# Patent

## Title
Polypeptides from non-typeable Haemophilus influenzae

## Abstract

Polypeptides comprising non-typeable Haemophilus influenzae (NTHi) amino acid sequences. Over 2500 specific NTHi proteins are disclosed. The invention also provides related polypeptides, nucleic acids, antibodies and methods. These can all be used in medicine for treating or preventing disease and/or infection caused by H. influenzae, such as otitis media.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a divisional of U.S. patent application Ser. No. 13/357,394, filed Jan. 24, 2012, now abandoned, which is a divisional of U.S. patent application Ser. No. 12/800,898, filed May 25, 2010, now U.S. Pat. No. 8,124,098, which is a continuation of U.S. patent application Ser. No. 11/596,557, filed Feb. 14, 2008, now U.S. Pat. No. 7,749,518, which is a 371 of PCT/IB05/01775, filed May 16, 2005, and claims priority to United Kingdom patent application no. 0410866.8, filed May 14, 2004, from which applications priority is claimed pursuant to 35 U.S.C. §§119/120 and which applications are incorporated herein by reference in their entireties.


INCORPORATION BY REFERENCE OF MATERIAL ON COMPACT DISC
This application incorporates by reference the Sequence Listing contained on the two compact discs (Copy 1 and Copy 2), filed concurrently herewith, containing the following file:
File name: PP022930.0003 SequenceList.txt; created Nov. 10, 2006; 6,676 KB in size.
TECHNICAL FIELD
This invention is in the field of Haemophilus influenzae immunology and vaccinology.
BACKGROUND ART
Haemophilus influenzae is a small, non-motile, Gram-negative coccobacillus. It is a respiratory pathogen that causes a wide spectrum of human infections, including: asymptomatic colonization of the upper respiratory tract (i.e. carriage); infections that extend from colonized mucosal surfaces to cause otitis media (inflammation of the middle ear), bronchitis, conjunctivitis, sinusitis, urinary tract infections and pneumonia; and invasive infections, such as bacteremia, septic arthritis, epiglottitis, pneumonia, empyema, pericarditis, cellulitis, osteomyelitis and meningitis. H. influenzae was the first bacterium for which a complete genome sequence was published [1].
H. influenzae strains are either capsulated (typeable) or non-capsulated (non-typeable), and there are six major serological types of capsulated strains (a to f). 95% of H. influenzae-caused invasive diseases are caused by H. influenzae type b (‘Hib’) strains. The most serious manifestation of Hib disease is meningitis, but the introduction in the 1980s of vaccines based on conjugated Hib capsular saccharides has hugely reduced incidence of this disease.
Although Hib infections can now be controlled by vaccination, other pathogenic H. influenzae strains remain a risk. For instance, non-typeable H. influenzae (NTHi) is responsible for otitis media (OM), particularly chronic OM. While OM is rarely associated with mortality, it is associated with significant morbidity. Hearing loss is the most common complication of OM, with behavioral, educational and language development delays being additional consequences of early onset OM with effusion. Acute OM is the most common bacterial infection in children in the USA. The non-typeable H. influenzae biogroup aegyptius causes epidemic conjunctivitis and Brazilian purpuric fever (BPF) [2], with BPF having a mortality of up to 70%.
To date, antibiotics are the main tool against the spectrum of clinical entities known collectively as OM, but widespread use of antibiotics for OM has met with controversy due to the emergence of multiple-antibiotic resistant microorganisms. Progress towards a vaccine is slow due to an incomplete understanding of both the pathogenesis of OM and the immune response to it.
The genome sequence of the serotype d strain KW20 [1,3] has been useful for understanding basic H. influenzae biology, but it has not been so useful in countering pathogenic H. influenzae strains, as serotype d strains are generally not pathogens.
It is an object of the invention to provide polypeptides for use in the development of vaccines for preventing and/or treating infections caused by non-typeable H. influenzae strains. In particular, it is an object to provide polypeptides for use in improved vaccines for preventing and/or treating otitis media. The polypeptides may also be useful for diagnostic purposes, and as targets for antibiotics.


DISCLOSURE OF THE INVENTION
Polypeptides
The invention provides polypeptides comprising the H. influenzae amino acid sequences disclosed in the examples. These amino acid sequences are the even SEQ ID NOs between 2 and 5080. There are thus 2540 amino acid sequences, and these are referred to as NTHnnnn, where nnnn is a number between 0001 and 2832 (there are 292 NTHnnnn numbers that have no sequence; see Table I). Further NTHi sequences of the invention are given as SEQ ID NOS: 5088 onwards.
The invention also provides polypeptides comprising amino acid sequences that have sequence identity to the H. influenzae amino acid sequences disclosed in the examples. Depending on the particular sequence, the degree of sequence identity is preferably greater than 50% (e.g. 60%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more). These polypeptides include homologs, orthologs, allelic variants and functional mutants. Typically, 50% identity or more between two polypeptide sequences is considered to be an indication of functional equivalence. Identity between polypeptides is preferably determined by the Smith-Waterman homology search algorithm as implemented in the MPSRCH program (Oxford Molecular), using an affine gap search with parameters gap open penalty=12 and gap extension penalty=1.
These polypeptide may, compared to the NTHi sequences of the examples, include one or more (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, etc.) conservative amino acid replacements i.e. replacements of one amino acid with another which has a related side chain. Genetically-encoded amino acids are generally divided into four families: (1) acidic i.e. aspartate, glutamate; (2) basic i.e. lysine, arginine, histidine; (3) non-polar i.e. alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan; and (4) uncharged polar i.e. glycine, asparagine, glutamine, cystine, serine, threonine, tyrosine. Phenylalanine, tryptophan, and tyrosine are sometimes classified jointly as aromatic amino acids. In general, substitution of single amino acids within these families does not have a major effect on the biological activity. The polypeptides may also include one or more (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, etc.) single amino acid deletions relative to the NTHi sequences of the examples. The polypeptides may also include one or more (e.g. 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, etc.) insertions (e.g. each of 1, 2, 3, 4 or 5 amino acids) relative to the NTHi sequences of the examples.
Preferred polypeptides of the invention are listed in Table II, including polypeptides that are lipidated, that are located in the outer membrane, that are located in the inner membrane, that are located in the periplasm, or that are not found in non-pathogenic H. influenzae strains. Particularly preferred polypeptides are those that fall into more than one of these categories e.g. polypeptides that are located in the outer membrane and are also not found in non-pathogenic H. influenzae strains.
A particularly preferred polypeptide is NTH0867. NTH0861, NTH0863 and NTH0865 are also preferred. As described below, these four proteins are embodied by SEQ ID NOS: 1566, 5095, 1570, 5094, 1574, 5093, 1578 and 5092. Within these eight SEQ ID NOS, 1566-1578 are preferred.
The invention further provides polypeptides comprising fragments of the H. influenzae amino acid sequences disclosed in the examples. The fragments should comprise at least n consecutive amino acids from the sequences and, depending on the particular sequence, n is 7 or more (e.g. 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100 or more).
The fragment may comprise at least one T-cell or, preferably, a B-cell epitope of the sequence. T- and B-cell epitopes can be identified empirically (e.g. using PEPSCAN [4,5] or similar methods), or they can be predicted (e.g. using the Jameson-Wolf antigenic index [6], matrix-based approaches [7], TEPITOPE [8], neural networks [9], OptiMer & EpiMer [10, 11], ADEPT [12], Tsites [13], hydrophilicity [14], antigenic index [15] or the methods disclosed in reference 16 etc.). Other preferred fragments are (a) the N-terminal signal peptides of the NTHi polypeptides of the invention, (b) the NTHi polypeptides, but without their N-terminal signal peptides, (c) the NTHi polypeptides, but without their N-terminal amino acid residue.
Polypeptides of the invention can be prepared in many ways e.g. by chemical synthesis (in whole or in part), by digesting longer polypeptides using proteases, by translation from RNA, by purification from cell culture (e.g. from recombinant expression), from the organism itself (e.g. after bacterial culture, or direct from patients), etc. A preferred method for production of peptides<40 amino acids long involves in vitro chemical synthesis [17,18]. Solid-phase peptide synthesis is particularly preferred, such as methods based on tBoc or Fmoc [19] chemistry. Enzymatic synthesis [20] may also be used in part or in full. As an alternative to chemical synthesis, biological synthesis may be used e.g. the polypeptides may be produced by translation. This may be carried out in vitro or in vivo.
Biological methods are in general restricted to the production of polypeptides based on L-amino acids, but manipulation of translation machinery (e.g. of aminoacyl tRNA molecules) can be used to allow the introduction of D-amino acids (or of other non natural amino acids, such as iodotyrosine or methylphenylalanine, azidohomoalanine, etc.) [21]. Where D-amino acids are included, however, it is preferred to use chemical synthesis. Polypeptides of the invention may have covalent modifications at the C-terminus and/or N-terminus.
Polypeptides of the invention can take various forms (e.g. native, fusions, glycosylated, non-glycosylated, lipidated, non-lipidated, phosphorylated, non-phosphorylated, myristoylated, non-myristoylated, monomeric, multimeric, particulate, denatured, etc.).
Polypeptides of the invention are preferably provided in purified or substantially purified form i.e. substantially free from other polypeptides (e.g. free from naturally-occurring polypeptides), particularly from other Haemophilus or host cell polypeptides, and are generally at least about 50% pure (by weight), and usually at least about 90% pure i.e. less than about 50%, and more preferably less than about 10% (e.g. 5%) of a composition is made up of other expressed polypeptides.
Polypeptides of the invention are preferably H. influenzae polypeptides. Polypeptides of the invention preferably have the function indicated in Table III for the relevant sequence.
Polypeptides of the invention may be attached to a solid support. Polypeptides of the invention may comprise a detectable label (e.g. a radioactive or fluorescent label, or a biotin label).
The term “polypeptide” refers to amino acid polymers of any length. The polymer may be linear or branched, it may comprise modified amino acids, and it may be interrupted by non-amino acids. The terms also encompass an amino acid polymer that has been modified naturally or by intervention; for example, disulfide bond formation, glycosylation, lipidation, acetylation, phosphorylation, or any other manipulation or modification, such as conjugation with a labeling component. Also included within the definition are, for example, polypeptides containing one or more analogs of an amino acid (including, for example, unnatural amino acids, etc.), as well as other modifications known in the art. Polypeptides can occur as single chains or associated chains. Polypeptides of the invention can be naturally or non-naturally glycosylated (i.e. the polypeptide has a glycosylation pattern that differs from the glycosylation pattern found in the corresponding naturally occurring polypeptide).
The invention provides polypeptides comprising a sequence —X—Y— or —Y—X—, wherein: —X— is an amino acid sequence as defined above and —Y— is not a sequence as defined above i.e. the invention provides fusion proteins. Where the N-terminus codon of a polypeptide-coding sequence is not ATG then that codon will be translated as the standard amino acid for that codon rather than as a Met, which occurs when the codon is a start codon.
The invention provides a process for producing polypeptides of the invention, comprising the step of culturing a host cell of to the invention under conditions which induce polypeptide expression.
The invention provides a process for producing a polypeptide of the invention, wherein the polypeptide is synthesised in part or in whole using chemical means.
The invention provides a composition comprising two or more polypeptides of the invention.
The invention also provides a hybrid polypeptide represented by the formula NH2-A-[-X-L-]n-B—COOH, wherein X is a polypeptide of the invention as defined above, L is an optional linker amino acid sequence, A is an optional N-terminal amino acid sequence, B is an optional C-terminal amino acid sequence, and n is an integer greater than 1. The value of n is between 2 and x, and the value of x is typically 3, 4, 5, 6, 7, 8, 9 or 10. Preferably n is 2, 3 or 4; it is more preferably 2 or 3; most preferably, n=2. For each n instances, —X— may be the same or different. For each n instances of [—X-L-], linker amino acid sequence -L- may be present or absent. For instance, when n=2 the hybrid may be NH2—X1-L1-X2-L2-COOH, NH2—X1—X2—COOH, NH2—X1-L1-X2—COOH, NH2—X1—X2-L2-COOH, etc. Linker amino acid sequence(s) -L- will typically be short (e.g. 20 or fewer amino acids i.e. 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1). Examples include short peptide sequences which facilitate cloning, poly-glycine linkers (i.e. Glyn where n=2, 3, 4, 5, 6, 7, 8, 9, 10 or more), and histidine tags (i.e. Hisn where n=3, 4, 5, 6, 7, 8, 9, 10 or more). Other suitable linker amino acid sequences will be apparent to those skilled in the art. -A- and —B— are optional sequences which will typically be short (e.g. 40 or fewer amino acids i.e. 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1). Examples include leader sequences to direct polypeptide trafficking, or short peptide sequences which facilitate cloning or purification (e.g. histidine tags i.e. Hisn where n=3, 4, 5, 6, 7, 8, 9, 10 or more). Other suitable N-terminal and C-terminal amino acid sequences will be apparent to those skilled in the art.
Various tests can be used to assess the in vivo immunogenicity of polypeptides of the invention. For example, polypeptides can be expressed recombinantly and used to screen patient sera by immunoblot. A positive reaction between the polypeptide and patient serum indicates that the patient has previously mounted an immune response to the protein in question i.e. the protein is an immunogen. This method can also be used to identify immunodominant proteins.
Antibodies
The invention provides antibodies that bind to polypeptides of the invention. These may be polyclonal or monoclonal and may be produced by any suitable means (e.g. by recombinant expression). To increase compatibility with the human immune system, the antibodies may be chimeric or humanised [e.g. refs. 22 & 23], or fully human antibodies may be used. The antibodies may include a detectable label (e.g. for diagnostic assays). Antibodies of the invention may be attached to a solid support. Antibodies of the invention are preferably neutralizing antibodies.
Monoclonal antibodies are particularly useful in identification and purification of the individual polypeptides against which they are directed. Monoclonal antibodies of the invention may also be employed as reagents in immunoassays, radioimmunoassays (RIA) or enzyme-linked immunosorbent assays (ELISA), etc. In these applications, the antibodies can be labelled with an analytically-detectable reagent such as a radioisotope, a fluorescent molecule or an enzyme. The monoclonal antibodies produced by the above method may also be used for the molecular identification and characterization (epitope mapping) of polypeptides of the invention.
Antibodies of the invention are preferably provided in purified or substantially purified form. Typically, the antibody will be present in a composition that is substantially free of other polypeptides e.g. where less than 90% (by weight), usually less than 60% and more usually less than 50% of the composition is made up of other polypeptides.
Antibodies of the invention can be of any isotype (e.g. IgA, IgG, IgM i.e. an α, γ or μ heavy chain), but will generally be IgG. Within the IgG isotype, antibodies may be IgG1, IgG2, IgG3 or IgG4 subclass. Antibodies of the invention may have a κ or a λ light chain.
Antibodies of the invention can take various forms, including whole antibodies, antibody fragments such as F(ab′)2 and F(ab) fragments, Fv fragments (non-covalent heterodimers), single-chain antibodies such as single chain Fv molecules (scFv), minibodies, oligobodies, etc. The term “antibody” does not imply any particular origin, and includes antibodies obtained through non-conventional processes, such as phage display.
The invention provides a process for detecting polypeptides of the invention, comprising the steps of: (a) contacting an antibody of the invention with a biological sample under conditions suitable for the formation of an antibody-antigen complexes; and (b) detecting said complexes.
The invention provides a process for detecting antibodies of the invention, comprising the steps of (a) contacting a polypeptide of the invention with a biological sample (e.g. a blood or serum sample) under conditions suitable for the formation of an antibody-antigen complexes; and (b) detecting said complexes.
Nucleic Acids
The invention provides nucleic acid comprising the H. influenzae nucleotide sequences disclosed in the examples. These nucleic acid sequences are the odd SEQ ID NOs between 1 and 5080.
The invention also provides nucleic acid comprising nucleotide sequences having sequence identity to the H. influenzae nucleotide sequences disclosed in the examples. Identity between sequences is preferably determined by the Smith-Waterman homology search algorithm as described above.
The invention also provides nucleic acid which can hybridize to the H. influenzae nucleic acid disclosed in the examples. Hybridization reactions can be performed under conditions of different “stringency”. Conditions that increase stringency of a hybridization reaction of widely known and published in the art [e.g. page 7.52 of reference 24]. Examples of relevant conditions include (in order of increasing stringency): incubation temperatures of 25° C., 37° C., 50° C., 55° C. and 68° C.; buffer concentrations of 10×SSC, 6×SSC, 1×SSC, 0.1×SSC (where SSC is 0.15 M NaCl and 15 mM citrate buffer) and their equivalents using other buffer systems; formamide concentrations of 0%, 25%, 50%, and 75%; incubation times from 5 minutes to 24 hours; 1, 2, or more washing steps; wash incubation times of 1, 2, or 15 minutes; and wash solutions of 6×SSC, 1×SSC, 0.1×SSC, or de-ionized water. Hybridization techniques and their optimization are well known in the art [e.g. see references 24-27, etc.].
In some embodiments, nucleic acid of the invention hybridizes to a target of the invention under low stringency conditions; in other embodiments it hybridizes under intermediate stringency conditions; in preferred embodiments, it hybridizes under high stringency conditions. An exemplary set of low stringency hybridization conditions is 50° C. and 10×SSC. An exemplary set of intermediate stringency hybridization conditions is 55° C. and 1×SSC. An exemplary set of high stringency hybridization conditions is 68° C. and 0.1×SSC.
Nucleic acid comprising fragments of these sequences are also provided. These should comprise at least n consecutive nucleotides from the H. influenzae sequences and, depending on the particular sequence, n is 10 or more (e.g. 12, 14, 15, 18, 20, 25, 30, 35, 40, 50, 60, 70, 80, 90, 100, 150, 200 or more).
The invention provides nucleic acid of formula 5′-X—Y—Z-3′, wherein: —X— is a nucleotide sequence consisting of x nucleotides; —Z— is a nucleotide sequence consisting of z nucleotides; —Y— is a nucleotide sequence consisting of either (a) a fragment of one of the odd-numbered SEQ ID NOS: 1 to 5079, or (b) the complement of (a); and said nucleic acid 5′-X—Y—Z-3′ is neither (i) a fragment of one of the odd-numbered SEQ ID NOS: 1 to 5079 nor (ii) the complement of (i). The —X— and/or —Z— moieties may comprise a promoter sequence (or its complement).
The invention also provides nucleic acid encoding the polypeptides and polypeptide fragments of the invention.
The invention includes nucleic acid comprising sequences complementary to the sequences disclosed in the sequence listing (e.g. for antisense or probing, or for use as primers), as well as the sequences in the orientation actually shown.
Nucleic acids of the invention can be used in hybridisation reactions (e.g. Northern or Southern blots, or in nucleic acid microarrays or ‘gene chips’) and amplification reactions (e.g. PCR, SDA, SSSR, LCR, TMA, NASBA, etc.) and other nucleic acid techniques.
Nucleic acid according to the invention can take various forms (e.g. single-stranded, double-stranded, vectors, primers, probes, labelled etc.). Nucleic acids of the invention may be circular or branched, but will generally be linear. Unless otherwise specified or required, any embodiment of the invention that utilizes a nucleic acid may utilize both the double-stranded form and each of two complementary single-stranded forms which make up the double-stranded form. Primers and probes are generally single-stranded, as are antisense nucleic acids.
Nucleic acids of the invention are preferably provided in purified or substantially purified form i.e. substantially free from other nucleic acids (e.g. free from naturally-occurring nucleic acids), particularly from other Haemophilus or host cell nucleic acids, generally being at least about 50% pure (by weight), and usually at least about 90% pure. Nucleic acids of the invention are preferably H. influenzae nucleic acids.
Nucleic acids of the invention may be prepared in many ways e.g. by chemical synthesis (e.g. phosphoramidite synthesis of DNA) in whole or in part, by digesting longer nucleic acids using nucleases (e.g. restriction enzymes), by joining shorter nucleic acids or nucleotides (e.g. using ligases or polymerases), from genomic or cDNA libraries, etc.
Nucleic acid of the invention may be attached to a solid support (e.g. a bead, plate, filter, film, slide, microarray support, resin, etc.). Nucleic acid of the invention may be labelled e.g. with a radioactive or fluorescent label, or a biotin label. This is particularly useful where the nucleic acid is to be used in detection techniques e.g. where the nucleic acid is a primer or as a probe.
The term “nucleic acid” includes in general means a polymeric form of nucleotides of any length, which contain deoxyribonucleotides, ribonucleotides, and/or their analogs. It includes DNA, RNA, DNA/RNA hybrids. It also includes DNA or RNA analogs, such as those containing modified backbones (e.g. peptide nucleic acids (PNAs) or phosphorothioates) or modified bases. Thus the invention includes mRNA, tRNA, rRNA, ribozymes, DNA, cDNA, recombinant nucleic acids, branched nucleic acids, plasmids, vectors, probes, primers, etc. Where nucleic acid of the invention takes the form of RNA, it may or may not have a 5′ cap.
Nucleic acids of the invention comprise NTHi sequences, but they may also comprise non-NTHi sequences (e.g. in nucleic acids of formula 5′-X—Y—Z-3′, as defined above). This is particularly useful for primers, which may thus comprise a first sequence complementary to a PCAV nucleic acid target and a second sequence which is not complementary to the nucleic acid target. Any such non-complementary sequences in the primer are preferably 5′ to the complementary sequences. Typical non-complementary sequences comprise restriction sites or promoter sequences.
Nucleic acids of the invention can be prepared in many ways e.g. by chemical synthesis (at least in part), by digesting longer nucleic acids using nucleases (e.g. restriction enzymes), by joining shorter nucleic acids (e.g. using ligases or polymerases), from genomic or cDNA libraries, etc.
Nucleic acids of the invention may be part of a vector i.e. part of a nucleic acid construct designed for transduction/transfection of one or more cell types. Vectors may be, for example, “cloning vectors” which are designed for isolation, propagation and replication of inserted nucleotides, “expression vectors” which are designed for expression of a nucleotide sequence in a host cell, “viral vectors” which is designed to result in the production of a recombinant virus or virus-like particle, or “shuttle vectors”, which comprise the attributes of more than one type of vector. Preferred vectors are plasmids. A “host cell” includes an individual cell or cell culture which can be or has been a recipient of exogenous nucleic acid. Host cells include progeny of a single host cell, and the progeny may not necessarily be completely identical (in morphology or in total DNA complement) to the original parent cell due to natural, accidental, or deliberate mutation and/or change. Host cells include cells transfected or infected in vivo or in vitro with nucleic acid of the invention.
Where a nucleic acid is DNA, it will be appreciated that “U” in a RNA sequence will be replaced by “T” in the DNA. Similarly, where a nucleic acid is RNA, it will be appreciated that “T” in a DNA sequence will be replaced by “U” in the RNA.
The term “complement” or “complementary” when used in relation to nucleic acids refers to Watson-Crick base pairing. Thus the complement of C is G, the complement of G is C, the complement of A is T (or U), and the complement of T (or U) is A. It is also possible to use bases such as I (the purine inosine) e.g. to complement pyrimidines (C or T). The terms also imply a direction—the complement of 5′-ACAGT-3′ is 5′-ACTGT-3′ rather than 5′-TGTCA-3′.
Nucleic acids of the invention can be used, for example: to produce polypeptides; as hybridization probes for the detection of nucleic acid in biological samples; to generate additional copies of the nucleic acids; to generate ribozymes or antisense oligonucleotides; as single-stranded DNA primers or probes; or as triple-strand forming oligonucleotides.
The invention provides a process for producing nucleic acid of the invention, wherein the nucleic acid is synthesised in part or in whole using chemical means.
The invention provides vectors comprising nucleotide sequences of the invention (e.g. cloning or expression vectors) and host cells transformed with such vectors.
The invention also provides a kit comprising primers (e.g. PCR primers) for amplifying a template sequence contained within a Haemophilus bacterium (e.g. H. influenzae) nucleic acid sequence, the kit comprising a first primer and a second primer, wherein the first primer is substantially complementary to said template sequence and the second primer is substantially complementary to a complement of said template sequence, wherein the parts of said primers which have substantial complementarity define the termini of the template sequence to be amplified. The first primer and/or the second primer may include a detectable label (e.g. a fluorescent label).
The invention also provides a kit comprising first and second single-stranded oligonucleotides which allow amplification of a Haemophilus template nucleic acid sequence contained in a single- or double-stranded nucleic acid (or mixture thereof), wherein: (a) the first oligonucleotide comprises a primer sequence which is substantially complementary to said template nucleic acid sequence; (b) the second oligonucleotide comprises a primer sequence which is substantially complementary to the complement of said template nucleic acid sequence; (c) the first oligonucleotide and/or the second oligonucleotide comprise(s) sequence which is not compementary to said template nucleic acid; and (d) said primer sequences define the termini of the template sequence to be amplified. The non-complementary sequence(s) of feature (c) are preferably upstream of (i.e. 5′ to) the primer sequences. One or both of these (c) sequences may comprise a restriction site [e.g. ref.28] or a promoter sequence [e.g. 29]. The first oligonucleotide and/or the second oligonucleotide may include a detectable label (e.g. a fluorescent label).
The template sequence may be any part of a genome sequence.
The invention provides a process for detecting nucleic acid of the invention, comprising the steps of: (a) contacting a nucleic probe according to the invention with a biological sample under hybridising conditions to form duplexes; and (b) detecting said duplexes.
The invention provides a process for detecting H. influenzae in a biological sample (e.g. blood), comprising the step of contacting nucleic acid according to the invention with the biological sample under hybridising conditions. The process may involve nucleic acid amplification (e.g. PCR, SDA, SSSR, LCR, TMA, NASBA, etc.) or hybridisation (e.g. microarrays, blots, hybridisation with a probe in solution etc.). PCR detection of H. influenzae in clinical samples has been reported [e.g. see refs. 30 & 31]. Clinical assays based on nucleic acid are described in general in ref. 32.
The invention provides a process for preparing a fragment of a target sequence, wherein the fragment is prepared by extension of a nucleic acid primer. The target sequence and/or the primer are nucleic acids of the invention. The primer extension reaction may involve nucleic acid amplification (e.g. PCR, SDA, SSSR, LCR, TMA, NASBA, etc.).
Nucleic acid amplification according to the invention may be quantitative and/or real-time.
For certain embodiments of the invention, nucleic acids are preferably at least 7 nucleotides in length (e.g. 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 50, 55, 60, 65, 70, 75, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190, 200, 225, 250, 275, 300 nucleotides or longer).
For certain embodiments of the invention, nucleic acids are preferably at most 500 nucleotides in length (e.g. 450, 400, 350, 300, 250, 200, 150, 140, 130, 120, 110, 100, 90, 80, 75, 70, 65, 60, 55, 50, 45, 40, 39, 38, 37, 36, 35, 34, 33, 32, 31, 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15 nucleotides or shorter).
Primers and probes of the invention, and other nucleic acids used for hybridization, are preferably between 10 and 30 nucleotides in length (e.g. 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides).
Pharmaceutical Compositions
The invention provides compositions comprising: (a) polypeptide, antibody, and/or nucleic acid of the invention; and (b) a pharmaceutically acceptable carrier. These compositions may be suitable as immunogenic compositions, for instance, or as diagnostic reagents, or as vaccines. Vaccines according to the invention may either be prophylactic (i.e. to prevent infection) or therapeutic (i.e. to treat infection), but will typically be prophylactic.
A ‘pharmaceutically acceptable carriers’ includes any carrier that does not itself induce the production of antibodies harmful to the individual receiving the composition. Suitable carriers are typically large, slowly metabolised macromolecules such as proteins, polysaccharides, polylactic acids, polyglycolic acids, polymeric amino acids, amino acid copolymers, sucrose, trehalose, lactose, and lipid aggregates (such as oil droplets or liposomes). Such carriers are well known to those of ordinary skill in the art. The vaccines may also contain diluents, such as water, saline, glycerol, etc. Additionally, auxiliary substances, such as wetting or emulsifying agents, pH buffering substances, and the like, may be present. Sterile pyrogen-free, phosphate-buffered physiologic saline is a typical carrier. A thorough discussion of pharmaceutically acceptable excipients is available in ref. 138.
Compositions of the invention may include an antimicrobial, particularly if packaged in a multiple dose format.
Compositions of the invention may comprise detergent e.g. a Tween (polysorbate), such as Tween 80. Detergents are generally present at low levels e.g. <0.01%.
Compositions of the invention may include sodium salts (e.g. sodium chloride) to give tonicity. A concentration of 10±2 mg/ml NaCl is typical.
Compositions of the invention will generally include a buffer. A phosphate buffer is typical.
Compositions of the invention may comprise a sugar alcohol (e.g. mannitol) or a disaccharide (e.g. sucrose or trehalose) e.g. at around 15-30 mg/ml (e.g. 25 mg/ml), particularly if they are to be lyophilised or if they include material which has been reconstituted from lyophilised material. The pH of a composition for lyophilisation may be adjusted to around 6.1 prior to lyophilisation.
Polypeptides of the invention may be administered in conjunction with other immunoregulatory agents. In particular, compositions will usually include a vaccine adjuvant. Adjuvants which may be used in compositions of the invention include, but are not limited to:
A. Mineral-Containing Compositions
Mineral containing compositions suitable for use as adjuvants in the invention include mineral salts, such as aluminium salts and calcium salts. The invention includes mineral salts such as hydroxides (e.g. oxyhydroxides), phosphates (e.g. hydroxyphosphates, orthophosphates), sulphates, etc. [e.g. see chapters 8 & 9 of ref. 33], or mixtures of different mineral compounds, with the compounds taking any suitable form (e.g. gel, crystalline, amorphous, etc.), and with adsorption being preferred. The mineral containing compositions may also be formulated as a particle of metal salt [34].
Aluminium phosphates are particularly preferred, particularly in compositions which include a H. influenzae saccharide antigen, and a typical adjuvant is amorphous aluminium hydroxyphosphate with PO4/Al molar ratio between 0.84 and 0.92, included at 0.6 mg Al3+/ml. Adsorption with a low dose of aluminium phosphate may be used e.g. between 50 and 100 μg Al3+ per conjugate per dose. Where there is more than one conjugate in a composition, not all conjugates need to be adsorbed.
B. Oil Emulsions
Oil emulsion compositions suitable for use as adjuvants in the invention include squalene-water emulsions, such as MF59 [Chapter 10 of ref 33; see also ref. 35] (5% Squalene, 0.5% Tween 80, and 0.5% Span 85, formulated into submicron particles using a microfluidizer). Complete Freund's adjuvant (CFA) and incomplete Freund's adjuvant (IFA) may also be used.
C. Saponin Formulations [Chapter 22 of Ref 33]
Saponin formulations may also be used as adjuvants in the invention. Saponins are a heterologous group of sterol glycosides and triterpenoid glycosides that are found in the bark, leaves, stems, roots and even flowers of a wide range of plant species. Saponin from the bark of the Quillaia saponaria Molina tree have been widely studied as adjuvants. Saponin can also be commercially obtained from Smilax ornata (sarsaprilla), Gypsophilla paniculata (brides veil), and Saponaria officianalis (soap root). Saponin adjuvant formulations include purified formulations, such as QS21, as well as lipid formulations, such as ISCOMs. QS21 is marketed as StimulonTM.
Saponin compositions have been purified using HPLC and RP-HPLC. Specific purified fractions using these techniques have been identified, including QS7, QS17, QS18, QS21, QH-A, QH-B and QH-C. Preferably, the saponin is QS21. A method of production of QS21 is disclosed in ref 36. Saponin formulations may also comprise a sterol, such as cholesterol [37].
Combinations of saponins and cholesterols can be used to form unique particles called immunostimulating complexes (ISCOMs) [chapter 23 of ref 33]. ISCOMs typically also include a phospholipid such as phosphatidylethanolamine or phosphatidylcholine. Any known saponin can be used in ISCOMs. Preferably, the ISCOM includes one or more of QuilA, QHA & QHC. ISCOMs are further described in refs. 37-39. Optionally, the ISCOMS may be devoid of additional detergent [40].
A review of the development of saponin based adjuvants can be found in refs. 41 & 42.
D. Virosomes and Virus-Like Particles
Virosomes and virus-like particles (VLPs) can also be used as adjuvants in the invention. These structures generally contain one or more proteins from a virus optionally combined or formulated with a phospholipid. They are generally non-pathogenic, non-replicating and generally do not contain any of the native viral genome. The viral proteins may be recombinantly produced or isolated from whole viruses. These viral proteins suitable for use in virosomes or VLPs include proteins derived from influenza virus (such as HA or NA), Hepatitis B virus (such as core or capsid proteins), Hepatitis E virus, measles virus, Sindbis virus, Rotavirus, Foot-and-Mouth Disease virus, Retrovirus, Norwalk virus, human Papilloma virus, HIV, RNA-phages, Qβ-phage (such as coat proteins), GA-phage, fr-phage, AP205 phage, and Ty (such as retrotransposon Ty protein p1). VLPs are discussed further in refs. 43-48. Virosomes are discussed further in, for example, ref 49
E. Bacterial or Microbial Derivatives
Adjuvants suitable for use in the invention include bacterial or microbial derivatives such as non-toxic derivatives of enterobacterial lipopolysaccharide (LPS), Lipid A derivatives, immunostimulatory oligonucleotides and ADP-ribosylating toxins and detoxified derivatives thereof.
Non-toxic derivatives of LPS include monophosphoryl lipid A (MPL) and 3-O-deacylated MPL (3dMPL). 3dMPL is a mixture of 3 de-O-acylated monophosphoryl lipid A with 4, 5 or 6 acylated chains. A preferred “small particle” form of 3 De-O-acylated monophosphoryl lipid A is disclosed in ref. 50. Such “small particles” of 3dMPL are small enough to be sterile filtered through a 0.22 μm membrane [50]. Other non-toxic LPS derivatives include monophosphoryl lipid A mimics, such as aminoalkyl glucosaminide phosphate derivatives e.g. RC-529 [51,52].
Lipid A derivatives include derivatives of lipid A from Escherichia coli such as OM-174. OM-174 is described for example in refs. 53 & 54.
Immunostimulatory oligonucleotides suitable for use as adjuvants in the invention include nucleotide sequences containing a CpG motif (a dinucleotide sequence containing an unmethylated cytosine linked by a phosphate bond to a guanosine). Double-stranded RNAs and oligonucleotides containing palindromic or poly(dG) sequences have also been shown to be immunostimulatory.
The CpG's can include nucleotide modifications/analogs such as phosphorothioate modifications and can be double-stranded or single-stranded. References 55, 56 and 57 disclose possible analog substitutions e.g. replacement of guanosine with 2′-deoxy-7-deazaguanosine. The adjuvant effect of CpG oligonucleotides is further discussed in refs. 58-63.
The CpG sequence may be directed to TLR9, such as the motif GTCGTT or TTCGTT [64]. The CpG sequence may be specific for inducing a Th1 immune response, such as a CpG-A ODN, or it may be more specific for inducing a B cell response, such a CpG-B ODN. CpG-A and CpG-B ODNs are discussed in refs. 65-67. Preferably, the CpG is a CpG-A ODN.
Preferably, the CpG oligonucleotide is constructed so that the 5′ end is accessible for receptor recognition. Optionally, two CpG oligonucleotide sequences may be attached at their 3′ ends to form “immunomers”. See, for example, refs. 64 & 68-70.
Bacterial ADP-ribosylating toxins and detoxified derivatives thereof may be used as adjuvants in the invention. Preferably, the protein is derived from E. coli (E. coli heat labile enterotoxin “LT”), cholera (“CT”), or pertussis (“PT”). The use of detoxified ADP-ribosylating toxins as mucosal adjuvants is described in ref. 71 and as parenteral adjuvants in ref. 72. The toxin or toxoid is preferably in the form of a holotoxin, comprising both A and B subunits. Preferably, the A subunit contains a detoxifying mutation; preferably the B subunit is not mutated. Preferably, the adjuvant is a detoxified LT mutant such as LT-K63, LT-R72, and LT-G192. The use of ADP-ribosylating toxins and detoxified derivatives thereof, particularly LT-K63 and LT-R72, as adjuvants can be found in refs. 73-80. Numerical reference for amino acid substitutions is preferably based on the alignments of the A and B subunits of ADP-ribosylating toxins set forth in ref. 81, specifically incorporated herein by reference in its entirety.
F. Human Immunomodulators
Human immunomodulators suitable for use as adjuvants in the invention include cytokines, such as interleukins (e.g. IL-1, IL-2, IL-4, IL-5, IL-6, IL-7, IL-12 [82], etc.) [83], interferons (e.g. interferon-γ), macrophage colony stimulating factor, and tumor necrosis factor.
G. Bioadhesives and Mucoadhesives
Bioadhesives and mucoadhesives may also be used as adjuvants in the invention. Suitable bioadhesives include esterified hyaluronic acid microspheres [84] or mucoadhesives such as cross-linked derivatives of poly(acrylic acid), polyvinyl alcohol, polyvinyl pyrollidone, polysaccharides and carboxymethylcellulose. Chitosan and derivatives thereof may also be used as adjuvants in the invention [85].
H. Microparticles
Microparticles may also be used as adjuvants in the invention. Microparticles (i.e. a particle of  ̃100 nm to  ̃150 μm in diameter, more preferably  ̃200 nm to  ̃30 μm in diameter, and most preferably  ̃500 nm to  ̃10 μm in diameter) formed from materials that are biodegradable and non-toxic (e.g. a poly(α-hydroxy acid), a polyhydroxybutyric acid, a polyorthoester, a polyanhydride, a polycaprolactone, etc.), with poly(lactide-co-glycolide) are preferred, optionally treated to have a negatively-charged surface (e.g. with SDS) or a positively-charged surface (e.g. with a cationic detergent, such as CTAB).
I. Liposomes (Chapters 13 & 14 of Ref 33)
Examples of liposome formulations suitable for use as adjuvants are described in refs. 86-88.
J. Polyoxyethylene Ether and Polyoxyethylene Ester Formulations
Adjuvants suitable for use in the invention include polyoxyethylene ethers and polyoxyethylene esters [89]. Such formulations further include polyoxyethylene sorbitan ester surfactants in combination with an octoxynol [90] as well as polyoxyethylene alkyl ethers or ester surfactants in combination with at least one additional non-ionic surfactant such as an octoxynol [91]. Preferred polyoxyethylene ethers are selected from the following group: polyoxyethylene-9-lauryl ether (laureth 9), polyoxyethylene-9-steoryl ether, polyoxytheylene-8-steoryl ether, polyoxyethylene-4-lauryl ether, polyoxyethylene-35-lauryl ether, and polyoxyethylene-23-lauryl ether.
K. Polyphosphazene (PCPP)
PCPP formulations are described, for example, in refs. 92 and 93.
L. Muramyl Peptides
Examples of muramyl peptides suitable for use as adjuvants in the invention include N-acetyl-muramyl-L-threonyl-D-isoglutamine (thr-MDP), N-acetyl-normuramyl-L-alanyl-D-isoglutamine (nor-MDP), and N-acetylmuramyl-L-alanyl-D-isoglutaminyl-L-alanine-2-(1′-2′-dipalmitoyl-sn-glycero-3-hydroxyphosphoryloxy)-ethylamine MTP-PE).
M. Imidazoquinolone Compounds.
Examples of imidazoquinolone compounds suitable for use adjuvants in the invention include Imiquamod and its homologues (e.g. “Resiquimod 3M”), described further in refs. 94 and 95.
The invention may also comprise combinations of aspects of one or more of the adjuvants identified above. For example, the following adjuvant compositions may be used in the invention: (1) a saponin and an oil-in-water emulsion [96]; (2) a saponin (e.g. QS21)+a non-toxic LPS derivative (e.g. 3dMPL) [97]; (3) a saponin (e.g. QS21)+a non-toxic LPS derivative (e.g. 3dMPL)+a cholesterol; (4) a saponin (e.g. QS21)+3dMPL+IL-12 (optionally+a sterol) [98]; (5) combinations of 3dMPL with, for example, QS21 and/or oil-in-water emulsions [99]; (6) SAF, containing 10% squalane, 0.4% Tween 80TM, 5% pluronic-block polymer L121, and thr-MDP, either microfluidized into a submicron emulsion or vortexed to generate a larger particle size emulsion. (7) RibiTM adjuvant system (RAS), (Ribi Immunochem) containing 2% squalene, 0.2% Tween 80, and one or more bacterial cell wall components from the group consisting of monophosphorylipid A (MPL), trehalose dimycolate (TDM), and cell wall skeleton (CWS), preferably MPL+CWS (DetoxTM); and (8) one or more mineral salts (such as an aluminum salt)+a non-toxic derivative of LPS (such as 3dMPL).
Other substances that act as immunostimulating agents are disclosed in chapter 7 of ref. 33.
The use of an aluminium hydroxide or aluminium phosphate adjuvant is particularly preferred, and antigens are generally adsorbed to these salts. Calcium phosphate is another preferred adjuvant.
The pH of compositions of the invention is preferably between 6 and 8, preferably about 7. Stable pH may be maintained by the use of a buffer. Where a composition comprises an aluminium hydroxide salt, it is preferred to use a histidine buffer [100]. The composition may be sterile and/or pyrogen-free. Compositions of the invention may be isotonic with respect to humans.
Compositions may be presented in vials, or they may be presented in ready-filled syringes. The syringes may be supplied with or without needles. A syringe will include a single dose of the composition, whereas a vial may include a single dose or multiple doses. Injectable compositions will usually be liquid solutions or suspensions. Alternatively, they may be presented in solid form (e.g. freeze-dried) for solution or suspension in liquid vehicles prior to injection.
Compositions of the invention may be packaged in unit dose form or in multiple dose form. For multiple dose forms, vials are preferred to pre-filled syringes. Effective dosage volumes can be routinely established, but a typical human dose of the composition for injection has a volume of 0.5 ml.
Where a composition of the invention is to be prepared extemporaneously prior to use (e.g. where a component is presented in lyophilised form) and is presented as a kit, the kit may comprise two vials, or it may comprise one ready-filled syringe and one vial, with the contents of the syringe being used to reactivate the contents of the vial prior to injection.
Immunogenic compositions used as vaccines comprise an immunologically effective amount of antigen(s), as well as any other components, as needed. By ‘immunologically effective amount’, it is meant that the administration of that amount to an individual, either in a single dose or as part of a series, is effective for treatment or prevention. This amount varies depending upon the health and physical condition of the individual to be treated, age, the taxonomic group of individual to be treated (e.g. non-human primate, primate, etc.), the capacity of the individual's immune system to synthesise antibodies, the degree of protection desired, the formulation of the vaccine, the treating doctor's assessment of the medical situation, and other relevant factors. It is expected that the amount will fall in a relatively broad range that can be determined through routine trials, and a typical quantity of each meningococcal saccharide antigen per dose is between 1 μg and 10 mg per antigen.
Pharmaceutical Uses
The invention also provides a method of treating a patient, comprising administering to the patient a therapeutically effective amount of a composition of the invention. The patient may either be at risk from the disease themselves or may be a pregnant woman (‘maternal immunisation’).
The invention provides nucleic acid, polypeptide, or antibody of the invention for use as medicaments (e.g. as immunogenic compositions or as vaccines) or as diagnostic reagents. It also provides the use of nucleic acid, polypeptide, or antibody of the invention in the manufacture of: (i) a medicament for treating or preventing disease and/or infection caused by H. influenzae; (ii) a diagnostic reagent for detecting the presence of H. influenzae or of antibodies raised against H. influenzae; and/or (iii) a reagent which can raise antibodies against H. influenzae. Said H. influenzae can be any serotype or strain, but is preferably a non-typeable H. influenzae. Said disease may be, for instance, otitis media (including acute otitis media), bronchitis, conjunctivitis, sinusitis, a urinary tract infection, pneumonia, bacteremia, septic arthritis, epiglottitis, pneumonia, empyema, pericarditis, cellulitis, osteomyelitis, lower respiratory tract infection or meningitis. The invention is particularly useful for preventing inflammation of the middle ear, by eliciting an immune response that prevents bacteria from moving from the throat to the middle ear via the eustachian tube, where the middle ear is then colonised.
The patient is preferably a human. Where the vaccine is for prophylactic use, the human is preferably a child (e.g. a toddler or infant); where the vaccine is for therapeutic use, the human is preferably an adult. A vaccine intended for children may also be administered to adults e.g. to assess safety, dosage, immunogenicity, etc.
One way of checking efficacy of therapeutic treatment involves monitoring NTHi infection after administration of the composition of the invention. One way of checking efficacy of prophylactic treatment involves monitoring immune responses against an administered polypeptide after administration. Immunogenicity of compositions of the invention can be determined by administering them to test subjects (e.g. children 12-16 months age, or animal models [e.g. a chinchilla model [146]) and then determining standard parameters including ELISA titres (GMT) of IgG. These immune responses will generally be determined around 4 weeks after administration of the composition, and compared to values determined before administration of the composition.
Where more than one dose of the composition is administered, more than one post-administration determination may be made.
Administration of polypeptide antigens is a preferred method of treatment for inducing immunity. Administration of antibodies of the invention is another preferred method of treatment. This method of passive immunisation is particularly useful for newborn children or for pregnant women. This method will typically use monoclonal antibodies, which will be humanised or fully human.
Compositions of the invention will generally be administered directly to a patient. Direct delivery may be accomplished by parenteral injection (e.g. subcutaneously, intraperitoneally, intravenously, intramuscularly, or to the interstitial space of a tissue), or by rectal, oral, vaginal, topical, transdermal, intranasal, ocular, aural, pulmonary or other mucosal administration. Intramuscular administration to the thigh or the upper arm is preferred. Injection may be via a needle (e.g. a hypodermic needle), but needle-free injection may alternatively be used. A typical intramuscular dose is 0.5 ml.
The invention may be used to elicit systemic and/or mucosal immunity.
Dosage treatment can be a single dose schedule or a multiple dose schedule. Multiple doses may be used in a primary immunisation schedule and/or in a booster immunisation schedule. A primary dose schedule may be followed by a booster dose schedule. Suitable timing between priming doses (e.g. between 4-16 weeks), and between priming and boosting, can be routinely determined.
Bacterial infections affect various areas of the body and so compositions may be prepared in various forms. For example, the compositions may be prepared as injectables, either as liquid solutions or suspensions. Solid forms suitable for solution in, or suspension in, liquid vehicles prior to injection can also be prepared (e.g. a lyophilised composition). The composition may be prepared for topical administration e.g. as an ointment, cream or powder. The composition be prepared for oral administration e.g. as a tablet or capsule, or as a syrup (optionally flavoured). The composition may be prepared for pulmonary administration e.g. as an inhaler, using a fine powder or a spray. The composition may be prepared as a suppository or pessary. The composition may be prepared for nasal, aural or ocular administration e.g. as spray, drops, gel or powder [e.g. refs 101 & 102].
Combinations
Within the >2500 proteins described in the examples, NTH0861, NTH0863, NTH0865 and NTH0867 are particularly preferred for use with the invention (particularly in vaccines), and these four proteins can be used in combinations. Thus the invention provides a composition comprising: (a) a NTH0861 protein; and (b) at least one further NTHi protein. The invention also provides a composition comprising: (a) a NTH0863 protein; and (b) at least one further NTHi protein. The invention also provides a composition comprising: (a) a NTH0865 protein; and (b) at least one further NTHi protein. The invention also provides a composition comprising: (a) a NTH0867 protein; and (b) at least one further NTHi protein. The further NTHi protein can be selected from proteins of the invention as described above.
The combinations are preferably selected within these four proteins, and so the invention provides a composition comprising two or more (i.e. 2, 3 or 4) of NTH0861, NTH0863, NTH0865 and/or NTH0867. Preferred compositions comprise: (1) NTH0861 and NTH0863; (2) NTH0861 and NTH0865; (3) NTH0861 and NTH0867; (4) NTH0863 and NTH0865; (5) NTH0863 and NTH0867; (6) NTH0865 and NTH0867; (7) NTH0861, NTH0863 and NTH0865; (8) NTH0861, NTH0863 and NTH0867; (9) NTH0863, NTH0865 and NTH0867; (10) NTH0861, NTH0865 and NTH0867; (11) NTH0861, NTH0863, NTH0865 and NTH0867.
The NTH0861 protein preferably comprises SEQ ID NO: 1566, SEQ ID NO: 5095, or an amino acid sequence having sequence identity (as described above) to SEQ ID NO: 1566 and/or to SEQ ID NO: 5095. The NTH0863 protein preferably comprises SEQ ID NO: 1570, SEQ ID NO: 5094, or an amino acid sequence having sequence identity (as described above) to SEQ ID NO: 1570 and/or to SEQ ID NO: 5094. The NTH0865 protein preferably comprises SEQ ID NO: 1574, SEQ ID NO: 5093, or an amino acid sequence having sequence identity (as described above) to SEQ ID NO: 1574 and/or to SEQ ID NO: 5093. The NTH0867 protein preferably comprises SEQ ID NO: 1578, SEQ ID NO: 5092, or an amino acid sequence having sequence identity (as described above) to SEQ ID NO: 1578 and/or to SEQ ID NO: 5092.
Further Antigenic Components of Compositions of the Invention
The invention also provides a composition comprising a polypeptide or the invention and one or more of the following further antigens:

    
    
        a saccharide antigen from N. meningitidis serogroup A, C, W135 and/or Y (preferably all four), such as the oligosaccharide disclosed in ref. 103 from serogroup C [see also ref. 104] or the oligosaccharides of ref. 105.
        a saccharide antigen from Streptococcus pneumoniae [e.g. 106, 107, 108].
        an antigen from hepatitis A virus, such as inactivated virus [e.g. 109, 110].
        an antigen from hepatitis B virus, such as the surface and/or core antigens [e.g. 110, 111].
        a diphtheria antigen, such as a diphtheria toxoid [e.g. chapter 3 of ref. 112] e.g. the CRM197 mutant [e.g. 113].
        a tetanus antigen, such as a tetanus toxoid [e.g. chapter 4 of ref. 112].
        an antigen from Bordetella pertussis, such as pertussis holotoxin (PT) and filamentous haemagglutinin (FHA) from B. pertussis, optionally also in combination with pertactin and/or agglutinogens 2 and 3 [e.g. refs. 114 & 115].
        a saccharide antigen from Haemophilus influenzae B [e.g. 104].
        polio antigen(s) [e.g. 116, 117] such as IPV.
        measles, mumps and/or rubella antigens [e.g. chapters 9, 10 & 11 of ref. 112].
        influenza antigen(s) [e.g. chapter 19 of ref. 112], such as the haemagglutinin and/or neuraminidase surface proteins.
        an antigen from Moraxella catarrhalis [e.g. 118].
        an protein antigen from Streptococcus agalactiae (group B streptococcus) [e.g. 119, 120].
        a saccharide antigen from Streptococcus agalactiae (group B streptococcus).
        an antigen from Streptococcus pyogenes (group A streptococcus) [e.g. 120, 121, 122].
        an antigen from Staphylococcus aureus [e.g. 123].
    
    


The composition may comprise one or more of these further antigens.
Toxic protein antigens may be detoxified where necessary (e.g. detoxification of pertussis toxin by chemical and/or genetic means [115]).
Where a diphtheria antigen is included in the composition it is preferred also to include tetanus antigen and pertussis antigens. Similarly, where a tetanus antigen is included it is preferred also to include diphtheria and pertussis antigens. Similarly, where a pertussis antigen is included it is preferred also to include diphtheria and tetanus antigens. DTP combinations are thus preferred.
Saccharide antigens are preferably in the form of conjugates. Carrier proteins for the conjugates include diphtheria toxin, tetanus toxin, the N. meningitidis outer membrane protein [124], synthetic peptides [125,126], heat shock proteins [127,128], pertussis proteins [129,130], protein D from H. influenzae [131], cytokines [132], lymphokines [132], streptococcal proteins, hormones [132], growth factors [132], toxin A or B from C. difficile [133], iron-uptake proteins [134], etc. A preferred carrier protein is the CRM197 diphtheria toxoid [135].
Antigens in the composition will typically be present at a concentration of at least 1 μg/ml each. In general, the concentration of any given antigen will be sufficient to elicit an immune response against that antigen.
As an alternative to using proteins antigens in the immunogenic compositions of the invention, nucleic acid (preferably DNA e.g. in the form of a plasmid) encoding the antigen may be used.
Antigens are preferably adsorbed to an aluminium salt.
Screening Methods
The invention provides a process for determining whether a test compound binds to a polypeptide of the invention. If a test compound binds to a polypeptide of the invention and this binding inhibits the life cycle of the H. influenzae bacterium, then the test compound can be used as an antibiotic or as a lead compound for the design of antibiotics. The process will typically comprise the steps of contacting a test compound with a polypeptide of the invention, and determining whether the test compound binds to said polypeptide. Preferred polypeptides of the invention for use in these processes are enzymes (e.g. tRNA synthetases), membrane transporters and ribosomal polypeptides. Suitable test compounds include polypeptides, polypeptides, carbohydrates, lipids, nucleic acids (e.g. DNA, RNA, and modified forms thereof), as well as small organic compounds (e.g. MW between 200 and 2000 Da). The test compounds may be provided individually, but will typically be part of a library (e.g. a combinatorial library). Methods for detecting a binding interaction include NMR, filter-binding assays, gel-retardation assays, displacement assays, surface plasmon resonance, reverse two-hybrid etc. A compound which binds to a polypeptide of the invention can be tested for antibiotic activity by contacting the compound with GBS bacteria and then monitoring for inhibition of growth. The invention also provides a compound identified using these methods.
Preferably, the process comprises the steps of: (a) contacting a polypeptide of the invention with one or more candidate compounds to give a mixture; (b) incubating the mixture to allow polypeptide and the candidate compound(s) to interact; and (c) assessing whether the candidate compound binds to the polypeptide or modulates its activity.
Once a candidate compound has been identified in vitro as a compound that binds to a polypeptide of the invention then it may be desirable to perform further experiments to confirm the in vivo function of the compound in inhibiting bacterial growth and/or survival. Thus the method comprise the further step of contacting the compound with a NTHi bacterium and assessing its effect.
The polypeptide used in the screening process may be free in solution, affixed to a solid support, located on a cell surface or located intracellularly. Preferably, the binding of a candidate compound to the polypeptide is detected by means of a label directly or indirectly associated with the candidate compound. The label may be a fluorophore, radioisotope, or other detectable label.
General
The invention provides a computer-readable medium (e.g. a floppy disk, a hard disk, a CD-ROM, a DVD etc.) and/or a computer memory and/or a computer database containing one or more of the sequences in the sequence listing.
The term “comprising” encompasses “including” as well as “consisting” e.g. a composition “comprising” X may consist exclusively of X or may include something additional e.g. X+Y.
The term “about” in relation to a numerical value x means, for example, x±10%.
The word “substantially” does not exclude “completely” e.g. a composition which is “substantially free” from Y may be completely free from Y. Where necessary, the word “substantially” may be omitted from the definition of the invention.
The N-terminus residues in the amino acid sequences in the sequence listing are given as the amino acid encoded by the first codon in the corresponding nucleotide sequence. Where the first codon is not ATG, it will be understood that it will be translated as methionine when the codon is a start codon, but will be translated as the indicated non-Met amino acid when the sequence is at the C-terminus of a fusion partner. The invention specifically discloses and encompasses each of the amino acid sequences of the sequence listing having a N-terminus methionine residue (e.g. a formyl-methionine residue) in place of any indicated non-Met residue.
Alternative start codons can be used in biology. The amino acid sequences in the sequence listing are based on particular start codons, but downstream start codons may alternatively be used. Thus the invention specifically discloses and encompasses each of the amino acid sequences of the sequence listing, starting at any methionine residue from the sequence that is downstream of the N-terminal residue shown in the sequence listing (e.g. SEQ ID NOS: 5088, 5089 & 5090).
As indicated in the above text, nucleic acids and polypeptides of the invention may include sequences that:

    
    
        (a) are identical (i.e. 100% identical) to the sequences disclosed in the sequence listing;
        (b) share sequence identity with the sequences disclosed in the sequence listing;
        (c) have 1, 2, 3, 4, 5, 6, 7, 8, 9 or 10 single nucleotide or amino acid alterations (deletions, insertions, substitutions), which may be at separate locations or may be contiguous, as compared to the sequences of (a) or (b); and
        (d) when aligned with a particular sequence from the sequence listing using a pairwise alignment algorithm, a moving window of x monomers (amino acids or nucleotides) moving from start (N-terminus or 5′) to end (C-terminus of 3′), such that for an alignment that extends to p monomers (where p>x) there are p−x+1 such windows, each window has at least x·y identical aligned monomers, where: x is selected from 20, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 150, 200; y is selected from 0.50, 0.60, 0.70, 0.75, 0.80, 0.85, 0.90, 0.91, 0.92, 0.93, 0.94, 0.95, 0.96, 0.97, 0.98, 0.99; and if x·y is not an integer then it is rounded up to the nearest integer. The preferred pairwise alignment algorithm is the Needleman-Wunsch global alignment algorithm [136], using default parameters (e.g. with Gap opening penalty=10.0, and with Gap extension penalty=0.5, using the EBLOSUM62 scoring matrix). This algorithm is conveniently implemented in the needle tool in the EMBOSS package [137].
    
    


The nucleic acids and polypeptides of the invention may additionally have further sequences to the N-terminus/5′ and/or C-terminus/3′ of these sequences (a) to (d).
The practice of the present invention will employ, unless otherwise indicated, conventional methods of chemistry, biochemistry, molecular biology, immunology and pharmacology, within the skill of the art. Such techniques are explained fully in the literature. See, e.g., references 138-145, etc.
MODES FOR CARRYING OUT THE INVENTION
Genome sequencing has been carried out on a low-passage clinical NTHi isolate (strain 86-028NP [146]). A total of 2540 coding sequences were identified in the genome, and these are given in the sequence listing together with their inferred translation products. Annotation of 1489 of the polypeptide sequences is given in Table III. From the sequenced material, polypeptide-coding sequences of particular interest were selected for further work, with particular attention to immunogenic proteins for vaccine development.
Lipoproteins
Of the 2540 coding sequences, the following 39 were identified as lipoproteins: NTH0094, NTH10163, NTH0167, NTH0255, NTH0289, NTH-0838, NTH-0909, NTH0997, NTH1000, NTH1016, NTH11174, NTH1298, NTH1313, NIH1413, NIH1416, NTH1552, NTH1623, NIH1675, NIH1680, NTH1739, NTH1873, NTH1922, NTH1942, NIH1974, NTH2142, NTH2169, NTH2251, NTH2349, NTH2356, NTH2358, NTH2524, NTH2588, NTH2595, NTH2641, NTH2673, NTH2715, NIH2754, NTH2758, and NTH2769. Lipoproteins are surface-exposed and, as such, they represent accessible immunological targets e.g. for diagnostic and for immunisation purposes. Moreover, it has been found in B. burgdorferi [147] that OspA protein is immunogenic in a lipidated form but is non-immunogenic in a non-lipidated form, and the authors concluded that post-translational lipid attachment is a critical determinant of OspA immunogenicity.
Outer Membrane
As H. influenzae is a Gram-negative bacterium, its cell wall includes an outer membrane. Of the 2540 coding sequences, the following 48 were identified as being located in this outer membrane: NTH0017, NTH0193, NTH0227, NTH0241, NTH0252, NTH0270, NTH0432, NTH0498, NTH0502, NTH0504, NTH0512, NTH0539, NTH0638, NTH0647, NTH0648, NTH0788, NTH0839, NTH0867, NTH0914, NTH1054, NTH1075, NTH1082, NTH1200, NTH1203, NTH1214, NTH1290, NTH1390, NTH1582, NTH1652, NTH1666, NTH1744, NTH1819, NTH1845, NTH1900, NTH1953, NTH1956, NTH1958, NTH1962, NTH2039, NTH2232, NTH2234, NTH2235, NTH2269, NTH2448, NTH2484, NTH2493, and NTH2727. Outer membrane proteins (OMPs) are surface-exposed and, as such, they represent accessible immunological targets e.g. for diagnostic and for immunisation purposes. OMPs are often invasins, adhesins, etc. which, if blocked, offers a means of preventing bacterial infection.
NTH1845 is an Aida-like autotransporter (‘Lav’) and is a preferred protein of the invention. It is conserved between NTHi strains, including one known to cause meningitis, but there is no corresponding gene in the Rd sequence or in strain R2846. It lies between the tmk and holb genes. A preferred form of NTH1845 starts at Met-22 (i.e. SEQ ID NO: 5090).
Periplasm
As H. influenzae is a Gram-negative bacterium, it has a periplasm between its cell cytoplasmic membrane and its outer membrane. Of the 2540 coding sequences, the following 105 were identified as being located in the periplasm: NTH0014, NTH1049, NTH0057, NTH0059, NTH0106, NTH0119, NTH0120, NTH0132, NTH0174, NTH0190, NTH0206, NTH0244, NTH0346, NTH0405, NTH0421, NTH0468, NTH0485, NTH0513, NTH0547, NTH0619, NTH0643, NTH0661, NTH0691, NTH0738, NTH0820, NTH0835, NTH0848, NTH0849, NTH0856, NTH0861, NTH0863, NTH0865, NTH0910, NTH0926, NTH0961, NTH1015, NTH1018, NTH1121, NTH1164, NTH1185, NTH1190, NTH1261, NTH1268, NTH1301, NTH1311, NTH1388, NTH1394, NTH1406, NTH1407, NTH1414, NTH1435, NTH1468, NTH1541, NTH1570, NTH1600, NTH1601, NTH1619, NTH1622, NTH1724, NTH1745, NTH1773, NTH1781, NTH1798, NTH1807, NTH1829, NTH1865, NTH1871, NTH1892, NTH1897, NTH1916, NTH1917, NTH1965, NTH1999, NTH2116, NTH2119, NTH2133, NTH2135, NTH2149, NTH2150, NTH2187, NTH2217, NTH2227, NTH2256, NTH2258, NTH2277, NTH2291, NTH2316, NTH2342, NTH2344, NTH2369, NTH2394, NTH2432, NTH2434, NTH2451, NTH2496, NTH2508, NTH2537, NTH2541, NTH2572, NTH2575, NTH2610, NTH2705, NTH2726, NTH2738, and NTH2778. Periplasmic proteins represent useful immunological targets e.g. for diagnostic and for immunisation purposes.
Inner Membrane
As H. influenzae is a Gram-negative bacterium, it has an inner membrane. Of the 2540 coding sequences, the following 740 were identified as being located in the inner membrane: NTH0002, NTH0015, NTH0019, NTH0020, NTH0021, NTH0025, NTH0032, NTH0034, NTH0035, NTH0041, NTH0043, NTH0045, NTH0048, NTH0050, NTH0052, NTH0060, NTH0061, NTH0067, NTH0073, NTH0076, NTH0085, NTH0089, NTH0091, NTH0097, NTH0107, NTH0110, NTH0116, NTH0118, NTH0121, NTH0128, NTH0134, NTH0135, NTH0151, NTH0155, NTH0157, NTH0158, NTH0180, NTH0184, NTH0185, NTH0186, NTH0189, NTH0199, NTH0203, NTH0208, NTH0209, NTH0223, NTH0224, NTH0228, NTH0232, NTH0237, NTH0238, NTH0242, NTH0247, NTH0248, NTH0251, NTH0253, NTH0254, NTH0256, NTH0263, NTH0269, NTH0278, NTH0279, NTH0280, NTH0290, NTH0295, NTH0297, NTH0302, NTH0307, NTH0311, NTH0317, NTH0320, NTH0321, NTH0325, NTH0326, NTH0333, NTH0334, NTH0341, NTH0347, NTH0351, NTH0352, NTH0353, NTH0356, NTH0358, NTH0366, NTH0371, NTH0372, NTH0388, NTH0397, NTH0400, NTH0401, NTH0402, NTH0407, NTH0411, NTH0412, NTH0417, NTH0418, NTH0420, NTH0426, NTH0427, NTH0434, NTH0435, NTH0437, NTH0444, NTH0453, NTH0455, NTH0457, NTH0459, NTH0460, NTH0461, NTH0462, NTH0463, NTH0465, NTH0469, NTH0473, NTH0475, NTH0478, NTH0484, NTH0489, NTH0490, NTH0493, NTH0496, NTH0507, NTH0509, NTH0518, NTH0524, NTH0526, NTH0528, NTH0529, NTH0544, NTH0545, NTH0549, NTH0565, NTH0566, NTH0574, NTH0580, NTH0581, NTH0584, NTH0585, NTH0586, NTH0587, NTH0590, NTH0617, NTH0618, NTH0622, NTH0624, NTH0626, NTH0630, NTH0636, NTH0637, NTH0642, NTH0644, NTH0646, NTH0654, NTH0656, NTH0658, NTH0673, NTH0675, NTH0676, NTH0677, NTH0678, NTH0680, NTH01694, NTH0696, NTH0702, NTH0703, NTH0706, NTH0709, NTH0710, NTH0712, NTH0715, NTH0718, NTH0728, NTH0730, NTH0740, NTH0744, NTH0745, NTH0749, NTH0750, NTH0755, NTH0762, NTH0764, NTH0765, NTH0771, NTH0774, NTH0794, NTH0795, NTH0796, NTH0797, NTH0798, NTH0802, NTH0803, NTH0804, NTH0813, NTH0814, NTH0815, NTH0821, NTH0822, NTH0827, NTH0829, NTH0834, NTH0836, NTH850, NTH0851, NTH0852, NTH0858, NTH0872, NTH0874, NTH0875, NTH0880, NTH0887, NTH0888, NTH0894, NTH0904, NTH0913, NTH0927, NTH0928, NTH0941, NTH0948, NTH0949, NTH0950, NTH0952, NTH0953, NTH0955, NTH0964, NTH0968, NTH0973, NTH0986, NTH0987, NTH0989, NTH0994, NTH0996, NTH1002, NTH1003, NTH1004, NTH1005, NTH1009, NTH1010, NTH1012, NTH1020, NTH1021, NTH1026, NTH1028, NTH1031, NTH1032, NTH1037, NTH1039, NTH1042, NTH1043, NTH1048, NTH1052, NTH1058, NTH1063, NTH1064, NTH1069, NTH1073, NTH1080, NTH1083, NTH1084, NTH1085, NTH1086, NTH1087, NTH1089, NTH1090, NTH1091, NTH1092, NTH1098, NTH1102, NTH1103, NTH1104, NTH1106, NTH1123, NTH1124, NTH1125, NTH1130, NTH1138, NTH1141, NTH1150, NTH1151, NTH1178, NTH1181, NTH1184, NTH1188, NTH1189, NTH1191, NTH1192, NTH1193, NTH1201, NTH1205, NTH1216, NTH1220, NTH1221, NTH1224, NTH1225, NTH1226, NTH1229, NTH1230, NTH1231, NTH1233, NTH1234, NTH1236, NTH1238, NTH1240, NTH1241, NTH1250, NTH1252, NTH1254, NTH1255, NTH1256, NTH1262, NTH1273, NTH1275, NTH1279, NTH1280, NTH1281, NTH1282, NTH1283, NTH1286, NTH1287, NTH1293, NTH1295, NTH1297, NTH1300, NTH1302, NTH1305, NTH1306, NTH1307, NTH1308, NTH1309, NTH1315, NTH1319, NTH1321, NTH1327, NTH1332, NTH1334, NTH1336, NTH1337, NTH1341, NTH1346, NTH1348, NTH1354, NTH1357, NTH1359, NTH1363, NTH1365, NTH1368, NTH1374, NTH1376, NTH1379, NTH1380, NTH1383, NTH1391, NTH1393, NTH1398, NTH1400, NTH1411, NTH1412, NTH1420, NTH1421, NTH1425, NTH1427, NTH1428, NTH1429, NTH1430, NTH1431, NTH1434, NTH1437, NTH1438, NTH1439, NTH1447, NTH1448, NTH1450, NTH1454, NTH1455, NTH1464, NTH1467, NTH1470, NTH1471, NTH1472, NTH1473, NTH1474, NTH1479, NTH1491, NTH1492, NTH1493, NTH1495, NTH1500, NTH1503, NTH1506, NTH1510, NTH1515, NTH1525, NTH1526, NTH1527, NTH1528, NTH1531, NTH1532, NTH1537, NTH1538, NTH1540, NTH1548, NTH1559, NTH1562, NTH1567, NTH1569, NTH1573, NTH1575, NTH1581, NTH1584, NTH1586, NTH1587, NTH1588, NTH1590, NTH1594, NTH1597, NTH1599, NTH1602, NTH1605, NTH1606, NTH1608, NTH1609, NTH1617, NTH1618, NTH1620, NTH1621, NTH1625, NTH1629, NTH1631, NTH1634, NTH1637, NTH1638, NTH1653, NTH1654, NTH1657, NTH1662, NTH1664, NTH1668, NTH1671, NTH1686, NTH1687, NTH1688, NTH1689, NTH1690, NTH1692, NTH1693, NTH1698, NTH1701, NTH1707, NTH1712, NTH1718, NTH1719, NTH1722, NTH1725, NTH1729, NTH1732, NTH1735, NTH1760, NTH1767, NTH1770, NTH1778, NTH1779, NTH1782, NTH1783, NTH1788, NTH1793, NTH1795, NTH1796, NTH1799, NTH1803, NTH1805, NTH1806, NTH1813, NTH1815, NTH1820, NTH1824, NTH1828, NTH1835, NTH1836, NTH1842, NTH1849, NTH1850, NTH1859, NTH1861, NTH1870, NTH1872, NTH1881, NTH1882, NTH1885, NTH1888, NTH1889, NTH1891, NTH1896, NTH1898, NTH1899, NTH1906, NTH1908, NTH1919, NTH1923, NTH1925, NTH1927, NTH1935, NTH1939, NTH1941, NTH1951, NTH1960, NTH1963, NTH1966, NTH1967, NTH1968, NTH1978, NTH1981, NTH1986, NTH1992, NTH1993, NTH1995, NTH1996, NTH1997, NTH1998, NTH2001, NTH2005, NTH2008, NTH2009, NTH2010, NTH2024, NTH2025, NTH2038, NTH2040, NTH2041, NTH2043, NTH2050, NTH2052, NTH2055, NTH2060, NTH2062, NTH2064, NTH2065, NTH2070, NTH2071, NTH2073, NTH2078, NTH2079, NTH2081, NTH2083, NTH2089, NTH2091, NTH2092, NTH2093, NTH2094, NTH2095, NTH2096, NTH2097, NTH2099, NTH2101, NTH2112, NTH2115, NTH2118, NTH2120, NTH2122, NTH2126, NTH2128, NTH2129, NTH2130, NTH2131, NTH2136, NTH2138, NTH2145, NTH2146, NTH2162, NTH2163, NTH2166, NTH2169, NTH2170, NTH2173, NTH2181, NTH2183, NTH2191, NTH2193, NTH2195, NTH2196, NTH2200, NTH2204, NTH2205, NTH2209, NTH2213, NTH2226, NTH2228, NTH2231, NTH2242, NTH2243, NTH2247, NTH2250, NTH2253, NTH2257, NTH2259, NTH2262, NTH2263, NTH2266, NTH2273, NTH2274, NTH2282, NTH2284, NTH2285, NTH2288, NTH2292, NTH2296, NTH2299, NTH2318, NTH2323, NTH2324, NTH2326, NTH2327, NTH2333, NTH2343, NTH2346, NTH2347, NTH2352, NTH2361, NTH2364, NTH2365, NTH2368, NTH2370, NTH2371, NTH2376, NTH2377, NTH2381, NTH2382, NTH2388, NTH2398, NTH2402, NTH2405, NTH2406, NTH2407, NTH2408, NTH2414, NTH2422, NTH2430, NTH2433, NTH2438, NTH2447, NTH2455, NTH2457, NTH2458, NTH2472, NTH2478, NTH2481, NTH2486, NTH2495, NTH2497, NTH2498, NTH2499, NTH2501, NTH2505, NTH2525, NTH2531, NTH2532, NTH2533, NTH2534, NTH2542, NTH2543, NTH2545, NTH2546, NTH2548, NTH2549, NTH2550, NTH2552, NTH2554, NTH2556, NTH2557, NTH2558, NTH2562, NTH2566, NTH2567, NTH2568, NTH2569, NTH2570, NTH2573, NTH2577, NTH2578, NTH2587, NTH2591, NTH2593, NTH2597, NTH2600, NTH2602, NTH2603, NTH2604, NTH2605, NTH2612, NTH2613, NTH2615, NTH2616, NTH2618, NTH2626, NTH2633, NTH2640, NTH2647, NTH2648, NTH2649, NTH2650, NTH2661, NTH2663, NTH2664, NTH2667, NTH2668, NTH2674, NTH2675, NTH2680, NTH2690, NTH2701, NTH2702, NTH2703, NTH2708, NTH2711, NTH2724, NTH2725, NTH2732, NTH2735, NTH2740, NTH2743, NTH2749, NTH2750, NTH2755, NTH2756, NTH2757, NTH2764, NTH2765, NTH2774, NTH2777, NTH2779, NTH2781, NTH2793, NTH2794, NTH2796, NTH2797, NTH2798, NTH2806, NTH2807, NTH2813, NTH2814, NTH2823, and NTH2824. Inner membrane proteins represent useful immunological targets e.g. for diagnostic and for immunisation purposes.
Of these proteins, NTH1069 in particular has been identified as a virulence-associated protein. A preferred form of this protein starts at Met-27 (i.e. SEQ ID NO: 5088). Another preferred form starts at Met-19 (SEQ ID NO: 5089).
Adhesin
An adhesin having amino acid sequence SEQ ID NO: 5091 has been identified in a NTHi strain isolated from a patient with meningitis. It is homologous to the Hia adhesin from N. meningitidis. 
H. influenzae Rd
The genome sequence of the serotype d strain KW20 [1,3] was published in 1995. As serotype d strains are generally not pathogens, but the sequenced NTHi strain is from a clinical infection, expressed NTHi sequences that are not seen in serotype d are likely to be the proteins that are involved in pathogenic mechanisms. Blocking these proteins, either by antibiotic treatment or by antibody binding, thus has therapeutic potential. Of the 2540 coding sequences, the following 613 are not seen in the Rd genome: NTH0001, NTH0002, NTH0004, NTH0005, NTH0012, NTH0016, NTH0021, NTH0022, NTH0024, NTH0032, NTH0033, NTH0034, NTH0035, NTH0036, NTH0037, NTH0038, NTH0040, NTH0045, NTH0050, NTH0051, NTH0052, NTH0053, NTH0064, NTH0089, NTH0092, NTH0097, NTH0101, NTH0104, NTH0110, NTH0114, NTH0122, NTH0123, NTH0124, NTH0125, NTH0129, NTH0135, NTH0136, NTH0138, NTH0140, NTH0146, NTH0148, NTH0151, NTH0153, NTH0154, NTH0159, NTH0161, NTH0164, NTH0169, NTH0173, NTH0176, NTH0177, NTH0187, NTH0191, NTH0192, NTH0193, NTH0194, NTH0195, NTH0197, NTH0198, NTH0199, NTH0226, NTH0235, NTH0236, NTH0238, NTH0250, NTH0251, NTH0254, NTH0255, NTH0256, NTH0264, NTH0265, NTH0278, NTH0279, NTH0280, NTH0282, NTH0283, NTH0284, NTH0285, NTH0289, NTH0297, NTH0298, NTH0299, NTH0300, NTH0302, NTH0307, NTH0308, NTH0312, NTH0313, NTH0319, NTH0327, NTH0328, NTH0331, NTH0334, NTH0335, NTH0339, NTH0341, NTH0348, NTH0363, NTH0371, NTH0375, NTH0378, NTH0379, NTH0384, NTH0385, NTH0396, NTH0407, NTH0408, NTH0411, NTH0417, NTH0419, NTH0420, NTH0424, NTH0429, NTH0430, NTH0431, NTH0432, NTH0433, NTH0434, NTH0435, NTH0438, NTH0455, NTH0478, NTH0484, NTH0485, NTH0486, NTH0487, NTH0488, NTH0489, NTH0498, NTH0500, NTH0501, NTH0506, NTH0509, NTH0510, NTH0511, NTH0520, NTH0523, NTH0526, NTH0527, NTH0531, NTH0534, NTH0536, NTH0539, NTH0559, NTH0561, NTH0573, NTH0577, NTH0579, NTH0580, NTH0581, NTH0582, NTH0583, NTH0584, NTH0585, NTH0586, NTH0588, NTH0599, NTH0603, NTH0604, NTH0606, NTH0615, NTH0617, NTH0631, NTH0637, NTH0644, NTH0645, NTH0653, NTH0662, NTH0663, NTH0664, NTH0667, NTH0668, NTH0673, NTH0677, NTH0680, NTH0681, NTH0683, NTH0687, NTH0690, NTH0691, NTH0692, NTH0694, NTH0695, NTH0696, NTH0706, NTH0707, NTH0711, NTH0715, NTH0716, NTH0717, NTH0721, NTH0724, NTH0725, NTH0726, NTH0728, NTH0729, NTH0730, NTH0749, NTH0752, NTH0756, NTH0768, NTH0776, NTH0792, NTH0797, NTH0818, NTH0827, NTH0832, NTH0839, NTH0841, NTH0843, NTH0844, NTH0862, NTH0864, NTH0866, NTH0867, NTH0877, NTH0879, NTH0885, NTH0886, NTH0892, NTH0895, NTH0896, NTH0900, NTH0901, NTH0904, NTH0906, NTH0921, NTH0924, NTH0928, NTH0929, NTH0930, NTH0931, NTH0932, NTH0933, NTH0937, NTH0938, NTH0942, NTH0949, NTH0953, NTH0955, NTH0961, NTH0964, NTH0970, NTH0971, NTH0972, NTH0973, NTH0985, NTH0987, NTH0991, NTH0992, NTH0993, NTH0994, NTH0995, NTH0996, NTH1007, NTH1016, NTH1017, NTH1020, NTH1025, NTH1026, NTH1027, NTH1028, NTH1029, NTH1037, NTH1040, NTH1049, NTH1067, NTH1069, NTH1070, NTH1073, NTH1082, NTH1086, NTH1089, NTH1090, NTH1108, NTH1111, NTH1112, NTH1114, NTH1115, NTH1116, NTH1122, NTH1129, NTH1131, NTH1142, NTH1149, NTH1150, NTH1153, NTH1157, NTH1159, NTH1161, NTH1162, NTH1176, NTH1178, NTH1179, NTH1193, NTH1195, NTH1196, NTH1204, NTH1205, NTH1207, NTH1208, NTH1209, NTH1210, NTH1211, NTH1214, NTH1216, NTH1220, NTH1225, NTH1234, NTH1235, NTH1237, NTH1241, NTH1244, NTH1245, NTH1246, NTH1247, NTH1248, NTH1249, NTH1250, NTH1251, NTH1252, NTH1253, NTH1270, NTH1271, NTH1294, NTH1299, NTH1313, NTH1315, NTH1316, NTH1325, NTH1330, NTH1333, NTH1337, NTH1339, NTH1342, NTH1353, NTH1361, NTH1367, NTH1374, NTH1375, NTH1381, NTH1382, NTH1390, NTH1391, NTH1395, NTH1396, NTH1399, NTH1414, NTH1415, NTH1418, NTH1419, NTH1437, NTH1441, NTH1454, NTH1456, NTH1471, NTH1474, NTH1487, NTH1489, NTH1490, NTH1491, NTH1492, NTH1493, NTH1494, NTH1495, NTH1496, NTH1497, NTH1504, NTH1516, NTH1540, NTH1543, NTH1555, NTH1563, NTH1564, NTH1567, NTH1571, NTH1573, NTH1574, NTH1580, NTH1587, NTH1598, NTH1599, NTH1600, NTH1601, NTH1602, NTH1603, NTH1605, NTH1606, NTH1607, NTH1611, NTH1612, NTH1615, NTH1616, NTH1626, NTH1627, NTH1628, NTH1647, NTH1656, NTH1657, NTH1658, NTH1676, NTH1677, NTH1687, NTH1697, NTH1702, NTH1703, NTH1713, NTH1734, NTH1740, NTH1742, NTH1744, NTH1745, NTH1748, NTH1749, NTH1751, NTH1752, NTH1753, NTH1754, NTH1755, NTH1756, NTH1757, NTH1758, NTH1759, NTH1760, NTH1765, NTH1769, NTH1770, NTH1778, NTH1798, NTH1804, NTH1811, NTH1812, NTH1815, NTH1816, NTH1817, NTH1818, NTH1820, NTH1821, NTH1822, NTH1829, NTH1832, NTH1833, NTH1837, NTH1842, NTH1845, NTH1854, NTH1857, NTH1904, NTH1910, NTH1914, NTH1916, NTH1920, NTH1921, NTH1922, NTH1945, NTH1946, NTH1947, NTH1948, NTH1956, NTH1962, NTH1964, NTH1968, NTH1989, NTH1994, NTH2019, NTH2031, NTH2035, NTH2043, NTH2056, NTH2060, NTH2069, NTH2075, NTH2093, NTH2096, NTH2109, NTH2110, NTH2112, NTH2113, NTH2114, NTH2117, NTH2156, NTH2159, NTH2170, NTH2197, NTH2198, NTH2199, NTH2206, NTH2207, NTH2216, NTH2217, NTH2219, NTH2220, NTH2221, NTH2222, NTH2223, NTH2226, NTH2229, NTH2245, NTH2273, NTH2284, NTH2287, NTH2305, NTH2309, NTH2315, NTH2316, NTH2323, NTH2326, NTH2330, NTH2332, NTH2343, NTH2349, NTH2353, NTH2362, NTH2363, NTH2364, NTH2386, NTH2414, NTH2442, NTH2451, NTH2455, NTH2456, NTH2457, NTH2458, NTH2460, NTH2461, NTH2463, NTH2464, NTH2466, NTH2467, NTH2468, NTH2471, NTH2480, NTH2481, NTH2482, NTH2483, NTH2484, NTH2485, NTH2486, NTH2487, NTH2488, NTH2500, NTH2510, NTH2524, NTH2525, NTH2527, NTH2528, NTH2536, NTH2537, NTH2549, NTH2562, NTH2563, NTH2572, NTH2573, NTH2575, NTH2584, NTH2585, NTH2590, NTH2604, NTH2607, NTH2608, NTH2609, NTH2635, NTH2647, NTH2648, NTH2650, NTH2655, NTH2664, NTH2668, NTH2679, NTH2684, NTH2693, NTH2694, NTH2696, NTH2697, NTH2703, NTH2704, NTH2706, NTH2707, NTH2708, NTH2709, NTH2710, NTH2711, NTH2712, NTH2713, NTH2715, NTH2716, NTH2718, NTH2719, NTH2720, NTH2721, NTH2723, NTH2724, NTH2725, NTH2726, NTH2727, NTH2729, NTH2730, NTH2731, NTH2737, NTH2744, NTH2753, NTH2778, NTH2781, NTH2783, NTH2784, NTH2785, NTH2791, NTH2804, NTH2806, NTH2809, NTH2810, and NTH2816.
NTH0861 to NTH0867
Protein NMB0419 from Neisseria meningitidis has been found to participate in the meningococcal invasion mechanism [2]. The protein was shown to modulate bacterial interaction with monolayers of human repiratory epithelial cells, promoting invasion. A homologous protein BPF001 is seen in H. influenzae biogroup aegyptius, but study of this protein was not possible.
The NTHi genome includes a region (SEQ ID NO: 5081) encoding a string of four polypeptides (NTH0861, NTH0863, NTH0865 and NTH0867) with strong similarity to NMB0419. This region and the four polypeptides are shown below:








GCCAGCTTGCTGCCTGCGGTCGACTCTANGAGACCCCTACAACAAAACATAATGCTAAAC



 


AAAAAATGTTTGGTTGTTTCAATTGTTGATTAATAAATGGACGATTTCTATGCGATTCAC


                     (SEQ ID NO: 1578) NTH0867   M  R  F  T


 


AAAAACACTTTTTACCACCGCACTTTTAGGTGCTTCTATCTTTTCTTTTCAATCCACCGC


 K  T  L  F  T  T  A  L  L  G  A  S  I  F  S  F  Q  S  T  A


 


TTGGGCGGATACGCTGGAACAGCAATTCCAACAAGGTTCTGAAGCCACTACGAGAGGCGA


 W  A  D  T  L  E  Q  Q  F  Q  Q  G  S  E  A  T  T  R  G  D


 


TTATCAAACCACCTTTAAATTTTTGTTACCTCTGGCGGAGCAGGGAAATGCAGAGGCTCA


 Y  Q  T  T  F  K  F  L  L  P  L  A  E  Q  G  N  A  E  A  Q


 


ATTGATGTTGGGCGTGATGTATGCAAGAGGAATAGGCGTCAAACAAGATGATTTTGAAGC


 L  M  L  G  V  M  Y  A  R  G  I  G  V  K  Q  D  D  F  E  A


 


GGTGAAGTGGTATCGCCAAGCGGCGGAGCAGGGATATGCAAATGCTCAAGCTATATTGGG


 V  K  W  Y  R  Q  A  A  E  Q  G  Y  A  N  A  Q  A  I  L  G


 


ATTCTCATATCTTTTAGGACAAAGCGGTGTTCAAGTAAATAAATCTTTAGCCAAAGAATG


 F  S  Y  L  L  G  Q  S  G  V  Q  V  N  K  S  L  A  K  E  W


 


GTTTGGTAAGGCTTGTGATAATGGTGATCAAAATGGTTGCGAATATTATGGCAAGTTAAA


 F  G  K  A     D  N  G  D  Q  N  G     E  Y  Y  G  K  L  N


 


TAGAGGGGAGCTCTAATGCCAACTTTACAATGCGAATTTTGGAATGTAGGGCAAGGGTTA


 R  G  E  L  *


 


TTTTCAAGTGGGCGTATTCAAATGGGAGACGCCCCAGCCTTTCATTGGGTTTATGGTTTG


 


CAAGTTCCTCATCATGGTTCAAAGCCAATTTTAGTGAATAAAAATAAAAGATTATCCATT


 


CATTCAATTTAATAGGAAAACAAATGAAACTCACAAAAACACTTCTTACCACCGCACTTT


(SEQ ID NO: 1574) 



            NTH0865    M  K  L  T  K  T  L  L  T  T  A  L  F



 


TCGGTGCTTCTATTTTTTCTTTTCAATCCACCGCTTGGGCGGATACGCCGGAACAGCAAT


  G  A  S  I  F  S  F  Q  S  T  A  W  A  D  T  P  E  Q  Q  F


 


TCCAACAAGGTTTAACCGCTTATGAGCAAAGCAACTATCAAACCGCCTTTAAACTTTGGT


  Q  Q  G  L  T  A  Y  E  Q  S  N  Y  Q  T  A  F  K  L  W  L


 


TACCTCTGGCGGAGCAGGGAGATGCACAGGCTCAAGGTGGTTTGGGCATGATGTATGAAA


  P  L  A  E  Q  G  D  A  Q  A  Q  G  G  L  G  M  M  Y  E  R


 


GAGGACTTGGCGTAAAACAAGAT CAAAGCAGTGAACTGGTATCGCAAAGCGGCGG


  G  L  G  V  K  Q  D  D  F  K  A  V  N  W  Y  R  K  A  A  R


 


AGCAGGGGGATGCAGATGCTCAATTAAATTTGGGTGCGATGTATGCAATCGGACGTGGCG


  Q  G  D  A  D  A  Q  L  N  L  G  A  M  Y  A  I  G  R  G  V


 


TAAAACAAGATGGTGT GGTGAAGTGGTTTCGCAAAGCGGCAGAGCAGGGAAATG


  K  Q  D  G  V  E  A  V  K  W  F  R  K  A  A  E  Q  G  N  A


 


CAAAGGCTCAAAATGGTTTGGGCATGATGTATGACGGAGGACTTGGCATAAAACAAGATT


  K  A  Q  N  G  L  G  M  M  Y  D  G  G  L  G  I  K  Q  D  Y


 


ATTTCAAAGCGGTGAAATGGCATCGCAAAGCGGCGGAGCAGGGATATGGAGGTGCTCAAG


  F  K  A  V  K  W  H  R  K  A  A  E  Q  G  Y  G  G  A  Q  V


 


TTATGTTGGGATTCTCATATCTTTCGGGAAAAGGTGTTCAAGTAAATAAATCTTTAGCCA


  M  L  G  F  S  Y  L  S  G  K  G  V  Q  V  N  K  S  L  A  K


 


AAGAATGGTTTGGTAAGGCTTGTGATAATGGTGAACAAGTGGGTTGTGAATATTATGGCA


  E  W  F  G  K  A     D  N  G  E  Q  V  G     E  Y  Y  G  K


 


AGCTAAATAGAGGGGAACGCTAATGCCAACTTTACAATGCGAATTTTGGAATGTAGGGCA


  L  N  R  G  E  R  *


 


AGGGTTATTTTCAAGTGGGCGTATTCAAATGGGAGACGCCCAAGCCTTTCATTGGGTTTA


 


TGGTTTGCAAGTTCCTCATCATGGTTCAAAGCCAATTTTAGTGAATAAAAATAAAAGATT


 


ATCCATTCATTCAATTTAATAGGAAAACAAA AAACTCACAAAAACACTTCTTACCAC


  (SEQ ID NO: 1570) NTH0863    M  K  L  T  K  T  L  L  T  T


 


CGCACTTTTCGGTGCTTCTGTATTTTCTTTTCAATCCACCGCTTGGGCGGATACGCTGGA


 A  L  F  G  A  S  V  F  S  F  Q  S  T  A  W  A  D  T  L  E


 


ACAGCAATTCCAACAAGGTTTAACCGCTTATGAGCAAAGCAACTATCAAACCGCCTTTAA


 Q  Q  F  Q  Q  G  L  T  A  Y  E  Q  S  N  Y  Q  T  A  F  K


 


ACTTTGGTTACCTATGGCAGAGCAGGGATATGCAAAGGCTCAATTTAATTTGGGCGTGAT


 L  W  L  P  M  A  E  Q  G  Y  A  K  A  Q  F  N  L  G  V  M


 


GTATGCTAAGGGGCAAGGCGTCAAACAAGATG TGAAGCGGTGAAGTGGTTTCGCAA


 Y  A  K  G  Q  G  V  K  Q  D  D  F  E  A  V  K  W  F  R  K


 


AGCGGCGGAGCAGGGATATGCAGAGGCTAAATTTAATTTGGGCCATATGTATTCTAAGGG


 A  A  E  Q  G  Y  A  E  A  K  F  N  L  G  H  M  Y  S  K  G


 


ACGAGGCGTCAAACAAGATGATTTTGAAGCAGTGAACTGGTATCGCAAAGCGGCGGAGCA


 R  G  V  K  Q  D  D  F  E  A  V  N  W  Y  R  K  A  A  E  Q


 


GGGAGATGCAGATGCTCAAGCTATATTGGGATTCTTATATCTTTTAGGAGAAAGAGGTGT


 G  D  A  D  A  Q  A  I  L  G  F  L  Y  L  L  G  E  R  G  V


 


CAAGTAAATAATTCTTTAGCCAAGNAATGGTNTGGTAAGGCTTGTGATAATGGTAATCAA


 K  *


 


AATGGCTGCGAATATTATGGCAAGCTAAATAGAGGGGAGCTCTAATGCCCACTTTTACAA


 


TGCGAATTNTGGAATGTAGGGCAAGGGTTATTTTCAAGTGGGCGTATTCAAGTGGAGACG


 


CNNCCAAGCCTTTCATTGGGTTTATGGTTTGCAAGTTCCTCATCATGGTTCANAGCCCAA


 


TTTAGTGNAATAAAAATAAAAGATTATCCATTCATTCAATTTAATAGGAAAACAAAATGA


                              (SEQ ID NO: 1566) NTH0861 M  K


 


AACTCACAAAAACACTTCTTACCACCGCACTTTTAGGTGCTTCTGTATTATCTTTTCAAT


  L  T  K  T  L  L  T  T  A  L  L  G  A  S  V  L  S  F  Q  S


 


CCACCGCTTGGGCGGATACGCTGGAACAGCAATTCCAACAAGGTTTAACCGCTTATGAGC


  T  A  W  A  D  T  L  E  Q  Q  F  Q  Q  G  L  T  A  Y  E  Q


 


AAAGCAACTATCAAACCGCCTTTAAACTTTGGTTACCTCTGGCGGAGCAGGGAGATGCAA


  S  N  Y  Q  T  A  F  K  L  W  L  P  L  A  E  Q  G  D  A  N


 


ATGTTCAATTTAATTTGGGCGTGATGTATGCTGAGGGGCAAGGCGTCAAACAAGATGATT


  V  Q  F  N  L  G  V  M  Y  A  E  G  Q  G  V  K  Q  D  D  F


 


TTGAAGCGGTGAAATGGTATCGCAAAGCGGCGGAGCAGGGAGATGCAAATGCTCAGGCTT


  E  A  V  K  W  Y  R  K  A  A  E  Q  G  D  A  N  A  Q  A  Y


 


ATTTAGGTTTGGCTTATACTGAAGGGCGTGGTGTAAGACAAGATTATACCGAAGCGGTGA


  L  G  L  A  Y  T  E  G  R  G  V  R  Q  D  Y  T  E  A  V  K


 


AGTGGTTTCGCAAAGCGGCGGAGCAGGGACATGCAAATGCTCAAGCTATATGGGATCTCT


  W  F  R  K  A  A  E  Q  G  H  A  N  A  Q  A  I  W  D  L  F


 


TTCTTTAGGGTACCGAGCCGAATCGATCCA


  L  *






The four coding sequences are aligned (ClustalW) below:









NTH0863
ATGAAACTCACAAAAACACTTCTTACCACCGCACTTTTCGGTGCTTCTGTATTTTCTTTT



 


NTH0867
ATGCGATTCACAAAAACACTTTTTACCACCGCACTTTTAGGTGCTTCTATCTTTTCTTTT


 


NTH0865
ATGAAACTCACAAAAACACTTCTTACCACCGCACTTTTCGGTGCTTCTATTTTTTCTTTT


 


NTH0861
ATGAAACTCACAAAAACACTTCTTACCACCGCACTTTTAGGTGCTTCTGTATTATCTTTT



***  * ************** **************** ********* * ** ******


 


NTH0863
CAATCCACCGCTTGGGCGGATACGCTGGAACAGCAATTCCAACAAGGTTTAACCGCTTAT


 


NTH0867
CAATCCACCGCTTGGGCGGATACGCTGGAACAGCAATTCCAACAAGGTTCTGAAGCCACT


 


NTH0865
CAATCCACCGCTTGGGCGGATACGCCGGAACAGCAATTCCAACAAGGTTTAACCGCTTAT


 


NTH0861
CAATCCACCGCTTGGGCGGATACGCTGGAACAGCAATTCCAACAAGGTTTAACCGCTTAT



************************* ***********************     **   *


 


NTH0863
GAGCAAAGCAACTATCAAACCGCCTTTAAACTTTGGTTACCTATGGCAGAGCAGGGATAT


 


NTH0867
ACGAGAGGCGATTATCAAACCACCTTTAAATTTTTGTTACCTCTGGCGGAGCAGGGAAAT


 


NTH0865
GAGCAAAGCAACTATCAAACCGCCTTTAAACTTTGGTTACCTCTGGCGGAGCAGGGAGAT


 


NTH0861
GAGCAAAGCAACTATCAAACCGCCTTTAAACTTTGGTTACCTCTGGCGGAGCAGGGAGAT



  *  * ** * ********* ******** *** ******* **** ********* **


 


NTH0863
GCAAAGGCTCAATTTAATTTGGGCGTGATGTATGCTAAGGGGCAAGGCGTCAAACAAGAT


 


NTH0867
GCAGAGGCTCAATTGATGTTGGGCGTGATGTATGCAAGAGGAATAGGCGTCAAACAAGAT


 


NTH0865
GCACAGGCTCAAGGTGGTTTGGGCATGATGTATGAAAGAGGACTTGGCGTAAAACAAGAT


 


NTH0861
GCAAATGTTCAATTTAATTTGGGCGTGATGTATGCTGAGGGGCAAGGCGTCAAACAAGAT



*** * * ****      ****** *********     **    ***** *********


 


NTH0863
GATTT-------------------------------------------------------


 


NTH0867
GATTT-------------------------------------------------------


 


NTH0865
GATTTCAAAGCAGTGAACTGGTATCGCAAAGCGGCGGAGCAGGGGGATGCAGATGCTCAA


 


NTH0861
GATTT-------------------------------------------------------



*****


 


NTH0863
-----------------------------------------------------TGAAGCG


 


NTH0867
-----------------------------------------------------TGAAGCG


 


NTH0865
TTAAATTTGGGTGCGATGTATGCAATCGGACGTGGCGTAAAACAAGATGGTGTTGAAGCG


 


NTH0861
-----------------------------------------------------TGAAGCG



                                                     *******


 


NTH0863
GTGAAGTGGTTTCGCAAAGCGGCGGAGCAGGGATATGCAGAGGCTAAATTTAATTTGGGC


 


NTH0867
GTGAAGTGGTATCGCCAAGCGGCGGAGCAGGGATATGCAAA-------------------


 


NTH0865
GTGAAGTGGTTTCGCAAAGCGGCAGAGCAGGGAAATGCAAAGGCTCAAAATGGTTTGGGC


 


NTH0861
GTGAAATGGTATCGCAAAGCGGCGGAGCAGGGAGATGCAAA-------------------



***** **** **** ******* ********* ***** *


 


NTH0863
CATATGTATTCTAAGGGACGAGGCGTCAAACAAGATGATTTTGAAGCAGTGAACTGGTAT


 


NTH0867
------------------------------------------------------------


 


NTH0865
ATGATGTATGACGGAGGACTTGGCATAAAACAAGATTATTTCAAAGCGGTGAAATGGCAT


 


NTH0861
------------------------------------------------------------


 


NTH0863
CGCAAAGCGGCGGAGCAGGGAGATGCAGATGCTCAAGCTATATTGGGATTCTTATATCTT


 


NTH0867
-----------------------------TGCTCAAGCTATATTGGGATTCTCATATCTT


 


NTH0865
CGCAAAGCGGCGGAGCAGGGATATGGAGGTGCTCAAGTTATGTTGGGATTCTCATATCTT


 


NTH0861
-----------------------------TGCTCAGGCTTATTTAGGTTTGGCTTATACT



                             ****** * *   ** ** **    ***  *


 


NTH0863
TTAGGAGAAAGAGGTGT-CAAGTAAATAATTCTTTAGCCAAGNAATGGTNTGGTAAGGCT


 


NTH0867
TTAGGACAAAGCGGTGTTCAAGTAAATAAATCTTTAGCCAAAGAATGGTTTGGTAAGGCT


 


NTH0865
TCGGGAAAA---GGTGTTCAAGTAAATAAATCTTTAGCCAAAGAATGGTTTGGTAAGGCT


 


NTH0861
GAAGGGCGT---GGTGTAAGACAAGATTATACCGAAGCGGTGAAGTGGTTTCGCAAAGC-



   **       *****   *  * ** *  *   ***     * **** * * ** **


 


NTH0863
TGTGATAATGGTAATCAAAATGGCTGCGAATATTATGGCAAGCTAAATAGAGGGGAGCTC


 


NTH0867
TGTGATAATGGTGATCAAAATGGTTGCGAATATTATGGCAAGTTAAATAGAGGGGAGCTC


 


NTH0865
TGTGATAATGGTGAACAAGTGGGTTGTGAATATTATGGCAAGCTAAATAGAGGGGAACGC


 


NTH0861
---------GGCGGAGCAGGGACATGCAAATGCT----CAAGCTATAT----GGGATCTC



         **      *      **  ***  *    **** ** **    **** * *


 


NTH0863
TAATGCCCACTTTTACAATGCGAATTNTGGAATGTAGGGCAAGGGTTATTTTCAAGTGGG


 


NTH0867
TAATGCCAACTTT-ACAATGCGAATTTTGGAATGTAGGGCAAGGGTTATTTTCAAGTGGG


 


NTH0865
TAATGCCAACTTT-ACAATGCGAATTTTGGAATGTAGGGCAAGGGTTATTTTCAAGTGGG


 


NTH0861
TTTCTTTAGGGTA-CCGAGCCGAATC----GATCCA------------------------



*          *   * *  *****      **  *


 


NTH0863
CGTATTCAAGTGGAGACGCNNCCAAGCCTTTCATTGGGTTTATGGTTTGCAAGTTCCTCA


 


NTH0867
CGTATTCAAATGG-GAGACGCCCCAGCCTTTCATTGGGTTTATGGTTTGCAAGTTCCTCA


 


NTH0865
CGTATTCAAATGG-GAGACGCCCAAGCCTTTCATTGGGTTTATGGTTTGCAAGTTCCTCA


 


NTH0861
------------------------------------------------------------


 


NTH0863
TCATGGTTCANAGCCCAATTTAGTGNAATAAAAATAAAAGATTATCCATTCATTCAATTT


 


NTH0867
TCATGGTTCAAAGCCAATTTTAGTGAA-TAAAAATAAAAGATTATCCATTCATTCAATTT


 


NTH0865
TCATGGTTCAAAGCCAATTTTAGTGAA-TAAAAATAAAAGATTATCCATTCATTCAATTT


 


NTH0861
------------------------------------------------------------


 








SEQ ID NO: 5083










NTH0863
AATAGGAAAACAAA



 








SEQ ID NO: 5085










NTH0867
AATAGGAAAACAA-



 








SEQ ID NO: 5084










NTH0865
AATAGGAAAACAAA



 








SEQ ID NO: 5082










NTH0861
--------------







The encoded polypeptides are aligned below, together with the bpf001 and NMB0419 sequences:









NTH0861
------------MKLTKTLLTTALLG---------ASVLSFQS---TAWADTLEQQFQQG



 


NTH0863
------------MKLTKTLLTTALFG---------ASVFSFQS---TAWADTLEQQFQQG


 


NTH0865
------------MKLTKTLLTTALFG---------ASIFSFQS---TAWADTPEQQFQQG


 


NTH0867
------------MRFTKTLFTTALLG---------ASIFSFQS---TAWADTLEQQFQQG


 


BPF001
------------MKLTKTLFTSALLG---------ASILSFHP---TVAAMDFGT--QVG


 


NMB0419
------------MKQTVKWLAAALIALGLNRAVWADDVSDFRENLQAAAQGNAAAQYNLG



            *: * . :::**:.          .: .*:    :.         : *


 


NTH0861
LTAYE----QSNYQTAFKLWLPLAEQ-GDANVQFNLGVMYAEGQGVKQDDFEAVKWYRKA


 


NTH0863
LTAYE----QSNYQTAFKLWLPMAEQ-GYAKAQFNLGVMYAKGQGVKQDDFEAVKWFRKA


 


NTH0865
LTAYE----QSNYQTAFKLWLPLAEQ-GDAQAQGGLGMMYERGLGVKQDDFKAVNWYRKA


 


NTH0867
SEATT----RGDYQTTFKFLLPLAEQ-GNAEAQLMLGVMYARGIGVKQDDFEAVKWYRQA


 


BPF001
IDAYR----KNDFAQAAEQFKDAGIVRGDPTAQLFLGRMYYNGEFFKQDYVEAAKWYRKA


 


NMB0419
AMYYKGRGVRRDDAEAVRWYRQAAEQ-GLAQAQYNLGWMYANGRGVRQDDTEAVRWYRQA



         : :   : .     .   * . .*  ** ** .*  .:**  :*..*:*:*


 


NTH0861
AEQG--------------------------------------------------------


 


NTH0863
AEQG--------------------------------------------------------


 


NTH0865
AEQGDADAQLNLGAMYAIGRGVKQDGVEAVKWFRKAAEQGNAKAQNGLGMMYDGGLGIKQ


 


NTH0867
AEQG--------------------------------------------------------


 


BPF001
AEQGEEFGLLFLG------------------------------------ETYEDGEGVEK


 


NMB0419
AAQGVVQAQYNLG------------------------------------VIYAEGRGVRQ



* **


 


NTH0861
----------------DANAQAYLGLAYTEGR-GVRQDYTEAVKWFRKAAEQGHANAQAI


 


NTH0863
----------------YAEAKFNLGHMYSKGR-GVKQDDFEAVNWYRKAAEQGDADAQAI


 


NTH0865
DYFKAVKWHRKAAEQGYGGAQVMLGFSYLSGK-GVQVNKSLAKEWFGKACDNGEQVGCEY


 


NTH0867
----------------YANAQAILGFSYLLGQSGVQVNKSLAKEWFGKACDNGDQNGCEY


 


BPF001
DYAEAAKLYRKAAEQGSAEGQMALGKMYRFGN-GVEKDYAEAIKLYRKSAEQGNFTALFF


 


NMB0419
DDVEAVRWFRQAAAQGVAQAQNNLGVMYAERR-GVRQDRALAQEWFGKACQNGDQDGCDN



                 . .:  **  *   . **. :   * : : *:.::*.  .


 








SEQ ID NO: 1566










NTH0861
WDLFL-----------------



 








SEQ ID NO: 1570










NTH0863
LGFLYLLGERGVK---------



 








SEQ ID NO: 1574










NTH0865
YGKLNR-GER------------



 








SEQ ID NO: 1578










NTH0867
YGKLNR-GEL------------



 








SEQ ID NO: 5086










BPF001
LGEMYDNGVGVKQNKAESQRII



 








SEQ ID NO: 5087










NMB0419
DQRLKAGY--------------




   :






The serial repeats of four closely-related genes that are also related to genes involved in bacterial invasion is noteworthy, and NTH0861, NTH0863, NTH0865 and NTH0867 are of particular interest for immunisation purposes. NTH0867 in particular is an outer-membrane protein that is not seen in the Rd genome, and is of special interest.
Moreover, as well as being caused by NTHi, acute otitis media is often caused by Moraxella catarrhalis and Streptococcus pneumoniae. Four proteins have been identified that in the NTHi genome that have homologs in the M. catarrhalis genome, namely NTH0861 (SEQ ID NO: 1566), NTH0863 (SEQ ID NO: 1570), NTH0865 (SEQ ID NO: 1574) and NTH0867 (SEQ ID NO: 1578). These proteins can thus be used as antigens for a general AOM vaccine. The corresponding M. catarrhalis antigens can also be used, either on their own or in combination with the NTHi antigens.
A variant of SEQ ID NO: 1566 is given as SEQ ID NO: 5095:




A variant of SEQ ID NO: 1570 is given as SEQ ID NO: 5094:




A variant of SEQ ID NO: 1574 is given as SEQ ID NO: 5093:




A variant of SEQ ID NO: 1578 is given as SEQ ID NO: 5092:




Preferred NTH0861 proteins have identity to both of SEQ ID NOS: 1566 and 5095. Preferred NTH0863 proteins have identity to both of SEQ ID NOS: 1570 and 5094. Preferred NTH0865 proteins have identity to both of SEQ ID NOS: 1574 and 5093. Preferred NTH0867 proteins have identity to both of SEQ ID NOS: 1578 and 5092.
It will be understood that the invention has been described by way of example only and modifications may be made whilst remaining within the scope and spirit of the invention.







TABLE I





MISSING NTHnnnn VALUES between NTH0001 and NTH2832


























0008
0031
0042
0054
0056
0066
0074
0077
0093
0111
0160
0162


0166
0171
0179
0210
0213
0214
0219
0229
0231
0276
0281
0288


0293
0322
0332
0357
0362
0381
0395
0398
0404
0406
0409
0410


0415
0439
0445
0446
0452
0466
0471
0491
0497
0516
0533
0538


0541
0546
0551
0553
0556
0569
0578
0598
0600
0610
0623
0639


0649
0666
0693
0713
0722
0727
0742
0746
0757
0763
0780
0789


0791
0793
0800
0809
0816
0855
0883
0891
0902
0911
0915
0916


0922
0943
0944
0957
0975
0978
0980
0998
0999
1013
1034
1044


1047
1055
1056
1065
1072
1076
1079
1099
1113
1118
1119
1128


1133
1134
1136
1146
1147
1158
1160
1170
1194
1199
1213
1219


1223
1232
1243
1257
1260
1288
1289
1296
1312
1317
1329
1335


1347
1350
1356
1358
1362
1364
1372
1377
1385
1452
1458
1469


1478
1481
1486
1488
1502
1517
1518
1529
1536
1547
1553
1557


1560
1566
1592
1595
1596
1604
1642
1649
1667
1669
1674
1691


1699
1711
1715
1721
1723
1727
1728
1731
1737
1741
1743
1746


1750
1761
1772
1784
1797
1810
1814
1823
1843
1844
1856
1864


1866
1878
1902
1909
1918
1957
1961
1979
1985
1987
1990
2004


2006
2015
2017
2023
2033
2037
2042
2054
2077
2080
2098
2104


2107
2125
2154
2167
2171
2174
2179
2194
2203
2210
2218
2237


2239
2240
2244
2254
2255
2267
2268
2270
2275
2278
2286
2290


2295
2300
2302
2312
2320
2334
2340
2355
2357
2366
2367
2374


2380
2400
2409
2431
2444
2459
2523
2540
2547
2551
2574
2580


2589
2601
2611
2614
2624
2628
2637
2639
2645
2652
2658
2662


2677
2692
2699
2700
2728
2734
2746
2760
2767
2773
2787
2799


2805
2808
2819
2822
















TABLE II





Preferred polypeptides






















NTH0001 
NTH0002 
NTH0004 
NTH0005 
NTH0012 
NTH0014 
NTH0015 
NTH0016


NTH0017 
NTH0019 
NTH0020 
NTH0021 
NTH0022 
NTH0024 
NTH0025 
NTH0032


NTH0033 
NTH0034 
NTH0035 
NTH0036 
NTH0037 
NTH0038 
NTH0040 
NTH0041


NTH0043 
NTH0045 
NTH0048 
NTH0049 
NTH0050 
NTH0051 
NTH0052 
NTH0053


NTH0057 
NTH0059 
NTH0060 
NTH0061 
NTH0064 
NTH0067 
NTH0073 
NTH0076


NTH0085 
NTH0089 
NTH0091 
NTH0092 
NTH0094 
NTH0097 
NTH0101 
NTH0104


NTH0106 
NTH0107 
NTH0110 
NTH0114 
NTH0116 
NTH0118 
NTH0119 
NTH0120


NTH0121 
NTH0122 
NTH0123 
NTH0124 
NTH0125 
NTH0128 
NTH0129 
NTH0132


NTH0134 
NTH0135 
NTH0136 
NTH0138 
NTH0140 
NTH0146 
NTH0148 
NTH0151


NTH0153 
NTH0154 
NTH0155 
NTH0157 
NTH0158 
NTH0159 
NTH0161 
NTH0163


NTH0164 
NTH0167 
NTH0169 
NTH0173 
NTH0174 
NTH0176 
NTH0177 
NTH0180


NTH0184 
NTH0185 
NTH0186 
NTH0187 
NTH0189 
NTH0190 
NTH0191 
NTH0192


NTH0193 
NTH0194 
NTH0195 
NTH0197 
NTH0198 
NTH0199 
NTH0203 
NTH0206


NTH0208 
NTH0209 
NTH0223 
NTH0224 
NTH0226 
NTH0227 
NTH0228 
NTH0232


NTH0235 
NTH0236 
NTH0237 
NTH0238 
NTH0241 
NTH0242 
NTH0244 
NTH0247


NTH0248 
NTH0250 
NTH0251 
NTH0252 
NTH0253 
NTH0254 
NTH0255 
NTH0256


NTH0263 
NTH0264 
NTH0265 
NTH0269 
NTH0270 
NTH0278 
NTH0279 
NTH0280


NTH0282 
NTH0283 
NTH0284 
NTH0285 
NTH0289 
NTH0290 
NTH0295 
NTH0297


NTH0298 
NTH0299 
NTH0300 
NTH0302 
NTH0307 
NTH0308 
NTH0310 
NTH0311


NTH0312 
NTH0313 
NTH0317 
NTH0319 
NTH0320 
NTH0321 
NTH0325 
NTH0326


NTH0327 
NTH0328 
NTH0331 
NTH0333 
NTH0334 
NTH0335 
NTH0339 
NTH0341


NTH0346 
NTH0347 
NTH0348 
NTH0351 
NTH0352 
NTH0353 
NTH0356 
NTH0358


NTH0363 
NTH0366 
NTH0371 
NTH0372 
NTH0375 
NTH0378 
NTH0379 
NTH0384


NTH0385 
NTH0388 
NTH0396 
NTH0397 
NTH0400 
NTH0401 
NTH0402 
NTH0405


NTH0407 
NTH0408 
NTH0411 
NTH0412 
NTH0417 
NTH0418 
NTH0419 
NTH0420


NTH0421 
NTH0424 
NTH0426 
NTH0427 
NTH0429 
NTH0430 
NTH0431 
NTH0432


NTH0433 
NTH0434 
NTH0435 
NTH0437 
NTH0438 
NTH0444 
NTH0453 
NTH0455


NTH0457 
NTH0459 
NTH0460 
NTH0461 
NTH0462 
NTH0463 
NTH0465 
NTH0468


NTH0469 
NTH0473 
NTH0475 
NTH0478 
NTH0484 
NTH0485 
NTH0486 
NTH0487


NTH0488 
NTH0489 
NTH0490 
NTH0493 
NTH0496 
NTH0498 
NTH0500 
NTH0501


NTH0502 
NTH0504 
NTH0506 
NTH0507 
NTH0509 
NTH0510 
NTH0511 
NTH0512


NTH0513 
NTH0518 
NTH0520 
NTH0523 
NTH0524 
NTH0526 
NTH0527 
NTH0528


NTH0529 
NTH0531 
NTH0534 
NTH0536 
NTH0539 
NTH0544 
NTH0545 
NTH0547


NTH0549 
NTH0559 
NTH0561 
NTH0565 
NTH0566 
NTH0573 
NTH0574 
NTH0577


NTH0579 
NTH0580 
NTH0581 
NTH0582 
NTH0583 
NTH0584 
NTH0585 
NTH0586


NTH0587 
NTH0588 
NTH0590 
NTH0599 
NTH0603 
NTH0604 
NTH0606 
NTH0615


NTH0617 
NTH0618 
NTH0619 
NTH0622 
NTH0624 
NTH0626 
NTH0630 
NTH0631


NTH0636 
NTH0637 
NTH0638 
NTH0642 
NTH0643 
NTH0644 
NTH0645 
NTH0646


NTH0647 
NTH0648 
NTH0653 
NTH0654 
NTH0656 
NTH0658 
NTH0661 
NTH0662


NTH0663 
NTH0664 
NTH0667 
NTH0668 
NTH0673 
NTH0675 
NTH0676 
NTH0677


NTH0678 
NTH0680 
NTH0681 
NTH0683 
NTH0687 
NTH0690 
NTH0691 
NTH0692


NTH0694 
NTH0695 
NTH0696 
NTH0702 
NTH0703 
NTH0706 
NTH0707 
NTH0709


NTH0710 
NTH0711 
NTH0712 
NTH0715 
NTH0716 
NTH0717 
NTH0718 
NTH0721


NTH0724 
NTH0725 
NTH0726 
NTH0728 
NTH0729 
NTH0730 
NTH0738 
NTH0740


NTH0744 
NTH0745 
NTH0749 
NTH0750 
NTH0752 
NTH0755 
NTH0756 
NTH0762


NTH0764 
NTH0765 
NTH0768 
NTH0771 
NTH0774 
NTH0776 
NTH0788 
NTH0792


NTH0794 
NTH0795 
NTH0796 
NTH0797 
NTH0798 
NTH0802 
NTH0803 
NTH0804


NTH0813 
NTH0814 
NTH0815 
NTH0818 
NTH0820 
NTH0821 
NTH0822 
NTH0827


NTH0829 
NTH0832 
NTH0834 
NTH0835 
NTH0836 
NTH0838 
NTH0839 
NTH0841


NTH0843 
NTH0844 
NTH0848 
NTH0849 
NTH0850 
NTH0851 
NTH0852 
NTH0856


NTH0858 
NTH0861 
NTH0862 
NTH0863 
NTH0864 
NTH0865 
NTH0866 
NTH0867


NTH0872 
NTH0874 
NTH0875 
NTH0877 
NTH0879 
NTH0880 
NTH0885 
NTH0886


NTH0887 
NTH0888 
NTH0892 
NTH0894 
NTH0895 
NTH0896 
NTH0900 
NTH0901


NTH0904 
NTH0906 
NTH0909 
NTH0910 
NTH0913 
NTH0914 
NTH0921 
NTH0924


NTH0926 
NTH0927 
NTH0928 
NTH0929 
NTH0930 
NTH0931 
NTH0932 
NTH0933


NTH0937 
NTH0938 
NTH0941 
NTH0942 
NTH0948 
NTH0949 
NTH0950 
NTH0952


NTH0953 
NTH0955 
NTH0961 
NTH0964 
NTH0968 
NTH0970 
NTH0971 
NTH0972


NTH0973 
NTH0985 
NTH0986 
NTH0987 
NTH0989 
NTH0991 
NTH0992 
NTH0993


NTH0994 
NTH0995 
NTH0996 
NTH0997 
NTH1000 
NTH1002 
NTH1003 
NTH1004


NTH1005 
NTH1007 
NTH1009 
NTH1010 
NTH1012 
NTH1015 
NTH1016 
NTH1017


NTH1018 
NTH1020 
NTH1021 
NTH1025 
NTH1026 
NTH1027 
NTH1028 
NTH1029


NTH1031 
NTH1032 
NTH1037 
NTH1039 
NTH1040 
NTH1042 
NTH1043 
NTH1048


NTH1049 
NTH1052 
NTH1054 
NTH1058 
NTH1063 
NTH1064 
NTH1067 
NTH1069


NTH1070 
NTH1073 
NTH1075 
NTH1080 
NTH1082 
NTH1083 
NTH1084 
NTH1085


NTH1086 
NTH1087 
NTH1089 
NTH1090 
NTH1091 
NTH1092 
NTH1098 
NTH1102


NTH1103 
NTH1104 
NTH1106 
NTH1108 
NTH1111 
NTH1112 
NTH1114 
NTH1115


NTH1116 
NTH1121 
NTH1122 
NTH1123 
NTH1124 
NTH1125 
NTH1129 
NTH1130


NTH1131 
NTH1138 
NTH1141 
NTH1142 
NTH1149 
NTH1150 
NTH1151 
NTH1153


NTH1157 
NTH1159 
NTH1161 
NTH1162 
NTH1164 
NTH1174 
NTH1176 
NTH1178


NTH1179 
NTH1181 
NTH1184 
NTH1185 
NTH1188 
NTH1189 
NTH1190 
NTH1191


NTH1192 
NTH1193 
NTH1195 
NTH1196 
NTH1200 
NTH1201 
NTH1203 
NTH1204


NTH1205 
NTH1207 
NTH1208 
NTH1209 
NTH1210 
NTH1211 
NTH1214 
NTH1216


NTH1220 
NTH1221 
NTH1224 
NTH1225 
NTH1226 
NTH1229 
NTH1230 
NTH1231


NTH1233 
NTH1234 
NTH1235 
NTH1236 
NTH1237 
NTH1238 
NTH1240 
NTH1241


NTH1244 
NTH1245 
NTH1246 
NTH1247 
NTH1248 
NTH1249 
NTH1250 
NTH1251


NTH1252 
NTH1253 
NTH1254 
NTH1255 
NTH1256 
NTH1261 
NTH1262 
NTH1268


NTH1270 
NTH1271 
NTH1273 
NTH1275 
NTH1279 
NTH1280 
NTH1281 
NTH1282


NTH1283 
NTH1286 
NTH1287 
NTH1290 
NTH1293 
NTH1294 
NTH1295 
NTH1297


NTH1298 
NTH1299 
NTH1300 
NTH1301 
NTH1302 
NTH1305 
NTH1306 
NTH1307


NTH1308 
NTH1309 
NTH1311 
NTH1313 
NTH1315 
NTH1316 
NTH1319 
NTH1321


NTH1325 
NTH1327 
NTH1330 
NTH1332 
NTH1333 
NTH1334 
NTH1336 
NTH1337


NTH1339 
NTH1341 
NTH1342 
NTH1346 
NTH1348 
NTH1353 
NTH1354 
NTH1357


NTH1359 
NTH1361 
NTH1363 
NTH1365 
NTH1367 
NTH1368 
NTH1374 
NTH1375


NTH1376 
NTH1379 
NTH1380 
NTH1381 
NTH1382 
NTH1383 
NTH1388 
NTH1390


NTH1391 
NTH1393 
NTH1394 
NTH1395 
NTH1396 
NTH1398 
NTH1399 
NTH1400


NTH1406 
NTH1407 
NTH1411 
NTH1412 
NTH1413 
NTH1414 
NTH1415 
NTH1416


NTH1418 
NTH1419 
NTH1420 
NTH1421 
NTH1425 
NTH1427 
NTH1428 
NTH1429


NTH1430 
NTH1431 
NTH1434 
NTH1435 
NTH1437 
NTH1438 
NTH1439 
NTH1441


NTH1447 
NTH1448 
NTH1450 
NTH1454 
NTH1455 
NTH1456 
NTH1464 
NTH1467


NTH1468 
NTH1470 
NTH1471 
NTH1472 
NTH1473 
NTH1474 
NTH1479 
NTH1487


NTH1489 
NTH1490 
NTH1491 
NTH1492 
NTH1493 
NTH1494 
NTH1495 
NTH1496


NTH1497 
NTH1500 
NTH1503 
NTH1504 
NTH1506 
NTH1510 
NTH1515 
NTH1516


NTH1525 
NTH1526 
NTH1527 
NTH1528 
NTH1531 
NTH1532 
NTH1537 
NTH1538


NTH1540 
NTH1541 
NTH1543 
NTH1548 
NTH1552 
NTH1555 
NTH1559 
NTH1562


NTH1563 
NTH1564 
NTH1567 
NTH1569 
NTH1570 
NTH1571 
NTH1573 
NTH1574


NTH1575 
NTH1580 
NTH1581 
NTH1582 
NTH1584 
NTH1586 
NTH1587 
NTH1588


NTH1590 
NTH1594 
NTH1597 
NTH1598 
NTH1599 
NTH1600 
NTH1601 
NTH1602


NTH1603 
NTH1605 
NTH1606 
NTH1607 
NTH1608 
NTH1609 
NTH1611 
NTH1612


NTH1615 
NTH1616 
NTH1617 
NTH1618 
NTH1619 
NTH1620 
NTH1621 
NTH1622


NTH1623 
NTH1625 
NTH1626 
NTH1627 
NTH1628 
NTH1629 
NTH1631 
NTH1634


NTH1637 
NTH1638 
NTH1647 
NTH1652 
NTH1653 
NTH1654 
NTH1656 
NTH1657


NTH1658 
NTH1662 
NTH1664 
NTH1666 
NTH1668 
NTH1671 
NTH1675 
NTH1676


NTH1677 
NTH1680 
NTH1686 
NTH1687 
NTH1688 
NTH1689 
NTH1690 
NTH1692


NTH1693 
NTH1697 
NTH1698 
NTH1701 
NTH1702 
NTH1703 
NTH1707 
NTH1712


NTH1713 
NTH1718 
NTH1719 
NTH1722 
NTH1724 
NTH1725 
NTH1729 
NTH1732


NTH1734 
NTH1735 
NTH1739 
NTH1740 
NTH1742 
NTH1744 
NTH1745 
NTH1748


NTH1749 
NTH1751 
NTH1752 
NTH1753 
NTH1754 
NTH1755 
NTH1756 
NTH1757


NTH1758 
NTH1759 
NTH1760 
NTH1765 
NTH1767 
NTH1769 
NTH1770 
NTH1773


NTH1778 
NTH1779 
NTH1781 
NTH1782 
NTH1783 
NTH1788 
NTH1793 
NTH1795


NTH1796 
NTH1798 
NTH1799 
NTH1803 
NTH1804 
NTH1805 
NTH1806 
NTH1807


NTH1811 
NTH1812 
NTH1813 
NTH1815 
NTH1816 
NTH1817 
NTH1818 
NTH1819


NTH1820 
NTH1821 
NTH1822 
NTH1824 
NTH1828 
NTH1829 
NTH1832 
NTH1833


NTH1835 
NTH1836 
NTH1837 
NTH1842 
NTH1845 
NTH1849 
NTH1850 
NTH1854


NTH1857 
NTH1859 
NTH1861 
NTH1865 
NTH1870 
NTH1871 
NTH1872 
NTH1873


NTH1881 
NTH1882 
NTH1885 
NTH1888 
NTH1889 
NTH1891 
NTH1892 
NTH1896


NTH1897 
NTH1898 
NTH1899 
NTH1900 
NTH1904 
NTH1906 
NTH1908 
NTH1910


NTH1914 
NTH1916 
NTH1917 
NTH1919 
NTH1920 
NTH1921 
NTH1922 
NTH1923


NTH1925 
NTH1927 
NTH1935 
NTH1939 
NTH1941 
NTH1942 
NTH1945 
NTH1946


NTH1947 
NTH1948 
NTH1951 
NTH1953 
NTH1956 
NTH1958 
NTH1960 
NTH1962


NTH1963 
NTH1964 
NTH1965 
NTH1966 
NTH1967 
NTH1968 
NTH1974 
NTH1978


NTH1981 
NTH1986 
NTH1989 
NTH1992 
NTH1993 
NTH1994 
NTH1995 
NTH1996


NTH1997 
NTH1998 
NTH1999 
NTH2001 
NTH2005 
NTH2008 
NTH2009 
NTH2010


NTH2019 
NTH2024 
NTH2025 
NTH2031 
NTH2035 
NTH2038 
NTH2039 
NTH2040


NTH2041 
NTH2043 
NTH2050 
NTH2052 
NTH2055 
NTH2056 
NTH2060 
NTH2062


NTH2064 
NTH2065 
NTH2069 
NTH2070 
NTH2071 
NTH2073 
NTH2075 
NTH2078


NTH2079 
NTH2081 
NTH2083 
NTH2089 
NTH2091 
NTH2092 
NTH2093 
NTH2094


NTH2095 
NTH2096 
NTH2097 
NTH2099 
NTH2101 
NTH2109 
NTH2110 
NTH2112


NTH2113 
NTH2114 
NTH2115 
NTH2116 
NTH2117 
NTH2118 
NTH2119 
NTH2120


NTH2122 
NTH2126 
NTH2128 
NTH2129 
NTH2130 
NTH2131 
NTH2133 
NTH2135


NTH2136 
NTH2138 
NTH2142 
NTH2145 
NTH2146 
NTH2149 
NTH2150 
NTH2156


NTH2159 
NTH2162 
NTH2163 
NTH2166 
NTH2169 
NTH2170 
NTH2173 
NTH2181


NTH2183 
NTH2187 
NTH2191 
NTH2193 
NTH2195 
NTH2196 
NTH2197 
NTH2198


NTH2199 
NTH2200 
NTH2204 
NTH2205 
NTH2206 
NTH2207 
NTH2209 
NTH2213


NTH2216 
NTH2217 
NTH2219 
NTH2220 
NTH2221 
NTH2222 
NTH2223 
NTH2226


NTH2227 
NTH2228 
NTH2229 
NTH2231 
NTH2232 
NTH2234 
NTH2235 
NTH2242


NTH2243 
NTH2245 
NTH2247 
NTH2250 
NTH2251 
NTH2253 
NTH2256 
NTH2257


NTH2258 
NTH2259 
NTH2262 
NTH2263 
NTH2266 
NTH2269 
NTH2273 
NTH2274


NTH2277 
NTH2282 
NTH2284 
NTH2285 
NTH2287 
NTH2288 
NTH2291 
NTH2292


NTH2296 
NTH2299 
NTH2305 
NTH2309 
NTH2315 
NTH2316 
NTH2318 
NTH2323


NTH2324 
NTH2326 
NTH2327 
NTH2330 
NTH2332 
NTH2333 
NTH2342 
NTH2343


NTH2344 
NTH2346 
NTH2347 
NTH2349 
NTH2352 
NTH2353 
NTH2356 
NTH2358


NTH2361 
NTH2362 
NTH2363 
NTH2364 
NTH2365 
NTH2368 
NTH2369 
NTH2370


NTH2371 
NTH2376 
NTH2377 
NTH2381 
NTH2382 
NTH2386 
NTH2388 
NTH2394


NTH2398 
NTH2402 
NTH2405 
NTH2406 
NTH2407 
NTH2408 
NTH2414 
NTH2414


NTH2422 
NTH2430 
NTH2432 
NTH2433 
NTH2434 
NTH2438 
NTH2442 
NTH2447


NTH2448 
NTH2451 
NTH2455 
NTH2456 
NTH2457 
NTH2458 
NTH2460 
NTH2461


NTH2463 
NTH2464 
NTH2466 
NTH2467 
NTH2468 
NTH2471 
NTH2472 
NTH2478


NTH2480 
NTH2481 
NTH2482 
NTH2483 
NTH2484 
NTH2485 
NTH2486 
NTH2487


NTH2488 
NTH2493 
NTH2495 
NTH2496 
NTH2497 
NTH2498 
NTH2499 
NTH2500


NTH2501 
NTH2505 
NTH2508 
NTH2510 
NTH2524 
NTH2525 
NTH2527 
NTH2528


NTH2531 
NTH2532 
NTH2533 
NTH2534 
NTH2536 
NTH2537 
NTH2541 
NTH2542


NTH2543 
NTH2545 
NTH2546 
NTH2548 
NTH2549 
NTH2550 
NTH2552 
NTH2554


NTH2556 
NTH2557 
NTH2558 
NTH2562 
NTH2563 
NTH2566 
NTH2567 
NTH2568


NTH2569 
NTH2570 
NTH2572 
NTH2573 
NTH2575 
NTH2577 
NTH2578 
NTH2584


NTH2585 
NTH2587 
NTH2588 
NTH2590 
NTH2591 
NTH2593 
NTH2595 
NTH2597


NTH2600 
NTH2602 
NTH2603 
NTH2604 
NTH2605 
NTH2607 
NTH2608 
NTH2609


NTH2610 
NTH2612 
NTH2613 
NTH2615 
NTH2616 
NTH2618 
NTH2626 
NTH2633


NTH2635 
NTH2640 
NTH2641 
NTH2647 
NTH2648 
NTH2649 
NTH2650 
NTH2655


NTH2661 
NTH2663 
NTH2664 
NTH2667 
NTH2668 
NTH2673 
NTH2674 
NTH2675


NTH2679 
NTH2680 
NTH2684 
NTH2690 
NTH2693 
NTH2694 
NTH2696 
NTH2697


NTH2701 
NTH2702 
NTH2703 
NTH2704 
NTH2705 
NTH2706 
NTH2707 
NTH2708


NTH2709 
NTH2710 
NTH2711 
NTH2712 
NTH2713 
NTH2715 
NTH2716 
NTH2718


NTH2719 
NTH2720 
NTH2721 
NTH2723 
NTH2724 
NTH2725 
NTH2726 
NTH2727


NTH2729 
NTH2730 
NTH2731 
NTH2732 
NTH2735 
NTH2737 
NTH2738 
NTH2740


NTH2743 
NTH2744 
NTH2749 
NTH2750 
NTH2753 
NTH2754 
NTH2755 
NTH2756


NTH2757 
NTH2758 
NTH2764 
NTH2765 
NTH2769 
NTH2774 
NTH2777 
NTH2778


NTH2779 
NTH2781 
NTH2783 
NTH2784 
NTH2785 
NTH2791 
NTH2793 
NTH2794


NTH2796 
NTH2797 
NTH2798 
NTH2804 
NTH2806 
NTH2807 
NTH2809 
NTH2810


NTH2813 
NTH2814 
NTH2816 
NTH2823
















TABLE III







Annotations


aa = length of polypeptide


PSORT = cellular location of polypeptide, according to PSORT algorithm










NTH
aa
PSORT
Annotation













0003
274
cytoplasm
Diaminopimelate epimerase (dapF)


0007
61
cytoplasm
tldD protein tldD


0010
158
cytoplasm
transcriptional regulator


0011
93
cytoplasm
usg-1 protein (usg1)


0013
274
cytoplasm
excinuclease ABC, subunit C (uvrC)


0014
64
periplasmic
excinuclease ABC, subunit C (uvrC)


0017
161
outer
2′,3′-cyclic-nucleotide 2′-phosphodiesterase (cpdB)


0018
130
cytoplasm
16s pseudouridylate 516 synthase (rsuA)


0019
98
inner 1
bicyclomycin resistance protein (bcr)


0020
181
inner 4
Na(+)-translocating NADH-quinone reductase, subunit


0023
110
cytoplasm
sigma-E factor regulatory protein (rseB)


0025
195
inner 1
sigma-E factor negative regulatory protein (mclA)


0026
157
cytoplasm
RNA polymerase sigma-E factor (rpoE)


0027
100
cytoplasm
cell division protein (ftsQ)


0028
37
cytoplasm
cell division protein (ftsA)


0029
34
cytoplasm
cell division protein (ftsA)


0030
268
cytoplasm
aspartate--ammonia ligase (asnA)


0039
311
cytoplasm
ADP-heptose--LPS heptosyltransferase II (rfaF)


0043
194
inner 3
sodium:dicarboxylate symporter protein


0044
79
cytoplasm
ferritin (rsgA)


0047
219
cytoplasm
heat shock protein (hslU)/ATP-dependent Clp protease, ATP-binding subunit


0048
55
inner 2
L-lactate permease (lctP)


0049
90
periplasmic
transferrin-binding protein or TonB-dependent receptor


0055
92
cytoplasm
heat shock protein (hslV)


0057
235
periplasmic
acid phosphatase


0058
206
cytoplasm
rod shape-determining protein (mreB) or cell division protein FtsA ftsA


0059
54
periplasmic
rod shape-determining protein (mreC)


0060
104
inner 0
ribosomal protein S8 (rpS8)


0061
313
inner 2
ribosomal protein L6 (rpL6)


0063
257
cytoplasm
fumarate (and nitrate) reduction regulatory protein (fnr)


0065
266
cytoplasm
thiamin ABC transporter, periplasmic-binding protein (tbpA)


0067
86
inner 1
thiamin ABC transporter, permease protein


0068
52
cytoplasm
UDP-N-acetylenolpyruvoylglucosamine reductase (murB)


0069
149
cytoplasm
RNA polymerase sigma-32 factor (rpoH)


0070
127
cytoplasm
RNA polymerase sigma-32 factor (rpoH)


0071
64
cytoplasm
NifR3/SMM1 family protein


0072
201
cytoplasm
acetolactate synthase III large subunit (ilvI)


0073
142
inner 1
acetolactate synthase III large subunit (ilvI)


0075
166
cytoplasm
acetolactate synthase III small subunit (ilvH)


0078
119
cytoplasm
orotate phosphoribosyltransferase (pyrE)


0079
36
cytoplasm
orotate phosphoribosyltransferase (pyrE)


0082
144
cytoplasm
DNA polymerase III, chi subunit (holC)


0083
85
cytoplasm
methylglyoxal synthase (mgsA)


0085
340
inner 7
cytochrome C-type biogenesis protein (ccmF)


0086
45
cytoplasm
cytochrome C-type biogenesis protein (ccmE)


0087
312
cytoplasm
histidyl-tRNA synthetase (hisS)


0088
214
cytoplasm
topoisomerase IV, subunit A (parC)


0091
212
inner 1
4-hydroxy-2-oxoglutarate


0094
338
lipo
zinc protease


0098
358
cytoplasm
homoserine O-acetyltransferase (met2)


0099
60
cytoplasm
DNA gyrase, subunit A (gyrA)


0100
56
cytoplasm
DNA gyrase, subunit A (gyrA)


0102
102
cytoplasm
universal stress protein A (uspA)


0103
290
cytoplasm
alanyl-tRNA synthetase (alaS)


0104
81
cytoplasm
alanyl-tRNA synthetase (alaS)


0105
557
cytoplasm
protective surface antigen D15 (Omp85)


0106
110
periplasmic
outer membrane protein


0107
257
inner 1
cell division protein (ftsZ)


0108
352
cytoplasm
cell division protein (ftsA)


0109
496
cytoplasm
DNA topoisomerase I (topA)


0112
259
cytoplasm
penicillin-binding protein 1B (ponB)


0113
35
cytoplasm
penicillin-binding protein 1B (ponB)


0115
279
cytoplasm
penicillin-binding protein 1A (ponA)


0116
310
inner 1
GTP-binding protein


0117
243
cytoplasm
phosphomannomutase (yhxB)


0118
84
inner 0
phosphomannomutase (yhxB)


0119
89
periplasmic
tonB protein


0120
147
periplasmic
biopolymer transport protein (exbD)


0121
49
inner 1
biopolymer transport protein (exbB)


0126
77
cytoplasm
integrase/recombinase


0128
111
inner 1
xanthine-guanine phosphoribosyltransferase (gptB)


0130
184
cytoplasm
aminoacyl-histidine dipeptidase (pepD)


0131
35
cytoplasm
aminoacyl-histidine dipeptidase (pepD)


0134
182
inner 1
phosphoribosylglycinamide formyltransferase (purN)


0137
58
cytoplasm
GTP-binding membrane protein (lepA)


0141
78
cytoplasm
uracil DNA glycosylase (ung)


0142
76
cytoplasm
aldose 1-epimerase (galM)


0143
129
cytoplasm
galactokinase (galK)


0144
197
cytoplasm
galactokinase (galK)


0145
346
cytoplasm
GTP-binding protein TypA


0147
179
cytoplasm
queuine tRNA-ribosyltransferase (tgt)


0150
239
cytoplasm
ribosomal large subunit pseudouridine synthase C


0152
463
cytoplasm
galactoside ABC transporter, ATP-binding protein (mglA)


0153
247
cytoplasm
hemagglutinin/hemolysin-related protein


0154
240
cytoplasm
hemagglutinin/hemolysin-related protein


0155
302
inner 7
phosphate permease


0157
124
inner 2
cytochrome D ubiquinol oxidase, subunit I (cydA) or iron(III) ABC





transporter, permease protein fbpB


0158
103
inner 2
cytochrome D ubiquinol oxidase, subunit II (cydB)


0163
154
lipo
15 kDa peptidoglycan-associated lipoprotein (lpp)


0165
165
cytoplasm
membrane-bound lytic murein transglycosylase C (mltC)


0167
194
lipo
membrane-bound lytic murein transglycosylase C (mltC)


0170
51
cytoplasm
hflK protein (hflK)


0174
40
periplasmic
tail specific protease (prc)


0178
116
cytoplasm
recombination protein (rec2) or competence protein ComA comA


0180
147
inner 2
ABC transporter, ATP-binding protein (msbA)


0185
220
inner 0
chorismate synthase (aroC)


0186
156
inner 2
ATP-binding transport protein (cydD)


0189
162
inner 2
rod shape-determining protein (mreD)


0190
188
periplasmic
rod shape-determining protein (mreC)


0196
68
cytoplasm
sigma factor


0200
68
cytoplasm
mercuric ion scavenger protein (merP)


0201
68
cytoplasm
mercuric ion scavenger protein (merP)


0202
68
cytoplasm
mercuric ion scavenger protein (merP)


0203
63
inner 0
orfJ protein


0204
306
cytoplasm
penicillin-binding protein 1A (ponA)


0205
38
cytoplasm
penicillin-binding protein 1A (ponA)


0207
175
cytoplasm
extragenic suppressor (suhB)


0208
64
inner 1
cytochrome C-type biogenesis


0209
117
inner 2
1,4-dihydroxy-2-naphthoate octaprenyltransferase (menA)


0212
203
cytoplasm
lysyl-tRNA synthetase analog (genX)


0215
204
cytoplasm
fumarate reductase, flavoprotein subunit (frdA) or succinate





dehydrogenase, flavoprotein subunit sdhA


0216
48
cytoplasm
fumarate reductase, flavoprotein subunit (frdA)


0217
40
cytoplasm
fumarate reductase, flavoprotein subunit (frdA)


0218
310
cytoplasm
nitrogen fixation protein (nifR3)


0220
99
cytoplasm
Hin recombinational enhancer binding protein (fis) or factor-for-inversion





stimulation protein Fis,


0221
48
cytoplasm
small protein B (smpB)


0222
222
cytoplasm
magnesium and cobalt transport protein (corA)


0223
91
inner 1
magnesium and cobalt transport protein (corA)


0225
426
cytoplasm
exoribonuclease II (rnb) or ribonuclease II family protein vacB


0233
114
cytoplasm
uridylate kinase (pyrH)


0234
41
cytoplasm
uridylate kinase (pyrH)


0236
35
cytoplasm
phospho-2-dehydro-3-deoxyheptonate aldolase (phenylalanine


0239
322
cytoplasm
heat shock (chaperone) protein (hscA)


0240
44
cytoplasm
heat shock (chaperone) protein (hscA)


0241
193
outer
usg-1 protein (usg1)


0242
268
inner 2
tryptophan synthase alpha subunit (trpA)


0243
58
cytoplasm
tryptophan synthase beta subunit (trpB)


0244
245
periplasmic
stationary phase survival protein SurA or peptidyl-prolyl cis-trans isomerase


0245
191
cytoplasm
pyrimidine operon regulatory protein (pyrR) or hypoxanthine-guanine





phosphoribosyltransferase,


0246
153
cytoplasm
mazG protein (mazG)


0247
159
inner 3
ATP synthase F0, subunit a (atpB)


0249
203
cytoplasm
glucose-inhibited division protein (gidB)


0257
289
cytoplasm
selenocysteine-specific elongation factor (selB)


0258
212
cytoplasm
pyruvate dehydrogenase, E1 component (aceE)


0259
61
cytoplasm
pyruvate dehydrogenase, E1 component (aceE)


0260
505
cytoplasm
ribonuclease E (rne)


0262
303
cytoplasm
ATP-dependent helicase (dinG)


0263
276
inner 7
thiamin ABC transporter, permease protein


0266
121
cytoplasm
N utilization substance protein B (nusB)


0267
160
cytoplasm
thiamin-monophosphate kinase (thiL)


0268
144
cytoplasm
thiamin-monophosphate kinase (thiL)


0269
163
inner 3
phosphatidylglycerophosphatase A (pgpA)


0272
44
cytoplasm
ribosomal protein L34 (rpL34)


0273
119
cytoplasm
ribonuclease P (rnpA)


0275
146
cytoplasm
impA protein


0277
218
cytoplasm
phospho-2-dehydro-3-deoxyheptonate aldolase (phenylalanine


0286
288
cytoplasm
GTP-binding protein


0287
422
cytoplasm
formate dehydrogenase, beta subunit (fdxH) or ferredoxin, 4Fe—4S bacterial





type


0291
109
cytoplasm
mannonate dehydratase (uxuA)


0292
46
cytoplasm
mannonate dehydratase (uxuA)


0294
171
cytoplasm
dihydroxyacid dehydratase (ilvD)


0295
308
inner 1
threonine deaminase (ilvA)


0296
239
cytoplasm
galactose-1-phosphate uridylyltransferase (galT)


0303
283
cytoplasm
hemoglobin-binding protein


0304
68
cytoplasm
ribosomal protein L24 (rpL24)


0305
123
cytoplasm
ribosomal protein L14 (rpL14)


0309
82
cytoplasm
inorganic pyrophosphatase (ppa)


0311
185
inner 4
phosphatidylglycerophosphate synthase (pgsA) or CDP-diacylglycerol--





glycerol-3-phosphate


0314
274
cytoplasm
dihydrolipoamide dehydrogenase (lpdA) or pyruvate dehydrogenase, E3





component, lipoamide


0315
38
cytoplasm
dihydrolipoamide dehydrogenase (lpdA)


0318
358
cytoplasm
DNA topoisomerase III (topB) or DNA topoisomerase I topA


0320
411
inner 1
Nqr6 subunit of Na-translocating NADH-quinone reductase


0321
191
inner 1
single-stranded DNA binding protein (ssb)


0323
141
cytoplasm
excinuclease ABC, subunit A (uvrA)


0324
319
cytoplasm
type IV pilus assembly protein pilF


0325
200
inner 1
pilus assembly protein PilG pilG


0326
386
inner 8
branched chain amino acid transport system II carrier


0329
395
cytoplasm
cystathionine beta-lyase (metC) or trans-sulfuration enzyme family protein


0330
109
cytoplasm
sanA protein (sanA)


0333
96
inner 1
folylpolyglutamate synthase/dihydrofolate synthase (folC)


0336
133
cytoplasm
short chain dehydrogenase/reductase or oxidoreductase, short-chain





dehydrogenase/reductase


0337
391
cytoplasm
tryptophan synthase beta subunit (trpB)


0340
151
cytoplasm
cell division protein (ftsH)


0342
147
cytoplasm
peptide methionine sulfoxide reductase pilB


0346
46
periplasmic
small protein A


0347
273
inner 7
transport protein


0349
66
cytoplasm
protease


0351
412
inner 1
penicillin-binding protein 1B (ponB)


0352
291
inner 5
carbon starvation protein A cstA


0354
227
cytoplasm
GTP pyrophosphokinase (relA)


0355
367
cytoplasm
GTP pyrophosphokinase (relA)


0356
65
inner 1
diacylglycerol kinase (dgkA)


0358
56
inner 1
diacylglycerol kinase (dgkA)


0359
275
cytoplasm
esterase


0360
216
cytoplasm
UDP-3-O-(3-hydroxymyristoyl)-glucosamine N-acyltransferase


0361
141
cytoplasm
translation elongation factor Ts (tsf) (EF-TS)


0365
91
cytoplasm
exodeoxyribonuclease III (xthA)


0366
432
inner 1
heme-hemopexin utilization protein A (hxuA)


0367
184
cytoplasm
carboxy-terminal tail specific protease (prc)


0368
204
cytoplasm
carboxy-terminal tail specific protease (prc)


0369
163
cytoplasm
dihydroxyacid dehydratase (ilvD)


0370
201
cytoplasm
acetohydroxy acid synthase II or acetolactate synthase III, large subunit ilvI


0372
306
inner 7
sodium-dependent transporter or sodium- and chloride-dependent





transporter


0373
42
cytoplasm
aminotransferase


0374
307
cytoplasm
aminotransferase


0376
128
cytoplasm
ribosomal protein L17 (rplQ)


0377
193
cytoplasm
DNA-directed RNA polymerase, alpha chain (rpoA)


0380
33
cytoplasm
acylneuraminate cytidylyltransferase (neuA)


0382
359
cytoplasm
peptidyl-prolyl cis-trans isomerse


0386
111
cytoplasm
DNA gyrase, subunit A (gyrA)


0387
52
cytoplasm
DNA gyrase, subunit A (gyrA)


0388
242
inner 3
sodium/proline symporter (proline permease) (putP)


0391
256
cytoplasm
anaerobic ribonucleoside-triphosphate reductase (nrdD)


0392
87
cytoplasm
anaerobic ribonucleoside-triphosphate reductase (nrdD)


0393
211
cytoplasm
aminotransferase


0394
117
cytoplasm
aerobic respiration control protein ARCA (arcA) or DNA-binding response





regulator


0397
444
inner 8
thiol:disulfide interchange protein (dsbD)


0399
362
cytoplasm
GTP-binding membrane protein (lepA)


0400
437
inner 9
sodium-dependent transporter


0401
206
inner 5
nitrite reductase, transmembrane protein (nrfD)


0402
138
inner 3
cytochrome C-type biogenesis protein or thiol:disulfide interchange protein





DsbD dsbD


0403
84
cytoplasm
peptide methionine sulfoxide reductase (msrA)


0405
299
periplasmic
peptide methionine sulfoxide reductase (msrA)


0418
297
inner 3
cytochrome D ubiquinol oxidase, subunit I (cydA)


0421
287
periplasmic
CTP synthetase (pyrG)


0423
385
cytoplasm
exodeoxyribonuclease VII, large subunit (xseA)


0425
92
cytoplasm
oligopeptide ABC transporter, ATP-binding protein (oppD)


0426
311
inner 6
oligopeptide ABC transporter, permease protein (oppC)


0427
232
inner 6
oligopeptide ABC transporter, permease protein (oppB) or iron(III) ABC





transporter, permease protein


0428
316
cytoplasm
cysteine synthetase (cysK)


0431
116
cytoplasm
C-5 cytosine-specific DNA-methylase


0436
341
cytoplasm
peptide chain release factor 3 (prfC)


0437
295
inner 1
enoyl-(acyl-carrier-protein) reductase (fabI)


0441
66
cytoplasm
L-2,4-diaminobutyrate decarboxylase


0442
222
cytoplasm
formamidopyrimidine-DNA glycosylase (fpg)


0443
160
cytoplasm
peptidase T (pepT)


0444
178
inner 0
fuculokinase (fucK)


0447
323
cytoplasm
L-fucose isomerase (fucI)


0448
119
cytoplasm
L-fucose isomerase (fucI)


0449
193
cytoplasm
dethiobiotin synthase (bioD-1)


0451
88
cytoplasm
GTP cyclohydrolase I (folE)


0453
113
inner 1
GTP cyclohydrolase I (folE)


0454
78
cytoplasm
GTP cyclohydrolase I (folE)


0456
212
cytoplasm
protein-PII uridylyl transferase (glnD)


0457
288
inner 9
undecaprenyl-phosphate alpha-N-acetylglucosaminyltransferase or





phospho-N-acetylmuramoyl-pentapeptide-transferase


0458
293
cytoplasm
penicillin tolerance protein (lytB)


0459
57
inner 1
lipoprotein signal peptidase (lspA)


0460
122
inner 1
lipoprotein signal peptidase (lspA)


0461
433
inner 2
YhbX/YhjW/YijP/YjdB family protein


0462
107
inner 2
transporter protein


0463
159
inner 3
transporter protein


0464
349
cytoplasm
2′,3′-cyclic-nucleotide 2′-phosphodiesterase (cpdB)


0465
73
inner 1
iron (chelated) ABC transporter, permease protein (yfeD)


0467
215
cytoplasm
transcriptional activator


0468
314
periplasmic
thiamine biosynthesis protein


0469
76
inner 1
ABC transporter, permease protein


0470
328
cytoplasm
alanyl-tRNA synthetase (alaS)


0472
122
cytoplasm
alanyl-tRNA synthetase (alaS)


0473
89
inner 0
phosphatidylserine decarboxylase proenzyme (psd)


0474
261
cytoplasm
glutathione reductase (gor) or 2-oxoglutarate dehydrogenase, E3





component,


0475
241
inner 5
phosphatidylglycerophosphatase B (pgpB)


0476
119
cytoplasm
GTP cyclohydrolase II (ribA)


0477
153
cytoplasm
DNA polymerase III, delta subunit (holA)


0479
369
cytoplasm
glycyl-tRNA synthetase, beta chain (glyS)


0480
305
cytoplasm
UDP-3-0-(3-hydroxymyristoyl) N-acetylglucosamine deacetylase


0481
116
cytoplasm
chorismate mutase/prephenate dehydratase (pheA)


0483
271
cytoplasm
urease accessory protein (ureH)


0490
179
inner 4
glutamate permease (gltS) sodium/glutamate symporter


0492
95
cytoplasm
ribosomal protein S6 modification protein (rimK) or glutathione synthetase





gshB


0493
123
inner 2
Na+/H+ antiporter (nhaC)


0494
326
cytoplasm
xylose operon regluatory protein (xylR)


0495
144
cytoplasm
lipopolysaccharide biosynthesis protein or lacto-N-neotetraose biosynthesis





glycosyl


0496
257
inner 1
lipopolysaccharide biosynthesis protein


0502
46
outer
penicillin-binding protein 7


0503
138
cytoplasm
transcription elongation factor (greA)


0504
115
outer
D-alanyl-D-alanine


0505
370
cytoplasm
D-alanyl-D-alanine or penicillin-binding protein 3


0506
38
cytoplasm
IS1016 family transposase


0507
158
inner 1
IS1016-V6 protein (IS1016-V6)


0508
111
cytoplasm
IS1016C2 transposase


0514
296
cytoplasm
aminopeptidase A/I (pepA)


0515
113
cytoplasm
stringent starvation protein B (sspB)


0517
312
cytoplasm
1-deoxyxylulose-5-phosphate synthase (dxs)


0518
150
inner 0
short chain dehydrogenase/reductase


0519
348
cytoplasm
phosphoribosylaminoimidazole synthetase (purM)


0521
40
cytoplasm
phosphoglycerate mutase (gpmA)


0522
70
cytoplasm
ribosomal protein L31 (rpL31)


0524
158
inner 0
A/G-specific adenine glycosylase (mutY)


0525
86
cytoplasm
A/G-specific adenine glycosylase (mutY)


0528
170
inner 2
formate dehydrogenase, gamma subunit (fdxI)


0529
319
inner 2
fdhE protein (fdhE)


0530
137
cytoplasm
DNA transformation protein (sxy)


0532
571
cytoplasm
immunoglobin A1 protease (iga1) or hemagglutinin/hemolysin-related





protein


0535
289
cytoplasm
threonyl-tRNA synthetase (thrS)


0540
184
cytoplasm
competence protein E (comE)


0542
213
cytoplasm
competence protein F (comF)


0543
220
cytoplasm
hflK protein (hflK) or stomatin/Mec-2 family protein


0544
295
inner 1
hflC protein (hflC) or stomatin/Mec-2 family protein


0547
74
periplasmic
sodium/proline symporter (proline permease) (putP)


0548
304
cytoplasm
cytoplasmic axial filament protein (cafA)


0549
108
inner 1
cytoplasmic axial filament protein (cafA)


0550
93
cytoplasm
cytoplasmic axial filament protein (cafA)


0552
217
cytoplasm
cell division protein (mukB)


0554
248
cytoplasm
killing protein suppressor (kicA)


0557
245
cytoplasm
fdhD protein (fdhD)


0558
38
cytoplasm
fdhD protein (fdhD)


0560
30
cytoplasm
phosphatidylserine decarboxylase proenzyme (psd)


0563
56
cytoplasm
ribosomal protein L32 (rpL32)


0564
225
cytoplasm
beta-ketoacyl-ACP synthase III (fabH) or 3-oxoacyl-(acyl-carrier-protein)





synthase III fabH


0565
368
inner 7
tryptophan-specific transport protein (mtr)


0566
409
inner 1
L-serine deaminase (sdaA)


0571
292
cytoplasm
cytidine deaminase (cdd)


0574
212
inner 2
lipoprotein


0575
65
cytoplasm
transcriptional regulator (bolA)


0576
158
cytoplasm
NADH:ubiquinone oxidoreducatase subunit A, Na translocating or Na(+)-





translocating NADH-quinone reductase, subunit


0580
160
inner 0
translation initiation factor 2 (infB)


0591
200
cytoplasm
beta-phosphoglucomutase pgmB


0592
462
cytoplasm
cell division protein (mukB)


0594
393
cytoplasm
traN-related protein


0595
31
cytoplasm
GTP cyclohydrolase II (ribA)


0596
57
cytoplasm
GTP cyclohydrolase II (ribA)


0597
345
cytoplasm
oligopeptide transporter, periplasmic-binding protein,


0599
32
cytoplasm
oligopeptide transporter, periplasmic-binding protein,


0601
240
cytoplasm
aminopeptidase P (pepP)


0604
37
cytoplasm
aldose 1-epimerase (galM)


0605
195
cytoplasm
aldose 1-epimerase (galM)


0607
318
cytoplasm
C-5 cytosine-specific DNA-methylase


0608
104
cytoplasm
killing protein (kicB)


0609
144
cytoplasm
DNA polymerase III, delta subunit (holA)


0611
69
cytoplasm
rare lipoprotein B


0613
75
cytoplasm
transcriptional regulator (nadR)


0614
310
cytoplasm
transcriptional regulator (nadR)


0616
69
cytoplasm
aerobic respiration control protein ARCA (arcA)


0618
368
inner 7
sodium/alanine symporter


0619
303
periplasmic
elongation factor Tu (tufB)


0622
218
inner 4
dedA protein


0626
164
inner 5
lic-1 operon protein (licB)


0627
321
cytoplasm
lic-1 operon protein (licA)


0628
235
cytoplasm
UDP-N-acetylenolpyruvoylglucosamine reductase (murB)


0629
179
cytoplasm
nitrate/nitrite sensor protein (narQ)


0630
151
inner 1
small major protein B (smpB)


0632
53
cytoplasm
6-phosphofructokinase (pfkA)


0633
290
cytoplasm
6-phosphofructokinase (pfkA)


0635
355
cytoplasm
type I modification enzyme (hsdM)


0636
158
inner 2
cysteine synthetase (cysZ)


0638
328
outer
cell division protein ZipA


0640
122
cytoplasm
ribosomal protein S12 (rps12)


0641
346
cytoplasm
glucose inhibited division protein (gidA)


0646
257
inner 5
Na+/H+ antiporter (nhaC)


0647
37
outer
Na+/H+ antiporter (nhaC)


0648
362
outer
colicin tolerance protein (tolB)


0650
497
cytoplasm
cell division protein (mukB)


0651
391
cytoplasm
heme-binding lipoprotein (dppA)


0652
78
cytoplasm
octaprenyl-diphosphate synthase (ispB)


0654
103
inner 1
ribosomal protein L21 (rpL21)


0655
85
cytoplasm
ribosomal protein L27 (rpL27)


0657
83
cytoplasm
GTP-binding protein (yhbZ)


0658
75
inner 1
lipopolysaccharide biosynthesis protein


0659
55
cytoplasm
lipopolysaccharide biosynthesis protein


0660
255
cytoplasm
molybdenum transport protein (modE)


0661
34
periplasmic
molybdenum ABC transporter, periplasmic-binding protein


0665
144
cytoplasm
single-stranded DNA binding protein (ssb)


0670
366
cytoplasm
histidinol-phosphate aminotransferase (hisH)


0671
31
cytoplasm
phosphoserine aminotransferase (serC)


0672
31
cytoplasm
phosphoserine aminotransferase (serC)


0674
140
cytoplasm
ribosomal protein L3 (rpL3)


0675
200
inner 1
ribosomal protein L4 (rpL4)


0676
139
inner 1
ribosomal protein L23 (rpL23)


0679
51
cytoplasm
ampD signalling protein (ampD)


0682
96
cytoplasm
hemolysin


0684
208
cytoplasm
spermidine/putrescine ABC transporter, ATP-binding protein


0685
52
cytoplasm
lysyl-tRNA synthetase analog (genX)


0686
227
cytoplasm
DNA-binding response regulator (cpxR)


0688
256
cytoplasm
aminoacyl-histidine dipeptidase (pepD)


0689
185
cytoplasm
integrase/recombinase (xerC)


0698
399
cytoplasm
nifS protein


0699
51
cytoplasm
nuclease


0701
153
cytoplasm
DnaA-related protein


0702
279
inner 7
uracil permease (uraA)


0703
129
inner 3
uracil permease (uraA)


0704
135
cytoplasm
uracil phosphoribosyltransferase (upp)


0705
341
cytoplasm
glutaminyl-tRNA synthetase (glnS)


0708
78
cytoplasm
cytoplasmic axial filament protein (cafA)


0709
258
inner 5
anaerobic C4-dicarboxylate membrane transporter protein


0710
43
inner 1
anaerobic C4-dicarboxylate membrane transporter protein


0714
169
cytoplasm
protein-export protein (secB)


0718
175
inner 1
glucose inhibited division protein (gidA)


0719
224
cytoplasm
threonyl-tRNA synthetase (thrS)


0720
194
cytoplasm
acyl carrier protein phosphodiesterase (acpD)


0723
146
cytoplasm
DNA topoisomerase I (topA)


0732
200
cytoplasm
recombination protein RecR (recR)


0733
202
cytoplasm
DNA topoisomerase III (topB)


0734
322
cytoplasm
S-adenosylmethionine synthetase (metX)


0735
193
cytoplasm
anthranilate synthase component II (trpG) or para-aminobenzoate synthase





glutamine


0736
210
cytoplasm
para-aminobenzoate synthetase component


0737
118
cytoplasm
folylpolyglutamate synthase/dihydrofolate synthase (folC)


0738
184
periplasmic
acetyl-CoA carboxylase, carboxyl transferase subunit beta


0739
93
cytoplasm
acetyl-CoA carboxylase, carboxyl transferase subunit beta


0740
177
inner 1
periplasmic serine protease


0741
321
cytoplasm
periplasmic serine protease


0743
269
cytoplasm
tRNA pseudouridylate synthase I (truA)


0745
235
inner 2
peptide ABC transporter, ATP-binding protein (sapF)


0747
37
cytoplasm
peptide ABC transporter, ATP-binding protein (sapF)


0748
44
cytoplasm
peptide ABC transporter, ATP-binding protein (sapD)


0751
86
cytoplasm
pseudouridine synthase RluD (rluD)


0753
198
cytoplasm
tRNA (guanine-N1)-methyltransferase (trmD)


0754
116
cytoplasm
ribosomal protein L19 (rpL19)


0758
235
cytoplasm
ribosomal protein S3 (rpS3)


0759
110
cytoplasm
ribosomal protein L22 (rpL22)


0760
91
cytoplasm
ribosomal protein S19 (rpS19)


0761
180
cytoplasm
ribosomal protein L2 (rpL2)


0762
221
inner 5
protein-export membrane protein (secD)


0764
406
inner 1
protein-export membrane protein (secD)


0765
97
inner 1
preprotein translocase, YajC subunit (yajC)


0769
37
cytoplasm
queuine tRNA-ribosyltransferase (tgt)


0770
371
cytoplasm
tRNA


0772
55
cytoplasm
thiamine biosynthesis lipoprotein ApbE lipoprotein


0773
35
cytoplasm
lipoprotein


0774
299
inner 1
thiamine biosynthesis lipoprotein ApbE lipoprotein


0777
63
cytoplasm
ribosomal protein L29 (rpL29)


0778
74
cytoplasm
ribosomal protein L16 (rpL16)


0779
335
cytoplasm
dihydrolipoamide acetyltransferase (aceF) or pyruvate dehydrogenase, E2





component,


0781
35
cytoplasm
dihydrolipoamide acetyltransferase (aceF)


0782
549
cytoplasm
pyruvate dehydrogenase, E1 component (aceE)


0787
297
cytoplasm
glycine cleavage system transcriptional activator (gcvA) or transcriptional





regulator, LysR family


0788
159
outer-hand
penicillin-binding protein 1A (ponA)


0790
164
cytoplasm
competence protein A (comA)


0794
168
inner 1
competence protein B (comB)


0795
134
inner 1
competence protein C (comC)


0796
172
inner 1
competence protein D (comD)


0798
166
inner 1
competence protein E (comE)


0801
583
cytoplasm
arginyl-tRNA synthetase (argS)


0802
100
inner 1
glutaredoxin (grx)


0803
406
inner 0
beta-ketoacyl-ACP synthase I (fabB)


0804
137
inner 1
monofunctional biosynthetic peptidoglycan transglycosylase


0805
101
cytoplasm
trp operon repressor (trpR)


0806
305
cytoplasm
soluble lytic murein transglycosylase


0807
267
cytoplasm
2-hydroxyacid (glycerate) dehydrogenase


0808
30
cytoplasm
2-dehydro-3-deoxyphosphooctonate aldolase (kdsA)


0810
249
cytoplasm
2-dehydro-3-deoxyphosphooctonate aldolase (kdsA)


0812
84
cytoplasm
hemK protein (hemK)


0813
202
inner 1
hemK protein (hemK)


0817
411
cytoplasm
hydrolase


0821
240
inner 1
transcriptional regulatory protein (ygiX)


0822
154
inner 1
sensor protein (ygiY)


0823
66
cytoplasm
sensor protein (ygiY)


0824
316
cytoplasm
glutamyl-tRNA synthetase (gltX)


0825
80
cytoplasm
glutamyl-tRNA synthetase (gltX)


0826
79
cytoplasm
glutamyl-tRNA synthetase (gltX)


0828
45
cytoplasm
ribonuclease PH (rph)


0829
278
inner 1
amidophosphoribosyltransferase (purF)


0830
484
cytoplasm
DNA gyrase, subunit A (gyrA)


0831
54
cytoplasm
DNA gyrase, subunit A (gyrA)


0833
583
cytoplasm
hemin receptor (hemR) or iron-regulated outer membrane protein FrpB frpB


0834
143
inner 2
colicin transport protein (tolQ) or biopolymer transport protein ExbB exbB


0835
139
periplasmic
colicin transport protein (tolR) or biopolymer transport protein ExbD exbD


0836
337
inner 1
outer membrane integrity protein (tolA) or IgA-specific serine





endopeptidase iga


0840
76
cytoplasm
ABC transporter, ATP-binding protein


0842
31
cytoplasm
type I restriction enzyme (hsdR)


0844
53
cytoplasm
modification methylase


0845
184
cytoplasm
ADP-heptose synthase (rfaE) or aut protein aut


0847
389
cytoplasm
argininosuccinate lyase (argH)


0848
295
periplasmic
glucosephosphate uridylyltransferase (galU) or UTP--glucose-1-phosphate





uridylyltransferase galU


0849
63
periplasmic
carbon storage regulator (csrA)


0850
461
inner 4
ATP-binding protein protein (cydD)


0851
94
inner 2
ATP-binding protein protein (cydD)


0852
160
inner 1
NAD(P)H oxidoreductase


0856
133
periplasmic
protease IV (sppA)


0857
152
cytoplasm
molybdenum ABC transporter, periplasmic-binding protein


0858
242
inner 5
molybdenum ABC transporter, permease protein (modB) or sulfate ABC





transporter, permease protein cysT


0859
40
cytoplasm
molybdenum ABC transporter, ATP-binding protein (modC)


0860
245
cytoplasm
molybdenum ABC transporter, ATP-binding protein (modC) or sulfate ABC





transporter, ATP-binding protein cysA


0868
119
cytoplasm
type I restriction/modification specificity protein (hsdS)


0869
90
cytoplasm
anthranilate synthase component I trpE


0873
145
cytoplasm
phosphoserine aminotransferase (serC)


0874
234
inner 2
succinyl-CoA synthetase, beta subunit (sucC)


0875
293
inner 1
succinyl-CoA synthetase, alpha subunit (sucD)


0882
93
cytoplasm
mazG protein (mazG)


0887
285
inner 1
3-oxoacyl-(acyl-carrier-protein) reductase fabG-2


0890
153
cytoplasm
DNA polymerase III, delta′ subunit (holB)


0892
41
cytoplasm
thiol:disulfide interchange protein (dsbD)


0893
60
cytoplasm
thiol:disulfide interchange protein (dsbD)


0897
234
cytoplasm
phosphoribosylaminoimidazolecarboxamide formyltransferase


0898
552
cytoplasm
ATP-dependent RNA helicase DeaD (deaD)


0900
64
cytoplasm
type I restriction/modification specificity protein (hsdS)


0903
248
cytoplasm
type I restriction enzyme (hsdR)


0905
106
cytoplasm
2-isopropylmalate synthase (leuA)


0907
373
cytoplasm
DNA processing chain A (dprA)


0910
106
periplasmic
nitrite reductase, Fe—S protein (nrfC)


0912
98
cytoplasm
nitrite reductase, cytochrome C-type protein (nrfB)


0913
277
inner 1
cell division protein FtsK-related protein


0914
205
outer
outer membrane lipoproteins carrier protein (lolA)


0918
286
cytoplasm
glycogen phosphorylase (glgP)


0919
323
cytoplasm
glycogen phosphorylase (glgP)


0920
117
cytoplasm
glycogen phosphorylase (glgP)


0923
253
cytoplasm
glycogen synthase (glgA)


0925
105
cytoplasm
phosphoglycerate mutase (gpmA)


0934
242
cytoplasm
3-ketoacyl-acyl carrier protein reductase (fabG)


0935
48
cytoplasm
malonyl CoA-acyl carrier protein transacylase (fabD)


0936
222
cytoplasm
malonyl CoA-acyl carrier protein transacylase (fabD)


0939
111
cytoplasm
3-oxoacyl-(acyl-carrier-protein) synthase III fabH


0945
125
cytoplasm
molybdopterin biosynthesis protein (moeB) or thiF protein thiF


0946
404
cytoplasm
molybdopterin biosynthesis protein (moeA)


0947
55
cytoplasm
GTP cyclohydrolase I (folE)


0950
353
inner 2
protease (sohB)


0954
274
cytoplasm
recombination associated protein RdgC rdgC


0956
354
cytoplasm
adenosylmethionine-8-amino-7-oxononanoate aminotransferase


0958
379
cytoplasm
8-amino-7-oxononanoate synthase (bioF)


0960
80
cytoplasm
ABC transporter, ATP-binding protein


0962
66
cytoplasm
ABC transporter, ATP-binding protein


0963
317
cytoplasm
ABC transporter, ATP-binding protein (msbA)


0965
313
cytoplasm
tetraacyldisaccharide 4′-kinase lpxK


0966
254
cytoplasm
3-deoxy-D-manno-octulosonate cytidylyltransferase (kdsB)


0967
77
cytoplasm
excinuclease ABC, subunit C (uvrC)


0969
204
cytoplasm
ABC transporter, ATP-binding protein


0974
90
cytoplasm
dethiobiotin synthase (bioD-2)


0976
223
cytoplasm
biotin synthesis protein BioC


0977
549
cytoplasm
long chain fatty acid coA ligase


0983
574
cytoplasm
phosphoenolpyruvate carboxylase (ppc)


0984
303
cytoplasm
gcpE protein (gcpE)


0988
226
cytoplasm
rbs repressor (rbsR)


0989
322
inner 1
ribokinase (rbsK) or ADP-heptose synthase


0990
156
cytoplasm
D-ribose ABC transporter, periplasmic-binding protein (rbsB)


0992
223
cytoplasm
baseplate assembly protein V


0994
52
inner 0
adhesin/invasin


0997
454
lipo
multidrug efflux pump channel protein mtrE


1001
273
cytoplasm
transcription termination factor (rho)


1002
230
inner 5
type 4 prepilin-like protein specific leader peptidase


1003
143
inner 1
pilus assembly protein PilG pilG


1007
39
cytoplasm
glycerol-3-phosphate regulon repressor (glpR)


1008
306
cytoplasm
fructose-1,6-bisphosphatase (fbp)


1012
233
inner 8
hydroxyacylglutathione hydrolase


1014
182
cytoplasm
tellurite resistance protein (tehB)


1015
541
periplasmic
oligopeptide ABC transporter, periplasmic-binding protein


1018
45
periplasmic
oligopeptide ABC transporter, permease protein (oppB)


1019
256
cytoplasm
methylenetetrahydrofolate


1021
428
inner 0
L-fucose permease (fucP) or glucose/galactose transporter gluP


1022
216
cytoplasm
L-fuculose phosphate aldolase (fucA)


1023
144
cytoplasm
fucose operon protein (fucU)


1024
30
cytoplasm
fuculokinase (fucK)


1030
492
cytoplasm
anaerobic glycerol-3-phosphate dehydrogenase, subunit A


1031
320
inner 1
anaerobic glycerol-3-phosphate dehydrogenase, subunit B


1032
242
inner 5
transporter


1033
116
cytoplasm
arsenate reductase


1041
70
cytoplasm
hypoxanthine phosphoribosyltransferase (hpt)


1043
460
inner 9
proton glutamate symport protein or sodium/dicarboxylate symporter family





protein


1045
155
cytoplasm
anaerobic ribonucleoside-triphosphate reductase activating


1046
242
cytoplasm
transport ATP-binding protein (cydC) ABC transporter


1048
212
inner 4
transport ATP-binding protein (cydC)


1050
359
cytoplasm
fructose-bisphosphate aldolase (fba)


1051
346
cytoplasm
ADP-heptose--LPS heptosyltransferase II rfaF


1053
56
cytoplasm
peptidyl-prolyl cis-trans isomerse


1054
201
outer
peptidyl-prolyl cis-trans isomerse


1057
452
cytoplasm
thiophene and furan oxidation protein (thdF)


1058
224
inner 2
inner membrane protein, 60 kDa (yidC)


1059
58
cytoplasm
ribosomal protein S18 (rpS18)


1060
149
cytoplasm
ribosomal protein L9 (rpL9)


1061
577
cytoplasm
heat shock protein (groEL)


1062
102
cytoplasm
chaperonin (groES)


1063
190
inner 4
urease, gamma subunit (ureA)


1064
216
inner 5
rod shape-determining protein (rodA) or cell division protein FtsW ftsW


1066
66
cytoplasm
penicillin-binding protein 2 (pbp2)


1068
66
cytoplasm
cell division protein FtsK-related protein


1071
447
cytoplasm
protease IV (sppA)


1074
286
cytoplasm
lic-1 operon protein (licD)


1075
213
outer
aminopeptidase A/I (pepA)


1077
141
cytoplasm
nucleoside diphosphate kinase (ndk)


1078
227
cytoplasm
GTP-binding protein (yhbZ)


1080
317
inner 1
phosphoribosylamine--glycine ligase (purD)


1081
198
cytoplasm
phosphoribosylaminoimidazolecarboxamide formyltransferase


1082
31
outer
phosphoribosylaminoimidazolecarboxamide formyltransferase


1083
45
inner 0
phosphoribosylaminoimidazolecarboxamide formyltransferase


1084
199
inner 0
sufI protein (sufI)


1085
125
inner 1
1-acyl-glycerol-3-phosphate acyltransferase (plsC)


1087
75
inner 1
1-acyl-glycerol-3-phosphate acyltransferase (plsC)


1091
199
inner 4
sodium- and chloride-dependent transporter


1092
217
inner 2
potassium/copper-transporting ATPase


1093
68
cytoplasm
mercuric ion scavenger protein (merP)


1094
68
cytoplasm
mercuric ion scavenger protein (merP)


1095
68
cytoplasm
mercuric ion scavenger protein (merP)


1096
144
cytoplasm
transcriptional regulator, merR family


1097
105
cytoplasm
met repressor (metJ)


1098
109
inner 1
transcription termination factor (rho)


1100
317
cytoplasm
fumarate reductase, flavoprotein subunit (frdA) or succinate





dehydrogenase, flavoprotein subunit sdhA


1101
276
cytoplasm
fumarate reductase, iron-sulfur protein (frdB) or succinate dehydrogenase,





iron-sulfur protein sdhB


1102
132
inner 3
fumarate reductase, 15 kDa hydrophobic protein (frdC)


1103
114
inner 1
fumarate reductase, 13 kDa hydrophobic protein (frdD)


1109
170
cytoplasm
terminase, small subunit


1116
51
cytoplasm
heme-hemopexin utilization protein A (hxuA)


1117
165
cytoplasm
heme-hemopexin utilization protein A (hxuA)


1120
118
cytoplasm
dihydroneopterin aldolase (folB)


1124
338
inner 1
nitrate/nitrite sensor protein (narQ)


1125
225
inner 1
topoisomerase IV, subunit A (parC)


1127
139
cytoplasm
glucose kinase


1132
202
cytoplasm
type I modification enzyme (hsdM)


1135
260
cytoplasm
type I modification enzyme (hsdM)


1137
362
cytoplasm
type I restriction/modification specificity protein (hsdS)


1138
226
inner 0
thiamin-phosphate pyrophosphorylase


1139
254
cytoplasm
phosphomethylpyrimidine kinase (thiD)


1140
32
cytoplasm
phosphomethylpyrimidine kinase (thiD)


1141
263
inner 1
hydroxyethylthiazole kinase


1143
70
cytoplasm
outer membrane protein NsgA


1144
51
cytoplasm
ribonuclease E (rne)


1145
75
cytoplasm
ribonuclease E (rne)


1148
42
cytoplasm
ribonuclease E (rne)


1151
180
inner 1
adenine phosphoribosyltransferase (apt)


1152
311
cytoplasm
DNA polymerase III, subunits gamma and tau (dnaX)


1154
221
cytoplasm
DNA polymerase III, subunits gamma and tau (dnaX)


1155
173
cytoplasm
DNA polymerase III, subunits gamma and tau (dnaX)


1156
60
cytoplasm
uracil phosphoribosyltransferase (upp)


1165
406
cytoplasm
nifS protein (nifS)


1166
151
cytoplasm
iscU protein (iscU)


1167
107
cytoplasm
HesB/YadR/YfhF family protein


1168
174
cytoplasm
co-chaperone Hsc20 (hscB)


1171
151
cytoplasm
heat shock protein (hscA)


1172
53
cytoplasm
D-lactate dehydrogenase (dld)


1173
36
cytoplasm
type I restriction enzyme EcoR124II R protein,


1174
183
lipo
lipoprotein (spr)


1175
194
cytoplasm
tldD protein tldD


1177
44
cytoplasm
hemoglobin-binding protein


1180
234
cytoplasm
peptidase E (pepE)


1182
386
cytoplasm
ribosomal protein S1 (rpS1)


1183
94
cytoplasm
integration host factor, beta-subunit (himD)


1186
194
cytoplasm
orotidine 5′-phosphate decarboxylase (pyrF)


1188
181
inner 1
lipopolysaccharide biosynthesis protein


1189
264
inner 1
alpha-1,2-N-acetylglucosamine transferase rfaK


1190
57
periplasmic
lipopolysaccharide biosynthesis protein


1191
304
inner 2
alpha-2,3-sialyltransferase


1192
160
inner 4
lipopolysaccharide biosynthesis protein


1197
124
cytoplasm
uridine kinase (udk)


1198
195
cytoplasm
deoxycytidine triphosphate deaminase (dcd)


1201
402
inner 10
drug resistance translocase family protein


1202
158
cytoplasm
GTP-binding protein


1203
55
outer
hemoglobin-binding protein


1206
736
cytoplasm
TonB-dependent receptor or hemoglobin receptor hmbR


1207
91
cytoplasm
transcriptional regulator, HTH_3 family


1212
230
cytoplasm
glycyl-tRNA synthetase, beta chain (glyS)


1218
244
cytoplasm
glycyl-tRNA synthetase, alpha chain (glyQ)


1228
198
cytoplasm
seryl-tRNA synthetase (serS)


1229
282
inner 2
cytochrome C-type biogenesis protein (nrfF)


1230
176
inner 1
thiol:disulfide interchange protein (dsbE)


1231
507
inner 9
cytochrome C-type biogenesis


1233
380
inner 1
glutamate dehydrogenase (gdhA)


1242
135
cytoplasm
transcriptional regulator


1253
266
cytoplasm
transcriptional regulatory protein


1254
101
inner 3
galactoside ABC transporter, permease protein (mglC)


1256
185
inner 6
intracellular septation protein A ispA


1258
154
cytoplasm
acyl CoA thioester hydrolase family protein


1261
158
periplasmic
soluble lytic murein transglycosylase


1263
229
cytoplasm
pyridoxamine phosphate oxidase (pdxH)


1264
162
cytoplasm
GTP-binding protein


1266
69
cytoplasm
NAD(P)H-flavin oxidoreductase


1267
386
cytoplasm
ATP-binding protein (mrp)


1268
460
periplasmic
methionyl-tRNA synthetase (metG)


1269
70
cytoplasm
phosphoribosylaminoimidazole carboxylase, catalytic


1272
596
cytoplasm
aminopeptidase N (pepN)


1273
175
inner 1
dihydrodipicolinate reductase (dapB)


1274
82
cytoplasm
ferredoxin


1276
329
cytoplasm
phenylalanyl-tRNA synthetase, alpha subunit (pheS)


1277
373
cytoplasm
phenylalanyl-tRNA synthetase, beta subunit (pheT)


1278
286
cytoplasm
DNA adenine methylase (dam)


1279
298
inner 1
3-dehydroquinate synthase (aroB)


1280
74
inner 2
NADH:ubiquinone oxidoreductase, Na translocating


1281
208
inner 6
NADH:ubiquinone oxidoreductase, Na translocating


1282
269
inner 1
NADH:ubiquinone oxidoreductase, Na translocating


1283
411
inner 7
NADH:ubiquinone oxidoreductase, subunit B (nqrB)


1284
48
cytoplasm
NADH:ubiquinone oxidoreducatase subunit A, Na translocating


1285
254
cytoplasm
NADH:ubiquinone oxidoreducatase subunit A, Na translocating


1286
85
inner 1
nitrogen fixation protein (rnfG)


1287
358
inner 9
Na(+)-translocating NADH-quinone reductase, subunit


1290
679
outer
ferredoxin, 4Fe—4S bacterial type


1291
58
cytoplasm
ferredoxin, 4Fe—4S bacterial type


1295
406
inner 1
polyribonucleotide nucleotidyltransferase pnp


1297
296
inner 1
polyribonucleotide nucleotidyltransferase pnp


1302
452
inner 1
O-succinylbenzoate--CoA ligase (menE) or long-chain-fatty-acid--CoA





ligase fadD-2


1303
201
cytoplasm
seqA protein (seqA)


1304
85
cytoplasm
esterase/lipase


1305
65
inner 1
esterase/lipase


1306
144
inner 0
esterase/lipase


1307
41
inner 1
iron (chelated) ABC transporter, permease protein (yfeD)


1308
147
inner 2
iron (chelated) ABC transporter, permease protein (yfeD)


1309
282
inner 8
iron (chelated) ABC transporter, permease protein (yfeC)


1310
306
cytoplasm
iron (chelated) transporter, ATP-binding protein (yfeB)


1311
293
periplasmic
iron (chelated) ABC transporter, periplasmic-binding protein


1313
154
lipo
outer membrane integrity protein (tolA) or IgA-specific serine





endopeptidase iga


1314
253
cytoplasm
penicillin-binding protein 7


1318
41
cytoplasm
transcriptional activator (ilvY)


1319
292
inner 9
rarD protein


1320
105
cytoplasm
glpE protein (glpE)


1321
263
inner 1
triosephosphate isomerase (tpiA)


1323
107
cytoplasm
integrase/recombinase (xerC)


1324
100
cytoplasm
dnaK suppressor protein (dksA)


1326
58
cytoplasm
poly(A) polymerase (pcnB)


1327
450
inner 10
C4-dicarboxylate transporter


1331
131
cytoplasm
uracil DNA glycosylase (ung)


1332
124
inner 2
bicyclomycin resistance protein (bcr)


1338
50
cytoplasm
gamma-glutamyl phosphate reductase (proA)


1339
47
cytoplasm
gamma-glutamyl phosphate reductase (proA)


1340
39
cytoplasm
gamma-glutamyl phosphate reductase (proA)


1341
319
inner 1
gamma-glutamyl phosphate reductase (proA)


1343
98
cytoplasm
heat shock protein (dnaJ)


1344
133
cytoplasm
acetyl-CoA carboxylase, biotin carboxyl carrier protein


1345
443
cytoplasm
acetyl-CoA carboxylase, biotin carboxylase (accC)


1348
320
inner 7
sodium/pantothenate symporter (panF)


1349
493
cytoplasm
cell division protein (ftsH)


1351
201
cytoplasm
dihydropteroate synthase (folP-2)


1352
445
cytoplasm
mrsA protein (mrsA) or phosphoglucomutase/phosphomannomutase family


1355
438
cytoplasm
DNA-directed RNA polymerase, beta′ chain (rpoC)


1357
172
inner 2
rod shape-determining protein (rodA)


1359
621
inner 1
penicillin-binding protein 2 (pbp2)


1361
193
cytoplasm
modification methylase NlaIV


1363
432
inner 1
3-phosphoshikimate-1-carboxyvinyltransferase (aroA) or 3-


1365
298
inner 1
formyltetrahydrofolate deformylase (purU) or phosphoribosylglycinamide





formyltransferase purN


1366
138
cytoplasm
DNA-binding protein H-NS (hns)


1369
66
cytoplasm
DNA polymerase III, alpha subunit (dnaE)


1370
35
cytoplasm
DNA polymerase III, alpha subunit (dnaE)


1371
847
cytoplasm
DNA polymerase III, alpha subunit (dnaE)


1373
118
cytoplasm
threonine deaminase (ilvA)


1378
196
cytoplasm
MutT/nudix family protein


1379
382
inner 1
glutamate 5-kinase (gamma-glutamyl kinase) (proB)


1380
128
inner 0
dihydrofolate reductase (folA)


1381
46
cytoplasm
dihydrofolate reductase (folA)


1383
392
inner 2
multidrug resistance protein A (emrA) or fatty acid efflux system protein





farA


1384
343
cytoplasm
poly(A) polymerase (pcnB)


1386
106
cytoplasm
2-amino-4-hydroxy-6-hydroxymethyldihydropteridine-


1388
432
periplasmic
N-acetylmuramoyl-L-alanine amidase


1389
227
cytoplasm
DNA mismatch repair protein (mutL)


1392
247
cytoplasm
hemY protein (hemY)


1393
175
inner 1
hemY protein (hemY)


1394
377
periplasmic
uroporphyrin-III C-methyltransferase (hemX)


1398
194
inner 0
transcriptional activator (ilvY)


1400
492
inner 1
ketol-acid reductoisomerase (ilvC)


1401
426
cytoplasm
anaerobic glycerol-3-phosphate dehydrogenase, subunit C


1402
30
cytoplasm
tRNA (guanine-N1)-methyltransferase (trmD)


1403
59
cytoplasm
16S rRNA processing protein RimM rimM


1404
81
cytoplasm
16S rRNA processing protein RimM rimM


1405
82
cytoplasm
ribosomal protein S16 (rpS16)


1407
603
periplasmic
5′-nucleotidase


1408
128
cytoplasm
shikimic acid kinase I (aroK)


1410
249
cytoplasm
stationary-phase survival protein (surE)


1411
128
inner 2
lipoprotein B (lppB)


1412
74
inner 1
lipoprotein B (lppB)


1416
354
lipo
lipoprotein NlpD


1417
56
cytoplasm
lipoprotein NlpD


1420
62
inner 1
phosphate ABC transporter, permease protein (pstC)


1421
282
inner 5
phosphate ABC transporter, permease protein (pstA) or sulfate ABC





transporter, permease protein cysT


1422
255
cytoplasm
amino acid ABC transporter, ATP-binding protein or sulfate ABC





transporter, ATP-binding protein cysA


1423
154
cytoplasm
phosphate regulon transcriptional regulatory protein (phoB) or DNA-binding





response regulator NULL


1424
72
cytoplasm
phosphate regulon transcriptional regulatory protein (phoB)


1425
425
inner 1
phosphate regulon sensor protein (phoR) or sensor histidine kinase NULL


1426
44
cytoplasm
exodeoxyribonuclease I (sbcB)


1427
474
inner 1
exodeoxyribonuclease I (sbcB)


1428
158
inner 1
aminopeptidase A/I (pepA)


1429
480
inner 5
high-affinity choline transport protein (betT)


1430
132
inner 2
high-affinity choline transport protein (betT)


1431
57
inner 0
sensor protein (ygiY)


1432
139
cytoplasm
high affinity ribose transport protein (rbsD)


1433
493
cytoplasm
D-ribose ABC transporter, ATP-binding protein (rbsA)


1434
323
inner 9
D-ribose ABC transporter, permease protein (rbsC)


1435
53
periplasmic
D-ribose ABC transporter, periplasmic-binding protein


1436
88
cytoplasm
D-ribose ABC transporter, periplasmic-binding protein (rbsB)


1438
246
inner 6
heme exporter protein C (ccmC) or cytochrome c-type biogenesis protein


1439
221
inner 6
heme exporter protein B (ccmB)


1440
212
cytoplasm
heme exporter ATP-binding protein A (ccmA) or amino acid ABC





transporter, ATP-binding protein


1442
215
cytoplasm
superoxide dismutase (sodA)


1443
231
cytoplasm
ABC transporter, ATP-binding protein


1445
105
cytoplasm
anti-sigma factor B antagonist


1446
99
cytoplasm
BolA/YrbA family protein


1447
424
inner 3
UDP-N-acetylglucosamine 1-carboxyvinyltransferase (murZ)


1448
110
inner 1
amino acid ABC transporter, periplasmic-binding protein


1449
135
cytoplasm
amino acid ABC transporter, periplasmic-binding protein


1450
234
inner 3
amino acid ABC transporter, permease protein


1456
51
cytoplasm
ATP-dependent Clp protease, ATPase subunit (clpB)


1457
246
cytoplasm
RNA methyltransferase, TrmH family


1459
782
cytoplasm
virulence-associated protein (vacB) or ribonuclease II family protein vacB


1460
83
cytoplasm
peptidyl-prolyl cis-trans isomerase, FkbP-type (slyD) or FKBP-type peptidyl-





prolyl cis-trans isomerase


1462
128
cytoplasm
ribosome binding factor A (rbfA)


1463
306
cytoplasm
tRNA pseudouridine 55 synthase (truB)


1464
379
inner 1
chorismate mutase/prephenate dehydrogenase (tyrA)


1467
38
inner 1
chorismate synthase (aroC)


1468
286
periplasmic
penicillin-insensitive murein endopeptidase (mepA)


1472
318
inner 2
lipid A biosynthesis (kdo)2-(lauroyl)-lipid IVA or HtrB/MsbB family protein


1473
126
inner 1
oligopeptide transporter, periplasmic-binding protein,


1475
696
cytoplasm
oligopeptidase A (prlC)


1476
292
cytoplasm
type I modification enzyme (hsdM)


1477
196
cytoplasm
type I modification enzyme (hsdM)


1480
204
cytoplasm
riboflavin synthase, alpha chain (ribE)


1482
212
cytoplasm
aminopeptidase N (pepN)


1483
140
cytoplasm
glutaminyl-tRNA synthetase (glnS)


1485
699
cytoplasm
4-alpha-glucanotransferase (malQ)


1499
273
cytoplasm
glutamine synthetase (glnA)


1500
96
inner 1
glutamine synthetase (glnA)


1501
50
cytoplasm
glutamine synthetase (glnA)


1503
347
inner 0
DTDP-glucose 4,6-dehydratase (rffG)


1505
527
cytoplasm
topoisomerase IV, subunit B (parE)


1506
315
inner 1
lipid A biosynthesis lauroyl acyltransferase (htrB)


1507
308
cytoplasm
ADP-heptose synthase (rfaE)


1508
83
cytoplasm
DNA-directed RNA polymerase, beta′ chain (rpoC)


1509
829
cytoplasm
DNA-directed RNA polymerase, beta′ chain (rpoC)


1510
332
inner 8
tellurite resistance protein (tehA)


1511
81
cytoplasm
ribosomal protein L13 (rpL13)


1512
153
cytoplasm
ribosomal protein S9 (rpS9)


1513
101
cytoplasm
urease, beta subunit (ureB)


1514
572
cytoplasm
urease, alpha subunit (ureC)


1515
185
inner 1
urease accessory protein (ureE)


1519
183
cytoplasm
urease accessory protein (ureF)


1520
107
cytoplasm
urease accessory protein (ureG)


1523
334
cytoplasm
ornithine carbamoyltransferase (arcB)


1524
310
cytoplasm
carbamate kinase (arcC)


1526
193
inner 3
efflux pump component MtrF mtrF


1527
113
inner 2
anaerobic C4-dicarboxylate membrane transporter protein


1528
136
inner 1
NADH dehydrogenase (ndh)


1530
315
cytoplasm
NADH dehydrogenase (ndh)


1531
410
inner 1
glycerol-3-phosphate acyltransferase (plsB)


1532
367
inner 0
glycerol-3-phosphate acyltransferase (plsB)


1533
75
cytoplasm
lexA repressor (lexA)


1534
121
cytoplasm
opacity protein or outer membrane protein NsgA nsgA


1537
227
inner 4
arginine ABC transporter, permease protein (artM)


1538
221
inner 4
arginine ABC transporter, permease protein (artQ)


1539
72
cytoplasm
arginine ABC transporter, periplasmic-binding protein (artI)


1541
99
periplasmic
arginine ABC transporter, periplasmic-binding protein


1542
243
cytoplasm
arginine ABC transporter, ATP-binding protein (artP)


1544
69
cytoplasm
phosphoheptose isomerase (gmhA)


1545
73
cytoplasm
shikimate 5-dehydrogenase-related protein


1546
267
cytoplasm
serine acetyltransferase (cysE)


1548
332
inner 1
glycerol-3-phosphate dehydrogenase (NAD+) (gpsA)


1549
567
cytoplasm
adenylate cyclase (cyaA)


1550
42
cytoplasm
adenylate cyclase (cyaA)


1551
228
cytoplasm
adenylate cyclase (cyaA)


1552
110
lipo
ribosomal-protein-alanine acetyltransferase (rimI)


1554
134
cytoplasm
DNA polymerase III, psi subunit (holD)


1556
222
cytoplasm
hemK protein hemK


1558
181
cytoplasm
GTP-binding protein (era)


1559
125
inner 0
GTP-binding protein (era)


1561
227
cytoplasm
ribonuclease III (rnc)


1562
349
inner 3
signal peptidase I (lepB)


1565
345
cytoplasm
tail fibre protein


1568
395
cytoplasm
tyrosyl tRNA synthetase (tyrS)


1569
315
inner 1
phosphoribosylpyrophosphate synthetase (prsA)


1575
72
inner 1
IS1016-V6 protein


1576
563
cytoplasm
glucose-6-phosphate isomerase (pgi)


1577
360
cytoplasm
alanine racemase, biosynthetic (alr)


1578
126
cytoplasm
replicative DNA helicase (dnaB)


1579
303
cytoplasm
replicative DNA helicase (dnaB)


1582
991
outer-hand
hemoglobin-binding protein


1583
237
cytoplasm
zinc protease


1584
276
inner 1
adenylosuccinate synthetase (purA)


1585
41
cytoplasm
adenylosuccinate synthetase (purA)


1586
297
inner 1
2,3,4,5-tetrahydropyridine-2-carboxylate


1588
336
inner 1
purine nucleotide synthesis repressor (purR)


1589
78
cytoplasm
phosphoenolpyruvate carboxylase (ppc)


1590
45
inner 1
ribosomal protein S1 (rpS1)


1591
244
cytoplasm
cytidylate kinase 2 (cmkB)


1593
291
cytoplasm
singlet oxygen resistance protein


1597
549
inner 1
D-lactate dehydrogenase (dld)


1609
462
inner 1
oxidoreductase


1610
199
cytoplasm
spermidine/putrescine ABC transporter, periplasmic-binding


1613
41
cytoplasm
carbonic anhydrase


1614
647
cytoplasm
ABC transporter, ATP-binding protein


1618
289
inner 6
cytochrome C-type biogenesis protein (ccmF)


1619
181
periplasmic
thiol:disulfide interchange protein (dsbE)


1624
152
cytoplasm
DNA ligase (lig)


1625
1027
inner 1
type I restriction enzyme (hsdR)


1627
123
cytoplasm
anticodon nuclease prrC


1629
177
inner 1
oligopeptide ABC transporter, ATP-binding protein (oppD) or sulfate ABC





transporter, ATP-binding protein cysA


1630
356
cytoplasm
oligopeptide ABC transporter, ATP-binding protein (oppF) or sulfate ABC





transporter, ATP-binding protein cysA


1631
292
inner 1
membrane protein (lapB)


1635
683
cytoplasm
5-methyltetrahydropteroyltriglutamate-homocysteine


1636
73
cytoplasm
5-methyltetrahydropteroyltriglutamate-homocysteine


1639
363
cytoplasm
GTP-binding protein


1640
194
cytoplasm
peptidyl-tRNA hydrolase (pth)


1645
163
cytoplasm
exodeoxyribonuclease VII, large subunit (xseA)


1646
183
cytoplasm
YhbX/YhjW/YijP/YjdB family protein


1648
242
cytoplasm
heat shock protein (dnaJ)


1650
320
cytoplasm
heat shock protein 70 (dnaK)


1651
327
cytoplasm
heat shock protein 70 (dnaK)


1653
411
inner 8
gluconate permease gntP


1659
269
cytoplasm
molybdenum cofactor biosynthesis protein A (moaA)


1662
337
inner 2
sugar isomerase, KpsF/GutQ family


1664
531
inner 1
single-stranded-DNA-specific exonuclease (recJ)


1665
39
cytoplasm
single-stranded-DNA-specific exonuclease (recJ)


1666
235
outer
thiol:disulfide interchange protein (dsbA)


1668
230
inner 1
pfs protein (pfs) or 5-methylthioadenosine


1670
565
cytoplasm
transferrin-binding protein or TonB-dependent receptor


1671
568
inner 1
lon protease or ATP-dependent protease La lon


1672
139
cytoplasm
3-hydroxydecanoyl-(acyl carrier-protein) dehydratase (fabA)


1678
155
cytoplasm
bacterioferritin comigratory protein (bcp)


1679
286
cytoplasm
dihydrodipicolinate synthetase (dapA)


1680
209
lipo
lipoprotein


1681
107
cytoplasm
sigma(54) modulation protein


1682
312
cytoplasm
glycosyl transferase


1688
613
inner 2
sensor histidine kinase


1690
145
inner 1
UDP-N-acetylglucosamine acetyltransferase (lpxA)


1692
403
inner 0
lipid-A-disaccharide synthetase (lpxB)


1693
197
inner 1
ribonuclease HII (rnhB)


1694
146
cytoplasm
modification methylase


1696
185
cytoplasm
ribosome releasing factor (rrf)


1698
226
inner 1
1-deoxy-D-xylulose 5-phosphate reductoisomerase (dxr)


1700
171
cytoplasm
1-deoxy-D-xylulose 5-phosphate reductoisomerase (dxr)


1704
370
cytoplasm
ribonucleoside-diphosphate reductase, alpha chain (nrdA)


1705
39
cytoplasm
ribonucleoside diphosphate reductase, beta chain (nrdB)


1706
311
cytoplasm
ribonucleoside diphosphate reductase, beta chain (nrdB)


1707
409
inner 1
2-oxoglutarate dehydrogenase E2 component, dihydrolipoamide


1708
222
cytoplasm
2-oxoglutarate dehydrogenase E1 component (sucA)


1709
184
cytoplasm
ribosomal protein S4 (rpS4)


1712
314
inner 2
phosphoserine phosphatase (serB)


1714
680
cytoplasm
transketolase 1 (tktA)


1716
333
cytoplasm
biotin synthetase (bioB)


1717
217
cytoplasm
thiamin ABC transporter, ATP-binding protein or spermidine/putrescine





ABC transporter, ATP-binding


1718
84
inner 1
thiamin ABC transporter, permease protein


1719
77
inner 1
molybdopeterin biosynthesis protein (mog)


1720
112
cytoplasm
nitrogen regulatory protein P-II (glnB)


1722
348
inner 6
transporter


1724
264
periplasmic
primosomal protein N′ (priA)


1725
487
inner 1
primosomal protein N′ (priA)


1726
102
cytoplasm
PTS system, glucose-specific IIA component (crr)


1729
581
inner 1
phosphoenolpyruvate-protein phosphotransferase (ptsI)


1730
92
cytoplasm
phosphocarrier protein HPr (ptsH)


1733
189
cytoplasm
oligoribonuclease orn


1735
294
inner 2
phenylalanyl-tRNA synthetase, beta subunit (pheT)


1736
53
cytoplasm
integration host factor, alpha-subunit (himA)


1738
47
cytoplasm
integration host factor, alpha-subunit (himA)


1739
161
lipo
lipoprotein (nlpC)


1747
87
cytoplasm
pyruvate kinase, type II (pykA)


1758
387
cytoplasm
modification methylase NlaIV


1766
90
cytoplasm
exodeoxyribonuclease, small subunit (xseB)


1767
296
inner 1
geranyltranstransferase (ispA)


1768
316
cytoplasm
1-deoxyxylulose-5-phosphate synthase (dxs)


1770
99
inner 1
glycosyl transferase


1771
464
cytoplasm
fumarate hydratase, class II (fumC)


1776
315
cytoplasm
dihydroorotate dehydrogenase (pyrD)


1780
669
cytoplasm
transferrin-binding protein 2 precursor (tbp2)


1781
560
periplasmic
transferrin-binding protein 1 precursor (tbp1)


1782
152
inner 1
deoxyuridinetriphosphatase (dut)


1783
400
inner 1
DNA/pantothenate metabolism flavoprotein (dfp)


1785
234
cytoplasm
DNA repair protein (radC)


1786
82
cytoplasm
ribosomal protein L28 (rpL28)


1787
56
cytoplasm
ribosomal protein L33 (rpL33)


1788
454
inner 1
L-2,4-diaminobutyrate:2-ketoglutarate 4-aminotransferase or acetylornithine





aminotransferase argD


1790
132
cytoplasm
virulence associated protein C (vapC)


1791
443
cytoplasm
L-2,4-diaminobutyrate decarboxylase


1792
434
cytoplasm
ATP-dependent RNA helicase (hrpa)


1793
780
inner 1
ATP-dependent RNA helicase (hrpa)


1794
122
cytoplasm
ATP-dependent helicase (hrpa)


1799
243
inner 5
cytochrome D ubiquinol oxidase, subunit II (cydB)


1800
198
cytoplasm
uxu operon regulator (uxuR)


1801
51
cytoplasm
mannonate dehydratase (uxuA)


1802
33
cytoplasm
acyl carrier protein (acpP)


1803
220
inner 5
anaerobic C4-dicarboxylate membrane transporter protein


1805
486
inner 5
NAD(P) transhydrogenase, subunit alpha (pntA)


1806
474
inner 7
NAD(P) transhydrogenase, subunit beta (pntB)


1807
305
periplasmic
transcriptional regulator


1808
70
cytoplasm
DNA topoisomerase I (topA)


1809
50
cytoplasm
signal recognition particle protein (ffh)


1812
88
cytoplasm
type I restriction enzyme (hsdR)


1813
646
inner 1
type I restriction enzyme (hsdR)


1815
418
inner 1
type I restriction/modification specificity protein (hsdS)


1819
545
outer
heme-hemopexin utilization protein B (hxuB)


1825
402
cytoplasm
xylose isomerase (xylA)


1826
493
cytoplasm
xylulose kinase


1827
308
cytoplasm
ADP-L-glycero-D-mannoheptose-6-epimerase (rfaD)


1828
167
inner 1
thioredoxin


1830
223
cytoplasm
deoxyribose-phosphate aldolase (deoC)


1831
509
cytoplasm
competence protein (comM)


1834
72
cytoplasm
glucose kinase


1835
288
inner 1
RpiR/YebK/YfhH family protein


1836
293
inner 0
N-acetylneuraminate lyase (nanA) or dihydrodipicolinate synthase dapA


1838
270
cytoplasm
glucosamine-6-phosphate isomerase (nagB)


1839
381
cytoplasm
N-acetylglucosamine-6-phosphate deacetylase (nagA)


1840
107
cytoplasm
outer membrane protein P2 (ompP2)


1841
38
cytoplasm
DNA polymerase III, delta′ subunit (holB)


1845
716
outer-hand
LavA virulence protein


1846
237
cytoplasm
thymidylate kinase


1848
265
cytoplasm
argininosuccinate synthetase (argG)


1855
97
cytoplasm
exoribonuclease II (rnb)


1858
188
cytoplasm
L-lactate dehydrogenase (lctD)


1859
269
inner 1
glutamate racemase (murI)


1860
693
cytoplasm
ATP-dependent DNA helicase (recG)


1861
515
inner 1
guanosine-3′,5′-bis(diphosphate) 3′-pyrophosphohydrolase


1867
69
cytoplasm
molybdenum-pterin binding protein (mopI)


1868
109
cytoplasm
desulfoviridin gamma subunit


1870
393
inner 1
killing protein (kicB)


1871
343
periplasmic
enolase (eno)


1875
508
cytoplasm
catalase (hktE)


1876
50
cytoplasm
glucosamine--fructose-6-phosphate aminotransferase (glmS)


1877
232
cytoplasm
glycogen synthase (glgA)


1879
174
cytoplasm
glucose-1-phosphate adenylyltransferase (glgC)


1880
283
cytoplasm
glucose-1-phosphate adenylyltransferase (glgC)


1881
435
inner 1
glycogen operon protein (glgX)


1882
229
inner 1
glycogen operon protein (glgX)


1883
685
cytoplasm
1,4-alpha-glucan branching enzyme (glgB)


1884
119
cytoplasm
ribosomal protein S10 (rpS10)


1885
315
inner 1
cys regulon transcriptional activator cysB


1886
217
cytoplasm
acetate CoA-transferase, alpha subunit


1887
233
cytoplasm
acetate CoA-transferase, beta subunit (atoA)


1888
344
inner 5
short-chain fatty acids transporter (atoE)


1889
84
inner 1
short-chain fatty acids transporter (atoE)


1890
393
cytoplasm
acetyl-CoA acetyltransferase (atoB)


1891
310
inner 4
cell division protein (ftsX)


1892
119
periplasmic
cell division ATP-binding protein (ftsE)


1893
129
cytoplasm
cell division ATP-binding protein (ftsE)


1894
175
cytoplasm
signal recognition particle-docking protein FtsY (ftsY)


1895
243
cytoplasm
peptide ABC transporter, ATP-binding protein (sapD)


1896
105
inner 2
peptide ABC transporter, permease protein (sapC)


1897
50
periplasmic
peptide ABC transporter, permease protein (sapC)


1898
184
inner 4
peptide ABC transporter, permease protein (sapC)


1899
321
inner 6
peptide ABC transporter, permease protein (sapB)


1900
564
outer
peptide ABC transporter, periplasmic-binding protein (sapA)


1903
72
cytoplasm
phosphoenolpyruvate carboxylase (ppc)


1905
337
cytoplasm
oxidoreductase


1906
624
inner 1
oxidoreductase


1908
323
inner 0
ferrochelatase (hemH)


1913
321
cytoplasm
thioredoxin reductase (trxB)


1915
127
cytoplasm
thiol peroxidase (tpx)


1917
286
periplasmic
phosphoribosylformylglycinamidine synthase (purL)


1919
960
inner 1
phosphoribosylformylglycinamidine synthase (purL)


1923
247
inner 0
lipooligosaccharide biosynthesis protein


1925
172
inner 5
glp protein


1926
235
cytoplasm
ribosomal large subunit pseudouridine synthase D


1927
923
inner 1
ATP-dependent helicase (hepA)


1928
249
cytoplasm
L-fucose operon activator (fucR) or transcriptional regulator, DeoR family


1929
568
cytoplasm
ABC transporter, ATP-binding protein


1932
440
cytoplasm
hemoglobin-binding protein


1933
158
cytoplasm
hemoglobin-binding protein


1934
140
cytoplasm
3,4-dihydroxy-2-butanone 4-phosphate synthase (ribB) or GTP





cyclohydrolase


1935
282
inner 1
lipooligosaccharide biosynthesis protein or lacto-N-neotetraose





biosynthesis glycosyl


1936
160
cytoplasm
rRNA methylase


1938
355
cytoplasm
signal recognition particle-docking protein FtsY (ftsY)


1939
622
inner 9
O-antigen acetylase


1940
380
cytoplasm
ribonuclease D (rnd)


1941
562
inner 2
long chain fatty acid coenzyme A ligase (fadD)


1942
183
lipo
outer membrane protein


1944
158
cytoplasm
ATP-dependent helicase (dinG)


1949
357
cytoplasm
hemagglutinin/hemolysin-related protein


1950
270
cytoplasm
traN-related protein


1953
232
outer
outer membrane protein P2 (ompP2)


1954
366
cytoplasm
queuosine biosynthesis protein (queA) or S-adenosylmethionine:tRNA


1958
1392
outer
Adhesion and penetration protein


1959
504
cytoplasm
excinuclease ABC, subunit A (uvrA)


1960
220
inner 1
excinuclease ABC, subunit A (uvrA)


1962
384
outer
membrane-bound lytic murein transglycosylase A


1963
261
inner 1
HesA/MoeB/ThiF family protein


1965
333
periplasmic
adhesin


1967
467
inner 1
NMB1183


1969
156
cytoplasm
transcriptional regulator (ttk)


1971
224
cytoplasm
catabolite gene activator (crp)


1972
392
cytoplasm
tRNA (uracil-5-)-methyltransferase trmA


1973
351
cytoplasm
beta-hexosaminidase (exoII) or glycosyl hydrolase, family 3


1975
299
cytoplasm
long-chain fatty acid transport protein (fadL) or outer membrane protein P1


1976
189
cytoplasm
methylated-DNA--protein-cysteine methyltransferase (dat1)


1977
87
cytoplasm
DNA mismatch repair protein (mutH)


1978
53
inner 0
DNA mismatch repair protein (mutH)


1980
71
cytoplasm
DNA mismatch repair protein (mutH)


1981
430
inner 1
cell cycle protein (mesJ)


1982
34
cytoplasm
pyridoxine kinase


1983
186
cytoplasm
acetyl-CoA carboxylase, carboxyl transferase subunit alpha


1984
141
cytoplasm
acetyl-CoA carboxylase, carboxyl transferase subunit alpha


1986
261
inner 9
membrane protein


1988
212
cytoplasm
ABC transporter, ATP-binding protein (yebM)


1989
127
cytoplasm
selenocysteine-specific elongation factor (selB)


1991
55
cytoplasm
selenocysteine-specific elongation factor (selB) or translation elongation





factor Tu tufA


1992
461
inner 1
L-seryl-tRNA selenium transferase (selA)


1993
861
inner 1
DNA mismatch repair protein (mutS)


1995
74
inner 2
tryptophan-specific transport protein (mtr)


1996
339
inner 5
tryptophan-specific transport protein (mtr)


1997
81
inner 2
ATP synthase F0, subunit a (atpB)


1998
88
inner 1
ATP synthase F0, subunit c (atpE)


1999
156
periplasmic
ATP synthase F0, subunit b (atpF)


2000
144
cytoplasm
ATP synthase F1, subunit delta (atpH)


2001
41
inner 0
ATP synthase F1, subunit delta (atpH)


2002
513
cytoplasm
ATP synthase F1, subunit alpha (atpA)


2003
289
cytoplasm
ATP synthase F1, subunit gamma (atpG)


2005
76
inner 1
ATP synthase F1, subunit beta (atpD)


2007
372
cytoplasm
ATP synthase F1, subunit beta (atpD)


2008
147
inner 1
ATP synthase F1, subunit epsilon (atpC)


2009
54
inner 1
tyrosine-specific transport protein (tyrP)


2010
117
inner 1
ribosomal protein L20 (rpL20)


2011
77
cytoplasm
exodeoxyribonuclease V, beta chain (recB)


2012
1086
cytoplasm
exodeoxyribonuclease V, beta chain (recB)


2013
288
cytoplasm
exodeoxyribonuclease V, alpha chain (recD)


2014
47
cytoplasm
exodeoxyribonuclease V, alpha chain (recD)


2016
194
cytoplasm
exodeoxyribonuclease V, alpha chain (recD)


2021
107
cytoplasm
virulence associated protein A (vapA)


2022
556
cytoplasm
ABC transporter, ATP-binding protein


2028
435
cytoplasm
transcription-repair coupling factor (mfd)


2029
228
cytoplasm
transcription-repair coupling factor (mfd)


2030
392
cytoplasm
transcription-repair coupling factor (mfd)


2031
36
cytoplasm
transcription-repair coupling factor (mfd)


2032
86
cytoplasm
leucyl-tRNA synthetase (leuS)


2034
688
cytoplasm
leucyl-tRNA synthetase (leuS)


2036
281
cytoplasm
undecaprenyl diphosphate synthase


2038
288
inner 7
CDP-diglyceride synthetase (cdsA)


2041
283
inner 2
protective surface antigen D15 Omp85


2044
256
cytoplasm
RNA polymerase sigma-70 factor (rpoD)


2045
300
cytoplasm
RNA polymerase sigma-70 factor (rpoD)


2046
347
cytoplasm
DNA primase (dnaG)


2047
191
cytoplasm
DNA primase (dnaG)


2048
52
cytoplasm
DNA primase (dnaG)


2049
71
cytoplasm
ribosomal protein S21 (rpS21)


2050
342
inner 1
O-sialoglycoprotein endopeptidase (gcp)


2051
206
cytoplasm
thymidine kinase (tdk)


2052
406
inner 10
tyrosine-specific transport protein (tyrP) or tryptophan transporter mtr


2053
86
cytoplasm
ferredoxin, 4Fe—4S bacterial type (fdx-2)


2058
263
cytoplasm
phosphoglycerate kinase (pgk)


2059
81
cytoplasm
phosphoglycerate kinase (pgk)


2061
207
cytoplasm
amino acid ABC transporter, ATP-binding protein


2062
79
inner 0
amino acid ABC transporter, ATP-binding protein


2065
230
inner 4
ribonuclease BN (rbn)


2066
53
cytoplasm
ribonuclease BN (rbn)


2070
273
inner 1
uridine phosphorylase (udp)


2071
438
inner 9
transport protein


2073
568
inner 1
2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate


2074
185
cytoplasm
menaquinone-specific isochorismate synthase (menF) or anthranilate





synthase component I trpE


2076
679
cytoplasm
excinuclease ABC, subunit B (uvrB)


2079
756
inner 4
malate oxidoreductase


2081
238
inner 5
tyrosine-specific transport protein (tyrP) or tryptophan transporter mtr


2083
228
inner 0
phosphoribosyl-AMP cyclohydrolase/phosphoribosyl-ATP


2084
258
cytoplasm
hisF cyclase (hisF)


2085
249
cytoplasm
phosphoribosylformimino-5-aminoimidazole carboxamide


2086
199
cytoplasm
amidotransferase (hisH)


2087
381
cytoplasm
imidazoleglycerol-phosphate dehydratase/


2088
367
cytoplasm
histidinol-phosphate aminotransferase (hisC)


2089
427
inner 1
histidinol dehydrogenase (hisD)


2090
35
cytoplasm
ATP phosphoribosyltransferase (hisG)


2091
199
inner 1
biotin operon repressor/biotin acetyl coenzyme A or BirA protein/Bvg





accessory factor


2092
488
inner 1
inosine-5′-monophosphate dehydrogenase (guaB)


2094
523
inner 1
GMP synthase (guaA)


2095
296
inner 7
rarD protein


2097
168
inner 0
transcriptional regulator


2099
321
inner 10
Na+/H+ antiporter (nhaA)


2100
32
cytoplasm
hemolysin


2101
522
inner 7
apolipoprotein N-acyltransferase (cutE)


2106
193
cytoplasm
recombination associated protein RdgC rdgC


2108
105
cytoplasm
recombination associated protein RdgC rdgC


2110
290
cytoplasm
integrase/recombinase


2115
158
inner 4
colicin V production protein (cvpA)


2118
441
inner 2
acetate kinase (ackA)


2119
331
periplasmic
phosphate acetyltransferase (pta)


2120
403
inner 1
phosphate acetyltransferase (pta)


2122
314
inner 1
adenine specific methylase


2123
323
cytoplasm
cys regulon transcriptional activator (cysB)


2124
71
cytoplasm
phosphoribosylaminoimidazole carboxylase, catalytic subunit


2126
362
inner 1
phosphoribosylaminoimidazole carboxylase, ATPase subunit


2127
396
cytoplasm
aspartate aminotransferase (aspC)


2128
220
inner 1
spermidine/putrescine ABC transporter, ATP-binding


2134
152
cytoplasm
mercuric resistance operon regulatory protein (merR2)


2138
560
inner 10
PTS system, fructose-specific IIBC component (fruA)


2139
313
cytoplasm
1-phosphofructokinase (fruK) or ADP-heptose synthase


2140
499
cytoplasm
PTS system, fructose-specific IIA/FPr component (fruB)


2143
92
cytoplasm
virulence associated protein D (vapD)


2146
101
inner 1
hypoxanthine phosphoribosyltransferase (hpt)


2147
451
cytoplasm
pmbA protein (pmbA)


2151
241
cytoplasm
ABC transporter, ATP-binding protein


2152
164
cytoplasm
nitrogen regulatory IIA protein (ptsN)


2155
202
cytoplasm
chorismate mutase/prephenate dehydratase (pheA)


2157
148
cytoplasm
ABC transporter, ATP-binding protein


2158
192
cytoplasm
histidinol-phosphatase


2160
221
cytoplasm
5,10 methylenetetrahydrofolate reductase (metF)


2161
89
cytoplasm
dethiobiotin synthase (bioD-1)


2162
313
inner 5
TRK system potassium uptake protein (trkH) or bis(5′-nucleosyl)-





tetraphosphatase, symmetrical/Trk


2163
191
inner 3
TRK system potassium uptake protein (trkH) or bis(5′-nucleosyl)-





tetraphosphatase, symmetrical/Trk


2166
288
inner 4
heat shock protein (htpX)


2168
130
cytoplasm
ribonuclease


2169
244
inner 0
lipoprotein (vacJ)


2172
185
cytoplasm
transcription antitermination protein (nusG)


2173
138
inner 3
preprotein translocase SecE subunit (secE)


2175
411
cytoplasm
ATP-dependent Clp protease, ATP-binding subunit (clpX)


2176
211
cytoplasm
ATP-dependent Clp protease, proteolytic subunit (clpP)


2177
394
cytoplasm
trigger factor (tig)


2178
52
cytoplasm
trigger factor (tig)


2180
89
cytoplasm
ribosomal protein S20 (rpS20)


2181
524
inner 11
virulence factor (mviN)


2182
312
cytoplasm
riboflavin kinase/FMN adenylyltransferase (ribF)


2183
484
inner 1
isoleucyl-tRNA synthetase ileS


2184
485
cytoplasm
isoleucyl-tRNA synthetase ileS


2185
102
cytoplasm
hit-related protein


2186
184
cytoplasm
lipoprotein


2187
393
periplasmic
penicillin-binding protein 5 (dacA)


2189
212
cytoplasm
lipoate biosynthesis protein B (lipB)


2190
320
cytoplasm
lipoate biosynthesis protein A (lipA)


2191
335
inner 1
citrate lyase ligase (citC)


2192
95
cytoplasm
citrate lyase, gamma chain (citD)


2193
291
inner 0
citrate lyase, beta chain (citE)


2195
500
inner 1
citrate lyase, alpha chain (citF)


2196
416
inner 1
citG protein (citG)


2200
256
inner 1
heme-hemopexin utilization protein A (hxuA)


2202
458
cytoplasm
DNA repair protein (radA)


2204
166
inner 1
leucine responsive regulatory protein (lrp)


2205
554
inner 5
cell division protein FtsK ftsK-1


2208
169
cytoplasm
polypeptide deformylase (def)


2209
318
inner 1
methionyl-tRNA formyltransferase (fmt)


2211
450
cytoplasm
sun protein (sun) or 16S RNA methyltransferase rsmB


2212
458
cytoplasm
TRK system potassium uptake protein (trkA)


2213
134
inner 2
large conductance mechanosensitive channel (mscL)


2215
40
cytoplasm
RNA polymerase sigma-E factor (rpoE)


2231
347
inner 1
lipopolysaccharide biosynthesis protein or ADP-heptose--LPS





heptosyltransferase II rfaF


2232
539
outer
heme-hemopexin utilization protein C or iron-regulated outer membrane





protein FrpB frpB


2233
170
cytoplasm
heme-hemopexin utilization protein C


2234
565
outer
heme-hemopexin utilization protein B (hxuB)


2235
758
outer-hand
heme-hemopexin utilization protein A (hxuA)


2236
231
cytoplasm
DNA ligase ligA-2


2238
327
cytoplasm
dipeptide ABC transporter, ATP-binding protein (dppF)


2241
330
cytoplasm
dipeptide ABC transporter, ATP-binding protein (dppD)


2242
295
inner 6
dipeptide ABC transporter, permease protein (dppC) or thiol:disulfide





interchange protein DsbD dsbD


2243
333
inner 5
dipeptide ABC transporter, permease protein (dppB)


2246
727
cytoplasm
DNA helicase II (uvrD)


2249
141
cytoplasm
6-pyruvoyl tetrahydrobiopterin synthase


2250
227
inner 0
aluminum resistance protein


2252
184
cytoplasm
branched-chain-amino-acid transaminase (ilvE)


2259
898
inner 1
exodeoxyribonuclease V, gamma chain (recC)


2260
163
cytoplasm
exodeoxyribonuclease V, gamma chain (recC)


2262
372
inner 1
riboflavin biosynthesis protein (ribD)


2263
357
inner 1
protease (degS)


2274
192
inner 0
molybdopterin-guanine dinucleotide biosynthesis protein


2277
216
periplasmic
periplasmic oxidoreductase (por) or thiol:disulfide interchange protein DsbA





dsbA-2


2280
363
cytoplasm
tRNA (uracil-5-)-methyltransferase (trmA)


2282
125
inner 1
sigma-E factor regulatory protein


2283
33
cytoplasm
sigma-E factor regulatory protein


2285
178
inner 0
molybdopterin-guanine dinucleotide biosynthesis protein B


2289
652
cytoplasm
ATP-dependent Clp protease, ATPase subunit (clpB)


2293
156
cytoplasm
DNA polymerase I (polA)


2294
785
cytoplasm
DNA polymerase I (polA)


2299
507
inner 0
N utilization substance protein A (nusA)


2301
855
cytoplasm
translation initiation factor 2 (infB)


2303
466
cytoplasm
type I restriction enzyme (hsdR)


2304
285
cytoplasm
type I restriction enzyme (hsdR)


2307
518
cytoplasm
anthranilate synthase component I (trpE)


2308
195
cytoplasm
anthranilate synthase component II (trpG) or para-aminobenzoate synthase





glutamine


2311
84
cytoplasm
anthanilate phosphoribosyltransferase (trpD)


2313
231
cytoplasm
anthanilate phosphoribosyltransferase (trpD)


2314
477
cytoplasm
indole-3-glycerol phosphate synthase/


2317
239
cytoplasm
valyl-tRNA synthetase (valS)


2318
425
inner 1
valyl-tRNA synthetase (valS)


2319
35
cytoplasm
valyl-tRNA synthetase (valS)


2321
150
cytoplasm
valyl-tRNA synthetase (valS)


2322
102
cytoplasm
valyl-tRNA synthetase (valS)


2324
42
inner 1
transport protein


2325
238
cytoplasm
purine-nucleoside phosphorylase (deoD) or 5-methylthioadenosine


2327
142
inner 0
ribosomal protein L11 (rpL11)


2328
229
cytoplasm
ribosomal protein L1 (rpL1)


2329
1298
cytoplasm
DNA-directed RNA polymerase, beta chain (rpoB)


2331
158
cytoplasm
iron(III) ABC transporter, periplasmic-binding protein


2333
506
inner 11
iron(III) ABC transporter, permease protein (hitB)


2335
356
cytoplasm
iron(III) ABC transporter, ATP-binding protein (hitC)


2338
377
cytoplasm
succinyl-diaminopimelate desuccinylase (dapE)


2341
631
cytoplasm
heat shock protein (htpG)


2344
106
periplasmic
organic solvent tolerance protein


2345
667
cytoplasm
organic solvent tolerance protein


2346
572
inner 1
prolyl-tRNA synthetase (proS)


2347
630
inner 1
ATP-dependent DNA helicase (recQ)


2348
113
cytoplasm
cyaY protein (cyaY)


2350
415
cytoplasm
diaminopimelate decarboxylase (lysA)


2351
208
cytoplasm
nitrate/nitrite response regulator protein (narP) or transcriptional regulator,





LuxR family


2354
203
cytoplasm
pseudouridine synthase RluD (rluD) or ribosomal large subunit





pseudouridine synthase D


2356
272
lipo
lipoprotein or competence lipoprotein ComL comL


2359
246
cytoplasm
pyruvate formate-lyase activating enzyme (act)


2360
772
cytoplasm
formate acetyltransferase (pfl)


2361
286
inner 6
formate transporter


2365
276
inner 2
sugar kinase


2368
377
inner 5
amino acid carrier protein


2371
158
inner 0
YgbB/YacN family protein


2373
146
cytoplasm
mioC protein (mioC) or sulfite reductase (NADPH) flavoprotein, alpha


2376
333
inner 1
glpX protein (glpX)


2381
551
inner 6
ABC transporter, ATP-binding protein


2382
360
inner 2
ATP-binding transport protein (cydD)


2383
228
cytoplasm
heat shock protein (grpE)


2385
520
cytoplasm
DNA repair protein (recN)


2387
38
cytoplasm
DNA repair protein (recN)


2388
981
inner 1
glutamate-ammonia-ligase adenylyltransferase (glnE)


2389
311
cytoplasm
tRNA delta(2)-isopentenylpyrophosphate transferase (trpX)


2390
390
cytoplasm
DNA mismatch repair protein (mutL)


2391
123
cytoplasm
thymidylate synthetase (thyA)


2392
173
cytoplasm
cytidine and deoxycytidylate deaminase family


2395
545
cytoplasm
preprotein translocase SecA subunit (secA)


2396
363
cytoplasm
preprotein translocase SecA subunit (secA)


2397
163
cytoplasm
mutator mutT protein (mutT)


2398
618
inner 10
glutathione-regulated potassium efflux system protein (kefC)


2399
254
cytoplasm
3-demethylubiquinone-9 3-methyltransferase ubiG


2401
245
cytoplasm
ribosomal protein S2 (rpS2)


2402
71
inner 1
preprotein translocase SecY subunit (secY)


2403
144
cytoplasm
ribosomal protein L15 (rpL15)


2404
59
cytoplasm
ribosomal protein L30 (rpL30)


2405
267
inner 1
glucosamine--fructose-6-phosphate aminotransferase (glmS)


2406
177
inner 3
disulfide bond formation protein B (dsbB)


2407
238
inner 5
Na+/H+ antiporter (nhaB)


2408
292
inner 5
Na+/H+ antiporter (nhaB)


2410
241
cytoplasm
fatty acid metabolism regulator protein (fadR)


2411
455
cytoplasm
phosphatidylserine synthase (pssA) or cardiolipin synthetase family protein


2412
201
cytoplasm
rRNA methylase


2413
232
cytoplasm
adenine specific methylase


2415
122
cytoplasm
ATP-dependent RNA helicase SrmB (srmB)


2416
287
cytoplasm
ATP-dependent RNA helicase SrmB (srmB)


2417
231
cytoplasm
protease


2418
203
cytoplasm
ATP phosphoribosyltransferase (hisG)


2421
410
cytoplasm
D-3-phosphoglycerate dehydrogenase (serA)


2422
219
inner 1
ribose 5-phosphate isomerase A (rpiA)


2423
383
cytoplasm
oxygen-independent coproporphyrinogen III oxidase


2424
658
cytoplasm
ATP-dependent proteinase (lon)


2428
298
cytoplasm
transcriptional regulator, araC family


2429
38
cytoplasm
ABC transporter, ATP-binding protein


2430
576
inner 4
ABC transporter, ATP-binding protein


2432
92
periplasmic
mercuric ion scavenger protein (merP)


2433
120
inner 3
mercuric ion transport protein (merT)


2435
472
cytoplasm
anaerobic dimethyl sulfoxide reductase, chain A (dmsA)


2436
352
cytoplasm
anaerobic dimethyl sulfoxide reductase, chain A (dmsA)


2437
205
cytoplasm
anaerobic dimethyl sulfoxide reductase, chain B (dmsB)


2438
279
inner 7
anaerobic dimethyl sulfoxide reductase, chain C (dmsC)


2440
166
cytoplasm
ferredoxin-type protein (napF) or NADH dehydrogenase I, I subunit nuol


2443
133
cytoplasm
2-isopropylmalate synthase (leuA)


2445
358
cytoplasm
3-isopropylmalate dehydrogenase (beta-IPM dehydrogenase)


2446
469
cytoplasm
3-isopropylmalate dehydratase, alpha subunit (leuC)


2447
200
inner 0
3-isopropylmalate dehydratase small subunit (leuD)


2448
1794
outer-hand
immunoglobin A1 protease (iga1) or IgA-specific serine endopeptidase iga


2449
378
cytoplasm
DNA/ATP binding protein (recF)


2450
366
cytoplasm
DNA polymerase III, beta subunit (dnaN)


2452
454
cytoplasm
chromosomal replication initiator protein (dnaA)


2453
118
cytoplasm
transferrin-binding protein 1 precursor (tbp1)


2454
231
cytoplasm
transferrin-binding protein 1 precursor (tbp1)


2457
199
inner 1
baseplate assembly protein V


2462
861
cytoplasm
tail fibre protein


2476
69
cytoplasm
aspartokinase I/homoserine dehydrogenase I (thrA)


2477
307
cytoplasm
aspartokinase I/homoserine dehydrogenase I (thrA)


2478
314
inner 1
homoserine kinase (thrB)


2479
425
cytoplasm
threonine synthase (thrC)


2480
238
cytoplasm
integrase/recombinase (xerC)


2491
176
cytoplasm
ferredoxin-type 4Fe—4S protein (napF)


2492
93
cytoplasm
napD protein (napD)


2493
832
outer-hand
Formate dehydrogenase major subunit


2494
279
cytoplasm
ferredoxin-type protein (napG)


2495
287
inner 4
ferredoxin-type 4Fe—4S protein (napH)


2496
150
periplasmic
periplasmic nitrate reductase (napB)


2497
200
inner 1
cytochrome C-type protein (napC)


2498
214
inner 0
adenylate kinase (adk)


2499
412
inner 10
permease or AmpG-related protein


2501
241
inner 0
UDP-glucose 4-epimerase (galE)


2502
82
cytoplasm
UDP-glucose 4-epimerase (galE)


2504
244
cytoplasm
iron(III) ABC transporter, ATP-binding protein fbpC


2505
176
inner 4
ABC transporter, permease protein


2508
241
periplasmic
FkbP-type peptidyl-prolyl cis-trans isomerase (fkpA) or macrophage





infectivity potentiator


2509
73
cytoplasm
slyX protein (slyX)


2511
33
cytoplasm
peroxiredoxin 2 family protein/glutaredoxin


2512
48
cytoplasm
peroxiredoxin 2 family protein/glutaredoxin


2513
117
cytoplasm
peroxiredoxin 2 family protein/glutaredoxin


2514
301
cytoplasm
hydrogen peroxide-inducible genes activator (oxyR) or transcriptional





regulator, LysR family


2517
158
cytoplasm
transcription elongation factor (greB)


2518
770
cytoplasm
transcription accessory protein (tex)


2519
736
cytoplasm
DNA gyrase, subunit B (gyrB)


2520
59
cytoplasm
DNA gyrase, subunit B (gyrB)


2521
234
cytoplasm
ribulose-phosphate 3-epimerase (dod)


2522
224
cytoplasm
phosphoglycolate phosphatase (gph)


2530
132
cytoplasm
transposase


2531
369
inner 8
multidrug resistance protein B (emrB) or fatty acid efflux system protein





farB


2532
256
inner 1
cell division protein (ftsN)


2533
1032
inner 12
acriflavine resistance protein (acrB) or multiple transferable resistance





system protein MtrD


2534
419
inner 1
lipoprotein or membrane fusion protein mtrC


2535
196
cytoplasm
transcriptional repressor (Bm3R1) or trancscriptional regulator MtrR mtrR


2538
418
cytoplasm
ATP-dependent RNA helicase (rhlB)


2541
210
periplasmic
kinase


2542
421
inner 1
serine hydroxymethyltransferase (serine methylase) (glyA)


2543
478
inner 3
YhbX/YhjW/YijP/YjdB family protein


2544
85
cytoplasm
phosphoribosylamine--glycine ligase (purD)


2545
101
inner 1
cell division protein (ftsQ)


2546
306
inner 0
D-alanine--D-alanine ligase (ddlB)


2548
475
inner 2
UDP-N-acetylmuramate--alanine ligase (murC)


2550
351
inner 1
UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide)


2552
394
inner 9
cell division protein (ftsW)


2553
437
cytoplasm
UDP-N-acetylmuramoylalanine--D-glutamate ligase (murD)


2554
360
inner 10
phospho-N-acetylmuramoyl-pentapeptide-transferase E (mraY)


2555
457
cytoplasm
UDP-MurNAc-pentapeptide synthetase (murF)


2556
488
inner 1
UDP-N-acetylmuramyl-tripeptide synthetase (murE)


2557
610
inner 1
penicillin-binding protein 3 (ftsI)


2558
107
inner 1
cell division protein (ftsL)


2561
208
cytoplasm
fuculokinase (fucK)


2564
68
cytoplasm
transcriptional regulatory protein (asnC)


2569
269
inner 0
sulfite synthesis pathway protein (cysQ) or inositol monophosphatase





family protein


2570
474
inner 0
glucose-6-phosphate 1-dehydrogenase (zwf)


2571
245
cytoplasm
oxidoreductase (devB)


2577
392
inner 1
6-phosphogluconate dehydrogenase, decarboxylating (gnd)


2578
76
inner 0
6-phosphogluconate dehydrogenase, decarboxylating (gnd)


2581
275
cytoplasm
diadenosine-tetraphosphatase (apaH) or bis(5′-nucleosyl)-





tetraphosphatase, symmetrical/Trk


2582
312
cytoplasm
lipooligosaccharide biosynthesis protein or lacto-N-neotetraose





biosynthesis glycosyl


2583
287
cytoplasm
dimethyladenosine transferase (ksgA)


2584
253
cytoplasm
lipopolysaccharide glycosyl transferase


2585
65
cytoplasm
lipopolysaccharide glycosyl transferase


2586
84
cytoplasm
translation initiation factor 1 (infA)


2587
480
inner 8
glycerol-3-phosphatase transporter (glpT)


2588
364
lipo
glycerophosphoryl diester phosphodiesterase (glpQ)


2591
217
inner 4
glycerol uptake facilitator protein (glpF)


2592
503
cytoplasm
glycerol kinase (glpK)


2593
155
inner 1
xanthine-guanine phosphoribosyltransferase (gptB)


2594
45
cytoplasm
glycerophosphoryl diester phosphodiesterase (glpQ)


2595
274
lipo
lipoprotein E (hel)


2597
132
inner 1
exopolyphosphatase


2598
212
cytoplasm
exopolyphosphatase


2600
133
inner 1
peptide chain release factor 3 (prfC)


2606
309
cytoplasm
transcriptional activator (metR)


2610
89
periplasmic
pyrroline-5-carboxylate reductase (proC)


2612
189
inner 0
pyrroline-5-carboxylate reductase (proC)


2617
297
cytoplasm
integrase/recombinase (xerD)


2619
335
cytoplasm
Holliday junction DNA helicase (ruvB)


2620
204
cytoplasm
Holliday junction DNA helicase (ruvA)


2621
190
cytoplasm
crossover junction endodeoxyribonuclease (ruvC)


2623
156
cytoplasm
datP pyrophosphohydrolase (ntpA)


2625
588
cytoplasm
aspartyl-tRNA synthetase (aspS)


2629
78
cytoplasm
virulence associated protein B (vapB)


2630
134
cytoplasm
virulence associated protein C


2631
135
cytoplasm
lactoylglutathione lyase (gloA)


2632
229
cytoplasm
ribonuclease T (rnt)


2636
188
cytoplasm
translation elongation factor P (efp)


2640
431
inner 1
opacity associated protein (oapA)


2641
134
lipo
opacity associated protein (oapB)


2642
236
cytoplasm
DNA repair protein (recO)


2643
438
cytoplasm
tRNA (uracil-5-)-methyltransferase trmA


2644
651
cytoplasm
elongation factor G (fusA)


2646
394
cytoplasm
elongation factor Tu (tufB)


2647
75
inner 2
chloride channel protein-related protein


2649
245
inner 3
chloride channel protein-related protein


2654
336
cytoplasm
tryptophanyl-tRNA synthetase (trpS)


2657
92
cytoplasm
adenylosuccinate lyase (purB)


2659
364
cytoplasm
adenylosuccinate lyase (purB)


2660
163
cytoplasm
ribosomal protein L10 (rpL10)


2661
126
inner 0
ribosomal protein L7/L12 (rpL7/L12)


2663
456
inner 0
UDP-N-acetylglucosamine pyrophosphorylase (glmU)


2665
311
cytoplasm
lysophospholipase L2 (pldB)


2666
371
cytoplasm
aspartate-semialdehyde dehydrogenase (asd)


2667
243
inner 4
transport protein


2670
136
cytoplasm
modulator of drug activity B (mdaB)


2671
42
cytoplasm
modulator of drug activity B (mdaB)


2672
676
cytoplasm
ATP-dependent DNA helicase (rep)


2674
156
inner 1
lipopolysaccharide core biosynthesis protein (kdtB)


2675
427
inner 2
3-deoxy-d-manno-octulosonic-acid transferase (kdtA)


2676
254
cytoplasm
lipopolysaccharide biosynthesis protein or beta-1,4-glucosyltransferase lgtF


2678
192
cytoplasm
DNA-3-methyladenine glycosidase I (tagI)


2680
268
inner 1
shikimate 5-dehydrogenase (aroE)


2682
178
cytoplasm
DNA topoisomerase I topA


2683
63
cytoplasm
ABC transporter, ATP-binding protein


2685
115
cytoplasm
anaerobic ribonucleoside-triphosphate reductase (nrdD)


2686
272
cytoplasm
anaerobic ribonucleoside-triphosphate reductase (nrdD)


2687
286
cytoplasm
acyl-CoA thioesterase II (tesB)


2688
469
cytoplasm
cysteinyl-tRNA synthetase (cysS)


2689
169
cytoplasm
peptidyl-prolyl cis-trans isomerase B (ppiB)


2698
107
cytoplasm
thioredoxin (trxM)


2701
335
inner 1
D-lactate dehydrogenase, fermentative (ldhA)


2702
393
inner 1
cystathionine gamma-synthase (metB)


2703
175
inner 1
ParA family protein


2705
451
periplasmic
replicative DNA helicase (dnaB)


2714
140
cytoplasm
single-stranded DNA binding protein (ssb)


2717
686
cytoplasm
DNA topoisomerase III (topB)


2722
156
cytoplasm
DNA repair protein (radC)


2733
150
cytoplasm
mutT protein mutT


2735
170
inner 3
transport protein


2736
280
cytoplasm
aspartate ammonia-lyase (aspA)


2738
236
periplasmic
aspartokinase I/homoserine dehydrogenase I (thrA)


2739
317
cytoplasm
transaldolase B (talB)


2740
217
inner 1
glyceraldehyde-3-phosphate dehydrogenase (gapdH)


2741
34
cytoplasm
inner membrane protein, 60 kDa (yidC)


2742
204
cytoplasm
inner membrane protein, 60 kDa (yidC)


2745
229
cytoplasm
sufI protein (sufI)


2747
167
cytoplasm
heat shock protein (hslU) or ATP-dependent Clp protease, ATP-binding





subunit


2748
94
cytoplasm
spermidine/putrescine ABC transporter, periplasmic-binding


2749
287
inner 8
drug resistance translocase family protein


2750
325
inner 2
potassium/copper-transporting ATPase or cation transport ATPase, E1-E2





family


2751
349
cytoplasm
2-oxoglutarate dehydrogenase E1 component (sucA)


2752
34
cytoplasm
2-oxoglutarate dehydrogenase E1 component (sucA)


2755
38
inner 1
serine transporter (sdaC)


2756
217
inner 4
serine transporter (sdaC)


2758
75
lipo
thermonuclease family protein


2761
144
cytoplasm
orfG protein


2762
51
cytoplasm
methionine aminopeptidase (map)


2763
343
cytoplasm
protein-PII uridylyltransferase glnD


2764
107
inner 4
transporter


2765
282
inner 5
protein-export membrane protein (secF)


2766
96
cytoplasm
recA protein (recA)


2768
152
cytoplasm
regulatory protein (recX)


2769
111
lipo
crcB protein


2772
163
cytoplasm
transcriptional regulatory protein (tyrR) or nitrogen assimilation regulatory





protein NtrX ntrX


2774
209
inner 1
glutathione transferase (bphH) or stringent starvation protein A sspA


2780
43
cytoplasm
CTP synthetase (pyrG)


2782
138
cytoplasm
CTP synthetase (pyrG)


2785
167
cytoplasm
transcriptional regulator


2786
93
cytoplasm
guanylate kinase (gmk)


2788
88
cytoplasm
DNA-directed RNA polymerase, omega chain (rpoZ)


2789
84
cytoplasm
guanosine-3′,5′-bis(diphosphate) 3′-pyrophosphohydrolase


2790
38
cytoplasm
guanosine-3′,5′-bis(diphosphate) 3′-pyrophosphohydrolase


2792
90
cytoplasm
S-adenosylmethionine:2-demethylmenaquinone methyltransferase


2795
120
cytoplasm
rbs repressor (rbsR)


2801
113
cytoplasm
ferredoxin (fdx-1) or ferredoxin, 2Fe—2S type fdx-2


2807
266
inner 1
modification methylase (hindIIIM)


2811
350
cytoplasm
asparaginyl-tRNA synthetase (asnS) or aspartyl-tRNA synthetase aspS


2812
31
cytoplasm
riboflavin synthase, beta chain (ribH)


2813
228
inner 3
PqiA family protein


2814
282
inner 1
pqiB protein pqiB


2815
112
cytoplasm
asparaginyl-tRNA synthetase (asnS) or aspartyl-tRNA synthetase aspS


2817
128
cytoplasm
carbonic anhydrase


2818
122
cytoplasm
transcriptional regulatory protein (tyrR)


2825
215
cytoplasm
pqiB protein pqiB


2827
194
cytoplasm
phosphoheptose isomerase gmhA


2831
233
cytoplasm
28 kDa outer membrane protein (hlpA)


2832
33
cytoplasm
glycerol-3-phosphate regulon repressor (glpR)









REFERENCES
The Contents of which are Hereby Incorporated by Reference


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## Claims

1. An immunogenic composition comprising an effective amount of (a) an isolated, immunogenic polypeptide, wherein the polypeptide comprises the amino acid sequence of SEQ ID NO: 1842 from Haemophilus influenzae strain 86-028NP, or the amino acid sequence of SEQ ID NO: 1842 that lacks a signal sequence; (b) a pharmaceutically acceptable carrier, and (c) an adjuvant.

2. The composition of claim 1, wherein the polypeptide comprises the amino acid sequence of SEQ ID NO:1842.

3. An immunogenic comprising an effective amount of (a) an isolated polypeptide that comprises an amino acid sequence with at least 95% sequence identity to the amino acid sequence of SEQ ID NO: 1842; (b) a pharmaceutically acceptable carrier, and (c) an adjuvant.

4. The composition of claim 1, wherein the adjuvant comprises an aluminium salt.

5. The composition of claim 2, wherein the adjuvant comprises an aluminium salt.

6. The composition of claim 3, wherein the adjuvant comprises an aluminium salt.

7. The composition of claim 1, wherein the adjuvant is an oil emulsion.

8. The composition of claim 2, wherein the adjuvant is an oil emulsion.

9. The composition of claim 3, wherein the adjuvant is an oil emulsion.

10. The composition of claim 7, wherein the adjuvant is MF59.

11. The composition of claim 8, wherein the adjuvant is MF59.

12. The composition of claim 9, wherein the adjuvant is MF59.

13. The composition of claim 7, wherein the adjuvant is Complete Freund's adjuvant or Incomplete Freund's adjuvant.

14. The composition of claim 8, wherein the adjuvant is Complete Freund's adjuvant or Incomplete Freund's adjuvant.

15. The composition of claim 9, wherein the adjuvant is Complete Freund's adjuvant or Incomplete Freund's adjuvant.