, encoding an alternative sialyltransferase, were identified in the strain 86-028NP genome (Hood et al.,  Mol Microbiol  39:341-50, 2001; Jones et al.,  J Biol Chem  277:14598-611, 2002), as well as a copy of the lsgB gene that encodes another sialyltransferase Jones et al.,  J Biol Chem  277:14598-611, 2002). 
         [0000]    
       
         
               
             
               
               
               
               
               
               
             
               
               
               
               
               
               
             
           
               
                 TABLE 9 
               
             
             
               
                   
               
               
                 NTHi genes involved in lipooligosaccharide biosynthesis 
               
             
          
           
               
                   
                   
                 Gene 
                 SEQ ID 
                   
                   
               
               
                 NTHI# 
                 HI# 
                 name 
                 NO: 
                 Function 
                 Contingency Repeats 
               
               
                   
               
             
          
           
               
                 68 
                 58 
                 kdsB 
                 831 
                 3-deoxy-D-manno-octulosonic acid 
                   
               
               
                   
                   
                   
                   
                 cytidylyltransferase 
                   
               
               
                 69 
                 59 
                 lpxK 
                 832 
                 Tetraacyldisaccharide 4′-kinase 
                   
               
               
                 72 
                 60 
                 msbA 
                 833 
                 Lipid A export ATP-binding protein msbA 
                   
               
               
                 296 
                 199 
                 msbB 
                 1029 
                 Lipid A biosynthesis (KDO)2-(lauroyl)-lipid 
                   
               
               
                   
                   
                   
                   
                 IVA acyltransferase 
                   
               
               
                 365 
                 258 
                 lgtC 
                 1090 
                 UDP-galactose--lipooligosaccharide 
                 GACA repeated 10 
               
               
                   
                   
                   
                   
                 galactosyltransferase 
                 times, in frame 
               
               
                 366 
                 260 
                 orfM 
                 1091 
                 Xanthosine triphosphate pyrophosphatase 
                   
               
               
                 367 
                 260.1 
                 kdkA 
                 1092 
                 3-deoxy-D-manno-octulosonic acid kinase 
                   
               
               
                 368 
                 261 
                 opsX 
                 1093 
                 ADP-heptose--lipooligosaccharide 
                   
               
               
                   
                   
                   
                   
                 heptosyltransferase I 
                   
               
               
                 383 
                 275 
                 lpt6 
                 1107 
                 PE-tn-6--lipooligosaccharide 
                   
               
               
                   
                   
                   
                   
                 phosphorylethanolamine transferase 
                   
               
               
                 471 
                 351 
                 galE 
                 1184 
                 UDP-glucose 4-epimerase 
                   
               
               
                 472 
                 352 
                 lic3A 
                 1185 
                 CMP-neu5Ac--lipooligosaccharide alpha 2-3  
                 CAAT repeated 18 
               
               
                   
                   
                   
                   
                 sialyltransferase 
                 times, in frame 
               
               
                 512 
                 391 
                   
                   
                 Predicted acyltransferase 
                 AGCA repeated 8 
               
               
                   
                   
                   
                   
                   
                 times, in frame 
               
               
                 649 
                 523 
                 waaQ 
                 1350 
                 ADP-heptose--lipooligosaccharide 
                   
               
               
                   
                   
                   
                   
                 heptosyltransferase III 
                   
               
               
                 677 
                 550 
                 lic2A 
                 1378 
                 UDP-galactose--lipooligosaccharide 
                 CAAT repeated 14 
               
               
                   
                   
                   
                   
                 galactosyltransferase 
                 times, in frame 
               
               
                 772 
                 652 
                 kdtA 
                 1462 
                 3-deoxy-D-manno-octulosonic acid 
                   
               
               
                   
                   
                   
                   
                 transferase 
                   
               
               
                 773 
                 653 
                 lgtF 
                 1463 
                 UDP-glucose--lipooligosaccharide 
                   
               
               
                   
                   
                   
                   
                 glucosyltransferase 
                   
               
               
                 892 
                 735 
                 lpxH 
                 1569 
                 UDP-2,3-diacylglucosamine hydrolase 
                   
               
               
                 899 
                 740 
                 pgmB 
                 1575 
                 phosphoglucomutase 
                   
               
               
                 913 
                   
                 lex2B 
                 1586 
                 UDP-glucose--lipooligosaccharide 
                   
               
               
                   
                   
                   
                   
                 glucosyltransferase 
                   
               
               
                 926 
                 765 
                 lpsA 
                 1597 
                 lipooligosaccharide glycosyltransferase 
                   
               
               
                 976 
                 812 
                 galU 
                 1644 
                 UTP--glucose-1-phosphate uridylyltransferase 
                   
               
               
                 1034 
                   
                 lic3A2 
                 1696 
                 CMP-neu5Ac--lipooligosaccharide alpha 2-3 
                 CAAT repeated 18 
               
               
                   
                   
                   
                   
                 sialyltransferase 
                 times, in frame 
               
               
                 1037 
                 873 
                 rmlB 
                 1698 
                 dTDP-glucose 4,6-dehydratase 
                   
               
               
                 1082 
                 915 
                 lpxC 
                 1739 
                 UDP-3-O-[3-hydroxymyristoyl] glucosamine 
                   
               
               
                   
                   
                   
                   
                 N-acyltransferase 
                   
               
               
                 1180 
                 1005 
                   
                   
                 Predicted PE--lipooligosaccharide 
                   
               
               
                   
                   
                   
                   
                 phosphorylethanolamine transferase 
                   
               
               
                 1220 
                 1060 
                 lpxB 
                 1858 
                 Lipid-A-disaccharide synthase 
                   
               
               
                 1222 
                 1061 
                 lpxA 
                 1859 
                 Acyl-[acyl-carrier-protein]--UDP-N- 
                   
               
               
                   
                   
                   
                   
                 acetylglucosamine O-acyltransferase 
                   
               
               
                 1224 
                 1064 
                   
                   
                 Predicted PE--lipooligosaccharide 
                   
               
               
                   
                   
                   
                   
                 phosphorylethanolamine transferase 
                   
               
               
                 1272 
                 1105 
                 rfaF 
                 1900 
                 ADP-heptose--lipooligosaccharide 
                   
               
               
                   
                   
                   
                   
                 heptosyltransferase II 
                   
               
               
                 1278 
                 1114 
                 rfaD 
                 1906 
                 ADP-L-glycero-D-manno-heptose-6- 
                   
               
               
                   
                   
                   
                   
                 epimerase 
                   
               
               
                 1312 
                 1144 
                 gmbA 
                 1934 
                 UDP-3-O-[3-hydroxymyristoyl] N- 
                   
               
               
                   
                   
                   
                   
                 acetylglucosamine deacetylase 
                   
               
               
                 1350 
                 1181 
                 gmhA 
                 1969 
                 Phosphoheptose isomerase 
                   
               
               
                 1474 
                 1578 
                 lgtD 
                 2079 
                 Putative UDP-glcNAc--lipooligosaccharide  
                   
               
               
                   
                   
                   
                   
                 N-Acetylglucosannine glycosyltransferase 
                   
               
               
                 1576 
                 1557 
                 kdsA 
                 2172 
                 Phospho-2-dehydro-3-deoxyoctonate 
                   
               
               
                   
                   
                   
                   
                 aldolase and 3-deoxy-D-manno-octulosonic 
                   
               
               
                   
                   
                   
                   
                 acid 8-phosphate synthetase 
                   
               
               
                 1594 
                 1540 
                 licD 
                 2189 
                 Phosphorylcholine transferase 
                   
               
               
                 1595 
                 1539 
                 ticC 
                 2190 
                 Protein licC, CTP--phosphocholine 
                   
               
               
                   
                   
                   
                   
                 cytidylyltransferase 
                   
               
               
                 1596 
                 1538 
                 licB 
                 2191 
                 Protein licB, putative cho;ine uptake protein 
                   
               
               
                 1597 
                 1537 
                 licA 
                 2192 
                 Protein licA, choline kinase 
                 CAAT repeated 15 
               
               
                   
                   
                   
                   
                   
                 times, in frame 
               
               
                 1606 
                 1527 
                 htr8 
                 2200 
                 Lipid A biosynthesis lauroyl acyltransferase 
                   
               
               
                 1607 
                 1526 
                 rfaE 
                 2201 
                 ADP-heptose synthase 
                   
               
               
                 1664 
                 1337 
                 mrsA 
                 2251 
                 Predicted phosphomannomutase 
                   
               
               
                 1750 
                   
                   
                   
                 Putative glycosyltransferase, glycosyl 
                 GACA repeated 14 
               
               
                   
                   
                   
                   
                 transferase family 8 protein 
                 times, in frame 
               
               
                 1769 
                   
                   
                   
                 Putative glycosyltransferase 
                 CCAA repeated 17 
               
               
                   
                   
                   
                   
                   
                 times, out of frame 
               
               
                 1891 
                 1279 
                 sia8 
                 2433 
                 CMP-neu5Ac synthetase 
                   
               
               
                 1921 
                 1244 
                   
                   
                 Possible polysaccharide biosynthesis protein 
                   
               
               
                 2002 
                 1695 
                 lsgF 
                 2548 
                 Putative UDP-galactose--lipooligosaccharide 
                   
               
               
                   
                   
                   
                   
                 galactosyltransferase 
                   
               
               
                 2003 
                 1696 
                 lsgE 
                 2549 
                 Putative UDP-galactose--lipooligosaccharide 
                   
               
               
                   
                   
                   
                   
                 galactosyltransferase 
                   
               
               
                 2004 
                 1697 
                 lsgD 
                 2550 
                 Putative UDP-glcNAc--lipooligosaccharide N- 
                   
               
               
                   
                   
                   
                   
                 Acetylglucosaminyl glycosyltransferase 
                   
               
               
                 2005 
                 1698 
                 lsgC 
                 2551 
                 Putative UDP-galactose--lipooligosaccharide 
                   
               
               
                   
                   
                   
                   
                 galactosyltransferase 
                   
               
               
                 2006 
                 1699 
                 lsg8 
                 2552 
                 CMP-N-acetylneuraminate-beta- 
                   
               
               
                   
                   
                   
                   
                 galactosamide-alpha-2,3-sialyltransferase 
                   
               
               
                 2007 
                 1700 
                 lsgA 
                 2553 
                 Putative lipooligosaccharide flippase 
                   
               
               
                 2025 
                 1716 
                 wecA 
                 2569 
                 Undecaprenyl-phosphate alpha-N- 
                   
               
               
                   
                   
                   
                   
                 acetylglucosaminyl 1-phosphate transferase 
               
               
                   
               
             
          
         
       
     
       Iron Acquisition 
       [0148]      H. influenzae  strains have an absolute requirement for either heme or iron, together with protophorphyrin IX (PPIX), the immediate precursor of heme (Evans et al.,  J Med Microbiol  7:359-65, 1974; White et al.,  J Bacteriol  85:842-50, 1963). Table 10 contains a list of genes involved in iron acquisition. Three haemoglobin and haemoglobin-haptoglobin binding proteins HgpA, HgpB and HgpC, were identified in  H. influenzae  type b, strain HI689 (Jin et al.,  Microbiology  145 (Pt 4):905-14, 1999; Morton et al.,  Infect Immun  67:2729-39, 1999; Ren et al.,  Infect Immun  66:4733-41, 1998). In strain HI689, these genes have CCAA tetranucleotide repeats and are known to be regulated by slip-strand mispairing. Two of these genes are present in strain 86-028NP. They both contain CCAA repeats; the hgpB gene is in-frame while the hgpC gene is out-of-frame. The derived amino acid sequence of a third gene that contains CCAA repeats is 45% identical to hgpA. We have designated this gene hgpD. This gene is out-of-frame. Homologues of the hxuABC genes of  H. influenzae  type b that encode heme and heme-hemopexin complexes (Cope et al.,  Infect Immun  69:2353-63, 2001; Cope et al.,  Infect Immun  66:4511-6, 1998; Cope et al.,  J Bacteriol  177:2644-53, 1995) as well as a homologue of the hemR receptor were identified. Strain 86-028NP also has the gene encoding the heme-binding lipoprotein HbpA (Heath et al.,  Pediatr Infect Dis J  20:300-5, 2001). Downstream of hbpA is NTHI1022, a hypothetical gene whose product is a member of COG0748, a cluster that includes putative heme utilization proteins. A homologue of the hup gene, recently identified in  H. influenzae  type b, that encodes a general heme utilization protein, was also identified (Morton et al.,  Microbiology  150:3923-33, 2004). 
         [0149]    In addition to the heme transport systems, iron transport systems were also identified. The hitABC genes encode the FbpABC proteins respectively, members of a highly specific ferric iron ABC transport system that was elegantly characterized by complementing a siderophore-deficient  E. coli  strain with the hitABC genes cloned from an  H. influenzae  type b strain (Anderson et al.,  J Bacteriol  186:6220-9, 2004). Transferrin-binding proteins 1 and 2 encoded by tbpAB (Gray-Owen et al.,  Infect Immun  63:1201-10, 1995; Gray-Owen et al.,  Infect Immun  63:3809-15, 1995) as well as genes designated hfeABCD that are homologues of an ABC transport system involved in iron uptake, originally characterized in  Yersinia pestis  (Bearden et al.,  J Bacteriol  180:1135-47, 1998) were identified. This latter gene cluster is also present in strain Rd. NTHI2035 encodes a putative homologue of the NRAMP family of Mn 2+  and Fe 2+  transporters (Richer et al.,  J. Mol Evol  57:363-7, 2003). 
         [0150]    As noted above,  H. influenzae  can use iron, together with PPIX, as a source of heme for growth in vitro. The hemH gene encoding ferrochelatase, which catalyzes the incorporation of iron into PPIX (Schlor et al.,  Infect Immun  68:3007-9, 2000), was identified. The gene encoding the global regulator, Fur, was also identified (Andrews et al.,  FEMS Microbiol Rev  27:215-37, 2003; Smoot et al.,  J Med Microbiol  48:629-3, 1999). 
         [0000]    
       
         
               
             
               
               
               
               
               
               
             
               
               
               
               
               
               
             
           
               
                 TABLE 10 
               
             
             
               
                   
               
               
                 NTHi Genes Involved in Iron Acquisition 
               
             
          
           
               
                   
                   
                 Gene 
                 SEQ ID 
                   
                   
               
               
                 NTHI# 
                 HI# 
                 name 
                 NO: 
                 Function 
                 Contingency Repeats 
               
               
                   
               
             
          
           
               
                 177 
                 97 
                 hitA 
                 931 
                 hFbpA, Iron-utilization periplasmic protein 
                   
               
               
                 179 
                 98 
                 hitB 
                 932 
                 hFbpB, Iron(III)-transport system permease 
                   
               
               
                   
                   
                   
                   
                 protein 
                   
               
               
                 180 
                 99 
                 hitC 
                 933 
                 hFbpC, Iron-utilization ATP-binding protein 
                   
               
               
                 202 
                 113 
                 hemR 
                 951 
                 Hemin receptor 
                   
               
               
                 284 
                 190 
                 fur 
                 1020 
                 Ferric uptake regulation protein 
                   
               
               
                 369 
                 262 
                 hxuC 
                 1094 
                 Heme/hemopexin-binding protein C 
                   
               
               
                   
                   
                   
                   
                 (Heme:hemopexin utilization protein C) 
                   
               
               
                 370 
                 263 
                 hxuB 
                 1095 
                 Heme/hemopexin-binding protein B 
                   
               
               
                   
                   
                   
                   
                 (Heme:hemopexin utilization protein B) 
                   
               
               
                 371 
                 264 
                 hxuA 
                 1096 
                 Heme/hemopexin-binding protein A 
                   
               
               
                   
                   
                   
                   
                 (Heme:hemopexin utilization protein A) 
                   
               
               
                 477 
                 359 
                 hfeD 
                 1090 
                 Putative ABC-type chelated iron transport 
                   
               
               
                   
                   
                   
                   
                 system, permease component 
                   
               
               
                 478 
                 360 
                 hfeC 
                 1191 
                 Putative ABC-type chelated iron transport 
                   
               
               
                   
                   
                   
                   
                 system, permease component 
                   
               
               
                 479 
                 361 
                 hfeB 
                 1192 
                 Putative ABC-type chelated iron transport 
                   
               
               
                   
                   
                   
                   
                 system, ATPase component 
                   
               
               
                 481 
                 362 
                 hfeA 
                 1193 
                 Putative periplasmic chelated iron binding 
                   
               
               
                   
                   
                   
                   
                 protein 
                   
               
               
                 736 
                   
                 hgpD 
                 1431 
                 Hemoglobin-haptoglobin binding protein D 
                 CCAA repeated 17 
               
               
                   
                   
                   
                   
                 (Hemoglobin-haptoglobin utilization protein D) 
                 times, out of frame 
               
               
                 782 
                 661 
                 hgpB 
                 1472 
                 Hemoglobin-haptoglobin binding protein B 
                 CCAA repeated 12 
               
               
                   
                   
                   
                   
                 (Hemoglobin-haptoglobin utilization protein B)  
                 times, in frame 
               
               
                 840 
                 712 
                 hgpC 
                 1523 
                 Hemoglobin-haptoglobin binding protein C 
                 CCAA repeated 20 
               
               
                   
                   
                   
                   
                 (Hemoglobin-haptoglobin utilization protein C) 
                 times, out of frame 
               
               
                 1021 
                 853 
                 hbpA 
                 1684 
                 Heme-binding protein A (Herein-binding 
                   
               
               
                   
                   
                   
                   
                 lipoprotein) 
                   
               
               
                 1168 
                 994 
                 tbp1 
                 1817 
                 Transferrin-binding protein 1 
                   
               
               
                 1169  
                 995 
                 tbp2 
                 1818 
                 Transferrin-binding protein 2 
                   
               
               
                 1329  
                 1160 
                 hemH 
                 1950 
                 Ferrochelatase 
                   
               
               
                 1390  
                 1217 
                 hup 
                 2004 
                 Heme utilization protein 
                   
               
               
                 2035 
                 1728 
                   
                 2577 
                 Mn2+ and Fe2+ transporter of the NRAMP 
                   
               
               
                   
                   
                   
                   
                 family 
               
               
                   
               
             
          
         
       
     
       Oxidative Stress 
       [0151]    Although necessary for growth, the active acquisition of iron can have deleterious effects on bacterial cells. Through the Fenton reaction, iron can react with hydrogen peroxide and generate highly reactive hydroxyl radicals. These products have profound effects, including lipid peroxidation and damage to both iron-containing enzymes and DNA (Imlay, Annu Rev Microbiol 57:395-418, 2003). The best-known defense system against hydroxyl radicals consists of superoxide dismutase A and B which convert highly reactive superoxide to hydrogen peroxide, which is then converted, by catalase, into water and oxygen (Demple, Annu Rev Genet 25:315-37, 1991). Strains 86-028NP and Rd contain the sodA gene (NTHI1251), but lack the sodB gene. Both strains also possess a catalase gene hktE (NTHI1099) (Bishai et al.,  J Bacteriol  176:2914-21, 1994), the oxyR gene (NTHI0704) encoding a primary regulator of genes involved in protection against oxidative stress (Maciver &amp; Hansen,  Infect Immun  64:4618-29, 1996; Pomposiello et al.,  Trends Biotechnol  19:109-14, 2001) and the gene encoding a chimeric peroxidase termed Prx/Grx that has a glutathione-dependent role in protection against small alkyl hydroperoxides (Pauwels et al.,  J Biol Chem  278:16658-66, 2003; Vergauwen et al.,  J Bacteriol  185:5555-62, 2003; Vergauwen et al.,  J Bacteriol  185:1572-81, 2003). We previously identified NTHI0212, a gene encoding a homologue of the  P. multocida  peroxiredoxin, TsaA that is absent in strain Rd (Munson et al.,  Infect Immun  72:3002-10, 2004). Strain 86-028NP, however, lacks AhpF, a dedicated alkyl hydroperoxide reductase known to be involved in the reduction of TsaA in  Salmonella  (Poole et al.,  Biochemistry  39:6602-15, 2000). Further protection against oxidative stress may be afforded by the ferritin-like proteins encoded by the ftnA and ftnB (NTHI1773 and NTHI1772, respectively) genes. Over-expression of these proteins were shown to protect an iron overloaded  E. coli  fur mutant against oxidative damage Touati et al.,  J Bacteriol  177:2305-14, 1995). A conserved hypothetical gene, NTHI1817, encodes a protein with homology to a DNA-binding ferritin-like protein. This is a member of the Dps family of non-specific DNA binding proteins, which in  S. enterica  have roles in protection against oxidative stress, both in the presence of iron and during phagocytosis, and are important for virulence in a murine model of  Salmonella  infection (Halsey et al.,  Infect Immun  72:1155-8, 2004) In  E. coli , Dps was shown to preferentially bind iron that had been oxidized by hydrogen peroxide, thus having an important role in abrogating the production of hydroxyl radicals generated via the Fenton reaction (Zhao et al.,  J Biol Chem  277:27689-96, 2002). 
       Secretion 
       [0152]    In addition to the Sec system, strain 86-028NP has genes that encode the TatA, B and C proteins, cytoplasmic membrane-associated proteins that are involved in a Sec-independent transport of proteins with twin arginines in their signal peptides (NTHI0279, NTHI0280 and NTHI0282) (Bolhuis et al.,  J Biol Chem  276:20213-9, 2001; Yen et al.,  Arch Microbiol  177:441-50, 2002). As previously reported, strain 86-028NP possesses NTHI0585, the gene encoding the autotransported protein Lav(Munson et al.,  Infect Immun  72:3002-10, 2004). This protein is absent in strain Rd, present in  Neisseria  and appears, within  Haemophilus , to be restricted to pathogenic strains (Davis et al.,  J Bacteriol  183:4626-35, 2001). Strain 86-028NP also has the gene encoding an IgA protease (NTHI1164) (Poulsen et al  J Bacteriol  174:2913-21, 1992), and as noted above, the gene encoding the Hap adhesin. Both are proteins of the autotransporter class. As described above, the HMW adhesins are members of the two-partner secretion pathway group of proteins. 
       Outer Membrane Proteins 
       [0153]    A number of outer membrane protein (OMP) encoding genes have been identified by homology to those in other  Haemophilus  isolates. These include the major OMPs that were all originally identified in  H. influenzae  type b; the surface expressed P1 (NTHI0522), the porin P2 (NTHI0225), the phosphomonoesterase and heme transporter P4 (NTHI0816), the adhesin P5 (NTHI1332) and the lipoprotein P6 (NTHI0501). Strain 86-028NP also shares a number of minor OMPs with other  Haemophilus  strains. These include D15 and the transferrin binding proteins from  H. influenzae  type b, as well as a homologue of OMP26, which was identified in NTHi strain 289 (Munson et al.,  Infect Immun  56:2235-42, 1988; Munson et al.,  Infect Immun  49:544-9, 1985; Munson et al.,  J Clin Invest  72:677-84, 1983; Reidl et al.,  J Exp Med  183:621-9, Reilly et al.,  J Bacteriol  181:6797-805, 1999; Reilly et al.,  FEBS Lett  494:19-23, 2001). All have subsequently been characterized in NTHi strains and analyzed as potential vaccine candidates (Poolman et al., Vaccine 19 Suppl 1:5108-15, 2000; Murphy et al.  Curr Opin Infect Dis  16:129-34, 2003; McMichael et al.,  Curr Opin Investig Drugs  4:953-8, 2003 Cripps et al.  Immunol Cell Biol  81:46-51, 2003; Bakaletz et al.  Ann Otol Rhinol Laryngol  Suppl 188:82-94, 2002). 
       Restriction Enzymes Systems: 
       [0154]    Strain 86-028NP lacks the HindII and HindIII type II restriction systems (Fleischmann et al.,  Science  269:496-512. 80, 1995; Nwankwo et al.,  Gene  150:75-80. 104, 1994, Smith, &amp; Marley.  Methods Enzynzol  65:104-8, 1980). In contrast, genes encoding the HaeII system that was originally identified in  H. aegyptius  (Slatko et al.,  Gene  74:45-50, 1988) are present in the strain 86-028NP genome but absent in strain Rd. Both strain 86-028NP and strain Rd have Hsd type restriction systems encoding a methytransferase (HsdM), a sequence recognition protein (HsdS) and a restriction enzyme (HsdR) (Roberts et al.,  Nucleic Acids Res  31:1805-12, 2003). These genes are adjacent in the strain Rd genome (HI1285-HI1287). The 86-028NP genome contains 3 hsd-like loci that each contain 4 genes. One hsd system is encoded by NTHI1838-NTHI1843. In this gene cluster, NTHI1841 encodes a hypothetical protein. A second hsd-like locus is encoded by NTHI0314-NTHI0318. In this gene cluster, NTHI0316 encodes a putative anticodon nuclease. This hsd-like system may be similar to the prr system in  E. coli  (Tyndall et al.,  J Mol Biol  237:266-74, 1994). A third hsd-locus is encoded by NTHI0188-NTHI0193. In this gene cluster, NTHI0190 encodes a predicted transcriptional regulator with a helix-turn-helix domain.