Patent Publication Number: US-2004043037-A1

Title: Staphylococcus aureus polynucleotides and sequences

Description:
CROSS REFERENCE TO RELATED APPLICATIONS  
     [0001] This application is a divisional of and claims priority under 35 U.S.C. § 120 to U.S. application Ser. No. 08/956,171, filed Oct. 20, 1997, which is a continuation-in-part of and claims priority under 35 U.S.C. § 120 to U.S. application Ser. No. 08/781,986, filed Jan. 3, 1997, which is a non-provisional of and claims benefit under 35 U.S.C. § 119(e) of U.S. Provisional Application No. 60/009,861, filed Jan. 5, 1996. 
    
    
     
       REFERENCE TO A SEQUENCE LISTING PROVIDED ON COMPACT DISC  
       [0002] This application refers to a “Sequence Listing”, which is provided as an electronic document on two identical compact discs (CD-R), labeled “Copy 1” and “Copy 2.” These compact discs each contain the electronic document, filename “PB248P1D1 sequence listing.txt” (6,143,385 bytes in size, created on Dec. 23, 2002), which is hereby incorporated in its entirety herein.  
       FIELD OF THE INVENTION  
       [0003] The present invention relates to the field of molecular biology. In particular, it relates to, among other things, nucleotide sequences of  Staphylococcus aureus,  contigs, ORFs, fragments, probes, primers and related polynucleotides thereof, peptides and polypeptides encoded by the sequences, and uses of the polynucleotides and sequences thereof, such as in fermentation, polypeptide production, assays and pharmaceutical development, among others.  
       BACKGROUND OF THE INVENTION  
       [0004] The genus Staphylococcus includes at least 20 distinct species. (For a review see Novick, R. P., The Staphylococcus as a Molecular Genetic System, Chapter 1, pgs. 1-37 in MOLECULAR BIOLOGY OF THE STAPHYLOCOCCI, R. Novick, Ed., VCH Publishers, New York (1990)). Species differ from one another by 80% or more, by hybridization kinetics, whereas strains within a species are at least 90% identical by the same measure.  
       [0005] The species  Staphylococcus aureus,  a gram-positive, facultatively aerobic, clump-forming  cocci,  is among the most important etiological agents of bacterial infection in humans, as discussed briefly below.  
       [0006] Human Health and  S. Aureus    
       [0007] Staphylococcus aureus  is a ubiquitous pathogen. (See, for instance, Mims et al., MEDICAL MICROBIOLOGY, Mosby-Year Book Europe Limited, London, UK (1993)). It is an etiological agent of a variety of conditions, ranging in severity from mild to fatal. A few of the more common conditions caused by  S. aureus  infection are bums, cellulitis, eyelid infections, food poisoning, joint infections, neonatal conjunctivitis, osteomyelitis, skin infections, surgical wound infection, scalded skin syndrome and toxic shock syndrome, some of which are described further below.  
       [0008] Burns  
       [0009] Burn wounds generally are sterile initially. However, they generally compromise physical and immune barriers to infection, cause loss of fluid and electrolytes and result in local or general physiological dysfunction. After cooling, contact with viable bacteria results in mixed colonization at the injury site. Infection may be restricted to the non-viable debris on the bum surface (“eschar”), it may progress into full skin infection and invade viable tissue below the eschar and it may reach below the skin, enter the lymphatic and blood circulation and develop into septicemia.  S. aureus  is among the most important pathogens typically found in burn wound infections. It can destroy granulation tissue and produce severe septicemia.  
       [0010] Cellulitis  
       [0011] Cellulitis, an acute infection of the skin that expands from a typically superficial origin to spread below the cutaneous layer, most commonly is caused by  S. aureus  in conjunction with  S. pyrogenes.  Cellulitis can lead to systemic infection. In fact, cellulitis can be one aspect of synergistic bacterial gangrene. This condition typically is caused by a mixture of  S. aureus  and  microaerophilic streptococci.  It causes necrosis and treatment is limited to excision of the necrotic tissue. The condition often is fatal.  
       [0012] Eyelid Infections  
       [0013] S. aureus  is the cause of styes and of sticky eye” in neonates, among other eye infections. Typically such infections are limited to the surface of the eye, and may occasionally penetrate the surface with more severe consequences.  
       [0014] Food Poisoning  
       [0015] Some strains of  S. aureus  produce one or more of five serologically distinct, heat and acid stable enterotoxins that are not destroyed by digestive process of the stomach and small intestine (enterotoxins A-E). Ingestion of the toxin, in sufficient quantities, typically results in severe vomiting, but not diarrhea. The effect does not require viable bacteria. Although the toxins are known, their mechanism of action is not understood.  
       [0016] Joint Infections  
       [0017] S. aureus  infects bone joints causing diseases such osteomyelitis.  
       [0018] Osteomyelitis  
       [0019] S. aureus  is the most common causative agent of haematogenous osteomyelitis. The disease tends to occur in children and adolescents more than adults and it is associated with non-penetrating injuries to bones. Infection typically occurs in the long end of growing bone, hence its occurrence in physically immature populations. Most often, infection is localized in the vicinity of sprouting capillary loops adjacent to epiphysial growth plates in the end of long, growing bones.  
       [0020] Skin Infections  
       [0021] S. aureus  is the most common pathogen of such minor skin infections as abscesses and boils. Such infections often are resolved by normal host response mechanisms, but they also can develop into severe internal infections. Recurrent infections of the nasal passages plague nasal carriers of  S. aureus.    
       [0022] Surgical Wound Infections  
       [0023] Surgical wounds often penetrate far into the body. Infection of such wound thus poses a grave risk to the patient.  S. aureus  is the most important causative agent of infections in surgical wounds.  S. aureus  is unusually adept at invading surgical wounds; sutured wounds can be infected by far fewer  S. aureus  cells then are necessary to cause infection in normal skin. Invasion of surgical wound can lead to severe  S. aureus  septicemia. Invasion of the blood stream by  S. aureus  can lead to seeding and infection of internal organs, particularly heart valves and bone, causing systemic diseases, such as endocarditis and osteomyelitis.  
       [0024] Scalded Skin Syndrome  
       [0025] S. aureus  is responsible for “scalded skin syndrome” (also called toxic epidermal necrosis, Ritter&#39;s disease and Lyell&#39;s disease). This diseases occurs in older children, typically in outbreaks caused by flowering of  S. aureus  strains produce exfoliation (also called scalded skin syndrome toxin). Although the bacteria initially may infect only a minor lesion, the toxin destroys intercellular connections, spreads epidermal layers and allows the infection to penetrate the outer layer of the skin, producing the desquamiation that typifies the diseases. Shedding of the outer layer of skin generally reveals normal skin below, but fluid lost in the process can produce severe injury in young children if it is not treated properly.  
       [0026] Toxic Shock Syndrome  
       [0027] Toxic shock syndrome is caused by strains of  S. aureus  that produce the so-called toxic shock syndrome toxin. The disease can be caused by  S. aureus  infection at any site, but it is too often erroneously viewed exclusively as a disease solely of women who use tampons. The disease involves toxaemia and septicemia, and can be fatal.  
       [0028] Nocosomial Infections  
       [0029] In the 1984 National Nocosomial Infection Surveillance Study (“NNIS”)  S. aureus  was the most prevalent agent of surgical wound infections in many hospital services, including medicine, surgery, obstetrics, pediatrics and newborns.  
       [0030] Resistance to Drugs of  S. aureus  Strains  
       [0031] Prior to the introduction of penicillin the prognosis for patients seriously infected with  S. aureus  was unfavorable. Following the introduction of penicillin in the early 1940s even the worst  S. aureus  infections generally could be treated successfully. The emergence of penicillin-resistant strains of  S. aureus  did not take long, however. Most strains of  S. aureus  encountered in hospital infections today do not respond to penicillin; although, fortunately, this is not the case for  S. aureus  encountered in community infections.  
       [0032] It is well known now that penicillin-resistant strains of  S. aureus  produce a lactamase which converts penicillin to pencillinoic acid, and thereby destroys antibiotic activity. Furthermore, the lactamase gene often is propagated episomally, typically on a plasmid, and often is only one of several genes on an episomal element that, together, confer multidrug resistance.  
       [0033] Methicillins, introduced in the 1960s, largely overcame the problem of penicillin resistance in  S. aureus . These compounds conserve the portions of penicillin responsible for antibiotic activity and modify or alter other portions that make penicillin a good substrate for inactivating lactamases. However, methicillin resistance has emerged in  S. aureus , along with resistance to many other antibiotics effective against this organism, including aminoglycosides, tetracycline, chloramphenicol, macrolides and lincosamides. In fact, methicillin-resistant strains of  S. aureus  generally are multiply drug resistant.  
       [0034] The molecular genetics of most types of drug resistance in  S. aureus  has been elucidated (See Lyon et al.,  Microbiology Reviews  51: 88-134 (1987)). Generally, resistance is mediated by plasmids, as noted above regarding penicillin resistance; however, several stable forms of drug resistance have been observed that apparently involve integration of a resistance element into the  S. aureus  genome itself.  
       [0035] Thus far each new antibiotic gives rise to resistance strains, stains emerge that are resistance to multiple drugs and increasingly persistent forms of resistance begin to emerge. Drug resistance of  S. aureus  infections already poses significant treatment difficulties, which are likely to get much worse unless new therapeutic agents are developed.  
       [0036] Molecular Genetics of  Staphylococcus Aureus    
       [0037] Despite its importance in, among other things, human disease, relatively little is known about the genome of this organism.  
       [0038] Most genetic studies of  S. aureus  have been carried out using the strain NCTC8325, which contains prophages psi11, psi12 and psi13, and the UV-cured derivative of this strain, 8325-4 (also referred to as RN450), which is free of the prophages.  
       [0039] These studies revealed that the  S. aureus  genome, like that of other  staphylococci,  consists of one circular, covalently closed, double-stranded DNA and a collection of so-called variable accessory genetic elements, such as prophages, plasmids, transposons and the like.  
       [0040] Physical characterization of the genome has not been carried out in any detail. Pattee et al. published a low resolution and incomplete genetic and physical map of the chromosome of  S. aureus  strain NCTC 8325. (Pattee et al. Genetic and Physical Mapping of Chromosome of  Staphylococcus aureus  NCTC 8325, Chapter 11, pgs. 163-169 in MOLECULAR BIOLOGY OF THE  STAPHYLOCOCCI,  R. P. Novick, Ed., VCH Publishers, New York, (1990) The genetic map largely was produced by mapping insertions of Tn551 and Tn4001, which, respectively, confer erythromycin and gentamicin resistance, and by analysis of SmaI-digested DNA by Pulsed Field Gel Electrophoresis (“PFGE”).  
       [0041] The map was of low resolution; even estimating the physical size of the genome was difficult, according to the investigators. The size of the largest SmaI chromosome fragment, for instance, was too large for accurate sizing by PFGE. To estimate its size, additional restriction sites had to be introduced into the chromosome using a transposon containing a SmaI recognition sequence.  
       [0042] In sum, most physical characteristics and almost all of the genes of  Staphylococcus aureus  are unknown. Among the few genes that have been identified, most have not been physically mapped or characterized in detail. Only a very few genes of this organism have been sequenced. (See, for instance Thomsberry, J.,  Antimicrobial Chemotherapy  21  Suppl C:  9-16 (1988), current versions of GENBANK and other nucleic acid databases, and references that relate to the genome of  S. aureus  such as those set out elsewhere herein.)  
       [0043] It is clear that the etiology of diseases mediated or exacerbated by  S. aureus  infection involves the programmed expression of  S. aureus  genes, and that characterizing the genes and their patterns of expression would add dramatically to our understanding of the organism and its host interactions. Knowledge of  S. aureus  genes and genomic organization would dramatically improve understanding of disease etiology and lead to improved and new ways of-preventing, ameliorating, arresting and reversing diseases. Moreover, characterized genes and genomic fragments of  S. aureus  would provide reagents for, among other things, detecting, characterizing and controlling  S. aureus  infections. There is a need therefore to characterize the genome of  S. aureus  and for polynucleotides and sequences of this organism.  
       SUMMARY OF THE INVENTION  
       [0044] The present invention is based on the sequencing of fragments of the  Staphylococcus aureus  genome. The primary nucleotide sequences which were generated are provided in SEQ ID NOS: 1-5,191.  
       [0045] The present invention provides the nucleotide sequence of several thousand contigs of the  Staphylococcus aureus  genome, which are listed in tables below and set out in the Sequence Listing submitted herewith, and representative fragments thereof, in a form which can be readily used, analyzed, and interpreted by a skilled artisan. In one embodiment, the present invention is provided as contiguous strings of primary sequence information corresponding to the nucleotide sequences depicted in SEQ ID NOS: 1-5,191.  
       [0046] The present invention further provides nucleotide sequences which are at least 95% identical to the nucleotide sequences of SEQ ID NOS: 1-5,191.  
       [0047] The nucleotide sequence of SEQ ID NOS: 1-5,191, a representative fragment thereof, or a nucleotide sequence which is at least 95% identical to the nucleotide sequence of SEQ ID NOS: 1-5,191 may be provided in a variety of mediums to facilitate its use. In one application of this embodiment, the sequences of the present invention are recorded on computer readable media. Such media includes, but is not limited to: magnetic storage media, such as floppy discs, hard disc storage medium, and magnetic tape; optical storage media such as CD-ROM; electrical storage media such as RAM and ROM; and hybrids of these categories such as magnetic/optical storage media.  
       [0048] The present invention further provides systems, particularly computer-based systems which contain the sequence information herein described stored in a data storage means. Such systems are designed to identify commercially important fragments of the  Staphylococcus aureus  genome.  
       [0049] Another embodiment of the present invention is directed to fragments of the  Staphylococcus aureus  genome having particular structural or functional attributes. Such fragments of the  Staphylococcus aureus  genome of the present invention include, but are not limited to, fragments which encode peptides, hereinafter referred to as open reading frames or ORFs,” fragments which modulate the expression of an operably linked ORF, hereinafter referred to as expression modulating fragments or EMFs,” and fragments which can be used to diagnose the presence of  Staphylococcus aureus  in a sample, hereinafter referred to as diagnostic fragments or “DFs.” 
       [0050] Each of the ORFs in fragments of the  Staphylococcus aureus  genome disclosed in Tables 1-3, and the EMFs found 5′ to the ORFs, can be used in numerous ways as polynucleotide reagents. For instance, the sequences can be used as diagnostic probes or amplification primers for detecting or determining the presence of a specific microbe in a sample, to selectively control gene expression in a host and in the production of polypeptides, such as polypeptides encoded by ORFs of the present invention, particular those polypeptides that have a pharmacological activity.  
       [0051] The present invention further includes recombinant constructs comprising one or more fragments of the  Staphylococcus aureus  genome of the present invention. The recombinant constructs of the present invention comprise vectors, such as a plasmid or viral vector, into which a fragment of the  Staphylococcus aureus  has been inserted.  
       [0052] The present invention further provides host cells containing any of the isolated fragments of the  Staphylococcus aureus  genome of the present invention. The host cells can be a higher eukaryotic host cell, such as a mammalian cell, a lower eukaryotic cell, such as a yeast cell, or a procaryotic cell such as a bacterial cell.  
       [0053] The present invention is further directed to isolated polypeptides and proteins encoded by ORFs of the present invention. A variety of methods, well known to those of skill in the art, routinely may be utilized to obtain any of the polypeptides and proteins of the present invention. For instance, polypeptides and proteins of the present invention having relatively short, simple amino acid sequences readily can be synthesized using commercially available automated peptide synthesizers. Polypeptides and proteins of the present invention also may be purified from bacterial cells which naturally produce the protein. Yet another alternative is to purify polypeptide and proteins of the present invention from cells which have been altered to express them.  
       [0054] The invention further provides polypeptides comprising  Staphylococcus aureus  epitopes and vaccine compositions comprising such polypeptides. Also provided are methods for vaccinating an individual against  Staphylococcus aureus  infection.  
       [0055] The invention further provides methods of obtaining homologs of the fragments of the  Staphylococcus aureus  genome of the present invention and homologs of the proteins encoded by the ORFs of the present invention. Specifically, by using the nucleotide and amino acid sequences disclosed herein as a probe or as primers, and techniques such as PCR cloning and colony/plaque hybridization, one skilled in the art can obtain homologs.  
       [0056] The invention further provides antibodies which selectively bind polypeptides and proteins of the present invention. Such antibodies include both monoclonal and polyclonal antibodies.  
       [0057] The invention further provides hybridomas which produce the above-described antibodies. A hybridoma is an immortalized cell line which is capable of secreting a specific monoclonal antibody.  
       [0058] The present invention further provides methods of identifying test samples derived from cells which express one of the ORFs of the present invention, or a homolog thereof. Such methods comprise incubating a test sample with one or more of the antibodies of the present invention, or one or more of the Dfs or antigens of the present invention, under conditions which allow a skilled artisan to determine if the sample contains the ORF or product produced therefrom.  
       [0059] In another embodiment of the present invention, kits are provided which contain the necessary reagents to carry out the above-described assays.  
       [0060] Specifically, the invention provides a compartmentalized kit to receive, in close confinement, one or more containers which comprises: (a) a first container comprising one of the antibodies, antigens, or one of the DFs of the present invention; and (b) one or more other containers comprising one or more of the following: wash reagents, reagents capable of detecting presence of bound antibodies, antigens or hybridized DFs.  
       [0061] Using the isolated proteins of the present invention, the present invention further provides methods of obtaining and identifying agents capable of binding to a polypeptide or protein encoded by one of the ORFs of the present invention. Specifically, such agents include, as further described below, antibodies, peptides, carbohydrates, pharmaceutical agents and the like. Such methods comprise steps of: (a)contacting an agent with an isolated protein encoded by one of the ORFs of the present invention; and (b)determining whether the agent binds to said protein.  
       [0062] The present genomic sequences of  Staphylococcus aureus  will be of great value to all laboratories working with this organism and for a variety of commercial purposes. Many fragments of the  Staphylococcus aureus  genome will be immediately identified by similarity searches against GenBank or protein databases and will be of immediate value to  Staphylococcus aureus  researchers and for immediate commercial value for the production of proteins or to control gene expression.  
       [0063] The methodology and technology for elucidating extensive genomic sequences of bacterial and other genomes has and will greatly enhance the ability to analyze and understand chromosomal organization. In particular, sequenced contigs and genomes will provide the models for developing tools for the analysis of chromosome structure and function, including the ability to identify genes within large segments of genomic DNA, the structure, position, and spacing of regulatory elements, the identification of genes with potential industrial applications, and the ability to do comparative genomic and molecular phylogeny. 
     
    
    
     BRIEF DESCRIPTION OF THE DRAWINGS  
     [0064]FIG. 1 is a block diagram of a computer system ( 102 ) that can be used to implement computer-based systems of present invention.  
     [0065]FIG. 2 is a schematic diagram depicting the data flow and computer programs used to collect, assemble, edit and annotate the contigs of the  Staphylococcus aureus  genome of the present invention. Both Macintosh and Unix platforms are used to handle the AB 373 and 377 sequence data files, largely as described in Kerlavage et al.,  Proceedings of the Twenty - Sixth Annual Hawaii International Conference on System Sciences,  585, IEEE Computer Society Press, Wash. D.C. (1993). Factura (AB) is a Macintosh program designed for automatic vector sequence removal and end-trimming of sequence files. The program Loadis runs on a Macintosh platform and parses the feature data extracted from the sequence files by Factura to the Unix based  Staphylococcus aureus  relational database. Assembly of contigs (and whole genome sequences) is accomplished by retrieving a specific set of sequence files and their associated features using extrseq, a Unix utility for retrieving sequences from an SQL database. The resulting sequence file is processed by seq_filter to trim portions of the sequences with more than 2% ambiguous nucleotides. The sequence files were assembled using TIGR Assembler, an assembly engine designed at The Institute for Genomic Research (TIGR”) for rapid and accurate assembly of thousands of sequence fragments. The collection of contigs generated by the assembly step is loaded into the database with the lassie program. Identification of open reading frames (ORFs) is accomplished by processing contigs with zorf. The ORFs are searched against  S. aureus  sequences from Genbank and against all protein sequences using the BLASTN and BLASTP programs, described in Altschul et al.,  J. Mol. Biol.  215: 403-410 (1990)). Results of the ORF determination and similarity searching steps were loaded into the database. As described below, some results of the determination and the searches are set out in Tables 1-3. 
    
    
     DETAILED DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS  
     [0066] The present invention is based on the sequencing of fragments of the  Staphylococcus aureus  genome and analysis of the sequences. The primary nucleotide sequences generated by sequencing the fragments are provided in SEQ ID NOS: 1-5,191. (As used herein, the “primary sequence” refers to the nucleotide sequence represented by the IUPAC nomenclature system.)  
     [0067] In addition to the aforementioned  Staphylococcus aureus  polynucleotide and polynucleotide sequences, the present invention provides the nucleotide sequences of SEQ ID NOS: 1-5,191, or representative fragments thereof, in a form which can be readily used, analyzed, and interpreted by a skilled artisan.  
     [0068] As used herein, a “representative fragment of the nucleotide sequence depicted in SEQ ID NOS: 1-5,191” refers to any portion of the SEQ ID NOS: 1-5,191 which is not presently represented within a publicly available database. Preferred representative fragments of the present invention are  Staphylococcus aureus  open reading frames (ORFS”), expression modulating fragment (EMFs”) and fragments which can be used to diagnose the presence of  Staphylococcus aureus  in sample (“DFs”). A non-limiting identification of preferred representative fragments is provided in Tables 1-3.  
     [0069] As discussed in detail below, the information provided in SEQ ID NOS: 1-5,191 and in Tables 1-3 together with routine cloning, synthesis, sequencing and assay methods will enable those skilled in the art to clone and sequence all “representative fragments” of interest, including open reading frames encoding a large variety of  Staphylococcus aureus  proteins.  
     [0070] While the presently disclosed sequences of SEQ ID NOS: 1-5,191 are highly accurate, sequencing techniques are not perfect and, in relatively rare instances, further investigation of a fragment or sequence of the invention may reveal a nucleotide sequence error present in a nucleotide sequence disclosed in SEQ ID NOS: 1-5,191. However, once the present invention is made available (i.e., once the information in SEQ ID NOS: 1-5,191 and Tables 1-3 has been made available), resolving a rare sequencing error in SEQ ID NOS: 1-5,191 will be well within the skill of the art. The present disclosure makes available sufficient sequence information to allow any of the described contigs or portions thereof to be obtained readily by straightforward application of routine techniques. Further sequencing of such polynucleotide may proceed in like manner using manual and automated sequencing methods which are employed ubiquitous in the art. Nucleotide sequence editing software is publicly available. For example, Applied Biosystem&#39;s (AB) AutoAssembler can be used as an aid during visual inspection of nucleotide sequences. By employing such routine techniques potential errors readily may be identified and the correct sequence then may be ascertained by targeting further sequencing effort, also of a routine nature, to the region containing the potential error.  
     [0071] Even if all of the very rare sequencing errors in SEQ ID NOS: 1-5,191 were corrected, the resulting nucleotide sequences would still be at least 95% identical, nearly all would be at least 99% identical, and the great majority would be at least 99.9% identical to the nucleotide sequences of SEQ ID NOS: 1-5,191.  
     [0072] As discussed elsewhere herein, polynucleotides of the present invention readily may be obtained by routine application of well known and standard procedures for cloning and sequencing DNA. Detailed methods for obtaining libraries and for sequencing are provided below, for instance. A wide variety of  Staphylococcus aureus  strains that can be used to prepare  S aureus  genomic DNA for cloning and for obtaining polynucleotides of the present invention are available to the public from recognized depository institutions, such as the American Type Culture Collection (ATCC”).  
     [0073] The nucleotide sequences of the genomes from different strains of  Staphylococcus aureus  differ somewhat. However, the nucleotide sequences of the genomes of all  Staphylococcus aureus  strains will be at least 95% identical, in corresponding part, to the nucleotide sequences provided in SEQ ID NOS: 1-5,191. Nearly all will be at least 99% identical and the great majority will be 99.9% identical.  
     [0074] Thus, the present invention further provides nucleotide sequences which are at least 95%, preferably 99% and most preferably 99.9% identical to the nucleotide sequences of SEQ ID NOS: 1-5,191, in a form which can be readily used, analyzed and interpreted by the skilled artisan.  
     [0075] Methods for determining whether a nucleotide sequence is at least 95%, at least 99% or at least 99.9% identical to the nucleotide sequences of SEQ ID NOS: 1-5,191 are routine and readily available to the skilled artisan. For example, the well known fasta algorithm described in Pearson and Lipman,  Proc. Natl. Acad. Sci. USA  85: 2444 (1988) can be used to generate the percent identity of nucleotide sequences. The  
     [0076] BLASTN program also can be used to generate an identity score of polynucleotides compared to one another.  
     COMPUTER RELATED EMBODIMENTS  
     [0077] The nucleotide sequences provided in SEQ ID NOS: 1-5,191, a representative fragment thereof, or a nucleotide sequence at least 95%, preferably at least 96%, 97%, 98% or 99% and most preferably at least 99.9% identical to a polynucleotide sequence of SEQ ID NOS: 1-5,191 may be “provided” in a variety of mediums to facilitate use thereof. As used herein, “provided” refers to a manufacture, other than an isolated nucleic acid molecule, which contains a nucleotide sequence of the present invention; i.e., a nucleotide sequence provided in SEQ ID NOS: 1-5,191, a representative fragment thereof, or a nucleotide sequence at least 95%, preferably at least 96%, 97%, 98% or 99% and most preferably at least 99.9% identical to a polynucleotide of SEQ ID NOS: 1-5,191. Such a manufacture provides a large portion of the  Staphylococcus aureus  genome and parts thereof (e.g., a  Staphylococcus aureus  open reading frame (ORF)) in a form which allows a skilled artisan to examine the manufacture using means not directly applicable to examining the  Staphylococcus aureus  genome or a subset thereof as it exists in nature or in purified form.  
     [0078] In one application of this embodiment, a nucleotide sequence of the present invention can be recorded on computer readable media. As used herein, “computer readable media” refers to any medium which can be read and accessed directly by a computer. Such media include, but are not limited to: magnetic storage media, such as floppy discs, hard disc storage medium, and magnetic tape; optical storage media such as CD-ROM; electrical storage media such as RAM and ROM; and hybrids of these categories, such as magnetic/optical storage media. A skilled artisan can readily appreciate how any of the presently known computer readable mediums can be used to create a manufacture comprising computer readable medium having recorded thereon a nucleotide sequence of the present invention. Likewise, it will be clear to those of skill how additional computer readable media that may be developed also can be used to create analogous manufactures having recorded thereon a nucleotide sequence of the present invention.  
     [0079] As used herein, “recorded” refers to a process for storing information on computer readable medium. A skilled artisan can readily adopt any of the presently know methods for recording information on computer readable medium to generate manufactures comprising the nucleotide sequence information of the present invention.  
     [0080] A variety of data storage structures are available to a skilled artisan for creating a computer readable medium having recorded thereon a nucleotide sequence of the present invention. The choice of the data storage structure will generally be based on the means chosen to access the stored information. In addition, a variety of data processor programs and formats can be used to store the nucleotide sequence information of the present invention on computer readable medium. The sequence information can be represented in a word processing text file, formatted in commercially-available software such as WordPerfect and MicroSoft Word, or represented in the form of an ASCII file, stored in a database application, such as DB2, Sybase, Oracle, or the like. A skilled artisan can readily adapt any number of data-processor structuring formats (e.g., text file or database) in order to obtain computer readable medium having recorded thereon the nucleotide sequence information of the present invention.  
     [0081] Computer software is publicly available which allows a skilled artisan to access sequence information provided in a computer readable medium. Thus, by providing in computer readable form the nucleotide sequences of SEQ ID NOS: 1-5,191, a representative fragment thereof, or a nucleotide sequence at least 95%, preferably at least 96%, 97%, 98% or 99% and most preferably at least 99.9% identical to a sequence of SEQ ID NOS: 1-5,191 the present invention enables the skilled artisan routinely to access the provided sequence information for a wide variety of purposes.  
     [0082] The examples which follow demonstrate how software which implements the BLAST (Altschul et al., J. Mol. Biol. 215:403-410 (1990)) and BLAZE (Brutlag et al., Comp. Chem. 17:203-207 (1993)) search algorithms on a Sybase system was used to identify open reading frames (ORFs) within the  Staphylococcus aureus  genome which contain homology to ORFs or proteins from both  Staphylococcus aureus  and from other organisms. Among the ORFs discussed herein are protein encoding fragments of the  Staphylococcus aureus  genome useful in producing commercially important proteins, such as enzymes used in fermentation reactions and in the production of commercially useful metabolites.  
     [0083] The present invention further provides systems, particularly computer-based systems, which contain the sequence information described herein. Such systems are designed to identify, among other things, commercially important fragments of the  Staphylococcus aureus  genome.  
     [0084] As used herein, “a computer-based system” refers to the hardware means, software means, and data storage means used to analyze the nucleotide sequence information of the present invention. The minimum hardware means of the computer-based systems of the present invention comprises a central processing unit (CPU), input means, output means, and data storage means. A skilled artisan can readily appreciate that any one of the currently available computer-based system are suitable for use in the present invention.  
     [0085] As stated above, the computer-based systems of the present invention comprise a data storage means having stored therein a nucleotide sequence of the present invention and the necessary hardware means and software means for supporting and implementing a search means.  
     [0086] As used herein, “data storage means” refers to memory which can store nucleotide sequence information of the present invention, or a memory access means which can access manufactures having recorded thereon the nucleotide sequence information of the present invention.  
     [0087] As used herein, “search means” refers to one or more programs which are implemented on the computer- based system to compare a target sequence or target structural motif with the sequence information stored within the data storage means. Search means are used to identify fragments or regions of the present genomic sequences which match a particular target sequence or target motif. A variety of known algorithms are disclosed publicly and a variety of commercially available software for conducting search means are and can be used in the computer-based systems of the present invention. Examples of such software includes, but is not limited to, MacPattern (EMBL), BLASTN and BLASTX (NCBIA). A skilled artisan can readily recognize that any one of the available algorithms or implementing software packages for conducting homology searches can be adapted for use in the present computer-based systems.  
     [0088] As used herein, a “target sequence” can be any DNA or amino acid sequence of six or more nucleotides or two or more amino acids. A skilled artisan can readily recognize that the longer a target sequence is, the less likely a target sequence will be present as a random occurrence in the database. The most preferred sequence length of a target sequence is from about 10 to 100 amino acids or from about 30 to 300 nucleotide residues. However, it is well recognized that searches for commercially important fragments, such as sequence fragments involved in gene expression and protein processing, may be of shorter length.  
     [0089] As used herein, “a target structural motif,” or “target motif,” refers to any rationally selected sequence or combination of sequences in which the sequence(s) are chosen based on a three-dimensional configuration which is formed upon the folding of the target motif. There are a variety of target motifs known in the art. Protein target motifs include, but are not limited to, enzymatic active sites and signal sequences. Nucleic acid target motifs include, but are not limited to, promoter sequences, hairpin structures and inducible expression elements (protein binding sequences).  
     [0090] A variety of structural formats for the input and output means can be used to input and output the information in the computer-based systems of the present invention. A preferred format for an output means ranks fragments of the  Staphylococcus aureus  genomic sequences possessing varying degrees of homology to the target sequence or target motif. Such presentation provides a skilled artisan with a ranking of sequences which contain various amounts of the target sequence or target motif and identifies the degree of homology contained in the identified fragment.  
     [0091] A variety of comparing means can be used to compare a target sequence or target motif with the data storage means to identify sequence fragments of the  Staphylococcus aureus  genome. In the present examples, implementing software which implement the BLAST and BLAZE algorithms, described in Altschul et al.,  J. Mol. Biol.  215: 403-410 (1990), was used to identify open reading frames within the  Staphylococcus aureus  genome. A skilled artisan can readily recognize that any one of the publicly available homology search programs can be used as the search means for the computer-based systems of the present invention. Of course, suitable proprietary systems that may be known to those of skill also may be employed in this regard.  
     [0092]FIG. 1 provides a block diagram of a computer system illustrative of embodiments of this aspect of present invention. The computer system  102  includes a processor  106  connected to a bus  104 . Also connected to the bus  104  are a main memory  108  (preferably implemented as random access memory, RAM) and a variety of secondary storage devices  110 , such as a hard drive  112  and a removable medium storage device  114 . The removable medium storage device  114  may represent, for example, a floppy disk drive, a CD-ROM drive, a magnetic tape drive, etc. A removable storage medium  116  (such as a floppy disk, a compact disk, a magnetic tape, etc.) containing control logic and/or data recorded therein may be inserted into the removable medium storage device  114 . The computer system  102  includes appropriate software for reading the control logic and/or the data from the removable medium storage device  114 , once it is inserted into the removable medium storage device  114 .  
     [0093] A nucleotide sequence of the present invention may be stored in a well known manner in the main memory  108 , any of the secondary storage devices  110 , and/or a removable storage medium  116 . During execution, software for accessing and processing the genomic sequence (such as search tools, comparing tools, etc.) reside in main memory  108 , in accordance with the requirements and operating parameters of the operating system, the hardware system and the software program or programs.  
     BIOCHEMICAL EMBODIMENTS  
     [0094] Other embodiments of the present invention are directed to isolated fragments of the  Staphylococcus aureus  genome. The fragments of the  Staphylococcus aureus  genome of the present invention include, but are not limited to fragments which encode peptides, hereinafter open reading frames (ORFs), fragments which modulate the expression of an operably linked ORF, hereinafter expression modulating fragments (EMFs) and fragments which can be used to diagnose the presence of  Staphylococcus aureus  in a sample, hereinafter diagnostic fragments (DFs).  
     [0095] As used herein, an “isolated nucleic acid molecule” or an “isolated fragment of the  Staphylococcus aureus  genome” refers to a nucleic acid molecule possessing a specific nucleotide sequence which has been subjected to purification means to reduce, from the composition, the number of compounds which are normally associated with the composition. Particularly, the term refers to the nucleic acid molecules having the sequences set out in SEQ ID NOS: 1-5,191, to representative fragments thereof as described above, to polynucleotides at least 95%, preferably at least 96%, 97%, 98% or 99% and especially preferably at least 99.9% identical in sequence thereto, also as set out above.  
     [0096] A variety of purification means can be used to generated the isolated fragments of the present invention. These include, but are not limited to methods which separate constituents of a solution based on charge, solubility, or size.  
     [0097] In one embodiment,  Staphylococcus aureus  DNA can be mechanically sheared to produce fragments of 15-20 kb in length. These fragments can then be used to generate an  Staphylococcus aureus  library by inserting them into lambda clones as described in the Examples below. Primers flanking, for example, an ORF, such as those enumerated in Tables 1-3 can then be generated using nucleotide sequence information provided in SEQ ID NOS: 1-5,191. Well known and routine techniques of PCR cloning then can be used to isolate the ORF from the lambda DNA library of  Staphylococcus aureus  genomic DNA. Thus, given the availability of SEQ ID NOS: 1-5,191, the information in Tables 1, 2 and 3, and the information that may be obtained readily by analysis of the sequences of SEQ ID NOS: 1-5,191 using methods set out above, those of skill will be enabled by the present disclosure to isolate any ORF-containing or other nucleic acid fragment of the present invention.  
     [0098] The isolated nucleic acid molecules of the present invention include, but are not limited to single stranded and double stranded DNA, and single stranded RNA.  
     [0099] As used herein, an “open reading frame,” ORF, means a series of triplets coding for amino acids without any termination codons and is a sequence translatable into protein.  
     [0100] Tables 1, 2 and 3 list ORFs in the  Staphylococcus aureus  genomic contigs of the present invention that were identified as putative coding regions by the GeneMark software using organism-specific second-order Markov probability transition matrices. It will be appreciated that other criteria can be used, in accordance with well known analytical methods, such as those discussed herein, to generate more inclusive, more restrictive or more selective lists.  
     [0101] Table 1 sets out ORFs in the  Staphylococcus aureus  contigs of the present invention that are at least 80 amino acids long and over a continuous region of at least 50 bases which are 95% or more identical (by BLAST analysis) to an  S. aureus  nucleotide sequence available through Genbank in November 1996.  
     [0102] Table 2 sets out ORFs in the  Staphylococcus aureus  contigs of the present invention that are not in Table 1 and match, with a BLASTP probability score of 0.01 or less, a polypeptide sequence available through Genbank by September 1996.  
     [0103] Table 3 sets out ORFs in the  Staphylococcus aureus  contigs of the present invention that do not match significantly, by BLASTP analysis, a polypeptide sequence available through Genbank by September 1996.  
     [0104] In each table, the first and second columns identify the ORF by, respectively, contig number (SEQ ID NO) and ORF number within the contig; the third column indicates the first nucleotide of the ORF, counting from the 5′ end of the contig strand shown in the sequence listing; and the fifth column indicates the length of each ORF in nucleotides. It will be appreciated that some ORFs are located on the reverse strand. The numbering identifying such ORFs also represents nucleotide positions counting from the 5′ end of the strand shown in the sequence listing.  
     [0105] In Tables 1 and 2, column five, lists the “match accession” for the closest matching sequence available through Genbank. These reference numbers are the databases entry numbers commonly used by those of skill in the art, who will be familiar with their denominators. Descriptions of the nomenclature are available from the National Center for Biotechnology Information. Column six in Tables 1 and 2 provides the “gene name” of the matching sequence; column seven provides the BLAST “similarity”; column eight provides the BLAST “identity” score from the comparison of the ORF and the homologous gene; and column nine indicates the length in nucleotides of the highest scoring “segment pair” identified by the BLAST identity analysis.  
     [0106] The concepts of percent identity and percent similarity of two polypeptide sequences is well understood in the art. For example, two polypeptides 10 amino acids in length which differ at three amino acid positions (e.g., at positions 1, 3 and 5) are said to have a percent identity of 70%. However, the same two polypeptides would be deemed to have a percent similarity of 80% if, for example at position 5, the amino acids moieties, although not identical, were “similar” (i.e., possessed similar biochemical characteristics). Many programs for analysis of nucleotide or amino acid sequence similarity, such as fasta and BLAST specifically list percent identity of a matching region as an output parameter. Thus, for instance, Tables 1 and 2 herein enumerate the percent identity “of the highest scoring segment pair” in each ORF and its listed relative. Further details concerning the algorithms and criteria used for homology searches are provided below and are described in the pertinent literature highlighted by the citations provided below.  
     [0107] It will be appreciated that other criteria can be used to generate more inclusive and more exclusive listings of the types set out in the tables. As those of skill will appreciate, narrow and broad searches both are useful. Thus, a skilled artisan can readily identify ORFs in contigs of the  Staphylococcus aureus  genome other than those listed in Tables 1-3, such as ORFs which are overlapping or encoded by the opposite strand of an identified ORF in addition to those ascertainable using the computer-based systems of the present invention.  
     [0108] As used herein, an “expression modulating fragment,” EMF, means a series of nucleotide molecules which modulates the expression of an operably linked ORF or EMF.  
     [0109] As used herein, a sequence is said to “modulate the expression of an operably linked sequence” when the expression of the sequence is altered by the presence of the EMF. EMFs include, but are not limited to, promoters, and promoter modulating sequences (inducible elements). One class of EMFs are fragments which induce the expression or an operably linked ORF in response to a specific regulatory factor or physiological event.  
     [0110] EMF sequences can be identified within the contigs of the  Staphylococcus aureus  genome by their proximity to the ORFs provided in Tables 1-3. An intergenic segment, or a fragment of the intergenic segment, from about 10 to 200 nucleotides in length, taken from any one of the ORFs of Tables 1-3 will modulate the expression of an operably linked ORF in a fashion similar to that found with the naturally linked ORF sequence. As used herein, an “intergenic segment” refers to fragments of the  Staphylococcus aureus  genome which are between two ORF(s) herein described. EMFs also can be identified using known EMFs as a target sequence or target motif in the computer-based systems of the present invention. Further, the two methods can be combined and used together.  
     [0111] The presence and activity of an EMF can be confirmed using an EMF trap vector. An EMF trap vector contains a cloning site linked to a marker sequence. A marker sequence encodes an identifiable phenotype, such as antibiotic resistance or a complementing nutrition auxotrophic factor, which can be identified or assayed when the EMF trap vector is placed within an appropriate host under appropriate conditions. As described above, a EMF will modulate the expression of an operably linked marker sequence. A more detailed discussion of various marker sequences is provided below.  
     [0112] A sequence which is suspected as being an EMF is cloned in all three reading frames in one or more restriction sites upstream from the marker sequence in the EMF trap vector. The vector is then transformed into an appropriate host using known procedures and the phenotype of the transformed host in examined under appropriate conditions. As described above, an EMF will modulate the expression of an operably linked marker sequence.  
     [0113] As used herein, a “diagnostic fragment,” DF, means a series of nucleotide molecules which selectively hybridize to  Staphylococcus aureus  sequences. DFs can be readily identified by identifying unique sequences within contigs of the  Staphylococcus aureus  genome, such as by using well-known computer analysis software, and by generating and testing probes or amplification primers consisting of the DF sequence in an appropriate diagnostic format which determines amplification or hybridization selectivity.  
     [0114] The sequences falling within the scope of the present invention are not limited to the specific sequences herein described, but also include allelic and species variations thereof. Allelic and species variations can be routinely determined by comparing the sequences provided in SEQ ID NOS: 1-5,191, a representative fragment thereof, or a nucleotide sequence at least 99% and preferably 99.9% identical to SEQ ID NOS: 1-5,191, with a sequence from another isolate of the same species.  
     [0115] Furthermore, to accommodate codon variability, the invention includes nucleic acid molecules coding for the same amino acid sequences as do the specific ORFs disclosed herein. In other words, in the coding region of an ORF, substitution of one codon for another which encodes the same amino acid is expressly contemplated.  
     [0116] Any specific sequence disclosed herein can be readily screened for errors by resequencing a particular fragment, such as an ORF, in both directions (i.e., sequence both strands). Alternatively, error screening can be performed by sequencing corresponding polynucleotides of  Staphylococcus aureus  origin isolated by using part or all of the fragments in question as a probe or primer.  
     [0117] Each of the ORFs of the  Staphylococcus aureus  genome disclosed in Tables 1, 2 and 3, and the EMFs found 5′ to the ORFs, can be used as polynucleotide reagents in numerous ways. For example, the sequences can be used as diagnostic probes or diagnostic amplification primers to detect the presence of a specific microbe in a sample, particular  Staphylococcus aureus . Especially preferred in this regard are ORF such as those of Table 3, which do not match previously characterized sequences from other organisms and thus are most likely to be highly selective for  Staphylococcus aureus . Also particularly preferred are ORFs that can be used to distinguish between strains of  Staphylococcus aureus , particularly those that distinguish medically important strain, such as drug-resistant strains.  
     [0118] In addition, the fragments of the present invention, as broadly described, can be used to control gene expression through triple helix formation or antisense DNA or RNA, both of which methods are based on the binding of a polynucleotide sequence to DNA or RNA. Triple helix-formation optimally results in a shut-off of RNA transcription from DNA, while antisense RNA hybridization blocks translation of an mRNA molecule into polypeptide. Information from the sequences of the present invention can be used to design antisense and triple helix-forming oligonucleotides. Polynucleotides suitable for use in these methods are usually 20 to 40 bases in length and are designed to be complementary to a region of the gene involved in transcription, for triple-helix formation, or to the mRNA itself, for antisense inhibition. Both techniques have been demonstrated to be effective in model systems, and the requisite techniques are well known and involve routine procedures. Triple helix techniques are discussed in, for example, Lee et al.,  Nucl. Acids Res.  6: 3073 (1979); Cooney et al,  Science  241: 456 (1988); and Dervan et al.,  Science  251: 1360 (1991). Antisense techniques in general are discussed in, for instance, Okano,  J. Neurochem.  56: 560 (1991) and OLIGODEOXYNUCLEOTIDES AS ANTISENSE INHIBITORS OF GENE EXPRESSION, CRC Press, Boca Raton, Fla. (1988)).  
     [0119] The present invention further provides recombinant constructs comprising one or more fragments of the  Staphylococcus aureus  genomic fragments and contigs of the present invention. Certain preferred recombinant constructs of the present invention comprise a vector, such as a plasmid or viral vector, into which a fragment of the  Staphylococcus aureus  genome has been inserted, in a forward or reverse orientation. In the case of a vector comprising one of the ORFs of the present invention, the vector may further comprise regulatory sequences, including for example, a promoter, operably linked to the ORF. For vectors comprising the EMFs of the present invention, the vector may further comprise a marker sequence or heterologous ORF operably linked to the EMF.  
     [0120] Large numbers of suitable vectors and promoters are known to those of skill in the art and are commercially available for generating the recombinant constructs of the present invention. The following vectors are provided by way of example. Useful bacterial vectors include phagescript, PsiX174, pBluescript SK and KS (+and −), pNH8a, pNH16a, pNH18a, pNH46a (available from Stratagene); pTrc99A, pKK223-3, pKK233-3, pDR540, pRIT5 (available from Pharmacia). Useful eukaryotic vectors include pWLneo, pSV2cat, pOG44, pXT1, pSG (available from Stratagene) pSVK3, pBPV, pMSG, pSVL (available from Pharmacia).  
     [0121] Promoter regions can be selected from any desired gene using CAT (chloramphenicol transferase) vectors or other vectors with selectable markers. Two appropriate vectors are pKK232-8 and pCM7. Particular named bacterial promoters include lacI, lacZ, T3, T7, gpt, lambda PR, and trc. Eukaryotic promoters include CMV immediate early, HSV thymidine kinase, early and late SV40, LTRs from retrovirus, and mouse metallothionein-I. Selection of the appropriate vector and promoter is well within the level of ordinary skill in the art.  
     [0122] The present invention further provides host cells containing any one of the isolated fragments of the  Staphylococcus aureus  genomic fragments and contigs of the present invention, wherein the fragment has been introduced into the host cell using known methods. The host cell can be a higher eukaryotic host cell, such as a mammalian cell, a lower eukaryotic host cell, such as a yeast cell, or a procaryotic cell, such as a bacterial cell.  
     [0123] A polynucleotide of the present invention, such as a recombinant construct comprising an ORF of the present invention, may be introduced into the host by a variety of well established techniques that are standard in the art, such as calcium phosphate transfection, DEAE, dextran mediated transfection and electroporation, which are described in, for instance, Davis, L. et al., BASIC METHODS IN MOLECULAR BIOLOGY (1986).  
     [0124] A host cell containing one of the fragments of the  Staphylococcus aureus  genomic fragments and contigs of the present invention, can be used in conventional manners to produce the gene product encoded by the isolated fragment (in the case of an ORF) or can be used to produce a heterologous protein under the control of the EMF.  
     [0125] The present invention further provides isolated polypeptides encoded by the nucleic acid fragments of the present invention or by degenerate variants of the nucleic acid fragments of the present invention. By “degenerate variant” is intended 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 polypeptide sequence.  
     [0126] Preferred nucleic acid fragments of the present invention are the ORFs depicted in Tables 2 and 3 which encode proteins.  
     [0127] A variety of methodologies known in the art can be utilized to obtain any one of the isolated polypeptides or proteins of the present invention. At the simplest level, the amino acid sequence can be synthesized using commercially available peptide synthesizers. This is particularly useful in producing small peptides and fragments of larger polypeptides. Such short fragments as may be obtained most readily by synthesis are useful, for example, in generating antibodies against the native polypeptide, as discussed further below.  
     [0128] In an alternative method, the polypeptide or protein is purified from bacterial cells which naturally produce the polypeptide or protein. One skilled in the art can readily employ well-known methods for isolating polypeptides and proteins to isolate and purify polypeptides or proteins of the present invention produced naturally by a bacterial strain, or by other methods. Methods for isolation and purification that can be employed in this regard include, but are not limited to, immunochromatography, HPLC, size-exclusion chromatography, ion-exchange chromatography, and immuno-affinity chromatography.  
     [0129] The polypeptides and proteins of the present invention also can be purified from cells which have been altered to express the desired polypeptide or protein. As used herein, a cell is said to be altered to express a desired polypeptide or protein when the cell, through genetic manipulation, is made to produce a polypeptide or protein which it normally does not produce or which the cell normally produces at a lower level. Those skilled in the art can readily adapt procedures for introducing and expressing either recombinant or synthetic sequences into eukaryotic or prokaryotic cells in order to generate a cell which produces one of the polypeptides or proteins of the present invention.  
     [0130] Any host/vector system can be used to express one or more of the ORFs of the present invention. These include, but are not limited to, eukaryotic hosts such as HeLa cells, CV-1 cell, COS cells, and Sf9 cells, as well as prokaryotic host such as  E. coli  and  B. subtilis.  The most preferred cells are those which do not normally express the particular polypeptide or protein or which expresses the polypeptide or protein at low natural level.  
     [0131] “Recombinant,” as used herein, means that a polypeptide or protein is derived from recombinant (e.g., microbial or mammalian) expression systems. “Microbial” refers to recombinant polypeptides or proteins made in bacterial or fungal (e.g., yeast) expression systems. As a product, “recombinant microbial” defines a polypeptide or protein essentially free of native endogenous substances and unaccompanied by associated native glycosylation. Polypeptides or proteins expressed in most bacterial cultures, e.g.,  E. coli,  will be free of glycosylation modifications; polypeptides or proteins expressed in yeast will have a glycosylation pattern different from that expressed in mammalian cells.  
     [0132] “Nucleotide sequence” refers to a heteropolymer of deoxyribonucleotides. Generally, DNA segments encoding the polypeptides and proteins provided by this invention are assembled from fragments of the  Staphylococcus aureus  genome and short oligonucleotide linkers, or from a series of oligonucleotides, to provide a synthetic gene which is capable of being expressed in a recombinant transcriptional unit comprising regulatory elements derived from a microbial or viral operon.  
     [0133] “Recombinant expression vehicle or vector” refers to a plasmid or phage or virus or vector, for expressing a polypeptide from a DNA (RNA) sequence. The expression vehicle can comprise a transcriptional unit comprising an assembly of (1) a genetic regulatory elements necessary for gene expression in the host, including elements required to initiate and maintain transcription at a level sufficient for suitable expression of the desired polypeptide, including, for example, promoters and, where necessary, an enhancers and a polyadenylation signal; (2) a structural or coding sequence which is transcribed into mRNA and translated into protein, and (3) appropriate signals to initiate translation at the beginning of the desired coding region and terminate translation at its end. Structural units intended for use in yeast or eukaryotic expression systems preferably include a leader sequence enabling extracellular secretion of translated protein by a host cell. Alternatively, where recombinant protein is expressed without a leader or transport sequence, it may include an N-terminal methionine residue. This residue may or may not be subsequently cleaved from the expressed recombinant protein to provide a final product.  
     [0134] “Recombinant expression system” means host cells which have stably integrated a recombinant transcriptional unit into chromosomal DNA or carry the recombinant transcriptional unit extra chromosomally. The cells can be prokaryotic or eukaryotic. Recombinant expression systems as defined herein will express heterologous polypeptides or proteins upon induction of the regulatory elements linked to the DNA segment or synthetic gene to be expressed.  
     [0135] Mature proteins can be expressed in mammalian cells, yeast, bacteria, or other cells under the control of appropriate promoters. Cell-free translation systems can also be employed to produce such proteins using RNAs derived from the DNA constructs of the present invention. Appropriate cloning and expression vectors for use with prokaryotic and eukaryotic hosts are described in Sambrook et al., MOLECULAR CLONING:A LABORATORY MANUAL, 2 nd  Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989), the disclosure of which is hereby incorporated by reference in its entirety.  
     [0136] Generally, recombinant expression vectors will include origins of replication and selectable markers permitting transformation of the host cell, e.g., the ampicillin resistance gene of  E. coli  and  S. cerevisiae  TRPI gene, and a promoter derived from a highly expressed gene to direct transcription of a downstream structural sequence. Such promoters can be derived from operons encoding glycolytic enzymes such as 3-phosphoglycerate kinase (PGK), alpha-factor, acid phosphatase, or heat shock proteins, among others. The heterologous structural sequence is assembled in appropriate phase with translation initiation and termination sequences, and preferably, a leader sequence capable of directing secretion of translated protein into the periplasmic space or extracellular medium. Optionally, the heterologous sequence can encode a fusion protein including an N-terminal identification peptide imparting desired characteristics, e.g., stabilization or simplified purification of expressed recombinant product.  
     [0137] Useful expression vectors for bacterial use are constructed by inserting a structural DNA sequence encoding a desired protein together with suitable translation initiation and termination signals in operable reading phase with a functional promoter. The vector will comprise one or more phenotypic selectable markers and an origin of replication to ensure maintenance of the vector and, when desirable, provide amplification within the host.  
     [0138] Suitable prokaryotic hosts for transformation include strains of  Staphylococcus aureus, E. coli, B. subtilis, Salmonella typhimurium  and various species within the genera Pseudomonas, Streptomyces, and Staphylococcus. Others may, also be employed as a matter of choice.  
     [0139] As a representative but non-limiting example, useful expression vectors for bacterial use can comprise a selectable marker and bacterial origin of replication derived from commercially available plasmids comprising genetic elements of the well known cloning vector pBR322 (ATCC 37017). Such commercial vectors include, for example, pKK223-3 (available form Pharmacia Fine Chemicals, Uppsala, Sweden) and GEM 1 (available from Promega Biotec, Madison, Wis., USA). These pBR322 “backbone” sections are combined with an appropriate promoter and the structural sequence to be expressed.  
     [0140] Following transformation of a suitable host strain and growth of the host strain to an appropriate cell density, the selected promoter, where it is inducible, is derepressed or induced by appropriate means (e.g., temperature shift or chemical induction) and cells are cultured for an additional period to provide for expression of the induced gene product. Thereafter cells are typically harvested, generally by centrifugation, disrupted to release expressed protein, generally by physical or chemical means, and the resulting crude extract is retained for further purification.  
     [0141] Various mammalian cell culture systems can also be employed to express recombinant protein. Examples of mammalian expression systems include the COS-7 lines of monkey kidney fibroblasts, described in Gluzman,  Cell  23: 175 (1981), and other cell lines capable of expressing a compatible vector, for example, the C127, 3T3, CHO, HeLa and BHK cell lines.  
     [0142] Mammalian expression vectors will comprise an origin of replication, a suitable promoter and enhancer, and also any necessary ribosome binding sites, polyadenylation site, splice donor and acceptor sites, transcriptional termination sequences, and 5′ flanking nontranscribed sequences. DNA sequences derived from the SV40 viral genome, for example, SV40 origin, early promoter, enhancer, splice, and polyadenylation sites may be used to provide the required nontranscribed genetic elements.  
     [0143] Recombinant polypeptides and proteins produced in bacterial culture is usually isolated by initial extraction from cell pellets, followed by one or more salting-out, aqueous ion exchange or size exclusion chromatography steps. Microbial cells employed in expression of proteins can be disrupted by any convenient method, including freeze-thaw cycling, sonication, mechanical disruption, or use of cell lysing agents. Protein refolding steps can be used, as necessary, in completing configuration of the mature protein. Finally, high performance liquid chromatography (HPLC) can be employed for final purification steps.  
     [0144] An additional aspect of the invention includes  Staphylococcus aureus  polypeptides which are useful as immunodiagnostic antigens and/or immunoprotective vaccines, collectively “immunologically useful polypeptides”. Such immunologically useful polypeptides may be selected from the ORFs disclosed herein based on techniques well known in the art and described elsewhere herein. The inventors have used the following criteria to select several immunologically useful polypeptides:  
     [0145] As is known in the art, an amino terminal type I signal sequence directs a nascent protein across the plasma and outer membranes to the exterior of the bacterial cell. Such outer membrane polypeptides are expected to be immunologically useful. According to Izard, J. W. et al., Mol. Microbiol. 13, 765-773; (1994), polypeptides containing type I signal sequences contain the following physical attributes: The length of the type I signal sequence is approximately 15 to 25 primarily hydrophobic amino acid residues with a net positive charge in the extreme amino terminus; the central region of the signal sequence must adopt an alpha-helical conformation in a hydrophobic environment; and the region surrounding the actual site of cleavage is ideally six residues long, with small side-chain amino acids in the −1 and −3 positions.  
     [0146] Also known in the art is the type IV signal sequence which is an example of the several types of functional signal sequences which exist in addition to the type I signal sequence detailed above. Although functionally related, the type IV signal sequence possesses a unique set of biochemical and physical attributes (Strom, M. S. and Lory, S., J. Bacteriol. 174, 7345-7351; 1992)). These are typically six to eight amino acids with a net basic charge followed by an additional sixteen to thirty primarily hydrophobic residues. The cleavage site of a type IV signal sequence is typically after the initial six to eight amino acids at the extreme amino terminus. In addition, all type IV signal sequences contain a phenylalanine residue at the +1 site relative to the cleavage site.  
     [0147] Studies of the cleavage sites of twenty-six bacterial lipoprotein precursors has allowed the definition of a consensus amino acid sequence for lipoprotein cleavage. Nearly three-fourths of the bacterial lipoprotein precursors examined contained the sequence L-(A,S)-(G,A)-C at positions −3 to +1, relative to the point of cleavage (Hayashi, S. and Wu, H. C. Lipoproteins in bacteria. J Bioenerg. Biomembr. 22, 451-471; 1990).  
     [0148] It is well known that most anchored proteins found on the surface of gram-positive bacteria possess a highly conserved carboxy terminal sequence. More than fifty such proteins from organisms such as  S. pyogenes, S. mutans, E. faecalis, S. pneumoniae,  and others, have been identified based on their extracellular location and carboxy terminal amino acid sequence (Fischetti, V. A. Gram-positive commensal bacteria deliver antigens to elicit mucosal and systemic immunity. ASM News 62, 405-410; 1996). The conserved region is comprised of six charged amino acids at the extreme carboxy terminus coupled to 15-20 hydrophobic amino acids presumed to function as a transmembrane domain. Immediately adjacent to the transmembrane domain is a six amino acid sequence conserved in nearly all proteins examined. The amino acid sequence of this region is L-P-X-G-X (SEQ ID NO:5256), where X is any amino acid.  
     [0149] Amino acid sequence similarities to proteins of known function by BLAST enables the assignment of putative functions to novel amino acid sequences and allows for the selection of proteins thought to function outside the cell wall. Such proteins are well known in the art and include “lipoprotein”, “periplasmic”, or “antigen”.  
     [0150] An algorithm for selecting antigenic and immunogenic  Staphylococcus aureus  polypeptides including the foregoing criteria was developed by the present inventors. Use of the algorithm by the inventors to select immunologically useful  Staphylococcus aureus  polypeptides resulted in the selection of several ORFs which are predicted to be outer membrane-associated proteins. These proteins are identified below, and shown in the Sequence Listing as SEQ ID NOS: 5,192 to 5,255. Thus the amino acid sequence of each of several antigenic  Staphylococcus aureus  polypeptides can be determined, for example, by locating the amino acid sequence of the ORF in the Sequence Listing. Likewise the polynucleotide sequence encoding each ORF can be found by locating the corresponding polynucleotide SEQ ID in Tables 1, 2, or 3, and finding the corresponding nucleotide sequence in the sequence listing.  
     [0151] As will be appreciated by those of ordinary skill in the art, although a polypeptide representing an entire ORF may be the closest approximation to a protein found in vivo, it is not always technically practical to express a complete ORF in vitro. It may be very challenging to express and purify a highly hydrophobic protein by common laboratory methods. As a result, the immunologically useful polypeptides described herein as SEQ ID NOS: 5,192-5,255 may have been modified slightly to simplify the production of recombinant protein, and are the preferred embodiments. In general, nucleotide sequences which encode highly hydrophobic domains, such as those found at the amino terminal signal sequence, are excluded for enhanced in vitro expression of the polypeptides. Furthermore, any highly hydrophobic amino acid sequences occurring at the carboxy terminus are also excluded. Such truncated polypeptides include for example the mature forms of the polypeptides expected to exist in nature.  
     [0152] Those of ordinary skill in the art can identify soluble portions the polypeptide, and in the case of truncated polypeptides sequences shown as SEQ ID NOS: 5,192-5,255, may obtain the complete predicted amino acid sequence of each polypeptide by translating the corresponding polynucleotides sequences of the corresponding ORF listed in Tables 1,2 and 3 and found in the sequence listing.  
     [0153] Accordingly, polypeptides comprising the complete amino acid sequence of an immunologically useful polypeptide selected from the group of polypeptides encoded by the ORFs shown as SEQ ID NOS: 5,192-5,255, or an amino acid sequence at least 95% identical thereto, preferably at least 97% identical thereto, and most preferably at least 99% identical thereto form an embodiment of the invention; in addition, polypeptides comprising an amino acid sequence selected from the group of amino acid sequences shown in the sequence listing as SEQ ID NOS: 5,191-5,255, or an amino acid sequence at least 95% identical thereto, preferably at least 97% identical thereto and most preferably 99% identical thereto, form an embodiment of the invention. Polynucleotides encoding the foregoing polypeptides also form part of the invention.  
     [0154] In another aspect, the invention provides a peptide or polypeptide comprising an epitope-bearing portion of a polypeptide of the invention, particularly those epitope-bearing portions (antigenic regions) identified in the sequence listing as SEQ ID NOS: 5,191-5,255. The epitope-bearing portion is an immunogenic or antigenic epitope of a polypeptide of the invention. An “immunogenic epitope” is defined as a part of a protein that elicits an antibody response when the whole protein is the immunogen. On the other hand, a region of a protein molecule to which an antibody can bind is defined as an “antigenic epitope.” The number of immunogenic epitopes of a protein generally is less than the number of antigenic epitopes. See, for instance, Geysen et al., Proc. Natl. Acad. Sci. USA 81:3998-4002 (1983).  
     [0155] As to the selection of peptides or polypeptides bearing an antigenic epitope (i.e., that contain a region of a protein molecule to which an antibody can bind), it is well known in that art that relatively short synthetic peptides that mimic part of a protein sequence are routinely capable of eliciting an antiserum that reacts with the partially mimicked protein. See, for instance, Sutcliffe, J. G., Shinnick, T. M., Green, N. and Learner, R. A. (1983) “Antibodies that react with predetermined sites on proteins”, Science, 219:660-666. Peptides capable of eliciting protein-reactive sera are frequently represented in the primary sequence of a protein, can be characterized by a set of simple chemical rules, and are confined neither to immunodominant regions of intact proteins (i.e., immunogenic epitopes) nor to the amino or carboxyl terminals.  
     [0156] Antigenic epitope-bearing peptides and polypeptides of the invention are therefore useful to raise antibodies, including monoclonal antibodies, that bind specifically to a polypeptide of the invention. See, for instance, Wilson et al., Cell 37:767-778 (1984) at 777.  
     [0157] Antigenic epitope-bearing peptides and polypeptides of the invention preferably contain a sequence of at least seven, more preferably at least nine and most preferably between about 15 to about 30 amino acids contained within the amino acid sequence of a polypeptide of the invention. Non-limiting examples of antigenic polypeptides or peptides that can be used to generate  S. aureus  specific antibodies include: a polypeptide comprising peptides shown below. These polypeptide fragments have been determined to bear antigenic epitopes of indicated  S. aureus  proteins by the analysis of the Jameson-Wolf antigenic index, a representative sample of which is shown in FIG. 3.  
     [0158] The epitope-bearing peptides and polypeptides of the invention may be produced by any conventional means. See, e.g., Houghten, R. A. (1985) General method for the rapid solid-phase synthesis of large numbers of peptides: specificity of antigen-antibody interaction at the level of individual amino acids. Proc. Natl. Acad. Sci. USA 82:5131-5135; this “Simultaneous Multiple Peptide Synthesis (SMPS)” process is further described in U.S. Pat. No. 4,631,211 to Houghten et al. (1986).  
     [0159] Epitope-bearing peptides and polypeptides of the invention are used to induce antibodies according to methods well known in the art. See, for instance, Sutcliffe et al., supra; Wilson et al., supra; Chow, M. et al., Proc. Natl. Acad. Sci. USA 82:910-914; and Bittle, F. J. et al., J. Gen. Virol. 66:2347-2354 (1985). Immunogenic epitope-bearing peptides of the invention, i.e., those parts of a protein that elicit an antibody response when the whole protein is the immunogen, are identified according to methods known in the art. See, for instance, Geysen et al., supra. Further still, U.S. Pat. No. 5,194,392 to Geysen (1990) describes a general method of detecting or determining the sequence of monomers (amino acids or other compounds) which is a topological equivalent of the epitope (i.e., a “mimotope”) which is complementary to a particular paratope (antigen binding site) of an antibody of interest. More generally, U.S. Pat. No. 4,433,092 to Geysen (1989) describes a method of detecting or determining a sequence of monomers which is a topographical equivalent of a ligand which is complementary to the ligand binding site of a particular receptor of interest. Similarly, U.S. Pat. No. 5,480,971 to Houghten, R. A. et al. (1996) on Peralkylated Oligopeptide Mixtures discloses linear C1-C7-alkyl peralkylated oligopeptides and sets and libraries of such peptides, as well as methods for using such oligopeptide sets and libraries for determining the sequence of a peralkylated oligopeptide that preferentially binds to an acceptor molecule of interest. Thus, non-peptide analogs of the epitope-bearing peptides of the invention also can be made routinely by these methods.  
     [0160] Immunologically useful polypeptides may be identified by an algorithm which locates novel  Staphylococcus aureus  outer membrane proteins, as is described above. Also listed are epitopes or “antigenic regions” of each of the identified polypeptides. The antigenic regions, or epitopes, are delineated by two numbers x-y, where x is the number of the first amino acid in the open reading frame included within the epitope and y is the number of the last amino acid in the open reading frame included within the epitope. For example, the first epitope in ORF 168-6 is comprised of amino acids 36 to 45 of SEQ ID NO: 5,192. The inventors have identified several epitopes for each of the antigenic polypeptides identified. Accordingly, forming part of the present invention are polypeptides comprising an amino acid sequence of one or more antigenic regions identified. The invention further provides polynucleotides encoding such polypeptides.  
     [0161] The present invention further includes isolated polypeptides, proteins and nucleic acid molecules which are substantially equivalent to those herein described. As used herein, substantially equivalent can refer both to nucleic acid and amino acid sequences, for example a mutant sequence, that varies from a reference sequence by one or more substitutions, deletions, or additions, the net effect of which does not result in an adverse functional dissimilarity between reference and subject sequences. For purposes of the present invention, sequences having equivalent biological activity, and equivalent expression characteristics are considered substantially equivalent. For purposes of determining equivalence, truncation of the mature sequence should be disregarded.  
     [0162] The invention further provides methods of obtaining homologs from other strains of  Staphylococcus aureus , of the fragments of the  Staphylococcus aureus  genome of the present invention and homologs of the proteins encoded by the ORFs of the present invention. As used herein, a sequence or protein of  Staphylococcus aureus  is defined as a homolog of a fragment of the  Staphylococcus aureus  fragments or contigs or a protein encoded by one of the ORFs of the present invention, if it shares significant homology to one of the fragments of the  Staphylococcus aureus  genome of the present invention or a protein encoded by one of the ORFs of the present invention. Specifically, by using the sequence disclosed herein as a probe or as primers, and techniques such as PCR cloning and colony/plaque hybridization, one skilled in the art can obtain homologs.  
     [0163] As used herein, two nucleic acid molecules or proteins are said to “share significant homology” if the two contain regions which possess greater than 85% sequence (amino acid or nucleic acid) homology. Preferred homologs in this regard are those with more than 90% homology. Especially preferred are those with 93% or more homology. Among especially preferred homologs those with 95% or more homology are particularly preferred. Very particularly preferred among these are those with 97% and even more particularly preferred among those are homologs with 99% or more homology. The most preferred homologs among these are those with 99.9% homology or more. It will be understood that, among measures of homology, identity is particularly preferred in this regard.  
     [0164] Region specific primers or probes derived from the nucleotide sequence provided in SEQ ID NOS: 1-5,191 or from a nucleotide sequence at least 95%, particularly at least 99%, especially at least 99.5% identical to a sequence of SEQ ID NOS: 1-5,191 can be used to prime DNA synthesis and PCR amplification, as well as to identify colonies containing cloned DNA encoding a homolog. Methods suitable to this aspect of the present invention are well known and have been described in great detail in many publications such as, for example, Innis et al., PCR PROTOCOLS, Academic Press, San Diego, Calif. (1990)).  
     [0165] When using primers derived from SEQ ID NOS: 1-5,191 or from a nucleotide sequence having an aforementioned identity to a sequence of SEQ ID NOS: 1-5,191, one skilled in the art will recognize that by employing high stringency conditions (e.g., annealing at 50-60° C. in 6× SSPC and 50% formamide, and washing at 50-65° C. in 0.5× SSPC) only sequences which are greater than 75% homologous to the primer will be amplified. By employing lower stringency conditions (e.g., hybridizing at 35-37° C. in 5× SSPC and 40-45% formamide, and washing at 42° C. in 0.5× SSPC), sequences which are greater than 40-50% homologous to the primer will also be amplified.  
     [0166] When using DNA probes derived from SEQ ID NOS: 1-5,191, or from a nucleotide sequence having an aforementioned identity to a sequence of SEQ ID NOS: 1-5,191, for colony/plaque hybridization, one skilled in the art will recognize that by employing high stringency conditions (e.g., hybridizing at 50-65° C. in 5× SSPC and 50% formamide, and washing at 50-65° C. in 0.5× SSPC), sequences having regions which are greater than 90% homologous to the probe can be obtained, and that by employing lower stringency conditions (e.g., hybridizing at 35-37° C. in 5× SSPC and 40-45% formamide, and washing at 42° C. in 0.5× SSPC), sequences having regions which are greater than 35-45% homologous to the probe will be obtained.  
     [0167] Any organism can be used as the source for homologs of the present invention so long as the organism naturally expresses such a protein or contains genes encoding the same. The most preferred organism for isolating homologs are bacterias which are closely related to  Staphylococcus aureus.    
     ILLUSTRATIVE USES OF COMPOSITIONS OF THE INVENTION  
     [0168] Each ORF provided in Tables 1 and 2 is identified with a function by homology to a known gene or polypeptide. As a result, one skilled in the art can use the polypeptides of the present invention for commercial, therapeutic and industrial purposes consistent with the type of putative identification of the polypeptide. Such identifications permit one skilled in the art to use the  Staphylococcus aureus  ORFs in a manner similar to the known type of sequences for which the identification is made; for example, to ferment a particular sugar source or to produce a particular metabolite. A variety of reviews illustrative of this aspect of the invention are available, including the following reviews on the industrial use of enzymes, for example, BIOCHEMICAL ENGINEERING AND BIOTECHNOLOGY HANDBOOK, 2 nd  Ed., Macmillan Publications, Ltd. NY (1991) and BIOCATALYSTS IN ORGANIC SYNTHESES, Tramper et al., Eds., Elsevier Science Publishers, Amsterdam, The Netherlands (1985). A variety of exemplary uses that illustrate this and similar aspects of the present invention are discussed below.  
     [0169] 1. Biosynthetic Enzymes  
     [0170] Open reading frames encoding proteins involved in mediating the catalytic reactions involved in intermediary and macromolecular metabolism, the biosynthesis of small molecules, cellular processes and other functions includes enzymes involved in the degradation of the intermediary products of metabolism, enzymes involved in central intermediary metabolism, enzymes involved in respiration, both aerobic and anaerobic, enzymes involved in fermentation, enzymes involved in ATP proton motor force conversion, enzymes involved in broad regulatory function, enzymes involved in amino acid synthesis, enzymes involved in nucleotide synthesis, enzymes involved in cofactor and vitamin synthesis, can be used for industrial biosynthesis.  
     [0171] The various metabolic pathways present in  Staphylococcus aureus  can be identified based on absolute nutritional requirements as well as by examining the various enzymes identified in Table 1-3 and SEQ ID NOS: 1-5,191.  
     [0172] Of particular interest are polypeptides involved in the degradation of intermediary metabolites as well as non-macromolecular metabolism. Such enzymes include amylases, glucose oxidases, and catalase.  
     [0173] Proteolytic enzymes are another class of commercially important enzymes. Proteolytic enzymes find use in a number of industrial processes including the processing of flax and other vegetable fibers, in the extraction, clarification and depectinization of fruit juices, in the extraction of vegetables&#39; oil and in the maceration of fruits and vegetables to give unicellular fruits. A detailed review of the proteolytic enzymes used in the food industry is provided in Rombouts et al.,  Symbiosis  21: 79 (1986) and Voragen et al. in BIOCATALYSTS IN AGRICULTURAL BIOTECHNOLOGY, Whitaker et al., Eds.,  American Chemical Society Symposium Series  389: 93 (1989).  
     [0174] The metabolism of sugars is an important aspect of the primary metabolism of  Staphylococcus aureus . Enzymes involved in the degradation of sugars, such as, particularly, glucose, galactose, fructose and xylose, can be used in industrial fermentation. Some of the important sugar transforming enzymes, from a commercial viewpoint, include sugar isomerases such as glucose isomerase. Other metabolic enzymes have found commercial use such as glucose oxidases which produces ketogulonic acid (KGA). KGA is an intermediate in the commercial production of ascorbic acid using the Reichstein&#39;s procedure, as described in Krueger et al.,  Biotechnology  6(A), Rhine et al., Eds., Verlag Press, Weinheim, Germany (1984).  
     [0175] Glucose oxidase (GOD) is commercially available and has been used in purified form as well as in an immobilized form for the deoxygenation of beer. See, for instance, Hartmeir et al.,  Biotechnology Letters  1: 21 (1979). The most important application of GOD is the industrial scale fermentation of gluconic acid. Market for gluconic acids which are used in the detergent, textile, leather, photographic, pharmaceutical, food, feed and concrete industry, as described, for example, in Bigelis et al., beginning on page 357 in GENE MANIPULATIONS AND FUNGI; Benett et al., Eds., Academic Press, New York (1985). In addition to industrial applications, GOD has found applications in medicine for quantitative determination of glucose in body fluids recently in biotechnology for analyzing syrups from starch and cellulose hydrosylates. This application is described in Owusu et al.,  Biochem. et Biophysica. Acta.  872: 83 (1986), for instance.  
     [0176] The main sweetener used in the world today is sugar which comes from sugar beets and sugar cane. In the field of industrial enzymes, the glucose isomerase process shows the largest expansion in the market today. Initially, soluble enzymes were used and later immobilized enzymes were developed (Krueger et al., Biotechnology, The Textbook of Industrial Microbiology, Sinauer Associated Incorporated, Sunderland, Mass. (1990)). Today, the use of glucose- produced high fructose syrups is by far the largest industrial business using immobilized enzymes. A review of the industrial use of these enzymes is provided by Jorgensen, Starch 40:307 (1988).  
     [0177] Proteinases, such as alkaline serine proteinases, are used as detergent additives and thus represent one of the largest volumes of microbial enzymes used in the industrial sector. Because of their industrial importance, there is a large body of published and unpublished information regarding the use of these enzymes in industrial processes. (See Faultman et al., Acid Proteases Structure Function and Biology, Tang, J., ed., Plenum Press, New York (1977) and Godfrey et al., Industrial Enzymes, MacMillan Publishers, Surrey, UK (1983) and Hepner et al, Report Industrial Enzymes by 1990, Hel Hepner &amp; Associates, London (1986)).  
     [0178] Another class of commercially usable proteins of the present invention are the microbial lipases, described by, for instance, Macrae et al., Philosophical Transactions of the Chiral Society of London 310:227 (1985) and Poserke, Journal of the American Oil Chemist Society 61:1758 (1984). A major use of lipases is in the fat and oil industry for the production of neutral glycerides using lipase catalyzed inter-esterification of readily available triglycerides. Application of lipases include the use as a detergent additive to facilitate the removal of fats from fabrics in the course of the washing procedures.  
     [0179] The use of enzymes, and in particular microbial enzymes, as catalyst for key steps in the synthesis of complex organic molecules is gaining popularity at a great rate. One area of great interest is the preparation of chiral intermediates. Preparation of chiral intermediates is of interest to a wide range of synthetic chemists particularly those scientists involved with the preparation of new pharmaceuticals, agrochemicals, fragrances and flavors. (See Davies et al., Recent Advances in the Generation of Chiral Intermediates Using Enzymes, CRC Press, Boca Raton, Fla. (1990)). The following reactions catalyzed by enzymes are of interest to organic chemists: hydrolysis of carboxylic acid esters, phosphate esters, amides and nitriles, esterification reactions, trans-esterification reactions, synthesis of amides, reduction of alkanones and oxoalkanates, oxidation of alcohols to carbonyl compounds, oxidation of sulfides to sulfoxides, and carbon bond forming reactions such as the aldol reaction.  
     [0180] When considering the use of an enzyme encoded by one of the ORFs of the present invention for biotransformation and organic synthesis it is sometimes necessary to consider the respective advantages and disadvantages of using a microorganism as opposed to an isolated enzyme. Pros and cons of using a whole cell system on the one hand or an isolated partially purified enzyme on the other hand, has been described in detail by Bud et al., Chemistry in Britain (1987), p. 127.  
     [0181] Amino transferases, enzymes involved in the biosynthesis and metabolism of amino acids, are useful in the catalytic production of amino acids. The advantages of using microbial based enzyme systems is that the amino transferase enzymes catalyze the stereo- selective synthesis of only L-amino acids and generally possess uniformly high catalytic rates. A description of the use of amino transferases for amino acid production is provided by Roselle-David,  Methods of Enzymology  136:479 (1987).  
     [0182] Another category of useful proteins encoded by the ORFs of the present invention include enzymes involved in nucleic acid synthesis, repair, and recombination. A variety of commercially important enzymes have previously been isolated from members of  Staphylococcus aureus . These include Sau3A and Sau96I.  
     [0183] 2. Generation of Antibodies  
     [0184] As described here, the proteins of the present invention, as well as homologs thereof, can be used in a variety procedures and methods known in the art which are currently applied to other proteins. The proteins of the present invention can further be used to generate an antibody which selectively binds the protein. Such antibodies can be either monoclonal or polyclonal antibodies, as well fragments of these antibodies, and humanized forms.  
     [0185] The invention further provides antibodies which selectively bind to one of the proteins of the present invention and hybridomas which produce these antibodies. A hybridoma is an immortalized cell line which is capable of secreting a specific monoclonal antibody.  
     [0186] In general, techniques for preparing polyclonal and monoclonal antibodies as well as hybridomas capable of producing the desired antibody are well known in the art (Campbell, A. M., MONOCLONAL ANTIBODY TECHNOLOGY: LABORATORY TECHNIQUES IN BIOCHEMISTRY AND MOLECULAR BIOLOGY, Elsevier Science Publishers, Amsterdam, The Netherlands (1984); St. Groth et al.,  J. Immunol. Methods  35: 1-21 (1980), Kohler and Milstein,  Nature  256: 495-497 (1975)), the trioma technique, the human B-cell hybridoma technique (Kozbor et al.,  Immunology Today- 4: 72 (1983), pgs. 77-96 of Cole et al., in MONOCLONAL ANTIBODIES AND CANCER THERAPY, Alan R. Liss, Inc. (1985)).  
     [0187] Any animal (mouse, rabbit, etc.) which is known to produce antibodies can be immunized with the pseudogene polypeptide. Methods for immunization are well known in the art. Such methods include subcutaneous or interperitoneal injection of the polypeptide. One skilled in the art will recognize that the amount of the protein encoded by the ORF of the present invention used for immunization will vary based on the animal which is immunized, the antigenicity of the peptide and the site of injection.  
     [0188] The protein which is used as an immunogen may be modified or administered in an adjuvant in order to increase the protein&#39;s antigenicity. Methods of increasing the antigenicity of a protein are well known in the art and include, but are not limited to coupling the antigen with a heterologous protein (such as globulin or galactosidase) or through the inclusion of an adjuvant during immunization.  
     [0189] For monoclonal antibodies, spleen cells from the immunized animals are removed, fused with myeloma cells, such as SP2/0-Ag14 myeloma cells, and allowed to become monoclonal antibody producing hybridoma cells.  
     [0190] Any one of a number of methods well known in the art can be used to identify the hybridoma cell which produces an antibody with the desired characteristics. These include screening the hybridomas with an ELISA assay, western blot analysis, or radioimmunoassay (Lutz et al.,  Exp. Cell Res.  175: 109-124 (1988)).  
     [0191] Hybridomas secreting the desired antibodies are cloned and the class and subclass is determined using procedures known in the art (Campbell, A. M., Monoclonal Antibody Technology: Laboratory Techniques in Biochemistry and Molecular Biology, Elsevier Science Publishers, Amsterdam, The Netherlands (1984)).  
     [0192] Techniques described for the production of single chain antibodies (U.S. Pat. No. 946,778) can be adapted to produce single chain antibodies to proteins of the present invention.  
     [0193] For polyclonal antibodies, antibody containing antisera is isolated from the immunized animal and is screened for the presence of antibodies with the desired specificity using one of the above-described procedures.  
     [0194] The present invention further provides the above- described antibodies in detectably labeled form. Antibodies can be detectably labeled through the use of radioisotopes, affinity labels (such as biotin, avidin, etc.), enzymatic labels (such as horseradish peroxidase, alkaline phosphatase, etc.) fluorescent labels (such as FITC or rhodamine, etc.), paramagnetic atoms, etc. Procedures for accomplishing such labeling are well-known in the art, for example see Stemberger et al., J. Histochem. Cytochem. 18:315 (1970); Bayer, E. A. et al., Meth. Enzym. 62:308 (1979); Engval, E. et al., Immunol.  109-129  (1972); Goding, J. W. J. Immunol. Meth. 13:215 (1976)).  
     [0195] The labeled antibodies of the present invention can be used for in vitro, in vivo, and in situ assays to identify cells or tissues in which a fragment of the  Staphyococcus aureus  genome is expressed.  
     [0196] The present invention further provides the above-described antibodies immoblized on a solid support. Examples of such solid supports include plastics such as polycarbonate, complex carbohydrates such as agarose and sepharose, acrylic resins and such as polyacrylamide and latex beads. Techniques for coupling antibodies to such solid supports are well known in the art (Weir, D. M. et al., “Handbook of Experimental Immunology” 4th Ed., Blackwell Scientific Publications, Oxford, England, Chapter 10 (1986); Jacoby, W. D. et al., Meth. Enzym. 34 Academic Press, N.Y. (1974)). The immobilized antibodies of the present invention can be used for in vitro, in vivo, and in situ assays as well as for immunoaffinity purification of the proteins of the present invention.  
     [0197] 3. Diagnostic Assays and Kits  
     [0198] The present invention further provides methods to identify the expression of one of the ORFs of the present invention, or homolog thereof, in a test sample, using one of the DFs, antigens or antibodies of the present invention.  
     [0199] In detail, such methods comprise incubating a test sample with one or more of the antibodies, or one or more of the DFs, or one or more antigens of the present invention and assaying for binding of the DFs, antigens or antibodies to components within the test sample.  
     [0200] Conditions for incubating a DF, antigen or antibody with a test sample vary. Incubation conditions depend on the format employed in the assay, the detection methods employed, and the type and nature of the DF or antibody used in the assay. One skilled in the art will recognize that any one of the commonly available hybridization, amplification or immunological assay formats can readily be adapted to employ the Dfs, antigens or antibodies of the present invention. Examples of such assays can be found in Chard, T., An Introduction to Radioimmunoassay and Related Techniques, Elsevier Science Publishers, Amsterdam, The Netherlands (1986); Bullock, G. R. et al., Techniques in inmunocytochemistry, Academic Press, Orlando, Fla. Vol. 1 (1982), Vol. 2 (1983), Vol. 3 (1985); Tijssen, P., Practice and Theory of Enzyme Immunoassays: Laboratory Techniques in Biochemistry; PCT publication W095/32291, and Molecular Biology, Elsevier Science Publishers, Amsterdam, The Netherlands (1985), all of which are hereby incorporated herein by reference.  
     [0201] The test samples of the present invention include cells, protein or membrane extracts of cells, or biological fluids such as sputum, blood, serum,, plasma, or urine. The test sample used in the above-described method will vary based on the assay format, nature of the detection method and the tissues, cells or extracts used as the sample to be assayed. Methods for preparing protein extracts or membrane extracts of cells are well known in the art and can be readily be adapted in order to obtain a sample which is compatible with the system utilized.  
     [0202] In another embodiment of the present invention, kits are provided which contain the necessary reagents to carry out the assays of the present invention.  
     [0203] Specifically, the invention provides a compartmentalized kit to receive, in close confinement, one or more containers which comprises:(a) a first container comprising one of the Dfs, antigens or antibodies of the present invention; and (b) one or more other containers comprising one or more of the following: wash reagents, reagents capable of detecting presence of a bound DF, antigen or antibody.  
     [0204] In detail, a compartmentalized kit includes any kit in which reagents are contained in separate containers. Such containers include small glass containers, plastic containers or strips of plastic or paper. Such containers allows one to efficiently transfer reagents from one compartment to another compartment such that the samples and reagents are not cross-contaminated, and the agents or solutions of each container can be added in a quantitative fashion from one compartment to another. Such containers will include a container which will accept the test sample, a container which contains the antibodies used in the assay, containers which contain wash reagents (such as phosphate buffered saline, Tris-buffers, etc.), and containers which contain the reagents used to detect the bound antibody, antigen or DF.  
     [0205] Types of detection reagents include labeled nucleic acid probes, labeled secondary antibodies, or in the alternative, if the primary antibody is labeled, the enzymatic, or antibody binding reagents which are capable of reacting with the labeled antibody. One skilled in the art will readily recognize that the disclosed Dfs, antigens and antibodies of the present invention can be readily incorporated into one of the established kit formats which are well known in the art.  
     [0206] 4. Screening Assay for Binding Agents  
     [0207] Using the isolated proteins of the present invention, the present invention further provides methods of obtaining and identifying agents which bind to a protein encoded by one of the ORFs of the present invention or to one of the fragments and the  Staphylococcus aureus  fragment and contigs herein described.  
     [0208] In general, such methods comprise steps of:  
     [0209] contacting an agent with an isolated protein encoded by one of the ORFs of the present invention, or an isolated fragment of the  Staphylococcus aureus  genome; and  
     [0210] determining whether the agent binds to said protein or said fragment.  
     [0211] The agents screened in the above assay can be, but are not limited to, peptides, carbohydrates, vitamin derivatives, or other pharmaceutical agents. The agents can be selected and screened at random or rationally selected or designed using protein modeling techniques.  
     [0212] For random screening, agents such as peptides, carbohydrates, pharmaceutical agents and the like are selected at random and are assayed for their ability to bind to the protein encoded by the ORF of the present invention.  
     [0213] Alternatively, agents may be rationally selected or designed. As used herein, an agent is said to be “rationally selected or designed” when the agent is chosen based on the configuration of the particular protein. For example, one skilled in the art can readily adapt currently available procedures to generate peptides, pharmaceutical agents and the like capable of binding to a specific peptide sequence in order to generate rationally designed antipeptide peptides, for example see Hurby et al., Application of Synthetic Peptides: Antisense Peptides,” In Synthetic Peptides, A User&#39;s Guide, W. H. Freeman, NY (1992), pp. 289-307, and Kaspczak et al., Biochemistry 28:9230-8 (1989), or pharmaceutical agents, or the like.  
     [0214] In addition to the foregoing, one class of agents of the present invention, as broadly described, can be used to control gene expression through binding to one of the ORFs or EMFs of the present invention. As described above, such agents can be randomly screened or rationally designed/selected. Targeting the ORF or EMF allows a skilled artisan to design sequence specific or element specific agents, modulating the expression of either a single ORF or multiple ORFs which rely on the same EMF for expression control.  
     [0215] One class of DNA binding agents are agents which contain base residues which hybridize or form a triple helix by binding to DNA or RNA. Such agents can be based on the classic phosphodiester, ribonucleic acid backbone, or can be a variety of sulfhydryl or polymeric derivatives which have base attachment capacity.  
     [0216] Agents suitable for use in these methods usually contain 20 to 40 bases and are designed to be complementary to a region of the gene involved in transcription (triple helix—see Lee et al., Nucl. Acids Res. 6:3073 (1979); Cooney et al., Science 241:456 (1988); and Dervan et al., Science 251: 1360 (1991)) or to the mRNA itself (antisense—Okano, J. Neurochem. 56:560 (1991); Oligodeoxynucleotides as Antisense Inhibitors of Gene Expression, CRC Press, Boca Raton, Fla. (1988)). Triple helix- formation optimally results in a shut-off of RNA transcription from DNA, while antisense RNA hybridization blocks translation of an mRNA molecule into polypeptide. Both techniques have been demonstrated to be effective in model systems. Information contained in the sequences of the present invention can be used to design antisense and triple helix-forming oligonucleotides, and other DNA binding agents.  
     [0217] 5. Pharmaceutical Compositions and Vaccines  
     [0218] The present invention further provides pharmaceutical agents which can be used to modulate the growth or pathogenicity of  Staphylococcus aureus , or another related organism, in vivo or in vitro. As used herein, a “pharmaceutical agent” is defined as a composition of matter which can be formulated using known techniques to provide a pharmaceutical compositions. As used herein, the “pharmaceutical agents of the present invention” refers the pharmaceutical agents which are derived from the proteins encoded by the ORFs of the present invention or are agents which are identified using the herein described assays.  
     [0219] As used herein, a pharmaceutical agent is said to “modulate the growth or pathogenicity of  Staphylococcus aureus  or a related organism, in vivo or in vitro,” when the agent reduces the rate of growth, rate of division, or viability of the organism in question. The pharmaceutical agents of the present invention can modulate the growth or pathogenicity of an organism in many fashions, although an understanding of the underlying mechanism of action is not needed to practice the use of the pharmaceutical agents of the present invention. Some agents will modulate the growth or pathogenicity by binding to an important protein thus blocking the biological activity of the protein, while other agents may bind to a component of the outer surface of the organism blocking attachment or rendering the organism more prone to act the bodies nature immune system. Alternatively, the agent may comprise a protein encoded by one of the ORFs of the present invention and serve as a vaccine. The development and use of vaccines derived from membrane associated polypeptides are well known in the art. The inventors have identified particularly preferred immunogenic  Staphylococcus aureus  polypeptides for use as vaccines. Such immunogenic polypeptides are described above and summarized below.  
     [0220] As used herein, a “related organism” is a broad term which refers to any organism whose growth or pathogenicity can be modulated by one of the pharmaceutical agents of the present invention. In general, such an organism will contain a homolog of the protein which is the target of the pharmaceutical agent or the protein used as a vaccine. As such, related organisms do not need to be bacterial but may be fungal or viral pathogens.  
     [0221] The pharmaceutical agents and compositions of the present invention may be administered in a convenient manner, such as by the oral, topical, intravenous, intraperitoneal, intramuscular, subcutaneous, intranasal or intradermal routes. The pharmaceutical compositions are administered in an amount which is effective for treating and/or prophylaxis of the specific indication. In general, they are administered in an amount of at least about 1 mg/kg body weight and in most cases they will be administered in an amount not in excess of about 1 g/kg body weight per day. In most cases, the dosage is from about 0.1 mg/kg to about 10 g/kg body weight daily, taking into account the routes of administration, symptoms, etc.  
     [0222] The agents of the present invention can be used in native form or can be modified to form a chemical derivative. As used herein, a molecule is said to be a “chemical derivative” of another molecule when it contains additional chemical moieties not normally a part of the molecule. Such moieties may improve the molecule&#39;s solubility, absorption, biological half life, etc. The moieties may alternatively decrease the toxicity of the molecule, eliminate or attenuate any undesirable side effect of the molecule, etc. Moieties capable of mediating such effects are disclosed in, among other sources, REMINGTON&#39;S PHARMACEUTICAL SCIENCES (1980) cited elsewhere herein.  
     [0223] For example, such moieties may change an immunological character of the functional derivative, such as affinity for a given antibody. Such changes in immunomodulation activity are measured by the appropriate assay, such as a competitive type immunoassay. Modifications of such protein properties as redox or thermal stability, biological half-life, hydrophobicity, susceptibility to proteolytic degradation or the tendency to aggregate with carriers or into multimers also may be effected in this way and can be assayed by methods well known to the skilled artisan.  
     [0224] The therapeutic effects of the agents of the present invention may be obtained by providing the agent to a patient by any suitable means (e.g., inhalation, intravenously, intramuscularly, subcutaneously, enterally, or parenterally). It is preferred to administer the agent of the present invention so as to achieve an effective concentration within the blood or tissue in which the growth of the organism is to be controlled. To achieve an effective blood concentration, the preferred method is to administer the agent by injection. The administration may be by continuous infusion, or by single or multiple injections.  
     [0225] In providing a patient with one of the agents of the present invention, the dosage of the administered agent will vary depending upon such factors as the patient&#39;s age, weight, height, sex, general medical condition, previous medical history, etc. In general, it is desirable to provide the recipient with a dosage of agent which is in the range of from about 1 pg/kg to 10 mg/kg (body weight of patient), although a lower or higher dosage may be administered. The therapeutically effective dose can be lowered by using combinations of the agents of the present invention or another agent.  
     [0226] As used herein, two or more compounds or agents are said to be administered “in combination” with each other when either (1) the physiological effects of each compound, or (2) the serum concentrations of each compound can be measured at the same time. The composition of the present invention can be administered concurrently with, prior to, or following the administration of the other agent.  
     [0227] The agents of the present invention are intended to be provided to recipient subjects in an amount sufficient to decrease the rate of growth (as defined above) of the target organism.  
     [0228] The administration of the agent(s) of the invention may be for either a “prophylactic” or “therapeutic” purpose. When provided prophylactically, the agent(s) are provided in advance of any symptoms indicative of the organisms growth. The prophylactic administration of the agent(s) serves to prevent, attenuate, or decrease the rate of onset of any subsequent infection. When provided therapeutically, the agent(s) are provided at (or shortly after) the onset of an indication of infection. The therapeutic administration of the compound(s) serves to attenuate the pathological symptoms of the infection and to increase the rate of recovery.  
     [0229] The agents of the present invention are administered to a subject, such as a mammal, or a patient, in a pharmaceutically acceptable form and in a therapeutically effective concentration. A composition is said to be “pharmacologically acceptable” if its administration can be tolerated by a recipient patient. Such an agent is said to be administered in a “therapeutically effective amount” if the amount administered is physiologically significant. An agent is physiologically significant if its presence results in a detectable change in the physiology of a recipient patient.  
     [0230] The agents of the present invention can be formulated according to known methods to prepare pharmaceutically useful compositions, whereby these materials, or their functional derivatives, are combined in admixture with a pharmaceutically acceptable carrier vehicle. Suitable vehicles and their formulation, inclusive of other human proteins, e.g., human serum albumin, are described, for example, in REMINGTON&#39;S PHARMACEUTICAL SCIENCES, 16 th  Ed., Osol, A., Ed., Mack Publishing, Easton Pa. (1980). In order to form a pharmaceutically acceptable composition suitable for effective administration, such compositions will contain an effective amount of one or more of the agents of the present invention, together with a suitable amount of carrier vehicle.  
     [0231] Additional pharmaceutical methods may be employed to control the duration of action. Control release preparations may be achieved through the use of polymers to complex or absorb one or more of the agents of the present invention. The controlled delivery may be effectuated by a variety of well known techniques, including formulation with macromolecules such as, for example, polyesters, polyamino acids, polyvinyl, pyrrolidone, ethylenevinylacetate, methylcellulose, carboxymethylcellulose, or protamine, sulfate, adjusting the concentration of the macromolecules and the agent in the formulation, and by appropriate use of methods of incorporation, which can be manipulated to effectuate a desired time course of release. Another possible method to control the duration of action by controlled release preparations is to incorporate agents of the present invention into particles of a polymeric material such as polyesters, polyamino acids, hydrogels, poly(lactic acid) or ethylene vinylacetate copolymers. Alternatively, instead of incorporating these agents into polymeric particles, it is possible to entrap these materials in microcapsules prepared, for example, by coacervation techniques or by interfacial polymerization with, for example, hydroxymethylcellulose or gelatine-microcapsules and poly(methylmethacylate) microcapsules, respectively, or in colloidal drug delivery systems, for example, liposomes, albumin microspheres, microemulsions, nanoparticles, and nanocapsules or in macroemulsions. Such techniques are disclosed in REMINGTON&#39;S PHARMACEUTICAL SCIENCES (1980).  
     [0232] The invention further provides a pharmaceutical pack or kit comprising one or more containers filled with one or more of the ingredients of the pharmaceutical compositions of the invention. Associated with such container(s) can be a notice in the form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals or biological products, which notice reflects approval by the agency of manufacture, use or sale for human administration.  
     [0233] In addition, the agents of the present invention may be employed in conjunction with other therapeutic compounds.  
     [0234] 6. Shot-Gun Approach to Megabase DNA Sequencing  
     [0235] The present invention further demonstrates that a large sequence can be sequenced using a random shotgun approach. This procedure, described in detail in the examples that follow, has eliminated the up front cost of isolating and ordering overlapping or contiguous subclones prior to the start of the sequencing protocols.  
     [0236] Certain aspects of the present invention are described in greater detail in the examples that follow. The examples are provided by way of illustration. Other aspects and embodiments of the present invention are contemplated by the inventors, as will be clear to those of skill in the art from reading the present disclosure.  
     ILLUSTRATIVE EXAMPLES  
     [0237] Libraries and Sequencing  
     [0238] 1. Shotgun Sequencing Probability Analysis  
     [0239] The overall strategy for a shotgun approach to whole genome sequencing follows from the Lander and Waterman (Landerman and Waterman, Genomics 2: 231 (1988)) application of the equation for the Poisson distribution. According to this treatment, the probability, P 0 , that any given base in a sequence of size L, in nucleotides, is not sequenced after a certain amount, n, in nucleotides, of random sequence has been determined can be calculated by the equation P 0 =e −m , where m is L/n, the fold coverage.” For instance, for a genome of 2.8 Mb, m=1 when 2.8 Mb of sequence has been randomly generated (1× coverage). At that point, P 0 =e −1 =0.37. The probability that any given base has not been sequenced is the same as the probability that any region of the whole sequence L has not been determined and, therefore, is equivalent to the fraction of the whole sequence that has yet to be determined. Thus, at one-fold coverage, approximately 37% of a polynucleotide of size L, in nucleotides has not been sequenced. When 14 Mb of sequence has been generated, coverage is 5× for a 0.2.8 Mb and the unsequenced fraction drops to 0.0067 or 0.67%. 5× coverage of a 2.8 Mb sequence can be attained by sequencing approximately 17,000 random clones from both insert ends with an average sequence read length of 410 bp.  
     [0240] Similarly, the total gap length, G, is determined by the equation G=Le −m , and the average gap size, g, follows the equation, g=L/n. Thus, 5× coverage leaves about 240 gaps averaging about 82 bp in size in a sequence of a polynucleotide 2.8 Mb long.  
     [0241] The treatment above is essentially that of Lander and Waterman,  Genomics  2: 231 (1988).  
     [0242] 2. Random Library Construction  
     [0243] In order to approximate the random model described above during actual sequencing, a nearly ideal library of cloned genomic fragments is required. The following library construction procedure was developed to achieve this end.  
     [0244] Staphylococcus aureus  DNA was prepared by phenol extraction. A mixture containing 600 ug DNA in 3.3 ml of 300 mM sodium acetate, 10 mM Tris-HCl, 1 mM Na-EDTA, 30% glycerol was sonicated for 1 min. at 0° C. in a Branson Model 450 Sonicator at the lowest energy setting using a 3 mm probe. The sonicated DNA was ethanol precipitated and redissolved in 500 ul TE buffer.  
     [0245] To create blunt-ends, a 100 ul aliquot of the resuspended DNA was digested with 5 units of BAL31 nuclease (New England BioLabs) for 10 min at 30° C. in 200 ul BAL31 buffer. The digested DNA was phenol-extracted, ethanol-precipitated, redissolved in 100 ul TE buffer, and then size-fractionated by electrophoresis through a 1.0% low melting temperature agarose gel. The section containing DNA fragments 1.6-2.0 kb in size was excised from the gel, and the LGT agarose was melted and the resulting solution was extracted with phenol to separate the agarose from the DNA. DNA was ethanol precipitated and redissolved in 20 ul of TE buffer for ligation to vector.  
     [0246] A two-step ligation procedure was used to produce a plasmid library with 97% inserts, of which &gt;99% were single inserts. The first ligation mixture (50 ul) contained 2 ug of DNA fragments, 2 ug pUC18 DNA (Pharmacia) cut with SmaI and dephosphorylated with bacterial alkaline phosphatase, and 10 units of T4 ligase (GIBCO/BRL) and was incubated at 14° C. for 4 hr. The ligation mixture then was phenol extracted and ethanol precipitated, and the precipitated DNA was dissolved in 20 ul TE buffer and electrophoresed on a 1.0% low melting agarose gel. Discrete bands in a ladder were visualized by ethidium bromide-staining and UV illumination and identified by size as insert (i), vector (v), v+i, v+2i, v+3i, etc. The portion of the gel containing v+i DNA was excised and the v+i DNA was recovered and resuspended into 20 ul TE. The v+i DNA then was blunt-ended by T4 polymerase treatment for 5 min. at 37° C. in a reaction mixture (50 ul) containing the v+i linears, 500 uM each of the 4 dNTPs, and 9 units of T4 polymerase (New England BioLabs), under recommended buffer conditions. After phenol extraction and ethanol precipitation the repaired v+i linears were dissolved in 20 ul TE. The final ligation to produce circles was carried out in a 50 ul reaction containing 5 ul of v+i linears and 5 units of T4 ligase at 14° C overnight. After 10 min. at 70° C. the following day, the reaction mixture was stored at −20° C.  
     [0247] This two-stage procedure resulted in a molecularly random collection of single-insert plasmid recombinants with minimal contamination from double-insert chimeras (&lt;1%) or free vector (&lt;3%).  
     [0248] Since deviation from randomness can arise from propagation the DNA in the host,  E. coli  host cells deficient in all recombination and restriction functions (A. Greener, Strategies 3 (1):5 (1990)) were used to prevent rearrangements, deletions, and loss of clones by restriction. Furthermore, transformed cells were plated directly on antibiotic diffusion plates to avoid the usual broth recovery phase which allows multiplication and selection of the most rapidly growing cells.  
     [0249] Plating was carried out as follows. A 100 ul aliquot of  Epicurian Coli  SURE II Supercompetent Cells (Stratagene 200152) was thawed on ice and transferred to a chilled Falcon 2059 tube on ice. A 1.7 ul aliquot of 1.42 M beta-mercaptoethanol was added to the aliquot of cells to a final concentration of 25 mM. Cells were incubated on ice for 10 min. A 1 ul aliquot of the final ligation was added to the cells and incubated on ice for 30 min. The cells were heat pulsed for 30 sec. at 42° C. and placed back on ice for 2 min. The outgrowth period in liquid culture was eliminated from this protocol in order to minimize the preferential growth of any given transformed cell. Instead the transformation mixture was plated directly on a nutrient rich SOB plate containing a 5 ml bottom layer of SOB agar (5% SOB agar: 20 g tryptone, 5 g yeast extract, 0.5 g NaCl, 1.5% Difco Agar per liter of media). The 5 ml bottom layer is supplemented with 0.4 ml of 50 mg/ml ampicillin per 100 ml SOB agar. The 15 ml top layer of SOB agar is supplemented with 1 ml X-Gal (2%), 1 ml MgCl 2  (1 M), and 1 ml MgSO 4 /100 ml SOB agar. The 15 ml top layer was poured just prior to plating. Our titer was approximately 100 colonies/10 ul aliquot of transformation.  
     [0250] All colonies were picked for template preparation regardless of size. Thus, only clones lost due to “poison” DNA or deleterious gene products would be deleted from the library, resulting in a slight increase in gap number over that expected.  
     [0251] 3. Random DNA Sequencing  
     [0252] High quality double stranded DNA plasmid templates were prepared using an alkaline lysis method developed in collaboration with 5Prime- - - &gt;3Prime Inc. (Boulder, Co.). Plasmid preparation was performed in a 96-well format for all stages of DNA preparation from bacterial growth through final DNA purification. Average template concentration was determined by running 25% of the samples on an agarose gel. DNA concentrations were not adjusted.  
     [0253] Templates were also prepared from a  Staphylococcus aureus  lambda genomic library. An unamplified library was constructed in Lambda DASH II vector (Stratagene).  Staphylococcus aureus  DNA (&gt;100 kb) was partially digested in a reaction mixture (200 ul) containing 50 ug DNA, 1× Sau3AI buffer, 20 units Sau3AI for 6 min. at 23 C. The digested DNA was phenol-extracted and centrifuges over a 10-40% sucrose gradient. Fractions containing genomic DNA of 15-25 kb were recovered by precipitation. One ul of fragments was used with 1 ul of DASHII vector (Stratagene) in the recommended ligation reaction. One ul of the ligation mixture was used per packaging reaction following the recommended protocol with the Gigapack II XL Packaging Extract Phage were plated directly without amplification from the packaging mixture (after dilution with 500 ul of recommended SM buffer and chloroform treatment). Yield was about 2.5×10 9  pfu/ul.  
     [0254] An amplified library was prepared from the primary packaging mixture according to the manufacturer&#39;s protocol. The amplified library is stored frozen in 7% dimethylsulfoxide. The phage titer is approximately 1×10 9  pfu/ml.  
     [0255] Mini-liquid lysates (0.1 ul) are prepared from randomly selected plaques and template is prepared by long range PCR. Samples are PCR amplified using modified T3 and T7 primers, and Elongase Supermix (LTI).  
     [0256] Sequencing reactions are carried out on plasmid templates using a combination of two workstations (BIOMEK 1000 and Hamilton Microlab 2200) and the Perkin-Elmer 9600 thermocycler with Applied Biosystems PRISM Ready Reaction Dye Primer Cycle Sequencing Kits for the M13 forward (M13-21) and the M13 reverse (M13RP1) primers. Dye terminator sequencing reactions are carried out on the lambda templates on a Perkin-Elmer 9600 Thermocycler using the Applied Biosystems Ready Reaction Dye Terminator Cycle Sequencing kits. Modified T7 and T3 primers are used to sequence the ends of the inserts from the Lambda DASH II library. Sequencing reactions are on a combination of AB 373 DNA Sequencers and ABI 377 DNA sequencers. All of the dye terminator sequencing reactions are analyzed using the 2×9 hour module on the AB 377. Dye primer reactions are analyzed on a combination of ABI 373 and ABI 377 DNA sequencers. The overall sequencing success rate very approximately is about 85% for M13-21 and M13RP1 sequences and 65% for dye-terminator reactions. The average usable read length is 485 bp for M13-21 sequences, 445bp for M13RP1 sequences, and 375 bp for dye-terminator reactions.  
     [0257] 4. Protocol for Automated Cycle Sequencing  
     [0258] The sequencing was carried out using Hamilton Microstation 2200, Perkin Elmer 9600 thermocyclers, ABI 373 and ABI 377 Automated DNA Sequencers. The Hamilton combines pre-aliquoted templates and reaction mixes consisting of deoxy- and dideoxynucleotides, the thermostable Taq DNA polymerase, fluorescently-labeled sequencing primers, and reaction buffer. Reaction mixes and templates were combined in the wells of a 96-well thermocycling plate and transferred to the Perkin Elmer 9600 thermocycler. Thirty consecutive cycles of linear amplification (i.e.., one primer synthesis) steps were performed including denaturation, annealing of primer and template, and extension; i.e., DNA synthesis. A heated lid with rubber gaskets on the thermocycling plate prevents evaporation without the need for an oil overlay.  
     [0259] Two sequencing protocols were used: one for dye-labeled primers and a second for dye-labeled dideoxy chain terminators. The shotgun sequencing involves use of four dye-labeled sequencing primers, one for each of the four terminator nucleotide. Each dye-primer was labeled with a different fluorescent dye, permitting the four individual reactions to be combined into one lane of the 373 or 377 DNA Sequencer for electrophoresis, detection, and base-calling. ABI currently supplies pre-mixed reaction mixes in bulk packages containing all the necessary non-template reagents for sequencing. Sequencing can be done with both plasmid and PCR- generated templates with both dye-primers and dye-terminators with approximately equal fidelity, although plasmid templates generally give longer usable sequences.  
     [0260] Thirty-two reactions were loaded per ABI 373 Sequencer each day and 96 samples can be loaded on an ABI 377 per day. Electrophoresis was run overnight (ABI 373) or for 2½ hours (ABI 377) following the manufacturer&#39;s protocols. Following electrophoresis and fluorescence detection, the ABI 373 or ABI 377 performs automatic lane tracking and base-calling. The lane-tracking was confirmed visually. Each sequence electropherogram (or fluorescence lane trace) was inspected visually and assessed for quality. Trailing sequences of low quality were removed and the sequence itself was loaded via software to a Sybase database (archived daily to 8 mm tape). Leading vector polylinker sequence was removed automatically by a software program. Average edited lengths of sequences from the standard ABI 373 or ABI 377 were around 400 bp and depend mostly on the quality of the template used for the sequencing reaction.  
     [0261] Imformatics  
     [0262] 1. Data Management  
     [0263] A number of information management systems for a large-scale sequencing lab have been developed. (For review see, for instance, Kerlavage et al.,  Proceedings of the Twenty - Sixth Annual Hawaii International Conference on System Sciences,  IEEE Computer Society Press, Wash. D.C., 585 (1993)) The system used to collect and assemble the sequence data was developed using the Sybase relational database management system and was designed to automate data flow wherever possible and to reduce user error. The database stores and correlates all information collected during the entire operation from template preparation to final analysis of the genome. Because the raw output of the ABI 373 Sequencers was based on a Macintosh platform and the data management system chosen was based on a Unix platform, it was necessary to design and implement a variety of multi- user, client-server applications which allow the raw data as well as analysis results to flow seamlessly into the database with a minimum of user effort.  
     [0264] 2. Assembly  
     [0265] An assembly engine (TIGR Assembler) developed for the rapid and accurate assembly of thousands of sequence fragments was employed to generate contigs. The TIGR assembler simultaneously clusters and assembles fragments of the genome. In order to obtain the speed necessary to assemble more than 10 4  fragments, the algorithm builds a hash table of 12 bp oligonucleotide subsequences to generate a list of potential sequence fragment overlaps. The number of potential overlaps for each fragment determines which fragments are likely to fall into repetitive elements. Beginning with a single seed sequence fragment, TIGR Assembler extends the current contig by attempting to add the best matching fragment based on oligonucleotide content. The contig and candidate fragment are aligned using a modified version of the Smith-Waterman algorithm which provides for optimal gapped alignments (Waterman, M. S.,  Methods in Enzymology  164: 765 (1988)). The contig is extended by the fragment only if strict criteria for the quality of the match are met. The match criteria include the minimum length of overlap, the maximum length of an unmatched end, and the minimum percentage match. These criteria are automatically lowered by the algorithm in regions of minimal coverage and raised in regions with a possible repetitive element. The number of potential overlaps for each fragment determines which fragments are likely to fall into repetitive elements. Fragments representing the boundaries of repetitive elements and potentially chimeric fragments are often rejected based on partial mismatches at the ends of alignments and excluded from the current contig. TIGR Assembler is designed to take advantage of clone size information coupled with sequencing from both ends of each template. It enforces the constraint that sequence fragments from two ends of the same template point toward one another in the contig and are located within a certain ranged of base pairs (definable for each clone based on the known clone size range for a given library).  
     [0266] 3. Identifying Genes  
     [0267] Tables 1, 2, and 3 list ORFs in the  Staphylococcus aureus  genomic contigs of the present invention that were identified as putative coding regions by the GeneMark software using organism-specific second-order Markov probability transition matrices. It will be appreciated that other criteria can be used, in accordance with well known analytical methods, such as those discussed herein, to generate more inclusive, more restrictive, or more selective lists.  
     [0268] Table 1 sets out ORFs in the  Staphylococcus aureus  contigs of the present invention that over a continuous region of at least 50 bases are 95% or more identical (by BLASTN analysis) to a nucleotide sequence available through Genbank in November 1996.  
     [0269] Table 2 sets out ORFs in the  Staphylococcus aureus  contigs of the present invention that are not in Table 1 and match, with a BLASTP probability score of 0.01 or less, polypeptide sequence available through a non-redundant database of known protein generated by combining the Swiss-Prot, PIR, and GenPept databases.  
     [0270] Table 3 sets out the remaining ORFs in the  Staphylococcus aureus  contigs of the present invention, which did not have significant matches to the public databases by the criteria described above.  
     [0271] Illustrative Applications  
     [0272] 1. Production of an Antibody to a  Staphylococcus aureus  Protein  
     [0273] Substantially pure protein or polypeptide is isolated from the transfected or transformed cells using any one of the methods known in the art. The protein can also be produced in a recombinant prokaryotic expression system, such as  E. coli,  or can by chemically synthesized. Concentration of protein in the final preparation is adjusted, for example, by concentration on an Amicon filter device, to the level of a few micrograms/ml. Monoclonal or polyclonal antibody to the protein can then be prepared as follows.  
     [0274] 2. Monoclonal Antibody Production by Hybridoma Fusion  
     [0275] Monoclonal antibody to epitopes of any of the peptides identified and isolated as described can be prepared from murine hybridomas according to the classical method of Kohler, G. and Milstein, C., Nature 256:495 (1975) or modifications of the methods thereof. Briefly, a mouse is repetitively inoculated with a few micrograms of the selected protein over a period of a few weeks. The mouse is then sacrificed, and the antibody producing cells of the spleen isolated. The spleen cells are fused by means of polyethylene glycol with mouse myeloma cells, and the excess unfused cells destroyed by growth of the system on selective media comprising aminopterin (HAT media). The successfully fused cells are diluted and aliquots of the dilution placed in wells of a microtiter plate where growth of the culture is continued. Antibody-producing clones are identified by detection of antibody in the supernatant fluid of the wells by immunoassay procedures, such as ELISA, as originally described by Engvall, E., Meth. Enzymol. 70:419 (1980), and modified methods thereof. Selected positive clones can be expanded and their monoclonal antibody product harvested for use. Detailed procedures for monoclonal antibody production are described in Davis, L. et al. Basic Methods in Molecular Biology Elsevier, New York. Section 21-2 (1989).  
     [0276] 3. Polyclonal Antibody Production by Immunization  
     [0277] Polyclonal antiserum containing antibodies to heterogenous epitopes of a single protein can be prepared by immunizing suitable animals with the expressed protein described above, which can be unmodified or modified to enhance immunogenicity. Effective polyclonal antibody production is affected by many factors related both to the antigen and the host species. For example, small molecules tend to be less immunogenic than other and may require the use of carriers and adjuvant. Also, host animals vary in response to site of inoculations and dose, with both inadequate or excessive doses of antigen resulting in low titer antisera. SmaII doses (ng level) of antigen administered at multiple intradermal sites appears to be most reliable. An effective immunization protocol for rabbits can be found in Vaitukaitis, J. et al., J. Clin. Endocrinol. Metab. 33:988-991 (1971).  
     [0278] Booster injections can be given at regular intervals, and antiserum harvested when antibody titer thereof, as determined semi-quantitatively, for example, by double immunodiffusion in agar against known concentrations of the antigen, begins to fall. See, for example, Ouchterlony, O. et al, Chap. 19 in: Handbook of Experimental Immunology, Wier, D., ed, Blackwell (1973). Plateau concentration of antibody is usually in the range of 0.1 to 0. 2 mg/ml of serum (about 12M). Affinity of the antisera for the antigen is determined by preparing competitive binding curves, as described, for example, by Fisher, D., Chap. 42 in: Manual of Clinical Immunology, second edition, Rose and Friedman, eds., Amer. Soc. For Microbiology, Wash., D.C. (1980)  
     [0279] Antibody preparations prepared according to either protocol are useful in quantitative immunoassays which determine concentrations of antigen-bearing substances in biological samples; they are also used semi-quantitatively or qualitatively to identify the presence of antigen in a biological sample. In addition, they are useful in various animal models of Staphylococcal disease known to those of skill in the art as a means of evaluating the protein used to make the antibody as a potential vaccine target or as a means of evaluating the antibody as a potential immunothereapeutic reagent.  
     [0280] 4. Preparation of PCR Primers and Amplification of DNA  
     [0281] Various fragments of the  Staphylococcus aureus  genome, such as those of Tables 1-3 and SEQ ID NOS: 1-5,191 can be used, in accordance with the present invention, to prepare PCR primers for a variety of uses. The PCR primers are preferably at least 15 bases, and more preferably at least 18 bases in length. When selecting a primer sequence, it is preferred that the primer pairs have approximately the same G/C ratio, so that melting temperatures are approximately the same. The PCR primers and amplified DNA of this Example find use in the Examples that follow.  
     [0282] 5. Gene Expression from DNA Sequences Corresponding to ORFs  
     [0283] A fragment of the  Staphylococcus aureus  genome provided in Tables 1-3 is introduced into an expression vector using conventional technology. Techniques to transfer cloned sequences into expression vectors that direct protein translation in mammalian, yeast, insect or bacterial expression systems are well known in the art. Commercially available vectors and expression systems are available from a variety of suppliers including Stratagene (La Jolla, Calif.), Promega (Madison, Wis.), and Invitrogen (San Diego, Calif.). If desired, to enhance expression and facilitate proper protein folding, the codon context and codon pairing of the sequence may be optimized for the particular expression organism, as explained by Hatfield et al., U.S. Pat. No. 5,082,767, incorporated herein by this reference.  
     [0284] The following is provided as one exemplary method to generate polypeptide(s) from cloned ORFs of the  Staphylococcus aureus  genome fragment. Bacterial ORFs generally lack a poly A addition signal. The addition signal sequence can be added to the construct by, for example, splicing out the poly A addition sequence from pSG5 (Stratagene) using BglI and SalI restriction endonuclease enzymes and incorporating it into the mammalian expression vector pXT1 (Stratagene) for use in eukaryotic expression systems. pXT1 contains the LTRs and a portion of the gag gene of Moloney Murine Leukemia Virus. The positions of the LTRs in the construct allow efficient stable transfection. The vector includes the Herpes Simplex thymidine kinase promoter and the selectable neomycin gene. The  Staphylococcus aureus  DNA is obtained by PCR from the bacterial vector using oligonucleotide primers complementary to the  Staphylococcus aureus  DNA and containing restriction endonuclease sequences for PstI incorporated into the 5′ primer and BglII at the 5′ end of the corresponding  Staphylococcus aureus  DNA 3′ primer, taking care to ensure that the  Staphylococcus aureus  DNA is positioned such that its followed with the poly A addition sequence. The purified fragment obtained from the resulting PCR reaction is digested with PstI, blunt ended with an exonuclease, digested with BglII, purified and ligated to pXT1, now containing a poly A addition sequence and digested BglII.  
     [0285] The ligated product is transfected into mouse NIH 3T3 cells using Lipofectin (Life Technologies, Inc., Grand Island, N.Y.) under conditions outlined in the product specification. Positive transfectants are selected after growing the transfected cells in 600 ug/ml G418 (Sigma, St. Louis, Mo.). The protein is preferably released into the supernatant. However if the protein has membrane binding domains, the protein may additionally be retained within the cell or expression may be restricted to the cell surface. Since it may be necessary to purify and locate the transfected product, synthetic 15-mer peptides synthesized from the predicted  Staphylococcus aureus  DNA sequence are injected into mice to generate antibody to the polypeptide encoded by the  Staphylococcus aureus  DNA.  
     [0286] Alternatively and if antibody production is not possible, the  Staphylococcus aureus  DNA sequence is additionally incorporated into eukaryotic expression vectors and expressed as, for example, a globin fusion. Antibody to the globin moiety then is used to purify the chimeric protein. Corresponding protease cleavage sites are engineered between the globin moiety and the polypeptide encoded by the  Staphylococcus aureus  DNA so that the latter may be freed from the formed by simple protease digestion. One useful expression vector for generating globin chimerics is pSG5 (Stratagene). This vector encodes a rabbit globin. Intron II of the rabbit globin gene facilitates splicing of the expressed transcript, and the polyadenylation signal incorporated into the construct increases the level of expression. These techniques are well known to those skilled in the art of molecular biology. Standard methods are published in methods texts such as Davis et al., cited elsewhere herein, and many of the methods are available from the technical assistance representatives from Stratagene, Life Technologies, Inc., or Promega. Polypeptides of the invention also may be produced using in vitro translation systems such as in vitro Express™ Translation Kit (Stratagene).  
     [0287] While the present invention has been described in some detail for purposes of clarity and understanding, one skilled in the art will appreciate that various changes in form and detail can be made without departing from the true scope of the invention.  
     [0288] All patents, patent applications and publications referred to above are hereby incorporated by reference.  
               TABLE 1                            S. aureus  - Coding regions containing known sequences                                                                             HSP   ORF        Contig ID   ORF ID   Start (nt)   Stop (nt)   match acession   match gene name   percent ident   nt length   nt length                                                         1   1   757   95   emb|X17301|SAHD     S. aureus  DNA for hld gene and for part of agr gene   100   663   663       1   2   2452   1631   emb|X52543|SAAG     S. aureus  agrA, agrB and hld genes   99   809   822       1   5   5651   4884   dbj|D14711|STAH     Staphylococcus aureus  HSP10 and HSP60 genes   98   223   768       5   1   439   71   emb|X72700|SAPV     S. aureus  genes for S and F components of Panton-Valentine leucocidins   81   216   369       5   4   3571   2111   emb|X72700|SAPV     S. aureus  genes for S and F components of Panton-Valentine leucocidins   95   424   1461       10   1   86   904   gb|L25288|     Staphylococcus aureus  gyrase-like protein alpha and beta subunit (grlA and   98   715   819                           grlB) genes, complete cds       16   5   5302   6246   gb|U35773|     Staphylococcus aureus  prolipoprotein diacylglyceryl transferase (lgt) gene, complete cds   94   251   945                                   16   6   6249   7091   gb|U35773|     Staphylococcus aureus  prolipoprotein diacylglyceryl transferase (lgt) gene,   99   843   843                           complete cds       16   7   7084   7584   gb|U35773|     Staphylococcus aureus  prolipoprotein diacylglyceryl transferase (lgt) gene,   99   342   501                           complete cds       20   1   549   103   gb|L19300|     Staphylococcus aureus  DNA sequence encoding three ORFs, complete cds; prophage phi-11   100   443   447                           sequence homology, 5′ flank       20   2   841   671   gb|L19300|     Staphylococcus aureus  DNA sequence encoding three ORFs, complete cds; prophage phi-11   91   137   171                           sequence homology, 5′ flank       20   3   1798   1586   gb|L19300|     Staphylococcus aureus  DNA sequence encoding three ORFs, complete cds; prophage phi-11   100   110   213                           sequence homology, 5′ flank       20   4   3825   2350   gb|M76714|     Staphylococcus aureus  peptidoglycan hydrolase gene, complete cds   100   948   1476       20   5   4282   3776   gb|M76714|     Staphylococcus aureus  peptidoglycan hydrolase gene, complete cds   100   309   507       26   1   2   145   gb|U41072|     Staphylococcus aureus  isoleucyl-tRNA synthetase (ileS) gene, partial cds   100   126   144       26   2   84   557   gb|U41072|     Staphylococcus aureus  isoleucyl-tRNA synthetase (ileS) gene, partial cds   99   430   474       26   3   763   3531   emb|X74219|SAIL     S. aureus  gene for isoleucyl-tRNA synthetase   99   2769   2769       29   3   1261   4392   gb|U66665|     Staphylococcus aureus  DNA fragment with class II promoter activity   100   117   3132       31   14   13463   11949   emb|X73889|SAP1     S. aureus  genes P1 and P2   99   1351   1515       31   15   13855   13469   emb|X73889|SAP1     S. aureus  genes P1 and P2   98   258   387       38   17   13112   11940   gb|M12715|     S. aureus  geh gene encoding lipase (glycerol ester hydrolase)   100   372   1173       38   19   13434   15518   gb|M12715|     S. aureus  geh gene encoding lipase (glycerol ester hydrolase)   100   2085   2085       46   2   519   1727   gb|U73374|     Staphylococcus aureus  type 8 capsule genes, cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G,   98   1209   1209                           cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,                           cap8O, cap8P, complete cds       46   3   1720   2295   gb|U73374|     Staphylococcus aureus  type 8 capsule genes, cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G,   98   576   576                           cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,                           cap8O, cap8P, complete cds       46   4   2259   3182   gb|U73374|     Staphylococcus aureus  type 8 capsule genes, cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G,   97   924   924                           cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,                           cap8O, cap8P, complete cds       46   5   3173   4498   gb|U73374|     Staphylococcus aureus  type 8 capsule genes, cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G,   98   1283   1326                           cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,                           cap8O, cap8P, complete cds       46   6   4536   5720   gb|U73374|     Staphylococcus aureus  type 8 capsule genes, cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G,   98   1185   1185                           cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,                           cap8O, cap8P, complete cds       46   7   6120   5785   gb|U73374|     Staphylococcus aureus  type 8 capsule genes, cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G,   99   278   336                           cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,                           cap8O, cap8P, complete cds       48   1   2   955   gb|L25893|     Staphylococcus aureus  recA gene, complete cds   99   954   954       50   3   2924   1383   emb|X85029|SAAH     S. aureus  AhpC gene   100   88   1542       50   4   3515   2922   emb|X85029|SAAH     S. aureus  AhpC gene   98   540   594       54   3   3392   1710   emb|X62992|SAFN     S. aureus  fnbB gene for fibronectin binding protein B   100   1668   1683       54   4   4122   3379   emb|X62992|SAFN     S. aureus  fnbB gene for fibronectin binding protein B   99   720   744       54   5   4562   4068   emb|X62992|SAFN     S. aureus  fnbB gene for fibronectin binding protein B   100   463   495       54   6   8300   5214   gb|J04151|     S. aureus  fibronectin-binding protein (fnbA) mRNA, complete cds   100   3087   3087       58   3   1743   2819   emb|X87104|SADN     S. aureus  mdr, pbp4 and taqD genes (SG511-55 isolate)   89   68   1077       58   4   2858   3280   emb|X91786|SAPB     S. aureus  abcA, pbp4, and tagD genes   99   423   423       58   5   4701   3397   emb|X91786|SAPB     S. aureus  abcA, pbp4, and tagD genes   99   1305   1305       58   6   5378   5079   gb|U29478|     Staphylococcus aureus  ABC transporter-like protein AbcA (abcA) gene,   100   300   300                           partial cds       58   7   5086   6840   emb|X91786|SAPB     S. aureus  abcA, pbp4, and tagD genes   99   1755   1755       72   1   445   2   gb|M21854|     S. aureus  agr gene encoding an accessory gene regulator protein, complete   100   444   444                           cds       72   2   1453   449   emb|X52543|SAAG     S. aureus  agrA, agrB and hld genes   99   673   1005       82   1   357   3917   emb|X64172|SARP     S. aureus  rp1L, orf202, rpoB(rif) and rpoC genes for ribosomal protein   99   2396   3561                           L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &amp;                           beta’ chains       82   2   4027   7677   emb|X89233|SARP     S. aureus  DNA for rpoC gene   99   3171   3651       82   3   7745   8068   gb|U20869|     Staphylococcus aureus  ribosomal protein S12 (rpsL) gene, complete cds,   100   320   324                           ribosomal protein S7 (rpsG) and ORF 1 genes, partial cds       82   4   8103   8579   gb|U20869|     Staphylococcus aureus  ribosomal protein S12 (rpsL) gene, complete cds,   100   477   477                           ribosomal protein S7 (rpsG) and ORF 1 genes, partial cds       82   5   8618   8821   gb|U20869|     Staphylococcus aureus  ribosomal protein S12 (rpsL) gene, complete cds,   100   154   204                           ribosomal protein S7 (rpsG) and ORF 1 genes, partial cds       84   1   18   191   gb|U73374|     Staphylococcus aureus  type 8 capsule genes, cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G,   98   164   174                           cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,                           cap8O, cap8P, complete cds       84   2   189   893   gb|U73374|     Staphylococcus aureus  type 8 capsule genes, cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G,   94   705   705                           cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,                           cap8O, cap8P, complete cds       84   3   887   1660   gb|U73374|     Staphylococcus aureus  type 8 capsule genes, cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G,   99   774   774                           cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,                           cap8O, cap8P, complete cds       84   4   1584   3503   gb|U73374|     Staphylococcus aureus  type 8 capsule genes, cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G,   98   1920   1920                           cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,                           cap8O, cap8P, complete cds       84   5   3394   4521   gb|U73374|     Staphylococcus aureus  type 8 capsule genes, cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G,   97   1128   1128                           cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,                           cap8O, cap8P, complete cds       84   6   4519   5643   gb|U73374|     Staphylococcus aureus  type 8 capsule genes, cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G,   97   1125   1125                           cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,                           cap8O, cap8P, complete cds       96   2   1245   3896   emb|Z18852|SACF     S. aureus  gene for clumping factor   83   660   2652       97   2   625   882   gb|U41072|     Staphylococcus aureus  isoleucyl-tRNA synthetase (ileS) gene, partial cds   97   68   258       111   1   3   452   gb|L41499|     Staphylococcus aureus  ORF1, partial cds, ORF2, ORF3, autolysin (atl) genes,   100   450   450                           complete cds       111   2   526   1041   gb|L41499|     Staphylococcus aureus  ORF1, partial cds, ORF2, ORF3, autolysin (atl) genes,   99   516   516                           complete cds       117   2   1278   1958   gb|M83994|     Staphylococcus aureus  prolipoprotein signal peptidase (lsp) gene, complete   100   61   681                           cds       118   4   3787   4254   dbj|D30690|STAN     Staphylococcus aureus  genes for ORF37; HSP20; HSP70; HSP40; ORF35, complete   99   467   468                           cds       130   4   2597   3640   emb|X13290|SATN     Staphylococcus aureus  multi-resistance plasmid pSK1 DNA containing   78   956   1044                           transposon Tn4003       130   5   3813   4265   emb|z16422|SADI     S. aureus  dfrB gene for dihydrofolate reductase   98   416   453       130   6   4309   5172   emb|z16422|SADI     S. aureus  dfrB gene for dihydrofolate reductase   98   607   864       136   4   5296   6207   emb|X71437|SAGY     S. aureus  genes gyrB, gyrA and recF (partial)   97   838   912       136   5   8987   6294   dbj|D10489|STAG     Staphylococcus aureus  genes for DNA gyrase A and B, complete cds   100   2694   2694       136   6   10940   8994   dbj|D10489|STAG     Staphylococcus aureus  genes for DNA gyrase A and B, complete cds   99   1947   1947       136   7   11765   10938   gb|S77055|   recF cluster: dnaA = replisome assembly protein...gyrB = DNA gyrase beta   99   822   828                           subunit [ Staphylococcus aureus , YB886, Genomic, 5 genes, 3573 nt]       143   3   2867   1563   gb|U36379|     Staphylococcus aureus  S-adenosylmethionine synthetase gene, complete cds   99   1305   1305       143   4   3100   4281   gb|L42943|     Staphylococcus aureus  (clone KIN50) phosphoenolpyruvate carboxykinase   100   1170   1182                           (pckA) gene, complete cds       143   5   4254   4718   gb|U51133|     Staphylococcus aureus  phosphoenolpyruvate carboxykinase (pcka) gene,   100   449   465                           complete cds       143   9   6977   7261   gb|U51132|     Staphylococcus aureus  o-succinylbenzoic acid CoA ligase (mene), and o-   100   75   285                           succinylbenzoic acid synthetase (menc) genes, complete cds       143   10   8361   7258   gb|U51132|     Staphylococcus aureus  o-succinylbenzoic acid CoA ligase (mene), and o-   100   1104   1104                           succinylbenzoic acid synthetase (menc) genes, complete cds       143   11   9748   8264   gb|U51132|     Staphylococcus aureus  o-succinylbenzoic acid CoA ligase (mene), and o-   100   1485   1485                           succinylbenzoic acid synthetase (menc) genes, complete cds       143   12   10320   9901   gb|U51132|     Staphylococcus aureus  o-succinylbenzoic acid CoA ligase (mene), and o-   100   332   420                           succinylbenzoic acid synthetase (mene) genes, complete cds       152   5   2454   3437   emb|X58434|SAPD     S. aureus  pdhB, pdhC and pdhD genes for pyruvate decarboxylase,   99   305   984                           dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase       152   6   3513   4820   emb|X58434|SAPD     S. aureus  pdhB, pdhC and pdhD genes for pyruvate decarboxylase,   98   1308   1308                           dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase       152   7   4818   6230   emb|X58434|SAPD     S. aureus  pdhB, pdhC and pdhD genes for pyruvate decarboxylase,   99   1413   1413                           dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase       153   1   387   1526   gb|S77055|   recF cluster: dnaA = replisome assembly protein.. .gyrB = DNA gyrase beta   99   1140   1140                           subunit [ Staphylococcus aureus , YB886, Genomic, 5 genes, 3573 nt]       153   2   1877   2152   gb|S77055|   recF cluster: dnaA = replisome assembly protein...gyrB = DNA gyrase beta   100   276   276                           subunit [ Staphylococcus aureus , YB886, Genomic, 5 genes, 3573 nt]       153   3   2143   2289   gb|S77055|   recF cluster; dnaA = replisome assembly protein...gyrB = DNA gyrase beta   99   113   147                           subunit [ Staphylococcus aureus , YB886, Genomic, 5 genes, 3573 nt]       154   10   9314   7836   gb|U06451|     Staphylococcus aureus  proline permease homolog (putP) gene, complete cds   91   154   1479       154   11   9615   9295   gb|U06451|     Staphylococcus aureus  proline permease homolog (putP) gene, complete cds   99   229   321       154   12   9943   10167   gb|U06451|     Staphylococcus aureus  proline permease homolog (putP) gene, complete cds   94   123   225       154   13   10089   11501   gb|U06451|     Staphylococcus aureus  proline permease homolog (putP) gene, complete cds   99   1326   1413       159   2   1212   229   dbj|D28879|STAP     Staphylococcus aureus  gene for penicillin-binding protein 1, complete cds   100   71   984       161   3   2270   1944   gb|M83994|     Staphylococcus aureus  prolipoprotein signal peptidase (lsp) gene, complete   92   203   327                           cds       162   1   705   4   gb|U21221|     Staphylococcus aureus  hyaluronate lyase (hysA) gene, complete cds   100   702   702       163   4   1263   1772   gb|U19770|     Staphylococcus aureus  pyrrolidone carboxyl peptidase (pcp) gene, complete   96   127   510                           cds       164   7   4774   9117   dbj|D86727|D867     Staphylococcus aureus  DNA for DNA polymerase III, complete cds   99   3470   4344       168   7   6447   5446   gb|U21636|     Staphylococcus aureus  cmp-binding-factor 1 (cbf1) and ORF X genes, complete   100   1002   1002                           cds       168   8   7961   6384   gb|U21636|     Staphylococcus aureus  cmp-binding-factor 1 (cbf1) and ORF X genes, complete   99   1158   1578                           cds       173   6   7801   6362   gb|J03479|     S. aureus  enzyme III-lac (lacF), enzyme II-lac (lacE), and phospho-beta-   100   1440   1440                           galactosidase (lacG) genes, complete cds       173   7   9522   7792   gb|J03479|     S. aureus  enzyme III-lac (lacF), enzyme II-lac (lacE), and phospho-beta-   99   1731   1731                           galactosidase (lacG) genes, complete cds       173   8   8285   8704   gb|J03479|     S. aureus  enzyme III-lac (lacF), enzyme II-lac (lacE), and phospho-beta-   100   420   420                           galactosidase (lacG) genes, complete cds       173   9   9839   9510   gb|J03479|     S. aureus  enzyme III-lac (lacF), enzyme II-lac (lacE), and phospho-beta-   100   330   330                           galactosidase (lacG) genes, complete cds       173   10   10829   9843   emb|X14827|SALA     Staphylococcus aureus  lacC and lacD genes   100   987   987       173   11   11774   10827   emb|X14827|SALA     Staphylococcus aureus  lacC and lacD genes   100   948   948       173   12   12305   11772   gb|M64724|     S. aureus  tagatose 6-phosphate isomerase gene, complete cds   100   534   534       173   13   12773   12303   gb|M32103|     Staphylococcus aureus  lac repressor (lacR) gene, complete cds and lacA   100   471   471                           repressor (lacA), partial cds       173   14   13866   13099   gb|M32103|     Staphylococcus aureus  lac repressor (lacR) gene, complete cds and lacA   100   768   768                           repressor (lacA), partial cds       178   1   2   655   gb|U52961|     Staphylococcus aureus  holin-like protein LrgA (lrgA) and LrgB (lrgB) genes,   100   115   654                           complete cds       178   2   1482   763   gh|U52961|     Staphylococcus aureus  holin-like protein LrgA (lrgA) and LrgB (lrgB) genes,   100   720   720                           complete cds       178   3   1909   1457   gb|U52961|     Staphylococcus aureus  holin-like protein LrgA (lrgA) and LrgB (lrgB) genes,   100   453   453                           complete cds       178   4   1551   1853   gb|U52961|     Staphylococcus aureus  holin-like protein LrgA (lrgA) and LrgB (lrgB) genes,   100   303   303                           complete cds       178   5   2777   2013   gb|L42945|     Staphylococcus aureus  lytS and lytR genes, complete cds   99   765   765       178   6   3025   2756   gb|L42945|     Staphylococcus aureus  lytS and lytR genes, complete cds   99   270   270       181   1   590   66   gb|M63177|     S. aureus  sigma factor (plaC) gene, complete cds   99   499   525       182   1   3   341   emb|X61307|SASP     Staphylococcus aureus  spa gene for protein A   98   277   339       182   2   690   2312   gb|J01786|     S. aureus  spa gene coding for protein A, complete csd   97   1332   1623       182   3   4251   2641   emb|X61307|SASP     Staphylococcus aureus  spa gene for protein A   99   119   1611       185   1   3   824   gb|U31979|     Staphylococcus aureus  chorismate synthase (aroC) and nucleoside diphosphate   90   132   822                           kinase (ndk) genes, complete cds, dehydroauinate synthase (aroB) and                           geranylgeranyl pyrophosphate synthetase homolog (gerCC) genes, partial cds       191   3   841   2760   emb|X17679|SACO     Staphylococcus aureus  coa gene for coagulase   99   1920   1920       191   4   2967   3143   emb|X16457|SAST     Staphylococcus aureus  gene for staphylocoagulase   99   177   177       191   5   4566   3364   emb|X16457|SAST     Staphylococcus aureus  gene for staphylocoagulase   99   250   1203       196   1   872   3   gb|L36472|     Staphylococcus aureus  lysyl-tRNA sythetase gene, complete cds, transfer RNA   99   870   870                           (tRNA) genes, 5S ribosomal RNA (5S rRNA) gene, 16S ribosomal RNA (16S                           rRNA) gene, 23S ribosomal RNA (23S rRNA) gene       198   3   1688   2011   emb|X93205|SAPT     S. aureus  ptsH and ptsI genes   99   324   324       198   4   2005   2310   emb|X93205|SAPT     S. aureus  ptsH and ptsI genes   97   304   306       202   1   163   1305   emb|X97985|SA12     S. aureus  orfs 1,2,3 &amp; 4   99   1143   1143       202   2   1303   2175   emb|X73889|SAP1     S. aureus  genes P1 and P2   94   444   873        210   1   1558   2   dbj|D17366|STAA     Staphylococcus aureus  atl gene for autolysin, complete cds and other ORFs   99   1552   1557       210   2   2232   1525   gb|L41499|     Staphylococcus aureus  ORF1, partial cds, ORF2, ORF3, autolysin (atl) genes,   99   684   708                           complete cds       214   11   7429   7770   dbj|D86240|D862     Staphylococcus aureus  gene for unkown function and dlt operon dltA, dltB,   96   157   342                           dltC and dltD genes, complete cds       216   3   398   1318   emb|X72700|SAPV     S. aureus  genes for S and F components of Panton-Valentine leucocidins   88   265   921       219   2   1073   336   dbj|D30690|STAN     Staphylococcus aureus  genes for ORF37; HSP20; HSP70; HSP40; ORF35, complete   100   60   738                           cds       219   3   2035   1091   dbj|D30690|STAN     Staphylococcus aureus  genes for ORF37; HSP20; HSP70; HSP40; ORF35, complete   99   945   945                           cds       219   4   3196   2033   dbj|D30690|STAN     Staphylococcus aureus  genes for ORF37; HSP20; HSP70; HSP40; ORF35, complete   99   1164   1164                           cds       219   5   5176   3308   dbj|D30690|STAN     Staphylococcus aureus  genes for ORF37; HSP20; HSP70; HSP40; ORF35, complete   98   1869   1869                           cds       219   6   5883   5209   dbj|D30690|STAN     Staphylococcus aureus  genes for ORF37; HSP20; HSP70; HSP40, ORF35, complete   99   675   675                           cds       219   7   6334   5867   dbj|D30690|STAN     Staphylococcus aureus  genes for ORF37; HSP20; HSP70; HSP40; ORF35, complete   98   468   468                           cds       221   8   10034   9252   gb|L19298|     Staphylococcus aureus  phosphatidylinositol-specific phospholipase C (plc)   91   67   783                           gene, complete cds       223   1   1506   157   gb|U73374|     Staphylococcus aureus  type 8 capsule genes, cap8A, cap8B, cap8C, cap8D,   99   102   1350                           cap8E, cap8F, cap8G, cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,                           cap8O, cap8P, complete cds       234   1   2   1357   emb|X97985|SA12     S. aureus  orfs 1,2,3 &amp; 4   100   176   1356       234   2   1694   2485   emb|X97985|SA12     S. aureus  orfs 1,2,3 &amp; 4   100   792   792       234   3   2648   3148   emb|X97985|SA12     S. aureus  orfs 1,2,3 &amp; 4   99   501   501       234   4   3120   4604   emb|X97985|SA12     S. aureus  orfs 1,2,3 &amp; 4   99   1305   1485       236   6   3826   5322   gb|U48826|     Staphylococcus aureus  elastin binding protein (ebpS) gene, complete cds   96   648   1497       248   1   2   403   emb|X62288|SAPE     S. aureus  DNA for penicillin-binding protein 2   100   103   402       248   2   388   852   gb|L25426|     Staphylococcus aureus  penicillin-binding protein 2 (pbp2) gene, complete   99   465   465                           cds       253   2   1093   647   gb|U46541|     Staphylococcus aureus  sarA gene, complete cds   96   447   447       254   2   150   1835   gb|U57060|     Staphylococcus aureus  scdA gene, complete cds   94   142   1686       254   3   1973   2728   gb|U57060|     Staphylococcus aureus  scdA gene, complete cds   99   756   756       260   1   2   1900   gb|M90693|     Staphylococcus aureus  glycerol ester hydrolase (lip) gene, complete cds   99   1213   1899       265   1   1   942   dbj|D21131|STAS     Staphylococcus aureus  gene for a participant in homogeneous expression of   99   941   942                           high-level methicillin resistance, complete cds       265   2   476   264   dbj|D21131|STAS     Staphylococcus aureus  gene for a participant in homogeneous expression of   99   213   213                           high-level methicillin resistance, complete cds       265   3   1765   1112   dbj|D21131|STAS     Staphylococcus aureus  gene for a participant in homogeneous expression of   98   69   654                           high-level methicillin resistance, complete cds       266   1   2   1018   dbj|D14711|STAH     Staphylococcus aureus  HSP10 and HSP60 genes   98   743   1017       282   1   1   525   gb|S72488|   hemB = porphobilinogen synthase [ Staphylococcus aureus , SA1959, Genomic, 1087   100   110   525                           nt]       282   2   516   1502   gb|S72488|   hemB = porphobilinogen synthase [ Staphylococcus aureus , SA1959, Genomic, 1087   100   952   987                           nt]       284   1   3   170   gb|M63176|     Staphylococcus aureus  helicase required for T181 replication (pcrA) gene,   98   84   168                           complete cds       284   2   282   1034   gb|M63176|     Staphylococcus aureus  helicase required for T181 replication (pcrA) gene,   100   712   753                           complete cds       284   3   1028   2026   gb|M63176|     Staphylococcus aureus  helicase required for T181 replication (pcrA) gene,   99   979   999                           complete cds       284   4   1990   2202   gb|M63176|     Staphylococcus aureus  helicase required for T181 replication (pcrA) gene,   98   187   213                           complete cds       289   3   1536   1991   gb|M32470|     S. aureus  Sau3AI-restriction-enzyme and Sau3AI-modification-enzyme genes,   99   338   456                           complete cds       303   1   2   868   gb|L01055|     Staphylococcus aureus  gamma-hemolysin components A, B and C (hlgA, hlgB,   99   867   867                           hglC) genes, complete cds       303   2   1409   2383   gb|L01055|     Staphylococcus aureus  gamma-hemolysin components A, B and C (hlgA, hlgB,   100   975   975                           hglC) genes, complete cds       303   3   2367   3161   gb|L01055|     Staphylococcus aureus  gamma-hemolysin components A, B and C (hlgA, hlgB,   99   793   795                           hglC) genes, complete cds       305   1   1355   3   dbj|D17366|STAA     Staphylococcus aureus  atl gene for autolysin, complete cds and other ORFs   99   1343   1353       311   1   1315   2   gb|L42945|     Staphylococcus aureus  lytS and lytR genes, complete cds   98   1314   1314       312   6   7019   7870   gb|L14017|     Staphylococcus aureus  methicillin-resistance protein (mecR) gene and   74   351   852                           unknown ORF, complete cds       323   1   1003   8   gb|U31175|     Staphylococcus aureus  D-specific D-2-hydroxyacid dehydrogenase (ddh) gene,   98   996   996                           complete cds       326   1   1   237   emb|Y00356|SASP     Staphylococcus aureus  V8 serine protease gene   100   108   237       338   1   388   89   emb|X64389|SALE     S. aureus  leuF-P83 gene for F component of leucocidin R   98   259   300       338   2   1088   348   emb|X64389|SALE     S. aureus  leuF-P83 gene for F component of leucocidin R   97   137   741       342   2   579   1754   gb|U06462|     Staphylococcus aureus  SA4 FtsZ (ftsZ) gene, complete cds   100   1176   1176       344   2   517   1248   emb|V01281|SANU     S. aureus  mRNA for nuclease   98   732   732       349   1   230   3   gb|M20393|     S. aureus  bacteriophage phi-11 attachment site (attB)   96   172   228       353   1   516   16   gb|M83994|     Staphylococcus aureus  prolipoprotein signal peptidase (lsp) gene, complete   100   187   501                           cds       353   2   1046   510   gb|M83994|     Staphylococcus aureus  prolipoprotein signal peptidase (lsp) gene, complete   99   537   537                           cds       356   1   3   674   gb|U20503|     Staphylococcus aureus  MHC class II analog gene, complete cds   75   671   672       361   1   1   903   gb|L19298|     Staphylococcus aureus  phosphatidylinositol-specific phospholipase C (plc)   98   747   903                           gene, complete cds       361   2   1103   1507   gb|L19298|     Staphylococcus aureus  phosphatidylinositol-specific phospholipase C (plc)   97   68   405                           gene, complete cds       373   1   3   1148   emb|X62288|SAPE     S. aureus  DNA for penicillin-binding protein 2   99   1146   1146       389   3   1248   592   emb|X62282|SATS     S. aureus  target site DNA for IS431 insertion   97   349   657       400   1   1   540   emb|X61716|SAHL     S. aureus  hlb gene encoding sphingomyelinase   99   389   540       400   2   1187   681   emb|X13404|SAHL     Staphylococcus aureus  hlb gene for beta-hemolysin   99   178   507       408   1   1049   288   gb|S76213|   asp23 = alkaline shock protein 23 (methicillin resistant) [ Staphylococcus     99   163   762                             aureus , 912, Genomic, 1360 nt]       418   1   2   217   gb|L41499|     Staphylococcus aureus  ORF1, partial cds, ORF2, ORF3, autolysin (at1) genes,   100   216   216                           complete cds       418   2   639   424   dbj|D17366|STAA     Staphylococcus aureus  at1 gene for autolysin, complete cds and other ORFs   100   188   216       421   2   1262   2509   gb|L43098|   Transposon Tn5404 and insertion sequences IS1181 and IS1182 (from   99   1248   1248                             Staphylococcus aureus ) DNA       422   1   2   325   gb|K02985|     S. aureus  (strain RN450) transposon Tn554 insertion site   96   200   324       427   1   434   3   dbj|D28879|STAP     Staphylococcus aureus  gene for penicillin-binding protein 1, complete cds   100   432   432       427   2   1122   415   dbj|D28879|STAP     Staphylococcus aureus  gene for penicillin-binding protein 1, complete cds   100   151   708       435   1   2   808   dbj|D86240|D862     Staphylococcus aureus  gene for unkown function and dlt operon dltA, dltB,   100   556   807                           dltC and dltD genes,complete cds       435   2   832   999   dbj|D86240|D862     Staphylococcus aureus  gene for unkown function and dlt operon dltA, dltB,   100   134   168                           dltC and dltD genes, complete cds       436   1   685   29   emb|X17688|SAFE     S. aureus  factor essential for expression of methicillin resistance (femA)   97   657   657                           gene, complete cds, and trpA gene, 3′ end       436   2   1657   911   emb|X17688|SAFE     S. aureus  factor essential for expression of methicillin resistance (femA)   100   294   747                           gene, complete cds, and trpA gene, 3′ end       442   1   347   1300   emb|X72700|SAPV     S. aureus  genes for S and F components of Panton-Valentine leucocidins   84   204   954       445   2   1906   2178   gb|L01055|     Staphylococcus aureus  gamma-hemolysin components A, B and C (hlgA, hlgB,   98   187   273                           hglC) genes, complete cds       447   1   167   1078   gb|U19770|     Staphylococcus aureus  pyrrolidone carboxyl peptidase (pcp) gene, complete   100   51   912                           cds       447   2   1176   1784   gb|U19770|     Staphylococcus aureus  pyrrolidone carboxyl peptidase (pcp) gene, complete   96   597   609                           cds       454   3   4319   1329   emb|Z18852|SACF     S. aureus  gene for clumping factor   75   653   2991       472   4   5479   3062   gb|L25288|     Staphylococcus aureus  gyrase-like protein alpha and beta subunit (grlA and   99   2418   2418                           grlB) genes, complete cds       472   5   6792   5464   gb|L25288|     Staphylococcus aureus  gyrase-like protein alpha and beta subunit (grlA and   99   1328   1329                           grlB) genes, complete cds       475   2   566   889   emb|X52543|SAAG     S. aureus  agrA, agrB and hld genes   100   76   324       481   4   1560   1198   emb|X64172|SARP     S. aureus  rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein   100   250   363                           L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &amp;                            beta′ chains       481   5   1244   1534   emb|X64172|SARP     S. aureus  rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein   100   224   291                           L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &amp;                           beta′ chains       487   2   1188   988   gb|M83994|     Staphylococcus aureus  prolipoprotein signal peptidase (lsp) gene, complete   98   72   201                           cds       489   1   1370   3   gb|U21221|     Staphylococcus aureus  hyaluronate lyase (hysA) gene, complete cds   99   1368   1368       503   2   653   171   gb|M83994|     Staphylococcus aureus  prolipoprotein signal peptidase (lsp) gene, complete   100   108   483                           cds       511   3   1613   2242   gb|L14017|     Staphylococcus aureus  methicillin-resistance protein (mecR) gene and   84   323   630                           unknown ORF, complete cds       511   4   2700   2278   gb|S76213|   asp23 = alkaline shock protein 23 (methicillin resistant) [ Staphylococcus     96   423   423                             aureus , 912, Genomic, 1360 nt]       520   2   758   1297   emb|X72014|SAFI     S. aureus  fib gene for fibrinogen-binding protein   99   540   540       520   3   1436   1801   emb|X72013|SAFI     S. aureus  fib gene for fibrinogen-binding protein   99   221   366       526   1   1092   34   dbj|D17366|STAA     Staphylococcus aureus  atl gene for autolysin, complete cds and other ORFs   99   641   1059       528   2   58   963   gb|L19300|     Staphylococcus aureus  DNA sequence encoding three ORFs, complete cds;   99   260   906                           prophage phi-11 sequence homology, 5′ flank       528   3   1098   2870   gb|L19300|     Staphylococcus aureus  DNA sequence encoding three ORFs, complete cds;   99   866   1773                           prophage phi-11 sequence homology, 5′ flank       530   1   3   434   gb|U31979|     Staphylococcus aureus  chorismate synthase (aroC) and nucleoside diphosphate   99   432   432                           kinase (ndk) genes, complete cds, dehydroauinate synthase (aroB) and                           geranylgeranyl pyrophosphate synthetase homolog (gerCC) genes, partial cds       530   2   1211   2395   gb|U31979|     Staphylococcus aureus  chorismate synthase (aroC) and nucleoside diphosphate   91   1185   1185                           kinase (ndk) genes; complete cds, dehydroauinate synthase (aroB) and                           geranylgeranyl pyrophosphate synthetase homolog (gerCC) genes, partial cds       530   3   2409   2801   gb|U31979|     Staphylococcus aureus  chorismate synthase (aroC) and nucleoside diphosphate   88   181   393                           kinase (ndk) genes, complete cds, dehydroauinate synthase (aroB) and                           geranylgeranyl pyrophosphate synthetase homolog (gerCC) genes, partial cds       530   4   2690   3484   gb|L05004|     Staphylococcus aureus  dehydroquinate synthase (aroB) gene, 3′ end cds; 3-   100   75   795                           phosphoshikimate-1-carboxyvinyltransferase (aroA) gene, complete cds;                           ORF3, complete cds       530   5   3482   4792   gb|L05004|     Staphylococcus aureus  dehydroquinate synthase (aroB) gene, 3′ end cds; 3-   99   905   1311                           phosphoshikimate-1-carboxyvinyltransferase (aroA) gene, complete cds;                           ORF3, complete cds       530   6   4790   5380   gb|L05004|     Staphylococcus aureus  dehydroquinate synthase (aroB) gene, 3′ end cds; 3-   100   196   591                           phosphoshikimate-1-carboxyvinyltransferase (aroA) gene, complete cds;                           ORF3, complete cds       539   1   3   338   emb|X76490|SAGL     S. aureus  (bb270) glnA and glnR genes   99   336   336       539   2   336   527   emb|X76490|SAGL     S. aureus  (bb270) glnA and glnR genes   100   189   192       554   1   365   3   gb|U73374|     Staphylococcus aureus  type 8 capsule genes, cap8A, cap8B, cap8C, cap8D,   100   54   363                           cap8E, cap8F, cap8G, cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,                           cap8O, cap8P, complete cds       554   2   1252   329   gb|U73374|     Staphylococcus aureus  type 8 capsule genes, cap8A, cap8B, cap8C, cap8D,   99   918   924                           cap8E, cap8F, cap8G, cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,                           cap8O, cap8P, complete cds       554   3   1374   1174   gb|U73374|     Staphylococcus aureus  type 8 capsule genes, cap8A, cap8B, cap8C, cap8D,   96   122   201                           cap8E, cap8F, cap8G, cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,                           cap8O, cap8P, complete cds       584   2   705   391   gb|U21221|     Staphylococcus aureus  hyaluronate lyase (hysA) gene, complete cds   99   306   315       587   3   1475   4288   emb|Z18852|SACF     S. aureus  gene for clumping factor   98   2588   2814       598   1   1953   25   dbj|D28879|STAP     Staphylococcus aureus  gene for penicillin-binding protein 1, complete cds   99   1873   1929       605   1   2   745   dbj|D86240|D862     Staphylococcus aureus  gene for unkown function and dlt operon dltA, dltB,   98   338   744                           dltC and dltD genes, complete cds       609   1   816   4   emb|X76490|SAGL     S. aureus  (bb270) glnA and glnR genes   100   495   813       614   1   642   4   gb|M32103|     Staphylococcus aureus  lac repressor (lacR) gene, complete cds and lacA   99   639   639                           repressor (lacA), partial cds       626   1   1255   2   gb|M63176|     Staphylococcus aureus  helicase required for T181 replication (pcrA) gene,   100   225   1254                           complete cds       626   2   2284   1253   gb|M63176|     Staphylococcus aureus  helicase required for T181 replication (pcrA) gene,   99   838   1032                           complete cds       629   1   1001   3   emb|X17688|SAFE     S. aureus  factor essential for expression of methicillin resistance (femA)   99   990   999                           gene, complete cds, and trpA gene, 3′ end       629   2   1195   983   emb|X17688|SAFE     S. aureus  factor essential for expression of methicillin resistance (femA)   98   194   213                           gene, complete cds, and trpA gene, 3′ end       631   2   3228   1330   emb|Z18852|SACF     S. aureus  gene for clumping factor   82   489   1899       632   1   3   551   emb|Z30588|SAST     S. aureus  (RN4220) genes for potential ABC transporter and potential   99   549   549                           membrane spanning protein       632   2   529   1323   emb|Z30588|SAST     S. aureus  (RN4220) genes for potential ABC transporter and potential   99   795   795                           membrane spanning protein       651   1   1070   231   gb|L19300|     Staphylococcus aureus  DNA sequence encoding three ORFs, complete cds;   99   478   840                           prophage phi-11 sequence homology, 5′ flank       657   2   1105   410   gb|L14017|     Staphylococcus aureus  methicillin-resistance protein (mecR) gene and   84   456   696                           unknown ORF, complete cds       662   1   456   4   emb|X13404|SAHL     Staphylococcus aureus  hlb gene for beta-hemolysin   100   369   453       662   2   230   475   emb|X13404|SAHL     Staphylococcus aureus  hlb gene for beta-hemolysin   100   246   246       662   3   746   1399   emb|X13404|SAHL     Staphylococcus aureus  hlb gene for beta-hemolysin   99   653   654       682   1   480   4   gb|M63177|     S. aureus  sigma factor (plaC) gene, complete cds   100   136   477       685   1   592   2   gb|U65000|     Staphylococcus aureus  type-I signal peptidase SpsA (spsA) gene, and type-I   98   534   591                           signal peptidase SpsB (spaB) gene, complete cds       685   2   1153   590   gb|U65000|     Staphylococcus aureus  type-I signal peptidase SpsA (spsA) gene, and type-I   96   564   564                           signal peptidase SpsB (spsB) gene, complete cds       697   1   3   527   gb|M63177|     S. aureus  sigma factor (plaC) gene, complete cds   100   195   525       697   2   485   784   gb|M63177|     S. aureus  sigma factor (plaC) gene, complete cds   97   280   300       710   1   15   503   dbj|D86240|D862     Staphylococcus aureus  gene for unkown function and dlt operon dltA, dltB,   99   217   489                           dltC and dltD genes, complete cds       733   1   26   205   gb|M80252|     Staphylococcus aureus  norA1199 gene (which mediates active efflux of   97   140   180                           fluoroguinolones), complete cds       741   1   1197   658   dbj|D83951|STAL     Staphylococcus aureus  DNA for LukM component, LukF-PV like component,   81   522   540                           complete cds       752   1   1   636   emb|Y00356|SASP     Staphylococcus aureus  V8 serine protease gene   99   618   636       752   2   588   956   emb|Y00356|SASP     Staphylococcus aureus  V8 serine protease gene   99   340   369       756   1   709   110   emb|X01645|SATO     Staphylococcus aureus  (Wood 46) gene for alpha-toxin   98   567   600       777   1   950   318   emb|Z49245|SA42     S. aureus  partial sod gene for superoxide dismutase   99   429   633       780   1   557   3   gb|U20503|     Staphylococcus aureus  MHC class II analog gene, complete cds   86   550   555       784   1   73   687   gb|U63529|     Staphylococcus aureus  novel antigen gene, complete cds   99   568   615       797   1   182   544   dbj|D14711|STAH     Staphylococcus aureus  HSP10 and HSP60 genes   98   363   363       798   1   302   72   emb|X58434|SAPD     S. aureus  pdhB, pdhC and pdhD genes for pyruvate decarboxylase,   95   196   231                           dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase       823   1   3   467   gb|S77055|   recF cluster: dnaA = replisome assembly protein...gyrB = DNA gyrase beta   99   156   465                           subunit [ Staphylococcus aureus , YB886, Genomic, 5 genes, 3573 nt]       848   1   175   2   gb|L25288|     Staphylococcus aureus  gyrase-like protein alpha and beta subunit (grlA and   99   174   174                           grlB) genes, complete cds       848   2   318   160   gb|L25288|     Staphylococcus aureus  gyrase-like protein alpha and beta subunit (grlA and   100   131   159                           grlB) genes, complete cds       866   1   397   2   emb|X64172|SARP     S. aureus  rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein   99   395   396                           L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &amp;                           beta′ chains       883   1   1   285   dbj|D90119|STAN     S. aureus  norA gene   99   131   285       884   1   334   62   emb|X52543|SAAG     S. aureus  agrA, agrB and hld genes   98   265   273       884   2   522   328   emb|X52543|SAAG     S. aureus  agrA, agrB and hld genes   100   195   195       912   2   517   681   emb|Z30588|SAST     S. aureus  (RN4220) genes for potential ABC transporter and potential   99   163   165                           membrane spanning protein       917   1   2   265   gb|M64724|     S. aureus  tagatose 6-phosphate isomerase gene, complete cds   99   247   264       917   2   238   396   gb|M64724|     S. aureus  tagatose 6-phosphate isomerase gene, complete cds   95   147   159       918   1   1215   4   emb|X93205|SAPT     S. aureus  ptsH and ptsI genes   99   1212   1212       967   1   1   411   dbj|D90119|STAN     S. aureus  norA gene   97   395   411       991   1   337   2   emb|X52543|SAAG     S. aureus  agrA, agrB and hld genes   99   336   336       1000   1   845   573   gb|L14017|     Staphylococcus aureus  methicillin-resistance protein (mecR) gene and   78   190   273                           unknown ORF, complete cds       1001   1   265   32   dbj|D86240|D862     Staphylococcus aureus  gene for unkown function and dlt operon dltA, dltB,   99   234   234                           dltC and dltD genes, complete cds       1010   1   1   285   gb|U21221|     Staphylococcus aureus  hyaluronate lyase (hysA) gene, complete cds   99   224   285       1046   1   330   4   emb|X72700|SAPV     S. aureus  genes for S and F components of Panton-Valentine leucocidins   85   205   327       1060   1   286   92   emb|X58434|SAPD     S. aureus  pdhB, pdhC and pdhD genes for pyruvate decarboxylase,   99   180   195                           dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase       1073   1   589   2   gb|K02985|     S. aureus  (strain RN450) transposon Tn554 insertion site   100   131   588       1079   1   3   230   dbj|D86240|D862     Staphylococcus aureus  gene for unkown function and dlt operon dltA, dltB,   99   228   228                           dltC and dltD genes, complete cds       1079   2   218   484   dbj|D86240|D862     Staphylococcus aureus  gene for unkown function and dlt operon dltA, dltB,   100   267   267                           dltC and dltD genes, complete cds       1079   3   460   645   dbj|D86240|D862     Staphylococcus aureus  gene for unkown function and dlt operon dltA, dltB,   100   186   186                           dltC and dltD genes, complete cds       1092   1   146   3   emb|X58434|SAPD     S. aureus  pdhB, pdhC and pdhD genes for pyruvate decarboxylase,   98   124   144                           dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase       1143   1   1   243   gb|M63177|     S. aureus  sigma factor (plaC) gene, complete cds   99   243   243       1157   1   2   136   emb|Z48003|SADN     S. aureus  gene for DNA polymerase III   97   127   135       1189   1   361   2   gb|S74031|   norA = NorA (ISP794) [ Staphylococcus aureus , NCTC 8325, Insertion, 1820 nt]   99   360   360       1190   1   2   283   gb|M21854|     S. aureus  agr gene encoding an accessory gene regulator protein, complete   100   282   282                           cds       1190   2   888   649   emb|X52543|SAAG     S. aureus  agrA, agrB and hld genes   100   240   240       1225   1   2   163   emb|X17679|SACO     Staphylococcus aureus  coa gene for coagulase   97   124   162       1243   1   2   529   dbj|D86240|D862     Staphylococcus aureus  gene for unkown function and dlt operon dltA, dltB,   99   495   528                           dltC and dltD genes, complete cds       1244   1   1   210   gb|S74031|   norA = NorA (ISP794) [ Staphylococcus aureus , NCTC 8325, Insertion, 1820 nt]   100   210   210       1301   1   41   472   emb|X76490|SAGL     S. aureus  (bb270) glnA and glnR genes   99   299   432       1315   1   18   326   emb|X64172|SARP     S. aureus  rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein   98   277   309                           L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &amp;                           beta′ chains       1519   1   2   175   dbj|D28879|STAP     Staphylococcus aureus  gene for penicillin-binding protein 1, complete cds   98   139   174       1663   1   675   4   dbj|D86240|D862     Staphylococcus aureus  gene for unkown function and dlt operon dltA, dltB,   98   672   672                           dltC and dltD genes, complete cds       1797   1   324   4   gb|U73374|     Staphylococcus aureus  type 8 capsule genes, cap8A, cap8B, cap8C, csp8D,   99   321   321                           cap8E, cap8F, cap8G, cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,                           cap8O, cap8P, complete cds       1857   1   1   192   gb|M90536|     Staphylococcus aureus  alpha-hemolysin gene, 3′ end   98   192   192       1923   1   2   181   emb|X17688|SAFE     S. aureus  factor essential for expression of methicillin resistance (femA)   100   180   180                           gene, complete cds, and trpA gene, 3′ end       1957   1   2   346   gb|U60589|     Staphylococcus aureus  novel antigen gene, complete cds   99   345   345       1988   1   1   402   dbj|D86240|D862     Staphylococcus aureus  gene for unkown function and dlt operon dltA, dltB,   100   402   402                           dltC and dltD genes, complete cds       2100   1   208   2   gb|M63177|     S. aureus  sigma factor (plaC) gene, complete cds   99   207   207       2199   1   1   402   gb|U66664|     Staphylococcus aureus  DNA fragment with class II promoter activity   99   131   402       2537   1   156   4   emb|X17688|SAFE     S. aureus  factor essential for expression of methicillin resistance (femA)   99   153   153                           gene, complete cds, and trpA gene, 3′ end       2891   1   2   400   gb|L25426|     Staphylococcus aureus  penicillin-binding protein 2 (pbp2) gene, complete   99   399   399                           cds       2950   1   398   18   dbj|D30690|STAN     Staphylococcus aureus  genes for ORF37; HSP20; HSP70; HSP40; ORF35, complete   100   358   381                           cds       2971   1   3   398   gb|U51132|     Staphylococcus aureus  o-succinylbenzoic acid CoA ligase (mene), and o-   97   272   396                           succinylbenzoic acid synthetase (menc) genes, complete cds       2978   1   328   38   gb|U31979|     Staphylococcus aureus  chorismate synthase (aroC) and nucleoside diphosphate   98   250   291                           kinase (ndk) genes, complete cds, dehydroauinate synthase (aroB) and                           geranylgeranyl pyrophosphate synthetase homolog (gerCC) genes, partial cds       2985   1   464   96   emb|X17679|SACO     Staphylococcus aureus  coa gene for coagulase   98   347   369       3006   1   1784   1398   gb|U11779|     Staphylococcus aureus  methicillin-resistant ATCC 33952 clone RRNV30 16S-23S   87   82   387                           rRNA spacer region       3008   1   238   2   dbj|D30690|STAN     Staphylococcus aureus  genes for ORF37; HSP20; HSP70; HSP40; ORF35, complete   88   178   237                           cds       3008   2   281   111   dbj|D30690|STAN     Staphylococcus aureus  genes for ORF37; HSP20; HSP70; HSP40; ORF35, complete   97   120   171                           cds       3011   1   398   3   emb|X62992|SAFN     S. aureus  fnbB gene for fibronectin binding protein B   93   72   396       3019   1   2   235   gb|J03479|     S. aureus  enzyme III-lac (lacF), enzyme II-lac (lacE), and phospho-beta-   97   234   234                           galactosidase (lacG) genes, complete cds       3023   1   81   233   gb|U06451|     Staphylococcus aureus  proline permease homolog (putP) gene, complete cds   87   100   153       3029   1   90   287   gb|U51133|     Staphylococcus aureus  phosphoenolpyruvate carboxykinase (pcka) gene,   100   135   198                           complete cds       3039   1   18   164   gb|U51133|     Staphylococcus aureus  phosphoenolpyruvate carboxykinase (pcka) gene,   97   135   147                           complete cds       3039   2   70   327   gb|U51133|     Staphylococcus aureus  phosphoenolpyruvate carboxykinase (pcka) gene,   77   183   258                           complete cds       3056   1   3   215   emb|X64172|SARP     S. aureus  rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein   99   213   213                           L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &amp;                           beta’ chains       3059   1   1   261   dbj|D30690|STAN     Staphylococcus aureus  genes for ORF37; HSP20; HSP70; HSP40; ORF35, complete   98   234   261                           cds       3073   1   27   284   gb|U06451|     Staphylococcus aureus  proline permease homolog (putP) gene, complete cds   99   229   258       3074   1   2   397   emb|X64172|SARP     S. aureus  rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein   96   250   396                           L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &amp;                           beta’ chains       3088   1   3   239   dbj|D86727|D867     Staphylococcus aureus  DNA for DNA polymerase III, complete cds   95   215   237       3097   1   244   44   emb|Z48003|SADN     S. aureus  gene for DNA polymerase III   97   160   201       3102   1   155   3   gb|J03479|     S. aureus  enzyme III-lac (lacF), enzyme II-lac (lacE), and phospho-beta-   97   142   153                           galactosidase (lacG) genes, complete cds       3121   1   398   228   emb|X58434|SAPD     S. aureus  pdhB, pdhC and pdhD genes for pyruvate decarboxylase,   100   88   171                           dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase       3125   1   233   3   emb|X89233|SARP     S. aureus  DNA for rpoC gene   98   192   231       3133   1   2   175   emb|Z18852|SACF     S. aureus  gene for clumping factor   96   154   174       3160   1   211   2   dbj|D10489|STAG     Staphylococcus aureus  genes for DNA gyrase A and B, complete cds   89   197   210       3176   1   1   378   emb|X58434|SAPD     S. aureus  pdhB, pdhC and pdhD genes for pyruvate decarboxylase,   96   91   378                           dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase       3192   1   211   2   gb|J03479|     S. aureus  enzyme III-lac (lacF), enzyme II-lac (lacE), and phospho-beta-   98   72   210                           galactosidase (lacG) genes, complete cds       3210   1   3   143   gb|M76714|     Staphylococcus aureus  peptidoglycan hydrolase gene, complete cds   96   141   141       3232   3   1282   458   gb|L14017|     Staphylococcus aureus  methicillin-resistance protein (mecR) gene and   71   257   825                           unknown ORF, complete cds       3538   1   2   394   emb|X89233|SARP     S. aureus  DNA for rpoC gene   99   350   393       3543   1   392   634   gb|L11530|     Staphylococcus aureus  transfer RNA sequence with two rRNAs   99   102   243       3555   1   320   3   emb|Z18852|SACF     S. aureus  gene for clumping factor   99   307   318       3559   1   3   182   emb|X17679|SACO     Staphylococcus aureus  coa gene for coagulase   100   141   180       3559   2   95   313   emb|X17679|SACO     Staphylococcus aureus  coa gene for coagulase   98   174   219       3563   1   141   4   gb|U35773|     Staphylococcus aureus  prolipoprotein diacylglyceryl transferase (lgt) gene,   100   79   138                           complete cds       3563   2   363   199   gb|U35773|     Staphylococcus aureus  prolipoprotein diacylglyceryl transferase (lgt) gene,   98   162   165                           complete cds       3566   1   3   422   emb|X16457|SAST     Staphylococcus aureus  gene for staphylocoagulase   98   175   420       3588   1   2   262   gb|L43098|   Transposon Tn5404 and insertion sequences IS1181 and IS1182 (from   99   253   261                             Staphylococcus aureus ) DNA       3593   1   3   350   gb|J03479|     S. aureus  enzyme III-lac (lacF), enzyme II-lac (lacE), and phospho-beta-   99   345   348                           galactosidase (lacG) genes, complete cds       3600   1   381   4   emb|Z18852|SACF     S. aureus  gene for clumping factor   72   346   378       3602   1   396   4   emb|Z18852|SACF     S. aureus  gene for clumping factor   98   319   393       3656   1   528   43   emb|Z18852|SACF     S. aureus  gene for clumping factor   84   403   486       3682   1   3   236   emb|X64172|SARP     S. aureus  rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein   100   231   234                           L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &amp;                           beta’ chains       3682   2   224   415   emb|X64172|SARP     S. aureus  rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein   100   112   192                           L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &amp;                           beta’ chains       3693   1   423   88   emb|X62992|SAFN     S. aureus  fnbB gene for fibronectin binding protein B   100   229   336       3702   1   354   115   gb|L11530|     Staphylococcus aureus  transfer RNA sequence with two rRNAs   96   81   240       3725   1   463   2   emb|Z18852|SACF     S. aureus  gene for clumping factor   71   367   462       3761   1   450   91   gb|L14017|     Staphylococcus aureus  methicillin-resistance protein (mecR) gene and   85   333   360                           unknown ORF, complete cds       3767   1   1   402   emb|X64172|SARP     S. aureus  rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein   98   387   402                           L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &amp;                           beta’ chains       3775   1   2   286   emb|X64172|SARP     S. aureus  rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein   100   227   285                           L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &amp;                           beta′ chains       3786   1   229   2   dbj|D10489|STAG     Staphylococcus aureus  genes for DNA gyrase A and B, complete cds   100   204   228       3786   2   366   190   dbj|D10489|STAG     Staphylococcus aureus  genes for DNA gyrase A and B, complete cds   95   123   177       3798   1   3   251   emb|X17679|SACO     Staphylococcus aureus  coa gene for coagulase   99   249   249       3813   1   398   3   gb|J04151|     S. aureus  fibronectin-binding protein (fnbA) mRNA, complete cds   98   396   396       3819   1   184   402   emb|X68425|SA23     S. aureus  gene for 23S rRNA   99   161   219       3844   1   468   4   gb|U48826|     Staphylococcus aureus  elastin binding protein (ebpS) gene, complete cds   87   204   465       3845   1   1   381   emb|X58434|SAPD     S. aureus  pdhB, pdhC and pdhD genes for pyruvate decarboxylase,   94   356   381                           dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase       3856   1   400   2   gb|L14017|     Staphylococcus aureus  methicillin-resistance protein (mecR) gene and   76   192   399                           unknown ORF, complete cds       3859   1   573   97   emb|Z18852|SACF     S. aureus  gene for clumping factor   85   347   477       3871   1   327   4   gb|M76714|     Staphylococcus aureus  peptidoglycan hydrolase gene, complete cds   100   299   324       3876   1   2   253   dbj|D10489|STAG     Staphylococcus aureus  genes for DNA gyrase A and B, complete cds   100   217   252       3877   1   288   4   gb|J03479|     S. aureus  enzyme III-lac (lacF), enzyme II-lac (lacE), and phospho-beta-   97   209   285                           galactosidase (lacG) genes, complete cds       3878   1   1   237   emb|X58434|SAPD     S. aureus  pdhB, pdhC and pdhD genes for pyruvate decarboxylase,   96   155   237                           dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase       3888   1   3   173   emb|X16457|SAST     Staphylococcus aureus  gene for staphylocoagulase   98   171   171       3893   1   1   183   emb|X89233|SARP     S. aureus  DNA for rpoC gene   100   170   183       3893   2   181   357   emb|X89233|SARP     S. aureus  DNA for rpoC gene   98   79   177       3894   1   3   485   emb|X64172|SARP     S. aureus  rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein   99   450   483                           L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &amp;                           beta’ chains       3895   1   420   4   gb|J04151|     S. aureus  fibronectin-binding protein (fnbA) mRNA, complete cds   99   411   417       3905   1   48   239   gb|L05004|     Staphylococcus aureus  dehydroquinate synthase (aroB) gene, 3′ end cds; 3-   100   159   192                           phosphoshikimate-1-carboxyvinyltransferase (aroA) gene, complete cds;                           ORF3, complete cds       3905   2   188   400   gb|L05004|     Staphylococcus aureus  dehydroquinate synthase (aroB) gene, 3′ end cds; 3-   97   88   213                           phosphoshikimate-1-carboxyvinyltransferase (aroA) gene, complete cds;                           ORF3, complete cds       3910   1   3   359   emb|X58434|SAPD     S. aureus  pdhB, pdhC and pdhD genes for pyruvate decarboxylase,   99   278   357                           dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase       3915   1   1   330   gb|L14017|     Staphylococcus aureus  methicillin-resistance protein (mecR) gene and   75   175   330                           unknown ORF, complete cds       3964   1   347   3   emb|Z48003|SADN     S. aureus  gene for DNA polymerase III   100   295   345       4007   1   199   390   emb|X16457|SAST     Staphylococcus aureus  gene for staphylocoagulase   98   163   192       4036   1   3   371   dbj|D10489|STAG     Staphylococcus aureus  genes for DNA gyrase A and B, complete cds   99   339   369       4046   1   348   4   emb|Z18852|SACF     S. aureus  gene for clumping factor   87   221   345       4060   1   1   375   emb|Z18852|SACF     S. aureus  gene for clumping factor   96   271   375       4061   1   432   4   emb|Z48003|SADN     S. aureus  gene for DNA polymerase III   99   429   429       4062   1   304   2   gb|L14017|     Staphylococcus aureus  methicillin-resistance protein (mecR) gene and   75   198   303                           unknown ORF, complete cds       4085   1   58   402   gb|U11786|     Staphylococcus aureus  methicillin-resistant ATCC 33952 clone RRNV42 16S-23S   98   127   345                           rRNA spacer region       4088   1   2   301   gb|L43098|   Transposon Tn5404 and insertion sequences IS1181 and IS1182 (from   99   227   300                             Staphylococcus aureus ) DNA       4093   1   2   277   emb|X58434|SAPD     S. aureus  pdhB, pdhC and pdhD genes for pyruvate decarboxylase,   99   276   276                           dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase       4097   1   1   402   emb|Z18852|SACF     S. aureus  gene for clumping factor   74   307   402       4116   1   22   402   gb|L05004|     Staphylococcus aureus  dehydroquinate synthase (aroB) gene, 3′ end cds; 3-   98   157   381                           phosphoshikimate-1-carboxyvinyltransferase (aroA) gene, complete cds;                           ORF3, complete cds       4125   1   240   401   gb|U73374|     Staphylococcus aureus  type 8 capsule genes, cap8A, cap8B, cap8C, cap8D,   100   86   162                           cap8E, cap8F, cap8G, cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,                           cap8O, cap8P, complete cds       4149   1   35   247   gb|J04151|     S. aureus  fibronectin-binding protein (fnbA) mRNA, complete cds   99   200   213       4151   1   366   103   gb|L14017|     Staphylococcus aureus  methicillin-resistance protein (mecR) gene and   87   150   264                           unknown ORF, complete cds       4154   1   398   42   emb|X64172|SARP     S. aureus  rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein   99   297   357                           L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &amp;                           beta’ chains       4179   1   1   294   emb|X64172|SARP     S. aureus  rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein   98   240   294                           L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &amp;                           beta’ chains       4203   1   1   255   emb|X89233|SARP     S. aureus  DNA for rpoC gene   99   239   255       4206   1   1   303   emb|Z18852|SACF     S. aureus  gene for clumping factor   100   236   303       4206   2   195   344   emb|Z18852|SACF     S. aureus  gene for clumping factor   95   65   150       4208   1   108   314   emb|X58434|SAPD     S. aureus  pdhB, pdhC and pdhD genes for pyruvate decarboxylase,   89   76   207                           dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase       4216   1   330   4   emb|X58434|SAPD     S. aureus  pdhB, pdhC and pdhD genes for pyruvate decarboxylase,   98   326   327                           dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase       4226   1   298   2   gb|L11530|     Staphylococcus aureus  transfer RNA sequence with two rRNAs   97   132   297       4260   1   216   383   gb|U11784|     Staphylococcus aureus  methicillin-resistant ATCC 33952 clone RRNV40 16S-23S   83   141   168                           rRNA spacer region       4272   1   179   3   emb|Z48003|SADN     S. aureus  gene for DNA polymerase III   100   164   177       4276   1   4   177   emb|X16457|SAST     Staphylococcus aureus  gene for staphylocoagulase   99   150   174       4277   1   1   270   emb|X64172|SARP     S. aureus  rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein   99   265   270                           L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &amp;                           beta’ chains       4282   1   377   63   emb|X64172|SARP     S. aureus  rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein   98   282   315                           L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &amp;                           beta’ chains       4291   1   191   3   emb|X64172|SARP     S. aureus  rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein   99   183   189                           L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &amp;                           beta’ chains       4295   1   3   329   emb|X16457|SAST     Staphylococcus aureus  gene for staphylocoagulase   94   144   327       4313   1   280   125   gb|L11530|     Staphylococcus aureus  transfer RNA sequence with two rRNAs   100   94   156       4315   1   3   185   gb|J03479|     S. aureus  enzyme III-lac (lacF), enzyme II-lac (lacE), and phospho-beta-   100   158   183                           galactosidase (lacG) genes, complete cds       4315   2   101   310   gb|J03479|     S. aureus  enzyme III-lac (lacF), enzyme II-lac (lacE), and phospho-beta-   98   75   210                           galactosidase (lacG) genes, complete cds       4327   1   1   294   gb|L43098|   Transposon Tn5404 and insertion sequences IS1181 and IS1182 (from   98   294   294                             Staphylococcus aureus ) DNA       4360   1   319   35   gb|U02910|     Staphylococcus aureus  ATCC 25923 16S rRNA gene, partial sequence   100   116   285       4364   1   3   146   emb|X64172|SARP     S. aureus  rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein   95   140   144                           L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &amp;                           beta’ chains       4388   1   167   310   emb|X62992|SAFN     S. aureus  fnbB gene for fibronectin binding protein B   73   119   144       4401   1   2   313   emb|X62992|SAFN     S. aureus  fnbB gene for fibronectin binding protein B   97   243   312       4421   1   36   281   dbj|D12572|STA2     Staphylococcus aureus  rrnA gene for 23S ribosomal RNA   100   112   246       4426   1   3   293   emb|Z18852|SACF     S. aureus  gene for clumping factor   85   185   291       4428   1   248   3   emb|X64172|SARP     S. aureus  rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein   100   139   246                           L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &amp;                           beta′ chains       4462   1   2   271   emb|X64172|SARP     S. aureus  rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein   99   270   270                           L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &amp;                           beta′ chains       4466   1   1   240   emb|Z18852|SACF     S. aureus  gene for clumping factor   99   231   240       4469   1   1   312   gb|J03479|     S. aureus  enzyme III-lac (lacF), enzyme II-lac (lacE), and phospho-beta-   99   265   312                           galactosidase (lacG) genes, complete cds       4485   1   3   263   gb|L43098|   Transposon Tn5404 and insertion sequences IS1181 and IS1182 (from   98   259   261                             Staphylococcus aureus ) DNA       4492   1   74   400   gb|M86227|     Staphylococcus aureus  DNA gyrase B subunit (gyrB) RecF homologue (recF) and   85   104   327                           DNA gyrase A subunit (gyrA) gene, complete cds       4497   1   269   3   emb|Z18852|SACF     S. aureus  gene for clumping factor   99   213   267       4529   1   2   172   emb|X64172|SARP     S. aureus  rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein   100   151   171                           L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &amp;                           beta′ chains       4547   1   1   300   emb|X62992|SAFN     S. aureus  fnbB gene for fibronectin binding protein B   100   157   300       4554   1   160   2   emb|Z18852|SACF     S. aureus  gene for clumping factor   84   126   159       4565   1   9   227   emb|Z18852|SACF     S. aureus  gene for clumping factor   84   213   219       4569   1   79   222   emb|Z18852|SACF     S. aureus  gene for clumping factor   98   127   144       4608   1   22   216   emb|X58434|SAPD     S. aureus  pdhB, pdhC and pdhD genes for pyruvate decarboxylase,   92   168   195                           dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase       4614   1   234   4   emb|Z18852|SACF     S. aureus  gene for clumping factor   86   169   231       4623   1   105   302   gb|J04151|     S. aureus  fibronectin-binding protein (fnbA) mRNA, complete cds   99   152   198       4632   1   18   206   gb|J03479|     S. aureus  enzyme III-lac (lacF), enzyme II-lac (lacE), and phospho-beta-   98   183   189                           galactosidase (lacG) genes, complete cds       4646   1   1   222   emb|Z18852|SACF     S. aureus  gene for clumping factor   84   100   222       4687   1   2   166   gb|J04151|     S. aureus  fibronectin-binding protein (fnbA) mRNA, complete cds   98   156   165       4695   1   158   3   gb|L14017|     Staphylococcus aureus  methicillin-resistance protein (mecR) gene and   75   155   156                           unknown ORF, complete cds       4703   1   1   153   emb|X58434|SAPD     S. aureus  pdhB, pdhC and pdhD genes for pyruvate decarboxylase,   98   103   153                           dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase                  
 
     [0289]               TABLE 2                            S. aureus  - Putative coding regions of novel proteins similar to known proteins                                                         Start   Stop   match                       Contig ID   ORF ID   (nt)   (nt)   acession   match gene name   % sim   % ident   length (nt)                                                         20   6   4679   4269   gi|511839   ORF1 [Staphylococcus bacteriophage phi 11]   100   100   411       149   3   1577   1122   pir|B49703|B497   int gene activator RinA - bacteriophage phi 11   100   100   456       149   5   1912   1715   gi|166161   Bacteriophage phi-11 int gene activator [Staphylococcus acteriophage phi   100   100   198                           11]       349   2   409   260   gi|166159   integrase (int) [Staphylococcus bacteriophage phi 11]   100   100   150       398   1   707   42   gi|166159   integrase (int) [Staphylococcus bacteriophage phi 11]   100   99   666       398   2   783   1001   gi|455128   excisionase (xis) [Staphylococcus bacteriophage phi 11]   100   100   219       502   4   1744   1574   gi|1204912     H. influenzae  predicted coding region HI0660 [ Haemophilus influenzae ]   100   71   171       849   1   2   262   gi|1373002   polyprotein [Bean common mosaic virus]   100   46   261       1349   1   140   3   gi|143359   protein synthesis initiation factor 2 (infB) [ Bacillus subtilis ] gi|49319   100   82   138                           IF2 gene product [ Bacillus subtilis ]       2880   1   21   308   gi|862933   protein kinase C inhibitor-I [ Homo sapiens ]   100   98   288       3085   1   216   4   gi|1354211   PET112-like protein [ Bacillus subtilis ]   100   100   213       4168   2   398   225   gi|1354211   PET112-like protein [ Bacillus subtilis ]   100   100   174       331   1   2   247   gi|426473   nusG gene product [ Staphylococcus carnosus ]   98   95   246       207   2   1272   1463   gi|460259   enolase [ Bacillus subtilis ]   97   90   192       331   2   395   850   gi|581638   L11 protein [ Staphylococcus carnosus ]   97   93   456       366   1   39   215   gi|166161   Bacteriophage phi-11 int gene activator [Staphylococcus acteriophage phi   97   95   177                           11]       680   3   718   936   gi|426473   nusG gene product [ Staphylococcus carnosus ]   97   97   219       3578   1   144   4   gi|1339950   large subunit of NADH-dependent glutamate synthase [ Plectonema boryanum ]   97   79   141       157   1   321   518   gi|1022726   unknown [ Staphylococcus haemolyticus ]   96   88   198       205   33   16147   15824   gi|1165302   S10 [ Bacillus subtilis ]   96   91   324       3919   1   48   401   gi|871784   Clp-like ATP-dependent protease binding subunit [ Bos taurus ]   96   81   354       4133   1   417   4   gi|1022726   unknown [ Staphylococcus haemolyticus ]   96   84   414       4168   1   355   2   gi|1354211   PET112-like protein [ Bacillus subtilis ]   96   95   354       4207   1   157   2   gi|602031   similar to trimethylamine DH [ Mycoplasma capricolum ]pir|S49950|S49950   96   86   156                           probable trimethylamine dehydrogenase (EC .5.99.7) -  Mycoplasma capricolum                             (SGC3) (fragment)       4227   2   152   331   gi|871784   Clp-like ATP-dependent protease binding subunit [ Bos taurus ]   96   81   180       4416   1   286   2   gi|1022726   unknown [ Staphylococcus haemolyticus ]   96   84   285       22   1   430   2   gi|511070   UreG [ Staphylococcus xylosus ]   95   88   429       22   7   4036   3710   gi|581787   urease gamma subunit [ Staphylococcus xylosus ]   95   79   327       82   6   8794   9114   pir|JG0008|JG00   ribosomal protein S7 -  Bacillus stearothermophilus     95   83   321       154   9   7838   6396   gi|1354211   PET112-like protein [ Bacillus subtilis ]   95   92   1443       186   3   2055   1312   gi|1514656   serine 0-acetyltransferase [ Staphylococcus xylosus ]   95   87   744       205   5   4014   3622   gi|142462   ribosomal protein S11 [ Bacillus subtilis ]   95   85   393       205   7   4793   4569   gi|142459   initiation factor 1 [ Bacillus subtilis ]   95   84   225       205   21   10991   10617   gi|1044974   ribosomal protein L14 [ Bacillus subtilis ]   95   93   375       259   5   6644   6000   sp|P47995|YSEA —     HYPOTHETICAL PROTEIN IN SECA 5′REGION (ORF1) (FRAGMENT).   95   85   645       302   3   795   1097   gi|40186   homologous to  E. coli  ribosomal protein L27 [ Bacillus subtilis ] i|143592 L27   95   89   303                           ribosomal protein [ Bacillus subtilis ] ir|C21895|C21895 ribosomal protein                           L27 -  Bacillus subtilis  p|P05657|RL27_BACSU 50S RIBOSOMAL PROTEIN L27                           (BL30) (BL24). i|40175 L24 gene prod       310   1   579   1523   gi|1177684   chorismate mutase [ Staphylococcus xylosus ]   95   92   945       414   1   2   163   pir|C48396|C483   ribosomal protein L34 -  Bacillus stearothermophilus     95   90   162       4185   2   125   277   gi|1276841   glutamate synthase (GOGAT) [ Porphyra purpurea ]   95   86   153       22   2   723   418   gi|511069   UreF [ Staphylococcus xylosus ]   94   91   306       22   5   3310   1574   gi|410516   urease alpha subunit [ Staphylococcus xylosus ]   94   85   1737       60   4   815   1372   gi|666116   glucose kinase [ Staphylococcus xylosus ]   94   87   558       205   18   9536   9060   gi|1044978   ribosomal protein S8 [ Bacillus subtilis ]   94   78   477       326   4   2542   1706   gi|557492   dihydroxynapthoic acid (DHNA) synthetase [ Bacillus subtilis ] gi|143186   94   85   837                           dihydroxynapthoic acid (DHNA) synthetase [ Bacillus subtilis ]       414   3   737   955   gi|467386   thiophen and furan oxidation [ Bacillus subtilis ]   94   77   219       426   3   1823   1386   gi|1263908   putative [ Staphylococcus epidermidis ]   94   87   438       534   1   2   355   gi|633650   enzyme II(mannitol) [ Staphylococcus carnosus ]   94   84   354       1017   1   2   229   gi|149435   putative [ Lactococcus lactis ]   94   73   228       3098   1   184   38   gi|413952   ipa-28d gene product [ Bacillus subtilis ]   94   50   147       3232   1   316   2   gi|1022725   unknown [ Staphylococcus haemolyticus ]   94   84   315       42   5   2089   2259   pir|B48396|B483   ribosomal protein L33 -  Bacillus stearothermophilus     93   81   171       101   2   1383   1021   gi|155345   arsenic efflux pump protein [Plasmid pSX267]   93   82   363       205   24   11865   11503   sp|P14577|RL16 —     50S RIBOSOMAL PROTEIN L16.   93   83   363       259   4   5673   3055   gi|499335   secA protein [ Staphylococcus carnosus ]   93   85   2619       275   1   1114   2   gi|633650   enzyme II(mannitol) [ Staphylococcus carnosus ]   93   86   1113       444   6   5773   5339   gi|1022726   unknown [ Staphylococcus haemolyticus ]   93   81   435       491   1   152   622   gi|46912   ribosomal protein L13 [ Staphylococcus carnosus ]   93   88   471       607   6   1674   2033   gi|1022726   unknown [ Staphylococcus haemolyticus ]   93   83   360       653   1   488   3   gi|580890   translation initiation factor IF3 (AA 1-172) [Bacillus tearothermophilus]   93   77   486       1864   1   3   194   gi|306553   ribosmal protein small subunit [ Homo sapiens ]   93   93   192       2997   1   28   300   gi|143390   carbamyl phosphate synthetase [ Bacillus subtilis ]   93   82   273       3232   2   596   285   gi|1022725   unknown [ Staphylococcus haemolyticus ]   93   84   312       3761   2   621   448   gi|1022725   unknown [ Staphylococcus haemolyticus ]   93   88   174       16   1   3   374   gi|142781   putative cytoplasmic protein; putative [ Bacillus subtilis ]   92   83   372                           sp|P37954|UVRB_BACSU EXCINUCLEASE ABC SUBUNIT B (DINA PROTEIN) FRAGMENT).       31   7   5915   6124   gi|1136430   KIAA0185 protein [ Homo sapiens ]   92   46   210       56   19   26483   27391   gi|467401   unknown [ Bacillus subtilis ]   92   80   909       69   6   5882   6130   gi|530200   trophoblastin [ Ovis aries ]   92   53   249       145   3   2038   1508   gi|1022725   unknown [ Staphylococcus haemolyticus ]   92   80   531       171   3   2362   1964   gi|517475   D-amino acid transaminase [ Staphylococcus haemolyticus ]   92   86   399       205   12   6962   6429   gi|49189   secY gene product [ Staphylococcus carnosus ]   92   85   534       205   19   10255   9698   gi|1044976   ribosomal protein L5 [ Bacillus subtilis ]   92   82   558       219   1   357   4   gi|1303812   YqeV [ Bacillus subtilis ]   92   88   354       344   3   1575   1805   gi|1405474   CspC protein [ Bacillus cereus ]   92   85   231       699   1   20   361   gi|413999   ipa-75d gene product [ Bacillus subtilis ]   92   81   342       1343   1   2   160   pir|A45434|A454   ribosomal protein L19 -  Bacillus stearothermophilus     92   84   159       1958   1   264   4   gi|407908   EIIscr [ Staphylococcus xylosus ]   92   80   261       3578   2   386   54   gi|1339950   large subunit of NADH-dependent glutamate synthase [ Plectonema boryanum ]   92   78   333       3585   1   324   4   gi|1339950   large subunit of NADH-dependent glutamate synthase [ Plectonema boryanum ]   92   81   321       3640   1   4   402   gi|1022726   unknown [ Staphylococcus haemolyticus ]   92   81   399       4362   1   14   178   gi|450688   hsdM gene of EcoprrI gene product [ Escherichia coli ] pir|S38437|S38437 hsdM   92   78   165                           protein -  Escherichia coli  pir|S09629|S09629 hypothetical protein A -                             Escherichia coli  (SUB 40-520)       4446   1   182   6   gi|1022725   unknown [ Staphylococcus haemolyticus ]   92   82   177       4549   1   232   2   gi|1022726   unknown [ Staphylococcus haemolyticus ]   92   80   231       4626   1   3   224   gi|1022725   unknown [ Staphylococcus haemolyticus ]   92   84   222       2   4   3980   4531   gi|535349   Codw [ Bacillus subtilis ]   91   74   552       28   1   2   1126   gi|1001376   hypothetical protein [Synechocystis sp.]   91   78   1125       60   5   1354   1701   gi|1226043   orf2 downstream of glucose kinase [ Staphylococcus xylosus ]   91   80   348       101   1   1036   83   gi|150728   arsenic efflux pump protein [Plasmid pI258]   91   80   954       187   2   412   1194   gi|142559   ATP synthase alpha subunit [ Bacillus megaterium ]   91   79   783       205   22   11298   11017   gi|40149   S17 protein (AA 1-87) [ Bacillus subtilis ]   91   83   282       206   7   8184   10262   gi|1072418   glcA gene product [ Staphylococcus carnosus ]   91   83   2079       306   2   2326   767   gi|143012   GMP synthetase [ Bacillus subtilis ]   91   78   1560       306   3   3826   2333   gi|467399   IMP dehydrogenase [ Bacillus subtilis ]   91   79   1494       310   3   2194   3207   gi|1177685   ccpA gene product [ Staphylococcus xylosus ]   91   81   1014       343   4   2974   3150   gi|949974   sucrose repressor [ Staphylococcus xylosus ]   91   82   177       480   3   1606   3042   gi|433991   ATP synthase subunit beta [ Bacillus subtilis ]   91   85   1437       536   3   1280   534   gi|143366   adenylosuccinate lyase (PUR-B) [ Bacillus subtilis ] pir|C29326|WZBSDS   91   79   747                           adenylosuccinate lyase (EC 4.3.2.2) -  Bacillus subtilis         552   1   615   166   gi|297874   fructose-bisphosphate aldolase [ Staphylococcus carnosus ] pir|A49943|A49943   91   79   450                           fructose-bisphosphate aldolase (EC 4.1.2.13) -  Staphylococcus carnosus                             (strain TM300)       637   1   1   1536   gi|143597   CTP synthetase [ Bacillus subtilis ]   91   79   1536       859   1   21   359   gi|385178   unknown [ Bacillus subtilis ]   91   66   339       1327   1   339   530   gi|496558   orfX [ Bacillus subtilis ]   91   71   192       2515   1   275   84   gi|511070   UreG [ Staphylococcus xylosus ]   91   85   192       2594   1   2   202   gi|146824   beta-cystathionase [ Escherichia coli ]   91   75   201       3764   1   425   3   gi|1022725   unknown [ Staphylococcus haemolyticus ]   91   78   423       4011   1   127   495   gi|1022726   unknown [ Staphylococcus haemolyticus ]   91   79   369       4227   1   1   177   gi|296464   ATPase [ Lactococcus lactis ]   91   66   177       42   3   815   1033   gi|520401   catalase [ Haemophilus influenzae ]   90   86   219       51   8   3717   4607   gi|580899   OppF gene product [ Bacillus subtilis ]   90   74   891       129   3   4001   2685   gi|1146206   glutamate dehydrogenase [ Bacillus subtilis ]   90   76   1317       164   17   16628   16933   sp|P05766|RS15 —     30S RIBOSOMAL PROTEIN S15 (BS18)   90   74   306       171   5   2819   2655   gi|517475   D-amino acid transaminase [ Staphylococcus haemolyticus ]   90   78   165       205   4   3550   2603   gi|142463   RNA polymerase alpha-core-subunit [ Bacillus subtilis ]   90   76   948       205   6   4410   4072   gi|1044989   ribosomal protein S13 [ Bacillus subtilis ]   90   73   339       205   10   6404   5643   gi|49189   secY gene product [ Staphylococcus carnosus ]   90   81   762       205   11   6472   6299   gi|49189   secY gene product [ Staphylococcus carnosus ]   90   78   174       205   27   13345   12998   gi|786157   Ribosomal Protein S19 [ Bacillus subtilis ]   90   79   348       205   31   15496   15134   gi|1165303   L3 [ Bacillus subtilis ]   90   79   363       260   5   5773   4523   gi|1161380   IcaA [ Staphylococcus epidermidis ]   90   78   1251       299   6   3378   3947   gi|467440   ‘phosphoribosylpyrophosphate synthetase [ Bacillus subtilis ] gi|40218 PRPP   90   78   570                           synthetase (AA 1-317) [ Bacillus subtilis ]       320   2   1025   1717   gi|312443   carbamoyl-phosphate synthase (glutamine-hydrolysing) [ Bacillus aldolyticus ]   90   75   693       330   4   1581   1769   gi|986963   beta-tubulin [Sporidiobolus pararoseus]   90   80   189       369   1   523   92   pir|S34762|S347   L-serine dehydratase beta chain - Clostridium sp.   90   77   432       557   1   3   188   gi|1511589     M. jannaschii  predicted coding region MJ1624 [ Methanococcus jannaschii ]   90   54   186       663   2   667   1200   gi|143786   tryptophanyl-tRNA synthetase (EC 6.1.1.2) [ Bacillus subtilis ]   90   73   534                           pir|JT0481|YWBS tryptophan-tRNA ligase (EC 6.1.1.2) -  Bacillus subtilis         717   1   1   261   gi|143065   hubst [ Bacillus stearothermophilus ]   90   79   261       745   4   865   671   gi|1205433     H. influenzae  predicted coding region HI1190 [ Haemophilus influenzae ]   90   81   195       1007   1   386   565   gi|143366   adenylosuccinate lyase (PUR-B) [ Bacillus subtilis ] pir|C29326|WZBSDS   90   77   180                           adenylosuccinate lyase EC 4.3.2.2) -  Bacillus subtilis         1054   1   331   83   gi|1033122   ORF_f729 [ Escherichia coli ]   90   50   249       1156   1   117   707   gi|1477776   ClpP [ Bacillus subtilis ]   90   80   591       1180   1   205   2   gi|1377831   unknown [ Bacillus subtilis ]   90   74   204       1253   1   1   462   gi|40046   phosphoglucose isomerase A (AA 1-449) [ Bacillus stearothermophilus ]   90   75   462                           ir|S15936|NUBSSA glucose-6-phosphate isomerase (EC 5.3.1.9) A -  Bacillus                               stearothermophilus         2951   1   3   269   gi|144816   formyltetrahydrofolate synthetase (FTHFS) (ttg start codon) (EC .3.4.3)   90   76   267                           [Moorella thermoacetica]       3140   1   166   5   gi|1070014   protein-dependent [ Bacillus subtilis ]   90   52   162       4594   1   3   233   gi|871784   Clp-like ATP-dependent protease binding subunit [ Bos taurus ]   90   76   231       87   1   1028   1750   gi|467327   unknown [ Bacillus subtilis ]   89   75   723       112   1   2   505   gi|153741   ATP-binding protein [Streptococcus mutans]   89   77   504       118   1   120   398   gi|1303804   YqeQ [ Bacillus subtilis ]   89   75   279       128   4   3545   3757   gi|460257   triose phosphate isomerase [ Bacillus subtilis ]   89   84   213       164   12   11667   12755   gi|39954   IF2 (aa 1-741) [ Bacillus stearothermophilus ]   89   80   1089       205   13   7405   6935   gi|216338   ORF for L15 ribosomal protein [ Bacillus subtilis ]   89   76   471       205   32   15823   15494   gi|1165303   L3 [ Bacillus subtilis ]   89   80   330       270   3   2207   2007   pir|C41902|C419   arsenate reductase (EC 1,—,—,—) -  Staphylococcus xylosus  plasmid pSX267   89   81   201       395   2   157   672   gi|520574   glutamate racemase [ Staphylococcus haemolyticus ]   89   80   516       494   1   3   839   gi|396259   protease [ Staphylococcus epidermidis ]   89   77   837       510   1   1   444   gi|40046   phosphoglucose isomerase A (AA 1-449) [ Bacillus stearothermophilus ]   89   74   444                           ir|S15936|NUBSSA glucose-6-phosphate isomerase (EC 5.3.1.9) A -  Bacillus                               stearothermophilus         615   1   1210   296   gi|1303812   YqeV [ Bacillus subtilis ]   89   74   915       841   1   18   341   gi|1165303   L3 [ Bacillus subtilis ]   89   80   324       1111   1   352   813   gi|47146   thermonuclease [Staphylococcus intermedius]   89   70   462       1875   1   2   256   gi|1205108   ATP-dependent protease binding subunit [ Haemophilus influenzae ]   89   82   255       2963   1   11   367   gi|467458   cell division protein [ Bacillus subtilis ]   89   83   357       3020   1   90   362   gi|1239988   hypothetical protein [ Bacillus subtilis ]   89   66   273       3565   1   2   400   gi|1256635   dihydroxy-acid dehydratase [ Bacillus subtilis ]   89   75   399       3586   1   105   314   gi|580832   ATP synthase subunit gamma [ Bacillus subtilis ]   89   82   210       3629   1   399   4   gi|1009366   Respiratory nitrate reductase [ Bacillus subtilis ]   89   78   396       3688   1   2   400   gi|1146206   glutamate dehydrogenase [ Bacillus subtilis ]   89   75   399       3699   1   399   4   gi|1339950   large subunit of NADH-dependent glutamate synthase [ Plectonema boryanum ]   89   75   396       4016   1   216   4   gi|1009366   Respiratory nitrate reductase [ Bacillus subtilis ]   89   71   213       4177   1   301   131   gi|149426   putative [ Lactococcus lactis ]   89   76   171       4436   1   302   3   gi|1022725   unknown [ Staphylococcus haemolyticus ]   89   80   300       4635   1   162   4   gi|1022725   unknown [ Staphylococcus haemolyticus ]   89   73   159       2   2   1330   2676   gi|520754   putative [ Bacillus subtilis ]   88   76   1347       42   2   468   848   sp|P42321|CATA —     CATALASE (EC 1.11.1.6).   88   76   381       53   5   4722   3055   gi|474177   alpha-D-1,4-glucosidase [ Staphylococcus xylosus ]   88   80   1668       56   16   18018   18617   gi|467411   recombination protein [ Bacillus subtilis ]   88   77   600       60   3   376   843   gi|666116   glucose kinase [ Staphylococcus xylosus ]   88   77   468       70   2   1245   907   gi|44095   replication initiator protein [ Listeria monocytogenes ]   88   74   339       82   8   11514   12719   pir|A60663|A606   translation elongation factor Tu -  Bacillus subtilis     88   79   1206       103   7   4179   4391   gi|167181   serine/threonine kinase receptor [Brassica napus]   88   77   213       114   8   7732   8232   gi|1022726   unknown [ Staphylococcus haemolyticus ]   88   72   501       118   2   308   2011   gi|1303804   YqeQ [ Bacillus subtilis ]   88   77   1704       141   3   657   1136   gi|1405446   transketolase [ Bacillus subtilis ]   88   72   480       148   7   5871   6116   gi|1118002   dihydropteroate synthase [ Staphylococcus haemolyticus ]   88   78   246       165   3   1428   2231   gi|40053   phenylalanyl-tRNA synthetase alpha subunit [ Bacillus subtilis ]   88   80   804                           ir|S11730|YFBSA phenylalanine-tRNA ligase (EC 6.1.1.20) alpha ain -                             Bacillus subtilis         205   28   14185   13343   gi|1165306   L2 [ Bacillus subtilis ]   88   82   843       225   1   898   227   gi|1303840   YqfS [ Bacillus subtilis ]   88   78   672       235   1   2   1975   gi|452309   valyl-tRNA synthetase [ Bacillus subtilis ]   88   76   1974       339   3   1566   1072   gi|1118002   dihydropteroate synthase [ Staphylococcus haemolyticus ]   88   73   495       443   4   2928   1531   gi|558559   pyrimidine nucleoside phosphorylase [ Bacillus subtilis ]   88   73   1398       532   1   3   419   gi|143797   valyl-tRNA synthetase [ Bacillus stearothermophilus ]sp|P11931|SYV_BACST   88   78   417                           VALYL-TRNA SYNTHETASE (EC 6.1.1.9) VALINE-TRNA LIGASE) (VALRS).       534   3   2504   2968   gi|153049   mannitol-specific enzyme-III [ Staphylococcus carnosus ]pir|JQ0088|JQ0088   88   82   465                           phosphotransferase system enzyme II (EC .7.1.69), mannitol-specific,                           factor III -  Staphylococcus carnosus  sp|P17876|PTMA_STACA PTS SYSTEM,                           MANNITOL-SPECIFIC IIA COMPONENT EIIA-MTL) (       705   2   399   214   gi|710018   nitrite reductase (nirB) [ Bacillus subtilis ]   88   70   186       1000   2   1309   794   gi|1022726   unknown [ Staphylococcus haemolyticus ]   88   78   516       1299   1   324   61   gi|401786   phosphomannomutase [ Mycoplasma pirum ]   88   55   264       1341   2   170   400   gi|39963   ribosomal protein L20 (AA 1-119) [ Bacillus stearothermophilus ]   88   82   231                           ir|S05348|R5BS20 ribosomal protein L20 -  Bacillus stearothermophilus         1386   1   41   214   pir|B47154|B471   signal recognition particle 54 K chain homolog Ffh -  Bacillus subtilis     88   71   174       1386   2   183   533   pir|B47154|B471   signal recognition particle 54 K chain homolog Ffh -  Bacillus subtilis     88   73   351       2949   1   399   94   gi|535350   CodX [ Bacillus subtilis ]   88   73   306       2984   1   5   169   gi|218277   O-acetylserine(thiol) lyase [Spinacia oleracea]   88   70   165       3035   1   1   138   gi|493083   dihydroxyacetone kinase [Citrobacter freundii]   88   67   138       3089   1   3   152   gi|606055   ORF_f746 [ Escherichia coli ]   88   88   150       3917   1   410   3   gi|143378   pyruvate decarboxylase (E-1) beta subunit [ Bacillus subtilis ]gi|1377836   88   77   408                           pyruvate decarboxylase E-1 beta subunit [ Bacillus subtilis ]       4199   1   342   4   gi|1405454   aconitase [ Bacillus subtilis ]   88   82   339       4201   1   369   4   gi|515938   glutamate synthase (ferredoxin) [Synechocystis sp.]pir|S46957|S46957   88   84   366                           glutamate synthase (ferredoxin) (EC 1.4.7.1) - ynechocystis sp.       4274   1   1   336   gi|515938   glutamate synthase (ferredoxin) [Synechocystis sp.]pir|S46957|S46957   88   84   336                           glutamate synthase (ferredoxin) (EC 1.4.7.1) - ynechocystis sp.       4308   1   399   4   gi|1146206   glutamate dehydrogenase [ Bacillus subtilis ]   88   71   396       2   5   4570   6000   gi|535350   CodX [ Bacillus subtilis ]   87   70   1431       52   8   6482   6183   gi|1064791   function umknown [ Bacillus subtilis ]   87   66   300       73   3   1584   2480   gi|142992   glycerol kinase (glpK) (EC 2.7.1.30) [ Bacillus subtilis ] pir|B45868|B45868   87   72   897                           glycerol kinase (EC 2.7.1.30) -  Bacillus subtilis  sp|P18157|GLPK_BACSU                           GLYCEROL KINASE (EC 2.7.1.30) (ATP: GLYCEROL-PHOSPHOTRANSFERASE)                           (GLYCEROKINASE) (GK).       98   12   8813   9100   gi|467433   unknown [ Bacillus subtilis ]   87   62   288       124   4   2988   1711   gi|556886   serine hydroxymethyltransferase [ Bacillus subtilis ] pir|S49363|S49363   87   77   1278                           serine hydroxymethyltransferase -  Bacillus subtilis         124   6   4032   3607   gi|556883   Unknown [ Bacillus subtilis ]   87   66   426       148   5   3741   4559   gi|467460   unknown [ Bacillus subtilis ]   87   70   819       164   13   12710   13810   gi|39954   IF2 (aa 1-741) [ Bacillus stearothermophilus ]   87   72   1101       177   2   1104   2126   gi|467385   unknown [ Bacillus subtilis ]   87   78   1023       199   1   1158   334   gi|143527   iron-sulfur protein [ Bacillus subtilis ]   87   77   825       199   2   2933   1149   pir|A27763|A277   succinate dehydrogenase (EC 1.3.99.1) flavoprotein -  Bacillus subtilis     87   80   1785       205   23   11543   11304   gi|1044972   ribosomal protein L29 [ Bacillus subtilis ]   87   78   240       205   25   12607   11939   gi|1165309   S3 [ Bacillus subtilis ]   87   75   669       222   1   1107   181   gi|1177249   rec233 gene product [ Bacillus subtilis ]   87   70   927       236   3   1333   1031   gi|1146198   ferredoxin [ Bacillus subtilis ]   87   80   303       246   5   2292   1999   gi|467373   ribosomal protein S18 [ Bacillus subtilis ]   87   77   294       260   2   3422   2655   gi|1161382   IcaC [ Staphylococcus epidermidis ]   87   72   768       320   3   1696   2391   gi|312443   carbamoyl-phosphate synthase (glutamine-hydrolysing) [ Bacillus aldolyticus ]   87   80   696       380   4   1165   1383   gi|142570   ATP synthase c subunit [ Bacillus firmus ]   87   80   219       414   4   900   1073   gi|467386   thiophen and furan oxidation [ Bacillus subtilis ]   87   77   174       425   2   794   585   gi|1046166   pilin repressor [ Mycoplasma genitalium ]   87   69   210       448   1   722   189   gi|405134   acetate kinase [ Bacillus subtilis ]   87   75   534       480   1   1   711   gi|142559   ATP synthase alpha subunit [ Bacillus megaterium ]   87   79   711       481   1   2   352   sp|Q06797|RL1_B   50S RIBOSOMAL PROTEIN L1 (BL1).   87   72   351       677   2   359   955   gi|460911   fructose-bisphosphate aldolase [ Bacillus subtilis ]   87   78   597       677   3   934   1284   gi|460911   fructose-bisphosphate aldolase [ Bacillus subtilis ]   87   78   351       876   1   3   452   gi|1146247   asparaginyl-tRNA synthetase [ Bacillus subtilis ]   87   79   450       1376   1   214   2   gi|1065555   F46H6.4 gene product [ Caenorhabditis elegans ]   87   75   213       2206   1   3   374   gi|215098   excisionase [Bacteriophage 154a]   87   72   372       2938   1   3   290   gi|508979   GTP-binding protein [ Bacillus subtilis ]   87   69   288       3081   2   126   308   gi|467399   IMP dehydrogenase [ Bacillus subtilis ]   87   72   183       3535   1   3   401   gi|1405454   aconitase [ Bacillus subtilis ]   87   80   399       4238   1   275   3   gi|603769   HutU protein, urocanase [ Bacillus subtilis ]   87   73   273       4   8   8736   7045   gi|603769   HutU protein, urocanase [ Bacillus subtilis ]   86   72   1692       22   6   3738   3286   gi|410515   urease beta subunit [ Staphylococcus xylosus ]   86   73   453       54   2   1572   664   gi|289287   UDP-glucose pyrophosphorylase [ Bacillus subtilis ]   86   70   909       124   3   1713   1090   gi|556887   uracil phosphoribosyltransferase [ Bacillus subtilis ] pir|S49364|S49364   86   74   624                           uracil phosphoribosyltransferase -  Bacillus subtilis         148   3   1349   3448   gi|467458   cell division protein [ Bacillus subtilis ]   86   75   2100       148   4   3638   3859   gi|467460   unknown [ Bacillus subtilis ]   86   73   222       152   3   1340   2086   gi|1377835   pyruvate decarboxylase E-1 alpha subunit [ Bacillus subtilis ]   86   75   747       164   18   17347   19467   gi|1184680   polynucleotide phosphorylase [ Bacillus subtilis ]   86   72   2121       180   2   554   1159   gi|143467   ribosomal protein S4 [ Bacillus subtilis ]   86   80   606       205   3   2592   2218   gi|142464   ribosomal protein L17 [ Bacillus subtilis ]   86   77   375       205   26   12990   12616   gi|40107   ribosomal protein L22 [Bacillus stearothermophilus] ir|S10612|S10612   86   75   375                           ribosomal protein L22 -  Bacillus stearothermophilus         246   7   3140   2817   gi|467375   ribosomal protein S6 [ Bacillus subtilis ]   86   70   324       299   3   1196   1540   gi|39656   spoVG gene product [ Bacillus megaterium ]   86   70   345       299   7   3884   4345   gi|467440   ‘phosphoribosylpyrophosphate synthetase [ Bacillus subtilis ] gi|40218 PRPP   86   78   462                           synthetase (AA 1-317) [ Bacillus subtilis ]       304   5   2170   2523   gi|666983   putative ATP binding subunit [ Bacillus subtilis ]   86   65   354       310   2   1487   1678   gi|1177684   chorismate mutase [ Staphylococcus xylosus ]   86   71   192       337   5   2086   3405   gi|487434   isocitrate dehydrogenase [ Bacillus subtilis ]   86   78   1320       339   2   1109   729   gi|1118003   dihydroneopterin aldolase [ Staphylococcus haemolyticus ]   86   77   381       358   2   2124   3440   gi|1146219   28.2% of identity to the  Escherichia coli  GTP-binding protein Era; putative   86   73   1317                           [ Bacillus subtilis ]       404   2   1015   2058   gi|1303817   YqfA [ Bacillus subtilis ]   86   78   1044       581   2   452   243   gi|40056   phoP gene product [ Bacillus subtilis ]   86   71   210       642   2   338   1075   gi|1176399   EpiF [ Staphylococcus epidermidis ]   86   72   738       770   1   347   72   gi|143328   phoP protein (put.); putative [ Bacillus subtilis ]   86   69   276       865   1   890   3   gi|1146247   asparaginyl-tRNA synthetase [ Bacillus subtilis ]   86   74   888       868   2   963   1133   gi|1002911   transmembrane protein [ Saccharomyces cerevisiae ]   86   69   171       904   1   1   162   gi|1303912   YqhW [ Bacillus subtilis ]   86   72   162       989   1   35   433   gi|1303993   YqkL [ Bacillus subtilis ]   86   76   399       1212   1   150   4   gi|414014   ipa-90d gene product [ Bacillus subtilis ]   86   70   147       1323   1   2   148   gi|40041   pyruvate dehydrogenase (lipoamide) [ Bacillus stearothermophilus ]   86   75   147                           ir|S10798|DEBSPF pyruvate dehydrogenase (lipoamide) (EC 1.2.4.1) pha chain -                             Bacillus stearothermophilus         3085   2   310   80   gi|1354211   PET112-like protein [ Bacillus subtilis ]   86   86   231       3847   1   1   228   gi|296464   ATPase [ Lactococcus lactis ]   86   63   228       4487   1   240   4   gi|1022726   unknown [ Staphylococcus haemolyticus ]   86   73   237       4583   1   187   2   gi|1022725   unknown [ Staphylococcus haemolyticus ]   86   79   186       25   5   4287   5039   gi|1502421   3-ketoacyl-acyl carrier protein reductase [ Bacillus subtilis ]   85   64   753       56   21   29395   28163   gi|1408507   pyrimidine nucleoside transport protein [ Bacillus subtilis ]   85   69   1233       68   2   332   1192   gi|467376   unknown [ Bacillus subtilis ]   85   74   861       73   2   880   1707   gi|142992   glycerol kinase (glpK) (EC 2.7.1.30) [ Bacillus subtilis ] pir|B45868|B45868   85   72   828                           glycerol kinase (EC 2.7.1.30) -  Bacillus subtilis  sp|P18157|GLPK_BACSU                           GLYCEROL KINASE (EC 2.7.1.30) (ATP: GLYCEROL-PHOSPHOTRANSFERASE)                           (GLYCEROKINASE) (GK).       106   4   1505   3490   gi|143766   (thrSv) (EC 6.1.1.3) [ Bacillus subtilis ]   85   74   1986       128   2   1153   2202   gi|311924   glycerladehyde-3-phosphate dehydrogenase [ Clostridium pasteurianum ]   85   75   1050                           pir|S34254|S34254 glyceraldehyde-3-phosphate dehydrogenase (EC .2.1.12) -                             Clostridium pasteurianum         129   4   5252   4038   gi|1064807   ORTHININE AMINOTRANSFERASE [ Bacillus subtilis ]   85   73   1215       138   6   3475   5673   gi|1072419   glcB gene product [ Staphylococcus carnosus ]   85   74   2199       189   1   2   169   gi|467385   unknown [ Bacillus subtilis ]   85   65   168       205   15   8106   7588   gi|1044981   ribosomal protein S5 [ Bacillus subtilis ]   85   75   519       205   20   10596   10264   pir|A02819|R5BS   ribosomal protein L24 -  Bacillus stearothermophilus     85   72   333       220   6   6101   5712   gi|48980   secA gene product [ Bacillus subtilis ]   85   66   390       231   4   3159   1441   gi|1002520   MutS [ Bacillus subtilis ]   85   70   1719       243   9   8013   8783   gi|414011   ipa-87r gene product [ Bacillus subtilis ]   85   72   771       249   2   3186   478   gi|1405454   aconitase [ Bacillus subtilis ]   85   73   2709       302   1   140   475   gi|40173   homolog of  E. coli  ribosomal protein L21 [ Bacillus subtilis ]   85   72   336                           ir|S18439|S18439 Ribosomal protein L21 -  Bacillus subtilis                             p|P26908|RL21_BACSU 50S RIBOSOMAL PROTEIN L21 [BL20].       333   1   2968   491   gi|442360   ClpC adenosine triphosphatase [ Bacillus subtilis ]   85   69   2478       364   6   6082   8196   gi|871784   Clp-like ATP-dependent protease binding subunit [ Bos taurus ]   85   68   2115       448   2   1339   686   gi|405134   acetate kinase [ Bacillus subtilis ]   85   68   654       747   1   853   455   gi|1373157   orf-X; hypothetical protein; Method: conceptual translation supplied by   85   73   399                           author [ Bacillus subtilis ]       886   2   159   467   gi|541768   hemin permease [ Yersinia enterocolitica ]   85   55   309       1089   1   606   4   pir|B47154|B471   signal recognition particle 54K chain homolog Ffh -  Bacillus subtilis     85   71   603       1163   1   409   2   gi|304155   diaminopimelate decarboxylase [ Bacillus methanolicus ] sp|P41023|DCDA_BACMT   85   62   408                           DIAMINOPIMELATE DECARBOXYLASE (EC 4.1.1.20) DAP DECARBOXYLASE].       1924   1   251   15   gi|215098   excisionase [Bacteriophage 154a]   85   73   237       2932   1   390   4   gi|1041099   Pyruvate Kinase [ Bacillus licheniformis ]   85   71   387       3030   1   3   275   gi|42370   pyruvate formate-lyase [AA 1-760] [ Escherichia coli ] ir|S01788|S01788   85   74   273                           formate C-acetyltransferase (EC 2.3.1.54) -  Escherichia coli         3111   1   299   3   gi|63568   limb deformity protein [ Gallus gallus ]   85   85   297       3778   1   316   2   gi|391840   beta-subunit of HDT [Pseudomonas fragi]   85   67   315       3835   1   1   387   gi|1204472   type I restriction enzyme ECOR124/3 I M protein [ Haemophilus influenzae ]   85   56   387       4042   1   3   386   gi|18178   formare acetyltransferase [ Chlamydomonas reinhardtii ] ir|S24997|S24997   85   70   384                           formate C-acetyltransferase (EC 2.3.1.54) -  Chlamydomonas reinhardtii         4053   1   35   340   gi|1204472   type I restriction enzyme ECOR124/3 I M protein [ Haemophilus influenzae ]   85   56   306       4108   1   2   181   gi|1072418   glcA gene product [ Staphylococcus carnosus ]   85   61   180       4300   1   330   85   gi|151932   fructose enzyme II [ Rhodobacter capsulatus ]   85   59   246       4392   1   355   83   gi|1022725   unknown [ Staphylococcus haemolyticus ]   85   74   273       4408   1   2   235   gi|871784   Clp-like ATP-dependent protease binding subunit [ Bos taurus ]   85   62   234       4430   1   291   4   gi|1009366   Respiratory nitrate reductase [ Bacillus subtilis ]   85   68   288       4555   1   2   253   gi|450688   hsdM gene of EcoprrI gene product [ Escherichia coli ] pir|S38437|S38437 hsdM   85   52   252                           protein -  Escherichia coli  pir|S09629|S09629 hypothetical protein A -                             Escherichia coli  (SUB 40-520)       4611   1   242   3   gi|1256635   dihydroxy-acid dehydratase [ Bacillus subtilis ]   85   65   240       4   10   10061   10591   gi|46982   fosB gene product [ Staphylococcus epidermidis ]   84   68   531       13   2   1172   996   gi|142450   ahrC protein [ Bacillus subtilis ]   84   56   177       16   4   1803   4652   gi|1277198   DNA repair protein [Deinococcus radiodurans]   84   67   2850       22   3   1128   721   gi|511069   UreF [ Staphylococcus xylosus ]   84   73   408       23   7   5055   5306   gi|603320   Yer082p [ Saccharomyces cerevisiae ]   84   61   252       53   11   11145   10693   gi|1303948   YqiW [ Bacillus subtilis ]   84   68   453       53   12   12770   11481   gi|142613   branched chain alpha-keto acid dehydrogenase E2 [ Bacillus subtilis ]   84   71   1290                           gi|1303944 BfmBB [ Bacillus subtilis ]       70   1   982   632   gi|46647   ORF (repE) [ Staphylococcus aureus ]   84   68   351       73   4   2512   4311   gi|142993   glycerol-3-phosphate dehydrogenase (glpD) (EC 1.1.99.5) [ Bacillus subtilis ]   84   74   1800       98   7   4324   6096   gi|467427   methionyl-tRNA synthetase [ Bacillus subtilis ]   84   66   1773       100   9   8680   7859   gi|1340128   ORF1 [ Staphylococcus aureus ]   84   78   822       117   3   1934   3208   gi|1237019   Srb [ Bacillus subtilis ]   84   68   1275       148   6   4720   5670   gi|467462   cysteine synthetase A [ Bacillus subtilis ]   84   69   951       152   4   2064   2456   gi|143377   pyruvate decarboxylase (E-1) alpha subunit [ Bacillus subtilis ]   84   70   393                           pir|B36718|DEBSPA pyruvate dehydrogenase (lipoamide) (EC 1.2.4.1) lpha                           chain -  Bacillus subtilis         169   7   3634   3861   gi|1001342   hypothetical protein [Synechocystis sp.]   84   66   228       171   4   2657   2322   gi|517475   D-amino acid transaminase [ Staphylococcus haemolyticus ]   84   71   336       186   6   6216   5491   gi|467475   unknown [ Bacillus subtilis ]   84   70   726       205   9   5692   5123   gi|216340   ORF for adenylate kinase [ Bacillus subtilis ]   84   71   570       224   2   915   1391   gi|288269   beta-fructofuranosidase [ Staphylococcus xylosus ]   84   70   477       251   1   92   388   gi|1303790   YqeI [ Bacillus subtilis ]   84   65   297       282   3   1526   2836   gi|143040   glutamate-1-semialdehyde 2,1-aminotransferase [ Bacillus subtilis ]   84   75   1311                           pir|D42728|D42728 glutamate-1-semialdehyde 2,1-aminomutase (EC.4.3.8) -                             Bacillus subtilis         307   5   2959   2780   gi|1070014   protein-dependent [ Bacillus subtilis ]   84   62   180       320   4   2343   4229   gi|143390   carbamyl phosphate synthetase [ Bacillus subtilis ]   84   70   1887       372   1   3   296   gi|1022725   unknown [ Staphylococcus haemolyticus ]   84   70   294       413   2   1341   481   gi|1256146   YbbQ [ Bacillus subtilis ]   84   65   861       439   1   3   392   gi|1046173   osmotically inducible protein [ Mycoplasma genitalium ]   84   53   390       461   3   1362   2270   gi|40211   threonine synthase (thrC) (AA 1-352) [ Bacillus subtilis ] ir|A25364|A25364   84   69   909                           threonine synthase (EC 4.2.99.2) -  Bacillus subtilis         487   1   3   299   gi|1144531   integrin-like protein alpha Intlp [ Candida albicans ]   84   46   297       491   2   624   905   pir|S08564|R3BS   ribosomal protein S9 -  Bacillus stearothermophilus     84   69   282       491   3   836   1033   pir|S08564|R3BS   ribosomal protein S9 -  Bacillus stearothermophilus     84   77   198       548   1   3   341   gi|431231   uracil permease [ Bacillus caldolyticus ]   84   74   339       728   2   1748   795   gi|912445   DNA polymerase [Bacillus caldotenax]   84   68   954       769   1   3   257   gi|1510953   cobalamin biosynthesis protein N [ Methanococcus jannaschii ]   84   38   255       954   1   156   4   gi|1405454   aconitase [ Bacillus subtilis ]   84   57   153       957   1   3   395   gi|143402   recombination protein (ttg start codon) [ Bacillus subtilis ] gi|1303923 RecN   84   68   393                           [ Bacillus subtilis ]       975   1   3   452   gi|885934   ClpB [Synechococcus sp.]   84   70   450       1585   1   3   257   gi|510140   ligoendopeptidase F [ Lactococcus lactis ]   84   56   255       2954   1   3   323   gi|603769   HutU protein, urocanase [ Bacillus subtilis ]   84   73   321       2996   1   348   46   gi|18178   formate acetyltransferase [ Chlamydomonas reinhardtii ] ir|S24997|S24997   84   65   303                           formate C-acetyltransferase (EC 2.3.1.54) -  Chlamydomonas reinhardtii         3766   1   375   13   gi|517205   67 kDa Myosin-crossreactive streptococcal antigen [ Streptococcus yogenes ]   84   72   363       4022   1   2   169   gi|1146206   glutamate dehydrogenase [ Bacillus subtilis ]   84   54   168       4058   1   312   4   gi|151932   fructose enzyme II [ Rhodobacter capsulatus ]   84   71   309       4108   2   106   351   gi|1072418   glcA gene product [ Staphylococcus carnosus ]   84   77   246       4183   1   3   308   gi|603769   HutU protein, urocanase [ Bacillus subtilis ]   84   72   306       4726   1   55   234   gi|146208   glutamate synthase large subunit (EC 2.6.1.53) [ Escherichia coli ]   84   73   180                           pir|A29617|A29617 glutamate synthase (NADPH) (EC 1.4.1.13) large hain -                             Escherichia coli         22   4   1576   1109   gi|393297   urease accessory protein [Bacillus sp.]   83   64   468       53   13   13745   12768   gi|142612   branched chain alpha-keto acid dehydrogenase E1-beta [ Bacillus subtilis ]   83   68   978       57   16   12872   12387   gi|143132   lactate dehydrogenase (AC 1.1.1.27) [ Bacillus caldolyticus ]   83   66   486                           pir|B29704|B29704 L-lactate dehydrogenase (EC 1.1.1.27) -  Bacillus                               aldolyticus         66   3   2274   1429   gi|1303894   YqhM [ Bacillus subtilis ]   83   63   846       66   5   4643   3168   gi|1212730   YqhK [ Bacillus subtilis ]   83   68   1476       70   3   1523   1182   gi|44095   replication initiator protein [ Listeria monocytogenes ]   83   73   342       90   1   377   1429   gi|155571   alcohol dehydrogenase I (adhA) (EC 1.1.1.1) [ Zymomonas mobilis ]   83   70   1053                           pir|A35260|A35260 alcohol dehydrogenase (EC 1.1.1.1) I -  Zymomonas obilis         95   2   708   2162   gi|506381   phospho-beta-glucosidase [ Bacillus subtilis ]   83   70   1455       137   1   68   694   gi|467391   initiation protein of replicaton [ Bacillus subtilis ]   83   77   627       140   4   2742   2275   gi|634107   kdpB [ Escherichia coli ]   83   65   468       142   3   2989   2510   gi|1212776   lumazine synthase (b-subunit) [ Bacillus amyloliquefaciens ]   83   69   480       161   12   5749   6696   gi|903307   ORF75 [ Bacillus subtilis ]   83   64   948       164   9   9880   11070   gi|49316   ORF2 gene product [ Bacillus subtilis ]   83   66   1191       164   14   14148   14546   gi|580902   ORF6 gene product [ Bacillus subtilis ]   83   60   399       170   2   2467   1790   gi|520844   orf4 [ Bacillus subtilis ]   83   64   678       186   2   1370   711   gi|289284   cysteinyl-tRNA synthetase [ Bacillus subtilis ]   83   72   660       205   14   7607   7392   gi|216337   ORF for L30 ribosomal protein [ Bacillus subtilis ]   83   74   216       237   6   3683   4540   gi|1510488   imidazoleglycerol-phosphate synthase (cyclase) [ Methanococcus jannaschii ]   83   60   858       301   1   638   291   gi|467419   unknown [ Bacillus subtilis ]   83   65   348       302   4   1421   2743   gi|508979   GTP-binding protein [ Bacillus subtilis ]   83   68   1323       321   4   3571   3209   gi|39844   fumarase (citG) (aa 1-462) [ Bacillus subtilis ]   83   68   363       367   1   2   352   gi|1039479   ORFU [ Lactococcus lactis ]   83   54   351       387   1   3   662   gi|806281   DNA polymerase I [ Bacillus stearothermophilus ]   83   70   660       527   2   916   1566   gi|396259   protease [ Staphylococcus epidermidis ]   83   67   651       533   1   179   3   gi|142455   alanine dehydrogenase (EC 1.4.1.1) [ Bacillus stearothermophilus ]   83   66   177                           pir|B34261|B34261 alanine dehydrogenase (EC 1.4.1.1) -  Bacillus                               stearothermophilus         536   4   1438   1259   gi|143366   adenylosuccinate lyase (PUR-B) [ Bacillus subtilis ] pir|C29326|WZBSDS   83   67   180                           adenylosuccinate lyase (EC 4.3.2.2) -  Bacillus subtilis         652   1   2   859   gi|520753   DNA topoisomerase I [ Bacillus subtilis ]   83   72   858       774   2   200   361   gi|1522665     M. jannaschii  predicted coding region MJECL28 [ Methanococcus jannaschii ]   83   58   162       897   1   120   296   gi|1064807   ORTHININE AMINOTRANSFERASE [ Bacillus subtilis ]   83   76   177       1213   1   3   491   gi|289288   lexA [ Bacillus subtilis ]   83   67   489       2529   1   150   4   gi|143786   tryptophanyl-tRNA synthetase (EC 6.1.1.2) [ Bacillus subtilis ]   83   69   147                           pir|JT0481|YWBS tryptophan - tRNA ligase (EC 6.1.1.2) -  Bacillus subtilis         2973   1   326   3   gi|1109687   ProZ [ Bacillus subtilis ]   83   58   324       3009   1   366   4   gi|882532   ORF_o294 [ Escherichia coli ]   83   65   363       3035   2   45   305   gi|950062   hypothetical yeast protein 1 [ Mycoplasma capricolum ] pir|S48578|S48578   83   59   261                           hypothetical protein -  Mycoplasma capricolum  SGC3) (fragment)       3906   1   67   309   gi|1353197   thioredoxin reductase [Eubacterium acidaminophilum]   83   61   243       4458   1   271   2   gi|397526   clumping factor [ Staphylococcus aureus ]   83   78   270       4570   1   223   2   gi|1022726   unknown [ Staphylococcus haemolyticus ]   83   74   222       4654   1   97   261   gi|1072419   glcB gene product [ Staphylococcus carnosus ]   83   79   165       16   2   295   1191   gi|153854   uvs402 protein [Streptococcus pneumoniae]   82   67   897       16   3   1193   1798   gi|153854   uvs402 protein [Streptococcus pneumoniae]   82   70   606       38   12   8724   7804   gi|1204400   N-acetylneuraminate lyase [ Haemophilus influenzae ]   82   58   921       42   4   988   2019   gi|841192   catalase [Bacteroides fragilis]   82   70   1032       51   6   2590   3489   gi|143607   sporulation protein [ Bacillus subtilis ]   82   69   900       56   11   12270   13925   gi|39431   oligo-1,6-glucosidase [ Bacillus cereus ]   82   60   1656       56   15   17673   18014   gi|467410   unknown [ Bacillus subtilis ]   82   66   342       61   2   881   3313   gi|143148   transfer RNA-Leu synthetase [ Bacillus subtilis ]   82   70   2433       82   7   9162   11318   gi|48240   elongation factor G (AA 1-691) [ Thermus aquaticus thermophilus ]   82   64   2157                           ir|S15928|EFTWG translation elongation factor G -  Thermus aquaticus                             p|P13551|EFG_THETH ELONGATION FACTOR G (EF-G).       85   2   3260   1050   gi|143369   phosphoribosylformyl glycinamidine synthetase II (PUR-Q) [ Bacillus subtilis ]   82   66   2211       102   6   3662   5380   gi|1256635   dihydroxy-acid dehydratase [Bacillus subtilis|   82   65   1719       117   4   3242   3493   pir|A47154|A471   orf1 5′ of Ffh -  Bacillus subtilis     82   53   252       128   6   4377   5933   gi|460258   phosphoglycerate mutase [ Bacillus subtilis ]   82   66   1557       129   2   1229   2182   gi|403373   glycerophosphoryl diester phosphodiesterase [ Bacillus subtilis ]   82   62   954                           pir|S37251|S37251 glycerophosphoryl diester phosphodiesterase - Bacillus                               subtilis         170   1   2   1441   gi|1377831   unknown [ Bacillus subtilis ]   82   67   1440       177   1   3   1094   gi|467386   thiophen and furan oxidation [ Bacillus subtilis ]   82   65   1092       184   4   3572   4039   gi|153566   ORF (19 K protein) [Enterococcus faecalis]   82   59   468       189   8   4225   3995   gi|1001878   CspL protein [ Listeria monocytogenes ]   82   73   231       206   19   20707   20048   gi|473916   lipopeptide antibiotics iturin A [ Bacillus subtilis ]sp|P39144|LP14_BACSU   82   50   660                           LIPOPEPTIDE ANTIBIOTICS ITURIN A AND SURFACTIN IOSYNTHESIS PROTEIN.       221   2   805   1722   gi|517205   67 kDa Myosin-crossreactive streptococcal antigen [ Streptococcus yogenes ]   82   63   918       223   4   3651   3436   gi|439619   [ Salmonella typhimurium  IS200 insertion sequence from SARA17, artial.],   82   69   216                           gene product [ Salmonella typhimurium ]       260   3   4296   3385   gi|1161381   IcaB [ Staphylococcus epidermidis ]   82   61   912       315   3   2855   846   gi|143397   quinol oxidase [ Bacillus subtilis ]   82   67   2010       321   10   7945   7370   gi|142981   ORF5; This ORF includes a region (aa23-103) containing a potential ron-   82   62   576                           sulphur centre homologous to a region of Rhodospirillum rubrum nd                           Chromatium vinosum; putative [ Bacillus stearothermophilus ]                           pir|PQ0299|PQ0299 hypothetical protein 5 (gldA 3′ region) -       331   3   1055   1342   gi|436574   ribosomal protein L1 [ Bacillus subtilis ]   82   71   288       370   2   262   618   gi|1303793   YqeL [ Bacillus subtilis ]   82   59   357       404   4   3053   4024   gi|1303821   YqfE [ Bacillus subtilis ]   82   68   972       405   4   3073   1706   gi|1303913   YqhX [ Bacillus subtilis ]   82   67   1368       436   3   2864   1632   gi|149521   tryptophan synthase beta subunit [ Lactococcus lactis ]pir|S35129|S35129   82   67   1233                           tryptophan synthase (EC 4.2.1.20) beta chain -  Lactococcus lactis subsp.                             lactis       441   4   2573   1752   gi|142952   glyceraldehyde-3-phosphate dehydrogenase [Bacillus tearothermophilus]   82   67   822       444   12   10415   11227   gi|1204354   spore germination and vegetative growth protein [ Haemophilus influenzae ]   82   67   813       446   1   3   191   gi|143387   aspartate transcarbamylase [ Bacillus subtilis ]   82   66   189       462   3   1007   1210   gi|142521   deoxyribodipyrimidine photolyase [ Bacillus subtilis ] pir|A37192|A37192 uvrB   82   64   204                           protein -  Bacillus subtilis  sp|P14951|UVRC_BACSU EXCINUCLEASE ABC SUBUNIT C.       537   1   784   8   gi|853767   UDP-N-acetylglucosamine 1-carboxyvinyltransferase [ Bacillus subtilis ]   82   61   777       680   2   407   700   gi|426472   secE gene product [ Staphylococcus carnosus ]   82   69   294       724   2   386   207   gi|143373   phosphoribosyl aminoimidazole carboxy formyl ormyltransferase/inosine   82   68   180                           monophosphate cyclohydrolase (PUR-H(J)) Bacillus subtilis)       763   1   213   4   gi|467458   cell division protein [ Bacillus subtilis ]   82   35   210       818   1   283   2   gi|1064787   function unknown [ Bacillus subtilis ]   82   69   282       858   1   175   1176   gi|143043   uroporphyrinogen decarboxylase [ Bacillus subtilis ] pir|B47045|B47045   82   71   1002                           uroporphyrinogen decarboxylase (EC 4.1.1.37) -  Bacillus subtilis         895   1   3   599   gi|1027507   ATP binding protein [Borrelia burgdorferi]   82   72   597       939   1   10   399   gi|143795   transfer RNA-Tyr synthetase [ Bacillus subtilis ]   82   60   390       961   1   1   306   gi|577647   gamma-hemolysin [ Staphylococcus aureus ]   82   69   306       1192   1   155   3   gi|146974   NH3-dependent NAD synthetase [ Escherichia coli ]   82   71   153       1317   1   49   375   gi|407908   EIIscr [ Staphylococcus xylosus ]   82   72   327       1341   1   1   150   gi|39962   ribosomal protein L35 (AA 1-66) [ Bacillus stearothermophilus ]   82   68   150                           ir|S05347|R5BS35 ribosomal protein L35 -  Bacillus earothermophilus         2990   2   349   131   gi|534855   ATPase subunit epsilon [ Bacillus stearothermophilus ]sp|P42009|ATPE_BACST   82   47   219                           ATP SYNTHASE EPSILON CHAIN (EC 3.6.1.34).       3024   1   45   224   gi|467402   unknown [ Bacillus subtilis ]   82   64   180       3045   1   139   2   gi|467335   ribosomal protein L9 [ Bacillus subtilis ]   82   60   138       3045   2   400   242   gi|467335   ribosomal protein L9 [ Bacillus subtilis ]   82   82   159       3091   1   238   2   gi|499335   secA protein [ Staphylococcus carnosus ]   82   78   237       3107   1   210   4   gi|546918   orfY 3′ of comK [Bacillus subtilis, E26, Peptide Partial, 140 aa]   82   64   207                           pir|S43612|S43612 hypothetical protein Y -  Bacillus subtilis                             sp|P40398|YHXD_BACSU HYPOTHETICAL PROTEIN IN COMK 3′ REGION (ORFY)                           FRAGMENT).       4332   1   2   319   gi|42086   nitrate reductase alpha subunit [ Escherichia coli ] p|P09152|NARG_ECOLI   82   75   318                           RESPIRATORY NITRATE REDUCTASE 1 ALPHA CHAIN (EC 7.99.4). (SUB 2-1247)       23   3   2574   1873   gi|1199573   spsB [Sphingomonas sp.]   81   64   702       42   1   321   4   gi|466778   lysine specific permease [ Escherichia coli ]   81   59   318       48   5   4051   4350   gi|1045937   M. genitalium predicted coding region MG246 [ Mycoplasma genitalium ]   81   62   300       51   4   1578   2579   pir|S16649|S166   dciAC protein -  Bacillus subtilis     81   55   1002       53   2   364   1494   gi|1303961   YqjJ [ Bacillus subtilis ]   81   67   1131       53   8   7971   6523   gi|146930   6-phosphogluconate dehydrogenase [ Escherichia coli ]   81   66   1449       54   9   10119   9481   gi|143016   permease [ Bacillus subtilis ]   81   65   639       54   10   11786   10212   gi|143015   gluconate kinase [ Bacillus subtilis ]   81   64   1575       57   17   13366   12749   pir|A25805|A258   L-lactate dehydrogenase (EC 1.1.1.27) -  Bacillus subtilis     81   74   618       81   2   2217   1726   gi|1222302   NifU-related protein [ Haemophilus influenzae ]   81   54   492       86   1   374   3   gi|414017   ipa-93d gene product [ Bacillus subtilis ]   81   70   372       103   6   4861   3284   gi|971342   nitrate reductase beta subunit [ Bacillus subtilis ] sp|P42176|NARH_BACSU   81   64   1578                           NITRATE REDUCTASE BETA CHAIN (EC 1.7.99.4).       120   15   10845   12338   gi|1524392   GbsA [ Bacillus subtilis ]   81   67   1494       128   5   3676   4413   gi|143319   triose phosphate isomerase [ Bacillus megaterium ]   81   64   738       131   9   9280   8252   gi|299163   alanine dehydrogenase [ Bacillus subtilis ]   81   68   1029       143   6   5471   4854   gi|439619   [Salmonella typhimurium IS200 insertion sequence from SARA17, artial.],   81   61   618                           gene product [ Salmonella typhimurium ]       169   1   43   825   gi|897795   30S ribosomal protein [ Pediococcus acidilactici ] sp|P49668|RS2_PEDAC 30S   81   65   783                           RIBOSOMAL PROTEN S2.       230   1   226   2   gi|1125826   short region of weak similarity to tyrosine-protein kinase receptors in a   81   54   225                           fibronectin type III-like domain [ Caenorhabditis elegans ]       233   5   2000   2677   gi|467404   unknown [ Bacillus subtilis ]   81   63   678       241   2   2149   1217   gi|16510   succinate - CoA ligase (GDP-forming) [ Arabidopsis thaliana ] ir|S30579|S30579   81   69   933                           succinate—CoA ligase (GDP-forming) (EC 6.2.1.4) pha chain -  Arabidopsis                               thaliana  (fragment)       256   1   1   981   pir|S09411|S094   spoIIIE protein - [ Bacillus subtilis ]   81   65   981       259   3   2691   1630   sp|P28367|RF2_B   PROBABLE PEPTIDE CHAIN RELEASE FACTOR 2 (RF-2) (FRAGMENT).   81   65   1062       275   2   1728   3581   gi|726480   L-glutamine-n-fructose-6-phosphate amidotransferase [ Bacillus subtilis ]   81   68   1854       285   1   735   4   gi|1204844     H. influenzae  predicted coding region HI0594 [ Haemophilus influenzae ]   81   63   732       296   1   99   1406   gi|467328   adenylosuccinate synthetase [ Bacillus subtilis ]   81   67   1308       302   9   5590   5889   gi|147485   queA [ Escherichia coli ]   81   64   300       317   2   1137   1376   gi|154961   resolvase [Transposon Tn917]   81   51   240       343   2   1034   1342   gi|405955   yeeD [ Escherichia coli ]   81   60   309       360   2   1404   2471   gi|1204570   aspartyl-tRNA synthetase [ Haemophilus influenzae ]   81   67   1068       364   5   5706   5161   gi|1204652   methylated-DNA-protein-cysteine methyltransferase [ Haemophilus influenzae ]   81   63   546       372   2   1135   563   gi|467416   unknown [ Bacillus subtilis ]   81   65   573       392   1   43   603   pir|S09411|S094   spoIIIE protein -  Bacillus subtilis     81   65   561       404   9   5252   6154   gi|606745   Bex [ Bacillus subtilis ]   81   65   903       426   2   1119   511   gi|39453   Manganese superoxide dismutase [Bacillus caldotenax] ir|S22053|S22053   81   66   609                           superoxide dismutase (EC 1.15.1.1) (Mn) -  Bacillus ldotenax         480   7   5653   5889   pir|C37083|C370   hypothetical protein II (ompH 3′ region) -  Salmonella typhimurium     81   57   237                           [fragment]       625   3   1105   2070   gi|1262360   protein kinase PknB [Mycobacterium leprae]   81   56   966       754   2   504   1064   gi|1303902   YqhU [ Bacillus subtilis ]   81   71   561       842   1   86   430   gi|1405446   transketolase [ Bacillus subtilis ]   81   68   345       953   1   400   2   gi|1205429   dipeptide transport ATP-binding protein [ Haemophilus influenzae ]   81   57   399       961   2   252   401   gi|487686   synergohymenotropic toxin [ Staphylococcus intermedius ] pir|S44944|S44944   81   72   150                           synergohymenotropic toxin -  Staphylococcus intermedius         1035   1   1   189   gi|1046138     M. genitalium  predicted coding region MG423 [ Mycoplasma genitalium ]   81   43   189       1280   1   449   228   gi|559164   helicase [Autographa californica nuclear polyhedrosis virus]   81   43   222                           sp|P24307|V143_NPVAC HELICASE.       3371   1   68   241   gi|1322245   mevalonate pyrophosphate decarboxylase [ Rattus norvegicus ]   81   62   174       3715   1   239   3   gi|537137   ORF_f388 [ Escherichia coli ]   81   58   237       3908   1   2   325   gi|439619   [Salmonella typhimurium IS200 insertion sequence from SARA17, artial.],   81   68   324                           gene product [ Salmonella typhimurium ]       3940   1   3   401   gi|296464   ATPase [ Lactococcus lactis ]   81   69   399       3954   1   1   318   gi|1224069   amidase [Moraxella catarrhalis]   81   68   318       4049   1   170   3   gi|603768   HutI protein, imidazolone-5-propionate hydrolase [ Bacillus subtilis ]   81   68   168                           gi|603768 HutI protein, imidazolone-5-propionate hydrolase  Bacillus                               subtilis ]       4209   1   1   324   gi|403373   glycerophosphoryl diester phosphodiesterase [ Bacillus subtilis ]   81   58   324                           pir|S37251|S37251 glycerophosphoryl diester phosphodiesterase -  Bacillus                               subtilis         4371   1   322   17   gi|216677   indolepyruvate decarboxylase [Enterobacter cloacae] pir|S16013|S16013   81   72   306                           indolepyruvate decarboxylase (EC 4.1.1.—) -  Enterobacter cloacae         4387   1   19   228   gi|460689   TVG [Thermoactinomyces vulgaris]   81   59   210       4391   1   306   31   gi|1524193   unknown [ Mycobacterium tuberculosis ]   81   67   276       4425   1   3   341   gi|143015   gluconate kinase [ Bacillus subtilis ]   81   66   339       9   1   847   101   gi|1064786   function unknown [ Bacillus subtilis ]   80   62   747       17   1   311   78   gi|559164   helicase [Autographa californica nuclear polyhedrosis virus]   80   40   234                           sp|P24307|V143_NPVAC HELICASE.       45   2   1159   2448   gi|1109684   ProV [ Bacillus subtilis ]   80   63   1290       45   5   4032   4733   gi|1109687   ProZ [ Bacillus subtilis ]   80   55   702       54   8   9502   8738   gi|563952   gluconate permease [ Bacillus licheniformis ]   80   62   765       62   12   7545   6238   gi|854655   Na/H antiporter system [Bacillus alcalophilus]   80   62   1308       62   14   8087   8683   gi|559713   ORF [ Homo sapiens ]   80   68   597       67   16   13781   14122   gi|305002   ORF_f356 [ Escherichia coli ]   80   65   342       70   13   10296   9097   gi|1303995   YqkN [ Bacillus subtilis ]   80   64   1200       98   9   6336   7130   gi|467428   unknown [ Bacillus subtilis ]   80   68   795       98   10   7294   7833   gi|467430   unknown [ Bacillus subtilis ]   80   64   540       98   11   7820   8737   gi|467431   high level kasgamycin resistance [ Bacillus subtilis ]   80   61   918       109   16   14154   14813   gi|580875   ipa-57d gene product [ Bacillus subtilis ]   80   63   660       112   15   14294   16636   gi|1072361   pyruvate-formate-lyase [ Clostridium pasteurianum ]   80   65   2343       139   1   726   4   gi|506699   CapC [ Staphylococcus aureus ]   80   58   723       139   2   1448   717   gi|506698   CapB [ Staphylococcus aureus ]   80   59   732       174   4   2870   2469   gi|1146242   aspartate 1-decarboxylase [ Bacillus subtilis ]   80   61   402       177   3   2102   2842   gi|467385   unknown [ Bacillus subtilis ]   80   70   741       184   6   5912   5700   gi|161953   85-kDa surface antigen [Trypanosoma cruzi]   80   46   213       186   4   3875   2382   gi|289282   glutamyl-tRNA synthetase [ Bacillus subtilis ]   80   65   1494       205   30   15140   14484   gi|40103   ribosomal protein L4 [ Bacillus stearothermophilus ]   80   66   657       207   1   140   1315   gi|460259   enolase [ Bacillus subtilis ]   80   67   1176       211   3   1078   1590   gi|410131   ORFX7 [ Bacillus subtilis ]   80   61   513       235   2   1962   2255   gi|143797   valyl-tRNA synthetase [ Bacillus stearothermophilus ] sp|P11931|SYV_BACST   80   55   294                           VALYL-TRNA SYNTHETASE (EC 6.1.1.9) VALINE-TRNA LIGASE) (VALRS).       239   1   1   1263   gi|143000   proton glutamate symport protein [ Bacillus stearothermophilus ]   80   59   1263                           pir|S26247|S26247 glutamate/aspartate transport protein -  Bacillus                               stearothermophilus         272   5   2461   2198   gi|709993   hypothetical protein [ Bacillus subtilis ]   80   54   264       301   3   1111   776   gi|467418   unknown [ Bacillus subtilis ]   80   58   336       310   4   4501   3305   gi|1177686   acuC gene product [ Staphylococcus xylosus ]   80   67   1197       310   6   5258   7006   gi|348053   acetyl-CoA synthetase [ Bacillus subtilis ]   80   67   1749       310   7   7410   9113   gi|1103865   formyl-tetrahydrofolate synthetase [Streptococcus mutans]   80   67   1704       325   3   1114   1389   gi|310325   outer capsid protein [Rotavirus sp.]   80   40   276       337   1   636   4   gi|537049   ORF_o470 [ Escherichia coli ]   80   55   633       374   2   929   1228   gi|1405448   YneF [ Bacillus subtilis ]   80   70   300       375   5   3062   3331   gi|467448   unknown [ Bacillus subtilis ]   80   68   270       388   1   267   587   gi|1064791   function unknown [ Bacillus subtilis ]   80   65   321       394   1   9   659   gi|304976   matches PS00017: ATP_GTP_A and PS00301: EFACTOR_GTP; similar to longation   80   65   651                           factor G, TetM/Tet0 tetracycline-resistance proteins  Escherichia coli ]       456   1   625   1263   gi|1146183   putative [ Bacillus subtilis ]   80   65   639       475   1   1   654   gi|288269   beta-fructofuranosidase [ Staphylococcus xylosus ]   80   66   654       544   2   1449   2240   gi|529754   speC [ Streptococcus pyogenes ]   80   50   792       622   4   1623   1871   gi|1483545   unknown [ Mycobacterium tuberculosis ]   80   65   249       719   1   1   1257   gi|1064791   function unknown [ Bacillus subtilis ]   80   68   1257       739   1   107   838   gi|666983   putative ATP binding subunit [ Bacillus subtilis ]   80   61   732       745   2   414   247   gi|1511600   coenzyme PQQ synthesis protein III [ Methanococcus jannaschii ]   80   61   168       822   1   17   679   gi|410141   ORFX17 [ Bacillus subtilis ]   80   68   663       827   2   836   681   gi|1205301   leukotoxin secretion ATP-binding protein [ Haemophilus influenzae ]   80   54   156       1044   1   3   149   gi|60632   vp2 [Marburg virus]   80   55   147       1220   2   413   255   pir|A61072|EPSG   gallidermin precursor -  Staphylococcus gallinarum     80   74   159       2519   1   75   275   gi|147556   dpj [ Escherichia coli ]   80   45   201       2947   1   279   55   gi|1184680   polynucleotide phosphorylase [ Bacillus subtilis ]   80   62   225       3120   1   2   226   gi|517205   67 kDa Myosin-crossreactive streptococcal antigen [ Streptococcus yogenes ]   80   65   225       3191   1   148   2   gi|151259   HMG-CoA reductase (EC 1.1.1.88) [ Pseudomonas mevalonii ] pir|A44756|A44756   80   59   147                           hydroxymethylglutaryl-CoA reductase (EC 1.1.1.88) Pseudomonas sp.       3560   2   285   434   gi|217130   photosystem I core protein B [Synechococcus vulcanus]   80   70   150       3655   1   47   346   gi|415855   deoxyribose aldolase [ Mycoplasma hominis ]   80   56   300       3658   2   324   584   gi|551531   2-nitropropane dioxygenase [Williopsis saturnus]   80   54   261       3769   1   400   2   gi|1339950   large subunit of NADH-dependent glutamate synthase [ Plectonema boryanum ]   80   68   399       3781   1   348   4   gi|166412   NADH-glutamate synthase [Medicago sativa]   80   62   345       3988   1   48   287   gi|1204696   fructose-permease IIBC component [ Haemophilus influenzae ]   80   69   240       4030   1   287   3   gi|1009366   Respiratory nitrate reductase [ Bacillus subtilis ]   80   60   285       4092   1   275   3   gi|1370207   orf6 [ Lactobacillus sake ]   80   69   273       4103   1   342   4   gi|39956   IIGlc [ Bacillus subtilis ]   80   65   339       4231   1   348   4   gi|289287   UDP-glucose pyrophosphorylase [ Bacillus subtilis ]   80   65   345       4265   1   299   3   gi|603768   HutI protein, imidazolone-5-propionate hydrolase [ Bacillus subtilis ]   80   63   297                           gi|603768 HutI protein, imidazolone-5-propionate hydrolase  Bacillus                               subtilis ]       4504   1   250   2   gi|1339950   large subunit of NADH-dependent glutamate synthase [ Plectonema boryanum ]   80   68   249       2   6   5998   6798   gi|535351   codY [ Bacillus subtilis ]   79   63   801       4   7   7051   5807   gi|603768   HutI protein, imidazolone-5-propionate hydrolase [ Bacillus subtilis ]   79   64   1245                           gi|603768 HutI protein, imidazolone-5-propionate hydrolase  Bacillus                               subtilis ]       25   6   5273   5515   pir|A36728|A367   acyl carrier protein -  Rhizobium meliloti     79   65   243       59   2   1173   1424   gi|147923   threonine dehydratase 2 (EC 4.2.1.16) [ Escherichia coli ]   79   75   252       60   1   1   204   gi|666115   orf1 upstream of glucose kinase [ Staphylococcus xylosus ]pir|S52351|S52351   79   60   204                           hypothetical protein 1 - Staphylococcus xylosus       81   1   1590   178   gi|466882   pps1; B1496_C2_189  [Mycobacterium leprae]   79   64   1413       85   7   6505   5987   gi|143364   phosphoribosyl aminoimidazole carboxylase I (PUR-E) [ Bacillus subtilis ]   79   60   519       89   6   4554   3448   gi|144906   product homologous to  E. coli  thioredoxin reductase: J. Biol. Chem. 1988)   79   35   1107                           263: 9015-9019, and to F52a protein of alkyl hydroperoxide eductase from                             S. typhimurium : J.Biol.Chem. (1990) 265: 10535-10540; pen reading frame A                           [ Clostridium pasteurianum ]       102   11   7489   8571   gi|143093   ketol-acid reductoisomerase [ Bacillus subtilis ] sp|P37253|ILVC_BACSU KETOL-   79   64   1083                           ACID REDUCTOISOMERASE (EC 1.1.1.86) ACETOHYDROXY-ACID ISOMEROREDUCTASE)                           (ALPHA-KETO-BETA-HYDROXYLACIL EDUCTOISOMERASE).       102   14   11190   12563   gi|149428   putative [ Lactococcus lactis ]   79   65   1374       127   9   7792   9372   gi|458688   PrfC/RF3 [ Dichelobacter nodosus ]   79   68   1581       139   3   1983   1426   gi|506697   CapA [ Staphylococcus aureus ]   79   55   558       144   2   1156   668   gi|1498296   peptide methionine sulfoxide reductase [Streptococcus pneumoniae]   79   47   489       148   2   529   1098   gi|467457   hypoxanthine-guanine phosphoribosyltransferase [ Bacillus subtilis ]   79   59   570                           gi|467457 hypoxanthine-guanine phosphoribosyltransferase [ Bacillus                               subtilis ]       150   1   591   217   gi|755602   unknown [ Bacillus subtilis ]   79   61   375       176   1   587   135   gi|297874   fructose-bisphosphate aldolase [ Staphylococcus carnosus ] pir|A49943|A49943   79   65   453                           fructose-bisphosphate aldolase (EC 4.1.2.13) -  Staphylococcus carnosus                             (strain TM300)       186   7   6874   6164   gi|1314298   ORF5; putative Sms protein; similar to Sms proteins from  Haemophilus     79   64   711                             influenzae  and  Escherichia coli  [ Listeria monocytogenes ]       205   16   8498   8109   gi|1044980   ribosomal protein L18 [ Bacillus subtilis ]   79   70   390       211   1   1   519   gi|1303994   YqkM [ Bacillus subtilis ]   79   62   519       223   2   2801   1419   gi|488430   alcohol dehydrogenase 2 [ Entamoeba histolytica ]   79   60   1383       243   8   7896   6877   gi|580883   ipa-88d gene product [ Bacillus subtilis ]   79   60   1020       279   4   3721   4329   gi|413930   ipa-6d gene product [ Bacillus subtilis ]   79   59   609       300   1   11   1393   gi|403372   glycerol 3-phosphate permease [ Bacillus subtilis ]   79   62   1383       307   3   1935   940   gi|950062   hypothetical yeast protein 1 [ Mycoplasma capricolum ] pir|S48578|S48578   79   60   996                           hypothetical protein -  Mycoplasma capricolum  SGC3) (fragment)       352   6   8886   7666   gi|216854   P47K [ Pseudomonas chlororaphis ]   79   59   1221       412   1   578   3   gi|143177   putative [ Bacillus subtilis ]   79   51   576       481   3   621   1124   gi|786163   Ribosomal Protein L10 [ Bacillus subtilis ]   79   66   504       516   1   352   2   gi|805090   NisF [ Lactococcus lactis ]   79   48   351       525   2   1426   395   gi|143371   phosphoribosyl aminoimidazole synthetase (PUR-M) [ Bacillus subtilis ]   79   61   1032                           pir|H29326|AJBSCL phosphoribosylformylglycinamidine cyclo-ligase EC                           6.3.3.1) -  Bacillus subtilis         538   4   2825   2202   gi|1370207   orf6 [ Lactobacillus sake ]   79   67   624       570   1   2   421   gi|476160   arginine permease substrate-binding subunit [ Listeria monocytogenes ]   79   61   420       645   8   2663   3241   gi|153898   transport protein [ Salmonella typhimurium ]   79   62   579       683   1   75   374   gi|1064795   function unknown [ Bacillus subtilis ]   79   62   300       816   3   3987   3274   gi|1407784   orf-1; novel antigen [ Staphylococcus aureus ]   79   62   714       2929   1   3   401   gi|1524397   glycine betaine transporter OpuD [ Bacillus subtilis ]   79   61   399       2937   1   202   47   pir|S52915|S529   nitrate reductase alpha chain -  Bacillus subtilis  (fragment)   79   58   156       2940   1   385   2   gi|149429   putative [ Lactococcus lactis ]   79   72   384       2946   1   286   2   gi|143267   2-oxoglutarate dehydrogenase (odhA; EC 1.2.4.2) [ Bacillus subtilis ]   79   61   285       2999   1   3   212   gi|710020   nitrite reductase (nirB) [ Bacillus subtilis ]   79   59   210       3022   1   332   150   gi|450686   3-phosphoglycerate kinase [Thermotoga maritima]   79   61   183       3064   1   3   314   gi|1204436   pyruvate formate-lyase [ Haemophilus influenzae ]   79   60   312       3083   1   2   220   gi|1149662   hypD gene product [Clostridium perfringens]   79   56   219       3126   1   411   121   gi|1339950   large subunit of NADH-dependent glutamate synthase [ Plectonema boryanum ]   79   55   291       3181   1   326   45   gi|1339950   large subunit of NADH-dependent glutamate synthase [ Plectonema boryanum ]   79   59   282       3345   1   3   476   gi|871784   Clp-like ATP-dependent protease binding subunit [ Bos taurus ]   79   63   474       3718   1   270   4   pir|C36889|C368   leuB protein, inactive -  Lactococcus lactis  subsp. lactis (strain IL1403)   79   71   267       3724   2   159   401   gi|1009366   Respiratory nitrate reductase [ Bacillus subtilis ]   79   64   243       3836   1   312   16   gi|1524193   unknown [ Mycobacterium tuberculosis ]   79   65   297       3941   1   2   334   gi|415855   deoxyribose aldolase [ Mycoplasma hominis ]   79   54   333       4113   1   3   341   gi|143015   gluconate kinase [ Bacillus subtilis ]   79   63   339       4501   1   209   12   gi|1022726   unknown [ Staphylococcus haemolyticus ]   79   66   198       4612   1   2   238   gi|460689   TVG [Thermoactinomyces vulgaris]   79   58   237       2   1   2   1213   gi|520753   DNA topoisomerase I [ Bacillus subtilis ]   78   64   1212       8   2   1220   174   gi|216151   DNA polymerase (gene L; ttg start codon) [Bacteriophage SP02] gi|579197   78   72   1047                           SP02 DNA polymerase (aa 1-648) [Bacteriophage SP02] pir|A21498|DJBPS2 DNA-                           directed DNA polymerase (EC 2.7.7.7) - phage P02       9   2   1089   838   gi|1064787   function unknown [ Bacillus subtilis ]   78   57   252       32   8   6803   7702   gi|146974   NH3-dependent NAD synthetase [ Escherichia coli ]   78   63   900       36   4   2941   3138   gi|290503   glutamate permease [ Escherichia coli ]   78   53   198       53   15   16221   14758   gi|1303941   YqiV [ Bacillus subtilis ]   78   58   1464       57   14   10520   12067   gi|1072418   glcA gene product [ Staphylococcus carnosus ]   78   65   1548       66   7   5812   4826   gi|1212729   YqhJ [ Bacillus subtilis ]   78   67   987       67   4   4029   4376   gi|466612   nikA [ Escherichia coli ]   78   71   348       91   9   10058   10942   gi|467380   stage 0 sporultion [ Bacillus subtilis ]   78   50   885       102   12   8574   10130   gi|149426   putative [ Lactococcus lactis ]   78   61   1557       112   6   3540   4463   gi|854234   cymG gene product [Klebsiella oxytoca]   78   56   924       124   2   1061   234   gi|405622   unknown [ Bacillus subtilis ]   78   60   828       130   3   1805   2260   gi|1256636   putative [ Bacillus subtilis ]   78   71   456       133   1   377   3   gi|168060   lamB [ Emericella nidulans ]   78   59   375       166   4   6163   5201   gi|451216   Mannosephosphate Isomerase [ Streptococcus mutans ]   78   63   963       186   1   795   4   gi|289284   cysteinyl-tRNA synthetase [ Bacillus subtilis ]   78   63   792       195   4   2315   1881   gi|1353874   unknown [ Rhodobacter capsulatus ]   78   58   435       199   3   3623   2967   gi|143525   succinate dehydrogenase cytochrome b-558 subunit [ Bacillus subtilis ]   78   57   657                           pir|A29843|DEBSSC succinate dehydrogenase (EC 1.3.99.1) cytochrome 558 -                             Bacillus subtilis         199   4   5557   3905   gi|142521   deoxyribodipyrimidine photolyase [ Bacillus subtilis ] pir|A37192|A37192 uvrB   78   62   1653                           protein -  Bacillus subtilis  sp|P14951|UVRC_BACSU EXCINUCLEASE ABC SUBUNIT                           C.       223   3   3523   3215   gi|439596   [ Escherichia coli  IS200 insertion sequence from ECOR63, partial.), ene   78   47   309                           product [ Escherichia coli ]       299   4   1865   2149   gi|467439   temperature sensitive cell division [ Bacillus subtilis ]   78   62   285       321   9   7315   6896   gi|142979   ORF3 is homologous to an ORF downstream of the spoT gene of  E. coli ; RF3   78   55   420                           [ Bacillus stearothermophilus ]       352   4   3714   3944   gi|349050   actin 1 [Pneumocystis carinii]   78   42   231       352   5   6093   4594   gi|903587   NADH dehydrogenase subunit 5 [ Bacillus subtilis ] sp|P39755|NDHF_BACSU NADH   78   58   1500                           DEHYDROGENASE SUBUNIT 5 (EC 1.6.5.3) NADH-UBIQUINONE OXIDOREDUCTASE CHAIN                           5).       376   1   2   583   gi|551693   dethiobiotin synthase [Bacillus sphaericus]   78   34   582       424   2   1595   1768   gi|1524117   alpha-acetolactate decarboxylase [ Lactococcus lactis ]   78   68   174       450   1   988   62   gi|1030068   NAD(P)H oxidoreductase, isoflavone reductase homologue [Solanum tuberosum]   78   63   927       558   1   562   362   gi|1511588   bifunctional protein [ Methanococcus jannaschii ]   78   60   201       670   3   1152   1589   gi|1122759   unknown [ Bacillus subtilis ]   78   64   438       714   1   64   732   gi|143460   37 kd minor sigma factor (rpoF, sigB; ttg start codon) [ Bacillus subtilis ]   78   57   669       814   1   3   368   gi|1377833   unknown [ Bacillus subtilis ]   78   59   366       981   1   692   3   gi|143802   GerC2 [ Bacillus subtilis ]   78   64   690       995   2   727   476   gi|296947   uridine kinase [ Escherichia coli ]   78   64   252       1045   1   3   401   gi|1407784   orf-1; novel antigen [ Staphylococcus aureus ]   78   61   399       1163   2   186   4   gi|410117   diaminopimelate decarboxylase [ Bacillus subtilis ]   78   54   183       2191   1   399   4   gi|215098   excisionase [Bacteriophage 154a]   78   65   396       2933   1   2   181   gi|1204436   pyruvate formate-lyase [ Haemophilus influenzae ]   78   73   180       3041   2   129   317   gi|624632   GltL [ Escherichia coli ]   78   53   189       3581   1   105   401   gi|763186   3-ketoacyl-coA thiolase [ Saccharomyces cerevisiae ]   78   55   297       3709   1   3   230   gi|460689   TVG [Thermoactinomyces vulgaris]   78   58   228       3974   1   265   2   gi|558839   unknown [ Bacillus subtilis ]   78   65   264       3980   1   3   401   gi|39956   IIGlc [ Bacillus subtilis ]   78   62   399       4056   1   354   61   gi|1256635   dihydroxy-acid dehydratase [ Bacillus subtilis ]   78   55   294       4114   1   316   2   pir|S09372|S093   hypothetical protein -  Trypanosoma brucei     78   62   315       4185   1   3   179   gi|1339950   large subunit of NADH-dependent glutamate synthase [ Plectonema boryanum ]   78   58   177       4235   1   329   3   gi|558839   unknown [ Bacillus subtilis ]   78   60   327       4352   1   302   63   gi|603768   HutI protein, imidazolone-5-propionate hydrolase [ Bacillus subtilis ]   78   63   240                           gi|603768 HutI protein, imidazolone-5-propionate hydrolase Bacillus                           subtilis]       4368   1   307   2   gi|1353678   heavy-metal transporting P-type ATPase [Proteus mirabilis]   78   59   306       4461   1   216   4   gi|1276841   glutamate synthase (GOGAT) [ Porphyra purpurea ]   78   36   213       4530   1   238   2   gi|39956   IIGlc [ Bacillus subtilis ]   78   65   237       3   2   2073   1177   gi|1109684   ProV [ Bacillus subtilis ]   77   56   897       12   2   1965   1504   gi|467335   ribosomal protein L9 [ Bacillus subtilis ]   77   59   462       27   1   2   388   gi|1212728   YqhI [ Bacillus subtilis ]   77   63   387       39   2   590   1252   gi|40054   phenylalanyl-tRNA synthetase beta subunit (AA 1-804) [ Bacillus subtilis ]   77   60   663       42   6   2704   2931   gi|606241   30S ribosomal subunit protein S14 [ Escherichia coli ] sp|P02370|RS14_ECOLI   77   65   228                           30S RIBOSOMAL PROTEIN S14. (SUB 2-101)       46   18   15459   16622   gi|297798   mitochondrial formate dehydrogenase precursor [Solanum tuberosum]   77   55   1164                           pir|JQ2272|JQ2272 formate dehydrogenase (EC 1.2.1.2) precursor,                           itochondrial - potato       100   4   4002   3442   gi|1340128   ORF1 [ Staphylococcus aureus ]   77   54   561       102   8   5378   5713   gi|1311482   acetolactate synthase [Thermus aquaticus]   77   57   336       109   7   4742   5383   gi|710637   Unknown [ Bacillus subtilis ]   77   56   642       117   1   2   1228   gi|1237015   ORF4 [ Bacillus subtilis ]   77   53   1227       124   10   7688   7053   gi|405819   thymidine kinase [ Bacillus subtilis ]   77   63   636       147   3   985   824   gi|849027   hypothetical 15.9-kDa protein [ Bacillus subtilis ]   77   37   162       152   10   7354   7953   gi|1205583   spermidine/putrescine transport ATP-binding protein [ Haemophilus     77   55   600                             influenzae ]       169   2   1004   1282   gi|473825   ‘elongation factor EF-Ts’ [ Escherichia coli ]   77   58   279       184   2   380   1147   gi|216314   esterase [ Bacillus stearothermophilus ]   77   60   768       189   7   3296   3868   gi|853809   ORF3 [Clostridium perfringens]   77   48   573       193   1   132   290   gi|1303788   YqeH [ Bacillus subtilis ]   77   54   159       195   8   8414   8088   gi|1499620     M. jannaschii  predicted coding region MJ0798 [ Methanococcus jannaschii ]   77   44   327       205   8   5204   4980   gi|216340   ORF for adenylate kinase [ Bacillus subtilis ]   77   61   225       205   29   14502   14209   gi|786155   Ribosomal Protein L23 [ Bacillus subtilis ]   77   62   294       211   5   1908   2084   gi|410132   ORFX8 [ Bacillus subtilis ]   77   47   177       217   5   3478   4416   gi|496254   fibronectin/fibrinogen-binding protein [ Streptococcus pyogenes ]   77   54   939       232   1   267   998   gi|1407784   orf-1; novel antigen [ Staphylococcus aureus ]   77   57   732       233   2   1346   873   gi|467408   unknown [ Bacillus subtilis ]   77   61   474       243   3   2299   1937   gi|516155   unconventional myosin [Sus scrofa]   77   32   363       299   1   68   769   gi|467436   unknown [ Bacillus subtilis ]   77   54   702       301   4   1283   1098   gi|950071   ATP-bind. pyrimidine kinase [ Mycoplasma capricolum ] pir|S48605|S48605   77   48   186                           hypothetical protein -  Mycoplasma capricolum  SGC3) (fragment)       302   5   2741   3211   gi|508980   pheB [ Bacillus subtilis ]   77   57   471       302   7   3835   4863   gi|147783   ruvB protein [ Escherichia coli ]   77   60   1029       307   9   4797   4192   gi|1070015   protein-dependent [ Bacillus subtilis ]   77   60   606       312   1   99   1391   gi|143165   malic enzyme (EC 1.1.1.38) [ Bacillus stearothermophilus ] pir|A33307|DEBSXS   77   62   1293                           malate dehydrogenase oxaloacetate-decarboxylating) (EC 1.1.1.38) -                             Bacillus tearothermophilus         312   2   1541   2443   gi|1399855   carboxyltransferase beta subunit [Synechococcus PCC7942]   77   58   903       321   5   4596   3526   gi|39844   fumarase (citG) (aa 1-462) [ Bacillus subtilis ]   77   65   1071       354   1   47   568   gi|1154634   YmaB [ Bacillus subtilis ]   77   57   522       365   1   2   1021   gi|143374   phosphoribosyl glycinamide synthetase (PUR-D; gtg start codon)  Bacillus     77   62   1020                             subtilis ]       374   1   1   708   gi|1405446   transketolase [ Bacillus subtilis ]   77   61   708       385   1   565   2   gi|533099   endonuclease III [ Bacillus subtilis ]   77   63   564       392   2   594   1940   gi|556014   UDP-N-acetyl muramate-alanine ligase [ Bacillus subtilis ]   77   65   1347                           sp|P40778|MURC_BACSU UDP-N-ACETYLMURAMATE-ALANINE LIGASE (EC .3.2.8)                           (UDP-N-ACETYLMURANOYL-L-ALANINE SYNTHETASE) (FRAGMENT).       405   5   3570   3061   gi|1303912   YqhW [ Bacillus subtilis ]   77   64   510       487   4   1302   1472   gi|432427   ORF1 gene product (Acinetobacter calcoaceticus)   77   48   171       522   1   2   562   pir|A01179|SYBS   tyrosine-tRNA ligase (EC 6.1.1.1) -  Bacillus stearothermophilus     77   63   561       523   2   1351   1115   gi|1387979   44% identity over 302 residues with hypothetical protein from Synechocystis   77   48   237                           sp, accession D64006_CD; expression induced by environmental stress; some                           similarity to glycosyl transferases; two potential membrane-spanning                           helices [ Bacillus subtil         536   2   612   241   gi|143366   adenylosuccinate lyase (PUR-B) [ Bacillus subtilis ] pir|C29326|WZBSDS   77   61   372                           adenylosuccinate lyase (EC 4.3.2.2) -  Bacillus subtilis         548   2   339   872   gi|143387   aspartate transcarbamylase [ Bacillus subtilis ]   77   56   534       597   1   2   481   gi|904198   hypothetical protein [ Bacillus subtilis ]   77   33   480       633   2   1313   879   gi|387577   ORF1A [ Bacillus subtilis ]   77   64   435       642   1   85   360   gi|46971   epiP gene product [ Staphylococcus epidermidis ]   77   61   276       659   1   125   1219   gi|1072381   glutamyl-aminopeptidase [ Lactococcus lactis ]   77   62   1095       670   4   1587   1820   gi|1122760   unknown [ Bacillus subtilis ]   77   58   234       789   1   2   391   gi|1377823   aminopeptidase [ Bacillus subtilis ]   77   65   390       815   1   10   573   gi|1303861   YqgN [ Bacillus subtilis ]   77   49   564       899   1   1   225   gi|1204844     H. influenzae  predicted coding region HI0594 [ Haemophilus influenzae ]   77   55   225       1083   1   3   188   gi|460828   B969 [ Saccharomyces cerevisiae ]   77   66   186       1942   1   209   3   gi|160047   p101/acidic basic repeat antigen [ Plasmodium falciparum ] pir|A29232|A29232   77   38   207                           101 K malaria antigen precursor -  Plasmodium alciparum  (strain Camp)       2559   1   1   171   gi|1499034     M. jannaschii  predicted coding region MJ0255 [ Methanococcus jannaschii ]   77   61   171       2933   2   243   401   gi|42370   pyruvate formate-lyase (AA 1-760) [ Escherichia coli ] ir|S01788|S01788   77   72   159                           formate C-acetyltransferase (EC 2.3.1.54) -  Echerichia coli         2966   1   56   292   gi|1524397   glycine betaine transporter OpuD [ Bacillus subtilis ]   77   45   237       2976   1   309   4   gi|40003   oxoglutarate dehydrogenase (NADP+) [ Bacillus subtilis ] p|P23129|ODO1_BACSU   77   60   306                           2-OXOGLUTARATE DEHYDROGENASE E1 COMPONENT (EC 2.4.2) (ALPHA-KETOGLUTARATE                           DEHYDROGENASE).       2979   2   400   122   gi|1204354   spore germination and vegetative growth protein [ Haemophilus influenzae ]   77   61   279       2988   1   377   153   gi|438465   Probable operon with orfF. Possible alternative initiation codon, ases   77   55   225                           2151-2153. Homology with acetyltransferases.; putative Bacillus subtilis]       2990   1   167   3   gi|142562   ATP synthase epsilon subunit [ Bacillus megaterium ] pir|B28599|PWBSEM H+−   77   63   165                           transporting ATP synthase (EC 3.6.1.34) psilon chain -  Bacillus megaterium         3032   1   3   389   gi|488430   alcohol dehydrogenase 2 [Entamoeba histolytica]   77   56   387       3057   1   1   195   gi|468764   mocR gene product (Rhizobium meliloti)   77   50   195       4008   1   400   74   gi|603768   HutI protein, imidazolone-5-propionate hydrolase [ Bacillus subtilis ]   77   52   327                           gi|603768 HutI protein, imidazolone-5-propionate hydrolase  Bacillus                               subtilis ]       4048   1   386   69   gi|216278   gramicidin S synthetase 1 [ Bacillus brevis ]   77   55   318       4110   1   3   368   pir|S52915|S529   nitrate reductase alpha chain -  Bacillus subtilis  (fragment)   77   61   366       4115   1   1   348   gi|517205   67 kDa Myosin-crossreactive streptococcal antigen [ Streptococcus yogenes ]   77   65   348       4225   1   297   4   gi|1322245   mevalonate pyrophosphate decarboxylase [ Rattus norvegicus ]   77   60   294       4611   2   327   160   gi|508979   GTP-binding protein [ Bacillus subtilis ]   77   57   168       4668   1   182   3   pir|S52915|S529   nitrate reductase alpha chain -  Bacillus subtilis  (fragment)   77   61   180       25   1   2   1627   gi|1150620   MmsA [Streptococcus pneumoniae]   76   58   1626       38   5   1488   2537   pir|A43577|A435   regulatory protein pfoR -  Clostridium perfringens     76   57   1050       52   5   2962   4041   gi|1161061   dioxygenase [Methylobacterium extorquens]   76   62   1080       56   20   27389   27955   gi|467402   unknown [ Bacillus subtilis ]   76   56   567       57   15   12046   12219   gi|1206040   weak similarity to keratin [ Caenorhabditis elegans ]   76   40   174       91   2   1062   2261   gi|475715   acetyl coenzyme A acetyltransferase (thiolase) [Clostridium cetobutylicum]   76   57   1200       98   2   818   1624   gi|467422   unknown [ Bacillus subtilis ]   76   62   807       98   5   2965   3228   gi|897793   y98 gene product [Pediococcus acidilactici]   76   52   264       98   8   5922   6326   gi|467427   methionyl-tRNA synthetase [ Bacillus subtilis ]   76   53   405       104   3   1322   1885   gi|216151   DNA polymerase (gene L; ttg start codon) [Bacteriophage SPO2] gi|579197   76   63   564                           SPO2 DNA polymerase (aa 1-648) [Bacteriophage SPO2) pir|A21498|DJBPS2 DNA-                           directed DNA polymerase (EC 2.7.7.7) - phage PO2       124   9   7055   5976   gi|853776   peptide chain release factor 1 [ Bacillus subtilis ] pir|S55437|S55437   76   58   1080                           peptide chain release factor 1 -  Bacillus subtilis         164   5   2832   3311   gi|1204976   prolyl-tRNA synthetase [ Haemophilus influenzae ]   76   53   480       168   2   1841   1065   gi|1177253   putative ATP-binding protein of ABC-type [ Bacillus subtilis ]   76   58   777       189   2   163   888   gi|467384   unknown [ Bacillus subtilis ]   76   63   726       235   3   2253   3518   gi|142936   folyl-polyglutamate synthetase [ Bacillus subtilis ] pir|B40646|B40646 folC -   76   53   1266                             Bacillus subtilis         236   1   335   925   gi|1146197   putative [ Bacillus subtilis ]   76   54   591       237   8   5323   5541   gi|1279261   F13G3.6 [ Caenorhabditis elegans ]   76   47   219       263   5   4585   3680   gi|1510348   dihydrodipicolinate synthase [ Methanococcus jannaschii ]   76   49   906       304   3   1051   1794   gi|666982   putative membrane spanning subunit [ Bacillus subtilis ]pir|S52382|S52382   76   60   744                           probable membrane spanning protein -  Bacillus subtilis         312   4   3611   4624   gi|143312   6-phospho-1-fructokinase (gtg start codon; EC 2.7.1.11) [Bacillus   76   56   1014                           tearothermophilus)       343   1   2   1036   gi|405956   yeeE [ Escherichia coli ]   76   59   1035       347   1   409   1701   gi|396304   acetylornithine deacetylase [ Escherichia coli ]   76   72   1293       358   1   672   1907   gi|1146215   39.0% identity to the  Escherichia coli  S1 ribosomal protein; putative   76   58   1236                           [ Bacillus subtilis ]       371   1   1   222   gi|537084   alternate gene name mgt; CG Site No. 497 [ Escherichia coli ]   76   61   222                           pir|S56468|S56468 mgtA protein -  Escherichia coli         379   4   4331   4858   gi|143268   dihydrolipoamide transsuccinylase (odhB; EC 2.3.1.61) [ Bacillus subtilis ]   76   61   528       404   5   4022   4492   gi|1303823   YqfG [ Bacillus subtilis ]   76   60   471       411   1   2   307   gi|486025   ORF YKL027w [ Saccharomyces cerevisiae ]   76   55   306       472   3   2854   1352   gi|1405464   AlsT [ Bacillus subtilis ]   76   57   1503       546   1   273   995   gi|153821   streptococcal pyrogenic exotoxin type C (speC) precursor Streptococcus   76   36   723                           pyogenes]       588   1   557   60   gi|1002520   MutS [ Bacillus subtilis ]   76   61   498       591   1   16   735   gi|885934   ClpB [Synechococcus sp.]   76   44   720       602   2   175   798   gi|1486422   OppD homologue [Rhizobium sp.]   76   52   624       619   2   290   33   gi|330613   major capsid protein [Human cytomegalovirus]   76   47   258       660   4   2568   3302   gi|904199   hypothetical protein [ Bacillus subtilis ]   76   55   735       677   1   228   4   gi|40177   spoOF gene product [ Bacillus subtilis ]   76   58   225       962   1   24   206   gi|142443   adenylosuccinate synthetase [ Bacillus subtilis ]sp|P29726|PURA_BACSU   76   67   183                           ADENYLOSUCCINATE SYNTHETASE (EC 6.3.4.4) IMP —ASPARTATE LIGASE).       978   1   580   2   gi|1511333     M. jannaschii  predicted coding region MJ1322 [ Methanococcus jannaschii ]   76   56   579       997   1   244   2   gi|467154   No definition line found [Mycobacterium leprae]   76   38   243       1563   1   266   3   gi|1303984   YqkG [ Bacillus subtilis ]   76   52   264       2184   1   182   3   gi|506706   CapJ [ Staphylococcus aureus ]   76   38   180       2572   1   1   387   gi|153898   transport protein [ Salmonella typhimurium ]   76   65   387       2942   1   29   400   gi|710020   nitrite reductase (nirB) [ Bacillus subtilis ]   76   59   372       2957   1   216   55   gi|1511251   hypothetical protein (SP: P42404) [Methanococcus janneschii]   76   47   162       2980   1   279   4   gi|1405464   AlsT [ Bacillus subtilis ]   76   53   276       3015   1   326   3   gi|408115   ornithine acetyltransferase [ Bacillus subtilis ]   76   61   324       3124   1   13   174   gi|882705   ORF_o401 ( Escherichia coli )   76   65   162       3179   1   3   161   gi|168477   ferredoxin-dependent glutamate synthase [ Zea mays ]pir|A38596|A38596   76   53   159                           glutamate synthase (ferredoxin) (EC 1.4.7.1)-  maize         3789   1   2   379   gi|39956   IIGlc [ Bacillus subtilis )   76   55   378       3892   1   3   314   gi|1510398   ferripyochelin binding protein [ Methanococcus jannaschii ]   76   52   312       3928   1   400   2   gi|143016   permease [ Bacillus subtilis ]   76   59   399       4159   1   386   15   sp|P80544|MRSP —     METHICILLIN-RESISTANT SURFACE PROTEIN (FRAGMENTS)   76   66   372       4204   1   17   331   gi|29646   ATPase [ Lactococcus lactis ]   76   56   315       4398   1   249   4   gi|987255   Menkes disease gene [ Homo sapiens ]   76   48   246       4506   1   2   313   gi|216746   (D-lactate dehydrogenase [ Lactobacillus plantarum ]   76   47   312       4546   1   247   17   gi|1339950   large subunit of NADH-dependent glutamate synthase [ Plectonema boryanum ]   76   61   231       4596   1   191   3   gi|560027   cellulose synthase [Acetobacter xylinum]   76   70   189       4   5   4337   3417   gi|882532   ORF_o294 [ Escherichia coli ]   75   59   921       6   1   164   952   gi|40960   OTCase [ Escherichia coli ]   75   56   789       12   3   3944   1953   gi|467336   unknown [ Bacillus subtilis ]   75   57   1992       23   18   17310   16348   gi|1296433   0-acetylserine sulfhydrylase B [Alcaligenes eutrophus]   75   55   963       25   3   2356   3393   gi|1502419   PlsX [ Bacillus subtilis ]   75   56   1038       36   8   5765   6037   gi|1256517   unknown [ Schizosaccharomyces pombe ]   75   45   273       46   13   11186   12058   gi|48972   nitrate transporter [Synechococcus sp.]   75   46   873       51   7   3474   3677   gi|143607   sporulation protein [ Bacillus subtilis ]   75   61   204       53   16   16590   16330   gi|143402   (recombination protein (ttg start codon) [ Bacillus subtilis ] gi|1303923 RecN   75   51   261                           [ Bacillus subtilis ]       74   3   2568   1564   gi|1204847   ornithine carbamoyltransferase [ Haemophilus influenzae ]   75   61   1005       85   3   3930   3232   gi|143368   phosphoribosylformyl glycinamidine synthetase I (PUR-L; gtg start odon)   75   63   699                           [ Bacillus subtilis ]       85   5   4878   4168   gi|143367   phosphoribosyl aminoidazole succinocarboxamide synthetase (PUR-C; tg start   75   55   711                           codon) [ Bacillus subtilis ]       85   8   6625   7530   gi|1303916   YqiA [ Bacillus subtilis ]   75   53   906       87   3   2340   3590   gi|1064813   homologous to sp: PHOR_BACSU [ Bacillus subtilis ]   75   56   1251       87   6   6084   6896   gi|1064810   function unknown [ Bacillus subtilis ]   75   61   813       108   2   1503   1162   gi|1001824   hypothetical protein [Synechocystis sp.]   75   51   342       110   3   1748   3727   gi|1147593   putative ppGpp synthetase [Streptomyces coelicolor]   75   55   1980       110   7   4353   5252   gi|1177251   clwD gene product [ Bacillus subtilis ]   75   75   900       120   14   10649   10032   gi|1524394   ORF-2 upstream of gbsAB operon [ Bacillus subtilis ]   75   55   618       121   5   2050   4221   gi|1154632   NrdE [ Bacillus subtilis ]   75   54   2172       124   1   143   3   gi|405622   unknown [ Bacillus subtilis ]   75   56   141       128   1   81   1139   gi|143316   (gap) gene products [ Bacillus megaterium ]   75   48   1059       130   8   5760   5903   gi|1256654   54.8% identity with Neisseria gonorrhoeae regulatory protein PilB; putative   75   62   144                           [ Bacillus subtilis ]       136   2   3185   1890   gi|467403   seryl-tRNA synthetase [ Bacillus subtilis ]   75   54   1296       161   10   5439   5798   gi|1001195   hypothetical protein [Synechocystis sp.]   75   55   360       172   4   2995   2171   gi|755153   ATP-binding protein [ Bacillus subtilis ]   75   52   825       179   1   1107   190   gi|143037   porphobilinogen deaminase [ Bacillus subtilis ]   75   58   918       195   10   9374   9219   sp|P25745|YCFB —     HYPOTHETICAL PROTEIN IN PURB 5′ REGION (ORF-15) (FRAGMENT)   75   60   156       200   4   2605   4596   gi|142440   ATP-dependent nuclease [ Bacillus subtilis ]   75   56   1992       206   3   5620   4340   gi|1256135   YbbF [ Bacillus subtilis ]   75   53   1281       216   2   159   389   gi|1052800   unknown [ Schizosaccharomyces pombe ]   75   58   231       229   1   29   847   gi|1205958   branched chain aa transport system II carrier protein [ Haemophilus     75   49   819                             influenzae ]       230   2   518   1714   gi|971337   nitrite extrusion protein [ Bacillus subtilis ]   75   53   1197       231   1   1122   4   gi|1002521   MutL [ Bacillus subtilis ]   75   54   1119       233   3   1314   1859   gi|467405   unknown [ Bacillus subtilis ]   75   59   546       269   1   164   3   gi|1511246   methyl coenzyme M reductase system, component A2 [ Methanococcus jannaschii ]   75   50   162       292   1   772   155   gi|1511604     M. jannaschii  predicted coding region MJ1651 [ Methanococcus jannaschii ]   75   46   618       304   4   1773   2261   gi|1205328   surfactin [ Haemophilus influenzae ]   75   55   489       312   3   2437   3387   gi|285621   undefined open reading frame [ Bacillus stearothermophilus ]   75   62   951       312   5   4622   6403   gi|1041097   Pyruvate Kinase [Bacillus psychrophilus]   75   57   1782       319   1   353   877   gi|1212728   YqhI [ Bacillus subtilis ]   75   54   525       320   5   4321   5031   gi|1070361   OMP decarboxylase [ Lactococcus lactis ]   75   56   711       320   6   5010   5642   gi|143394   OMP-PRPP transferase [ Bacillus subtilis ]   75   60   633       337   4   1519   2088   gi|487433   citrate synthase II [ Bacillus subtilis ]   75   58   570       394   2   669   1271   gi|304976   matches PS00017: ATP_GTP_A and PS00301: EFACTOR_GTP; similar to longation   75   51   603                           factor G, TetM/TetO tetracycline-resistance proteins  Escherichia coli ]       423   1   127   570   gi|1183839   unknown [Pseudomonas aeruginosa]   75   59   444       433   2   1603   1929   gi|149211   acetolactate synthase [Klebsiella pneumoniae]   75   63   327       446   2   176   1540   gi|312441   dihydroorotase [ Bacillus caldolyticus ]   75   62   1365       486   1   249   4   gi|1149682   potF gene product [Clostridium perfringens]   75   55   246       496   1   3   794   gi|143582   spoIIIEA protein [ Bacillus subtilis ]   75   59   792       498   2   824   1504   gi|143328   phoP protein (put.); putative [ Bacillus subtilis ]   75   47   681       499   2   1061   1624   gi|1387979   44% identity over 302 residues with hypothetical protein from Synechocystis   75   51   564                           sp, accession D64006_CD; expression induced by environmental stress; some                           similarity to glycosyl transferases; two potential membrane-spanning                           helices [Bacillus subtil       568   1   453   265   pir|JC4110|JC41   triacylglycerol lipase (EC 3.1.1.3) 2 -  Mycoplasma mycoides  subsp. mycoides   75   50   189                           (SGC3)       613   2   233   36   gi|330993   tegument protein [Saimiriine herpesvirus 2]   75   75   198       621   1   1   525   gi|529754   speC [ Streptococcus pyogenes ]   75   43   525       642   5   1809   2474   gi|1176401   EpiG [ Staphylococcus epidermidis ]   75   51   666       646   2   454   657   gi|172442   ribonuclease P [ Saccharomyces cerevisiae ]   75   37   204       657   1   3   347   gi|882541   ORF_o236 [ Escherichia coli ]   75   47   345       750   1   832   2   gi|46971   epiP gene product [ Staphylococcus epidermidis ]   75   57   831       754   1   2   481   gi|1303901   YqhT [ Bacillus subtilis ]   75   57   480       763   2   393   223   gi|1205145   multidrug resistance protein [ Haemophilus influenzae ]   75   51   171       775   1   482   3   pir|B36889|B368   leuA protein, inactive -  Lactococcus lactis  subsp. lactis (strain IL1403)   75   63   480       793   1   1   180   gi|143316   [gap] gene products [ Bacillus megaterium ]   75   57   180       800   1   160   2   gi|509411   NFRA protein [Azorhizobium caulinodans]   75   34   159       811   1   560   3   gi|143434   Rho Factor [ Bacillus subtilis ]   75   60   558       940   1   329   165   gi|1276985   arginase [ Bacillus caldovelox ]   75   50   165       971   2   37   252   gi|1001373   hypothetical protein [Synechocystis sp.]   75   58   216       1059   1   232   80   gi|726480   L-glutamine-D-fructose-6-phosphate amidotransferase [ Bacillus subtilis ]   75   67   153       1109   2   219   374   gi|143331   alkaline phosphatase regulatory protein [ Bacillus subtilis ]   75   53   156                           pir|A27650|A27650 regulatory protein phoR -  Bacillus subtilis                             sp|P23545|PHOR_BACSU ALKALINE PHOSPHATASE SYNTHESIS SENSOR PROTEIN HOR (EC                           2.7.3.—).       1268   1   137   3   gi|304135   ornithine acetyltransferase [ Bacillus stearothermophilus ]   75   63   135                           sp|Q07908|ARGJ_BACST GLUTAMATE N-ACETYLTRANSFERASE (EC 2.3.1.35) ORNITHINE                           ACETYLTRANSFERASE) (ORNITHINE TRANSACETYLASE) (OATASE)/MINO-ACID                           ACETYLTRANSFERASE (EC 2.3.1.1) (N-ACETYLGLUTAMATE YNTHA       1500   1   163   2   gi|1205488   excinuclease ABC subunit B [ Haemophilus influenzae ]   75   57   162       1529   1   400   2   gi|1002521   MutL [ Bacillus subtilis ]   75   54   399       3010   1   387   4   gi|1204435   pyruvate formate-lyase activating enzyme [ Haemophilus influenzae ]   75   54   384       3105   1   1   180   gi|1041097   Pyruvate Kinase [ Bacillus psychrophilus ]   75   57   180       3117   1   45   212   gi|899317   peptide synthetase module [Microcystis aeruginosa]pir|S49111|S49111   75   42   168                           probable amino acid activating domain -  Microcystis aeruginosa  (fragment)                           (SUB 144-528)       3139   2   139   345   gi|145294   adenine phosphoribosyl-transferase [ Escherichia coli ]   75   66   207       3880   1   310   2   gi|1009366   Respiratory nitrate reductase [ Bacillus subtilis ]   75   58   309       3911   1   48   401   gi|433991   ATP synthase subunit beta [ Bacillus subtilis ]   75   68   354       3957   1   2   379   pir|D36889|D368   3-isopropylmalate dehydratase (EC 4.2.1.33) chain leuC -  Lactococcus lactis     75   65   378                           subsp. lactis (strain IL1403)       4005   1   5   259   gi|216746   D-lactate dehydrogenase [ Lactobacillus plantarum ]   75   48   255       4080   1   73   333   gi|415855   deoxyribose aldolase [ Mycoplasma hominis ]   75   59   261       4111   1   1   339   gi|149435   putative [ Lactococcus lactis ]   75   57   339       4136   1   303   4   gi|450688   hsdM gene of EcoprrI gene product [ Escherichia coli ] pir|S38437|S38437 hsdM   75   56   300                           protein -  Escherichia coli  pir|S09629|S09629 hypothetical protein A -                             Escherichia coli  (SUB 40-520)       4144   1   336   4   gi|48972   nitrate transporter [Synechococcus sp.]   75   49   333       4237   1   374   84   gi|1339950   large subunit of NADH-dependent glutamate synthase [ Plectonema boryanum ]   75   55   291       4306   2   73   318   gi|294260   major surface glycoprotein [Pneumocystis carinii]   75   68   246       4343   1   359   3   gi|1204652   methylated-DNA-protein-cysteine methyltransferase [ Haemophilus influenzae ]   75   52   357       4552   1   312   4   gi|296464   ATPase [ Lactococcus lactis ]   75   55   309       38   9   5776   6126   gi|443793   NupC [ Escherichia coli ]   74   50   351       50   8   6221   5532   gi|1239988   hypothetical protein [ Bacillus subtilis ]   74   55   690       56   9   10770   12221   gi|1000451   TreP [ Bacillus subtilis ]   74   57   1452       64   2   1622   978   gi|41015   aspartate-tRNA ligase [ Escherichia coli ]   74   57   645       66   6   4848   4633   gi|1212729   YqhJ [ Bacillus subtilis ]   74   47   216       67   18   14334   14897   gi|1510631   endoglucanase [ Methanococcus jannaschii ]   74   52   564       102   15   12561   13136   gi|149429   putative [ Lactococcus lactis ]   74   67   576       102   16   13121   14419   gi|149435   putative [ Lactococcus lactis ]   74   57   1299       108   4   3902   2931   gi|39478   ATP binding protein of transport ATPases [ Bacillus firmus ] ir|S15486|S15486   74   59   972                           ATP-binding protein -  Bacillus firmus  p|P26946|YATR_BACFI HYPOTHETICAL                           ATP-BINDING TRANSPORT PROTEIN.       116   5   7093   5612   gi|1205430   dipeptide transport system permease protein [ Haemophilus influenzae     74   49   1482       120   7   4342   4803   gi|146970   ribonucleoside triphosphate reductase [ Escherichia coli ] pir|A47331|A47331   74   58   462                           anaerobic ribonucleotide reductase -  Escherichia coli         121   7   5961   6581   gi|1107528   ttg start [ Campylobacter coli ]   74   51   621       128   3   2320   3531   gi|143318   phosphoglycerate kinase [ Bacillus megaterium ]   74   57   1212       130   7   5237   5791   gi|1256653   DNA-binding protein [ Bacillus subtilis ]   74   60   555       136   3   5150   3555   gi|143076   histidase [ Bacillus subtilis ]   74   58   1596       145   2   664   1368   gi|407773   devA gene product [Anabaena sp.]   74   45   705       152   1   277   2   gi|1377833   unknown [ Bacillus subtilis ]   74   54   276       164   10   11064   11375   gi|580900   ORF3 gene product [ Bacillus subtilis ]   74   52   312       175   2   2624   2139   gi|642656   unknown [Rhizobium meliloti]   74   34   486       175   9   5612   5160   gi|854656   Na/H antiporter system ORF2 [ Bacillus alcalophilus ]   74   46   453       195   11   10339   9332   gi|1204430   hypothetical protein (SP: P25745) [ Haemophilus influenzae ]   74   55   1008       205   17   9059   8499   gi|1044979   ribosomal protein L6 [ Bacillus subtilis ]   74   64   561       236   7   5574   6710   gi|1146207   putative [ Bacillus subtilis ]   74   63   1137       241   3   3334   2147   gi|694121   malate thiokinase [Methylobacterium extorquens]   74   52   1188       246   6   2799   2293   gi|467374   single strand DNA binding protein [ Bacillus subtilis ]   74   64   507       249   4   5313   4075   gi|1524397   glycine betaine transporter OpuD [ Bacillus subtilis ]   74   55   1239       261   7   4081   3773   gi|809542   CbrB protein [Erwinia chrysanthemi]   74   42   309       278   6   4665   3616   gi|1204872   ATP-binding protein [ Haemophilus influenzae ]   74   54   1050       309   1   666   112   gi|1205579   hypothetical protein (GB: U14003_302) [ Haemophilus influenzae ]   74   53   555       315   2   862   251   gi|143398   quinol oxidase [ Bacillus subtilis ]   74   57   612       320   1   1   1065   gi|143389   glutaminase of carbamyl phosphate synthetase [ Bacillus subtilis ]   74   60   1065                           pir|E39845|E39845 carbamoyl-phosphate synthase glutamine-hydrolyzing) (EC                           6.3.5.5), pyrimidine-repressible, small hain -  Bacillus subtilis         380   2   382   1128   gi|534857   ATPase subunit a [ Bacillus stearothermophilus ]   74   56   747       405   2   1311   880   gi|1303915   YqhZ [ Bacillus subtilis ]   74   65   432       433   5   2503   3270   gi|473902   alpha-acetolactate synthase [ Lactococcus lactis ]   74   56   768       452   1   1   942   gi|413982   ipa-58r gene product [ Bacillus subtilis ]   74   52   942       461   1   3   1193   gi|558494   homoserine dehydrogenase [ Bacillus subtilis ]   74   51   1191       461   2   1174   1407   gi|40211   threonine synthase (thrC) (AA 1-352) [ Bacillus subtilis ] ir|A25364|A25364   74   56   234                           threonine synthase (EC 4.2.99.2) -  Bacillus subtilis         462   2   402   734   gi|142520   thioredoxin [ Bacillus subtilis ]   74   62   333       478   1   320   66   gi|1499005   glycyl-tRNA synthetase [ Methanococcus jannaschii ]   74   52   255       501   2   739   1740   gi|217040   acid glycoprotein [ Streptococcus pyogenes ]   74   58   1002       551   2   2791   1499   gi|143040   glutamate-1-semialdehyde 2,1-aminotransferase [ Bacillus subtilis ]   74   51   1293                           pir|D42728|D42728 glutamate-1-semialdehyde 2,1-aminomutase (EC .4.3.8) -                             Bacillus subtilis         573   1   1   477   gi|1006605   hypothetical protein [Synechocystis sp.]   74   45   477       596   2   1298   816   gi|1303853   YqgF [ Bacillus subtilis ]   74   55   483       618   2   1758   592   gi|1146237   21.4% of identity to trans-acting transcription factor of Sacharomyces   74   55   1167                           cerevisiae; 25% of identity to sucrose synthase of Zee mays; putative                           [ Bacillus subtilis ]       659   2   1269   1595   gi|1072380   ORF3 [ Lactococcus lactis ]   74   62   327       724   1   188   3   gi|143374   phosphoribosyl glycinamide synthetase (PUR-D; gtg start codon)  Bacillus     74   58   186                             subtilis ]       743   2   604   1209   gi|153833   ORF1; putative [Streptococcus parasanguis]   74   50   606       836   1   2   259   gi|143458   ORF V [ Bacillus subtilis ]   74   47   258       989   2   443   724   gi|1303994   YqkM [ Bacillus subtilis ]   74   46   282       1106   1   1   492   gi|46970   epiD gene product [ Staphylococcus epidermidis ]   74   54   492       1135   2   373   528   gi|413948   ipa-24d gene product [ Bacillus subtilis ]   74   48   156       1234   1   452   87   gi|495245   recJ gene product [ Erwinia chrysanthemi ]   74   36   366       2586   1   2   238   gi|1149701   sbcC gene product [ Clostridium perfringens ]   74   62   237       2959   1   400   2   gi|1405454   aconitase [ Bacillus subtilis ]   74   60   399       2962   1   363   76   gi|450686   3-phosphoglycerate kinase [ Thermotoga maritima ]   74   58   288       2983   1   3   191   gi|1303893   YqhL [ Bacillus subtilis ]   74   56   189       3018   1   2   223   gi|143040   glutamate-1-semialdehyde 2,1-aminotransferase [ Bacillus subtilis ]   74   56   222                           pir|D42728|D42728 glutamate-1-semialdehyde 2,1-aminomutase (EC .4.3.8) -                           Bacillus&#39; subtilis       3038   1   256   2   pir|S52915|S529   nitrate reductase alpha chain -  Bacillus subtilis  (fragment)   74   57   255       3062   1   189   4   gi|1107528   ttg start [ Campylobacter coli ]   74   51   186       4035   1   184   360   gi|1022725   unknown [ Staphylococcus haemolyticus ]   74   64   177       4045   1   305   3   gi|1510977   M. jannaachii predicted coding region MJ0938 [ Methanococcus jannaschii ]   74   41   303       4283   1   304   137   gi|520844   orf4 [ Bacillus subtilis ]   74   58   168       4449   1   3   221   gi|580910   peptide-synthetase ORF1 [ Bacillus subtilis ]   74   54   219       4587   1   231   4   gi|1370207   orf6 [ Lactobacillus sake ]   74   59   228       4603   1   29   214   gi|146208   glutamate synthase large subunit (EC 2.6.1.53) [ Escherichia coli ]   74   60   186                           pir|A29617|A29617 glutamate synthase (NADPH) (EC 1.4.1.13) large hain-                             Escherichia coli         4670   1   184   2   gi|1256135   YbbF [ Bacillus subtilis ]   74   61   183       5   10   7162   6371   gi|143727   putative [ Bacillus subtilis ]   73   42   792       11   2   1372   290   gi|166338   dihydroorotate dehydrogenase [Agrocybe aegerita]   73   55   1083       14   1   1020   16   gi|143373   phosphoribosyl aminoimidazole carboxy formyl ormyltransferase/inosine   73   54   1005                           monophosphate cyclohydrolase (PUR-H(J))  Bacillus subtilis ]       23   5   4635   3844   gi|1468939   meso-2,3-butanediol dehydrogenase (D-acetoin forming) [Klebsiella   73   58   792                           pneumoniae]       23   17   16360   15341   gi|297060   ornithine cyclodeaminase [Rhizobium meliloti]   73   37   1020       29   2   692   1273   gi|467442   stage V sporulation [ Bacillus subtilis ]   73   54   582       31   5   4914   3361   gi|414000   ipa-76d gene product [ Bacillus subtilis ]   73   55   1554       37   8   7402   6146   gi|1429259   pepT gene product [ Bacillus subtilis ]   73   59   1257       37   9   7562   7386   gi|168367   alpha-isopropylmalate isomerase (put.); putative [Rhizomucor ircinelloides]   73   52   177       38   7   3931   4896   gi|405885   yeiN [ Escherichia coli ]   73   58   966       44   6   4238   3435   gi|580895   unknown [ Bacillus subtilis ]   73   53   804       44   11   7767   8306   gi|42009   moaB gene product [Eacherichia coli]   73   50   540       45   3   2439   3080   gi|1109685   ProW [ Bacillus subtilis ]   73   47   642       54   13   13794   13552   gi|413931   ipa-7d gene product [ Bacillus subtilis ]   73   61   243       59   4   1430   2248   gi|147923   threonine dehydratase 2 (EC 4.2.1.16) [ Escherichia coli ]   73   53   819       65   1   730   2   gi|677944   AppF [ Bacillus subtilis ]   73   56   729       80   2   860   345   gi|580932   murD gene product [ Bacillus subtilis ]   73   53   516       102   13   10124   11179   gi|580891   3-isopropylmalate dehydrogenase (AA 1-365) [ Bacillus subtilis ]   73   55   1056                           pir|A26522|A26522 3-isopropylmalate dehydrogenase (EC 1.1.1.85) -  Bacillus                               subtilis         109   2   2600   1707   gi|1510849     M. jannaschii  predicted coding region MJ0775 [ Methanococcus jannaschii ]   73   40   894       120   8   4782   5756   gi|146970   ribonucleoside triphosphate reductase [ Escherichia coli ] pir|A47331|A47331   73   56   975                           anaerobic ribonucleotide reductase -  Escherichia coli         120   9   5726   6223   gi|1204333   anaerobic ribonucleoside-triphosphate reductase [ Haemophilus influenzae ]   73   62   498       132   5   4151   4363   gi|871048   HPSR2 - heavy chain potential motor protein [Giardia inrestinalis]   73   43   213       140   6   4324   2696   gi|634107   kdpB [Eacherichia coli]   73   59   1629       142   6   5939   4918   gi|410125   ribG gene product [ Bacillus subtilis ]   73   57   1122       149   4   1717   1568   gi|460892   heparin binding protein-44, HBP-44 [mice, Peptide, 360 aa]   73   53   150                           pir|JX0281|JX0281 heparin-binding protein-44 precursor - mouse gi|220434                           ORF [ Mus musculus ] (SUB 2-360)       158   1   1   1431   gi|882504   ORF_f560 [ Eacherichia coli ]   73   57   1431       174   6   4525   3698   gi|1146240   ketopantoate hydroxymethyltransferase [ Bacillus subtilis ]   73   55   828       175   8   5178   4819   gi|854657   Na/H antiporter system ORF3 [ Bacillus alcalophilus )   73   56   360       186   5   5493   4393   gi|467477   unknown [ Bacillus subtilis ]   73   48   1101       249   6   5729   5175   gi|1524397   glycine betaine transporter OpuD [ Bacillus subtilis ]   73   56   555       265   4   1873   2280   gi|39848   U3 [ Bacillus subtilis ]   73   41   408       270   1   328   582   gi|780461   220 kDa polyprotein [African swine fever virus]   73   53   255       278   4   3618   2953   gi|1208965   hypothetical 23.3 kd protein [ Eacherichia coli ]   73   49   666       279   3   3593   2202   gi|1185288   isochorismate synthase [ Bacillus subtilis ]   73   58   1392       291   4   1207   1575   gi|1511440   glutamine - fructose-6-phosphate transaminase ( Methanococcus jannaschii )   73   63   369       299   2   735   1166   gi|467437   unknown [ Bacillus subtilis ]   73   58   432       299   5   2050   3234   gi|467439   temperature sensitive cell division [ Bacillus subtilis ]   73   53   1185       334   1   728   219   gi|536655   ORF YBR244w [Saccharomyces cerevisise]   73   43   510       336   2   1036   245   gi|790943   urea amidolyase [ Bacillus subtilis ]   73   51   792       374   3   1389   1874   gi|1405451   YneJ [ Bacillus subtilis ]   73   55   486       433   4   1916   2554   gi|473902   alpha-aceholactate synthase [ Lactococcus lactis ]   73   54   639       509   2   1028   261   gi|467483   unknown [ Bacillus subtilis ]   73   56   768       513   1   918   127   gi|1146220   NAD+ dependent glycerol-3-phosphate dehydrogenase [ Bacillus subtilis ]   73   56   792       533   2   239   733   gi|1510605   hypothetical protein (SP: P42297) [ Methanococcus jannaschii ]   73   44   495       546   2   1148   2815   gi|41748   hsdM protein (AA 1-520) [Eacherichia coli]   73   52   1668       549   1   382   2   gi|1314847   CinA [ Bacillus subtilis ]   73   57   381       567   1   675   4   gi|410137   ORFX13 [ Bacillus subtilis ]   73   58   672       716   2   654   1112   gi|1256623   exodeoxyribonuclease [ Bacillus subtilis ]   73   56   459       772   1   3   677   gi|142010   Shows 70.2% similarity and 48.6% identity to the EnvM protein of almonella   73   57   675                           typhimurium [Anabaena sp.]       774   1   3   209   gi|409286   bmrU [ Bacillus subtilis ]   73   52   207       782   1   1   402   gi|143320   [gap] gene products [ Bacillus megaterium ]   73   56   402       789   2   451   762   gi|1063246   low homology to P14 protein of Heamophilus influenzar and 14.2 kDa protein   73   56   312                           of  Escherichia coli  [ Bacillus subtilis ]       796   1   3   911   gi|853754   ABC transporter [ Bacillus subtilis ]   73   58   909       806   3   949   689   gi|143786   tryptophanyl-tRNA synthetase (EC 6.1.1.2) [ Bacillus subtilis ]   73   51   261                           pir|JT0481|YWBS tryptophan-tRNA ligase (EC 6.1.1.2) -  Bacillus subtilis         816   2   3097   1355   gi|41748   hsdM protein (AA 1-520) [ Escherichia coli ]   73   52   1743       839   1   400   2   gi|886906   argininosuccinate synthetase [ Streptomyces clavuligerus ] pir|S57659|S57659   73   59   399                           argininosuccinate synthase (EC 6.3.4.5) - treptomyces clavuligerus       857   1   3   290   gi|348052   acetoin utilization protein [ Bacillus subtilis ]   73   50   288       1008   1   398   6   gi|40100   rodC (tag3) polypeptide (AA 1-746) [ Bacillus subtilis ] ir|S06049|S06049   73   41   393                           rodC protein -  Bacillus subtilis  p|P13485|TAGF_BACSU TECHOIC ACID                           BIOSYNTHESIS PROTEIN F.       1018   1   1   213   gi|529357   No definition line found [ Caenorhabditis elegans ] sp|P46975|STT3_CAEEL   73   53   213                           OLIGOSACCHARYL TRANSFERASE STT3 SUBUNIT OMOLOG.       1033   1   3   491   gi|142706   comG1 gene product [ Bacillus subtilis ]   73   51   489       1174   1   204   13   gi|1149513   alpha3a subunit of laminin 5 [ Homo sapiens ]   73   60   192       1175   1   329   3   gi|473817   ‘ORF’ [ Escherichia coli ]   73   57   327       1187   1   3   209   gi|580870   ipa-37d qoxA gene product [ Bacillus subtilis ]   73   52   207       1206   1   72   245   gi|144816   formyltetrahydrofolate synthetase (FTHFS) (ttg start codon) (EC .3.4.3)   73   43   174                           [Moorella thermoacetica]       1454   1   241   59   gi|1213253   unknown [ Schizosaccharomyces pombe ]   73   53   183       1469   1   260   3   gi|1303787   YqeG [ Bacillus subtilis ]   73   55   258       1761   1   189   4   gi|9135   Mst26Aa gene product [ Drosophila simulans ]   73   34   186       1849   1   243   19   gi|162307   DNA topoisomerase II [ Trypanosoma cruzi ]   73   60   225       2055   1   2   400   gi|559381   P47K protein [Rhodococcus erythropolis]   73   34   399       2556   1   2   244   gi|145925   fecB [ Escherichia coli ]   73   62   243       2947   2   400   251   gi|1184680   polynucleotide phosphorylase [ Bacillus subtilis ]   73   51   150       2956   1   375   4   gi|143397   quinol oxidase [ Bacillus subtilis ]   73   58   372       3037   1   329   3   gi|143091   acetolactate synthase [ Bacillus subtilis ]   73   55   327       3115   1   194   3   gi|323866   overlapping out-of-phase protein [Eggplant mosaic virus]   73   53   192                           sp|P20129|V70K_EPMV 70 KD PROTEIN.       3603   2   527   354   gi|1439521   glutaryl-CoA dehydrogenase precursor [ Mus musculus ]   73   48   174       3743   1   400   2   gi|450688   hsdM gene of EcoprrI gene product [ Escherichia coli ]pir|S38437|S38437 hsdM   73   54   399                           protein -  Escherichia coli  pir|S09629|S09629 hypothetical protein A -                             Escherichia coli  (SUB 40-520)       3752   1   359   78   gi|1524193   unknown (Mycobacterium tuberculosis]   73   59   282       3852   1   2   181   gi|216746   D-lactate dehydrogenase [ Lactobacillus plantarum ]   73   68   180       3914   1   239   3   pir|S13490|S134   Hydroxymethylglutaryl-CoA synthase (EC 4.1.3.5) - Chicken (fragment)   73   53   237       3914   2   343   116   gi|528991   unknown [ Bacillus subtilis ]   73   38   228       4069   1   2   316   gi|40003   oxoglutarate dehydrogenase (NADP+) [ Bacillus subtilis ] p|P23129|OD01_BACSU   73   55   315                           2-OXOGLUTARATE DEHYDROGENASE E1 COMPONENT (EC 2.4.2) (ALPHA-KETOGLUTARATE                           DEHYDROGENASE).       4165   1   365   15   gi|1439521   glutaryl-CoA dehydrogenase precursor [ Mus musculus ]   73   48   351       4196   1   1   177   gi|809660   deoxyribose-phosphate aldolase [ Bacillus subtilis ] pir|S49455|S49455   73   60   177                           deoxyribose-phosphate aldolase (EC 4.1.2.4) -  Bacillus subtilis         4202   1   378   184   gi|528991   unknown [ Bacillus subtilis )   73   38   195       4314   1   2   193   gi|436797   N-acyl-L-amino acid amidohydrolase [ Bacillus stearothermophilus ]   73   47   192                           sp|P37112|AMA_BACST N-ACYL-L-AMINO ACID AMIDOHYDROLASE (EC .5.1.14)                           (AMINOACYLASE).       4393   1   3   263   gi|216267   ORF2 [ Bacillus megaterium )   73   47   261       35   2   903   1973   gi|1146196   phosphoglycerate dehydrogenase [ Bacillus subtilis ]   72   53   1071       38   22   17877   16660   gi|602031   similar to trimethylamine DH [ Mycoplasma capricolum ] pir|S49950|S49950   72   54   1218                           probable trimethylamine dehydrogenase (EC .5.99.7) -  Mycoplasma capricolum                             (SGC3) (fragment)       38   23   18134   19162   gi|413968   ipa-44d gene product [ Bacillus subtilis ]   72   54   1029       44   19   11895   12953   gi|516272   unknown [ Bacillus subtilis ]   72   49   1059       48   7   6248   7117   gi|43499   pyruvate synthase [Halobacterium halobium)   72   49   870       50   7   5691   4819   gi|1205399   proton glutamate symport protein [ Haemophilus influenzae ]   72   53   873       53   9   9259   7997   gi|1303956   YqjE [ Bacillus subtilis ]   72   52   1263       56   23   29549   29995   gi|467471   unknown [ Bacillus subtilis ]   72   47   447       69   4   4123   2948   gi|1354775   pfoS/R [Treponema pallidum]   72   46   1176       69   5   4377   4982   gi|904198   hypothetical protein [ Bacillus subtilis ]   72   43   606       73   1   2   856   gi|142997   glycerol uptake facilitator [ Bacillus subtilis ]   72   59   855       98   13   9371   10258   gi|467435   unknown [ Bacillus subtilis ]   72   50   888       127   1   1   1593   gi|217144   alanine carrier protein [thermophilic bacterium PS3] pir|A45111|A45111   72   56   1593                           alanine transport protein - thermophilic acterium PS-3       131   1   2600   3   gi|153952   polymerase III polymerase subunit (dnaE) [ Salmonella typhimurium ]   72   53   2598                           pir|A45915|A45915 DNA-directed DNA polymerase (EC 2.7.7.7) III lpha chain -                             Salmonella typhimurium         141   4   1040   1978   gi|1405446   transketolase [ Bacillus subtilis ]   72   54   939       149   8   2535   2251   gi|606234   secY [ Escherichia coli ]   72   44   285       149   17   5245   5018   gi|1304472   DNA polymerase [Unidentified phycodnavirus clone OTU4]   72   55   228       154   1   1   210   gi|1205620   ferritin like protein [ Haemophilus influenzae ]   72   40   210       155   1   1320   433   gi|391610   farnesyl diphosphate synthase [ Bacillus stearothermophilus ]   72   57   888                           pir|JX0257|JX0257 geranyltranstransferase (EC 2.5.1.10) -  Bacillus                               stearothermophilus         180   1   2   328   gi|433630   A180 [ Saccharomyces cerevisiae ]   72   62   327       184   3   1145   3553   gi|1205110   virulence associated protein homolog [ Haemophilus influenzae ]   72   49   2409       195   2   1279   635   gi|1001730   hypothetical protein [Synechocystis sp.]   72   45   645       206   13   14646   15869   gi|1064807   ORTHININE AMINOTRANSFERASE [ Bacillus subtilis ]   72   50   1224       209   2   462   932   gi|1204666   hypothetical protein (GB: X73124_53) [ Haemophilus influenzae ]   72   60   471       215   2   522   280   gi|881513   insulin receptor homolog [ Drosophila melanogaster ] pir|S57245|S57245   72   63   243                           insulin receptor homolog - fruit fly ( Drosophila elanogaster ) (SUB 46-                           2146)       224   1   2   790   gi|949974   sucrose repressor [ Staphylococcus xylosus ]   72   54   789       233   1   765   4   gi|1408493   homologous to SwissProt: YIDA_ECOLI hypothetical protein [ Bacillus subtilis ]   72   52   762       240   1   220   1485   gi|537049   ORF_o470 [ Escherichia coli ]   72   52   1266       245   1   3   1340   gi|1204578   hypothetical protein (GB: U06949_1) [ Haemophilus influenzae ]   72   46   1338       259   2   1245   382   gi|1340128   ORF1 [ Staphylococcus aureus ]   72   59   864       304   2   285   1094   gi|1205330   glutamine-binding periplasmic protein [ Haemophilus influenzae ]   72   52   810       307   10   5039   4752   gi|1070015   protein-dependent [ Bacillus subtilis ]   72   53   288       315   1   260   3   gi|143399   quinol oxidase [ Bacillus subtilis ]   72   55   258       316   11   9308   8994   gi|1204445   hypothetical protein (SP: P27857) [ Haemophilus influenzae ]   72   52   315       337   3   926   1609   gi|487433   citrate synthase II [ Bacillus subtilis ]   72   55   684       364   7   10493   8448   gi|1510643   ferrous iron transport protein B [ Methanococcus jannaschii ]   72   53   2046       409   2   340   1263   gi|1402944   orfRM1 gene product [ Bacillus subtilis ]   72   49   924       441   3   1590   1003   gi|312379   highly conserved among eubacteria [ Clostridium acetobutylicum ]   72   48   588                           pir|S34312|S34312 hypothetical protein V -  Clostridium cetobutylicum         453   6   2505   2356   pir|S00601|BXSA   antibacterial protein 3 -  Staphylococcus haemolyticus     72   70   150       460   1   2   625   gi|1016162   ABC transporter subunit [Cyanophora paradoxa]   72   51   624       463   1   1628   3   gi|666014   The polymorphysm (RFLP) of this gene is associated with usceptibility to   72   60   1626                           essential hypertension. The SA gene product has light homology to acetyl-                           CoA synthetase [ Homo sapiens ]       480   4   3047   3466   gi|433992   ATP synthase subunit epsilon [ Bacillus subtilis ]   72   53   420       502   1   586   86   gi|310859   ORF2 [synechococcus sp.]   72   50   501       519   1   81   1184   gi|1303704   YrkE [ Bacillus subtilis ]   72   54   1104       559   1   3   746   gi|1107530   ceuD gene product [ Campylobacter coli ]   72   56   744       575   1   573   4   gi|1303866   Yqgs [ Bacillus subtilis ]   72   56   570       671   1   2   592   gi|1204497   protein-export membrane protein [ Haemophilus influenzae ]   72   44   591       679   2   295   1251   gi|563258   virulence-associated protein E [ Dichelobacter nodosus ]   72   52   957       687   2   295   957   gi|1146214   44% identical amino acids with the  Escherichia coli  smba supress; putative   72   49   663                           [ Bacillus subtilis ]       837   1   1   435   gi|1146183   putative [ Bacillus subtilis ]   72   54   435       868   1   150   788   gi|1377842   unknown [ Bacillus subtilis ]   72   55   639       922   1   130   432   gi|1088269   unknown protein [Azotobacter vinelandii]   72   58   303       941   1   2   238   gi|153929   NADPH-sulfite reducatase flavoprotein component [Salmonella yphimurium]   72   49   237       980   1   421   2   gi|853767   UDP-N-acetylglucosamine 1-carboxyvinyltransferase [ Bacillus subtilis ]   72   59   420       1209   1   213   43   gi|144735   neurotoxin type B [Clostridium botulinum]   72   44   171       1469   2   474   277   gi|1205458   hypothetical protein (GB: D26562_47) [ Haemophilus influenzae ]   72   63   198       1956   1   365   3   gi|154409   hexosephosphate transport protein [ Salmonella typhimurium ]   72   44   363                           pir|B41853|B41853 hexose phosphate transport system regulatory rotein uhpB -                           salmonella typhimurium       2101   1   3   401   gi|1303950   YqiY [ Bacillus subtilis ]   72   50   399       2503   1   399   229   gi|149713   formate dehydrogenase [ Methanobacterium formicicum ] pir|A42712|A42712   72   56   171                           formate dehydrogenase (EC 1.2.1.2) -  Methanobacterium formicicum         2967   1   3   155   gi|1212729   YqhJ [ Bacillus subtilis ]   72   46   153       3004   1   185   3   gi|665999   hypothetical protein [ Bacillus subtilis ]   72   55   183       3109   1   141   4   gi|413968   ipa-44d gene product [ Bacillus subtilis ]   72   45   138       3171   1   3   287   gi|515938   glutamate synthase (ferredoxin) [Synechocystis sp.] pir|S46957|S46957   72   52   285                           glutamate synthase (ferredoxin) (EC 1.4.7.1) - Synechocystis sp.       3771   1   26   367   gi|1408501   homologous to N-acyl-L-amino acid amidohydrolase of  Bacillus     72   63   342                             stearothermophilus  [ Bacillus subtilis ]       3951   1   1   222   gi|1500409     M. jannaschii  predicted coding region MJ1519 [ Methanococcus jannaschii ]   72   38   222       4190   1   362   3   gi|39956   IIGlc [ Bacillus subtilis ]   72   57   360       4444   1   3   347   gi|1009366   Respiratory nitrate reductase [ Bacillus subtilis ]   72   55   345       6   2   931   1200   gi|537095   ornithine carbamoyltransferase [ Escherichia coli ]   71   55   270       11   15   10859   10368   gi|532309   25 kDa protein [ Escherichia coli ]   71   47   492       19   2   1248   2435   gi|1244574   D-alanine; D-alanine ligase [ Enterococcus hirae ]   71   52   1188       21   2   898   1488   gi|149629   anthranilate synthase component 2 [ Leptospira biflexa ] pir|C32840|C32840   71   45   591                           anthranilate synthase (EC 4.1.3.27) component II  Leptospira biflexa         34   1   1   567   gi|1303983   YqkF [ Bacillus subtilis ]   71   59   567       37   3   2806   2420   gi|1209681   glutamate-rich protein [ Bacillus firmus ]   71   50   387       38   18   12250   12462   gi|927645   arginyl endopeptidase [Porphyromonas gingivalis]   71   50   213       39   3   1246   4431   pir|S09411|S094   spoIIIE protein -  Bacillus subtilis     71   49   3186       53   14   14760   13750   gi|142611   branched chain alpha-keto acid dehydrogenase E1-alpha [ Bacillus subtilis ]   71   58   1011       54   11   12625   11789   gi|143014   gnt repressor [ Bacillus subtilis ]   71   46   837       57   7   5860   4568   gi|508175   EIIC domain of PTS-dependent Gat transport and phosphorylation Escherichia   71   48   1293                           coli]       57   18   13897   14334   gi|1063247   high homology to flavohemoprotein (Haemoglobin-like protein) of Alcaligenes   71   56   438                           eutrophus and Saccharomyces cerevisiae [ Bacillus subtilis ]       62   16   9831   10955   gi|1303926   YgiG [ Bacillus subtilis ]   71   54   1125       70   12   8505   8966   gi|147198   phnE protein [ Escherichia coli ]   71   38   462       86   5   2089   1784   gi|904205   hypothetical protein [ Bacillus subtilis ]   71   51   306       96   7   7601   8269   gi|709991   hypothetical protein [ Bacillus subtilis ]   71   49   669       100   6   4822   5931   gi|1060848   Opine dehydrogenase [Arthrobacter sp.]   71   45   1110       103   1   532   2   gi|143089   iep protein [ Bacillus subtilis ]   71   41   531       109   18   15312   15695   gi|413985   ipa-61d gene product [ Bacillus subtilis ]   71   57   384       113   1   316   2   gi|663254   probable protein kinase [ Saccharomyces cerevisiae ]   71   57   315       114   5   5603   4608   gi|143156   membrane bound protein [ Bacillus subtilis ]   71   40   996       133   2   1723   359   gi|1303913   YqhX [ Bacillus subtilis ]   71   53   1365       149   19   5895   5455   gi|529650   G40P [Bacteriophage SPP1]   71   51   441       154   5   3087   2539   gi|425488   repressor protein [Streptococcus sobrinus]   71   47   549       164   11   11354   11689   gi|49318   ORF4 gene product [ Bacillus subtilis ]   71   52   336       169   5   1936   2745   gi|1403403   unknown [ Mycobacterium tuberculosis ]   71   56   810       193   2   272   1234   gi|1303788   YqeH [ Bacillus subtilis ]   71   49   963       205   1   895   47   gi|1215694   GlnQ [ Mycoplasma pneumoniae ]   71   46   849       233   4   1849   2022   gi|633732   ORF1 [ Campylobacter jejuni ]   71   50   174       237   7   4501   5169   gi|149384   HisIE [ Lactococcus lactis ]   71   54   669       272   4   2273   1698   gi|709993   hypothetical protein [ Bacillus subtilis ]   71   48   576       274   2   618   1496   gi|143035   NAD(P)H: glutamyl-transfer RNA reductase [ Bacillus subtilis ]   71   53   879                           pir|A35252|A35252 5-aminolevulinate synthase (EC 2.3.1.37) -  Bacillus                               subtilis         276   5   2720   2091   gi|303562   ORF210 [ Escherichia coli ]   71   50   630       287   1   136   660   gi|310634   20 kDa protein [Streptococcus gordonii]   71   53   525       288   6   2771   2220   gi|1256625   putative [ Bacillus subtilis ]   71   47   552       301   6   2461   1430   gi|467417   similar to lysine decarboxylase [ Bacillus subtilis ]   71   57   1032       306   4   5222   3837   gi|1256618   transport protein [ Bacillus subtilis ]   71   56   1386       307   2   925   314   gi|602683   orfC [ Mycoplasma capricolum ]   71   45   612       310   5   5146   4499   gi|348052   acetoin utilization protein [ Bacillus subtilis ]   71   51   648       322   1   2   1303   gi|1001819   hypothetical protein [Synechocystis sp.]   71   46   1302       333   4   3995   3819   gi|467473   unknown [ Bacillus subtilis ]   71   57   177       350   2   548   922   gi|551879   ORF 1 [ Lactococcus lactis ]   71   55   375       375   4   1860   3071   gi|467447   unknown [ Bacillus subtilis ]   71   57   1212       380   5   1560   2102   gi|142557   ATP synthase b subunit [ Bacillus megaterium ]   71   43   543       414   2   251   637   gi|580904   homologous to  E. coli  rnpA [ Bacillus subtilis ]   71   49   387       424   1   335   1354   gi|581305   L-lactate dehydrogenase [ Lactobacillus plantarum ]   71   57   1020       436   4   3270   2839   pir|PN0501|PN05   phosphoribosylanthranilate isomerase (EC 5.3.1.24) -  Bacillus subtilis     71   66   432                           [fragment]       482   1   3   1280   gi|410142   ORFX18 [ Bacillus subtilis ]   71   49   1278       525   3   1844   1416   gi|143370   Phosphoribosylpyrophosphate amidotransferase [PUR-F; EC 2.4.2.14]  Bacillus     71   56   429                             subtilis ]       529   4   2047   1355   gi|606150   ORF_f309 [ Escherichia coli ]   71   43   693       563   1   22   969   gi|1237015   ORF4 [ Bacillus subtilis ]   71   53   948       581   1   255   4   gi|1301730   T25G3.2 [ Caenorhabditis elegans ]   71   47   252       612   2   913   758   gi|153968   fimbriae Z [ Salmonella typhimurium ]   71   55   156       613   1   1   654   gi|466778   lysine specific permease [ Escherichia coli ]   71   50   654       618   1   623   3   gi|1146238   poly(A) polymerase [ Bacillus subtilis ]   71   52   621       630   1   586   2   gi|1486243   unknown [ Bacillus subtilis ]   71   53   585       691   1   641   156   gi|289260   comE ORF1 [ Bacillus subtilis ]   71   51   486       694   2   149   427   gi|12971   NADH dehydrogenase subunit V (AA 1-605) [ Gallus gallus ] ir|s10197|S10197   71   47   279                           NADH dehydrogenase (ubiquinone) (EC 1.6.5.3) chain - chicken mitochondrion                           (SGC1)       715   2   169   777   gi|1303830   YqfL [ Bacillus subtilis ]   71   53   609       746   2   970   467   gi|1377843   unknown [ Bacillus subtilis ]   71   52   504       748   1   802   167   gi|1405459   YneS [ Bacillus subtilis ]   71   49   636       753   1   524   30   gi|1510389     M. jannaschii  predicted coding region MJ0296 [ Methanococcus jannaschii ]   71   53   495       761   1   3   215   gi|475972   pentafunctional enzyme [Pneumocystis carinii]   71   47   213       783   1   703   203   gi|536655   ORF YBR244w [ Saccharomyces cerevisiae ]   71   52   501       800   3   987   682   gi|1204326   tRNA delta (2)-isopentenylpyrophosphate transferase [ Haemophilus influenzae ]   71   48   306       806   1   116   286   gi|1419075   cbiM gene product [ Methanobacterium thermoautotrophicum ]   71   50   171       931   1   488   3   gi|893358   PgsA [ Bacillus subtilis ]   71   56   486       1041   1   2   262   gi|1408507   pyrimidine nucleoside transport protein [ Bacillus subtilis ]   71   45   261       1070   1   2   172   gi|709993   hypothetical protein [ Bacillus subtilis ]   71   46   171       1176   1   57   365   gi|151259   HMG-CoA reductase (EC 1.1.1.88) [ Pseudomonas mevalonii ] pir|A44756|A44756   71   49   309                           hydroxymethylglutaryl-CoA reductase (EC 1.1.1.88) Pseudomonas sp.       1181   1   184   2   gi|46971   epiP gene product [ Staphylococcus epidermidis ]   71   50   183       1281   1   3   290   gi|153016   ORF 419 protein [ Staphylococcus aureus ]   71   50   288       1348   1   229   2   gi|602683   orfc [ Mycoplasma capricolum ]   71   48   228       2002   1   379   2   gi|1008177   ORF YJL046w [ Saccharomyces cerevisiae ]   71   48   378       2119   1   2   217   gi|1046088   arginyl-tRNA synthetase [ Mycoplasma genitalium ]   71   50   216       2418   1   3   320   gi|1499771     M. jannaschii  predicted coding region MJ0936 [ Methanococcus jannaschii ]   71   57   318       2961   1   2   187   gi|312443   carbamoyl-phosphate synthase (glutamine-hydrolysing) [ Bacillus aldolyticus ]   71   57   186       2999   2   67   306   gi|710020   nitrite reductase (nirB) [ Bacillus subtilis ]   71   43   240       3033   1   2   184   gi|1262335   YmaA [ Bacillus subtilis ]   71   57   183       3584   1   3   338   gi|401716   beta-isopropylmalate dehydrogenase [ Neurospora crassa ]   71   55   336       3715   2   399   55   gi|563952   gluconate permease [ Bacillus licheniformis ]   71   59   345       3785   1   387   4   gi|47382   acyl-CoA-dehydrogenase [Streptomyces purpurascens]   71   57   384       3875   1   272   3   gi|1001541   hypothetical protein [Synechocystis sp.]   71   38   270       4135   1   320   3   gi|142695   S-adenosyl-L-methionine: uroporphyrinogen III methyltransferase Bacillus   71   52   318                           megaterium]       4249   1   63   239   gi|1205363   deoxyribose aldolase [ Haemophilus influenzae ]   71   63   177       4508   1   267   4   gi|1197667   vitellogenin [ Anolis pulchellus ]   71   46   264       1976   1   237   22   gi|9806   lysine-rich aspartic acid-rich protein [Plasmodium chabaudi]   56   33   216                           r|S22183|S22183 lysine/aspartic acid-rich protein - Plasmodiom baudi       2161   1   2   400   gi|1237015   ORF4 [ Bacillus subtilis ]   56   27   399       2958   1   183   4   gi|466685   No definition line found [ Escherichia coli ]   56   26   180       2979   1   212   3   gi|1204354   spore germination and vegetative growth protein [ Haemophilus infiuenzae ]   56   40   210       2994   2   326   126   gi|836646   phosphoribosylformimino-praic ketoisomerase [Rhodobacter phaeroides]   56   29   201       3026   1   179   328   gi|143306   penicllin V amidase [Bacillus sphaericus]   56   30   150       3189   1   146   3   gi|1166604   Similar to aldehyde dehydrogenase [ Caenorhabditis elegans ]   56   37   144       3770   1   63   401   gi|1129145   acetyl-CoA C-acyltransferase [ Mangifera indica ]   56   43   339       4054   2   361   2   gi|1205355   Na+/H+ antiporter [ Haemophilus influenzae ]   56   31   360       4145   1   1   324   gi|726095   long-chain acyl-CoA dehydrogenase [ Mus musculus ]   56   36   324       4200   1   254   3   gi|155588   glucose-fructose oxidoreductase [ Zymomonas mobilis |pir|A42289|A42289   56   40   252                           glucose-fructose oxidoreductase (EC 1.1.—.—) recursor -  Zymomonas mobilis         4273   1   355   35   gi|308861   GTG start codon [ Lactococcus lactis ]   56   33   321       1   3   3436   2777   gi|5341   Putative orF YCLX8c, len: 192 [ Saccharomyces cerevisiae ] r|S53591|S53591   55   25   660                           hypothetical protein - yeast (Saccharomyces evisiae)       11   12   8505   7633   gi|216773   haloacetate dehalogenase H-1 [Moraxella sp.]   55   32   873       12   4   4534   3935   gi|467337   unknown [ Bacillus subtilis ]   55   26   600       19   5   5404   5844   gi|1001719   hypothetical protein [Synechocystis sp.]   55   25   441       23   13   12339   10591   gi|474190   iucA gene product [ Escherichia coli ]   55   30   1749       32   7   5368   6888   gi|1340096   unknown [ Mycobacterium tuberculosis ]   55   37   1521       34   3   1808   1047   gi|1303968   YqjQ [ Bacillus subtilis ]   55   39   762       34   5   3412   2864   gi|1303962   Yqjk [ Bacillus subtilis ]   55   33   549       36   1   647   3   gi|606045   ORF_o118 [ Escherichia coli ]   55   27   645       36   6   5243   4266   gi|1001341   hypothetical protein [Synechocystis sp.]   55   31   978       47   3   3054   3821   gi|1001819   hypothetical protein [Synechocystis sp.]   55   21   768       49   1   1127   189   gi|403373   glycerophosphoryl diester phosphodiesterase [ Bacillus subtilis ]   55   36   939                           pir|S37251|S37251 glycerophosphoryl diester phosphodiesterase -  Bacillus                               subtilis         67   11   8966   9565   gi|153053   norA1199 protein [ Staphylococcus aureus ]   55   23   600       75   3   881   1273   gi|41698   L-histidinol: NAD+ oxidoreductase (EC 1.1.1.23) (aa 1-434)  Escherichia coli )   55   33   393       82   9   14194   13001   gi|1136221   carboxypeptidase [ Sulfolobus solfataricus ]   55   35   1194       87   4   3517   4917   gi|1064812   function unknown [ Bacillus subtilis ]   55   26   1401       88   2   1172   1636   gi|882463   protein-N(pi)-phosphohistldine-sugar phosphotransferase [ Escherichia coli ]   55   35   465       92   1   127   516   gi|1377832   unknown [ Bacillus subtilis ]   55   36   390       100   2   836   2035   gi|1370274   zeaxanthin epoxidase [ Nicotiana plumbaginifolia ]   55   36   1200       100   5   4658   4179   gi|396660   unknown open reading frame [ Buchnera aphidicola ]   55   29   480       108   3   2986   1706   gi|1499866     M. jannaschii  predicted coding region MJ1024 [Methanococcus jannaschli]   55   31   1281       114   3   1834   1052   gi|1511367   formate dehydrogenase, alpha subunit [ Methanococcus jannaschii ]   55   29   783       144   3   1476   1147   gi|1100787   unkown [ Saccharomyces cerevisiae ]   55   35   330       165   5   5508   4804   gi|1045884   M. genitalium predicted coding region MG199 [ Hycoplasma genitalium ]   55   27   705       189   5   2205   2576   gi|142569   ATP synthase a subunit [ Bacillus firmus ]   55   35   372       191   6   6857   4578   gi|559411   B0272.3 [ Caenorhabditis elegans ]   55   39   2280       194   2   364   636   gi|1145768   K7 kinesin-like protein [ Dictyostelium discoideum ]   55   34   273       209   4   1335   1676   gi|473357   thi4 gene product [ Schizosaccharomyces pombe ]   55   35   342       211   2   1145   597   gi|410130   ORFX6 [ Bacillus subtilis ]   55   37   549       213   2   644   1372   gi|633692   TrsA [ Yersinia enterocolitica ]   55   28   729       214   7   4144   5481   gi|1001793   hypothetical protein [Synechocystis sp.]   55   30   1338       221   7   9197   6921   gi|466520   pocR [ Salmonella typhimurium ]   55   32   2277       233   8   4817   3726   gi|1237063   unknown [ Mycobacterium tuberculosis ]   55   38   1092       236   4   1375   2340   gi|1146199   putative [ Bacillus subtilis ]   55   32   966       243   2   380   1885   gi|459907   mercuric reductase (Plasmid pI258]   55   29   1506       258   1   394   2   gi|455006   orf6 [ Rhodococcus fascians ]   55   36   393       281   1   126   938   gi|1408493   homologous to SwissProt: YIDA_ECOLI hypothetical protein [ Bacillus subtilis ]   55   35   813       316   3   1323   2102   gi|1486447   LuxA homologue [Rhizobium sp.]   55   30   780       326   5   2744   2520   gi|1296824   proline iminopeptidase [ Lactobacillus helveticus ]   55   36   225       351   2   1429   536   gi|1204820   hydrogen peroxide-inducible activator [ Haemophilus influenzae ]   55   28   894       353   4   2197   2412   gi|1272475   chitin synthase [ Emericella nidulans ]   55   50   216       380   1   14   379   gi|142554   ATP synthase i subunit [ Bacillus megaterium ]   55   37   366       383   1   232   2   gi|289272   ferrichrome-binding protein [ Bacillus subtilis ]   55   36   231       386   1   3   938   gi|1510251   DNA helicase, putative [ Methanococcus jannaschii ]   55   30   936       410   2   1208   1891   gi|1205144   multidrug resistance protein [ Haemophilus influenzae ]   55   27   684       483   2   411   833   gi|413934   ipa-10r gene product [ Bacillus subtilis ]   55   26   423       529   3   1433   1089   gi|606150   ORF_f309 [ Escherichia coli ]   55   33   345       555   1   585   82   gi|143407   para-aminobenzoic acid synthase, component I (pab) [ Bacillus subtilis ]   55   28   504       565   1   202   2   gi|1223961   CDP-tyvelose epimerase [ Yersinia pseudotuberculosis ]   55   41   201       582   1   452   153   gi|1256643   20.2% identity with NADH dehydrogenase of the Leishmania major   55   36   300                           mitochondrion; putative [ Bacillus subtilis ]       645   5   2057   1854   gi|210824   fusion protein F [Bovine respiratory syncytial virus] pir|JQ1481|VGNZBA   55   25   204                           fusion glycoprotein precursor - bovine espiratory syncytial virus (strain                           A51908)       672   2   957   2216   gi|1511333     M. jannaschii  predicted coding region MJ1322 [ Methanococcus jannaschii ]   55   36   1260       730   1   479   3   gi|537007   ORF_f379 [ Escherichia coli ]   55   30   477       737   1   945   31   gi|536963   CG Site No. 18166 [ Escherichia coli ]   55   30   915       742   2   228   572   gi|304160   product unknown [ Bacillus subtilis ]   55   38   345       817   2   903   595   gi|1136289   histidine kinase A [ Dictyostelium discoideum ]   55   29   309       819   1   355   128   gi|558073   polymorphic antigen [ Plasmodium falciparum ]   55   22   228       832   2   724   296   gi|40367   ORFC [Clostridium acetobutylicum]   55   32   429       840   1   386   3   gi|1205875   pseudouridylate synthase I [ Haemophilus influenzae ]   55   39   384       1021   1   23   529   gi|48563   beta-lactamase [ Yersinia enterocolitica ]   55   38   507       1026   1   60   335   gi|47804   Opp C (AA1-301) [ Salmonella typhimurium ]   55   26   276       1525   1   1   282   gi|1477533   sarA [ Staphylococcus aureus ]   55   29   282       1814   2   224   985   gi|1046078   M. genitalium predicted coding region MG369 [ Mycoplasma genitalium ]   55   38   762       3254   1   254   81   gi|413968   ipa-44d gene product [ Bacillus subtilis ]   55   30   174       3695   1   345   4   gi|216773   haloacetate dehalogenase H-1 [Moraxella sp.]   55   32   342       3721   1   1   312   gi|42029   ORF1 gene product [ Escherichia coli ]   55   31   312       3799   1   3   272   gi|42029   ORF1 gene product [ Escherichia coli ]   55   38   270       3889   1   22   423   gi|1129145   acetyl-CoA C-acyltransferase [ Mangifera indica ]   55   45   402       3916   1   2   385   gi|529754   speC [ Streptococcus pyogenes ]   55   38   384       3945   1   4   198   gi|476252   phase 1 flagellin [ Salmonella enterica ]   55   36   195       4074   1   246   4   gi|42029   ORF1 gene product [ Escherichia coli ]   55   38   243       4184   1   2   343   gi|1524267   unknown [ Hycobacterium tuberculosis ]   55   28   342       4284   1   14   208   gi|1100774   ferredoxin-dependent glutamate synthase [Synechocystis sp.]   55   36   195       4457   2   378   112   gi|180189   cerebellar-degeneration-related antigen (CDR34) [ Homo sapiens ] gi|182737   55   38   267                           cerebellar degeneration-associated protein [ Homo sapiens ]                           pir|A29770|A29770 cerebellar degeneration-related protein - human       4514   1   2   244   gi|216773   haloacetate dehalogenase H-1 [Moraxella sp.]   55   32   243       4599   1   217   2   gi|1129145   acetyl-CoA C-acyltransferase [ Mangifera indica ]   55   42   216       4606   1   210   4   gi|386120   myosin alpha heavy chain (S2 subfragment) [rabbits, masseter, eptide   55   27   207                           Partial, 234 aa]       5   8   4932   4516   gi|536069   ORF YBL047c [ Saccharomyces cerevisiae ]   54   27   417       12   7   6165   5164   gi|1205504   homoserine acetyltransferase [ Haemophilus influenzae ]   54   30   1002       23   16   15326   13566   gi|474192   iucC gene product [ Escherichia coli ]   54   31   1761       35   1   2   979   gi|48054   small subunit of soluble hydrogenase (AA 1-384) [Synechococcus sp.]   54   36   978                           ir|S06919|HQYCSS soluble hydrogenase (EC 1.12.—.—) small chain -                           nechococcus sp. (PCC 6716)       37   11   8667   7897   gi|537207   ORF_f277 [ Escherichia coli ]   54   38   771       37   12   8165   8332   gi|1160967   palmitoyl-protein thioesterase [ Homo sapiens ]   54   37   168       46   15   13025   13804   gi|438473   protein is hydrophobic, with homology to  E. coli  ProW; putative  Bacillus     54   28   780                             subtilis ]       56   2   203   736   gi|1256139   YbbJ [ Bacillus subtilis ]   54   34   534       57   13   10179   9241   gi|1151248   inosine-uridine preferring nucleoside hydrolase [Crithidia fasciculata]   54   32   939       66   2   516   1133   gi|1335781   Cap [ Drosophila melanogaster ]   54   29   618       70   10   8116   8646   gi|1399823   PhoE [Rhizobium meliloti]   54   31   531       70   15   11801   11046   sp|P02983|TCR_S   TETRACYCLINE RESISTANCE PROTEIN.   54   29   756       87   5   4915   5706   gi|1064811   function unknown [ Bacillus subtilis ]   54   33   792       92   4   2289   1573   gi|1205366   oligopeptide transport ATP-binding protein [ Haemophilus influenzae ]   54   33   717       103   2   1556   516   gi|710495   protein kinase [ Bacillus brevis ]   54   33   1041       105   2   2095   605   gi|143727   putative [ Bacillus subtilis ]   54   30   1491       112   4   2337   2732   gi|153724   MalC [Streptococcus pneumoniae]   54   41   396       127   2   1720   2493   gi|144297   acetyl esterase (XynC) [ Caldocellum saccharolyticum ] pir|B37202|B37202   54   34   774                           acetylesterase (EC 3.1.1.6) (XynC) -  Caldocellum accharolyticum         138   5   1600   3306   gi|42473   pyruvate oxidase [ Escherichia coli ]   54   36   1707       152   2   525   1172   gi|1377834   unknown [ Bacillus subtilis ]   54   23   648       161   9   4831   5469   gi|903305   ORF73 [ Bacillus subtilis ]   54   28   639       161   13   6694   7251   gi|1511039   phosphate transport system regulatory protein [ Methanococcus jannaschii ]   54   32   558       164   6   3263   4543   gi|1204976   prolyl-tRNA synthetase [ Haemophilus influenzae ]   54   34   1281       164   20   21602   22243   gi|143582   spoIIIEA protein [ Bacillus subtilis ]   54   32   642       171   6   4250   2817   gi|436965   [malA] gene products [ Bacillus stearothermophilus ] pir|S43914|S43914   54   37   1434                           hypothetical protein 1 -  Bacillus stearothermophilus         206   18   19208   19720   gi|1240016   R09E10.3 [ Caenorhabditis elegans ]   54   38   513       218   2   1090   1905   gi|467378   unknown [ Bacillus subtilis ]   54   26   816       220   1   663   4   gi|1353761   myosin II heavy chain [Naegleria fowleri]   54   22   660       220   13   12655   13059   pir|S00485|S004   gene 11-1 protein precursor -  Plasmodium falciparum  (fragments)   54   35   405       221   3   2030   3709   gi|1303813   YqeW [ Bacillus subtilis ]   54   34   1680       272   7   4219   3383   gi|62964   arylamine N-acetyltransferase (AA 1-290) [Gallus gallus] ir|S06652|XYCHY3   54   33   837                           arylamine N-acetyltransferase (EC 2.3.1.5) (clone NAT-3) - chicken       316   7   4141   4701   gi|682769   mccE gene product [ Escherichia coli ]   54   31   561       316   10   6994   8742   gi|413951   ipa-27d gene product [ Bacillus subtilis ]   54   28   1749       338   3   2214   1051   gi|490328   LORF F [unidentified]   54   28   1164       341   4   3201   3614   gi|171959   myosin-like protein [ Saccharomyces cerevisiae ]   54   25   414       346   1   912   4   gi|396400   similar to eukaryotic Na+/H+ exchangers [ Escherichia coli ]   54   34   909                           sp|P32703|YJCE_ECOLI HYPOTHETICAL 60.5 KD PROTEIN IN SOXR-ACS NTERGENIC                           REGION (0549).       348   2   623   1351   gi|537109   ORF_f343a [ Escherichia coli ]   54   34   729       378   2   1007   1942   sp|P02983|TCR_S   TETRACYCLINE RESISTANCE PROTEIN   54   31   936       408   6   4351   5301   gi|474190   iucA gene product [ Escherichia coli ]   54   29   951       444   9   7934   8854   gi|216267   ORF2 [ Bacillus megaterium ]   54   32   921       463   2   2229   1741   gi|304160   product unknown [ Bacillus subtilis ]   54   50   489       502   2   1133   570   gi|1205015   hypothetical protein (SP: P10120) [ Haemophilus influenzae ]   54   38   564       505   6   5357   4452   gi|1500558   2-hydroxyhepta-2,4-diene-1,7-dioate isomerase [ Methanococcus jannaschii ]   54   41   906       550   1   1522   308   gi|40100   rodC (tag3) polypeptide (AA 1-746) [ Bacillus subtilis ] ir|S06049|S06049   54   35   1215                           rodC protein -  Bacillus subtilis  p|P13485|TAGF_BACSU TECHOIC ACID                           BIOSYNTHESIS PROTEIN F.       551   5   3305   4279   gi|950197   unknown [Corynebacterium glutamicum]   54   34   975       558   2   958   560   gi|485090   No definition line found [ Caenorhabditis elegans ]   54   32   399       580   1   91   936   gi|331906   fused envelope glycoprotein precursor [Friend spleen focus-forming irus]   54   45   846       603   3   554   757   gi|1323423   ORF YGR234w [ Saccharomyces cerevisiae ]   54   36   204       617   1   25   249   gi|219959   ornithine transcarbamylase [ Homo sapiens ]   54   40   225       622   3   1097   1480   gi|1303873   YqgZ [ Bacillus subtilis ]   54   25   384       623   1   3   404   gi|1063250   low homology to P20 protein of Bacillus lichiniformis and bleomycin   54   45   402                           acetyltransferase of Streptomyces verticillus [ Bacillus subtilis ]       689   1   1011   475   gi|552446   NADH dehydrogenase subunit 4 [Apis mellifera ligustica]pir|S52968|S52968   54   30   537                           NADH dehydrogenase chain 4 - honeybee itochondrion (SGC4)       725   2   686   1441   gi|987096   sensory protein kinase [ Streptomyces hygroscopicus ]   54   26   756       956   1   1   249   pir|S30782|S307   integrin homolog - yeast [ Saccharomyces cerevisiae ]   54   24   249       978   2   859   581   gi|1301994   ORF YNL091w [ Saccharomyces cerevisiae ]   54   33   279       1314   1   3   281   gi|1001108   hypothetical protein [Synechocystis sp.]   54   33   279       2450   1   1   228   gi|1045057   ch-TOG [ Homo sapiens ]   54   32   228       2934   1   1   387   gi|580870   ipa-37d qoxA gene product [ Bacillus subtilis ]   54   36   387       2970   1   251   3   sp|P37348|YECE —     HYPOTHETICAL PROTEIN IN ASPS 5′REGION (FRAGMENT).   54   42   249       3002   1   1   309   gi|44027   Tma protein [ Lactococcus lactis ]   54   33   309       3561   1   9   464   gi|151259   HMG-CoA reductase (EC 1.1.1.88) [ Pseudomonas mevalonii ] pir|A44756|A44756   54   35   456                           hydroxymethylglutaryl-CoA reductase (EC 1.1.1.88) Pseudomonas sp.       3572   1   72   401   gi|450688   hsdM gene of EcoprrI gene product [ Escherichia coli ] pir|S38437|S38437 hsdM   54   36   330                           protein -  Escherichia coli  pir|S09629|S09629 hypothetical protein A -                             Escherichia coli  (SUB 40-520)       3829   1   400   2   gi|1322245   mevalonate pyrophosphate decarboxylase [ Rattus norvegicus ]   54   29   399       3909   1   1   273   gi|29865   CENP-E [ Homo sapiens ]   54   30   273       3921   1   3   209   pir|S24325|S243   glucan 1,4-beta-glucosidase (EC 3.2.1.74) -  Pseudomonas fluorescens  subsp.   54   34   207                           cellulosa       4438   1   285   4   gi|1196657   unknown protein [ Mycoplasma pneumoniae ]   54   30   282       4459   1   3   272   gi|1046081   hypothetical protein (GB: D26185_10) [ Mycoplasma genitalium ]   54   38   270       4564   1   3   221   gi|216267   ORF2 [ Bacillus megaterium ]   54   38   219       23   12   10685   8832   gi|474192   iucC gene product [ Escherichia coli ]   53   35   1854       23   14   13579   12317   gi|42029   ORF1 gene product [ Escherichia coli ]   53   32   1263       24   3   3940   3440   gi|1369947   c2 gene product [Bacteriophage B1]   53   36   501       26   4   3818   4618   gi|1486247   unknown [ Bacillus subtilis ]   53   37   801       38   6   2856   3998   gi|405880   yeil [ Escherichia coli ]   53   40   1143       38   10   7806   6232   gi|1399954   thyroid sodium/iodide symporter NIS [ Rattus norvegicus ]   53   29   1575       56   10   12100   11876   pir|A54592|A545   110k actin filament-associated protein - chicken   53   32   225       57   6   4583   4119   pir|A00341|DEZP   alcohol dehydrogenase (EC 1.1.1.1) - fission yeast [ Schizosaccharomyces     53   39   465                             pombe ]       57   12   8932   7349   gi|1480429   putative transcriptional regulator [ Bacillus stearothermophilus ]   53   30   1584       67   12   9496   10218   gi|1511555   quinolone resistance norA protein protein [ Methanococcus jannaschii ]   53   31   723       69   3   2382   1639   gi|1087017   arabinogalactan-protein, AGP [ Nicotiana alata , cell-suspension culture   53   30   744                           filtrate, Peptide, 461 aa]       79   1   3   1031   gi|1523802   glucanase [ Anabaena variabilis ]   53   32   1029       80   1   338   3   gi|452428   ATPase 3 [ Plasmodium falciparum ]   53   36   336       88   4   1910   2524   gi|537034   ORF_o488 [ Escherichia coli ]   53   25   615       88   5   2467   3282   gi|537034   ORF_o488 [ Escherichia coli ]   53   29   816       92   8   5505   5140   gi|399598   amphotropic murine retrovirus receptor [ Rattus norvegicus ]   53   33   366       94   5   3239   2061   gi|173038   tropomyosin (TPM1) [ Saccharomyces cerevisiae ]   53   25   1179       99   5   4207   5433   sp|P28246|BCR_E   BICYCLOMYCIN RESISTANCE PROTEIN (SULFONAMIDE RESISTANCE PROTEIN)   53   30   1227       120   3   1639   2262   gi|576655   ORF1 [Vibrio anguillarum]   53   35   624       120   11   7257   8897   gi|1524397   glycine betaine transporter OpuD [ Bacillus subtilis ]   53   33   1641       127   6   5685   4477   gi|1256630   putative [ Bacillus subtilis ]   53   32   1209       147   2   255   557   gi|581648   epiB gene product [ Staphylococcus epidermidis ]   53   34   303       158   4   4256   3807   gi|151004   mucoidy regulatory protein AlgR [Pseudomonas aeruginosa] pir|A32802|A32802   53   32   450                           regulatory protein algR —Pseudomonas aeruginosa sp|P26275|ALGR_PSEAE                           POSITIVE ALGINATE BIOSYNTHESIS REGULATORY ROTEIN.       171   7   5421   5125   gi|1510669   hypothetical protein (GP: D64044_18) [ Methanococcus jannaschii ]   53   34   297       191   9   11483   9879   gi|298085   acetoacetate decarboxylase [Clostridium acetobutylicum] pir|B49346|B49346   53   31   1605                           butyrate—acetoacetate CoA-transferase (EC .8.3.9) small chain -                           Clostridium acetobutylicum sp|P33752|CTFA_CLOAB BUTYRATE-ACETOACETATE COA-                           TRANSFERASE SUBUNIT (EC 2.8.3.9) (COAT A)       203   5   3763   4326   gi|143456   rpoE protein (ttg start codon) [ Bacillus subtilis ]   53   29   564       206   17   18204   18971   gi|304136   acetylglutamate kinase [ Bacillus stearothermophilus ] sp|Q07905|ARGB_BACST   53   36   768                           ACETYLGLUTAMATE KINASE (EC 2.7.2.8) (NAG INASE) (AGK) (N-ACETYL-L-                           GLUTAMATE 5-PHOSPHOTRANSFERASE).       212   10   4021   4221   gi|9878   protein kinase [ Plasmodium falciparum ]   53   28   201       231   2   1350   1120   gi|537506   paramyosin [ Dirofilaria immitis ]   53   34   231       272   6   2719   3249   pir|A33141|A331   hypothetical protein (gtfD 3′ region) -  Streptococcus mutans     53   34   531       308   3   927   2576   gi|606292   ORF_o696 [ Escherichia coli ]   53   33   1650       320   7   5645   5884   gi|160596   RNA polymerase III largest subunit [ Plasmodium falciparum ]   53   33   240                           sp|P27625|RPC1_PLAFA DNA-DIRECTED RNA POLYMERASE III LARGEST UBUNIT (EC                           2.7.7.6).       327   1   218   901   gi|854601   unknown [ Schizosaccharomyces pombe ]   53   31   684       341   2   212   2500   gi|633732   ORF1 [ Campylobacter jejuni ]   53   31   2289       351   1   383   3   sp|P31675|YABM —     HYPOTHETICAL 42.7 KD PROTEIN IN TBPA-LEUD INTERGENIC REGION (ORF104).   53   32   381       433   7   4731   4375   gi|1001961   MHC class II analog [ Staphylococcus aureus ]   53   30   357       454   2   980   720   pir|A60328|A603   40K cell wall protein precursor (sr 5′ region) -  Streptococcus mutans     53   27   261                           (strain OMZ175, serotype f)       470   4   1123   1761   gi|516826   rat GCP360 [ Rattus rattus ]   53   30   639       483   1   217   2   gi|1480429   putative transcriptional regulator [ Bacillus stearothermophilus ]   53   33   216       544   1   516   1259   gi|46587   ORF 1 (AA 1-121) (1 is 2nd base in codon) [ Staphylococcus aureus ]   53   38   744                           ir|S15765|S15765 hypothetical protein 1 (hlb 5′ region) -  Staphylococcus                             aureus (fragment)       558   10   3754   3551   gi|15140   res gene [Bacteriophage P1]   53   32   204       603   2   339   620   gi|507738   Hmp [Vibrio parahaemolyticus]   53   26   282       693   1   941   213   gi|153123   toxic shock syndrome toxin-1 precursor [ Staphylococcus aureus ]   53   38   729                           pir|A24606|XCSAS1 toxic shock syndrome toxin-1 precursor -  Staphylococcus                               aureus         766   1   2   673   gi|687600   orfA2; orfA2 forms an operon with orfA1 [ Listeria monocytogenes ]   53   43   672       781   1   335   3   gi|1204551   pilin biogenesis protein [ Haemophilus influenzae ]   53   26   333       801   1   3   545   gi|1279400   SapA protein [ Escherichia coli ]   53   25   543       803   1   2   910   gi|695278   lipase-like enzyme [Alcaligenes eutrophus]   53   30   909       872   1   590   3   gi|298032   EF [ Streptococcus suis ]   53   30   588       910   1   2   184   gi|1044936   unknown [ Schizosaccharomyces pombe ]   53   29   183       943   1   399   4   gi|290508   similar to unidentified ORF near 47 minutes [ Escherichia coli ]   53   30   396                           sp|P31436|YICK_ECOLI HYPOTHETICAL 43.5 KD PROTEIN IN SELC-NLPA NTERGENIC                           REGION.       988   1   504   4   gi|142441   ORF 3; putative [ Bacillus subtilis ]   53   28   501       1064   1   3   434   gi|305080   myosin heavy chain [Entamoeba histolytica]   53   26   432       1366   1   3   452   gi|308852   transmembrane protein [ Lactococcus lactis ]   53   33   450       1758   1   397   2   gi|1001774   hypothetical protein [Synechocystis sp.]   53   30   396       1897   1   1   447   gi|1303949   YqiX [ Bacillus subtilis ]   53   27   447       2381   1   400   2   gi|1146243   22.4% identity with  Escherichia coli  DNA-damage inducible protein ...;   53   37   399                           putative [ Bacillus subtilis ]       3537   1   1   327   gi|450688   hsdM gene of EcoprrI gene product [ Escherichia coli ] pir|S38437|S38437 hsdM   53   35   327                           protein -  Escherichia coli  pir|S09629|S09629 hypothetical protein A -                             Escherichia coli  [SUB 40-520]       3747   2   137   397   gi|1477486   transposase [Burkholderia cepacia]   53   53   261       11   5   3049   3441   gi|868224   No definition line found [ Caenorhabditis elegans ]   52   33   393       15   5   2205   2369   gi|215966   G41 protein (gtg start codon) [Bacteriophage T4]   52   34   165       19   3   2429   3808   gi|1205379   UDP-murnac-pentapeptide synthetase [ Haemophilus influenzae ]   52   31   1380       24   1   3462   4   gi|579124   predicted 86.4 kd protein; 52 Kd observed [Mycobacteriophage 15]   52   32   3459                           pir|S30971|S30971 gene 26 protein - Mycobacterium phage L5                           sp|Q05233|VG26_BPML5 MINOR TAIL PROTEIN GP26. (SUB 2-837)       37   5   3015   3935   gi|1500543   P115 protein [ Methanococcus jannaschii ]   52   25   921       38   13   8795   9703   gi|46851   glucose kinase [Streptomyces coelicolor]   52   29   909       44   16   10617   11066   gi|42012   moaE gene product [ Escherichia coli ]   52   36   450       46   1   3   521   gi|1040957   NADH dehydrogenase subunit 6 [Anopheles trinkae]   52   25   519       51   10   5531   6280   gi|388269   traC [Plasmid pAD1]   52   32   750       56   5   2826   1684   gi|181949   endothelial differentiation protein (edg-1) [ Homo sapiens ]   52   23   1143                           pir|A35300|A35300 G protein-coupled receptor edg-1 - human                           sp|P21453|EDG1_HUMAN PROBABLE G PROTEIN-COUPLED RECEPTOR EDG-1.       57   5   4173   3496   gi|304153   sorbitol dehydrogenase [ Bacillus subtilis ]   52   27   678       62   5   2870   2376   gi|1072399   phaE gene product [Rhizobium meliloti]   52   25   495       62   6   3651   2857   gi|46485   NADH dehydrogenase [Synechococcus PCC7942]   52   27   795       67   14   11355   12962   gi|1511365   glutamate synthase (NADPH), subunit alpha [ Methanococcus jannaschii ]   52   30   1608       67   21   16935   18158   gi|1204393   hypothetical protein (SP: P31122) [ Haemophilus influenzae ]   52   25   1224       70   4   1997   1809   gi|7227   cytoplasmic dynein heavy chain [ Dictyostelium discoldeum ]r|A44357|A44357   52   36   189                           dynein heavy chain, cytosolic - slime mold  Dictyostelium discoideum )       96   10   10005   10664   gi|1408485   B65G gene product [ Bacillus subtilis ]   52   26   660       103   5   3351   2716   gi|1009368   Respiratory nitrate reductase [ Bacillus subtilis ]   52   42   636       109   3   3350   2598   gi|699274   lmbE gene product [Mycobacterium leprae]   52   39   753       109   19   15732   17300   gi|1526981   amino acid permease YeeF like protein [ Salmonella typhimurium ]   52   30   1569       121   3   981   550   gi|732931   unknown [ Saccharomyces cerevisiae ]   52   32   432       125   3   865   1680   gi|1296975   puT gene product [Porphyromonas gingivalis]   52   38   816       130   2   659   1807   gi|1256634   25.8% identity over 120 aa with the Synenococcus sp. MpeV protein; putative   52   36   1149                           [ Bacillus subtilis ]       149   1   583   2   gi|1225943   PBSX terminase [ Bacillus subtilis ]   52   33   582       149   14   4415   4143   gi|1510368     M. jannaschii  predicted coding region MJ0272 [ Methanococcus jannaschii ]   52   35   273       167   1   216   1001   gi|146025   cell division protein [ Escherichia coli ]   52   43   786       188   1   120   1256   gi|474915   orf 337; translated orf similarity to SW: BCR_ECOLI bicyclomycin esistance   52   26   1137                           protein of  Escherichia coli  [ Coxiella burnetii ] pir|S44207|S44207                           hypothetical protein 337 - Coxiella burnetii (SUB -338)       195   9   8760   8359   gi|3028   mitochondrial outer membrane 72K protein [ Neurospora crassa ]   52   25   402                           r|A36682|A36682 72K mitochondrial outer membrane protein -  Neurospora crassa         200   3   2065   2607   gi|142439   ATP-dependent nuclease [ Bacillus subtilis ]   52   35   543       203   4   2776   3684   gi|303698   BltD [ Bacillus subtilis ]   52   25   909       227   8   5250   5651   gi|305080   myosin heavy chain [ Entamoeba histolytica ]   52   24   402       242   1   21   1424   gi|1060877   EmrY [ Escherichia coli ]   52   32   1404       249   5   4526   4753   pir|C37222|C372   cytochrome P450 1A1, hepatic - dog (fragment)   52   23   228       255   1   1055   3   gi|143290   penicillin-binding protein [ Bacillus subtills ]   52   28   1053       276   7   3664   3365   gi|1001610   hypothetical protein [Synechocystis sp.]   52   30   300       276   8   4055   3654   gi|416235   orf L3 [ Mycoplasma capricolum ]   52   26   402       289   2   1449   1042   gi|150900   GTP phosphohydrolase [Proteus vulgaris]   52   34   408       325   1   1   279   gi|1204874   polypeptide deformylase (formylmethionine deformylase) [ Haemophilus     52   33   279                             influenzae ]       340   1   1010   3   gi|1215695   peptide transport system protein SapF homolog; SapF homolog [ Mycoplasma     52   33   1008                             pneumoniae ]       375   3   340   1878   gi|467446   similar to SpoVB [ Bacillus subtilis ]   52   28   1539       424   4   3262   2420   gi|1478239   unknown [ Mycobacterium tuberculosis ]   52   34   843       430   1   3   575   pir|A42606|A426   orfA 5′ to orf405 -  Saccharopolyspora erythraea  (fragment)   52   28   573       444   4   3712   2696   gi|1408494   homologous to penicillin acylase [ Bacillus subtilis ]   52   31   1017       465   1   903   4   gi|143331   alkaline phosphatase regulatory protein [ Bacillus subtilis ]   52   36   900                           pir|A27650|A27650 regulatory protein phoR -  Bacillus subtilis                             sp|P23545|PHOR_BACSU ALKALINE PHOSPHATASE SYNTHESIS SENSOR PROTEIN HOR (EC                           2.7.3.—)       469   5   4169   3633   gi|755152   highly hydrophobic integral membrane protein [ Bacillus subtilis ]   52   32   537                           sp|P42953|TAGG_BACSU TEICHOIC ACID TRANSLOCATION PERMEASE PROTEIN AGG.       495   1   633   4   gi|1204607   transcription activator [ Haemophilus influenzae ]   52   25   630       505   7   5762   5520   gi|142440   ATP-dependent nuclease [ Bacillus subtilis ]   52   28   243       517   2   1162   1614   gi|166162   Bacteriophage phi-11 int gene activator [Staphylococcus acteriophage phi   52   35   453                           11]       543   2   444   1295   gi|1215693   putative orf; GT9_orf434 [ Mycoplasma pneumoniae ]   52   25   852       586   1   1   336   gi|581648   epiB gene product [ Staphylococcus epidermidis ]   52   36   336       773   1   426   4   gi|1279769   FdhC [Methanobacterium thermofomicicum]   52   30   423       1120   2   100   330   gi|142439   ATP-dependent nuclease [ Bacillus subtilis ]   52   35   231       1614   1   347   3   gi|289262   comE ORF3 [ Bacillus subtilis ]   52   28   345       2495   1   1   324   gi|216151   DNA polymerase (gene L; ttg start codon) [Bacteriophage SP02] gi|579197   52   34   324                           SP02 DNA polymerase (aa 1-648) [Bacteriophage SPO2] pir|A21498|DJBPS2 DNA-                           directed DNA polymerase (EC 2.7.7.7) - phage PO2       2931   1   285   4   gi|1256136   YbbG [ Bacillus subtilis ]   52   30   282       2943   1   320   63   gi|41713   hisA ORF (AA 1-245) [ Escherichia coli ]   52   35   258       2993   1   295   2   gi|298032   EF [ Streptococcus suis ]   52   34   294       3667   1   307   2   gi|849025   hypothetical 64.7-kDa protein [ Bacillus subtilis ]   52   36   306       3944   1   260   42   gi|1218040   BAA [ Bacillus licheniformis ]   52   36   219       3954   2   347   81   gi|854064   U87 [Human herpesvirus 6]   52   50   267       3986   1   90   401   gi|1205919   Na+ and Cl− dependent gamma-aminobutryic acid transporter [ Haemophilus     52   33   312                             influenzae ]       4002   1   3   389   gi|40003   oxoglutarate dehydrogenase (NADP+) [ Bacillus subtilis ] p|P23129|ODO1_BACSU   52   42   387                           2-OXOGLUTARATE DEHYDROGENASE E1 COMPONENT (EC 2.4.2) (ALPHA-KETOGLUTARATE                           DEHYDROGENASE).       4020   1   1   249   gi|159388   ornithine decarboxylase [Leishmania donovani]   52   47   249       4098   1   220   2   gi|409795   No definition line found [ Escherichia coli ]   52   32   219       4248   1   3   212   gi|965077   Adr6p [Seccharomyces cerevisiae]   52   40   210       7   1   3   575   gi|895747   putative cel operon regulator [ Bacillus subtilis ]   51   28   573       21   4   2479   3276   gi|1510962   indole-3-glycerol phosphate synthase [ Methanococcus jannaschii ]   51   32   798       22   9   5301   5966   gi|1303933   YqiN [ Bacillus subtilis ]   51   25   666       43   3   1283   1050   gi|1519460   Srp1 [ Schizosaccharomyces pombe ]   51   31   234       44   17   11042   11305   gi|42011   moaD gene product [ Escherichia coli ]   51   35   264       51   11   6453   6731   gi|495471   vacuolating toxin [Helicobacter pylori]   51   37   279       52   4   2537   2995   gi|1256652   25% identity to the  E. coli  regulatory protein MprA; putative [Bacillus   51   32   459                           subtilis]       57   10   6843   6355   gi|508173   EIIA domain of PTS-dependent Gat transport and phosphorylation Escherichia   51   32   489                           coli]       59   1   29   1111   gi|299163   alanine dehydrogenase [ Bacillus subtilis ]   51   33   1083       67   20   15791   16576   gi|1510977     M. jannaschii  predicted coding region MJ0938 [ Methanococcus jannaschii ]   51   24   786       69   2   1218   877   gi|467359   unknown [ Bacillus subtilis ]   51   34   342       71   1   3   1196   gi|298032   EF [ Streptococcus suis ]   51   32   1194       78   2   176   3   gi|1161242   proliferating cell nuclear antigen [Styela clava]   51   28   174       99   4   3357   4040   gi|642795   TFIID subunit TAFII55 [ Homo sapiens ]   51   25   684       109   1   1428   4   gi|580920   rodD (gtaA) polypeptide (AA 1-673) [ Bacillus subtilis ] pir|S06048|S06048   51   27   1425                           probable rodD protein -  Bacillus subtilis  sp|P13484|TAGE_BACSU PROBABLE                           POLY (GLYCEROL-PHOSPHATE) LPHA-GLUCOSYLTRANSFERASE (EC 2.4.1.52) (TECHOIC                           ACID BIOSYNTHESIS ROTEIN E)       109   9   6007   6693   gi|1204815   hypothetical protein (SP: P32662) [ Haemophilus influenzae ]   51   23   687       112   3   1066   2352   pir|S05330|S053   maltose-binding protein precursor -  Enterobacter aerogenes     51   42   1287       112   13   12855   11278   gi|405857   yehU [ Escherichia coli ]   51   29   1578       114   9   8967   8209   gi|435098   orf1 [ Mycoplasma capricolum ]   51   30   759       115   1   1   912   gi|1431110   ORF YDL085w [ Saccharomyces cerevisiae ]   51   25   912       127   10   9647   10477   gi|1204314     H. influenzae  predicted coding region HI0056 [ Haemophilus influenzae ]   51   37   831       152   9   6814   7356   gi|431929   MunI regulatory protein [Mycoplasma sp.]   51   38   543       154   2   575   1153   gi|1237044   unknown [ Mycobacterium tuberculosis ]   51   36   579       154   7   5634   4681   gi|409286   bmrU [ Bacillus subtilis ]   51   27   954       171   8   6236   5529   gi|1205484   hypothetical protein (SP: P33918) [ Haemophilus influenzae ]   51   32   708       184   1   1   291   gi|466886   B1496_C3_206 [Mycobacterium leprae]   51   33   291       212   5   1501   2139   pir|A45605|A456   mature-parasite-infected erythrocyte surface antigen MESA -  Plasmodium     51   23   639                             falciparum         228   2   707   1378   gi|8204   nuclear protein [ Drosophila melanogaster ]   51   27   672       236   8   7481   6825   gi|49272   Asparaginase [ Bacillus licheniformis ]   51   31   657       243   4   3546   2455   gi|1511102   melvalonate kinase [ Methanococcus jannaschii ]   51   29   1092       257   4   3373   3206   gi|1204579     H. influenzae  predicted coding region HI0326 [ Haemophilus influenzae ]   51   22   168       258   3   1609   821   gi|160299   glutamic acid-rich protein [ Plasmodium falciparum ] pir|A54514|A54514   51   34   789                           glutamic acid-rich protein precursor -  Plasmodium falciparum         265   5   2419   3591   gi|580841   F1 [ Bacillus subtilis ]   51   32   1173       298   2   518   748   gi|1336162   SCPB [Streptococcus agalactiae|   51   34   231       316   9   5817   7049   gi|413953   ipa-29d gene product [ Bacillus subtilis ]   51   39   1233       332   2   2057   339   gi|1209012   mutS [ Thermus aquaticus thermophilus ]   51   26   1719       364   4   3816   4991   gi|528991   unknown [ Bacillus subtilis ]   51   32   1176       440   2   448   684   gi|2819   transferase (GAL10) (AA 1-687) [Kluyveromyces lactis] r|S01407|XUVKG   51   32   237                           UDPglucose 4-epimerase (EC 5.1.3.2) - yeast uyveromyces marxianus var.                           lactis)       495   2   1177   1001   gi|297861   protease G [Erwinia chrysanthemi]   51   41   177       495   3   1718   1149   gi|1513317   serine rich protein [Entamoeba histolytica]   51   25   570       506   1   421   2   gi|455320   cII protein [Bacteriophage P4]   51   33   420       600   1   983   492   gi|587532   orf, len: 201, CAI: 0.16 [ Saccharomyces cerevisiae ] pir|S48818|S48818   51   30   492                           hypothetical protein - yeast (Saccharomyces erevisiae)       607   3   479   934   gi|1511524   hypothetical protein (SP: P37002) [ Methanococcus jannaschii ]   51   40   456       686   2   127   600   gi|493017   endocarditis specific antigen [Enterococcus faecalis]   51   30   474       726   1   33   230   gi|1353851   unknown [Prochlorococcus marinus]   51   45   198       861   1   176   652   gi|410145   dehydroquinate dehydratase [ Bacillus subtilis ]   51   34   477       869   1   393   4   gi|40100   rodC (tag3) polypeptide (AA 1-746) [ Bacillus subtilis ] ir|S06049|S06049   51   23   390                           rodC protein -  Bacillus subtilis  p|P13485|TAGF_BACSU TECHOIC ACID                           BIOSYNTHESIS PROTEIN F.       1003   1   322   2   gi|1279707   hypothetical phosphoglycerate mutase [ Saccharomyces cerevisiae ]   51   39   321       1046   2   624   382   gi|510257   glycosyltransferase [ Escherichia coli ]   51   29   243       1467   1   352   2   gi|1511175     M. jannaschii  predicted coding region MJ1177 [ Methanococcus jannaschii ]   51   32   351       2558   1   230   3   sp|P10582|DPOM —     DNA POLYMERASE (EC 2.7.7.7) (S-1 DNA ORF 3).   51   26   228       3003   1   399   19   gi|809543   CbrC protein [ Erwinia chrysanthemi ]   51   27   381       3604   1   1   399   pir|JC4210|JC42   3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) - mouse   51   37   399       3732   1   2   316   gi|145906   acyl-CoA synthetase [ Escherichia coli ]   51   33   315       3791   1   2   274   gi|1061351   semaphorin III family homolog [ Homo sapiens ]   51   37   273       3995   1   46   336   gi|216346   surfactin synthetase [ Bacillus subtilis ]   51   38   291       4193   1   307   2   gi|42749   ribosomal protein L12 (AA 1-179) [ Escherichia coli ] ir|S04776|XXECPL   51   25   306                           peptide N-acetyltransferase rimL (EC 2.3.1.—) -  Echerichia coli         4539   1   185   3   gi|1408494   homologous to penicillin acylase [ Bacillus subtilis ]   51   40   183       4562   1   239   36   gi|1458280   coded for by  C. elegans  cDNA cm01e7; Similar to hydroxymethylglutaryl-CoA   51   35   204                           synthase [ Caenorhabditis elegans ]       1   4   3576   4859   gi|559160   GRAIL score: null; cap site and late promoter motifs present pstream;   50   44   1284                           putative [Autographa californica nuclear polyhedrosis irus]       11   7   4044   5165   gi|1146207   putative [ Bacillus subtilis ]   50   35   1122       11   13   9496   8483   gi|1208451   hypothetical protein [Synechocystis sp.]   50   39   1014       19   1   1018   2   gi|413966   ipa-42d gene product [ Bacillus subtilis ]   50   29   1017       20   11   8407   8228   gi|1323159   ORF YGR103w [ Saccharomyces cerevisiae ]   50   28   180       24   5   4824   4240   gi|496280   structural protein [Bacteriophage Tuc2009]   50   29   585       34   4   1926   2759   gi|1303966   Yqj0 [ Bacillus subtilis ]   50   36   834       38   30   22865   23440   gi|1072179   Similar to dihydroflavonol-4-reductase (maize, petunia, tomato)   50   32   576                           [ Caenorhabditis elegans ]       47   2   1705   2976   gi|153015   FemA protein [ Staphylococcus aureus ]   50   29   1272       56   13   15290   15841   gi|606096   ORF_f167; end overlaps end of o100 by 14 bases; start overlaps f174, ther   50   30   552                           starts possible [ Escherichia coli ]       57   1   1077   19   gi|640922   xylitol dehydrogenase (unidentified hemiascomycete)   50   29   1059       58   2   628   1761   gi|143725   putative [ Bacillus subtilis ]   50   29   1134       88   6   3884   3375   gi|1072179   Similar to dihydroflavonol-4-reductase (maize, petunia, tomato)   50   32   510                           [ Caenorhabditis elegans ]       89   5   3356   3012   gi|1276658   ORF174 gene product [ Porphyra purpurea ]   50   25   345       141   1   3   239   gi|476024   carbamoyl phosphate synthetase II [ Plasmodium falciparum ]   50   33   237       151   1   186   626   gi|1403441   unknown [ Mycobacterium tuberculosis ]   50   35   441       166   7   9623   8181   gi|895747   putative cel operon regulator [ Bacillus subtilis ]   50   32   1443       201   6   5096   4908   gi|160229   circumsporozoite protein [Plasmodium reichenowi]   50   42   189       206   22   29555   28326   gi|1052754   LmrP integral membrane protein [ Lactococcus lactis ]   50   24   1230       211   4   1523   1927   gi|410131   ORFX7 [ Bacillus subtilis ]   50   29   405       214   4   2411   3295   sp|P37348|YECE —     HYPOTHETICAL PROTEIN IN ASPS 5′ REGION (FRAGMENT)   50   37   885       228   7   4406   3744   gi|313580   envelope protein [Human immunodeficiency virus type 1] pir|S35835|S35835   50   35   663                           envelope protein - human immunodeficiency virus type 1 (fragment) (SUB 1-                           77)       272   2   1723   398   gi|1408485   B65G gene product [ Bacillus subtilis ]   50   22   1326       273   2   984   352   gi|984186   phosphoglycerate mutase [ Saccharomyces cerevisiae ]   50   28   633       328   2   1605   703   gi|148896   lipoprotein [ Haemophilus influenzae ]   50   26   903       332   4   3802   2135   gi|1526547   DNA polymerase family X [Thermus aquaticus]   50   27   1668       342   5   3473   3931   gi|456562   G-box binding factor [ Dictyostelium discoideum ]   50   35   459       352   1   741   4   gi|288301   ORF2 gene product [ Bacillus megaterium ]   50   29   738       408   7   5299   5523   gi|11665   ORF2136 [Marchantia polymorpha]   50   27   225       420   3   650   1825   gi|757842   UDP-sugar hydrolase [ Escherichia coli ]   50   30   1176       464   1   1   591   gi|487282   Na+ -ATPase subunit J [ Enterococcus hirae ]   50   29   591       472   2   864   310   gi|551875   Bg1R [ Lactococcus lactis ]   50   23   555       520   1   23   541   gi|567036   CapE [ Staphylococcus aureus ]   50   27   519       529   1   6   410   gi|1256652   25% identity to the  E. coli  regulatory protein MprA; putative [ Bacillus     50   34   405                             subtilis ]       534   5   6059   4392   gi|295671   selected as a weak suppressor of a mutant of the subunit AC40 of DNA   50   18   1668                           ependant RNA polymerase I and III [ Saccharomyces cerevisiae ]       647   1   1497   4   gi|405568   TraI protein shares sequence similarity with a family of opoisomerases   50   31   1494                           [Plasmid pSK41]       664   3   711   289   gi|410007   leukocidin F component [ Staphylococcus aureus , MRSA No. 4, Peptide, 23 aa]   50   32   423       678   1   1   627   gi|298032   EF [ Streptococcus suis ]   50   29   627       755   3   947   1171   gi|150572   cytochrome c1 precursor (EC 1.10.2.2) [ Paracoccus denitrificans ] gi|45465   50   37   225                           cytochrome c1 (AA 1-450) [ Paracoccus denitrificans ] pir|C29413|C29413                           ubiquinol - cytochrome-c reductase (EC 1.10.2.2) ytochrome c1 precursor -                           Paracoccus denitrificans sp|P13627|CY1       827   1   683   3   gi|142020   heterocyst differentiation protein [Anabaena sp.]   50   21   681       892   1   3   752   gi|1408485   B65G gene product [ Bacillus subtilis ]   50   27   750       910   2   438   887   gi|1204727   tyrosine-specific transport protein [ Haemophilus influenzae ]   50   25   450       933   1   524   760   gi|1205451   cell division inhibitor [ Haemophilus influenzae ]   50   32   237       973   1   236   48   gi|886947   orf3 gene product [ Saccharomyces cerevisiae ]   50   40   189       1009   1   429   205   gi|153727   M protein [group G streptococcus]   50   28   225       1027   1   257   3   gi|413934   ipa-10r gene product [ Bacillus subtilis ]   50   25   255       1153   2   326   96   gi|773676   nccA [Alcaligenes xylosoxydans]   50   36   231       1222   1   400   2   gi|1408485   B65G gene product [ Bacillus subtilis ]   50   21   399       1350   1   399   106   gi|289272   ferrichrome-binding protein [ Bacillus subtilis ]   50   32   294       2945   1   184   2   gi|171704   hexaprenyl pyrophosphate synthetase (COQ1) [Saccharomyces erevisiae]   50   34   183       2968   2   804   4   gi|397526   clumping factor [ Staphylococcus aureus ]   50   33   801       2998   2   394   131   gi|495696   F54E7.3 gene product [ Caenorhabditis elegans ]   50   40   264       3046   2   306   106   pir|S13819|S138   acyl carrier protein -  Anabaena variabilis  (fragment)   50   32   201       3063   1   275   3   gi|474190   iucA gene product [ Escherichia coli ]   50   29   273       3174   1   3   146   gi|151900   alcohol dehydrogenase [Rhodobacter sphaeroides]   50   31   144       3792   1   314   3   gi|1001423   hypothetical protein [Synechocystis sp.]   50   35   312       3800   1   2   262   gi|144733   NAD-dependent beta-hydroxybutyryl coenzyme A dehydrogenase Clostridium   50   28   261                           acetobutylicum]       3946   1   188   3   gi|576765   cytochrome b [Myrmecia pilosula]   50   38   186       3984   1   291   4   sp|P37348|YECE —     HYPOTHETICAL PROTEIN IN ASPS 5′ REGION (FRAGMENT).   50   37   288       37   10   7885   7520   gi|1204367   hypothetical protein (GB: U14003_278) [ Haemophilus influenzae ]   49   30   366       46   16   13802   14848   gi|466860   acd: B1308_F1_34 [Mycobacterium leprae]   49   24   1047       59   5   2267   3601   gi|606304   ORF_o462 [ Escherichia coli ]   49   27   1335       112   18   17884   18615   gi|559502   ND4 protein (AA 1-409) [ Caenorhabditis elegans ]   49   25   732       138   9   6973   7902   gi|303953   esterase [Acinetobacter calcoaceticus]   49   29   930       217   6   4401   5138   gi|496254   fibronectin/fibrinogen-blnding protein [ Streptococcus pyogenes ]   49   31   738       220   12   11803   12657   gi|397526   clumping factor [ Staphylococcus aureus ]   49   31   855       228   4   1842   2492   pir|S23692|S236   hypothetical protein 9 -  Plasmodium falciparum     49   24   651       268   1   2614   212   gi|143047   ORFB [ Bacillus subtilis ]   49   26   2403       271   2   1164   1373   gi|1001257   hypothetical protein [Synechocystis sp.]   49   38   210       300   3   3180   2020   gi|1510796   hypothetical protein (GP: X91006_2) [ Methanococcus jannaschii ]   49   26   1161       381   1   1142   3   gi|396301   matches PS00041: Bacterial regulatory proteins, araC family ignature   49   29   1140                           [ Escherichia coli ]       466   1   3   947   gi|1303863   YqgP [ Bacillus subtilis ]   49   26   945       666   1   191   3   gi|633112   ORF1 [Streptococcus sobrinus]   49   29   189       670   2   403   1014   gi|1122758   unknown [ Bacillus subtilis ]   49   32   612       709   1   795   157   gi|143830   xpaC [ Bacillus subtilis ]   49   29   639       831   1   473   3   gi|401786   phosphomannomutase [ Mycoplasma pirum ]   49   29   471       1052   1   213   4   gi|1303799   YqeN [ Bacillus subtilis ]   49   21   210       1800   1   172   2   gi|216300   peptidoglycan synthesis enzyme [ Bacillus subtilis ] sp|P37585|MURG_BACSU   49   28   171                           MURG PROTEIN UPD-N-ACETYLGLUCOSAMINE—N-ACETYLMURAMYL-                           PENTAPEPTIDE) PYROPHOSPHORYL-UNDECAPRENOL N-ACETYLGLUCOSAMINE RANSFERASE).       2430   1   2   376   sp|P27434|YFGA —     HYPOTHETICAL 36.2 KD PROTEIN IN NDK-GCPE INTERGENIC REGION.   49   26   375       3096   1   273   4   gi|516360   surfactin synthetase [ Bacillus subtilis ]   49   25   270       32   4   3100   2429   gi|1217963   hepatocyte nuclear factor 4 gamma (HNF4gamma) [ Homo sapiens ]   48   36   672       38   1   1   609   gi|1205790     H. influenzae  predicted coding region HI1555 [ Haemophilus influenzae ]   48   28   609       45   6   5021   6427   gi|1524267   unknown [ Mycobacterium tuberculosis ]   48   20   1407       59   14   16346   31096   gi|1197336   Lmp3 protein [ Mycoplasma hominis ]   48   28   14751       61   1   3   608   gi|1511555   quinolone resistance norA protein protein [ Methanococcus jannaschii ]   48   30   606       61   3   3311   3646   gi|1303893   YqhL [ Bacillus subtilis ]   48   29   336       114   1   98   415   gi|671708   su(s) homolog; similar to Drosophila melanogaster suppressor of able   48   25   318                           (su(s)) protein, Swiss-Prot Accession Number P22293 Drosophila virilis)       121   1   610   89   gi|1314584   unknown [Sphingomonas S88]   48   29   522       136   1   1280   546   gi|1205968     H. influenzae  predicted coding region HI1738 [ Haemophilus influenzae ]   48   23   735       171   10   8220   9557   gi|1208454   hypothetical protein [Synechocystis sp.]   48   34   1338       175   1   1814   3   gi|396400   similar to eukaryotic Na+/H+ exchangers [ Escherichia coli ]   48   29   1812                           sp|P32703|YJCE_ECOLI HYPOTHETICAL 60.5 KD PROTEIN IN SOXR-ACS NTERGENIC                           REGION (O549).       194   1   2   385   gi|1510493     M. jannaschii  predicted coding region MJ0419 [ Methanococcus jannaschii ]   48   25   384       197   1   452   3   gi|1045714   spermidine/putrescine transport ATP-binding protein [ Mycoplasma genitalium ]   48   25   450       203   1   1   396   gi|940288   protein localized in the nucleoli of pea nuclei; ORF; putative Pisum   48   29   396                           sativum]       204   1   698   33   gi|529202   No definition line found [ Caenorhabditis elegans ]   48   25   666       206   20   27760   20705   gi|511490   gramicidin S synthetase 2 [ Bacillus brevis ]   48   27   7056       212   1   2   166   gi|295899   nucleolin [ Xenopus laevis ]   48   34   165       220   10   11426   10200   gi|44073   SecY protein [ Lactococcus lactis ]   48   23   1227       243   6   5491   4532   gi|1184118   mevalonate kinase [ Methanobacterium thermoautotrophicum ]   48   30   960       264   4   3308   1182   gi|1015903   ORF YJR151c [ Saccharomyces cerevisiae ]   48   26   2127       441   1   768   4   gi|142863   replication initiation protein [ Bacillus subtilis ] pir|B26580|B26580   48   23   765                           replication initiation protein -  Bacillus subtilis         444   5   3898   5298   gi|145836   putative [ Escherichia coli ]   48   24   1401       484   2   388   1110   gi|146551   transmembrane protein (kdpD) [ Escherichia coli ]   48   18   723       542   3   1425   2000   pir|S28969|S289   N-carbamoylsarcosine amidohydrolase (EC 3.5.1.59) - Arthrobacter sp.   48   27   576       566   1   3   1019   gi|153490   tetracenomycin C resistance and export protein [ Streptomyces laucescens ]   48   24   1017       611   1   2   730   gi|1103507   unknown [ Schizosaccharomyces pombe ]   48   38   729       624   1   665   75   gi|144859   ORF B [Clostridium perfringens]   48   26   591       846   1   508   2   gi|537506   paramyosin [ Dirofilaria immitis ]   48   27   507       1020   1   66   950   gi|1499876   magnesium and cobalt transport protein [ Methanococcus jannaschii ]   48   30   885       1227   1   1   174   gi|493730   lipoxygenase [ Pisum sativum ]   48   35   174       1266   1   1   405   gi|882452   ORF_f211; alternate name yggA; orf5 of X14436 [ Escherichia coli ] gi|41425   48   24   405                           ORF5 (AA 1-197) [ Escherichia coli ] (SUB 15-211)       2071   1   381   55   gi|1408486   HS74A gene product [ Bacillus subtilis ]   48   25   327       2398   1   233   3   gi|1500401   reverse gyrase [ Methanococcus jannaschii ]   48   40   231       2425   1   246   16   pir|H48563|H485   G1 protein - fowlpox virus (strain HP444) (fragment)   48   40   231       2432   1   225   4   gi|1353703   Trio [ Homo sapiens ]   48   33   222       2453   1   399   4   gi|142850   division initiation protein [ Bacillus subtilis ]   48   29   396       2998   1   236   3   gi|577569   PepV [ Lactobacillus delbrueckii ]   48   31   234       3042   1   14   280   gi|945219   mucin [ Homo sapiens ]   48   35   267       3686   1   1   405   gi|145836   putative [ Escherichia coli ]   48   25   405       4027   2   301   110   pir|S51177|S511   trans-activator protein - Equine infectious anemia virus   48   32   192       4   2   2232   823   gi|1303989   YqkI [ Bacillus subtilis ]   47   24   1410       24   2   599   1084   gi|540083   PC4-1 gene product [Bradysia hygida]   47   28   486       36   10   6925   6326   gi|1209223   esterase [ Acinetobacter lwoffii ]   47   26   600       43   2   196   1884   gi|1403455   unknown [ Mycobacterium tuberculosis ]   47   27   1689       44   22   15108   14098   gi|1511555   quinolone resistance norA protein protein [ Methanococcus jannaschii ]   47   31   1011       69   7   6710   6279   gi|438466   Possible operon with orfG. Hydrophilic, no homologue in the atabase;   47   29   432                           putative [ Bacillus subtilis ]       81   4   4279   3536   gi|466882   ppsl; B1496_C2_189 [Mycobacterium leprae]   47   24   744       120   12   8863   8591   gi|927340   D9509.27p; CAI: 0.12 [ Saccharomyces cerevisiae ]   47   38   273       142   1   1174   326   gi|486143   ORF YKL094w [ Saccharomyces cerevisiae ]   47   32   849       168   1   1093   8   gi|1177254   hypothetical EcsB protein [ Bacillus subtilis ]   47   29   1086       263   1   943   2   gi|142822   D-alanine racemase cds [ Bacillus subtilis ]   47   34   942       279   1   561   13   gi|516608   2 predicted membrane helices, homology with B. subtilis men Orf3 Rowland   47   31   549                           et. al. unpublished Accession number M74183), approximately 1 minutes on                           updated Rudd map; putative [ Escherichia coli ] sp|P37355|YFBB_ECOLI                           HYPOTHETICAL 26.7 KD PROTEIN IN MEND-MENB       345   2   1676   732   gi|1204835   hippuricase [ Haemophilus influenzae ]   47   28   945       389   2   152   400   gi|456562   G-box binding factor [ Dictyostelium discoideum ]   47   32   249       391   1   1   831   gi|1420856   myo-inositol transporter [ Schizosaccharomyces pombe ]   47   19   831       404   3   2072   2773   gi|1255425   C33G8.2 gene product [ Caenorhabditis elegans ]   47   17   702       529   5   2145   3107   gi|1303973   YqjV [ Bacillus subtilis ]   47   29   963       565   2   1257   193   gi|142824   processing protease [ Bacillus subtilis ]   47   28   1065       654   1   483   4   gi|243353   ORF 5′ of ECRF3 [herpesvirus saimiri HVS, host-squirrel monkey, eptide, 407   47   23   480                           aa]       692   1   115   633   gi|150756   40 kDa protein [Plasmid pJM1]   47   25   519       765   1   819   4   gi|1256621   26.7% of identity in 165 aa to a Thermophilic bacterium hypothetical   47   28   816                           protein 6; putative [ Bacillus subtilis ]       825   2   211   1023   gi|397526   clumping factor [ Staphylococcus aureus ]   47   32   813       914   1   1   615   gi|558073   polymorphic antigen [ Plasmodium falciparum ]   47   29   615       1076   1   1   753   gi|1147557   Aspartate aminotransferase [Bacillus circulans]   47   33   753       1351   1   398   3   gi|755153   ATP-binding protein [ Bacillus subtilis ]   47   20   396       4192   1   3   293   gi|145836   putative [ Escherichia coli ]   47   24   291       5   6   4361   4014   gi|305080   myosin heavy chain [Entamoeba histolytica]   46   30   348       11   4   2777   3058   gi|603639   Ye1040p [ Saccharomyces cerevisiae ]   46   28   282       46   11   10300   10082   gi|1246901   ATP-dependent DNA ligase [ Candida albicans ]   46   28   219       61   4   3941   7930   gi|298032   EF [ Streptococcus suis ]   46   35   3990       132   4   4093   3158   gi|1511057   hypothetical protein SP: P45869 [ Methanococcus jannaschii ]   46   25   936       170   4   3652   2585   pir|S51910|S519   G4 protein - sauroleishmania tarentolae   46   26   1068       191   7   8284   7025   gi|1041334   F54D5.7 [ Caenorhabditis elegans ]   46   25   1260       253   1   1   396   gi|1204449   dihydrolipoamide acetyltransferase [ Haemophilus influenzae ]   46   35   396       264   3   437   973   gi|180189   cerebellar-degeneration-related antigen (CDR34) [ Homo sapiens ] gi|182737   46   29   537                           cerebellar degeneration-associated protein [ Homo sapiens ]                           pir|A29770|A29770 cerebellar degeneration-related protein - human       273   1   285   85   gi|607573   envelope glycoprotein C2V3 region [Human immunodeficiency virus type]   46   35   201       350   1   3   563   gi|537052   ORF_E286 [ Escherichia coli ]   46   35   561       384   1   2   862   gi|1221884   (urea?) amidolyase [ Haemophilus influenzae ]   46   31   861       410   4   1876   2490   gi|1110518   proton antiporter efflux pump [ Mycobacterium smegmatis ]   46   24   615       432   1   1455   247   gi|1197634   orf4; putative transporter; Method: conceptual translation supplied by   46   27   1209                           author [ Mycobacterium smegmatis ]       458   1   1211   3   gi|15470   portal protein [Bacteriophage SPP1]   46   30   1209       517   5   2477   4192   gi|1523812   orf5 [Bacteriophage A2]   46   23   1716       540   3   1285   1058   gi|215635   pacA [Bacteriophage P1]   46   30   228       587   2   649   1242   gi|537148   ORF_f181 [ Escherichia coli ]   46   29   594       1218   1   391   35   gi|1205456   single-stranded-DNA-specific exonuclease [ Haemophilus influenzae ]   46   30   357       3685   1   1   402   gi|450688   hsdM gene of EcoprrI gene product [ Escherichia coli ] pir|S38437|S38437 hsdM   46   33   402                           protein -  Escherichia coli  pir|S09629|S09629 hypothetical protein A -                             Escherichia coli  (SUB 40-520)       4176   1   338   3   gi|951460   FIM-C.1 gene product [ Xenopus laevis ]   46   31   336       37   7   4813   5922   gi|606064   ORF_f408 [ Escherichia coli ]   45   24   1110       38   16   11699   12004   gi|452192   protein tyrosine phosphatase (PTP-BAS, type 2) [ Homo sapiens ]   45   24   306       87   2   1748   2407   gi|1064813   homologous to sp: PHOR_BACSU [ Bacillus subtilis ]   45   23   660       103   12   13385   12588   gi|1001307   hypothetical protein [Synechocystis sp.]   45   22   798       112   14   13811   12831   gi|1204389     H. influenzae  predicted coding region HI0131 [ Haemophilus influenzae ]   45   23   981       145   4   3461   2439   gi|220578   open reading frame [ Mus musculus ]   45   20   1023       170   6   4965   3601   gi|238657   AppC = cytochrome d oxidase, subunit I homolog [ Escherichia coli , K12,   45   27   1365                           eptide, 514 aa]       206   2   4346   3462   gi|1222056   aminotransferase [ Haemophilus influenzae ]   45   27   885       228   1   60   716   gi|160299   glutamic acid-rich protein [ Plasmodium falciparum ] pir|A54514|A54514   45   23   657                           glutamic acid-rich protein precursor -  Plasmodium alciparum         288   1   2   1015   gi|1255425   C33G8.2 gene product [ Caenorhabditis elegans ]   45   23   1014       313   3   3128   1917   gi|581140   NADH dehydrogenase [ Escherichia coli ]   45   30   1212       332   1   459   4   gi|870966   F47A4.2 [ Caenorhabditis elegans ]   45   20   456       344   1   3   221   gi|171225   kinesin-related protein [ Saccharomyces cerevisiae ]   45   26   219       441   2   1073   645   gi|142863   replication initiation protein [ Bacillus subtilis ] pir|B26580|B26580   45   27   429                           replication initiation protein -  Bacillus subtilis         672   1   2   982   gi|1511334     M. jannaschii  predicted coding region MJ1323 [ Methanococcus jannaschii ]   45   22   981       763   3   851   357   gi|606180   ORF_f310 [ Escherichia coli ]   45   24   495       886   3   379   846   gi|726426   similar to protein kinases and  C. elegans  proteins F37C12.8 and 37C12.5   45   30   468                           [ Caenorhabditis elegans ]       948   1   3   473   gi|156400   myosin heavy chain (isozyme unc-54) [ Caenorhabditis elegans ]   45   25   471                           pir|A93958|MWKW myosin heavy chain B -  Caenorhabditis elegans                             sp|P02566|MYSB_CAEEL MYOSIN HEAVY CHAIN B (MHC B).       1158   1   2   376   gi|441155   ransmission-blocking target antigen [ Plasmodium falciparum ]   45   35   375       2551   1   4   285   gi|1276705   ORF287 gene product [ Porphyra purpurea ]   45   28   282       3967   1   42   374   gi|976025   MrsA [ Escherichia coli ]   45   28   333       52   7   5846   4761   gi|467378   unknown [ Bacillus subtilis ]   44   22   1086       138   8   6475   6849   gi|173028   thioredoxin II [ Saccharomyces cerevisiae ]   44   28   375       221   5   5617   4202   gi|153490   tetracenomycin C resistance and export protein [ Streptomyces laucescens ]   44   21   1416       252   2   1122   913   gi|1204989   hypothetical protein (GB: U00022_9) [ Haemophilus influenzae ]   44   30   210       263   2   2093   921   gi|1136221   carboxypeptidase [ Sulfolobus solfataricus ]   44   26   1173       365   4   3524   2085   gi|1296822   orf1 gene product [ Lactobacillus helveticus ]   44   31   1440       543   3   1315   1833   gi|1063250   low homology to P20 protein of Bacillus lichiniformis and bleomycin   44   24   519                           acetyltransferase of Streptomyces verticillus [ Bacillus subtilis ]       544   4   3942   4892   gi|951460   FIM-C.1 gene product [ Xenopus laevis ]   44   32   951       792   1   613   2   gi|205680   high molecular weight neurofilament [ Rattus norveglcus ]   44   28   612       44   18   11303   11911   gi|1511614   molybdopterin-guanine dinucleotide biosynthesis protein A [ Methanococcus     43   27   609                             jannaschii ]       59   8   3665   5128   gi|153490   tetracenomycin C resistance and export protein [ Streptomyces laucescens ]   43   21   1464       59   10   5536   7527   gi|153022   lipase Staphylococcus epidermidis]   43   22   1992       99   1   681   16   gi|1419051   unknown [ Mycobacterium tuberculosis ]   43   21   666       310   8   9402   12134   gi|397526   clumping factor [ Staphylococcus aureus ]   43   21   2733       432   3   2303   1824   pir|A60540|A605   sporozoite surface protein 2 -  Plasmodium yoelii  (fragment)   43   29   480       519   3   2547   3122   sp|Q06530|DHSU —     SULFIDE DEHYDROGENASE (FLAVOCYTOCHROME C) FLAVOPROTEIN CHAIN PRECURSOR (EC   43   23   576                           1.8.2.—) (FC) (FCSD).       4   13   12053   13321   gi|295671   selected as a weak suppressor of a mutant of the subunit AC40 of DNA   42   18   1269                           ependant RNA polymerase I and III [ Saccharomyces cerevisiae ]       94   2   1091   414   gi|501027   ORF2 [Trypanosoma brucei]   42   31   678       127   4   4550   3309   gi|42029   ORF1 gene product [ Escherichia coli ]   42   21   1242       297   3   1036   557   gi|142790   ORF1; putative [ Bacillus firmus ]   42   25   480       344   6   3525   2953   gi|40320   ORF 2 (AA 1-203) [Bacillus thuringiensis]   42   30   573       512   1   1115   63   gi|405957   yeeF [ Escherichia coli ]   42   23   1053       631   1   1223   12   gi|580920   rodD (gtaA) polypeptide (AA 1-673) [ Bacillus subtilis ] pir|S06048|S06048   42   24   1212                           probable rodD protein -  Bacillus subtilis  sp|P13484|TAGE_BACSU PROBABLE                           POLY(GLYCEROL-PHOSPHATE) LPHA-GLUCOSYLTRANSFERASE (EC 2.4.1.52) (TECHOIC                           ACID BIOSYNTHESIS ROTEIN E).       685   3   1739   1119   gi|1303784   YqeD [ Bacillus subtilis ]   42   19   621       4132   1   395   3   gi|1022910   protein tyrosine phosphatase [ Dictyostelium discoideum ]   42   25   393       86   2   884   393   gi|309506   spermidine/spermine N1-acetyltransferase [Mus saxicola] pir|S43430|S43430   41   30   492                           spermidine/spermine N1-acetyltransferase - spiny ouse ( Mus saxicola )       191   12   14075   13353   gi|1124957   orf4 gene product [ Methanosarcina barkeri ]   41   22   723       212   6   2150   3127   gi|15873   observed 35.2 Kd protein [Mycobacteriophage 15]   41   26   978       213   3   1263   2000   gi|633692   TrsA [ Yersinia enterocolitica ]   41   18   738       408   4   2625   3386   gi|1197634   orf4; putative transporter; Method: conceptual translation supplied by   41   24   762                           author [ Mycobacterium smegmatis ]       542   1   3   1103   gi|457146   rhoptry protein [Plasmodium, yoelii]   41   21   1101       924   1   2   475   pir|JH0148|JH01   nucleolin - rat   41   30   474       1562   1   1   402   gi|552184   asparagine-rich antigen Pfa35-2 [ Plasmodium falciparum ] pir|S27826|S27826   40   20   402                           asparagine-rich antigen Pfa35-2 -  Plasmodium alciparum  (fragment)       2395   1   261   4   pir|S42251|S422   hypothetical protein 5 - fowlpox virus   40   18   258       4077   1   3   305   gi|1055055   coded for by  C. elegans  cDNA yk37g1.5; coded for by  C. elegans  cDNA   39   21   303                           yk5c9.5; coded for by  C. elegans  cDNA yk1a9.5; alternatively spliced form                           of F52C9.8b [ Caenorhabditis elegans ]       958   1   503   3   gi|1255425   C33G8.2 gene product [ Caenorhabditis elegans ]   37   25   501       59   12   8294   10636   gi|535260   STARP antigen [Plasmodium reichenowi]   36   24   2343       63   5   3550   8079   gi|298032   EF [ Streptococcus suis ]   36   19   4530       544   3   2507   3601   gi|1015903   ORF YJR151c [ Saccharomyces cerevisiae ]   35   22   1095       63   4   1949   3574   gi|552195   circumsporozoite protein (Plasmodium falciparum) sp|P05691|CSP_PLAFL   32   27   1626                           CIRCUMSPOROZOITE PROTEIN (CS) (FRAGMENT).                    
     [0290]               TABLE 3                            S. aureus  - Putative coding regions of       novel proteins not similar to known proteins                                     Contig   ORF   Start   Stop           ID   ID   (nt)   (nt)                                                 4   1   692   150           4   3   1712   2278           4   4   3032   2361           4   14   12585   12097           5   2   1601   663           5   3   1532   1771           5   7   4550   4359           5   9   6422   4905           5   12   8547   8383           6   4   1982   1605           8   1   176   3           11   8   5144   5983           11   9   5968   6498           11   10   6284   6096           11   16   10954   11271           12   5   4942   4532           12   6   4596   4862           15   3   1650   1405           16   10   10835   10407           18   2   917   741           20   9   7764   6403           20   10   8230   7889           20   12   8803   8405           20   13   10470   8782           23   1   339   4           23   6   5485   4832           23   8   5942   5508           23   9   6881   6111           23   15   12618   12830           24   4   4185   3814           24   6   5241   4840           25   2   1824   2402           31   2   505   849           31   3   1177   1524           31   4   2454   3005           32   2   765   1388           32   9   7952   8575           32   10   8591   8728           32   11   9379   9020           32   12   10087   9377           34   2   1049   783           36   7   5226   5801           36   11   7261   6947           36   12   7424   7621           37   4   2964   2770           38   2   980   375           38   11   6425   6868           38   20   16371   15760           38   26   20253   20804           38   27   20722   21264           39   1   1   627           40   1   404   3           43   1   428   60           44   4   2324   1974           44   5   2484   3263           44   14   10129   9671           44   20   13536   13348           44   21   13596   13994           45   7   6297   6019           46   8   6365   6520           46   12   10449   10976           46   17   15032   15424           47   1   288   1079           48   9   7620   7778           50   1   962   312           50   2   1316   1011           51   1   370   2           51   5   2245   1970           53   1   287   132           53   7   6319   5933           54   7   8709   8404           55   1   326   60           55   3   786   520           56   1   1   261           56   3   1228   905           56   4   1560   1150           56   17   18712   18332           57   4   3521   3348           57   8   5436   5822           58   9   8553   8221           59   3   1366   1509           59   6   2802   2578           59   7   3570   3370           59   9   4563   4180           59   11   7518   8378           59   13   10401   16403           62   2   1521   346           62   11   5440   5757           63   1   1   336           67   1   900   1781           67   2   1774   2610           67   3   2591   3904           67   8   6955   6800           68   1   78   326           70   6   5199   3637           70   11   8645   8355           77   3   1192   794           79   2   1228   947           79   3   1411   1791           83   1   2   403           85   9   8300   8653           85   10   8781   8593           86   3   1232   1038           87   8   9187   9366           88   3   1620   1922           89   1   3   161           89   7   4878   4714           91   1   550   2           91   3   3141   2344           92   2   449   928           92   3   1467   976           92   9   5638   6024           94   1   332   3           94   3   1813   1181           94   4   2197   1811           96   11   10601   11050           99   6   4523   4374           99   7   4784   4554           100   8   7287   6916           102   7   4368   4039           103   3   2035   1574           104   1   2   694           104   2   699   1277           105   1   693   151           105   3   2655   2077           106   1   3   221           106   3   1209   1355           107   1   542   3           109   4   3651   3277           109   13   11625   11996           109   14   11981   12268           109   20   17401   17688           110   1   2   760           114   10   8764   9384           116   1   1   309           116   3   4462   2651           116   8   9976   8903           116   9   10158   10003           120   5   3320   2937           120   6   3869   3468           120   13   9290   9844           121   2   417   569           126   3   818   546           127   3   2648   3196           127   5   4084   4395           131   6   6438   6103           132   2   715   1695           134   1   2   667           135   2   258   4           135   3   729   334           138   1   3   152           138   7   6008   6463           140   1   1032   4           140   2   1513   1007           140   5   2387   2743           142   2   1360   2388           142   7   7586   6342           143   7   6502   5714           144   1   640   53           146   1   2   511           146   3   502   1350           146   4   2540   1407           146   5   2874   3071           147   1   1   339           149   11   3615   3274           149   12   3785   3534           149   13   4145   3783           149   15   4610   4413           149   16   5049   4603           149   18   5491   5243           149   21   7054   6692           149   23   8521   7826           149   24   9106   8531           149   25   9897   9115           150   2   1587   871           154   3   1508   1221           154   8   6398   6210           154   14   12147   11590           154   15   12803   12075           156   1   315   593           157   3   1183   2232           158   2   1064   657           159   3   452   808           161   2   876   1808           161   6   4279   3905           161   7   4540   4277           161   8   4717   4538           161   11   5638   5459           163   2   840   76           163   5   2344   1892           163   7   2647   2342           163   9   4905   5132           164   3   1147   956           166   3   4854   4495           168   4   2500   2868           168   5   3595   4158           170   3   2517   2777           171   2   1450   623           171   11   11125   9674           172   1   3   278           172   2   1149   358           173   1   708   127           173   5   6114   5227           174   2   593   1105           175   3   2552   2890           175   5   3335   2850           175   7   4342   4506           182   4   4986   4495           184   5   5702   5361           188   2   1210   1755           188   4   2647   2994           189   6   2614   3039           190   3   1998   2564           191   1   1   153           191   2   669   388           191   10   11786   13039           191   11   12363   11824           192   1   91   426           195   3   1932   1558           195   5   2606   2313           198   2   1016   1591           201   1   170   625           203   2   783   1466           206   6   7815   6700           206   12   13636   13325           206   21   27960   27712           212   2   170   817           212   3   796   1167           212   7   3128   3436           212   9   3749   4075           213   1   1   705           214   2   570   64           214   6   3738   3412           214   9   6600   6995           214   10   7469   7074           217   1   965   3           218   1   178   657           218   3   1776   2156           220   2   1369   887           220   3   2262   1273           220   7   7208   6141           220   8   8661   7078           220   9   10216   8636           221   4   2613   2131           221   9   10757   10086           226   1   3   659           226   2   1459   722           226   3   1476   1961           227   1   2   487           227   2   460   975           227   4   1855   2121           227   5   2052   2345           227   6   3768   2776           227   9   5591   6367           228   5   2503   2877           228   6   2846   3526           233   7   3762   3580           236   2   579   349           238   2   1391   807           239   2   905   393           241   5   4334   4173           242   2   1363   1049           243   1   127   576           244   1   647   3           244   2   1962   889           245   2   1258   902           246   1   69   215           246   4   738   1733           249   3   3712   3518           250   1   249   4           254   1   1   156           256   2   956   1144           257   3   3227   2754           260   4   4580   4254           261   4   2196   2606           261   6   3214   3681           264   2   155   439           264   5   4533   3814           264   6   4739   5107           267   2   931   539           268   4   4700   4260           272   1   446   30           272   3   1200   1439           272   9   4691   4909           272   10   6035   5601           276   4   1746   1901           278   1   224   553           278   5   3299   3448           278   7   4849   5127           285   2   551   736           288   3   1756   1950           288   5   2055   2276           289   1   1055   3           290   2   1932   1630           291   2   332   622           291   5   1545   2051           295   3   1349   1092           295   4   2141   1554           295   5   2220   2762           297   2   465   142           298   1   2   205           300   2   1928   1476           301   7   2624   2454           304   1   3   194           306   1   109   654           306   5   4036   4257           307   1   339   4           307   8   3645   3995           308   1   1   654           308   2   599   78           308   4   2332   2021           313   2   1919   1524           314   1   10   702           316   2   982   1341           316   6   2758   3165           317   1   2   1114           317   3   3458   2346           321   6   5217   4789           321   7   6140   5961           321   8   6794   6138           322   2   543   259           326   2   165   1112           326   3   1117   1467           328   1   469   2           328   5   3276   3100           329   1   3   719           329   2   781   1212           329   3   1471   1833           330   1   289   2           330   3   1447   1623           332   3   2204   2055           332   7   4971   5138           333   2   3128   2961           335   1   433   2           337   2   95   526           340   2   1356   1054           341   1   3   281           341   3   2476   3192           341   5   3618   3944           341   6   3929   4558           344   5   2889   2581           345   1   768   4           346   2   221   592           350   3   1410   1598           352   2   1765   1352           352   3   4596   1876           352   7   7967   8404           352   8   8906   9247           352   9   9854   9537           359   1   1   546           362   1   3   656           364   2   1808   1458           364   8   10714   10454           365   2   1313   1014           365   5   4090   3500           365   7   4980   6239           366   3   520   1719           367   3   906   1085           368   1   494   240           375   1   2   136           380   3   1097   843           389   1   1   276           390   1   2   877           390   2   1373   1549           391   2   560   369           395   1   197   3           396   1   1068   4           398   3   1141   938           399   1   178   669           401   3   566   847           402   2   100   465           404   8   5370   5179           408   2   2269   1031           408   3   2672   2469           408   5   3524   4423           410   3   1890   1669           413   1   488   96           416   1   320   33           416   2   578   847           416   3   1590   985           417   1   3   179           417   2   161   616           420   2   513   238           422   2   357   677           431   2   856   1407           432   2   446   1084           433   1   1   417           433   3   2033   1755           434   1   535   128           434   2   1235   381           440   1   1   450           442   2   1269   3320           443   3   1520   1167           444   1   1   696           444   7   6366   5971           451   1   614   288           453   2   636   376           453   8   3833   4786           453   9   4512   4306           453   10   4731   4525           455   1   219   4           455   2   472   930           459   1   265   687           462   1   2   247           466   2   907   320           467   1   349   44           468   1   2   250           469   1   925   362           469   3   2386   3372           469   4   3464   3706           470   1   77   538           470   6   3694   3290           470   7   5686   5042           470   9   7351   8181           470   10   8175   9773           471   1   500   60           471   2   1017   472           476   1   70   267           477   1   2   760           477   3   1764   2081           477   4   2066   2332           480   5   4016   4261           481   2   480   4           486   3   613   774           487   6   1795   2112           488   1   359   3           492   1   127   675           493   1   2   520           493   2   496   1242           502   3   1149   1571           504   1   346   2           505   5   4150   3734           511   2   1232   723           512   2   583   747           515   1   609   812           517   4   2179   2511           520   4   2097   2360           520   6   3669   3430           527   1   1   498           528   1   335   33           529   2   1104   529           530   7   5298   5534           536   1   156   4           538   1   736   110           538   3   2203   2880           538   5   3121   2711           538   6   3731   3114           540   1   664   332           540   2   1031   567           541   1   89   433           541   2   432   145           542   2   1048   1272           545   2   734   456           551   1   1129   113           555   2   704   516           558   3   1154   951           558   4   1458   1156           558   5   1821   1537           558   6   2020   1874           558   7   2322   2008           558   8   2802   2551           558   9   3453   2920           560   1   475   921           565   3   1485   1264           571   1   156   4           571   3   994   1206           577   1   2   199           577   2   163   453           579   1   1   477           579   2   1200   616           583   1   996   4           585   1   539   132           587   1   22   573           588   2   1372   848           588   3   1554   1366           590   1   47   334           592   2   1141   827           593   1   2   775           593   2   817   1122           595   1   87   890           596   3   1435   1277           602   1   8   169           603   5   1071   1469           606   1   322   768           607   5   1226   1008           610   1   541   53           612   1   3   500           616   1   650   309           617   2   491   246           622   1   36   347           625   4   2046   2549           627   1   67   210           628   1   452   3           631   3   4004   3219           634   1   759   70           636   1   189   368           636   2   1063   197           637   2   1994   1665           638   1   227   1081           639   1   261   4           639   2   811   245           641   1   118   444           642   3   1331   1047           642   4   1847   1434           643   1   3   608           645   4   1534   1758           645   6   2025   2321           645   7   2488   2036           648   1   2   1045           660   1   77   601           660   2   576   872           661   1   961   197           664   2   89   304           667   1   3   413           668   1   1   330           671   2   516   220           673   1   3   338           674   2   584   303           679   1   1   237           679   3   1589   1906           688   1   835   434           688   2   1077   802           694   1   3   143           696   2   432   46           706   1   224   81           709   3   1183   1449           711   1   3   908           715   1   3   167           716   1   2   637           721   1   133   570           722   1   383   3           723   1   829   2           723   2   1112   726           727   1   2   472           729   1   268   441           731   1   130   828           735   1   2   214           736   1   3   782           738   1   2   298           742   1   3   230           745   3   780   412           748   2   282   464           749   1   344   3           751   1   452   3           755   1   97   522           755   2   520   918           758   2   400   137           764   2   746   459           767   1   1   405           768   1   2   373           771   1   534   10           778   1   902   69           785   1   1023   256           787   1   631   2           791   1   3   224           799   1   15   260           804   1   304   711           805   1   3   680           808   1   219   842           810   1   1112   3           810   2   1442   1110           812   1   38   979           817   1   358   2           818   2   487   1104           819   2   1032   535           819   3   1419   1090           820   1   195   1064           828   1   255   4           829   1   48   800           830   1   291   4           832   1   298   2           835   1   320   796           840   3   491   709           845   1   457   2           850   2   303   449           853   1   359   3           860   1   2   256           864   1   18   410           864   2   383   715           864   6   1676   1828           870   1   1   588           873   1   454   2           875   1   294   4           877   1   1020   379           878   1   544   107           879   1   785   3           881   1   1   243           882   1   389   604           890   1   2   508           905   1   398   3           906   1   544   236           912   1   188   3           913   1   3   290           913   2   547   2           915   1   6   161           915   2   169   402           921   1   126   386           927   1   808   38           928   1   2   385           929   1   2   400           932   1   2   400           934   1   1   384           936   1   528   4           937   1   2   616           945   1   220   645           945   2   649   1242           946   1   950   198           949   1   1   270           951   1   3   362           955   1   3   143           960   1   400   77           963   1   1   162           965   1   346   2           966   1   606   133           969   1   3   302           971   1   12   170           974   1   161   3           976   1   348   4           977   1   2   211           982   1   982   38           984   1   296   3           987   1   3   467           993   1   1   525           994   1   549   178           1004   1   318   79           1014   1   313   2           1015   1   2   463           1016   1   145   2           1019   1   660   115           1022   1   474   109           1024   1   299   3           1024   2   276   431           1030   1   338   3           1032   1   179   3           1040   1   399   4           1043   1   3   269           1044   2   115   399           1047   1   1   159           1051   1   354   4           1051   2   733   233           1063   1   2   400           1069   1   2   148           1069   2   533   297           1075   1   399   91           1077   1   97   405           1081   1   58   438           1086   1   1   384           1087   2   246   431           1088   1   3   374           1096   1   238   2           1098   1   509   3           1100   1   511   2           1100   2   1158   796           1101   1   353   3           1102   1   194   3           1107   1   2   580           1114   1   3   422           1115   1   2   268           1119   1   22   267           1129   1   40   342           1132   1   181   2           1133   1   376   143           1144   1   225   4           1147   1   280   2           1153   1   1   153           1154   1   3   818           1159   1   1   330           1161   1   186   31           1164   1   254   81           1171   1   19   240           1171   2   108   299           1183   1   2   379           1195   1   179   3           1196   1   1   189           1200   1   33   197           1203   2   129   464           1222   2   105   401           1232   1   1   387           1240   1   2   175           1247   1   311   102           1271   1   221   30           1286   1   2   595           1295   1   1   165           1306   1   185   3           1314   2   158   631           1316   1   58   570           1359   1   193   2           1370   1   1   402           1371   1   1   345           1374   1   357   4           1378   1   2   400           1392   1   3   413           1411   1   202   432           1433   1   167   3           1450   1   2   256           1453   1   149   3           1471   1   398   75           1477   1   639   409           1502   1   399   4           1518   1   126   449           1534   1   143   3           1546   1   3   401           1547   1   255   4           1583   1   3   350           1587   1   3   563           1602   2   170   679           1629   1   1   402           1665   1   235   2           1760   1   314   3           1762   1   3   200           1876   2   119   286           1895   1   2   379           1931   1   400   2           1976   2   383   51           2055   2   252   401           2056   1   167   3           2150   1   263   3           2157   1   399   4           2164   1   283   2           2175   1   218   400           2212   1   331   170           2338   1   367   2           2342   1   3   167           2352   1   166   2           2352   2   398   174           2355   1   47   352           2356   1   341   3           2359   1   152   3           2421   1   150   4           2422   1   306   43           2443   1   263   99           2454   1   3   158           2463   1   253   2           2485   1   3   374           2557   1   246   4           2575   1   2   355           2582   1   3   284           2607   1   1   294           2930   1   17   400           2939   1   242   18           2944   1   3   359           2945   2   399   97           2952   1   2   190           2953   1   399   61           2964   1   166   2           2969   1   144   4           2977   1   2   373           2981   2   334   167           2986   1   7   279           2991   1   363   118           2995   1   1   321           3007   1   191   39           3017   1   308   48           3018   2   136   351           3025   1   197   3           3040   1   180   4           3046   1   185   3           3049   1   278   3           3050   1   3   314           3052   1   253   2           3065   1   2   157           3070   1   190   23           3075   1   222   4           3080   1   1   285           3092   1   162   4           3093   1   250   89           3100   1   52   237           3103   1   47   298           3118   1   174   4           3123   1   2   145           3127   1   1   147           3138   1   169   2           3142   1   203   18           3144   1   386   108           3151   1   170   3           3155   2   202   384           3168   1   12   176           3205   1   145   2           3282   1   1   150           3303   2   239   400           3371   2   211   399           3558   1   2   148           3558   2   36   401           3568   1   377   3           3595   1   380   3           3618   1   2   238           3618   2   130   402           3622   1   86   358           3622   2   398   132           3642   1   439   2           3649   1   398   15           3651   1   314   3           3664   1   467   637           3674   1   55   402           3677   1   311   3           3704   1   1   402           3726   1   269   3           3765   1   256   2           3779   1   357   160           3794   1   135   4           3794   2   377   87           3796   2   375   112           3801   1   262   50           3806   1   298   143           3807   1   42   389           3815   1   400   2           3827   1   3   320           3842   1   392   3           3853   1   399   127           3855   1   1   324           3857   1   2   235           3861   1   297   4           3865   1   399   103           3897   1   3   173           3897   2   143   400           3898   2   225   401           3921   2   103   342           3927   1   70   375           3930   1   76   234           3946   2   382   113           3951   2   105   377           3965   1   344   42           3973   1   400   5           3981   1   3   311           3998   1   3   356           4001   1   296   111           4003   1   90   335           4018   1   2   259           4018   2   186   401           4021   1   1   345           4043   1   3   344           4054   1   3   344           4066   1   1   150           4070   1   1   324           4072   2   187   390           4073   1   1   285           4077   2   127   372           4083   1   3   359           4090   1   27   368           4101   1   103   297           4105   1   1   306           4107   1   286   2           4119   1   339   49           4121   1   372   4           4123   1   3   230           4127   1   3   341           4128   1   2   331           4130   1   415   62           4146   1   97   381           4157   1   3   206           4186   1   254   3           4224   1   256   2           4239   1   1   348           4242   1   356   3           4252   1   296   3           4253   1   1   174           4256   1   323   78           4258   2   334   170           4267   1   144   4           4271   1   2   304           4287   1   163   23           4289   1   319   167           4302   1   153   305           4304   1   1   186           4304   2   96   314           4306   1   2   151           4318   1   289   2           4322   1   5   148           4331   1   221   3           4331   2   364   200           4338   1   399   70           4346   1   277   83           4367   2   117   311           4373   1   2   268           4381   1   326   78           4384   1   309   4           4397   1   9   311           4402   1   1   249           4403   1   328   50           4406   1   3   317           4411   1   2   280           4411   2   398   99           4412   1   2   364           4418   1   3   230           4424   1   398   195           4443   1   215   3           4471   1   323   3           4478   1   271   2           4482   1   50   289           4489   1   302   3           4491   1   12   206           4495   1   3   179           4496   1   252   4           4500   1   130   306           4511   1   248   3           4518   1   1   246           4526   1   241   2           4527   1   2   163           4532   1   3   239           4542   1   11   175           4567   1   36   200           4573   1   1   231           4578   1   322   2           4619   1   1   180           4620   1   176   3           4662   1   1   246           4669   1   2   157           4680   1   28   183           4690   1   174   4                        
     [0291] 
    
     
       
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                 SEQUENCE LISTING 
               
            
           
           
               
            
               
                 The patent application contains a lengthy “Sequence Listing” section. A copy of the “Sequence Listing” is available in electronic form from the USPTO 
               
               
                 web site (http://seqdata.uspto.gov/sequence.html?DocID=20040043037). An electronic copy of the “Sequence Listing” will also be available from the 
               
               
                 USPTO upon request and payment of the fee set forth in 37 CFR 1.19(b)(3).