Staphylococcus aureus polynucleotides and sequences

Abstract

The present invention provides polynucleotide sequences of the genome of Staphylococcus aureus, polypeptide sequences encoded by the polynucleotide sequences, corresponding polynucleotides and polypeptides, vectors and hosts comprising the polynucleotides, and assays and other uses thereof. The present invention further provides polynucleotide and polypeptide sequence information stored on computer readable media, and computer-based systems and methods which facilitate its use.

Description

REFERENCE TO A SEQUENCE LISTING PROVIDED ON COMPACT DISC

[0002] This application refers to a “Sequence Listing”, which is provided as an electronic document on two identical compact discs (CD-R), labeled “Copy 1” and “Copy 2.” These compact discs each contain the electronic document, filename “PB248P1D1 sequence listing.txt” (6,143,385 bytes in size, created on Dec. 23, 2002), which is hereby incorporated in its entirety herein.

FIELD OF THE INVENTION

[0003] The present invention relates to the field of molecular biology. In particular, it relates to, among other things, nucleotide sequences of Staphylococcus aureus, contigs, ORFs, fragments, probes, primers and related polynucleotides thereof, peptides and polypeptides encoded by the sequences, and uses of the polynucleotides and sequences thereof, such as in fermentation, polypeptide production, assays and pharmaceutical development, among others.

BACKGROUND OF THE INVENTION

[0004] The genus Staphylococcus includes at least 20 distinct species. (For a review see Novick, R. P., The Staphylococcus as a Molecular Genetic System, Chapter 1, pgs. 1-37 in MOLECULAR BIOLOGY OF THE STAPHYLOCOCCI, R. Novick, Ed., VCH Publishers, New York (1990)). Species differ from one another by 80% or more, by hybridization kinetics, whereas strains within a species are at least 90% identical by the same measure.

[0005] The species Staphylococcus aureus, a gram-positive, facultatively aerobic, clump-forming cocci, is among the most important etiological agents of bacterial infection in humans, as discussed briefly below.

[0006] Human Health and S. Aureus

[0007] Staphylococcus aureus is a ubiquitous pathogen. (See, for instance, Mims et al., MEDICAL MICROBIOLOGY, Mosby-Year Book Europe Limited, London, UK (1993)). It is an etiological agent of a variety of conditions, ranging in severity from mild to fatal. A few of the more common conditions caused by S. aureus infection are bums, cellulitis, eyelid infections, food poisoning, joint infections, neonatal conjunctivitis, osteomyelitis, skin infections, surgical wound infection, scalded skin syndrome and toxic shock syndrome, some of which are described further below.

[0008] Burns

[0009] Burn wounds generally are sterile initially. However, they generally compromise physical and immune barriers to infection, cause loss of fluid and electrolytes and result in local or general physiological dysfunction. After cooling, contact with viable bacteria results in mixed colonization at the injury site. Infection may be restricted to the non-viable debris on the bum surface (“eschar”), it may progress into full skin infection and invade viable tissue below the eschar and it may reach below the skin, enter the lymphatic and blood circulation and develop into septicemia. S. aureus is among the most important pathogens typically found in burn wound infections. It can destroy granulation tissue and produce severe septicemia.

[0010] Cellulitis

[0011] Cellulitis, an acute infection of the skin that expands from a typically superficial origin to spread below the cutaneous layer, most commonly is caused by S. aureus in conjunction with S. pyrogenes. Cellulitis can lead to systemic infection. In fact, cellulitis can be one aspect of synergistic bacterial gangrene. This condition typically is caused by a mixture of S. aureus and microaerophilic streptococci. It causes necrosis and treatment is limited to excision of the necrotic tissue. The condition often is fatal.

[0012] Eyelid Infections

[0013] S. aureus is the cause of styes and of sticky eye” in neonates, among other eye infections. Typically such infections are limited to the surface of the eye, and may occasionally penetrate the surface with more severe consequences.

[0014] Food Poisoning

[0015] Some strains of S. aureus produce one or more of five serologically distinct, heat and acid stable enterotoxins that are not destroyed by digestive process of the stomach and small intestine (enterotoxins A-E). Ingestion of the toxin, in sufficient quantities, typically results in severe vomiting, but not diarrhea. The effect does not require viable bacteria. Although the toxins are known, their mechanism of action is not understood.

[0016] Joint Infections

[0017] S. aureus infects bone joints causing diseases such osteomyelitis.

[0018] Osteomyelitis

[0019] S. aureus is the most common causative agent of haematogenous osteomyelitis. The disease tends to occur in children and adolescents more than adults and it is associated with non-penetrating injuries to bones. Infection typically occurs in the long end of growing bone, hence its occurrence in physically immature populations. Most often, infection is localized in the vicinity of sprouting capillary loops adjacent to epiphysial growth plates in the end of long, growing bones.

[0020] Skin Infections

[0021] S. aureus is the most common pathogen of such minor skin infections as abscesses and boils. Such infections often are resolved by normal host response mechanisms, but they also can develop into severe internal infections. Recurrent infections of the nasal passages plague nasal carriers of S. aureus.

[0022] Surgical Wound Infections

[0023] Surgical wounds often penetrate far into the body. Infection of such wound thus poses a grave risk to the patient. S. aureus is the most important causative agent of infections in surgical wounds. S. aureus is unusually adept at invading surgical wounds; sutured wounds can be infected by far fewer S. aureus cells then are necessary to cause infection in normal skin. Invasion of surgical wound can lead to severe S. aureus septicemia. Invasion of the blood stream by S. aureus can lead to seeding and infection of internal organs, particularly heart valves and bone, causing systemic diseases, such as endocarditis and osteomyelitis.

[0024] Scalded Skin Syndrome

[0025] S. aureus is responsible for “scalded skin syndrome” (also called toxic epidermal necrosis, Ritter's disease and Lyell's disease). This diseases occurs in older children, typically in outbreaks caused by flowering of S. aureus strains produce exfoliation (also called scalded skin syndrome toxin). Although the bacteria initially may infect only a minor lesion, the toxin destroys intercellular connections, spreads epidermal layers and allows the infection to penetrate the outer layer of the skin, producing the desquamiation that typifies the diseases. Shedding of the outer layer of skin generally reveals normal skin below, but fluid lost in the process can produce severe injury in young children if it is not treated properly.

[0026] Toxic Shock Syndrome

[0027] Toxic shock syndrome is caused by strains of S. aureus that produce the so-called toxic shock syndrome toxin. The disease can be caused by S. aureus infection at any site, but it is too often erroneously viewed exclusively as a disease solely of women who use tampons. The disease involves toxaemia and septicemia, and can be fatal.

[0028] Nocosomial Infections

[0029] In the 1984 National Nocosomial Infection Surveillance Study (“NNIS”) S. aureus was the most prevalent agent of surgical wound infections in many hospital services, including medicine, surgery, obstetrics, pediatrics and newborns.

[0030] Resistance to Drugs of S. aureus Strains

[0031] Prior to the introduction of penicillin the prognosis for patients seriously infected with S. aureus was unfavorable. Following the introduction of penicillin in the early 1940s even the worst S. aureus infections generally could be treated successfully. The emergence of penicillin-resistant strains of S. aureus did not take long, however. Most strains of S. aureus encountered in hospital infections today do not respond to penicillin; although, fortunately, this is not the case for S. aureus encountered in community infections.

[0032] It is well known now that penicillin-resistant strains of S. aureus produce a lactamase which converts penicillin to pencillinoic acid, and thereby destroys antibiotic activity. Furthermore, the lactamase gene often is propagated episomally, typically on a plasmid, and often is only one of several genes on an episomal element that, together, confer multidrug resistance.

[0033] Methicillins, introduced in the 1960s, largely overcame the problem of penicillin resistance in S. aureus. These compounds conserve the portions of penicillin responsible for antibiotic activity and modify or alter other portions that make penicillin a good substrate for inactivating lactamases. However, methicillin resistance has emerged in S. aureus, along with resistance to many other antibiotics effective against this organism, including aminoglycosides, tetracycline, chloramphenicol, macrolides and lincosamides. In fact, methicillin-resistant strains of S. aureus generally are multiply drug resistant.

[0034] The molecular genetics of most types of drug resistance in S. aureus has been elucidated (See Lyon et al., Microbiology Reviews 51: 88-134 (1987)). Generally, resistance is mediated by plasmids, as noted above regarding penicillin resistance; however, several stable forms of drug resistance have been observed that apparently involve integration of a resistance element into the S. aureus genome itself.

[0035] Thus far each new antibiotic gives rise to resistance strains, stains emerge that are resistance to multiple drugs and increasingly persistent forms of resistance begin to emerge. Drug resistance of S. aureus infections already poses significant treatment difficulties, which are likely to get much worse unless new therapeutic agents are developed.

[0036] Molecular Genetics of Staphylococcus Aureus

[0037] Despite its importance in, among other things, human disease, relatively little is known about the genome of this organism.

[0038] Most genetic studies of S. aureus have been carried out using the strain NCTC8325, which contains prophages psi11, psi12 and psi13, and the UV-cured derivative of this strain, 8325-4 (also referred to as RN450), which is free of the prophages.

[0039] These studies revealed that the S. aureus genome, like that of other staphylococci, consists of one circular, covalently closed, double-stranded DNA and a collection of so-called variable accessory genetic elements, such as prophages, plasmids, transposons and the like.

[0040] Physical characterization of the genome has not been carried out in any detail. Pattee et al. published a low resolution and incomplete genetic and physical map of the chromosome of S. aureus strain NCTC 8325. (Pattee et al. Genetic and Physical Mapping of Chromosome of Staphylococcus aureus NCTC 8325, Chapter 11, pgs. 163-169 in MOLECULAR BIOLOGY OF THE STAPHYLOCOCCI, R. P. Novick, Ed., VCH Publishers, New York, (1990) The genetic map largely was produced by mapping insertions of Tn551 and Tn4001, which, respectively, confer erythromycin and gentamicin resistance, and by analysis of SmaI-digested DNA by Pulsed Field Gel Electrophoresis (“PFGE”).

[0041] The map was of low resolution; even estimating the physical size of the genome was difficult, according to the investigators. The size of the largest SmaI chromosome fragment, for instance, was too large for accurate sizing by PFGE. To estimate its size, additional restriction sites had to be introduced into the chromosome using a transposon containing a SmaI recognition sequence.

[0042] In sum, most physical characteristics and almost all of the genes of Staphylococcus aureus are unknown. Among the few genes that have been identified, most have not been physically mapped or characterized in detail. Only a very few genes of this organism have been sequenced. (See, for instance Thomsberry, J., Antimicrobial Chemotherapy 21 Suppl C: 9-16 (1988), current versions of GENBANK and other nucleic acid databases, and references that relate to the genome of S. aureus such as those set out elsewhere herein.)

[0043] It is clear that the etiology of diseases mediated or exacerbated by S. aureus infection involves the programmed expression of S. aureus genes, and that characterizing the genes and their patterns of expression would add dramatically to our understanding of the organism and its host interactions. Knowledge of S. aureus genes and genomic organization would dramatically improve understanding of disease etiology and lead to improved and new ways of-preventing, ameliorating, arresting and reversing diseases. Moreover, characterized genes and genomic fragments of S. aureus would provide reagents for, among other things, detecting, characterizing and controlling S. aureus infections. There is a need therefore to characterize the genome of S. aureus and for polynucleotides and sequences of this organism.

SUMMARY OF THE INVENTION

[0044] The present invention is based on the sequencing of fragments of the Staphylococcus aureus genome. The primary nucleotide sequences which were generated are provided in SEQ ID NOS: 1-5,191.

[0045] The present invention provides the nucleotide sequence of several thousand contigs of the Staphylococcus aureus genome, which are listed in tables below and set out in the Sequence Listing submitted herewith, and representative fragments thereof, in a form which can be readily used, analyzed, and interpreted by a skilled artisan. In one embodiment, the present invention is provided as contiguous strings of primary sequence information corresponding to the nucleotide sequences depicted in SEQ ID NOS: 1-5,191.

[0046] The present invention further provides nucleotide sequences which are at least 95% identical to the nucleotide sequences of SEQ ID NOS: 1-5,191.

[0047] The nucleotide sequence of SEQ ID NOS: 1-5,191, a representative fragment thereof, or a nucleotide sequence which is at least 95% identical to the nucleotide sequence of SEQ ID NOS: 1-5,191 may be provided in a variety of mediums to facilitate its use. In one application of this embodiment, the sequences of the present invention are recorded on computer readable media. Such media includes, but is not limited to: magnetic storage media, such as floppy discs, hard disc storage medium, and magnetic tape; optical storage media such as CD-ROM; electrical storage media such as RAM and ROM; and hybrids of these categories such as magnetic/optical storage media.

[0048] The present invention further provides systems, particularly computer-based systems which contain the sequence information herein described stored in a data storage means. Such systems are designed to identify commercially important fragments of the Staphylococcus aureus genome.

[0049] Another embodiment of the present invention is directed to fragments of the Staphylococcus aureus genome having particular structural or functional attributes. Such fragments of the Staphylococcus aureus genome of the present invention include, but are not limited to, fragments which encode peptides, hereinafter referred to as open reading frames or ORFs,” fragments which modulate the expression of an operably linked ORF, hereinafter referred to as expression modulating fragments or EMFs,” and fragments which can be used to diagnose the presence of Staphylococcus aureus in a sample, hereinafter referred to as diagnostic fragments or “DFs.”

[0050] Each of the ORFs in fragments of the Staphylococcus aureus genome disclosed in Tables 1-3, and the EMFs found 5′ to the ORFs, can be used in numerous ways as polynucleotide reagents. For instance, the sequences can be used as diagnostic probes or amplification primers for detecting or determining the presence of a specific microbe in a sample, to selectively control gene expression in a host and in the production of polypeptides, such as polypeptides encoded by ORFs of the present invention, particular those polypeptides that have a pharmacological activity.

[0051] The present invention further includes recombinant constructs comprising one or more fragments of the Staphylococcus aureus genome of the present invention. The recombinant constructs of the present invention comprise vectors, such as a plasmid or viral vector, into which a fragment of the Staphylococcus aureus has been inserted.

[0052] The present invention further provides host cells containing any of the isolated fragments of the Staphylococcus aureus genome of the present invention. The host cells can be a higher eukaryotic host cell, such as a mammalian cell, a lower eukaryotic cell, such as a yeast cell, or a procaryotic cell such as a bacterial cell.

[0053] The present invention is further directed to isolated polypeptides and proteins encoded by ORFs of the present invention. A variety of methods, well known to those of skill in the art, routinely may be utilized to obtain any of the polypeptides and proteins of the present invention. For instance, polypeptides and proteins of the present invention having relatively short, simple amino acid sequences readily can be synthesized using commercially available automated peptide synthesizers. Polypeptides and proteins of the present invention also may be purified from bacterial cells which naturally produce the protein. Yet another alternative is to purify polypeptide and proteins of the present invention from cells which have been altered to express them.

[0054] The invention further provides polypeptides comprising Staphylococcus aureus epitopes and vaccine compositions comprising such polypeptides. Also provided are methods for vaccinating an individual against Staphylococcus aureus infection.

[0055] The invention further provides methods of obtaining homologs of the fragments of the Staphylococcus aureus genome of the present invention and homologs of the proteins encoded by the ORFs of the present invention. Specifically, by using the nucleotide and amino acid sequences disclosed herein as a probe or as primers, and techniques such as PCR cloning and colony/plaque hybridization, one skilled in the art can obtain homologs.

[0056] The invention further provides antibodies which selectively bind polypeptides and proteins of the present invention. Such antibodies include both monoclonal and polyclonal antibodies.

[0057] The invention further provides hybridomas which produce the above-described antibodies. A hybridoma is an immortalized cell line which is capable of secreting a specific monoclonal antibody.

[0058] The present invention further provides methods of identifying test samples derived from cells which express one of the ORFs of the present invention, or a homolog thereof. Such methods comprise incubating a test sample with one or more of the antibodies of the present invention, or one or more of the Dfs or antigens of the present invention, under conditions which allow a skilled artisan to determine if the sample contains the ORF or product produced therefrom.

[0059] In another embodiment of the present invention, kits are provided which contain the necessary reagents to carry out the above-described assays.

[0060] Specifically, the invention provides a compartmentalized kit to receive, in close confinement, one or more containers which comprises: (a) a first container comprising one of the antibodies, antigens, or one of the DFs of the present invention; and (b) one or more other containers comprising one or more of the following: wash reagents, reagents capable of detecting presence of bound antibodies, antigens or hybridized DFs.

[0061] Using the isolated proteins of the present invention, the present invention further provides methods of obtaining and identifying agents capable of binding to a polypeptide or protein encoded by one of the ORFs of the present invention. Specifically, such agents include, as further described below, antibodies, peptides, carbohydrates, pharmaceutical agents and the like. Such methods comprise steps of: (a)contacting an agent with an isolated protein encoded by one of the ORFs of the present invention; and (b)determining whether the agent binds to said protein.

[0062] The present genomic sequences of Staphylococcus aureus will be of great value to all laboratories working with this organism and for a variety of commercial purposes. Many fragments of the Staphylococcus aureus genome will be immediately identified by similarity searches against GenBank or protein databases and will be of immediate value to Staphylococcus aureus researchers and for immediate commercial value for the production of proteins or to control gene expression.

[0063] The methodology and technology for elucidating extensive genomic sequences of bacterial and other genomes has and will greatly enhance the ability to analyze and understand chromosomal organization. In particular, sequenced contigs and genomes will provide the models for developing tools for the analysis of chromosome structure and function, including the ability to identify genes within large segments of genomic DNA, the structure, position, and spacing of regulatory elements, the identification of genes with potential industrial applications, and the ability to do comparative genomic and molecular phylogeny.

BRIEF DESCRIPTION OF THE DRAWINGS

[0064] FIG. 1 is a block diagram of a computer system (102) that can be used to implement computer-based systems of present invention.

[0065] FIG. 2 is a schematic diagram depicting the data flow and computer programs used to collect, assemble, edit and annotate the contigs of the Staphylococcus aureus genome of the present invention. Both Macintosh and Unix platforms are used to handle the AB 373 and 377 sequence data files, largely as described in Kerlavage et al., Proceedings of the Twenty-Sixth Annual Hawaii International Conference on System Sciences, 585, IEEE Computer Society Press, Wash. D.C. (1993). Factura (AB) is a Macintosh program designed for automatic vector sequence removal and end-trimming of sequence files. The program Loadis runs on a Macintosh platform and parses the feature data extracted from the sequence files by Factura to the Unix based Staphylococcus aureus relational database. Assembly of contigs (and whole genome sequences) is accomplished by retrieving a specific set of sequence files and their associated features using extrseq, a Unix utility for retrieving sequences from an SQL database. The resulting sequence file is processed by seq_filter to trim portions of the sequences with more than 2% ambiguous nucleotides. The sequence files were assembled using TIGR Assembler, an assembly engine designed at The Institute for Genomic Research (TIGR”) for rapid and accurate assembly of thousands of sequence fragments. The collection of contigs generated by the assembly step is loaded into the database with the lassie program. Identification of open reading frames (ORFs) is accomplished by processing contigs with zorf. The ORFs are searched against S. aureus sequences from Genbank and against all protein sequences using the BLASTN and BLASTP programs, described in Altschul et al., J. Mol. Biol. 215: 403-410 (1990)). Results of the ORF determination and similarity searching steps were loaded into the database. As described below, some results of the determination and the searches are set out in Tables 1-3.

DETAILED DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS

[0066] The present invention is based on the sequencing of fragments of the Staphylococcus aureus genome and analysis of the sequences. The primary nucleotide sequences generated by sequencing the fragments are provided in SEQ ID NOS: 1-5,191. (As used herein, the “primary sequence” refers to the nucleotide sequence represented by the IUPAC nomenclature system.)

[0067] In addition to the aforementioned Staphylococcus aureus polynucleotide and polynucleotide sequences, the present invention provides the nucleotide sequences of SEQ ID NOS: 1-5,191, or representative fragments thereof, in a form which can be readily used, analyzed, and interpreted by a skilled artisan.

[0068] As used herein, a “representative fragment of the nucleotide sequence depicted in SEQ ID NOS: 1-5,191” refers to any portion of the SEQ ID NOS: 1-5,191 which is not presently represented within a publicly available database. Preferred representative fragments of the present invention are Staphylococcus aureus open reading frames (ORFS”), expression modulating fragment (EMFs”) and fragments which can be used to diagnose the presence of Staphylococcus aureus in sample (“DFs”). A non-limiting identification of preferred representative fragments is provided in Tables 1-3.

[0069] As discussed in detail below, the information provided in SEQ ID NOS: 1-5,191 and in Tables 1-3 together with routine cloning, synthesis, sequencing and assay methods will enable those skilled in the art to clone and sequence all “representative fragments” of interest, including open reading frames encoding a large variety of Staphylococcus aureus proteins.

[0070] While the presently disclosed sequences of SEQ ID NOS: 1-5,191 are highly accurate, sequencing techniques are not perfect and, in relatively rare instances, further investigation of a fragment or sequence of the invention may reveal a nucleotide sequence error present in a nucleotide sequence disclosed in SEQ ID NOS: 1-5,191. However, once the present invention is made available (i.e., once the information in SEQ ID NOS: 1-5,191 and Tables 1-3 has been made available), resolving a rare sequencing error in SEQ ID NOS: 1-5,191 will be well within the skill of the art. The present disclosure makes available sufficient sequence information to allow any of the described contigs or portions thereof to be obtained readily by straightforward application of routine techniques. Further sequencing of such polynucleotide may proceed in like manner using manual and automated sequencing methods which are employed ubiquitous in the art. Nucleotide sequence editing software is publicly available. For example, Applied Biosystem's (AB) AutoAssembler can be used as an aid during visual inspection of nucleotide sequences. By employing such routine techniques potential errors readily may be identified and the correct sequence then may be ascertained by targeting further sequencing effort, also of a routine nature, to the region containing the potential error.

[0071] Even if all of the very rare sequencing errors in SEQ ID NOS: 1-5,191 were corrected, the resulting nucleotide sequences would still be at least 95% identical, nearly all would be at least 99% identical, and the great majority would be at least 99.9% identical to the nucleotide sequences of SEQ ID NOS: 1-5,191.

[0072] As discussed elsewhere herein, polynucleotides of the present invention readily may be obtained by routine application of well known and standard procedures for cloning and sequencing DNA. Detailed methods for obtaining libraries and for sequencing are provided below, for instance. A wide variety of Staphylococcus aureus strains that can be used to prepare S aureus genomic DNA for cloning and for obtaining polynucleotides of the present invention are available to the public from recognized depository institutions, such as the American Type Culture Collection (ATCC”).

[0073] The nucleotide sequences of the genomes from different strains of Staphylococcus aureus differ somewhat. However, the nucleotide sequences of the genomes of all Staphylococcus aureus strains will be at least 95% identical, in corresponding part, to the nucleotide sequences provided in SEQ ID NOS: 1-5,191. Nearly all will be at least 99% identical and the great majority will be 99.9% identical.

[0074] Thus, the present invention further provides nucleotide sequences which are at least 95%, preferably 99% and most preferably 99.9% identical to the nucleotide sequences of SEQ ID NOS: 1-5,191, in a form which can be readily used, analyzed and interpreted by the skilled artisan.

[0075] Methods for determining whether a nucleotide sequence is at least 95%, at least 99% or at least 99.9% identical to the nucleotide sequences of SEQ ID NOS: 1-5,191 are routine and readily available to the skilled artisan. For example, the well known fasta algorithm described in Pearson and Lipman, Proc. Natl. Acad. Sci. USA 85: 2444 (1988) can be used to generate the percent identity of nucleotide sequences. The

[0076] BLASTN program also can be used to generate an identity score of polynucleotides compared to one another.

COMPUTER RELATED EMBODIMENTS

[0077] The nucleotide sequences provided in SEQ ID NOS: 1-5,191, a representative fragment thereof, or a nucleotide sequence at least 95%, preferably at least 96%, 97%, 98% or 99% and most preferably at least 99.9% identical to a polynucleotide sequence of SEQ ID NOS: 1-5,191 may be “provided” in a variety of mediums to facilitate use thereof. As used herein, “provided” refers to a manufacture, other than an isolated nucleic acid molecule, which contains a nucleotide sequence of the present invention; i.e., a nucleotide sequence provided in SEQ ID NOS: 1-5,191, a representative fragment thereof, or a nucleotide sequence at least 95%, preferably at least 96%, 97%, 98% or 99% and most preferably at least 99.9% identical to a polynucleotide of SEQ ID NOS: 1-5,191. Such a manufacture provides a large portion of the Staphylococcus aureus genome and parts thereof (e.g., a Staphylococcus aureus open reading frame (ORF)) in a form which allows a skilled artisan to examine the manufacture using means not directly applicable to examining the Staphylococcus aureus genome or a subset thereof as it exists in nature or in purified form.

[0078] In one application of this embodiment, a nucleotide sequence of the present invention can be recorded on computer readable media. As used herein, “computer readable media” refers to any medium which can be read and accessed directly by a computer. Such media include, but are not limited to: magnetic storage media, such as floppy discs, hard disc storage medium, and magnetic tape; optical storage media such as CD-ROM; electrical storage media such as RAM and ROM; and hybrids of these categories, such as magnetic/optical storage media. A skilled artisan can readily appreciate how any of the presently known computer readable mediums can be used to create a manufacture comprising computer readable medium having recorded thereon a nucleotide sequence of the present invention. Likewise, it will be clear to those of skill how additional computer readable media that may be developed also can be used to create analogous manufactures having recorded thereon a nucleotide sequence of the present invention.

[0079] As used herein, “recorded” refers to a process for storing information on computer readable medium. A skilled artisan can readily adopt any of the presently know methods for recording information on computer readable medium to generate manufactures comprising the nucleotide sequence information of the present invention.

[0080] A variety of data storage structures are available to a skilled artisan for creating a computer readable medium having recorded thereon a nucleotide sequence of the present invention. The choice of the data storage structure will generally be based on the means chosen to access the stored information. In addition, a variety of data processor programs and formats can be used to store the nucleotide sequence information of the present invention on computer readable medium. The sequence information can be represented in a word processing text file, formatted in commercially-available software such as WordPerfect and MicroSoft Word, or represented in the form of an ASCII file, stored in a database application, such as DB2, Sybase, Oracle, or the like. A skilled artisan can readily adapt any number of data-processor structuring formats (e.g., text file or database) in order to obtain computer readable medium having recorded thereon the nucleotide sequence information of the present invention.

[0081] Computer software is publicly available which allows a skilled artisan to access sequence information provided in a computer readable medium. Thus, by providing in computer readable form the nucleotide sequences of SEQ ID NOS: 1-5,191, a representative fragment thereof, or a nucleotide sequence at least 95%, preferably at least 96%, 97%, 98% or 99% and most preferably at least 99.9% identical to a sequence of SEQ ID NOS: 1-5,191 the present invention enables the skilled artisan routinely to access the provided sequence information for a wide variety of purposes.

[0082] The examples which follow demonstrate how software which implements the BLAST (Altschul et al., J. Mol. Biol. 215:403-410 (1990)) and BLAZE (Brutlag et al., Comp. Chem. 17:203-207 (1993)) search algorithms on a Sybase system was used to identify open reading frames (ORFs) within the Staphylococcus aureus genome which contain homology to ORFs or proteins from both Staphylococcus aureus and from other organisms. Among the ORFs discussed herein are protein encoding fragments of the Staphylococcus aureus genome useful in producing commercially important proteins, such as enzymes used in fermentation reactions and in the production of commercially useful metabolites.

[0083] The present invention further provides systems, particularly computer-based systems, which contain the sequence information described herein. Such systems are designed to identify, among other things, commercially important fragments of the Staphylococcus aureus genome.

[0084] As used herein, “a computer-based system” refers to the hardware means, software means, and data storage means used to analyze the nucleotide sequence information of the present invention. The minimum hardware means of the computer-based systems of the present invention comprises a central processing unit (CPU), input means, output means, and data storage means. A skilled artisan can readily appreciate that any one of the currently available computer-based system are suitable for use in the present invention.

[0085] As stated above, the computer-based systems of the present invention comprise a data storage means having stored therein a nucleotide sequence of the present invention and the necessary hardware means and software means for supporting and implementing a search means.

[0086] As used herein, “data storage means” refers to memory which can store nucleotide sequence information of the present invention, or a memory access means which can access manufactures having recorded thereon the nucleotide sequence information of the present invention.

[0087] As used herein, “search means” refers to one or more programs which are implemented on the computer- based system to compare a target sequence or target structural motif with the sequence information stored within the data storage means. Search means are used to identify fragments or regions of the present genomic sequences which match a particular target sequence or target motif. A variety of known algorithms are disclosed publicly and a variety of commercially available software for conducting search means are and can be used in the computer-based systems of the present invention. Examples of such software includes, but is not limited to, MacPattern (EMBL), BLASTN and BLASTX (NCBIA). A skilled artisan can readily recognize that any one of the available algorithms or implementing software packages for conducting homology searches can be adapted for use in the present computer-based systems.

[0088] As used herein, a “target sequence” can be any DNA or amino acid sequence of six or more nucleotides or two or more amino acids. A skilled artisan can readily recognize that the longer a target sequence is, the less likely a target sequence will be present as a random occurrence in the database. The most preferred sequence length of a target sequence is from about 10 to 100 amino acids or from about 30 to 300 nucleotide residues. However, it is well recognized that searches for commercially important fragments, such as sequence fragments involved in gene expression and protein processing, may be of shorter length.

[0089] As used herein, “a target structural motif,” or “target motif,” refers to any rationally selected sequence or combination of sequences in which the sequence(s) are chosen based on a three-dimensional configuration which is formed upon the folding of the target motif. There are a variety of target motifs known in the art. Protein target motifs include, but are not limited to, enzymatic active sites and signal sequences. Nucleic acid target motifs include, but are not limited to, promoter sequences, hairpin structures and inducible expression elements (protein binding sequences).

[0090] A variety of structural formats for the input and output means can be used to input and output the information in the computer-based systems of the present invention. A preferred format for an output means ranks fragments of the Staphylococcus aureus genomic sequences possessing varying degrees of homology to the target sequence or target motif. Such presentation provides a skilled artisan with a ranking of sequences which contain various amounts of the target sequence or target motif and identifies the degree of homology contained in the identified fragment.

[0091] A variety of comparing means can be used to compare a target sequence or target motif with the data storage means to identify sequence fragments of the Staphylococcus aureus genome. In the present examples, implementing software which implement the BLAST and BLAZE algorithms, described in Altschul et al., J. Mol. Biol. 215: 403-410 (1990), was used to identify open reading frames within the Staphylococcus aureus genome. A skilled artisan can readily recognize that any one of the publicly available homology search programs can be used as the search means for the computer-based systems of the present invention. Of course, suitable proprietary systems that may be known to those of skill also may be employed in this regard.

[0092] FIG. 1 provides a block diagram of a computer system illustrative of embodiments of this aspect of present invention. The computer system 102 includes a processor 106 connected to a bus 104. Also connected to the bus 104 are a main memory 108 (preferably implemented as random access memory, RAM) and a variety of secondary storage devices 110, such as a hard drive 112 and a removable medium storage device 114. The removable medium storage device 114 may represent, for example, a floppy disk drive, a CD-ROM drive, a magnetic tape drive, etc. A removable storage medium 116 (such as a floppy disk, a compact disk, a magnetic tape, etc.) containing control logic and/or data recorded therein may be inserted into the removable medium storage device 114. The computer system 102 includes appropriate software for reading the control logic and/or the data from the removable medium storage device 114, once it is inserted into the removable medium storage device 114.

[0093] A nucleotide sequence of the present invention may be stored in a well known manner in the main memory 108, any of the secondary storage devices 110, and/or a removable storage medium 116. During execution, software for accessing and processing the genomic sequence (such as search tools, comparing tools, etc.) reside in main memory 108, in accordance with the requirements and operating parameters of the operating system, the hardware system and the software program or programs.

BIOCHEMICAL EMBODIMENTS

[0094] Other embodiments of the present invention are directed to isolated fragments of the Staphylococcus aureus genome. The fragments of the Staphylococcus aureus genome of the present invention include, but are not limited to fragments which encode peptides, hereinafter open reading frames (ORFs), fragments which modulate the expression of an operably linked ORF, hereinafter expression modulating fragments (EMFs) and fragments which can be used to diagnose the presence of Staphylococcus aureus in a sample, hereinafter diagnostic fragments (DFs).

[0095] As used herein, an “isolated nucleic acid molecule” or an “isolated fragment of the Staphylococcus aureus genome” refers to a nucleic acid molecule possessing a specific nucleotide sequence which has been subjected to purification means to reduce, from the composition, the number of compounds which are normally associated with the composition. Particularly, the term refers to the nucleic acid molecules having the sequences set out in SEQ ID NOS: 1-5,191, to representative fragments thereof as described above, to polynucleotides at least 95%, preferably at least 96%, 97%, 98% or 99% and especially preferably at least 99.9% identical in sequence thereto, also as set out above.

[0096] A variety of purification means can be used to generated the isolated fragments of the present invention. These include, but are not limited to methods which separate constituents of a solution based on charge, solubility, or size.

[0097] In one embodiment, Staphylococcus aureus DNA can be mechanically sheared to produce fragments of 15-20 kb in length. These fragments can then be used to generate an Staphylococcus aureus library by inserting them into lambda clones as described in the Examples below. Primers flanking, for example, an ORF, such as those enumerated in Tables 1-3 can then be generated using nucleotide sequence information provided in SEQ ID NOS: 1-5,191. Well known and routine techniques of PCR cloning then can be used to isolate the ORF from the lambda DNA library of Staphylococcus aureus genomic DNA. Thus, given the availability of SEQ ID NOS: 1-5,191, the information in Tables 1, 2 and 3, and the information that may be obtained readily by analysis of the sequences of SEQ ID NOS: 1-5,191 using methods set out above, those of skill will be enabled by the present disclosure to isolate any ORF-containing or other nucleic acid fragment of the present invention.

[0098] The isolated nucleic acid molecules of the present invention include, but are not limited to single stranded and double stranded DNA, and single stranded RNA.

[0099] As used herein, an “open reading frame,” ORF, means a series of triplets coding for amino acids without any termination codons and is a sequence translatable into protein.

[0100] Tables 1, 2 and 3 list ORFs in the Staphylococcus aureus genomic contigs of the present invention that were identified as putative coding regions by the GeneMark software using organism-specific second-order Markov probability transition matrices. It will be appreciated that other criteria can be used, in accordance with well known analytical methods, such as those discussed herein, to generate more inclusive, more restrictive or more selective lists.

[0101] Table 1 sets out ORFs in the Staphylococcus aureus contigs of the present invention that are at least 80 amino acids long and over a continuous region of at least 50 bases which are 95% or more identical (by BLAST analysis) to an S. aureus nucleotide sequence available through Genbank in November 1996.

[0102] Table 2 sets out ORFs in the Staphylococcus aureus contigs of the present invention that are not in Table 1 and match, with a BLASTP probability score of 0.01 or less, a polypeptide sequence available through Genbank by September 1996.

[0103] Table 3 sets out ORFs in the Staphylococcus aureus contigs of the present invention that do not match significantly, by BLASTP analysis, a polypeptide sequence available through Genbank by September 1996.

[0104] In each table, the first and second columns identify the ORF by, respectively, contig number (SEQ ID NO) and ORF number within the contig; the third column indicates the first nucleotide of the ORF, counting from the 5′ end of the contig strand shown in the sequence listing; and the fifth column indicates the length of each ORF in nucleotides. It will be appreciated that some ORFs are located on the reverse strand. The numbering identifying such ORFs also represents nucleotide positions counting from the 5′ end of the strand shown in the sequence listing.

[0105] In Tables 1 and 2, column five, lists the “match accession” for the closest matching sequence available through Genbank. These reference numbers are the databases entry numbers commonly used by those of skill in the art, who will be familiar with their denominators. Descriptions of the nomenclature are available from the National Center for Biotechnology Information. Column six in Tables 1 and 2 provides the “gene name” of the matching sequence; column seven provides the BLAST “similarity”; column eight provides the BLAST “identity” score from the comparison of the ORF and the homologous gene; and column nine indicates the length in nucleotides of the highest scoring “segment pair” identified by the BLAST identity analysis.

[0106] The concepts of percent identity and percent similarity of two polypeptide sequences is well understood in the art. For example, two polypeptides 10 amino acids in length which differ at three amino acid positions (e.g., at positions 1, 3 and 5) are said to have a percent identity of 70%. However, the same two polypeptides would be deemed to have a percent similarity of 80% if, for example at position 5, the amino acids moieties, although not identical, were “similar” (i.e., possessed similar biochemical characteristics). Many programs for analysis of nucleotide or amino acid sequence similarity, such as fasta and BLAST specifically list percent identity of a matching region as an output parameter. Thus, for instance, Tables 1 and 2 herein enumerate the percent identity “of the highest scoring segment pair” in each ORF and its listed relative. Further details concerning the algorithms and criteria used for homology searches are provided below and are described in the pertinent literature highlighted by the citations provided below.

[0107] It will be appreciated that other criteria can be used to generate more inclusive and more exclusive listings of the types set out in the tables. As those of skill will appreciate, narrow and broad searches both are useful. Thus, a skilled artisan can readily identify ORFs in contigs of the Staphylococcus aureus genome other than those listed in Tables 1-3, such as ORFs which are overlapping or encoded by the opposite strand of an identified ORF in addition to those ascertainable using the computer-based systems of the present invention.

[0108] As used herein, an “expression modulating fragment,” EMF, means a series of nucleotide molecules which modulates the expression of an operably linked ORF or EMF.

[0109] As used herein, a sequence is said to “modulate the expression of an operably linked sequence” when the expression of the sequence is altered by the presence of the EMF. EMFs include, but are not limited to, promoters, and promoter modulating sequences (inducible elements). One class of EMFs are fragments which induce the expression or an operably linked ORF in response to a specific regulatory factor or physiological event.

[0110] EMF sequences can be identified within the contigs of the Staphylococcus aureus genome by their proximity to the ORFs provided in Tables 1-3. An intergenic segment, or a fragment of the intergenic segment, from about 10 to 200 nucleotides in length, taken from any one of the ORFs of Tables 1-3 will modulate the expression of an operably linked ORF in a fashion similar to that found with the naturally linked ORF sequence. As used herein, an “intergenic segment” refers to fragments of the Staphylococcus aureus genome which are between two ORF(s) herein described. EMFs also can be identified using known EMFs as a target sequence or target motif in the computer-based systems of the present invention. Further, the two methods can be combined and used together.

[0111] The presence and activity of an EMF can be confirmed using an EMF trap vector. An EMF trap vector contains a cloning site linked to a marker sequence. A marker sequence encodes an identifiable phenotype, such as antibiotic resistance or a complementing nutrition auxotrophic factor, which can be identified or assayed when the EMF trap vector is placed within an appropriate host under appropriate conditions. As described above, a EMF will modulate the expression of an operably linked marker sequence. A more detailed discussion of various marker sequences is provided below.

[0112] A sequence which is suspected as being an EMF is cloned in all three reading frames in one or more restriction sites upstream from the marker sequence in the EMF trap vector. The vector is then transformed into an appropriate host using known procedures and the phenotype of the transformed host in examined under appropriate conditions. As described above, an EMF will modulate the expression of an operably linked marker sequence.

[0113] As used herein, a “diagnostic fragment,” DF, means a series of nucleotide molecules which selectively hybridize to Staphylococcus aureus sequences. DFs can be readily identified by identifying unique sequences within contigs of the Staphylococcus aureus genome, such as by using well-known computer analysis software, and by generating and testing probes or amplification primers consisting of the DF sequence in an appropriate diagnostic format which determines amplification or hybridization selectivity.

[0114] The sequences falling within the scope of the present invention are not limited to the specific sequences herein described, but also include allelic and species variations thereof. Allelic and species variations can be routinely determined by comparing the sequences provided in SEQ ID NOS: 1-5,191, a representative fragment thereof, or a nucleotide sequence at least 99% and preferably 99.9% identical to SEQ ID NOS: 1-5,191, with a sequence from another isolate of the same species.

[0115] Furthermore, to accommodate codon variability, the invention includes nucleic acid molecules coding for the same amino acid sequences as do the specific ORFs disclosed herein. In other words, in the coding region of an ORF, substitution of one codon for another which encodes the same amino acid is expressly contemplated.

[0116] Any specific sequence disclosed herein can be readily screened for errors by resequencing a particular fragment, such as an ORF, in both directions (i.e., sequence both strands). Alternatively, error screening can be performed by sequencing corresponding polynucleotides of Staphylococcus aureus origin isolated by using part or all of the fragments in question as a probe or primer.

[0117] Each of the ORFs of the Staphylococcus aureus genome disclosed in Tables 1, 2 and 3, and the EMFs found 5′ to the ORFs, can be used as polynucleotide reagents in numerous ways. For example, the sequences can be used as diagnostic probes or diagnostic amplification primers to detect the presence of a specific microbe in a sample, particular Staphylococcus aureus. Especially preferred in this regard are ORF such as those of Table 3, which do not match previously characterized sequences from other organisms and thus are most likely to be highly selective for Staphylococcus aureus. Also particularly preferred are ORFs that can be used to distinguish between strains of Staphylococcus aureus, particularly those that distinguish medically important strain, such as drug-resistant strains.

[0118] In addition, the fragments of the present invention, as broadly described, can be used to control gene expression through triple helix formation or antisense DNA or RNA, both of which methods are based on the binding of a polynucleotide sequence to DNA or RNA. Triple helix-formation optimally results in a shut-off of RNA transcription from DNA, while antisense RNA hybridization blocks translation of an mRNA molecule into polypeptide. Information from the sequences of the present invention can be used to design antisense and triple helix-forming oligonucleotides. Polynucleotides suitable for use in these methods are usually 20 to 40 bases in length and are designed to be complementary to a region of the gene involved in transcription, for triple-helix formation, or to the mRNA itself, for antisense inhibition. Both techniques have been demonstrated to be effective in model systems, and the requisite techniques are well known and involve routine procedures. Triple helix techniques are discussed in, for example, Lee et al., Nucl. Acids Res. 6: 3073 (1979); Cooney et al, Science 241: 456 (1988); and Dervan et al., Science 251: 1360 (1991). Antisense techniques in general are discussed in, for instance, Okano, J. Neurochem. 56: 560 (1991) and OLIGODEOXYNUCLEOTIDES AS ANTISENSE INHIBITORS OF GENE EXPRESSION, CRC Press, Boca Raton, Fla. (1988)).

[0119] The present invention further provides recombinant constructs comprising one or more fragments of the Staphylococcus aureus genomic fragments and contigs of the present invention. Certain preferred recombinant constructs of the present invention comprise a vector, such as a plasmid or viral vector, into which a fragment of the Staphylococcus aureus genome has been inserted, in a forward or reverse orientation. In the case of a vector comprising one of the ORFs of the present invention, the vector may further comprise regulatory sequences, including for example, a promoter, operably linked to the ORF. For vectors comprising the EMFs of the present invention, the vector may further comprise a marker sequence or heterologous ORF operably linked to the EMF.

[0120] Large numbers of suitable vectors and promoters are known to those of skill in the art and are commercially available for generating the recombinant constructs of the present invention. The following vectors are provided by way of example. Useful bacterial vectors include phagescript, PsiX174, pBluescript SK and KS (+and −), pNH8a, pNH16a, pNH18a, pNH46a (available from Stratagene); pTrc99A, pKK223-3, pKK233-3, pDR540, pRIT5 (available from Pharmacia). Useful eukaryotic vectors include pWLneo, pSV2cat, pOG44, pXT1, pSG (available from Stratagene) pSVK3, pBPV, pMSG, pSVL (available from Pharmacia).

[0121] Promoter regions can be selected from any desired gene using CAT (chloramphenicol transferase) vectors or other vectors with selectable markers. Two appropriate vectors are pKK232-8 and pCM7. Particular named bacterial promoters include lacI, lacZ, T3, T7, gpt, lambda PR, and trc. Eukaryotic promoters include CMV immediate early, HSV thymidine kinase, early and late SV40, LTRs from retrovirus, and mouse metallothionein-I. Selection of the appropriate vector and promoter is well within the level of ordinary skill in the art.

[0122] The present invention further provides host cells containing any one of the isolated fragments of the Staphylococcus aureus genomic fragments and contigs of the present invention, wherein the fragment has been introduced into the host cell using known methods. The host cell can be a higher eukaryotic host cell, such as a mammalian cell, a lower eukaryotic host cell, such as a yeast cell, or a procaryotic cell, such as a bacterial cell.

[0123] A polynucleotide of the present invention, such as a recombinant construct comprising an ORF of the present invention, may be introduced into the host by a variety of well established techniques that are standard in the art, such as calcium phosphate transfection, DEAE, dextran mediated transfection and electroporation, which are described in, for instance, Davis, L. et al., BASIC METHODS IN MOLECULAR BIOLOGY (1986).

[0124] A host cell containing one of the fragments of the Staphylococcus aureus genomic fragments and contigs of the present invention, can be used in conventional manners to produce the gene product encoded by the isolated fragment (in the case of an ORF) or can be used to produce a heterologous protein under the control of the EMF.

[0125] The present invention further provides isolated polypeptides encoded by the nucleic acid fragments of the present invention or by degenerate variants of the nucleic acid fragments of the present invention. By “degenerate variant” is intended nucleotide fragments which differ from a nucleic acid fragment of the present invention (e.g., an ORF) by nucleotide sequence but, due to the degeneracy of the Genetic Code, encode an identical polypeptide sequence.

[0126] Preferred nucleic acid fragments of the present invention are the ORFs depicted in Tables 2 and 3 which encode proteins.

[0127] A variety of methodologies known in the art can be utilized to obtain any one of the isolated polypeptides or proteins of the present invention. At the simplest level, the amino acid sequence can be synthesized using commercially available peptide synthesizers. This is particularly useful in producing small peptides and fragments of larger polypeptides. Such short fragments as may be obtained most readily by synthesis are useful, for example, in generating antibodies against the native polypeptide, as discussed further below.

[0128] In an alternative method, the polypeptide or protein is purified from bacterial cells which naturally produce the polypeptide or protein. One skilled in the art can readily employ well-known methods for isolating polypeptides and proteins to isolate and purify polypeptides or proteins of the present invention produced naturally by a bacterial strain, or by other methods. Methods for isolation and purification that can be employed in this regard include, but are not limited to, immunochromatography, HPLC, size-exclusion chromatography, ion-exchange chromatography, and immuno-affinity chromatography.

[0129] The polypeptides and proteins of the present invention also can be purified from cells which have been altered to express the desired polypeptide or protein. As used herein, a cell is said to be altered to express a desired polypeptide or protein when the cell, through genetic manipulation, is made to produce a polypeptide or protein which it normally does not produce or which the cell normally produces at a lower level. Those skilled in the art can readily adapt procedures for introducing and expressing either recombinant or synthetic sequences into eukaryotic or prokaryotic cells in order to generate a cell which produces one of the polypeptides or proteins of the present invention.

[0130] Any host/vector system can be used to express one or more of the ORFs of the present invention. These include, but are not limited to, eukaryotic hosts such as HeLa cells, CV-1 cell, COS cells, and Sf9 cells, as well as prokaryotic host such as E. coli and B. subtilis. The most preferred cells are those which do not normally express the particular polypeptide or protein or which expresses the polypeptide or protein at low natural level.

[0131] “Recombinant,” as used herein, means that a polypeptide or protein is derived from recombinant (e.g., microbial or mammalian) expression systems. “Microbial” refers to recombinant polypeptides or proteins made in bacterial or fungal (e.g., yeast) expression systems. As a product, “recombinant microbial” defines a polypeptide or protein essentially free of native endogenous substances and unaccompanied by associated native glycosylation. Polypeptides or proteins expressed in most bacterial cultures, e.g., E. coli, will be free of glycosylation modifications; polypeptides or proteins expressed in yeast will have a glycosylation pattern different from that expressed in mammalian cells.

[0132] “Nucleotide sequence” refers to a heteropolymer of deoxyribonucleotides. Generally, DNA segments encoding the polypeptides and proteins provided by this invention are assembled from fragments of the Staphylococcus aureus genome and short oligonucleotide linkers, or from a series of oligonucleotides, to provide a synthetic gene which is capable of being expressed in a recombinant transcriptional unit comprising regulatory elements derived from a microbial or viral operon.

[0133] “Recombinant expression vehicle or vector” refers to a plasmid or phage or virus or vector, for expressing a polypeptide from a DNA (RNA) sequence. The expression vehicle can comprise a transcriptional unit comprising an assembly of (1) a genetic regulatory elements necessary for gene expression in the host, including elements required to initiate and maintain transcription at a level sufficient for suitable expression of the desired polypeptide, including, for example, promoters and, where necessary, an enhancers and a polyadenylation signal; (2) a structural or coding sequence which is transcribed into mRNA and translated into protein, and (3) appropriate signals to initiate translation at the beginning of the desired coding region and terminate translation at its end. Structural units intended for use in yeast or eukaryotic expression systems preferably include a leader sequence enabling extracellular secretion of translated protein by a host cell. Alternatively, where recombinant protein is expressed without a leader or transport sequence, it may include an N-terminal methionine residue. This residue may or may not be subsequently cleaved from the expressed recombinant protein to provide a final product.

[0134] “Recombinant expression system” means host cells which have stably integrated a recombinant transcriptional unit into chromosomal DNA or carry the recombinant transcriptional unit extra chromosomally. The cells can be prokaryotic or eukaryotic. Recombinant expression systems as defined herein will express heterologous polypeptides or proteins upon induction of the regulatory elements linked to the DNA segment or synthetic gene to be expressed.

[0135] Mature proteins can be expressed in mammalian cells, yeast, bacteria, or other cells under the control of appropriate promoters. Cell-free translation systems can also be employed to produce such proteins using RNAs derived from the DNA constructs of the present invention. Appropriate cloning and expression vectors for use with prokaryotic and eukaryotic hosts are described in Sambrook et al., MOLECULAR CLONING:A LABORATORY MANUAL, 2nd Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (1989), the disclosure of which is hereby incorporated by reference in its entirety.

[0136] Generally, recombinant expression vectors will include origins of replication and selectable markers permitting transformation of the host cell, e.g., the ampicillin resistance gene of E. coli and S. cerevisiae TRPI gene, and a promoter derived from a highly expressed gene to direct transcription of a downstream structural sequence. Such promoters can be derived from operons encoding glycolytic enzymes such as 3-phosphoglycerate kinase (PGK), alpha-factor, acid phosphatase, or heat shock proteins, among others. The heterologous structural sequence is assembled in appropriate phase with translation initiation and termination sequences, and preferably, a leader sequence capable of directing secretion of translated protein into the periplasmic space or extracellular medium. Optionally, the heterologous sequence can encode a fusion protein including an N-terminal identification peptide imparting desired characteristics, e.g., stabilization or simplified purification of expressed recombinant product.

[0137] Useful expression vectors for bacterial use are constructed by inserting a structural DNA sequence encoding a desired protein together with suitable translation initiation and termination signals in operable reading phase with a functional promoter. The vector will comprise one or more phenotypic selectable markers and an origin of replication to ensure maintenance of the vector and, when desirable, provide amplification within the host.

[0138] Suitable prokaryotic hosts for transformation include strains of Staphylococcus aureus, E. coli, B. subtilis, Salmonella typhimurium and various species within the genera Pseudomonas, Streptomyces, and Staphylococcus. Others may, also be employed as a matter of choice.

[0139] As a representative but non-limiting example, useful expression vectors for bacterial use can comprise a selectable marker and bacterial origin of replication derived from commercially available plasmids comprising genetic elements of the well known cloning vector pBR322 (ATCC 37017). Such commercial vectors include, for example, pKK223-3 (available form Pharmacia Fine Chemicals, Uppsala, Sweden) and GEM 1 (available from Promega Biotec, Madison, Wis., USA). These pBR322 “backbone” sections are combined with an appropriate promoter and the structural sequence to be expressed.

[0140] Following transformation of a suitable host strain and growth of the host strain to an appropriate cell density, the selected promoter, where it is inducible, is derepressed or induced by appropriate means (e.g., temperature shift or chemical induction) and cells are cultured for an additional period to provide for expression of the induced gene product. Thereafter cells are typically harvested, generally by centrifugation, disrupted to release expressed protein, generally by physical or chemical means, and the resulting crude extract is retained for further purification.

[0141] Various mammalian cell culture systems can also be employed to express recombinant protein. Examples of mammalian expression systems include the COS-7 lines of monkey kidney fibroblasts, described in Gluzman, Cell 23: 175 (1981), and other cell lines capable of expressing a compatible vector, for example, the C127, 3T3, CHO, HeLa and BHK cell lines.

[0142] Mammalian expression vectors will comprise an origin of replication, a suitable promoter and enhancer, and also any necessary ribosome binding sites, polyadenylation site, splice donor and acceptor sites, transcriptional termination sequences, and 5′ flanking nontranscribed sequences. DNA sequences derived from the SV40 viral genome, for example, SV40 origin, early promoter, enhancer, splice, and polyadenylation sites may be used to provide the required nontranscribed genetic elements.

[0143] Recombinant polypeptides and proteins produced in bacterial culture is usually isolated by initial extraction from cell pellets, followed by one or more salting-out, aqueous ion exchange or size exclusion chromatography steps. Microbial cells employed in expression of proteins can be disrupted by any convenient method, including freeze-thaw cycling, sonication, mechanical disruption, or use of cell lysing agents. Protein refolding steps can be used, as necessary, in completing configuration of the mature protein. Finally, high performance liquid chromatography (HPLC) can be employed for final purification steps.

[0144] An additional aspect of the invention includes Staphylococcus aureus polypeptides which are useful as immunodiagnostic antigens and/or immunoprotective vaccines, collectively “immunologically useful polypeptides”. Such immunologically useful polypeptides may be selected from the ORFs disclosed herein based on techniques well known in the art and described elsewhere herein. The inventors have used the following criteria to select several immunologically useful polypeptides:

[0145] As is known in the art, an amino terminal type I signal sequence directs a nascent protein across the plasma and outer membranes to the exterior of the bacterial cell. Such outer membrane polypeptides are expected to be immunologically useful. According to Izard, J. W. et al., Mol. Microbiol. 13, 765-773; (1994), polypeptides containing type I signal sequences contain the following physical attributes: The length of the type I signal sequence is approximately 15 to 25 primarily hydrophobic amino acid residues with a net positive charge in the extreme amino terminus; the central region of the signal sequence must adopt an alpha-helical conformation in a hydrophobic environment; and the region surrounding the actual site of cleavage is ideally six residues long, with small side-chain amino acids in the −1 and −3 positions.

[0146] Also known in the art is the type IV signal sequence which is an example of the several types of functional signal sequences which exist in addition to the type I signal sequence detailed above. Although functionally related, the type IV signal sequence possesses a unique set of biochemical and physical attributes (Strom, M. S. and Lory, S., J. Bacteriol. 174, 7345-7351; 1992)). These are typically six to eight amino acids with a net basic charge followed by an additional sixteen to thirty primarily hydrophobic residues. The cleavage site of a type IV signal sequence is typically after the initial six to eight amino acids at the extreme amino terminus. In addition, all type IV signal sequences contain a phenylalanine residue at the +1 site relative to the cleavage site.

[0147] Studies of the cleavage sites of twenty-six bacterial lipoprotein precursors has allowed the definition of a consensus amino acid sequence for lipoprotein cleavage. Nearly three-fourths of the bacterial lipoprotein precursors examined contained the sequence L-(A,S)-(G,A)-C at positions −3 to +1, relative to the point of cleavage (Hayashi, S. and Wu, H. C. Lipoproteins in bacteria. J Bioenerg. Biomembr. 22, 451-471; 1990).

[0148] It is well known that most anchored proteins found on the surface of gram-positive bacteria possess a highly conserved carboxy terminal sequence. More than fifty such proteins from organisms such as S. pyogenes, S. mutans, E. faecalis, S. pneumoniae, and others, have been identified based on their extracellular location and carboxy terminal amino acid sequence (Fischetti, V. A. Gram-positive commensal bacteria deliver antigens to elicit mucosal and systemic immunity. ASM News 62, 405-410; 1996). The conserved region is comprised of six charged amino acids at the extreme carboxy terminus coupled to 15-20 hydrophobic amino acids presumed to function as a transmembrane domain. Immediately adjacent to the transmembrane domain is a six amino acid sequence conserved in nearly all proteins examined. The amino acid sequence of this region is L-P-X-G-X (SEQ ID NO:5256), where X is any amino acid.

[0149] Amino acid sequence similarities to proteins of known function by BLAST enables the assignment of putative functions to novel amino acid sequences and allows for the selection of proteins thought to function outside the cell wall. Such proteins are well known in the art and include “lipoprotein”, “periplasmic”, or “antigen”.

[0150] An algorithm for selecting antigenic and immunogenic Staphylococcus aureus polypeptides including the foregoing criteria was developed by the present inventors. Use of the algorithm by the inventors to select immunologically useful Staphylococcus aureus polypeptides resulted in the selection of several ORFs which are predicted to be outer membrane-associated proteins. These proteins are identified below, and shown in the Sequence Listing as SEQ ID NOS: 5,192 to 5,255. Thus the amino acid sequence of each of several antigenic Staphylococcus aureus polypeptides can be determined, for example, by locating the amino acid sequence of the ORF in the Sequence Listing. Likewise the polynucleotide sequence encoding each ORF can be found by locating the corresponding polynucleotide SEQ ID in Tables 1, 2, or 3, and finding the corresponding nucleotide sequence in the sequence listing.

[0151] As will be appreciated by those of ordinary skill in the art, although a polypeptide representing an entire ORF may be the closest approximation to a protein found in vivo, it is not always technically practical to express a complete ORF in vitro. It may be very challenging to express and purify a highly hydrophobic protein by common laboratory methods. As a result, the immunologically useful polypeptides described herein as SEQ ID NOS: 5,192-5,255 may have been modified slightly to simplify the production of recombinant protein, and are the preferred embodiments. In general, nucleotide sequences which encode highly hydrophobic domains, such as those found at the amino terminal signal sequence, are excluded for enhanced in vitro expression of the polypeptides. Furthermore, any highly hydrophobic amino acid sequences occurring at the carboxy terminus are also excluded. Such truncated polypeptides include for example the mature forms of the polypeptides expected to exist in nature.

[0152] Those of ordinary skill in the art can identify soluble portions the polypeptide, and in the case of truncated polypeptides sequences shown as SEQ ID NOS: 5,192-5,255, may obtain the complete predicted amino acid sequence of each polypeptide by translating the corresponding polynucleotides sequences of the corresponding ORF listed in Tables 1,2 and 3 and found in the sequence listing.

[0153] Accordingly, polypeptides comprising the complete amino acid sequence of an immunologically useful polypeptide selected from the group of polypeptides encoded by the ORFs shown as SEQ ID NOS: 5,192-5,255, or an amino acid sequence at least 95% identical thereto, preferably at least 97% identical thereto, and most preferably at least 99% identical thereto form an embodiment of the invention; in addition, polypeptides comprising an amino acid sequence selected from the group of amino acid sequences shown in the sequence listing as SEQ ID NOS: 5,191-5,255, or an amino acid sequence at least 95% identical thereto, preferably at least 97% identical thereto and most preferably 99% identical thereto, form an embodiment of the invention. Polynucleotides encoding the foregoing polypeptides also form part of the invention.

[0154] In another aspect, the invention provides a peptide or polypeptide comprising an epitope-bearing portion of a polypeptide of the invention, particularly those epitope-bearing portions (antigenic regions) identified in the sequence listing as SEQ ID NOS: 5,191-5,255. The epitope-bearing portion is an immunogenic or antigenic epitope of a polypeptide of the invention. An “immunogenic epitope” is defined as a part of a protein that elicits an antibody response when the whole protein is the immunogen. On the other hand, a region of a protein molecule to which an antibody can bind is defined as an “antigenic epitope.” The number of immunogenic epitopes of a protein generally is less than the number of antigenic epitopes. See, for instance, Geysen et al., Proc. Natl. Acad. Sci. USA 81:3998-4002 (1983).

[0155] As to the selection of peptides or polypeptides bearing an antigenic epitope (i.e., that contain a region of a protein molecule to which an antibody can bind), it is well known in that art that relatively short synthetic peptides that mimic part of a protein sequence are routinely capable of eliciting an antiserum that reacts with the partially mimicked protein. See, for instance, Sutcliffe, J. G., Shinnick, T. M., Green, N. and Learner, R. A. (1983) “Antibodies that react with predetermined sites on proteins”, Science, 219:660-666. Peptides capable of eliciting protein-reactive sera are frequently represented in the primary sequence of a protein, can be characterized by a set of simple chemical rules, and are confined neither to immunodominant regions of intact proteins (i.e., immunogenic epitopes) nor to the amino or carboxyl terminals.

[0156] Antigenic epitope-bearing peptides and polypeptides of the invention are therefore useful to raise antibodies, including monoclonal antibodies, that bind specifically to a polypeptide of the invention. See, for instance, Wilson et al., Cell 37:767-778 (1984) at 777.

[0157] Antigenic epitope-bearing peptides and polypeptides of the invention preferably contain a sequence of at least seven, more preferably at least nine and most preferably between about 15 to about 30 amino acids contained within the amino acid sequence of a polypeptide of the invention. Non-limiting examples of antigenic polypeptides or peptides that can be used to generate S. aureus specific antibodies include: a polypeptide comprising peptides shown below. These polypeptide fragments have been determined to bear antigenic epitopes of indicated S. aureus proteins by the analysis of the Jameson-Wolf antigenic index, a representative sample of which is shown in FIG. 3.

[0158] The epitope-bearing peptides and polypeptides of the invention may be produced by any conventional means. See, e.g., Houghten, R. A. (1985) General method for the rapid solid-phase synthesis of large numbers of peptides: specificity of antigen-antibody interaction at the level of individual amino acids. Proc. Natl. Acad. Sci. USA 82:5131-5135; this “Simultaneous Multiple Peptide Synthesis (SMPS)” process is further described in U.S. Pat. No. 4,631,211 to Houghten et al. (1986).

[0159] Epitope-bearing peptides and polypeptides of the invention are used to induce antibodies according to methods well known in the art. See, for instance, Sutcliffe et al., supra; Wilson et al., supra; Chow, M. et al., Proc. Natl. Acad. Sci. USA 82:910-914; and Bittle, F. J. et al., J. Gen. Virol. 66:2347-2354 (1985). Immunogenic epitope-bearing peptides of the invention, i.e., those parts of a protein that elicit an antibody response when the whole protein is the immunogen, are identified according to methods known in the art. See, for instance, Geysen et al., supra. Further still, U.S. Pat. No. 5,194,392 to Geysen (1990) describes a general method of detecting or determining the sequence of monomers (amino acids or other compounds) which is a topological equivalent of the epitope (i.e., a “mimotope”) which is complementary to a particular paratope (antigen binding site) of an antibody of interest. More generally, U.S. Pat. No. 4,433,092 to Geysen (1989) describes a method of detecting or determining a sequence of monomers which is a topographical equivalent of a ligand which is complementary to the ligand binding site of a particular receptor of interest. Similarly, U.S. Pat. No. 5,480,971 to Houghten, R. A. et al. (1996) on Peralkylated Oligopeptide Mixtures discloses linear C1-C7-alkyl peralkylated oligopeptides and sets and libraries of such peptides, as well as methods for using such oligopeptide sets and libraries for determining the sequence of a peralkylated oligopeptide that preferentially binds to an acceptor molecule of interest. Thus, non-peptide analogs of the epitope-bearing peptides of the invention also can be made routinely by these methods.

[0160] Immunologically useful polypeptides may be identified by an algorithm which locates novel Staphylococcus aureus outer membrane proteins, as is described above. Also listed are epitopes or “antigenic regions” of each of the identified polypeptides. The antigenic regions, or epitopes, are delineated by two numbers x-y, where x is the number of the first amino acid in the open reading frame included within the epitope and y is the number of the last amino acid in the open reading frame included within the epitope. For example, the first epitope in ORF 168-6 is comprised of amino acids 36 to 45 of SEQ ID NO: 5,192. The inventors have identified several epitopes for each of the antigenic polypeptides identified. Accordingly, forming part of the present invention are polypeptides comprising an amino acid sequence of one or more antigenic regions identified. The invention further provides polynucleotides encoding such polypeptides.

[0161] The present invention further includes isolated polypeptides, proteins and nucleic acid molecules which are substantially equivalent to those herein described. As used herein, substantially equivalent can refer both to nucleic acid and amino acid sequences, for example a mutant sequence, that varies from a reference sequence by one or more substitutions, deletions, or additions, the net effect of which does not result in an adverse functional dissimilarity between reference and subject sequences. For purposes of the present invention, sequences having equivalent biological activity, and equivalent expression characteristics are considered substantially equivalent. For purposes of determining equivalence, truncation of the mature sequence should be disregarded.

[0162] The invention further provides methods of obtaining homologs from other strains of Staphylococcus aureus, of the fragments of the Staphylococcus aureus genome of the present invention and homologs of the proteins encoded by the ORFs of the present invention. As used herein, a sequence or protein of Staphylococcus aureus is defined as a homolog of a fragment of the Staphylococcus aureus fragments or contigs or a protein encoded by one of the ORFs of the present invention, if it shares significant homology to one of the fragments of the Staphylococcus aureus genome of the present invention or a protein encoded by one of the ORFs of the present invention. Specifically, by using the sequence disclosed herein as a probe or as primers, and techniques such as PCR cloning and colony/plaque hybridization, one skilled in the art can obtain homologs.

[0163] As used herein, two nucleic acid molecules or proteins are said to “share significant homology” if the two contain regions which possess greater than 85% sequence (amino acid or nucleic acid) homology. Preferred homologs in this regard are those with more than 90% homology. Especially preferred are those with 93% or more homology. Among especially preferred homologs those with 95% or more homology are particularly preferred. Very particularly preferred among these are those with 97% and even more particularly preferred among those are homologs with 99% or more homology. The most preferred homologs among these are those with 99.9% homology or more. It will be understood that, among measures of homology, identity is particularly preferred in this regard.

[0164] Region specific primers or probes derived from the nucleotide sequence provided in SEQ ID NOS: 1-5,191 or from a nucleotide sequence at least 95%, particularly at least 99%, especially at least 99.5% identical to a sequence of SEQ ID NOS: 1-5,191 can be used to prime DNA synthesis and PCR amplification, as well as to identify colonies containing cloned DNA encoding a homolog. Methods suitable to this aspect of the present invention are well known and have been described in great detail in many publications such as, for example, Innis et al., PCR PROTOCOLS, Academic Press, San Diego, Calif. (1990)).

[0165] When using primers derived from SEQ ID NOS: 1-5,191 or from a nucleotide sequence having an aforementioned identity to a sequence of SEQ ID NOS: 1-5,191, one skilled in the art will recognize that by employing high stringency conditions (e.g., annealing at 50-60° C. in 6× SSPC and 50% formamide, and washing at 50-65° C. in 0.5× SSPC) only sequences which are greater than 75% homologous to the primer will be amplified. By employing lower stringency conditions (e.g., hybridizing at 35-37° C. in 5× SSPC and 40-45% formamide, and washing at 42° C. in 0.5× SSPC), sequences which are greater than 40-50% homologous to the primer will also be amplified.

[0166] When using DNA probes derived from SEQ ID NOS: 1-5,191, or from a nucleotide sequence having an aforementioned identity to a sequence of SEQ ID NOS: 1-5,191, for colony/plaque hybridization, one skilled in the art will recognize that by employing high stringency conditions (e.g., hybridizing at 50-65° C. in 5× SSPC and 50% formamide, and washing at 50-65° C. in 0.5× SSPC), sequences having regions which are greater than 90% homologous to the probe can be obtained, and that by employing lower stringency conditions (e.g., hybridizing at 35-37° C. in 5× SSPC and 40-45% formamide, and washing at 42° C. in 0.5× SSPC), sequences having regions which are greater than 35-45% homologous to the probe will be obtained.

[0167] Any organism can be used as the source for homologs of the present invention so long as the organism naturally expresses such a protein or contains genes encoding the same. The most preferred organism for isolating homologs are bacterias which are closely related to Staphylococcus aureus.

ILLUSTRATIVE USES OF COMPOSITIONS OF THE INVENTION

[0168] Each ORF provided in Tables 1 and 2 is identified with a function by homology to a known gene or polypeptide. As a result, one skilled in the art can use the polypeptides of the present invention for commercial, therapeutic and industrial purposes consistent with the type of putative identification of the polypeptide. Such identifications permit one skilled in the art to use the Staphylococcus aureus ORFs in a manner similar to the known type of sequences for which the identification is made; for example, to ferment a particular sugar source or to produce a particular metabolite. A variety of reviews illustrative of this aspect of the invention are available, including the following reviews on the industrial use of enzymes, for example, BIOCHEMICAL ENGINEERING AND BIOTECHNOLOGY HANDBOOK, 2nd Ed., Macmillan Publications, Ltd. NY (1991) and BIOCATALYSTS IN ORGANIC SYNTHESES, Tramper et al., Eds., Elsevier Science Publishers, Amsterdam, The Netherlands (1985). A variety of exemplary uses that illustrate this and similar aspects of the present invention are discussed below.

[0169] 1. Biosynthetic Enzymes

[0170] Open reading frames encoding proteins involved in mediating the catalytic reactions involved in intermediary and macromolecular metabolism, the biosynthesis of small molecules, cellular processes and other functions includes enzymes involved in the degradation of the intermediary products of metabolism, enzymes involved in central intermediary metabolism, enzymes involved in respiration, both aerobic and anaerobic, enzymes involved in fermentation, enzymes involved in ATP proton motor force conversion, enzymes involved in broad regulatory function, enzymes involved in amino acid synthesis, enzymes involved in nucleotide synthesis, enzymes involved in cofactor and vitamin synthesis, can be used for industrial biosynthesis.

[0171] The various metabolic pathways present in Staphylococcus aureus can be identified based on absolute nutritional requirements as well as by examining the various enzymes identified in Table 1-3 and SEQ ID NOS: 1-5,191.

[0172] Of particular interest are polypeptides involved in the degradation of intermediary metabolites as well as non-macromolecular metabolism. Such enzymes include amylases, glucose oxidases, and catalase.

[0173] Proteolytic enzymes are another class of commercially important enzymes. Proteolytic enzymes find use in a number of industrial processes including the processing of flax and other vegetable fibers, in the extraction, clarification and depectinization of fruit juices, in the extraction of vegetables' oil and in the maceration of fruits and vegetables to give unicellular fruits. A detailed review of the proteolytic enzymes used in the food industry is provided in Rombouts et al., Symbiosis 21: 79 (1986) and Voragen et al. in BIOCATALYSTS IN AGRICULTURAL BIOTECHNOLOGY, Whitaker et al., Eds., American Chemical Society Symposium Series 389: 93 (1989).

[0174] The metabolism of sugars is an important aspect of the primary metabolism of Staphylococcus aureus. Enzymes involved in the degradation of sugars, such as, particularly, glucose, galactose, fructose and xylose, can be used in industrial fermentation. Some of the important sugar transforming enzymes, from a commercial viewpoint, include sugar isomerases such as glucose isomerase. Other metabolic enzymes have found commercial use such as glucose oxidases which produces ketogulonic acid (KGA). KGA is an intermediate in the commercial production of ascorbic acid using the Reichstein's procedure, as described in Krueger et al., Biotechnology 6(A), Rhine et al., Eds., Verlag Press, Weinheim, Germany (1984).

[0175] Glucose oxidase (GOD) is commercially available and has been used in purified form as well as in an immobilized form for the deoxygenation of beer. See, for instance, Hartmeir et al., Biotechnology Letters 1: 21 (1979). The most important application of GOD is the industrial scale fermentation of gluconic acid. Market for gluconic acids which are used in the detergent, textile, leather, photographic, pharmaceutical, food, feed and concrete industry, as described, for example, in Bigelis et al., beginning on page 357 in GENE MANIPULATIONS AND FUNGI; Benett et al., Eds., Academic Press, New York (1985). In addition to industrial applications, GOD has found applications in medicine for quantitative determination of glucose in body fluids recently in biotechnology for analyzing syrups from starch and cellulose hydrosylates. This application is described in Owusu et al., Biochem. et Biophysica. Acta. 872: 83 (1986), for instance.

[0176] The main sweetener used in the world today is sugar which comes from sugar beets and sugar cane. In the field of industrial enzymes, the glucose isomerase process shows the largest expansion in the market today. Initially, soluble enzymes were used and later immobilized enzymes were developed (Krueger et al., Biotechnology, The Textbook of Industrial Microbiology, Sinauer Associated Incorporated, Sunderland, Mass. (1990)). Today, the use of glucose- produced high fructose syrups is by far the largest industrial business using immobilized enzymes. A review of the industrial use of these enzymes is provided by Jorgensen, Starch 40:307 (1988).

[0177] Proteinases, such as alkaline serine proteinases, are used as detergent additives and thus represent one of the largest volumes of microbial enzymes used in the industrial sector. Because of their industrial importance, there is a large body of published and unpublished information regarding the use of these enzymes in industrial processes. (See Faultman et al., Acid Proteases Structure Function and Biology, Tang, J., ed., Plenum Press, New York (1977) and Godfrey et al., Industrial Enzymes, MacMillan Publishers, Surrey, UK (1983) and Hepner et al, Report Industrial Enzymes by 1990, Hel Hepner & Associates, London (1986)).

[0178] Another class of commercially usable proteins of the present invention are the microbial lipases, described by, for instance, Macrae et al., Philosophical Transactions of the Chiral Society of London 310:227 (1985) and Poserke, Journal of the American Oil Chemist Society 61:1758 (1984). A major use of lipases is in the fat and oil industry for the production of neutral glycerides using lipase catalyzed inter-esterification of readily available triglycerides. Application of lipases include the use as a detergent additive to facilitate the removal of fats from fabrics in the course of the washing procedures.

[0179] The use of enzymes, and in particular microbial enzymes, as catalyst for key steps in the synthesis of complex organic molecules is gaining popularity at a great rate. One area of great interest is the preparation of chiral intermediates. Preparation of chiral intermediates is of interest to a wide range of synthetic chemists particularly those scientists involved with the preparation of new pharmaceuticals, agrochemicals, fragrances and flavors. (See Davies et al., Recent Advances in the Generation of Chiral Intermediates Using Enzymes, CRC Press, Boca Raton, Fla. (1990)). The following reactions catalyzed by enzymes are of interest to organic chemists: hydrolysis of carboxylic acid esters, phosphate esters, amides and nitriles, esterification reactions, trans-esterification reactions, synthesis of amides, reduction of alkanones and oxoalkanates, oxidation of alcohols to carbonyl compounds, oxidation of sulfides to sulfoxides, and carbon bond forming reactions such as the aldol reaction.

[0180] When considering the use of an enzyme encoded by one of the ORFs of the present invention for biotransformation and organic synthesis it is sometimes necessary to consider the respective advantages and disadvantages of using a microorganism as opposed to an isolated enzyme. Pros and cons of using a whole cell system on the one hand or an isolated partially purified enzyme on the other hand, has been described in detail by Bud et al., Chemistry in Britain (1987), p. 127.

[0181] Amino transferases, enzymes involved in the biosynthesis and metabolism of amino acids, are useful in the catalytic production of amino acids. The advantages of using microbial based enzyme systems is that the amino transferase enzymes catalyze the stereo- selective synthesis of only L-amino acids and generally possess uniformly high catalytic rates. A description of the use of amino transferases for amino acid production is provided by Roselle-David, Methods of Enzymology 136:479 (1987).

[0182] Another category of useful proteins encoded by the ORFs of the present invention include enzymes involved in nucleic acid synthesis, repair, and recombination. A variety of commercially important enzymes have previously been isolated from members of Staphylococcus aureus. These include Sau3A and Sau96I.

[0183] 2. Generation of Antibodies

[0184] As described here, the proteins of the present invention, as well as homologs thereof, can be used in a variety procedures and methods known in the art which are currently applied to other proteins. The proteins of the present invention can further be used to generate an antibody which selectively binds the protein. Such antibodies can be either monoclonal or polyclonal antibodies, as well fragments of these antibodies, and humanized forms.

[0185] The invention further provides antibodies which selectively bind to one of the proteins of the present invention and hybridomas which produce these antibodies. A hybridoma is an immortalized cell line which is capable of secreting a specific monoclonal antibody.

[0186] In general, techniques for preparing polyclonal and monoclonal antibodies as well as hybridomas capable of producing the desired antibody are well known in the art (Campbell, A. M., MONOCLONAL ANTIBODY TECHNOLOGY: LABORATORY TECHNIQUES IN BIOCHEMISTRY AND MOLECULAR BIOLOGY, Elsevier Science Publishers, Amsterdam, The Netherlands (1984); St. Groth et al., J. Immunol. Methods 35: 1-21 (1980), Kohler and Milstein, Nature 256: 495-497 (1975)), the trioma technique, the human B-cell hybridoma technique (Kozbor et al., Immunology Today-4: 72 (1983), pgs. 77-96 of Cole et al., in MONOCLONAL ANTIBODIES AND CANCER THERAPY, Alan R. Liss, Inc. (1985)).

[0187] Any animal (mouse, rabbit, etc.) which is known to produce antibodies can be immunized with the pseudogene polypeptide. Methods for immunization are well known in the art. Such methods include subcutaneous or interperitoneal injection of the polypeptide. One skilled in the art will recognize that the amount of the protein encoded by the ORF of the present invention used for immunization will vary based on the animal which is immunized, the antigenicity of the peptide and the site of injection.

[0188] The protein which is used as an immunogen may be modified or administered in an adjuvant in order to increase the protein's antigenicity. Methods of increasing the antigenicity of a protein are well known in the art and include, but are not limited to coupling the antigen with a heterologous protein (such as globulin or galactosidase) or through the inclusion of an adjuvant during immunization.

[0189] For monoclonal antibodies, spleen cells from the immunized animals are removed, fused with myeloma cells, such as SP2/0-Ag14 myeloma cells, and allowed to become monoclonal antibody producing hybridoma cells.

[0190] Any one of a number of methods well known in the art can be used to identify the hybridoma cell which produces an antibody with the desired characteristics. These include screening the hybridomas with an ELISA assay, western blot analysis, or radioimmunoassay (Lutz et al., Exp. Cell Res. 175: 109-124 (1988)).

[0191] Hybridomas secreting the desired antibodies are cloned and the class and subclass is determined using procedures known in the art (Campbell, A. M., Monoclonal Antibody Technology: Laboratory Techniques in Biochemistry and Molecular Biology, Elsevier Science Publishers, Amsterdam, The Netherlands (1984)).

[0192] Techniques described for the production of single chain antibodies (U.S. Pat. No. 946,778) can be adapted to produce single chain antibodies to proteins of the present invention.

[0193] For polyclonal antibodies, antibody containing antisera is isolated from the immunized animal and is screened for the presence of antibodies with the desired specificity using one of the above-described procedures.

[0194] The present invention further provides the above- described antibodies in detectably labeled form. Antibodies can be detectably labeled through the use of radioisotopes, affinity labels (such as biotin, avidin, etc.), enzymatic labels (such as horseradish peroxidase, alkaline phosphatase, etc.) fluorescent labels (such as FITC or rhodamine, etc.), paramagnetic atoms, etc. Procedures for accomplishing such labeling are well-known in the art, for example see Stemberger et al., J. Histochem. Cytochem. 18:315 (1970); Bayer, E. A. et al., Meth. Enzym. 62:308 (1979); Engval, E. et al., Immunol. 109-129 (1972); Goding, J. W. J. Immunol. Meth. 13:215 (1976)).

[0195] The labeled antibodies of the present invention can be used for in vitro, in vivo, and in situ assays to identify cells or tissues in which a fragment of the Staphyococcus aureus genome is expressed.

[0196] The present invention further provides the above-described antibodies immoblized on a solid support. Examples of such solid supports include plastics such as polycarbonate, complex carbohydrates such as agarose and sepharose, acrylic resins and such as polyacrylamide and latex beads. Techniques for coupling antibodies to such solid supports are well known in the art (Weir, D. M. et al., “Handbook of Experimental Immunology” 4th Ed., Blackwell Scientific Publications, Oxford, England, Chapter 10 (1986); Jacoby, W. D. et al., Meth. Enzym. 34 Academic Press, N.Y. (1974)). The immobilized antibodies of the present invention can be used for in vitro, in vivo, and in situ assays as well as for immunoaffinity purification of the proteins of the present invention.

[0197] 3. Diagnostic Assays and Kits

[0198] The present invention further provides methods to identify the expression of one of the ORFs of the present invention, or homolog thereof, in a test sample, using one of the DFs, antigens or antibodies of the present invention.

[0199] In detail, such methods comprise incubating a test sample with one or more of the antibodies, or one or more of the DFs, or one or more antigens of the present invention and assaying for binding of the DFs, antigens or antibodies to components within the test sample.

[0200] Conditions for incubating a DF, antigen or antibody with a test sample vary. Incubation conditions depend on the format employed in the assay, the detection methods employed, and the type and nature of the DF or antibody used in the assay. One skilled in the art will recognize that any one of the commonly available hybridization, amplification or immunological assay formats can readily be adapted to employ the Dfs, antigens or antibodies of the present invention. Examples of such assays can be found in Chard, T., An Introduction to Radioimmunoassay and Related Techniques, Elsevier Science Publishers, Amsterdam, The Netherlands (1986); Bullock, G. R. et al., Techniques in inmunocytochemistry, Academic Press, Orlando, Fla. Vol. 1 (1982), Vol. 2 (1983), Vol. 3 (1985); Tijssen, P., Practice and Theory of Enzyme Immunoassays: Laboratory Techniques in Biochemistry; PCT publication W095/32291, and Molecular Biology, Elsevier Science Publishers, Amsterdam, The Netherlands (1985), all of which are hereby incorporated herein by reference.

[0201] The test samples of the present invention include cells, protein or membrane extracts of cells, or biological fluids such as sputum, blood, serum,, plasma, or urine. The test sample used in the above-described method will vary based on the assay format, nature of the detection method and the tissues, cells or extracts used as the sample to be assayed. Methods for preparing protein extracts or membrane extracts of cells are well known in the art and can be readily be adapted in order to obtain a sample which is compatible with the system utilized.

[0202] In another embodiment of the present invention, kits are provided which contain the necessary reagents to carry out the assays of the present invention.

[0203] Specifically, the invention provides a compartmentalized kit to receive, in close confinement, one or more containers which comprises:(a) a first container comprising one of the Dfs, antigens or antibodies of the present invention; and (b) one or more other containers comprising one or more of the following: wash reagents, reagents capable of detecting presence of a bound DF, antigen or antibody.

[0204] In detail, a compartmentalized kit includes any kit in which reagents are contained in separate containers. Such containers include small glass containers, plastic containers or strips of plastic or paper. Such containers allows one to efficiently transfer reagents from one compartment to another compartment such that the samples and reagents are not cross-contaminated, and the agents or solutions of each container can be added in a quantitative fashion from one compartment to another. Such containers will include a container which will accept the test sample, a container which contains the antibodies used in the assay, containers which contain wash reagents (such as phosphate buffered saline, Tris-buffers, etc.), and containers which contain the reagents used to detect the bound antibody, antigen or DF.

[0205] Types of detection reagents include labeled nucleic acid probes, labeled secondary antibodies, or in the alternative, if the primary antibody is labeled, the enzymatic, or antibody binding reagents which are capable of reacting with the labeled antibody. One skilled in the art will readily recognize that the disclosed Dfs, antigens and antibodies of the present invention can be readily incorporated into one of the established kit formats which are well known in the art.

[0206] 4. Screening Assay for Binding Agents

[0207] Using the isolated proteins of the present invention, the present invention further provides methods of obtaining and identifying agents which bind to a protein encoded by one of the ORFs of the present invention or to one of the fragments and the Staphylococcus aureus fragment and contigs herein described.

[0208] In general, such methods comprise steps of:

[0209] contacting an agent with an isolated protein encoded by one of the ORFs of the present invention, or an isolated fragment of the Staphylococcus aureus genome; and

[0210] determining whether the agent binds to said protein or said fragment.

[0211] The agents screened in the above assay can be, but are not limited to, peptides, carbohydrates, vitamin derivatives, or other pharmaceutical agents. The agents can be selected and screened at random or rationally selected or designed using protein modeling techniques.

[0212] For random screening, agents such as peptides, carbohydrates, pharmaceutical agents and the like are selected at random and are assayed for their ability to bind to the protein encoded by the ORF of the present invention.

[0213] Alternatively, agents may be rationally selected or designed. As used herein, an agent is said to be “rationally selected or designed” when the agent is chosen based on the configuration of the particular protein. For example, one skilled in the art can readily adapt currently available procedures to generate peptides, pharmaceutical agents and the like capable of binding to a specific peptide sequence in order to generate rationally designed antipeptide peptides, for example see Hurby et al., Application of Synthetic Peptides: Antisense Peptides,” In Synthetic Peptides, A User's Guide, W. H. Freeman, NY (1992), pp. 289-307, and Kaspczak et al., Biochemistry 28:9230-8 (1989), or pharmaceutical agents, or the like.

[0214] In addition to the foregoing, one class of agents of the present invention, as broadly described, can be used to control gene expression through binding to one of the ORFs or EMFs of the present invention. As described above, such agents can be randomly screened or rationally designed/selected. Targeting the ORF or EMF allows a skilled artisan to design sequence specific or element specific agents, modulating the expression of either a single ORF or multiple ORFs which rely on the same EMF for expression control.

[0215] One class of DNA binding agents are agents which contain base residues which hybridize or form a triple helix by binding to DNA or RNA. Such agents can be based on the classic phosphodiester, ribonucleic acid backbone, or can be a variety of sulfhydryl or polymeric derivatives which have base attachment capacity.

[0216] Agents suitable for use in these methods usually contain 20 to 40 bases and are designed to be complementary to a region of the gene involved in transcription (triple helix—see Lee et al., Nucl. Acids Res. 6:3073 (1979); Cooney et al., Science 241:456 (1988); and Dervan et al., Science 251: 1360 (1991)) or to the mRNA itself (antisense—Okano, J. Neurochem. 56:560 (1991); Oligodeoxynucleotides as Antisense Inhibitors of Gene Expression, CRC Press, Boca Raton, Fla. (1988)). Triple helix- formation optimally results in a shut-off of RNA transcription from DNA, while antisense RNA hybridization blocks translation of an mRNA molecule into polypeptide. Both techniques have been demonstrated to be effective in model systems. Information contained in the sequences of the present invention can be used to design antisense and triple helix-forming oligonucleotides, and other DNA binding agents.

[0217] 5. Pharmaceutical Compositions and Vaccines

[0218] The present invention further provides pharmaceutical agents which can be used to modulate the growth or pathogenicity of Staphylococcus aureus, or another related organism, in vivo or in vitro. As used herein, a “pharmaceutical agent” is defined as a composition of matter which can be formulated using known techniques to provide a pharmaceutical compositions. As used herein, the “pharmaceutical agents of the present invention” refers the pharmaceutical agents which are derived from the proteins encoded by the ORFs of the present invention or are agents which are identified using the herein described assays.

[0219] As used herein, a pharmaceutical agent is said to “modulate the growth or pathogenicity of Staphylococcus aureus or a related organism, in vivo or in vitro,” when the agent reduces the rate of growth, rate of division, or viability of the organism in question. The pharmaceutical agents of the present invention can modulate the growth or pathogenicity of an organism in many fashions, although an understanding of the underlying mechanism of action is not needed to practice the use of the pharmaceutical agents of the present invention. Some agents will modulate the growth or pathogenicity by binding to an important protein thus blocking the biological activity of the protein, while other agents may bind to a component of the outer surface of the organism blocking attachment or rendering the organism more prone to act the bodies nature immune system. Alternatively, the agent may comprise a protein encoded by one of the ORFs of the present invention and serve as a vaccine. The development and use of vaccines derived from membrane associated polypeptides are well known in the art. The inventors have identified particularly preferred immunogenic Staphylococcus aureus polypeptides for use as vaccines. Such immunogenic polypeptides are described above and summarized below.

[0220] As used herein, a “related organism” is a broad term which refers to any organism whose growth or pathogenicity can be modulated by one of the pharmaceutical agents of the present invention. In general, such an organism will contain a homolog of the protein which is the target of the pharmaceutical agent or the protein used as a vaccine. As such, related organisms do not need to be bacterial but may be fungal or viral pathogens.

[0221] The pharmaceutical agents and compositions of the present invention may be administered in a convenient manner, such as by the oral, topical, intravenous, intraperitoneal, intramuscular, subcutaneous, intranasal or intradermal routes. The pharmaceutical compositions are administered in an amount which is effective for treating and/or prophylaxis of the specific indication. In general, they are administered in an amount of at least about 1 mg/kg body weight and in most cases they will be administered in an amount not in excess of about 1 g/kg body weight per day. In most cases, the dosage is from about 0.1 mg/kg to about 10 g/kg body weight daily, taking into account the routes of administration, symptoms, etc.

[0222] The agents of the present invention can be used in native form or can be modified to form a chemical derivative. As used herein, a molecule is said to be a “chemical derivative” of another molecule when it contains additional chemical moieties not normally a part of the molecule. Such moieties may improve the molecule's solubility, absorption, biological half life, etc. The moieties may alternatively decrease the toxicity of the molecule, eliminate or attenuate any undesirable side effect of the molecule, etc. Moieties capable of mediating such effects are disclosed in, among other sources, REMINGTON'S PHARMACEUTICAL SCIENCES (1980) cited elsewhere herein.

[0223] For example, such moieties may change an immunological character of the functional derivative, such as affinity for a given antibody. Such changes in immunomodulation activity are measured by the appropriate assay, such as a competitive type immunoassay. Modifications of such protein properties as redox or thermal stability, biological half-life, hydrophobicity, susceptibility to proteolytic degradation or the tendency to aggregate with carriers or into multimers also may be effected in this way and can be assayed by methods well known to the skilled artisan.

[0224] The therapeutic effects of the agents of the present invention may be obtained by providing the agent to a patient by any suitable means (e.g., inhalation, intravenously, intramuscularly, subcutaneously, enterally, or parenterally). It is preferred to administer the agent of the present invention so as to achieve an effective concentration within the blood or tissue in which the growth of the organism is to be controlled. To achieve an effective blood concentration, the preferred method is to administer the agent by injection. The administration may be by continuous infusion, or by single or multiple injections.

[0225] In providing a patient with one of the agents of the present invention, the dosage of the administered agent will vary depending upon such factors as the patient's age, weight, height, sex, general medical condition, previous medical history, etc. In general, it is desirable to provide the recipient with a dosage of agent which is in the range of from about 1 pg/kg to 10 mg/kg (body weight of patient), although a lower or higher dosage may be administered. The therapeutically effective dose can be lowered by using combinations of the agents of the present invention or another agent.

[0226] As used herein, two or more compounds or agents are said to be administered “in combination” with each other when either (1) the physiological effects of each compound, or (2) the serum concentrations of each compound can be measured at the same time. The composition of the present invention can be administered concurrently with, prior to, or following the administration of the other agent.

[0227] The agents of the present invention are intended to be provided to recipient subjects in an amount sufficient to decrease the rate of growth (as defined above) of the target organism.

[0228] The administration of the agent(s) of the invention may be for either a “prophylactic” or “therapeutic” purpose. When provided prophylactically, the agent(s) are provided in advance of any symptoms indicative of the organisms growth. The prophylactic administration of the agent(s) serves to prevent, attenuate, or decrease the rate of onset of any subsequent infection. When provided therapeutically, the agent(s) are provided at (or shortly after) the onset of an indication of infection. The therapeutic administration of the compound(s) serves to attenuate the pathological symptoms of the infection and to increase the rate of recovery.

[0229] The agents of the present invention are administered to a subject, such as a mammal, or a patient, in a pharmaceutically acceptable form and in a therapeutically effective concentration. A composition is said to be “pharmacologically acceptable” if its administration can be tolerated by a recipient patient. Such an agent is said to be administered in a “therapeutically effective amount” if the amount administered is physiologically significant. An agent is physiologically significant if its presence results in a detectable change in the physiology of a recipient patient.

[0230] The agents of the present invention can be formulated according to known methods to prepare pharmaceutically useful compositions, whereby these materials, or their functional derivatives, are combined in admixture with a pharmaceutically acceptable carrier vehicle. Suitable vehicles and their formulation, inclusive of other human proteins, e.g., human serum albumin, are described, for example, in REMINGTON'S PHARMACEUTICAL SCIENCES, 16th Ed., Osol, A., Ed., Mack Publishing, Easton Pa. (1980). In order to form a pharmaceutically acceptable composition suitable for effective administration, such compositions will contain an effective amount of one or more of the agents of the present invention, together with a suitable amount of carrier vehicle.

[0231] Additional pharmaceutical methods may be employed to control the duration of action. Control release preparations may be achieved through the use of polymers to complex or absorb one or more of the agents of the present invention. The controlled delivery may be effectuated by a variety of well known techniques, including formulation with macromolecules such as, for example, polyesters, polyamino acids, polyvinyl, pyrrolidone, ethylenevinylacetate, methylcellulose, carboxymethylcellulose, or protamine, sulfate, adjusting the concentration of the macromolecules and the agent in the formulation, and by appropriate use of methods of incorporation, which can be manipulated to effectuate a desired time course of release. Another possible method to control the duration of action by controlled release preparations is to incorporate agents of the present invention into particles of a polymeric material such as polyesters, polyamino acids, hydrogels, poly(lactic acid) or ethylene vinylacetate copolymers. Alternatively, instead of incorporating these agents into polymeric particles, it is possible to entrap these materials in microcapsules prepared, for example, by coacervation techniques or by interfacial polymerization with, for example, hydroxymethylcellulose or gelatine-microcapsules and poly(methylmethacylate) microcapsules, respectively, or in colloidal drug delivery systems, for example, liposomes, albumin microspheres, microemulsions, nanoparticles, and nanocapsules or in macroemulsions. Such techniques are disclosed in REMINGTON'S PHARMACEUTICAL SCIENCES (1980).

[0232] The invention further provides a pharmaceutical pack or kit comprising one or more containers filled with one or more of the ingredients of the pharmaceutical compositions of the invention. Associated with such container(s) can be a notice in the form prescribed by a governmental agency regulating the manufacture, use or sale of pharmaceuticals or biological products, which notice reflects approval by the agency of manufacture, use or sale for human administration.

[0233] In addition, the agents of the present invention may be employed in conjunction with other therapeutic compounds.

[0234] 6. Shot-Gun Approach to Megabase DNA Sequencing

[0235] The present invention further demonstrates that a large sequence can be sequenced using a random shotgun approach. This procedure, described in detail in the examples that follow, has eliminated the up front cost of isolating and ordering overlapping or contiguous subclones prior to the start of the sequencing protocols.

[0236] Certain aspects of the present invention are described in greater detail in the examples that follow. The examples are provided by way of illustration. Other aspects and embodiments of the present invention are contemplated by the inventors, as will be clear to those of skill in the art from reading the present disclosure.

ILLUSTRATIVE EXAMPLES

[0237] Libraries and Sequencing

[0238] 1. Shotgun Sequencing Probability Analysis

[0239] The overall strategy for a shotgun approach to whole genome sequencing follows from the Lander and Waterman (Landerman and Waterman, Genomics 2: 231 (1988)) application of the equation for the Poisson distribution. According to this treatment, the probability, P0, that any given base in a sequence of size L, in nucleotides, is not sequenced after a certain amount, n, in nucleotides, of random sequence has been determined can be calculated by the equation P0=e−m, where m is L/n, the fold coverage.” For instance, for a genome of 2.8 Mb, m=1 when 2.8 Mb of sequence has been randomly generated (1× coverage). At that point, P0=e−1=0.37. The probability that any given base has not been sequenced is the same as the probability that any region of the whole sequence L has not been determined and, therefore, is equivalent to the fraction of the whole sequence that has yet to be determined. Thus, at one-fold coverage, approximately 37% of a polynucleotide of size L, in nucleotides has not been sequenced. When 14 Mb of sequence has been generated, coverage is 5× for a 0.2.8 Mb and the unsequenced fraction drops to 0.0067 or 0.67%. 5× coverage of a 2.8 Mb sequence can be attained by sequencing approximately 17,000 random clones from both insert ends with an average sequence read length of 410 bp.

[0240] Similarly, the total gap length, G, is determined by the equation G=Le−m, and the average gap size, g, follows the equation, g=L/n. Thus, 5× coverage leaves about 240 gaps averaging about 82 bp in size in a sequence of a polynucleotide 2.8 Mb long.

[0241] The treatment above is essentially that of Lander and Waterman, Genomics 2: 231 (1988).

[0242] 2. Random Library Construction

[0243] In order to approximate the random model described above during actual sequencing, a nearly ideal library of cloned genomic fragments is required. The following library construction procedure was developed to achieve this end.

[0244] Staphylococcus aureus DNA was prepared by phenol extraction. A mixture containing 600 ug DNA in 3.3 ml of 300 mM sodium acetate, 10 mM Tris-HCl, 1 mM Na-EDTA, 30% glycerol was sonicated for 1 min. at 0° C. in a Branson Model 450 Sonicator at the lowest energy setting using a 3 mm probe. The sonicated DNA was ethanol precipitated and redissolved in 500 ul TE buffer.

[0245] To create blunt-ends, a 100 ul aliquot of the resuspended DNA was digested with 5 units of BAL31 nuclease (New England BioLabs) for 10 min at 30° C. in 200 ul BAL31 buffer. The digested DNA was phenol-extracted, ethanol-precipitated, redissolved in 100 ul TE buffer, and then size-fractionated by electrophoresis through a 1.0% low melting temperature agarose gel. The section containing DNA fragments 1.6-2.0 kb in size was excised from the gel, and the LGT agarose was melted and the resulting solution was extracted with phenol to separate the agarose from the DNA. DNA was ethanol precipitated and redissolved in 20 ul of TE buffer for ligation to vector.

[0246] A two-step ligation procedure was used to produce a plasmid library with 97% inserts, of which >99% were single inserts. The first ligation mixture (50 ul) contained 2 ug of DNA fragments, 2 ug pUC18 DNA (Pharmacia) cut with SmaI and dephosphorylated with bacterial alkaline phosphatase, and 10 units of T4 ligase (GIBCO/BRL) and was incubated at 14° C. for 4 hr. The ligation mixture then was phenol extracted and ethanol precipitated, and the precipitated DNA was dissolved in 20 ul TE buffer and electrophoresed on a 1.0% low melting agarose gel. Discrete bands in a ladder were visualized by ethidium bromide-staining and UV illumination and identified by size as insert (i), vector (v), v+i, v+2i, v+3i, etc. The portion of the gel containing v+i DNA was excised and the v+i DNA was recovered and resuspended into 20 ul TE. The v+i DNA then was blunt-ended by T4 polymerase treatment for 5 min. at 37° C. in a reaction mixture (50 ul) containing the v+i linears, 500 uM each of the 4 dNTPs, and 9 units of T4 polymerase (New England BioLabs), under recommended buffer conditions. After phenol extraction and ethanol precipitation the repaired v+i linears were dissolved in 20 ul TE. The final ligation to produce circles was carried out in a 50 ul reaction containing 5 ul of v+i linears and 5 units of T4 ligase at 14° C overnight. After 10 min. at 70° C. the following day, the reaction mixture was stored at −20° C.

[0247] This two-stage procedure resulted in a molecularly random collection of single-insert plasmid recombinants with minimal contamination from double-insert chimeras (<1%) or free vector (<3%).

[0248] Since deviation from randomness can arise from propagation the DNA in the host, E. coli host cells deficient in all recombination and restriction functions (A. Greener, Strategies 3 (1):5 (1990)) were used to prevent rearrangements, deletions, and loss of clones by restriction. Furthermore, transformed cells were plated directly on antibiotic diffusion plates to avoid the usual broth recovery phase which allows multiplication and selection of the most rapidly growing cells.

[0249] Plating was carried out as follows. A 100 ul aliquot of Epicurian Coli SURE II Supercompetent Cells (Stratagene 200152) was thawed on ice and transferred to a chilled Falcon 2059 tube on ice. A 1.7 ul aliquot of 1.42 M beta-mercaptoethanol was added to the aliquot of cells to a final concentration of 25 mM. Cells were incubated on ice for 10 min. A 1 ul aliquot of the final ligation was added to the cells and incubated on ice for 30 min. The cells were heat pulsed for 30 sec. at 42° C. and placed back on ice for 2 min. The outgrowth period in liquid culture was eliminated from this protocol in order to minimize the preferential growth of any given transformed cell. Instead the transformation mixture was plated directly on a nutrient rich SOB plate containing a 5 ml bottom layer of SOB agar (5% SOB agar: 20 g tryptone, 5 g yeast extract, 0.5 g NaCl, 1.5% Difco Agar per liter of media). The 5 ml bottom layer is supplemented with 0.4 ml of 50 mg/ml ampicillin per 100 ml SOB agar. The 15 ml top layer of SOB agar is supplemented with 1 ml X-Gal (2%), 1 ml MgCl2 (1 M), and 1 ml MgSO4/100 ml SOB agar. The 15 ml top layer was poured just prior to plating. Our titer was approximately 100 colonies/10 ul aliquot of transformation.

[0250] All colonies were picked for template preparation regardless of size. Thus, only clones lost due to “poison” DNA or deleterious gene products would be deleted from the library, resulting in a slight increase in gap number over that expected.

[0251] 3. Random DNA Sequencing

[0252] High quality double stranded DNA plasmid templates were prepared using an alkaline lysis method developed in collaboration with 5Prime- - - >3Prime Inc. (Boulder, Co.). Plasmid preparation was performed in a 96-well format for all stages of DNA preparation from bacterial growth through final DNA purification. Average template concentration was determined by running 25% of the samples on an agarose gel. DNA concentrations were not adjusted.

[0253] Templates were also prepared from a Staphylococcus aureus lambda genomic library. An unamplified library was constructed in Lambda DASH II vector (Stratagene). Staphylococcus aureus DNA (>100 kb) was partially digested in a reaction mixture (200 ul) containing 50 ug DNA, 1× Sau3AI buffer, 20 units Sau3AI for 6 min. at 23 C. The digested DNA was phenol-extracted and centrifuges over a 10-40% sucrose gradient. Fractions containing genomic DNA of 15-25 kb were recovered by precipitation. One ul of fragments was used with 1 ul of DASHII vector (Stratagene) in the recommended ligation reaction. One ul of the ligation mixture was used per packaging reaction following the recommended protocol with the Gigapack II XL Packaging Extract Phage were plated directly without amplification from the packaging mixture (after dilution with 500 ul of recommended SM buffer and chloroform treatment). Yield was about 2.5×109 pfu/ul.

[0254] An amplified library was prepared from the primary packaging mixture according to the manufacturer's protocol. The amplified library is stored frozen in 7% dimethylsulfoxide. The phage titer is approximately 1×109 pfu/ml.

[0255] Mini-liquid lysates (0.1 ul) are prepared from randomly selected plaques and template is prepared by long range PCR. Samples are PCR amplified using modified T3 and T7 primers, and Elongase Supermix (LTI).

[0256] Sequencing reactions are carried out on plasmid templates using a combination of two workstations (BIOMEK 1000 and Hamilton Microlab 2200) and the Perkin-Elmer 9600 thermocycler with Applied Biosystems PRISM Ready Reaction Dye Primer Cycle Sequencing Kits for the M13 forward (M13-21) and the M13 reverse (M13RP1) primers. Dye terminator sequencing reactions are carried out on the lambda templates on a Perkin-Elmer 9600 Thermocycler using the Applied Biosystems Ready Reaction Dye Terminator Cycle Sequencing kits. Modified T7 and T3 primers are used to sequence the ends of the inserts from the Lambda DASH II library. Sequencing reactions are on a combination of AB 373 DNA Sequencers and ABI 377 DNA sequencers. All of the dye terminator sequencing reactions are analyzed using the 2×9 hour module on the AB 377. Dye primer reactions are analyzed on a combination of ABI 373 and ABI 377 DNA sequencers. The overall sequencing success rate very approximately is about 85% for M13-21 and M13RP1 sequences and 65% for dye-terminator reactions. The average usable read length is 485 bp for M13-21 sequences, 445bp for M13RP1 sequences, and 375 bp for dye-terminator reactions.

[0257] 4. Protocol for Automated Cycle Sequencing

[0258] The sequencing was carried out using Hamilton Microstation 2200, Perkin Elmer 9600 thermocyclers, ABI 373 and ABI 377 Automated DNA Sequencers. The Hamilton combines pre-aliquoted templates and reaction mixes consisting of deoxy- and dideoxynucleotides, the thermostable Taq DNA polymerase, fluorescently-labeled sequencing primers, and reaction buffer. Reaction mixes and templates were combined in the wells of a 96-well thermocycling plate and transferred to the Perkin Elmer 9600 thermocycler. Thirty consecutive cycles of linear amplification (i.e.., one primer synthesis) steps were performed including denaturation, annealing of primer and template, and extension; i.e., DNA synthesis. A heated lid with rubber gaskets on the thermocycling plate prevents evaporation without the need for an oil overlay.

[0259] Two sequencing protocols were used: one for dye-labeled primers and a second for dye-labeled dideoxy chain terminators. The shotgun sequencing involves use of four dye-labeled sequencing primers, one for each of the four terminator nucleotide. Each dye-primer was labeled with a different fluorescent dye, permitting the four individual reactions to be combined into one lane of the 373 or 377 DNA Sequencer for electrophoresis, detection, and base-calling. ABI currently supplies pre-mixed reaction mixes in bulk packages containing all the necessary non-template reagents for sequencing. Sequencing can be done with both plasmid and PCR- generated templates with both dye-primers and dye-terminators with approximately equal fidelity, although plasmid templates generally give longer usable sequences.

[0260] Thirty-two reactions were loaded per ABI 373 Sequencer each day and 96 samples can be loaded on an ABI 377 per day. Electrophoresis was run overnight (ABI 373) or for 2½ hours (ABI 377) following the manufacturer's protocols. Following electrophoresis and fluorescence detection, the ABI 373 or ABI 377 performs automatic lane tracking and base-calling. The lane-tracking was confirmed visually. Each sequence electropherogram (or fluorescence lane trace) was inspected visually and assessed for quality. Trailing sequences of low quality were removed and the sequence itself was loaded via software to a Sybase database (archived daily to 8 mm tape). Leading vector polylinker sequence was removed automatically by a software program. Average edited lengths of sequences from the standard ABI 373 or ABI 377 were around 400 bp and depend mostly on the quality of the template used for the sequencing reaction.

[0261] Imformatics

[0262] 1. Data Management

[0263] A number of information management systems for a large-scale sequencing lab have been developed. (For review see, for instance, Kerlavage et al., Proceedings of the Twenty-Sixth Annual Hawaii International Conference on System Sciences, IEEE Computer Society Press, Wash. D.C., 585 (1993)) The system used to collect and assemble the sequence data was developed using the Sybase relational database management system and was designed to automate data flow wherever possible and to reduce user error. The database stores and correlates all information collected during the entire operation from template preparation to final analysis of the genome. Because the raw output of the ABI 373 Sequencers was based on a Macintosh platform and the data management system chosen was based on a Unix platform, it was necessary to design and implement a variety of multi- user, client-server applications which allow the raw data as well as analysis results to flow seamlessly into the database with a minimum of user effort.

[0264] 2. Assembly

[0265] An assembly engine (TIGR Assembler) developed for the rapid and accurate assembly of thousands of sequence fragments was employed to generate contigs. The TIGR assembler simultaneously clusters and assembles fragments of the genome. In order to obtain the speed necessary to assemble more than 104 fragments, the algorithm builds a hash table of 12 bp oligonucleotide subsequences to generate a list of potential sequence fragment overlaps. The number of potential overlaps for each fragment determines which fragments are likely to fall into repetitive elements. Beginning with a single seed sequence fragment, TIGR Assembler extends the current contig by attempting to add the best matching fragment based on oligonucleotide content. The contig and candidate fragment are aligned using a modified version of the Smith-Waterman algorithm which provides for optimal gapped alignments (Waterman, M. S., Methods in Enzymology 164: 765 (1988)). The contig is extended by the fragment only if strict criteria for the quality of the match are met. The match criteria include the minimum length of overlap, the maximum length of an unmatched end, and the minimum percentage match. These criteria are automatically lowered by the algorithm in regions of minimal coverage and raised in regions with a possible repetitive element. The number of potential overlaps for each fragment determines which fragments are likely to fall into repetitive elements. Fragments representing the boundaries of repetitive elements and potentially chimeric fragments are often rejected based on partial mismatches at the ends of alignments and excluded from the current contig. TIGR Assembler is designed to take advantage of clone size information coupled with sequencing from both ends of each template. It enforces the constraint that sequence fragments from two ends of the same template point toward one another in the contig and are located within a certain ranged of base pairs (definable for each clone based on the known clone size range for a given library).

[0266] 3. Identifying Genes

[0267] Tables 1, 2, and 3 list ORFs in the Staphylococcus aureus genomic contigs of the present invention that were identified as putative coding regions by the GeneMark software using organism-specific second-order Markov probability transition matrices. It will be appreciated that other criteria can be used, in accordance with well known analytical methods, such as those discussed herein, to generate more inclusive, more restrictive, or more selective lists.

[0268] Table 1 sets out ORFs in the Staphylococcus aureus contigs of the present invention that over a continuous region of at least 50 bases are 95% or more identical (by BLASTN analysis) to a nucleotide sequence available through Genbank in November 1996.

[0269] Table 2 sets out ORFs in the Staphylococcus aureus contigs of the present invention that are not in Table 1 and match, with a BLASTP probability score of 0.01 or less, polypeptide sequence available through a non-redundant database of known protein generated by combining the Swiss-Prot, PIR, and GenPept databases.

[0270] Table 3 sets out the remaining ORFs in the Staphylococcus aureus contigs of the present invention, which did not have significant matches to the public databases by the criteria described above.

[0271] Illustrative Applications

[0272] 1. Production of an Antibody to a Staphylococcus aureus Protein

[0273] Substantially pure protein or polypeptide is isolated from the transfected or transformed cells using any one of the methods known in the art. The protein can also be produced in a recombinant prokaryotic expression system, such as E. coli, or can by chemically synthesized. Concentration of protein in the final preparation is adjusted, for example, by concentration on an Amicon filter device, to the level of a few micrograms/ml. Monoclonal or polyclonal antibody to the protein can then be prepared as follows.

[0274] 2. Monoclonal Antibody Production by Hybridoma Fusion

[0275] Monoclonal antibody to epitopes of any of the peptides identified and isolated as described can be prepared from murine hybridomas according to the classical method of Kohler, G. and Milstein, C., Nature 256:495 (1975) or modifications of the methods thereof. Briefly, a mouse is repetitively inoculated with a few micrograms of the selected protein over a period of a few weeks. The mouse is then sacrificed, and the antibody producing cells of the spleen isolated. The spleen cells are fused by means of polyethylene glycol with mouse myeloma cells, and the excess unfused cells destroyed by growth of the system on selective media comprising aminopterin (HAT media). The successfully fused cells are diluted and aliquots of the dilution placed in wells of a microtiter plate where growth of the culture is continued. Antibody-producing clones are identified by detection of antibody in the supernatant fluid of the wells by immunoassay procedures, such as ELISA, as originally described by Engvall, E., Meth. Enzymol. 70:419 (1980), and modified methods thereof. Selected positive clones can be expanded and their monoclonal antibody product harvested for use. Detailed procedures for monoclonal antibody production are described in Davis, L. et al. Basic Methods in Molecular Biology Elsevier, New York. Section 21-2 (1989).

[0276] 3. Polyclonal Antibody Production by Immunization

[0277] Polyclonal antiserum containing antibodies to heterogenous epitopes of a single protein can be prepared by immunizing suitable animals with the expressed protein described above, which can be unmodified or modified to enhance immunogenicity. Effective polyclonal antibody production is affected by many factors related both to the antigen and the host species. For example, small molecules tend to be less immunogenic than other and may require the use of carriers and adjuvant. Also, host animals vary in response to site of inoculations and dose, with both inadequate or excessive doses of antigen resulting in low titer antisera. SmaII doses (ng level) of antigen administered at multiple intradermal sites appears to be most reliable. An effective immunization protocol for rabbits can be found in Vaitukaitis, J. et al., J. Clin. Endocrinol. Metab. 33:988-991 (1971).

[0278] Booster injections can be given at regular intervals, and antiserum harvested when antibody titer thereof, as determined semi-quantitatively, for example, by double immunodiffusion in agar against known concentrations of the antigen, begins to fall. See, for example, Ouchterlony, O. et al, Chap. 19 in: Handbook of Experimental Immunology, Wier, D., ed, Blackwell (1973). Plateau concentration of antibody is usually in the range of 0.1 to 0. 2 mg/ml of serum (about 12M). Affinity of the antisera for the antigen is determined by preparing competitive binding curves, as described, for example, by Fisher, D., Chap. 42 in: Manual of Clinical Immunology, second edition, Rose and Friedman, eds., Amer. Soc. For Microbiology, Wash., D.C. (1980)

[0279] Antibody preparations prepared according to either protocol are useful in quantitative immunoassays which determine concentrations of antigen-bearing substances in biological samples; they are also used semi-quantitatively or qualitatively to identify the presence of antigen in a biological sample. In addition, they are useful in various animal models of Staphylococcal disease known to those of skill in the art as a means of evaluating the protein used to make the antibody as a potential vaccine target or as a means of evaluating the antibody as a potential immunothereapeutic reagent.

[0280] 4. Preparation of PCR Primers and Amplification of DNA

[0281] Various fragments of the Staphylococcus aureus genome, such as those of Tables 1-3 and SEQ ID NOS: 1-5,191 can be used, in accordance with the present invention, to prepare PCR primers for a variety of uses. The PCR primers are preferably at least 15 bases, and more preferably at least 18 bases in length. When selecting a primer sequence, it is preferred that the primer pairs have approximately the same G/C ratio, so that melting temperatures are approximately the same. The PCR primers and amplified DNA of this Example find use in the Examples that follow.

[0282] 5. Gene Expression from DNA Sequences Corresponding to ORFs

[0283] A fragment of the Staphylococcus aureus genome provided in Tables 1-3 is introduced into an expression vector using conventional technology. Techniques to transfer cloned sequences into expression vectors that direct protein translation in mammalian, yeast, insect or bacterial expression systems are well known in the art. Commercially available vectors and expression systems are available from a variety of suppliers including Stratagene (La Jolla, Calif.), Promega (Madison, Wis.), and Invitrogen (San Diego, Calif.). If desired, to enhance expression and facilitate proper protein folding, the codon context and codon pairing of the sequence may be optimized for the particular expression organism, as explained by Hatfield et al., U.S. Pat. No. 5,082,767, incorporated herein by this reference.

[0284] The following is provided as one exemplary method to generate polypeptide(s) from cloned ORFs of the Staphylococcus aureus genome fragment. Bacterial ORFs generally lack a poly A addition signal. The addition signal sequence can be added to the construct by, for example, splicing out the poly A addition sequence from pSG5 (Stratagene) using BglI and SalI restriction endonuclease enzymes and incorporating it into the mammalian expression vector pXT1 (Stratagene) for use in eukaryotic expression systems. pXT1 contains the LTRs and a portion of the gag gene of Moloney Murine Leukemia Virus. The positions of the LTRs in the construct allow efficient stable transfection. The vector includes the Herpes Simplex thymidine kinase promoter and the selectable neomycin gene. The Staphylococcus aureus DNA is obtained by PCR from the bacterial vector using oligonucleotide primers complementary to the Staphylococcus aureus DNA and containing restriction endonuclease sequences for PstI incorporated into the 5′ primer and BglII at the 5′ end of the corresponding Staphylococcus aureus DNA 3′ primer, taking care to ensure that the Staphylococcus aureus DNA is positioned such that its followed with the poly A addition sequence. The purified fragment obtained from the resulting PCR reaction is digested with PstI, blunt ended with an exonuclease, digested with BglII, purified and ligated to pXT1, now containing a poly A addition sequence and digested BglII.

[0285] The ligated product is transfected into mouse NIH 3T3 cells using Lipofectin (Life Technologies, Inc., Grand Island, N.Y.) under conditions outlined in the product specification. Positive transfectants are selected after growing the transfected cells in 600 ug/ml G418 (Sigma, St. Louis, Mo.). The protein is preferably released into the supernatant. However if the protein has membrane binding domains, the protein may additionally be retained within the cell or expression may be restricted to the cell surface. Since it may be necessary to purify and locate the transfected product, synthetic 15-mer peptides synthesized from the predicted Staphylococcus aureus DNA sequence are injected into mice to generate antibody to the polypeptide encoded by the Staphylococcus aureus DNA.

[0286] Alternatively and if antibody production is not possible, the Staphylococcus aureus DNA sequence is additionally incorporated into eukaryotic expression vectors and expressed as, for example, a globin fusion. Antibody to the globin moiety then is used to purify the chimeric protein. Corresponding protease cleavage sites are engineered between the globin moiety and the polypeptide encoded by the Staphylococcus aureus DNA so that the latter may be freed from the formed by simple protease digestion. One useful expression vector for generating globin chimerics is pSG5 (Stratagene). This vector encodes a rabbit globin. Intron II of the rabbit globin gene facilitates splicing of the expressed transcript, and the polyadenylation signal incorporated into the construct increases the level of expression. These techniques are well known to those skilled in the art of molecular biology. Standard methods are published in methods texts such as Davis et al., cited elsewhere herein, and many of the methods are available from the technical assistance representatives from Stratagene, Life Technologies, Inc., or Promega. Polypeptides of the invention also may be produced using in vitro translation systems such as in vitro Express™ Translation Kit (Stratagene).

[0287] While the present invention has been described in some detail for purposes of clarity and understanding, one skilled in the art will appreciate that various changes in form and detail can be made without departing from the true scope of the invention.

[0288] All patents, patent applications and publications referred to above are hereby incorporated by reference.

TABLE 1
S. aureus - Coding regions containing known sequences
							HSP	ORF
Contig ID	ORF ID	Start (nt)	Stop (nt)	match acession	match gene name	percent ident	nt length	nt length
1	1	757	95	emb|X17301|SAHD	S. aureus DNA for hld gene and for part of agr gene	100	663	663
1	2	2452	1631	emb|X52543|SAAG	S. aureus agrA, agrB and hld genes	99	809	822
1	5	5651	4884	dbj|D14711|STAH	Staphylococcus aureus HSP10 and HSP60 genes	98	223	768
5	1	439	71	emb|X72700|SAPV	S. aureus genes for S and F components of Panton-Valentine leucocidins	81	216	369
5	4	3571	2111	emb|X72700|SAPV	S. aureus genes for S and F components of Panton-Valentine leucocidins	95	424	1461
10	1	86	904	gb|L25288|	Staphylococcus aureus gyrase-like protein alpha and beta subunit (grlA and	98	715	819
					grlB) genes, complete cds
16	5	5302	6246	gb|U35773|	Staphylococcus aureus prolipoprotein diacylglyceryl transferase (lgt) gene, complete cds	94	251	945
16	6	6249	7091	gb|U35773|	Staphylococcus aureus prolipoprotein diacylglyceryl transferase (lgt) gene,	99	843	843
					complete cds
16	7	7084	7584	gb|U35773|	Staphylococcus aureus prolipoprotein diacylglyceryl transferase (lgt) gene,	99	342	501
					complete cds
20	1	549	103	gb|L19300|	Staphylococcus aureus DNA sequence encoding three ORFs, complete cds; prophage phi-11	100	443	447
					sequence homology, 5′ flank
20	2	841	671	gb|L19300|	Staphylococcus aureus DNA sequence encoding three ORFs, complete cds; prophage phi-11	91	137	171
					sequence homology, 5′ flank
20	3	1798	1586	gb|L19300|	Staphylococcus aureus DNA sequence encoding three ORFs, complete cds; prophage phi-11	100	110	213
					sequence homology, 5′ flank
20	4	3825	2350	gb|M76714|	Staphylococcus aureus peptidoglycan hydrolase gene, complete cds	100	948	1476
20	5	4282	3776	gb|M76714|	Staphylococcus aureus peptidoglycan hydrolase gene, complete cds	100	309	507
26	1	2	145	gb|U41072|	Staphylococcus aureus isoleucyl-tRNA synthetase (ileS) gene, partial cds	100	126	144
26	2	84	557	gb|U41072|	Staphylococcus aureus isoleucyl-tRNA synthetase (ileS) gene, partial cds	99	430	474
26	3	763	3531	emb|X74219|SAIL	S. aureus gene for isoleucyl-tRNA synthetase	99	2769	2769
29	3	1261	4392	gb|U66665|	Staphylococcus aureus DNA fragment with class II promoter activity	100	117	3132
31	14	13463	11949	emb|X73889|SAP1	S. aureus genes P1 and P2	99	1351	1515
31	15	13855	13469	emb|X73889|SAP1	S. aureus genes P1 and P2	98	258	387
38	17	13112	11940	gb|M12715|	S. aureus geh gene encoding lipase (glycerol ester hydrolase)	100	372	1173
38	19	13434	15518	gb|M12715|	S. aureus geh gene encoding lipase (glycerol ester hydrolase)	100	2085	2085
46	2	519	1727	gb|U73374|	Staphylococcus aureus type 8 capsule genes, cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G,	98	1209	1209
					cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,
					cap8O, cap8P, complete cds
46	3	1720	2295	gb|U73374|	Staphylococcus aureus type 8 capsule genes, cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G,	98	576	576
					cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,
					cap8O, cap8P, complete cds
46	4	2259	3182	gb|U73374|	Staphylococcus aureus type 8 capsule genes, cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G,	97	924	924
					cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,
					cap8O, cap8P, complete cds
46	5	3173	4498	gb|U73374|	Staphylococcus aureus type 8 capsule genes, cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G,	98	1283	1326
					cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,
					cap8O, cap8P, complete cds
46	6	4536	5720	gb|U73374|	Staphylococcus aureus type 8 capsule genes, cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G,	98	1185	1185
					cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,
					cap8O, cap8P, complete cds
46	7	6120	5785	gb|U73374|	Staphylococcus aureus type 8 capsule genes, cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G,	99	278	336
					cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,
					cap8O, cap8P, complete cds
48	1	2	955	gb|L25893|	Staphylococcus aureus recA gene, complete cds	99	954	954
50	3	2924	1383	emb|X85029|SAAH	S. aureus AhpC gene	100	88	1542
50	4	3515	2922	emb|X85029|SAAH	S. aureus AhpC gene	98	540	594
54	3	3392	1710	emb|X62992|SAFN	S. aureus fnbB gene for fibronectin binding protein B	100	1668	1683
54	4	4122	3379	emb|X62992|SAFN	S. aureus fnbB gene for fibronectin binding protein B	99	720	744
54	5	4562	4068	emb|X62992|SAFN	S. aureus fnbB gene for fibronectin binding protein B	100	463	495
54	6	8300	5214	gb|J04151|	S. aureus fibronectin-binding protein (fnbA) mRNA, complete cds	100	3087	3087
58	3	1743	2819	emb|X87104|SADN	S. aureus mdr, pbp4 and taqD genes (SG511-55 isolate)	89	68	1077
58	4	2858	3280	emb|X91786|SAPB	S. aureus abcA, pbp4, and tagD genes	99	423	423
58	5	4701	3397	emb|X91786|SAPB	S. aureus abcA, pbp4, and tagD genes	99	1305	1305
58	6	5378	5079	gb|U29478|	Staphylococcus aureus ABC transporter-like protein AbcA (abcA) gene,	100	300	300
					partial cds
58	7	5086	6840	emb|X91786|SAPB	S. aureus abcA, pbp4, and tagD genes	99	1755	1755
72	1	445	2	gb|M21854|	S. aureus agr gene encoding an accessory gene regulator protein, complete	100	444	444
					cds
72	2	1453	449	emb|X52543|SAAG	S. aureus agrA, agrB and hld genes	99	673	1005
82	1	357	3917	emb|X64172|SARP	S. aureus rp1L, orf202, rpoB(rif) and rpoC genes for ribosomal protein	99	2396	3561
					L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &
					beta’ chains
82	2	4027	7677	emb|X89233|SARP	S. aureus DNA for rpoC gene	99	3171	3651
82	3	7745	8068	gb|U20869|	Staphylococcus aureus ribosomal protein S12 (rpsL) gene, complete cds,	100	320	324
					ribosomal protein S7 (rpsG) and ORF 1 genes, partial cds
82	4	8103	8579	gb|U20869|	Staphylococcus aureus ribosomal protein S12 (rpsL) gene, complete cds,	100	477	477
					ribosomal protein S7 (rpsG) and ORF 1 genes, partial cds
82	5	8618	8821	gb|U20869|	Staphylococcus aureus ribosomal protein S12 (rpsL) gene, complete cds,	100	154	204
					ribosomal protein S7 (rpsG) and ORF 1 genes, partial cds
84	1	18	191	gb|U73374|	Staphylococcus aureus type 8 capsule genes, cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G,	98	164	174
					cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,
					cap8O, cap8P, complete cds
84	2	189	893	gb|U73374|	Staphylococcus aureus type 8 capsule genes, cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G,	94	705	705
					cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,
					cap8O, cap8P, complete cds
84	3	887	1660	gb|U73374|	Staphylococcus aureus type 8 capsule genes, cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G,	99	774	774
					cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,
					cap8O, cap8P, complete cds
84	4	1584	3503	gb|U73374|	Staphylococcus aureus type 8 capsule genes, cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G,	98	1920	1920
					cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,
					cap8O, cap8P, complete cds
84	5	3394	4521	gb|U73374|	Staphylococcus aureus type 8 capsule genes, cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G,	97	1128	1128
					cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,
					cap8O, cap8P, complete cds
84	6	4519	5643	gb|U73374|	Staphylococcus aureus type 8 capsule genes, cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G,	97	1125	1125
					cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,
					cap8O, cap8P, complete cds
96	2	1245	3896	emb|Z18852|SACF	S. aureus gene for clumping factor	83	660	2652
97	2	625	882	gb|U41072|	Staphylococcus aureus isoleucyl-tRNA synthetase (ileS) gene, partial cds	97	68	258
111	1	3	452	gb|L41499|	Staphylococcus aureus ORF1, partial cds, ORF2, ORF3, autolysin (atl) genes,	100	450	450
					complete cds
111	2	526	1041	gb|L41499|	Staphylococcus aureus ORF1, partial cds, ORF2, ORF3, autolysin (atl) genes,	99	516	516
					complete cds
117	2	1278	1958	gb|M83994|	Staphylococcus aureus prolipoprotein signal peptidase (lsp) gene, complete	100	61	681
					cds
118	4	3787	4254	dbj|D30690|STAN	Staphylococcus aureus genes for ORF37; HSP20; HSP70; HSP40; ORF35, complete	99	467	468
					cds
130	4	2597	3640	emb|X13290|SATN	Staphylococcus aureus multi-resistance plasmid pSK1 DNA containing	78	956	1044
					transposon Tn4003
130	5	3813	4265	emb|z16422|SADI	S. aureus dfrB gene for dihydrofolate reductase	98	416	453
130	6	4309	5172	emb|z16422|SADI	S. aureus dfrB gene for dihydrofolate reductase	98	607	864
136	4	5296	6207	emb|X71437|SAGY	S. aureus genes gyrB, gyrA and recF (partial)	97	838	912
136	5	8987	6294	dbj|D10489|STAG	Staphylococcus aureus genes for DNA gyrase A and B, complete cds	100	2694	2694
136	6	10940	8994	dbj|D10489|STAG	Staphylococcus aureus genes for DNA gyrase A and B, complete cds	99	1947	1947
136	7	11765	10938	gb|S77055|	recF cluster: dnaA = replisome assembly protein...gyrB = DNA gyrase beta	99	822	828
					subunit [Staphylococcus aureus, YB886, Genomic, 5 genes, 3573 nt]
143	3	2867	1563	gb|U36379|	Staphylococcus aureus S-adenosylmethionine synthetase gene, complete cds	99	1305	1305
143	4	3100	4281	gb|L42943|	Staphylococcus aureus (clone KIN50) phosphoenolpyruvate carboxykinase	100	1170	1182
					(pckA) gene, complete cds
143	5	4254	4718	gb|U51133|	Staphylococcus aureus phosphoenolpyruvate carboxykinase (pcka) gene,	100	449	465
					complete cds
143	9	6977	7261	gb|U51132|	Staphylococcus aureus o-succinylbenzoic acid CoA ligase (mene), and o-	100	75	285
					succinylbenzoic acid synthetase (menc) genes, complete cds
143	10	8361	7258	gb|U51132|	Staphylococcus aureus o-succinylbenzoic acid CoA ligase (mene), and o-	100	1104	1104
					succinylbenzoic acid synthetase (menc) genes, complete cds
143	11	9748	8264	gb|U51132|	Staphylococcus aureus o-succinylbenzoic acid CoA ligase (mene), and o-	100	1485	1485
					succinylbenzoic acid synthetase (menc) genes, complete cds
143	12	10320	9901	gb|U51132|	Staphylococcus aureus o-succinylbenzoic acid CoA ligase (mene), and o-	100	332	420
					succinylbenzoic acid synthetase (mene) genes, complete cds
152	5	2454	3437	emb|X58434|SAPD	S. aureus pdhB, pdhC and pdhD genes for pyruvate decarboxylase,	99	305	984
					dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase
152	6	3513	4820	emb|X58434|SAPD	S. aureus pdhB, pdhC and pdhD genes for pyruvate decarboxylase,	98	1308	1308
					dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase
152	7	4818	6230	emb|X58434|SAPD	S. aureus pdhB, pdhC and pdhD genes for pyruvate decarboxylase,	99	1413	1413
					dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase
153	1	387	1526	gb|S77055|	recF cluster: dnaA = replisome assembly protein.. .gyrB = DNA gyrase beta	99	1140	1140
					subunit [Staphylococcus aureus, YB886, Genomic, 5 genes, 3573 nt]
153	2	1877	2152	gb|S77055|	recF cluster: dnaA = replisome assembly protein...gyrB = DNA gyrase beta	100	276	276
					subunit [Staphylococcus aureus, YB886, Genomic, 5 genes, 3573 nt]
153	3	2143	2289	gb|S77055|	recF cluster; dnaA = replisome assembly protein...gyrB = DNA gyrase beta	99	113	147
					subunit [Staphylococcus aureus, YB886, Genomic, 5 genes, 3573 nt]
154	10	9314	7836	gb|U06451|	Staphylococcus aureus proline permease homolog (putP) gene, complete cds	91	154	1479
154	11	9615	9295	gb|U06451|	Staphylococcus aureus proline permease homolog (putP) gene, complete cds	99	229	321
154	12	9943	10167	gb|U06451|	Staphylococcus aureus proline permease homolog (putP) gene, complete cds	94	123	225
154	13	10089	11501	gb|U06451|	Staphylococcus aureus proline permease homolog (putP) gene, complete cds	99	1326	1413
159	2	1212	229	dbj|D28879|STAP	Staphylococcus aureus gene for penicillin-binding protein 1, complete cds	100	71	984
161	3	2270	1944	gb|M83994|	Staphylococcus aureus prolipoprotein signal peptidase (lsp) gene, complete	92	203	327
					cds
162	1	705	4	gb|U21221|	Staphylococcus aureus hyaluronate lyase (hysA) gene, complete cds	100	702	702
163	4	1263	1772	gb|U19770|	Staphylococcus aureus pyrrolidone carboxyl peptidase (pcp) gene, complete	96	127	510
					cds
164	7	4774	9117	dbj|D86727|D867	Staphylococcus aureus DNA for DNA polymerase III, complete cds	99	3470	4344
168	7	6447	5446	gb|U21636|	Staphylococcus aureus cmp-binding-factor 1 (cbf1) and ORF X genes, complete	100	1002	1002
					cds
168	8	7961	6384	gb|U21636|	Staphylococcus aureus cmp-binding-factor 1 (cbf1) and ORF X genes, complete	99	1158	1578
					cds
173	6	7801	6362	gb|J03479|	S. aureus enzyme III-lac (lacF), enzyme II-lac (lacE), and phospho-beta-	100	1440	1440
					galactosidase (lacG) genes, complete cds
173	7	9522	7792	gb|J03479|	S. aureus enzyme III-lac (lacF), enzyme II-lac (lacE), and phospho-beta-	99	1731	1731
					galactosidase (lacG) genes, complete cds
173	8	8285	8704	gb|J03479|	S. aureus enzyme III-lac (lacF), enzyme II-lac (lacE), and phospho-beta-	100	420	420
					galactosidase (lacG) genes, complete cds
173	9	9839	9510	gb|J03479|	S. aureus enzyme III-lac (lacF), enzyme II-lac (lacE), and phospho-beta-	100	330	330
					galactosidase (lacG) genes, complete cds
173	10	10829	9843	emb|X14827|SALA	Staphylococcus aureus lacC and lacD genes	100	987	987
173	11	11774	10827	emb|X14827|SALA	Staphylococcus aureus lacC and lacD genes	100	948	948
173	12	12305	11772	gb|M64724|	S. aureus tagatose 6-phosphate isomerase gene, complete cds	100	534	534
173	13	12773	12303	gb|M32103|	Staphylococcus aureus lac repressor (lacR) gene, complete cds and lacA	100	471	471
					repressor (lacA), partial cds
173	14	13866	13099	gb|M32103|	Staphylococcus aureus lac repressor (lacR) gene, complete cds and lacA	100	768	768
					repressor (lacA), partial cds
178	1	2	655	gb|U52961|	Staphylococcus aureus holin-like protein LrgA (lrgA) and LrgB (lrgB) genes,	100	115	654
					complete cds
178	2	1482	763	gh|U52961|	Staphylococcus aureus holin-like protein LrgA (lrgA) and LrgB (lrgB) genes,	100	720	720
					complete cds
178	3	1909	1457	gb|U52961|	Staphylococcus aureus holin-like protein LrgA (lrgA) and LrgB (lrgB) genes,	100	453	453
					complete cds
178	4	1551	1853	gb|U52961|	Staphylococcus aureus holin-like protein LrgA (lrgA) and LrgB (lrgB) genes,	100	303	303
					complete cds
178	5	2777	2013	gb|L42945|	Staphylococcus aureus lytS and lytR genes, complete cds	99	765	765
178	6	3025	2756	gb|L42945|	Staphylococcus aureus lytS and lytR genes, complete cds	99	270	270
181	1	590	66	gb|M63177|	S. aureus sigma factor (plaC) gene, complete cds	99	499	525
182	1	3	341	emb|X61307|SASP	Staphylococcus aureus spa gene for protein A	98	277	339
182	2	690	2312	gb|J01786|	S. aureus spa gene coding for protein A, complete csd	97	1332	1623
182	3	4251	2641	emb|X61307|SASP	Staphylococcus aureus spa gene for protein A	99	119	1611
185	1	3	824	gb|U31979|	Staphylococcus aureus chorismate synthase (aroC) and nucleoside diphosphate	90	132	822
					kinase (ndk) genes, complete cds, dehydroauinate synthase (aroB) and
					geranylgeranyl pyrophosphate synthetase homolog (gerCC) genes, partial cds
191	3	841	2760	emb|X17679|SACO	Staphylococcus aureus coa gene for coagulase	99	1920	1920
191	4	2967	3143	emb|X16457|SAST	Staphylococcus aureus gene for staphylocoagulase	99	177	177
191	5	4566	3364	emb|X16457|SAST	Staphylococcus aureus gene for staphylocoagulase	99	250	1203
196	1	872	3	gb|L36472|	Staphylococcus aureus lysyl-tRNA sythetase gene, complete cds, transfer RNA	99	870	870
					(tRNA) genes, 5S ribosomal RNA (5S rRNA) gene, 16S ribosomal RNA (16S
					rRNA) gene, 23S ribosomal RNA (23S rRNA) gene
198	3	1688	2011	emb|X93205|SAPT	S. aureus ptsH and ptsI genes	99	324	324
198	4	2005	2310	emb|X93205|SAPT	S. aureus ptsH and ptsI genes	97	304	306
202	1	163	1305	emb|X97985|SA12	S. aureus orfs 1,2,3 & 4	99	1143	1143
202	2	1303	2175	emb|X73889|SAP1	S. aureus genes P1 and P2	94	444	873
210	1	1558	2	dbj|D17366|STAA	Staphylococcus aureus atl gene for autolysin, complete cds and other ORFs	99	1552	1557
210	2	2232	1525	gb|L41499|	Staphylococcus aureus ORF1, partial cds, ORF2, ORF3, autolysin (atl) genes,	99	684	708
					complete cds
214	11	7429	7770	dbj|D86240|D862	Staphylococcus aureus gene for unkown function and dlt operon dltA, dltB,	96	157	342
					dltC and dltD genes, complete cds
216	3	398	1318	emb|X72700|SAPV	S. aureus genes for S and F components of Panton-Valentine leucocidins	88	265	921
219	2	1073	336	dbj|D30690|STAN	Staphylococcus aureus genes for ORF37; HSP20; HSP70; HSP40; ORF35, complete	100	60	738
					cds
219	3	2035	1091	dbj|D30690|STAN	Staphylococcus aureus genes for ORF37; HSP20; HSP70; HSP40; ORF35, complete	99	945	945
					cds
219	4	3196	2033	dbj|D30690|STAN	Staphylococcus aureus genes for ORF37; HSP20; HSP70; HSP40; ORF35, complete	99	1164	1164
					cds
219	5	5176	3308	dbj|D30690|STAN	Staphylococcus aureus genes for ORF37; HSP20; HSP70; HSP40; ORF35, complete	98	1869	1869
					cds
219	6	5883	5209	dbj|D30690|STAN	Staphylococcus aureus genes for ORF37; HSP20; HSP70; HSP40, ORF35, complete	99	675	675
					cds
219	7	6334	5867	dbj|D30690|STAN	Staphylococcus aureus genes for ORF37; HSP20; HSP70; HSP40; ORF35, complete	98	468	468
					cds
221	8	10034	9252	gb|L19298|	Staphylococcus aureus phosphatidylinositol-specific phospholipase C (plc)	91	67	783
					gene, complete cds
223	1	1506	157	gb|U73374|	Staphylococcus aureus type 8 capsule genes, cap8A, cap8B, cap8C, cap8D,	99	102	1350
					cap8E, cap8F, cap8G, cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,
					cap8O, cap8P, complete cds
234	1	2	1357	emb|X97985|SA12	S. aureus orfs 1,2,3 & 4	100	176	1356
234	2	1694	2485	emb|X97985|SA12	S. aureus orfs 1,2,3 & 4	100	792	792
234	3	2648	3148	emb|X97985|SA12	S. aureus orfs 1,2,3 & 4	99	501	501
234	4	3120	4604	emb|X97985|SA12	S. aureus orfs 1,2,3 & 4	99	1305	1485
236	6	3826	5322	gb|U48826|	Staphylococcus aureus elastin binding protein (ebpS) gene, complete cds	96	648	1497
248	1	2	403	emb|X62288|SAPE	S. aureus DNA for penicillin-binding protein 2	100	103	402
248	2	388	852	gb|L25426|	Staphylococcus aureus penicillin-binding protein 2 (pbp2) gene, complete	99	465	465
					cds
253	2	1093	647	gb|U46541|	Staphylococcus aureus sarA gene, complete cds	96	447	447
254	2	150	1835	gb|U57060|	Staphylococcus aureus scdA gene, complete cds	94	142	1686
254	3	1973	2728	gb|U57060|	Staphylococcus aureus scdA gene, complete cds	99	756	756
260	1	2	1900	gb|M90693|	Staphylococcus aureus glycerol ester hydrolase (lip) gene, complete cds	99	1213	1899
265	1	1	942	dbj|D21131|STAS	Staphylococcus aureus gene for a participant in homogeneous expression of	99	941	942
					high-level methicillin resistance, complete cds
265	2	476	264	dbj|D21131|STAS	Staphylococcus aureus gene for a participant in homogeneous expression of	99	213	213
					high-level methicillin resistance, complete cds
265	3	1765	1112	dbj|D21131|STAS	Staphylococcus aureus gene for a participant in homogeneous expression of	98	69	654
					high-level methicillin resistance, complete cds
266	1	2	1018	dbj|D14711|STAH	Staphylococcus aureus HSP10 and HSP60 genes	98	743	1017
282	1	1	525	gb|S72488|	hemB = porphobilinogen synthase [Staphylococcus aureus, SA1959, Genomic, 1087	100	110	525
					nt]
282	2	516	1502	gb|S72488|	hemB = porphobilinogen synthase [Staphylococcus aureus, SA1959, Genomic, 1087	100	952	987
					nt]
284	1	3	170	gb|M63176|	Staphylococcus aureus helicase required for T181 replication (pcrA) gene,	98	84	168
					complete cds
284	2	282	1034	gb|M63176|	Staphylococcus aureus helicase required for T181 replication (pcrA) gene,	100	712	753
					complete cds
284	3	1028	2026	gb|M63176|	Staphylococcus aureus helicase required for T181 replication (pcrA) gene,	99	979	999
					complete cds
284	4	1990	2202	gb|M63176|	Staphylococcus aureus helicase required for T181 replication (pcrA) gene,	98	187	213
					complete cds
289	3	1536	1991	gb|M32470|	S. aureus Sau3AI-restriction-enzyme and Sau3AI-modification-enzyme genes,	99	338	456
					complete cds
303	1	2	868	gb|L01055|	Staphylococcus aureus gamma-hemolysin components A, B and C (hlgA, hlgB,	99	867	867
					hglC) genes, complete cds
303	2	1409	2383	gb|L01055|	Staphylococcus aureus gamma-hemolysin components A, B and C (hlgA, hlgB,	100	975	975
					hglC) genes, complete cds
303	3	2367	3161	gb|L01055|	Staphylococcus aureus gamma-hemolysin components A, B and C (hlgA, hlgB,	99	793	795
					hglC) genes, complete cds
305	1	1355	3	dbj|D17366|STAA	Staphylococcus aureus atl gene for autolysin, complete cds and other ORFs	99	1343	1353
311	1	1315	2	gb|L42945|	Staphylococcus aureus lytS and lytR genes, complete cds	98	1314	1314
312	6	7019	7870	gb|L14017|	Staphylococcus aureus methicillin-resistance protein (mecR) gene and	74	351	852
					unknown ORF, complete cds
323	1	1003	8	gb|U31175|	Staphylococcus aureus D-specific D-2-hydroxyacid dehydrogenase (ddh) gene,	98	996	996
					complete cds
326	1	1	237	emb|Y00356|SASP	Staphylococcus aureus V8 serine protease gene	100	108	237
338	1	388	89	emb|X64389|SALE	S. aureus leuF-P83 gene for F component of leucocidin R	98	259	300
338	2	1088	348	emb|X64389|SALE	S. aureus leuF-P83 gene for F component of leucocidin R	97	137	741
342	2	579	1754	gb|U06462|	Staphylococcus aureus SA4 FtsZ (ftsZ) gene, complete cds	100	1176	1176
344	2	517	1248	emb|V01281|SANU	S. aureus mRNA for nuclease	98	732	732
349	1	230	3	gb|M20393|	S. aureus bacteriophage phi-11 attachment site (attB)	96	172	228
353	1	516	16	gb|M83994|	Staphylococcus aureus prolipoprotein signal peptidase (lsp) gene, complete	100	187	501
					cds
353	2	1046	510	gb|M83994|	Staphylococcus aureus prolipoprotein signal peptidase (lsp) gene, complete	99	537	537
					cds
356	1	3	674	gb|U20503|	Staphylococcus aureus MHC class II analog gene, complete cds	75	671	672
361	1	1	903	gb|L19298|	Staphylococcus aureus phosphatidylinositol-specific phospholipase C (plc)	98	747	903
					gene, complete cds
361	2	1103	1507	gb|L19298|	Staphylococcus aureus phosphatidylinositol-specific phospholipase C (plc)	97	68	405
					gene, complete cds
373	1	3	1148	emb|X62288|SAPE	S. aureus DNA for penicillin-binding protein 2	99	1146	1146
389	3	1248	592	emb|X62282|SATS	S. aureus target site DNA for IS431 insertion	97	349	657
400	1	1	540	emb|X61716|SAHL	S. aureus hlb gene encoding sphingomyelinase	99	389	540
400	2	1187	681	emb|X13404|SAHL	Staphylococcus aureus hlb gene for beta-hemolysin	99	178	507
408	1	1049	288	gb|S76213|	asp23 = alkaline shock protein 23 (methicillin resistant) [Staphylococcus	99	163	762
					aureus, 912, Genomic, 1360 nt]
418	1	2	217	gb|L41499|	Staphylococcus aureus ORF1, partial cds, ORF2, ORF3, autolysin (at1) genes,	100	216	216
					complete cds
418	2	639	424	dbj|D17366|STAA	Staphylococcus aureus at1 gene for autolysin, complete cds and other ORFs	100	188	216
421	2	1262	2509	gb|L43098|	Transposon Tn5404 and insertion sequences IS1181 and IS1182 (from	99	1248	1248
					Staphylococcus aureus) DNA
422	1	2	325	gb|K02985|	S. aureus (strain RN450) transposon Tn554 insertion site	96	200	324
427	1	434	3	dbj|D28879|STAP	Staphylococcus aureus gene for penicillin-binding protein 1, complete cds	100	432	432
427	2	1122	415	dbj|D28879|STAP	Staphylococcus aureus gene for penicillin-binding protein 1, complete cds	100	151	708
435	1	2	808	dbj|D86240|D862	Staphylococcus aureus gene for unkown function and dlt operon dltA, dltB,	100	556	807
					dltC and dltD genes,complete cds
435	2	832	999	dbj|D86240|D862	Staphylococcus aureus gene for unkown function and dlt operon dltA, dltB,	100	134	168
					dltC and dltD genes, complete cds
436	1	685	29	emb|X17688|SAFE	S. aureus factor essential for expression of methicillin resistance (femA)	97	657	657
					gene, complete cds, and trpA gene, 3′ end
436	2	1657	911	emb|X17688|SAFE	S. aureus factor essential for expression of methicillin resistance (femA)	100	294	747
					gene, complete cds, and trpA gene, 3′ end
442	1	347	1300	emb|X72700|SAPV	S. aureus genes for S and F components of Panton-Valentine leucocidins	84	204	954
445	2	1906	2178	gb|L01055|	Staphylococcus aureus gamma-hemolysin components A, B and C (hlgA, hlgB,	98	187	273
					hglC) genes, complete cds
447	1	167	1078	gb|U19770|	Staphylococcus aureus pyrrolidone carboxyl peptidase (pcp) gene, complete	100	51	912
					cds
447	2	1176	1784	gb|U19770|	Staphylococcus aureus pyrrolidone carboxyl peptidase (pcp) gene, complete	96	597	609
					cds
454	3	4319	1329	emb|Z18852|SACF	S. aureus gene for clumping factor	75	653	2991
472	4	5479	3062	gb|L25288|	Staphylococcus aureus gyrase-like protein alpha and beta subunit (grlA and	99	2418	2418
					grlB) genes, complete cds
472	5	6792	5464	gb|L25288|	Staphylococcus aureus gyrase-like protein alpha and beta subunit (grlA and	99	1328	1329
					grlB) genes, complete cds
475	2	566	889	emb|X52543|SAAG	S. aureus agrA, agrB and hld genes	100	76	324
481	4	1560	1198	emb|X64172|SARP	S. aureus rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein	100	250	363
					L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &
					beta′ chains
481	5	1244	1534	emb|X64172|SARP	S. aureus rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein	100	224	291
					L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &
					beta′ chains
487	2	1188	988	gb|M83994|	Staphylococcus aureus prolipoprotein signal peptidase (lsp) gene, complete	98	72	201
					cds
489	1	1370	3	gb|U21221|	Staphylococcus aureus hyaluronate lyase (hysA) gene, complete cds	99	1368	1368
503	2	653	171	gb|M83994|	Staphylococcus aureus prolipoprotein signal peptidase (lsp) gene, complete	100	108	483
					cds
511	3	1613	2242	gb|L14017|	Staphylococcus aureus methicillin-resistance protein (mecR) gene and	84	323	630
					unknown ORF, complete cds
511	4	2700	2278	gb|S76213|	asp23 = alkaline shock protein 23 (methicillin resistant) [Staphylococcus	96	423	423
					aureus, 912, Genomic, 1360 nt]
520	2	758	1297	emb|X72014|SAFI	S. aureus fib gene for fibrinogen-binding protein	99	540	540
520	3	1436	1801	emb|X72013|SAFI	S. aureus fib gene for fibrinogen-binding protein	99	221	366
526	1	1092	34	dbj|D17366|STAA	Staphylococcus aureus atl gene for autolysin, complete cds and other ORFs	99	641	1059
528	2	58	963	gb|L19300|	Staphylococcus aureus DNA sequence encoding three ORFs, complete cds;	99	260	906
					prophage phi-11 sequence homology, 5′ flank
528	3	1098	2870	gb|L19300|	Staphylococcus aureus DNA sequence encoding three ORFs, complete cds;	99	866	1773
					prophage phi-11 sequence homology, 5′ flank
530	1	3	434	gb|U31979|	Staphylococcus aureus chorismate synthase (aroC) and nucleoside diphosphate	99	432	432
					kinase (ndk) genes, complete cds, dehydroauinate synthase (aroB) and
					geranylgeranyl pyrophosphate synthetase homolog (gerCC) genes, partial cds
530	2	1211	2395	gb|U31979|	Staphylococcus aureus chorismate synthase (aroC) and nucleoside diphosphate	91	1185	1185
					kinase (ndk) genes; complete cds, dehydroauinate synthase (aroB) and
					geranylgeranyl pyrophosphate synthetase homolog (gerCC) genes, partial cds
530	3	2409	2801	gb|U31979|	Staphylococcus aureus chorismate synthase (aroC) and nucleoside diphosphate	88	181	393
					kinase (ndk) genes, complete cds, dehydroauinate synthase (aroB) and
					geranylgeranyl pyrophosphate synthetase homolog (gerCC) genes, partial cds
530	4	2690	3484	gb|L05004|	Staphylococcus aureus dehydroquinate synthase (aroB) gene, 3′ end cds; 3-	100	75	795
					phosphoshikimate-1-carboxyvinyltransferase (aroA) gene, complete cds;
					ORF3, complete cds
530	5	3482	4792	gb|L05004|	Staphylococcus aureus dehydroquinate synthase (aroB) gene, 3′ end cds; 3-	99	905	1311
					phosphoshikimate-1-carboxyvinyltransferase (aroA) gene, complete cds;
					ORF3, complete cds
530	6	4790	5380	gb|L05004|	Staphylococcus aureus dehydroquinate synthase (aroB) gene, 3′ end cds; 3-	100	196	591
					phosphoshikimate-1-carboxyvinyltransferase (aroA) gene, complete cds;
					ORF3, complete cds
539	1	3	338	emb|X76490|SAGL	S. aureus (bb270) glnA and glnR genes	99	336	336
539	2	336	527	emb|X76490|SAGL	S. aureus (bb270) glnA and glnR genes	100	189	192
554	1	365	3	gb|U73374|	Staphylococcus aureus type 8 capsule genes, cap8A, cap8B, cap8C, cap8D,	100	54	363
					cap8E, cap8F, cap8G, cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,
					cap8O, cap8P, complete cds
554	2	1252	329	gb|U73374|	Staphylococcus aureus type 8 capsule genes, cap8A, cap8B, cap8C, cap8D,	99	918	924
					cap8E, cap8F, cap8G, cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,
					cap8O, cap8P, complete cds
554	3	1374	1174	gb|U73374|	Staphylococcus aureus type 8 capsule genes, cap8A, cap8B, cap8C, cap8D,	96	122	201
					cap8E, cap8F, cap8G, cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,
					cap8O, cap8P, complete cds
584	2	705	391	gb|U21221|	Staphylococcus aureus hyaluronate lyase (hysA) gene, complete cds	99	306	315
587	3	1475	4288	emb|Z18852|SACF	S. aureus gene for clumping factor	98	2588	2814
598	1	1953	25	dbj|D28879|STAP	Staphylococcus aureus gene for penicillin-binding protein 1, complete cds	99	1873	1929
605	1	2	745	dbj|D86240|D862	Staphylococcus aureus gene for unkown function and dlt operon dltA, dltB,	98	338	744
					dltC and dltD genes, complete cds
609	1	816	4	emb|X76490|SAGL	S. aureus (bb270) glnA and glnR genes	100	495	813
614	1	642	4	gb|M32103|	Staphylococcus aureus lac repressor (lacR) gene, complete cds and lacA	99	639	639
					repressor (lacA), partial cds
626	1	1255	2	gb|M63176|	Staphylococcus aureus helicase required for T181 replication (pcrA) gene,	100	225	1254
					complete cds
626	2	2284	1253	gb|M63176|	Staphylococcus aureus helicase required for T181 replication (pcrA) gene,	99	838	1032
					complete cds
629	1	1001	3	emb|X17688|SAFE	S. aureus factor essential for expression of methicillin resistance (femA)	99	990	999
					gene, complete cds, and trpA gene, 3′ end
629	2	1195	983	emb|X17688|SAFE	S. aureus factor essential for expression of methicillin resistance (femA)	98	194	213
					gene, complete cds, and trpA gene, 3′ end
631	2	3228	1330	emb|Z18852|SACF	S. aureus gene for clumping factor	82	489	1899
632	1	3	551	emb|Z30588|SAST	S. aureus (RN4220) genes for potential ABC transporter and potential	99	549	549
					membrane spanning protein
632	2	529	1323	emb|Z30588|SAST	S. aureus (RN4220) genes for potential ABC transporter and potential	99	795	795
					membrane spanning protein
651	1	1070	231	gb|L19300|	Staphylococcus aureus DNA sequence encoding three ORFs, complete cds;	99	478	840
					prophage phi-11 sequence homology, 5′ flank
657	2	1105	410	gb|L14017|	Staphylococcus aureus methicillin-resistance protein (mecR) gene and	84	456	696
					unknown ORF, complete cds
662	1	456	4	emb|X13404|SAHL	Staphylococcus aureus hlb gene for beta-hemolysin	100	369	453
662	2	230	475	emb|X13404|SAHL	Staphylococcus aureus hlb gene for beta-hemolysin	100	246	246
662	3	746	1399	emb|X13404|SAHL	Staphylococcus aureus hlb gene for beta-hemolysin	99	653	654
682	1	480	4	gb|M63177|	S. aureus sigma factor (plaC) gene, complete cds	100	136	477
685	1	592	2	gb|U65000|	Staphylococcus aureus type-I signal peptidase SpsA (spsA) gene, and type-I	98	534	591
					signal peptidase SpsB (spaB) gene, complete cds
685	2	1153	590	gb|U65000|	Staphylococcus aureus type-I signal peptidase SpsA (spsA) gene, and type-I	96	564	564
					signal peptidase SpsB (spsB) gene, complete cds
697	1	3	527	gb|M63177|	S. aureus sigma factor (plaC) gene, complete cds	100	195	525
697	2	485	784	gb|M63177|	S. aureus sigma factor (plaC) gene, complete cds	97	280	300
710	1	15	503	dbj|D86240|D862	Staphylococcus aureus gene for unkown function and dlt operon dltA, dltB,	99	217	489
					dltC and dltD genes, complete cds
733	1	26	205	gb|M80252|	Staphylococcus aureus norA1199 gene (which mediates active efflux of	97	140	180
					fluoroguinolones), complete cds
741	1	1197	658	dbj|D83951|STAL	Staphylococcus aureus DNA for LukM component, LukF-PV like component,	81	522	540
					complete cds
752	1	1	636	emb|Y00356|SASP	Staphylococcus aureus V8 serine protease gene	99	618	636
752	2	588	956	emb|Y00356|SASP	Staphylococcus aureus V8 serine protease gene	99	340	369
756	1	709	110	emb|X01645|SATO	Staphylococcus aureus (Wood 46) gene for alpha-toxin	98	567	600
777	1	950	318	emb|Z49245|SA42	S. aureus partial sod gene for superoxide dismutase	99	429	633
780	1	557	3	gb|U20503|	Staphylococcus aureus MHC class II analog gene, complete cds	86	550	555
784	1	73	687	gb|U63529|	Staphylococcus aureus novel antigen gene, complete cds	99	568	615
797	1	182	544	dbj|D14711|STAH	Staphylococcus aureus HSP10 and HSP60 genes	98	363	363
798	1	302	72	emb|X58434|SAPD	S. aureus pdhB, pdhC and pdhD genes for pyruvate decarboxylase,	95	196	231
					dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase
823	1	3	467	gb|S77055|	recF cluster: dnaA = replisome assembly protein...gyrB = DNA gyrase beta	99	156	465
					subunit [Staphylococcus aureus, YB886, Genomic, 5 genes, 3573 nt]
848	1	175	2	gb|L25288|	Staphylococcus aureus gyrase-like protein alpha and beta subunit (grlA and	99	174	174
					grlB) genes, complete cds
848	2	318	160	gb|L25288|	Staphylococcus aureus gyrase-like protein alpha and beta subunit (grlA and	100	131	159
					grlB) genes, complete cds
866	1	397	2	emb|X64172|SARP	S. aureus rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein	99	395	396
					L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &
					beta′ chains
883	1	1	285	dbj|D90119|STAN	S. aureus norA gene	99	131	285
884	1	334	62	emb|X52543|SAAG	S. aureus agrA, agrB and hld genes	98	265	273
884	2	522	328	emb|X52543|SAAG	S. aureus agrA, agrB and hld genes	100	195	195
912	2	517	681	emb|Z30588|SAST	S. aureus (RN4220) genes for potential ABC transporter and potential	99	163	165
					membrane spanning protein
917	1	2	265	gb|M64724|	S. aureus tagatose 6-phosphate isomerase gene, complete cds	99	247	264
917	2	238	396	gb|M64724|	S. aureus tagatose 6-phosphate isomerase gene, complete cds	95	147	159
918	1	1215	4	emb|X93205|SAPT	S. aureus ptsH and ptsI genes	99	1212	1212
967	1	1	411	dbj|D90119|STAN	S. aureus norA gene	97	395	411
991	1	337	2	emb|X52543|SAAG	S. aureus agrA, agrB and hld genes	99	336	336
1000	1	845	573	gb|L14017|	Staphylococcus aureus methicillin-resistance protein (mecR) gene and	78	190	273
					unknown ORF, complete cds
1001	1	265	32	dbj|D86240|D862	Staphylococcus aureus gene for unkown function and dlt operon dltA, dltB,	99	234	234
					dltC and dltD genes, complete cds
1010	1	1	285	gb|U21221|	Staphylococcus aureus hyaluronate lyase (hysA) gene, complete cds	99	224	285
1046	1	330	4	emb|X72700|SAPV	S. aureus genes for S and F components of Panton-Valentine leucocidins	85	205	327
1060	1	286	92	emb|X58434|SAPD	S. aureus pdhB, pdhC and pdhD genes for pyruvate decarboxylase,	99	180	195
					dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase
1073	1	589	2	gb|K02985|	S. aureus (strain RN450) transposon Tn554 insertion site	100	131	588
1079	1	3	230	dbj|D86240|D862	Staphylococcus aureus gene for unkown function and dlt operon dltA, dltB,	99	228	228
					dltC and dltD genes, complete cds
1079	2	218	484	dbj|D86240|D862	Staphylococcus aureus gene for unkown function and dlt operon dltA, dltB,	100	267	267
					dltC and dltD genes, complete cds
1079	3	460	645	dbj|D86240|D862	Staphylococcus aureus gene for unkown function and dlt operon dltA, dltB,	100	186	186
					dltC and dltD genes, complete cds
1092	1	146	3	emb|X58434|SAPD	S. aureus pdhB, pdhC and pdhD genes for pyruvate decarboxylase,	98	124	144
					dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase
1143	1	1	243	gb|M63177|	S. aureus sigma factor (plaC) gene, complete cds	99	243	243
1157	1	2	136	emb|Z48003|SADN	S. aureus gene for DNA polymerase III	97	127	135
1189	1	361	2	gb|S74031|	norA = NorA (ISP794) [Staphylococcus aureus, NCTC 8325, Insertion, 1820 nt]	99	360	360
1190	1	2	283	gb|M21854|	S. aureus agr gene encoding an accessory gene regulator protein, complete	100	282	282
					cds
1190	2	888	649	emb|X52543|SAAG	S. aureus agrA, agrB and hld genes	100	240	240
1225	1	2	163	emb|X17679|SACO	Staphylococcus aureus coa gene for coagulase	97	124	162
1243	1	2	529	dbj|D86240|D862	Staphylococcus aureus gene for unkown function and dlt operon dltA, dltB,	99	495	528
					dltC and dltD genes, complete cds
1244	1	1	210	gb|S74031|	norA = NorA (ISP794) [Staphylococcus aureus, NCTC 8325, Insertion, 1820 nt]	100	210	210
1301	1	41	472	emb|X76490|SAGL	S. aureus (bb270) glnA and glnR genes	99	299	432
1315	1	18	326	emb|X64172|SARP	S. aureus rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein	98	277	309
					L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &
					beta′ chains
1519	1	2	175	dbj|D28879|STAP	Staphylococcus aureus gene for penicillin-binding protein 1, complete cds	98	139	174
1663	1	675	4	dbj|D86240|D862	Staphylococcus aureus gene for unkown function and dlt operon dltA, dltB,	98	672	672
					dltC and dltD genes, complete cds
1797	1	324	4	gb|U73374|	Staphylococcus aureus type 8 capsule genes, cap8A, cap8B, cap8C, csp8D,	99	321	321
					cap8E, cap8F, cap8G, cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,
					cap8O, cap8P, complete cds
1857	1	1	192	gb|M90536|	Staphylococcus aureus alpha-hemolysin gene, 3′ end	98	192	192
1923	1	2	181	emb|X17688|SAFE	S. aureus factor essential for expression of methicillin resistance (femA)	100	180	180
					gene, complete cds, and trpA gene, 3′ end
1957	1	2	346	gb|U60589|	Staphylococcus aureus novel antigen gene, complete cds	99	345	345
1988	1	1	402	dbj|D86240|D862	Staphylococcus aureus gene for unkown function and dlt operon dltA, dltB,	100	402	402
					dltC and dltD genes, complete cds
2100	1	208	2	gb|M63177|	S. aureus sigma factor (plaC) gene, complete cds	99	207	207
2199	1	1	402	gb|U66664|	Staphylococcus aureus DNA fragment with class II promoter activity	99	131	402
2537	1	156	4	emb|X17688|SAFE	S. aureus factor essential for expression of methicillin resistance (femA)	99	153	153
					gene, complete cds, and trpA gene, 3′ end
2891	1	2	400	gb|L25426|	Staphylococcus aureus penicillin-binding protein 2 (pbp2) gene, complete	99	399	399
					cds
2950	1	398	18	dbj|D30690|STAN	Staphylococcus aureus genes for ORF37; HSP20; HSP70; HSP40; ORF35, complete	100	358	381
					cds
2971	1	3	398	gb|U51132|	Staphylococcus aureus o-succinylbenzoic acid CoA ligase (mene), and o-	97	272	396
					succinylbenzoic acid synthetase (menc) genes, complete cds
2978	1	328	38	gb|U31979|	Staphylococcus aureus chorismate synthase (aroC) and nucleoside diphosphate	98	250	291
					kinase (ndk) genes, complete cds, dehydroauinate synthase (aroB) and
					geranylgeranyl pyrophosphate synthetase homolog (gerCC) genes, partial cds
2985	1	464	96	emb|X17679|SACO	Staphylococcus aureus coa gene for coagulase	98	347	369
3006	1	1784	1398	gb|U11779|	Staphylococcus aureus methicillin-resistant ATCC 33952 clone RRNV30 16S-23S	87	82	387
					rRNA spacer region
3008	1	238	2	dbj|D30690|STAN	Staphylococcus aureus genes for ORF37; HSP20; HSP70; HSP40; ORF35, complete	88	178	237
					cds
3008	2	281	111	dbj|D30690|STAN	Staphylococcus aureus genes for ORF37; HSP20; HSP70; HSP40; ORF35, complete	97	120	171
					cds
3011	1	398	3	emb|X62992|SAFN	S. aureus fnbB gene for fibronectin binding protein B	93	72	396
3019	1	2	235	gb|J03479|	S. aureus enzyme III-lac (lacF), enzyme II-lac (lacE), and phospho-beta-	97	234	234
					galactosidase (lacG) genes, complete cds
3023	1	81	233	gb|U06451|	Staphylococcus aureus proline permease homolog (putP) gene, complete cds	87	100	153
3029	1	90	287	gb|U51133|	Staphylococcus aureus phosphoenolpyruvate carboxykinase (pcka) gene,	100	135	198
					complete cds
3039	1	18	164	gb|U51133|	Staphylococcus aureus phosphoenolpyruvate carboxykinase (pcka) gene,	97	135	147
					complete cds
3039	2	70	327	gb|U51133|	Staphylococcus aureus phosphoenolpyruvate carboxykinase (pcka) gene,	77	183	258
					complete cds
3056	1	3	215	emb|X64172|SARP	S. aureus rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein	99	213	213
					L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &
					beta’ chains
3059	1	1	261	dbj|D30690|STAN	Staphylococcus aureus genes for ORF37; HSP20; HSP70; HSP40; ORF35, complete	98	234	261
					cds
3073	1	27	284	gb|U06451|	Staphylococcus aureus proline permease homolog (putP) gene, complete cds	99	229	258
3074	1	2	397	emb|X64172|SARP	S. aureus rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein	96	250	396
					L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &
					beta’ chains
3088	1	3	239	dbj|D86727|D867	Staphylococcus aureus DNA for DNA polymerase III, complete cds	95	215	237
3097	1	244	44	emb|Z48003|SADN	S. aureus gene for DNA polymerase III	97	160	201
3102	1	155	3	gb|J03479|	S. aureus enzyme III-lac (lacF), enzyme II-lac (lacE), and phospho-beta-	97	142	153
					galactosidase (lacG) genes, complete cds
3121	1	398	228	emb|X58434|SAPD	S. aureus pdhB, pdhC and pdhD genes for pyruvate decarboxylase,	100	88	171
					dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase
3125	1	233	3	emb|X89233|SARP	S. aureus DNA for rpoC gene	98	192	231
3133	1	2	175	emb|Z18852|SACF	S. aureus gene for clumping factor	96	154	174
3160	1	211	2	dbj|D10489|STAG	Staphylococcus aureus genes for DNA gyrase A and B, complete cds	89	197	210
3176	1	1	378	emb|X58434|SAPD	S. aureus pdhB, pdhC and pdhD genes for pyruvate decarboxylase,	96	91	378
					dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase
3192	1	211	2	gb|J03479|	S. aureus enzyme III-lac (lacF), enzyme II-lac (lacE), and phospho-beta-	98	72	210
					galactosidase (lacG) genes, complete cds
3210	1	3	143	gb|M76714|	Staphylococcus aureus peptidoglycan hydrolase gene, complete cds	96	141	141
3232	3	1282	458	gb|L14017|	Staphylococcus aureus methicillin-resistance protein (mecR) gene and	71	257	825
					unknown ORF, complete cds
3538	1	2	394	emb|X89233|SARP	S. aureus DNA for rpoC gene	99	350	393
3543	1	392	634	gb|L11530|	Staphylococcus aureus transfer RNA sequence with two rRNAs	99	102	243
3555	1	320	3	emb|Z18852|SACF	S. aureus gene for clumping factor	99	307	318
3559	1	3	182	emb|X17679|SACO	Staphylococcus aureus coa gene for coagulase	100	141	180
3559	2	95	313	emb|X17679|SACO	Staphylococcus aureus coa gene for coagulase	98	174	219
3563	1	141	4	gb|U35773|	Staphylococcus aureus prolipoprotein diacylglyceryl transferase (lgt) gene,	100	79	138
					complete cds
3563	2	363	199	gb|U35773|	Staphylococcus aureus prolipoprotein diacylglyceryl transferase (lgt) gene,	98	162	165
					complete cds
3566	1	3	422	emb|X16457|SAST	Staphylococcus aureus gene for staphylocoagulase	98	175	420
3588	1	2	262	gb|L43098|	Transposon Tn5404 and insertion sequences IS1181 and IS1182 (from	99	253	261
					Staphylococcus aureus) DNA
3593	1	3	350	gb|J03479|	S. aureus enzyme III-lac (lacF), enzyme II-lac (lacE), and phospho-beta-	99	345	348
					galactosidase (lacG) genes, complete cds
3600	1	381	4	emb|Z18852|SACF	S. aureus gene for clumping factor	72	346	378
3602	1	396	4	emb|Z18852|SACF	S. aureus gene for clumping factor	98	319	393
3656	1	528	43	emb|Z18852|SACF	S. aureus gene for clumping factor	84	403	486
3682	1	3	236	emb|X64172|SARP	S. aureus rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein	100	231	234
					L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &
					beta’ chains
3682	2	224	415	emb|X64172|SARP	S. aureus rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein	100	112	192
					L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &
					beta’ chains
3693	1	423	88	emb|X62992|SAFN	S. aureus fnbB gene for fibronectin binding protein B	100	229	336
3702	1	354	115	gb|L11530|	Staphylococcus aureus transfer RNA sequence with two rRNAs	96	81	240
3725	1	463	2	emb|Z18852|SACF	S. aureus gene for clumping factor	71	367	462
3761	1	450	91	gb|L14017|	Staphylococcus aureus methicillin-resistance protein (mecR) gene and	85	333	360
					unknown ORF, complete cds
3767	1	1	402	emb|X64172|SARP	S. aureus rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein	98	387	402
					L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &
					beta’ chains
3775	1	2	286	emb|X64172|SARP	S. aureus rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein	100	227	285
					L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &
					beta′ chains
3786	1	229	2	dbj|D10489|STAG	Staphylococcus aureus genes for DNA gyrase A and B, complete cds	100	204	228
3786	2	366	190	dbj|D10489|STAG	Staphylococcus aureus genes for DNA gyrase A and B, complete cds	95	123	177
3798	1	3	251	emb|X17679|SACO	Staphylococcus aureus coa gene for coagulase	99	249	249
3813	1	398	3	gb|J04151|	S. aureus fibronectin-binding protein (fnbA) mRNA, complete cds	98	396	396
3819	1	184	402	emb|X68425|SA23	S. aureus gene for 23S rRNA	99	161	219
3844	1	468	4	gb|U48826|	Staphylococcus aureus elastin binding protein (ebpS) gene, complete cds	87	204	465
3845	1	1	381	emb|X58434|SAPD	S. aureus pdhB, pdhC and pdhD genes for pyruvate decarboxylase,	94	356	381
					dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase
3856	1	400	2	gb|L14017|	Staphylococcus aureus methicillin-resistance protein (mecR) gene and	76	192	399
					unknown ORF, complete cds
3859	1	573	97	emb|Z18852|SACF	S. aureus gene for clumping factor	85	347	477
3871	1	327	4	gb|M76714|	Staphylococcus aureus peptidoglycan hydrolase gene, complete cds	100	299	324
3876	1	2	253	dbj|D10489|STAG	Staphylococcus aureus genes for DNA gyrase A and B, complete cds	100	217	252
3877	1	288	4	gb|J03479|	S. aureus enzyme III-lac (lacF), enzyme II-lac (lacE), and phospho-beta-	97	209	285
					galactosidase (lacG) genes, complete cds
3878	1	1	237	emb|X58434|SAPD	S. aureus pdhB, pdhC and pdhD genes for pyruvate decarboxylase,	96	155	237
					dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase
3888	1	3	173	emb|X16457|SAST	Staphylococcus aureus gene for staphylocoagulase	98	171	171
3893	1	1	183	emb|X89233|SARP	S. aureus DNA for rpoC gene	100	170	183
3893	2	181	357	emb|X89233|SARP	S. aureus DNA for rpoC gene	98	79	177
3894	1	3	485	emb|X64172|SARP	S. aureus rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein	99	450	483
					L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &
					beta’ chains
3895	1	420	4	gb|J04151|	S. aureus fibronectin-binding protein (fnbA) mRNA, complete cds	99	411	417
3905	1	48	239	gb|L05004|	Staphylococcus aureus dehydroquinate synthase (aroB) gene, 3′ end cds; 3-	100	159	192
					phosphoshikimate-1-carboxyvinyltransferase (aroA) gene, complete cds;
					ORF3, complete cds
3905	2	188	400	gb|L05004|	Staphylococcus aureus dehydroquinate synthase (aroB) gene, 3′ end cds; 3-	97	88	213
					phosphoshikimate-1-carboxyvinyltransferase (aroA) gene, complete cds;
					ORF3, complete cds
3910	1	3	359	emb|X58434|SAPD	S. aureus pdhB, pdhC and pdhD genes for pyruvate decarboxylase,	99	278	357
					dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase
3915	1	1	330	gb|L14017|	Staphylococcus aureus methicillin-resistance protein (mecR) gene and	75	175	330
					unknown ORF, complete cds
3964	1	347	3	emb|Z48003|SADN	S. aureus gene for DNA polymerase III	100	295	345
4007	1	199	390	emb|X16457|SAST	Staphylococcus aureus gene for staphylocoagulase	98	163	192
4036	1	3	371	dbj|D10489|STAG	Staphylococcus aureus genes for DNA gyrase A and B, complete cds	99	339	369
4046	1	348	4	emb|Z18852|SACF	S. aureus gene for clumping factor	87	221	345
4060	1	1	375	emb|Z18852|SACF	S. aureus gene for clumping factor	96	271	375
4061	1	432	4	emb|Z48003|SADN	S. aureus gene for DNA polymerase III	99	429	429
4062	1	304	2	gb|L14017|	Staphylococcus aureus methicillin-resistance protein (mecR) gene and	75	198	303
					unknown ORF, complete cds
4085	1	58	402	gb|U11786|	Staphylococcus aureus methicillin-resistant ATCC 33952 clone RRNV42 16S-23S	98	127	345
					rRNA spacer region
4088	1	2	301	gb|L43098|	Transposon Tn5404 and insertion sequences IS1181 and IS1182 (from	99	227	300
					Staphylococcus aureus) DNA
4093	1	2	277	emb|X58434|SAPD	S. aureus pdhB, pdhC and pdhD genes for pyruvate decarboxylase,	99	276	276
					dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase
4097	1	1	402	emb|Z18852|SACF	S. aureus gene for clumping factor	74	307	402
4116	1	22	402	gb|L05004|	Staphylococcus aureus dehydroquinate synthase (aroB) gene, 3′ end cds; 3-	98	157	381
					phosphoshikimate-1-carboxyvinyltransferase (aroA) gene, complete cds;
					ORF3, complete cds
4125	1	240	401	gb|U73374|	Staphylococcus aureus type 8 capsule genes, cap8A, cap8B, cap8C, cap8D,	100	86	162
					cap8E, cap8F, cap8G, cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N,
					cap8O, cap8P, complete cds
4149	1	35	247	gb|J04151|	S. aureus fibronectin-binding protein (fnbA) mRNA, complete cds	99	200	213
4151	1	366	103	gb|L14017|	Staphylococcus aureus methicillin-resistance protein (mecR) gene and	87	150	264
					unknown ORF, complete cds
4154	1	398	42	emb|X64172|SARP	S. aureus rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein	99	297	357
					L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &
					beta’ chains
4179	1	1	294	emb|X64172|SARP	S. aureus rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein	98	240	294
					L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &
					beta’ chains
4203	1	1	255	emb|X89233|SARP	S. aureus DNA for rpoC gene	99	239	255
4206	1	1	303	emb|Z18852|SACF	S. aureus gene for clumping factor	100	236	303
4206	2	195	344	emb|Z18852|SACF	S. aureus gene for clumping factor	95	65	150
4208	1	108	314	emb|X58434|SAPD	S. aureus pdhB, pdhC and pdhD genes for pyruvate decarboxylase,	89	76	207
					dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase
4216	1	330	4	emb|X58434|SAPD	S. aureus pdhB, pdhC and pdhD genes for pyruvate decarboxylase,	98	326	327
					dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase
4226	1	298	2	gb|L11530|	Staphylococcus aureus transfer RNA sequence with two rRNAs	97	132	297
4260	1	216	383	gb|U11784|	Staphylococcus aureus methicillin-resistant ATCC 33952 clone RRNV40 16S-23S	83	141	168
					rRNA spacer region
4272	1	179	3	emb|Z48003|SADN	S. aureus gene for DNA polymerase III	100	164	177
4276	1	4	177	emb|X16457|SAST	Staphylococcus aureus gene for staphylocoagulase	99	150	174
4277	1	1	270	emb|X64172|SARP	S. aureus rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein	99	265	270
					L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &
					beta’ chains
4282	1	377	63	emb|X64172|SARP	S. aureus rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein	98	282	315
					L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &
					beta’ chains
4291	1	191	3	emb|X64172|SARP	S. aureus rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein	99	183	189
					L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &
					beta’ chains
4295	1	3	329	emb|X16457|SAST	Staphylococcus aureus gene for staphylocoagulase	94	144	327
4313	1	280	125	gb|L11530|	Staphylococcus aureus transfer RNA sequence with two rRNAs	100	94	156
4315	1	3	185	gb|J03479|	S. aureus enzyme III-lac (lacF), enzyme II-lac (lacE), and phospho-beta-	100	158	183
					galactosidase (lacG) genes, complete cds
4315	2	101	310	gb|J03479|	S. aureus enzyme III-lac (lacF), enzyme II-lac (lacE), and phospho-beta-	98	75	210
					galactosidase (lacG) genes, complete cds
4327	1	1	294	gb|L43098|	Transposon Tn5404 and insertion sequences IS1181 and IS1182 (from	98	294	294
					Staphylococcus aureus) DNA
4360	1	319	35	gb|U02910|	Staphylococcus aureus ATCC 25923 16S rRNA gene, partial sequence	100	116	285
4364	1	3	146	emb|X64172|SARP	S. aureus rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein	95	140	144
					L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &
					beta’ chains
4388	1	167	310	emb|X62992|SAFN	S. aureus fnbB gene for fibronectin binding protein B	73	119	144
4401	1	2	313	emb|X62992|SAFN	S. aureus fnbB gene for fibronectin binding protein B	97	243	312
4421	1	36	281	dbj|D12572|STA2	Staphylococcus aureus rrnA gene for 23S ribosomal RNA	100	112	246
4426	1	3	293	emb|Z18852|SACF	S. aureus gene for clumping factor	85	185	291
4428	1	248	3	emb|X64172|SARP	S. aureus rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein	100	139	246
					L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &
					beta′ chains
4462	1	2	271	emb|X64172|SARP	S. aureus rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein	99	270	270
					L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &
					beta′ chains
4466	1	1	240	emb|Z18852|SACF	S. aureus gene for clumping factor	99	231	240
4469	1	1	312	gb|J03479|	S. aureus enzyme III-lac (lacF), enzyme II-lac (lacE), and phospho-beta-	99	265	312
					galactosidase (lacG) genes, complete cds
4485	1	3	263	gb|L43098|	Transposon Tn5404 and insertion sequences IS1181 and IS1182 (from	98	259	261
					Staphylococcus aureus) DNA
4492	1	74	400	gb|M86227|	Staphylococcus aureus DNA gyrase B subunit (gyrB) RecF homologue (recF) and	85	104	327
					DNA gyrase A subunit (gyrA) gene, complete cds
4497	1	269	3	emb|Z18852|SACF	S. aureus gene for clumping factor	99	213	267
4529	1	2	172	emb|X64172|SARP	S. aureus rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein	100	151	171
					L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &
					beta′ chains
4547	1	1	300	emb|X62992|SAFN	S. aureus fnbB gene for fibronectin binding protein B	100	157	300
4554	1	160	2	emb|Z18852|SACF	S. aureus gene for clumping factor	84	126	159
4565	1	9	227	emb|Z18852|SACF	S. aureus gene for clumping factor	84	213	219
4569	1	79	222	emb|Z18852|SACF	S. aureus gene for clumping factor	98	127	144
4608	1	22	216	emb|X58434|SAPD	S. aureus pdhB, pdhC and pdhD genes for pyruvate decarboxylase,	92	168	195
					dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase
4614	1	234	4	emb|Z18852|SACF	S. aureus gene for clumping factor	86	169	231
4623	1	105	302	gb|J04151|	S. aureus fibronectin-binding protein (fnbA) mRNA, complete cds	99	152	198
4632	1	18	206	gb|J03479|	S. aureus enzyme III-lac (lacF), enzyme II-lac (lacE), and phospho-beta-	98	183	189
					galactosidase (lacG) genes, complete cds
4646	1	1	222	emb|Z18852|SACF	S. aureus gene for clumping factor	84	100	222
4687	1	2	166	gb|J04151|	S. aureus fibronectin-binding protein (fnbA) mRNA, complete cds	98	156	165
4695	1	158	3	gb|L14017|	Staphylococcus aureus methicillin-resistance protein (mecR) gene and	75	155	156
					unknown ORF, complete cds
4703	1	1	153	emb|X58434|SAPD	S. aureus pdhB, pdhC and pdhD genes for pyruvate decarboxylase,	98	103	153
					dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase

[0289]

TABLE 2
S. aureus - Putative coding regions of novel proteins similar to known proteins
		Start	Stop	match
Contig ID	ORF ID	(nt)	(nt)	acession	match gene name	% sim	% ident	length (nt)
20	6	4679	4269	gi|511839	ORF1 [Staphylococcus bacteriophage phi 11]	100	100	411
149	3	1577	1122	pir|B49703|B497	int gene activator RinA - bacteriophage phi 11	100	100	456
149	5	1912	1715	gi|166161	Bacteriophage phi-11 int gene activator [Staphylococcus acteriophage phi	100	100	198
					11]
349	2	409	260	gi|166159	integrase (int) [Staphylococcus bacteriophage phi 11]	100	100	150
398	1	707	42	gi|166159	integrase (int) [Staphylococcus bacteriophage phi 11]	100	99	666
398	2	783	1001	gi|455128	excisionase (xis) [Staphylococcus bacteriophage phi 11]	100	100	219
502	4	1744	1574	gi|1204912	H. influenzae predicted coding region HI0660 [Haemophilus influenzae]	100	71	171
849	1	2	262	gi|1373002	polyprotein [Bean common mosaic virus]	100	46	261
1349	1	140	3	gi|143359	protein synthesis initiation factor 2 (infB) [Bacillus subtilis] gi|49319	100	82	138
					IF2 gene product [Bacillus subtilis]
2880	1	21	308	gi|862933	protein kinase C inhibitor-I [Homo sapiens]	100	98	288
3085	1	216	4	gi|1354211	PET112-like protein [Bacillus subtilis]	100	100	213
4168	2	398	225	gi|1354211	PET112-like protein [Bacillus subtilis]	100	100	174
331	1	2	247	gi|426473	nusG gene product [Staphylococcus carnosus]	98	95	246
207	2	1272	1463	gi|460259	enolase [Bacillus subtilis]	97	90	192
331	2	395	850	gi|581638	L11 protein [Staphylococcus carnosus]	97	93	456
366	1	39	215	gi|166161	Bacteriophage phi-11 int gene activator [Staphylococcus acteriophage phi	97	95	177
					11]
680	3	718	936	gi|426473	nusG gene product [Staphylococcus carnosus]	97	97	219
3578	1	144	4	gi|1339950	large subunit of NADH-dependent glutamate synthase [Plectonema boryanum]	97	79	141
157	1	321	518	gi|1022726	unknown [Staphylococcus haemolyticus]	96	88	198
205	33	16147	15824	gi|1165302	S10 [Bacillus subtilis]	96	91	324
3919	1	48	401	gi|871784	Clp-like ATP-dependent protease binding subunit [Bos taurus]	96	81	354
4133	1	417	4	gi|1022726	unknown [Staphylococcus haemolyticus]	96	84	414
4168	1	355	2	gi|1354211	PET112-like protein [Bacillus subtilis]	96	95	354
4207	1	157	2	gi|602031	similar to trimethylamine DH [Mycoplasma capricolum]pir|S49950|S49950	96	86	156
					probable trimethylamine dehydrogenase (EC .5.99.7) - Mycoplasma capricolum
					(SGC3) (fragment)
4227	2	152	331	gi|871784	Clp-like ATP-dependent protease binding subunit [Bos taurus]	96	81	180
4416	1	286	2	gi|1022726	unknown [Staphylococcus haemolyticus]	96	84	285
22	1	430	2	gi|511070	UreG [Staphylococcus xylosus]	95	88	429
22	7	4036	3710	gi|581787	urease gamma subunit [Staphylococcus xylosus]	95	79	327
82	6	8794	9114	pir|JG0008|JG00	ribosomal protein S7 - Bacillus stearothermophilus	95	83	321
154	9	7838	6396	gi|1354211	PET112-like protein [Bacillus subtilis]	95	92	1443
186	3	2055	1312	gi|1514656	serine 0-acetyltransferase [Staphylococcus xylosus]	95	87	744
205	5	4014	3622	gi|142462	ribosomal protein S11 [Bacillus subtilis]	95	85	393
205	7	4793	4569	gi|142459	initiation factor 1 [Bacillus subtilis]	95	84	225
205	21	10991	10617	gi|1044974	ribosomal protein L14 [Bacillus subtilis]	95	93	375
259	5	6644	6000	sp|P47995|YSEA—	HYPOTHETICAL PROTEIN IN SECA 5′REGION (ORF1) (FRAGMENT).	95	85	645
302	3	795	1097	gi|40186	homologous to E. coli ribosomal protein L27 [Bacillus subtilis] i|143592 L27	95	89	303
					ribosomal protein [Bacillus subtilis] ir|C21895|C21895 ribosomal protein
					L27 - Bacillus subtilis p|P05657|RL27_BACSU 50S RIBOSOMAL PROTEIN L27
					(BL30) (BL24). i|40175 L24 gene prod
310	1	579	1523	gi|1177684	chorismate mutase [Staphylococcus xylosus]	95	92	945
414	1	2	163	pir|C48396|C483	ribosomal protein L34 - Bacillus stearothermophilus	95	90	162
4185	2	125	277	gi|1276841	glutamate synthase (GOGAT) [Porphyra purpurea]	95	86	153
22	2	723	418	gi|511069	UreF [Staphylococcus xylosus]	94	91	306
22	5	3310	1574	gi|410516	urease alpha subunit [Staphylococcus xylosus]	94	85	1737
60	4	815	1372	gi|666116	glucose kinase [Staphylococcus xylosus]	94	87	558
205	18	9536	9060	gi|1044978	ribosomal protein S8 [Bacillus subtilis]	94	78	477
326	4	2542	1706	gi|557492	dihydroxynapthoic acid (DHNA) synthetase [Bacillus subtilis] gi|143186	94	85	837
					dihydroxynapthoic acid (DHNA) synthetase [Bacillus subtilis]
414	3	737	955	gi|467386	thiophen and furan oxidation [Bacillus subtilis]	94	77	219
426	3	1823	1386	gi|1263908	putative [Staphylococcus epidermidis]	94	87	438
534	1	2	355	gi|633650	enzyme II(mannitol) [Staphylococcus carnosus]	94	84	354
1017	1	2	229	gi|149435	putative [Lactococcus lactis]	94	73	228
3098	1	184	38	gi|413952	ipa-28d gene product [Bacillus subtilis]	94	50	147
3232	1	316	2	gi|1022725	unknown [Staphylococcus haemolyticus]	94	84	315
42	5	2089	2259	pir|B48396|B483	ribosomal protein L33 - Bacillus stearothermophilus	93	81	171
101	2	1383	1021	gi|155345	arsenic efflux pump protein [Plasmid pSX267]	93	82	363
205	24	11865	11503	sp|P14577|RL16—	50S RIBOSOMAL PROTEIN L16.	93	83	363
259	4	5673	3055	gi|499335	secA protein [Staphylococcus carnosus]	93	85	2619
275	1	1114	2	gi|633650	enzyme II(mannitol) [Staphylococcus carnosus]	93	86	1113
444	6	5773	5339	gi|1022726	unknown [Staphylococcus haemolyticus]	93	81	435
491	1	152	622	gi|46912	ribosomal protein L13 [Staphylococcus carnosus]	93	88	471
607	6	1674	2033	gi|1022726	unknown [Staphylococcus haemolyticus]	93	83	360
653	1	488	3	gi|580890	translation initiation factor IF3 (AA 1-172) [Bacillus tearothermophilus]	93	77	486
1864	1	3	194	gi|306553	ribosmal protein small subunit [Homo sapiens]	93	93	192
2997	1	28	300	gi|143390	carbamyl phosphate synthetase [Bacillus subtilis]	93	82	273
3232	2	596	285	gi|1022725	unknown [Staphylococcus haemolyticus]	93	84	312
3761	2	621	448	gi|1022725	unknown [Staphylococcus haemolyticus]	93	88	174
16	1	3	374	gi|142781	putative cytoplasmic protein; putative [Bacillus subtilis]	92	83	372
					sp|P37954|UVRB_BACSU EXCINUCLEASE ABC SUBUNIT B (DINA PROTEIN) FRAGMENT).
31	7	5915	6124	gi|1136430	KIAA0185 protein [Homo sapiens]	92	46	210
56	19	26483	27391	gi|467401	unknown [Bacillus subtilis]	92	80	909
69	6	5882	6130	gi|530200	trophoblastin [Ovis aries]	92	53	249
145	3	2038	1508	gi|1022725	unknown [Staphylococcus haemolyticus]	92	80	531
171	3	2362	1964	gi|517475	D-amino acid transaminase [Staphylococcus haemolyticus]	92	86	399
205	12	6962	6429	gi|49189	secY gene product [Staphylococcus carnosus]	92	85	534
205	19	10255	9698	gi|1044976	ribosomal protein L5 [Bacillus subtilis]	92	82	558
219	1	357	4	gi|1303812	YqeV [Bacillus subtilis]	92	88	354
344	3	1575	1805	gi|1405474	CspC protein [Bacillus cereus]	92	85	231
699	1	20	361	gi|413999	ipa-75d gene product [Bacillus subtilis]	92	81	342
1343	1	2	160	pir|A45434|A454	ribosomal protein L19 - Bacillus stearothermophilus	92	84	159
1958	1	264	4	gi|407908	EIIscr [Staphylococcus xylosus]	92	80	261
3578	2	386	54	gi|1339950	large subunit of NADH-dependent glutamate synthase [Plectonema boryanum]	92	78	333
3585	1	324	4	gi|1339950	large subunit of NADH-dependent glutamate synthase [Plectonema boryanum]	92	81	321
3640	1	4	402	gi|1022726	unknown [Staphylococcus haemolyticus]	92	81	399
4362	1	14	178	gi|450688	hsdM gene of EcoprrI gene product [Escherichia coli] pir|S38437|S38437 hsdM	92	78	165
					protein - Escherichia coli pir|S09629|S09629 hypothetical protein A -
					Escherichia coli (SUB 40-520)
4446	1	182	6	gi|1022725	unknown [Staphylococcus haemolyticus]	92	82	177
4549	1	232	2	gi|1022726	unknown [Staphylococcus haemolyticus]	92	80	231
4626	1	3	224	gi|1022725	unknown [Staphylococcus haemolyticus]	92	84	222
2	4	3980	4531	gi|535349	Codw [Bacillus subtilis]	91	74	552
28	1	2	1126	gi|1001376	hypothetical protein [Synechocystis sp.]	91	78	1125
60	5	1354	1701	gi|1226043	orf2 downstream of glucose kinase [Staphylococcus xylosus]	91	80	348
101	1	1036	83	gi|150728	arsenic efflux pump protein [Plasmid pI258]	91	80	954
187	2	412	1194	gi|142559	ATP synthase alpha subunit [Bacillus megaterium]	91	79	783
205	22	11298	11017	gi|40149	S17 protein (AA 1-87) [Bacillus subtilis]	91	83	282
206	7	8184	10262	gi|1072418	glcA gene product [Staphylococcus carnosus]	91	83	2079
306	2	2326	767	gi|143012	GMP synthetase [Bacillus subtilis]	91	78	1560
306	3	3826	2333	gi|467399	IMP dehydrogenase [Bacillus subtilis]	91	79	1494
310	3	2194	3207	gi|1177685	ccpA gene product [Staphylococcus xylosus]	91	81	1014
343	4	2974	3150	gi|949974	sucrose repressor [Staphylococcus xylosus]	91	82	177
480	3	1606	3042	gi|433991	ATP synthase subunit beta [Bacillus subtilis]	91	85	1437
536	3	1280	534	gi|143366	adenylosuccinate lyase (PUR-B) [Bacillus subtilis] pir|C29326|WZBSDS	91	79	747
					adenylosuccinate lyase (EC 4.3.2.2) - Bacillus subtilis
552	1	615	166	gi|297874	fructose-bisphosphate aldolase [Staphylococcus carnosus] pir|A49943|A49943	91	79	450
					fructose-bisphosphate aldolase (EC 4.1.2.13) - Staphylococcus carnosus
					(strain TM300)
637	1	1	1536	gi|143597	CTP synthetase [Bacillus subtilis]	91	79	1536
859	1	21	359	gi|385178	unknown [Bacillus subtilis]	91	66	339
1327	1	339	530	gi|496558	orfX [Bacillus subtilis]	91	71	192
2515	1	275	84	gi|511070	UreG [Staphylococcus xylosus]	91	85	192
2594	1	2	202	gi|146824	beta-cystathionase [Escherichia coli]	91	75	201
3764	1	425	3	gi|1022725	unknown [Staphylococcus haemolyticus]	91	78	423
4011	1	127	495	gi|1022726	unknown [Staphylococcus haemolyticus]	91	79	369
4227	1	1	177	gi|296464	ATPase [Lactococcus lactis]	91	66	177
42	3	815	1033	gi|520401	catalase [Haemophilus influenzae]	90	86	219
51	8	3717	4607	gi|580899	OppF gene product [Bacillus subtilis]	90	74	891
129	3	4001	2685	gi|1146206	glutamate dehydrogenase [Bacillus subtilis]	90	76	1317
164	17	16628	16933	sp|P05766|RS15—	30S RIBOSOMAL PROTEIN S15 (BS18)	90	74	306
171	5	2819	2655	gi|517475	D-amino acid transaminase [Staphylococcus haemolyticus]	90	78	165
205	4	3550	2603	gi|142463	RNA polymerase alpha-core-subunit [Bacillus subtilis]	90	76	948
205	6	4410	4072	gi|1044989	ribosomal protein S13 [Bacillus subtilis]	90	73	339
205	10	6404	5643	gi|49189	secY gene product [Staphylococcus carnosus]	90	81	762
205	11	6472	6299	gi|49189	secY gene product [Staphylococcus carnosus]	90	78	174
205	27	13345	12998	gi|786157	Ribosomal Protein S19 [Bacillus subtilis]	90	79	348
205	31	15496	15134	gi|1165303	L3 [Bacillus subtilis]	90	79	363
260	5	5773	4523	gi|1161380	IcaA [Staphylococcus epidermidis]	90	78	1251
299	6	3378	3947	gi|467440	‘phosphoribosylpyrophosphate synthetase [Bacillus subtilis] gi|40218 PRPP	90	78	570
					synthetase (AA 1-317) [Bacillus subtilis]
320	2	1025	1717	gi|312443	carbamoyl-phosphate synthase (glutamine-hydrolysing) [Bacillus aldolyticus]	90	75	693
330	4	1581	1769	gi|986963	beta-tubulin [Sporidiobolus pararoseus]	90	80	189
369	1	523	92	pir|S34762|S347	L-serine dehydratase beta chain - Clostridium sp.	90	77	432
557	1	3	188	gi|1511589	M. jannaschii predicted coding region MJ1624 [Methanococcus jannaschii]	90	54	186
663	2	667	1200	gi|143786	tryptophanyl-tRNA synthetase (EC 6.1.1.2) [Bacillus subtilis]	90	73	534
					pir|JT0481|YWBS tryptophan-tRNA ligase (EC 6.1.1.2) - Bacillus subtilis
717	1	1	261	gi|143065	hubst [Bacillus stearothermophilus]	90	79	261
745	4	865	671	gi|1205433	H. influenzae predicted coding region HI1190 [Haemophilus influenzae]	90	81	195
1007	1	386	565	gi|143366	adenylosuccinate lyase (PUR-B) [Bacillus subtilis] pir|C29326|WZBSDS	90	77	180
					adenylosuccinate lyase EC 4.3.2.2) - Bacillus subtilis
1054	1	331	83	gi|1033122	ORF_f729 [Escherichia coli]	90	50	249
1156	1	117	707	gi|1477776	ClpP [Bacillus subtilis]	90	80	591
1180	1	205	2	gi|1377831	unknown [Bacillus subtilis]	90	74	204
1253	1	1	462	gi|40046	phosphoglucose isomerase A (AA 1-449) [Bacillus stearothermophilus]	90	75	462
					ir|S15936|NUBSSA glucose-6-phosphate isomerase (EC 5.3.1.9) A - Bacillus
					stearothermophilus
2951	1	3	269	gi|144816	formyltetrahydrofolate synthetase (FTHFS) (ttg start codon) (EC .3.4.3)	90	76	267
					[Moorella thermoacetica]
3140	1	166	5	gi|1070014	protein-dependent [Bacillus subtilis]	90	52	162
4594	1	3	233	gi|871784	Clp-like ATP-dependent protease binding subunit [Bos taurus]	90	76	231
87	1	1028	1750	gi|467327	unknown [Bacillus subtilis]	89	75	723
112	1	2	505	gi|153741	ATP-binding protein [Streptococcus mutans]	89	77	504
118	1	120	398	gi|1303804	YqeQ [Bacillus subtilis]	89	75	279
128	4	3545	3757	gi|460257	triose phosphate isomerase [Bacillus subtilis]	89	84	213
164	12	11667	12755	gi|39954	IF2 (aa 1-741) [Bacillus stearothermophilus]	89	80	1089
205	13	7405	6935	gi|216338	ORF for L15 ribosomal protein [Bacillus subtilis]	89	76	471
205	32	15823	15494	gi|1165303	L3 [Bacillus subtilis]	89	80	330
270	3	2207	2007	pir|C41902|C419	arsenate reductase (EC 1,—,—,—) - Staphylococcus xylosus plasmid pSX267	89	81	201
395	2	157	672	gi|520574	glutamate racemase [Staphylococcus haemolyticus]	89	80	516
494	1	3	839	gi|396259	protease [Staphylococcus epidermidis]	89	77	837
510	1	1	444	gi|40046	phosphoglucose isomerase A (AA 1-449) [Bacillus stearothermophilus]	89	74	444
					ir|S15936|NUBSSA glucose-6-phosphate isomerase (EC 5.3.1.9) A - Bacillus
					stearothermophilus
615	1	1210	296	gi|1303812	YqeV [Bacillus subtilis]	89	74	915
841	1	18	341	gi|1165303	L3 [Bacillus subtilis]	89	80	324
1111	1	352	813	gi|47146	thermonuclease [Staphylococcus intermedius]	89	70	462
1875	1	2	256	gi|1205108	ATP-dependent protease binding subunit [Haemophilus influenzae]	89	82	255
2963	1	11	367	gi|467458	cell division protein [Bacillus subtilis]	89	83	357
3020	1	90	362	gi|1239988	hypothetical protein [Bacillus subtilis]	89	66	273
3565	1	2	400	gi|1256635	dihydroxy-acid dehydratase [Bacillus subtilis]	89	75	399
3586	1	105	314	gi|580832	ATP synthase subunit gamma [Bacillus subtilis]	89	82	210
3629	1	399	4	gi|1009366	Respiratory nitrate reductase [Bacillus subtilis]	89	78	396
3688	1	2	400	gi|1146206	glutamate dehydrogenase [Bacillus subtilis]	89	75	399
3699	1	399	4	gi|1339950	large subunit of NADH-dependent glutamate synthase [Plectonema boryanum]	89	75	396
4016	1	216	4	gi|1009366	Respiratory nitrate reductase [Bacillus subtilis]	89	71	213
4177	1	301	131	gi|149426	putative [Lactococcus lactis]	89	76	171
4436	1	302	3	gi|1022725	unknown [Staphylococcus haemolyticus]	89	80	300
4635	1	162	4	gi|1022725	unknown [Staphylococcus haemolyticus]	89	73	159
2	2	1330	2676	gi|520754	putative [Bacillus subtilis]	88	76	1347
42	2	468	848	sp|P42321|CATA—	CATALASE (EC 1.11.1.6).	88	76	381
53	5	4722	3055	gi|474177	alpha-D-1,4-glucosidase [Staphylococcus xylosus]	88	80	1668
56	16	18018	18617	gi|467411	recombination protein [Bacillus subtilis]	88	77	600
60	3	376	843	gi|666116	glucose kinase [Staphylococcus xylosus]	88	77	468
70	2	1245	907	gi|44095	replication initiator protein [Listeria monocytogenes]	88	74	339
82	8	11514	12719	pir|A60663|A606	translation elongation factor Tu - Bacillus subtilis	88	79	1206
103	7	4179	4391	gi|167181	serine/threonine kinase receptor [Brassica napus]	88	77	213
114	8	7732	8232	gi|1022726	unknown [Staphylococcus haemolyticus]	88	72	501
118	2	308	2011	gi|1303804	YqeQ [Bacillus subtilis]	88	77	1704
141	3	657	1136	gi|1405446	transketolase [Bacillus subtilis]	88	72	480
148	7	5871	6116	gi|1118002	dihydropteroate synthase [Staphylococcus haemolyticus]	88	78	246
165	3	1428	2231	gi|40053	phenylalanyl-tRNA synthetase alpha subunit [Bacillus subtilis]	88	80	804
					ir|S11730|YFBSA phenylalanine-tRNA ligase (EC 6.1.1.20) alpha ain -
					Bacillus subtilis
205	28	14185	13343	gi|1165306	L2 [Bacillus subtilis]	88	82	843
225	1	898	227	gi|1303840	YqfS [Bacillus subtilis]	88	78	672
235	1	2	1975	gi|452309	valyl-tRNA synthetase [Bacillus subtilis]	88	76	1974
339	3	1566	1072	gi|1118002	dihydropteroate synthase [Staphylococcus haemolyticus]	88	73	495
443	4	2928	1531	gi|558559	pyrimidine nucleoside phosphorylase [Bacillus subtilis]	88	73	1398
532	1	3	419	gi|143797	valyl-tRNA synthetase [Bacillus stearothermophilus]sp|P11931|SYV_BACST	88	78	417
					VALYL-TRNA SYNTHETASE (EC 6.1.1.9) VALINE-TRNA LIGASE) (VALRS).
534	3	2504	2968	gi|153049	mannitol-specific enzyme-III [Staphylococcus carnosus]pir|JQ0088|JQ0088	88	82	465
					phosphotransferase system enzyme II (EC .7.1.69), mannitol-specific,
					factor III - Staphylococcus carnosus sp|P17876|PTMA_STACA PTS SYSTEM,
					MANNITOL-SPECIFIC IIA COMPONENT EIIA-MTL) (
705	2	399	214	gi|710018	nitrite reductase (nirB) [Bacillus subtilis]	88	70	186
1000	2	1309	794	gi|1022726	unknown [Staphylococcus haemolyticus]	88	78	516
1299	1	324	61	gi|401786	phosphomannomutase [Mycoplasma pirum]	88	55	264
1341	2	170	400	gi|39963	ribosomal protein L20 (AA 1-119) [Bacillus stearothermophilus]	88	82	231
					ir|S05348|R5BS20 ribosomal protein L20 - Bacillus stearothermophilus
1386	1	41	214	pir|B47154|B471	signal recognition particle 54 K chain homolog Ffh - Bacillus subtilis	88	71	174
1386	2	183	533	pir|B47154|B471	signal recognition particle 54 K chain homolog Ffh - Bacillus subtilis	88	73	351
2949	1	399	94	gi|535350	CodX [Bacillus subtilis]	88	73	306
2984	1	5	169	gi|218277	O-acetylserine(thiol) lyase [Spinacia oleracea]	88	70	165
3035	1	1	138	gi|493083	dihydroxyacetone kinase [Citrobacter freundii]	88	67	138
3089	1	3	152	gi|606055	ORF_f746 [Escherichia coli]	88	88	150
3917	1	410	3	gi|143378	pyruvate decarboxylase (E-1) beta subunit [Bacillus subtilis]gi|1377836	88	77	408
					pyruvate decarboxylase E-1 beta subunit [Bacillus subtilis]
4199	1	342	4	gi|1405454	aconitase [Bacillus subtilis]	88	82	339
4201	1	369	4	gi|515938	glutamate synthase (ferredoxin) [Synechocystis sp.]pir|S46957|S46957	88	84	366
					glutamate synthase (ferredoxin) (EC 1.4.7.1) - ynechocystis sp.
4274	1	1	336	gi|515938	glutamate synthase (ferredoxin) [Synechocystis sp.]pir|S46957|S46957	88	84	336
					glutamate synthase (ferredoxin) (EC 1.4.7.1) - ynechocystis sp.
4308	1	399	4	gi|1146206	glutamate dehydrogenase [Bacillus subtilis]	88	71	396
2	5	4570	6000	gi|535350	CodX [Bacillus subtilis]	87	70	1431
52	8	6482	6183	gi|1064791	function umknown [Bacillus subtilis]	87	66	300
73	3	1584	2480	gi|142992	glycerol kinase (glpK) (EC 2.7.1.30) [Bacillus subtilis] pir|B45868|B45868	87	72	897
					glycerol kinase (EC 2.7.1.30) - Bacillus subtilis sp|P18157|GLPK_BACSU
					GLYCEROL KINASE (EC 2.7.1.30) (ATP: GLYCEROL-PHOSPHOTRANSFERASE)
					(GLYCEROKINASE) (GK).
98	12	8813	9100	gi|467433	unknown [Bacillus subtilis]	87	62	288
124	4	2988	1711	gi|556886	serine hydroxymethyltransferase [Bacillus subtilis] pir|S49363|S49363	87	77	1278
					serine hydroxymethyltransferase - Bacillus subtilis
124	6	4032	3607	gi|556883	Unknown [Bacillus subtilis]	87	66	426
148	5	3741	4559	gi|467460	unknown [Bacillus subtilis]	87	70	819
164	13	12710	13810	gi|39954	IF2 (aa 1-741) [Bacillus stearothermophilus]	87	72	1101
177	2	1104	2126	gi|467385	unknown [Bacillus subtilis]	87	78	1023
199	1	1158	334	gi|143527	iron-sulfur protein [Bacillus subtilis]	87	77	825
199	2	2933	1149	pir|A27763|A277	succinate dehydrogenase (EC 1.3.99.1) flavoprotein - Bacillus subtilis	87	80	1785
205	23	11543	11304	gi|1044972	ribosomal protein L29 [Bacillus subtilis]	87	78	240
205	25	12607	11939	gi|1165309	S3 [Bacillus subtilis]	87	75	669
222	1	1107	181	gi|1177249	rec233 gene product [Bacillus subtilis]	87	70	927
236	3	1333	1031	gi|1146198	ferredoxin [Bacillus subtilis]	87	80	303
246	5	2292	1999	gi|467373	ribosomal protein S18 [Bacillus subtilis]	87	77	294
260	2	3422	2655	gi|1161382	IcaC [Staphylococcus epidermidis]	87	72	768
320	3	1696	2391	gi|312443	carbamoyl-phosphate synthase (glutamine-hydrolysing) [Bacillus aldolyticus]	87	80	696
380	4	1165	1383	gi|142570	ATP synthase c subunit [Bacillus firmus]	87	80	219
414	4	900	1073	gi|467386	thiophen and furan oxidation [Bacillus subtilis]	87	77	174
425	2	794	585	gi|1046166	pilin repressor [Mycoplasma genitalium]	87	69	210
448	1	722	189	gi|405134	acetate kinase [Bacillus subtilis]	87	75	534
480	1	1	711	gi|142559	ATP synthase alpha subunit [Bacillus megaterium]	87	79	711
481	1	2	352	sp|Q06797|RL1_B	50S RIBOSOMAL PROTEIN L1 (BL1).	87	72	351
677	2	359	955	gi|460911	fructose-bisphosphate aldolase [Bacillus subtilis]	87	78	597
677	3	934	1284	gi|460911	fructose-bisphosphate aldolase [Bacillus subtilis]	87	78	351
876	1	3	452	gi|1146247	asparaginyl-tRNA synthetase [Bacillus subtilis]	87	79	450
1376	1	214	2	gi|1065555	F46H6.4 gene product [Caenorhabditis elegans]	87	75	213
2206	1	3	374	gi|215098	excisionase [Bacteriophage 154a]	87	72	372
2938	1	3	290	gi|508979	GTP-binding protein [Bacillus subtilis]	87	69	288
3081	2	126	308	gi|467399	IMP dehydrogenase [Bacillus subtilis]	87	72	183
3535	1	3	401	gi|1405454	aconitase [Bacillus subtilis]	87	80	399
4238	1	275	3	gi|603769	HutU protein, urocanase [Bacillus subtilis]	87	73	273
4	8	8736	7045	gi|603769	HutU protein, urocanase [Bacillus subtilis]	86	72	1692
22	6	3738	3286	gi|410515	urease beta subunit [Staphylococcus xylosus]	86	73	453
54	2	1572	664	gi|289287	UDP-glucose pyrophosphorylase [Bacillus subtilis]	86	70	909
124	3	1713	1090	gi|556887	uracil phosphoribosyltransferase [Bacillus subtilis] pir|S49364|S49364	86	74	624
					uracil phosphoribosyltransferase - Bacillus subtilis
148	3	1349	3448	gi|467458	cell division protein [Bacillus subtilis]	86	75	2100
148	4	3638	3859	gi|467460	unknown [Bacillus subtilis]	86	73	222
152	3	1340	2086	gi|1377835	pyruvate decarboxylase E-1 alpha subunit [Bacillus subtilis]	86	75	747
164	18	17347	19467	gi|1184680	polynucleotide phosphorylase [Bacillus subtilis]	86	72	2121
180	2	554	1159	gi|143467	ribosomal protein S4 [Bacillus subtilis]	86	80	606
205	3	2592	2218	gi|142464	ribosomal protein L17 [Bacillus subtilis]	86	77	375
205	26	12990	12616	gi|40107	ribosomal protein L22 [Bacillus stearothermophilus] ir|S10612|S10612	86	75	375
					ribosomal protein L22 - Bacillus stearothermophilus
246	7	3140	2817	gi|467375	ribosomal protein S6 [Bacillus subtilis]	86	70	324
299	3	1196	1540	gi|39656	spoVG gene product [Bacillus megaterium]	86	70	345
299	7	3884	4345	gi|467440	‘phosphoribosylpyrophosphate synthetase [Bacillus subtilis] gi|40218 PRPP	86	78	462
					synthetase (AA 1-317) [Bacillus subtilis]
304	5	2170	2523	gi|666983	putative ATP binding subunit [Bacillus subtilis]	86	65	354
310	2	1487	1678	gi|1177684	chorismate mutase [Staphylococcus xylosus]	86	71	192
337	5	2086	3405	gi|487434	isocitrate dehydrogenase [Bacillus subtilis]	86	78	1320
339	2	1109	729	gi|1118003	dihydroneopterin aldolase [Staphylococcus haemolyticus]	86	77	381
358	2	2124	3440	gi|1146219	28.2% of identity to the Escherichia coli GTP-binding protein Era; putative	86	73	1317
					[Bacillus subtilis]
404	2	1015	2058	gi|1303817	YqfA [Bacillus subtilis]	86	78	1044
581	2	452	243	gi|40056	phoP gene product [Bacillus subtilis]	86	71	210
642	2	338	1075	gi|1176399	EpiF [Staphylococcus epidermidis]	86	72	738
770	1	347	72	gi|143328	phoP protein (put.); putative [Bacillus subtilis]	86	69	276
865	1	890	3	gi|1146247	asparaginyl-tRNA synthetase [Bacillus subtilis]	86	74	888
868	2	963	1133	gi|1002911	transmembrane protein [Saccharomyces cerevisiae]	86	69	171
904	1	1	162	gi|1303912	YqhW [Bacillus subtilis]	86	72	162
989	1	35	433	gi|1303993	YqkL [Bacillus subtilis]	86	76	399
1212	1	150	4	gi|414014	ipa-90d gene product [Bacillus subtilis]	86	70	147
1323	1	2	148	gi|40041	pyruvate dehydrogenase (lipoamide) [Bacillus stearothermophilus]	86	75	147
					ir|S10798|DEBSPF pyruvate dehydrogenase (lipoamide) (EC 1.2.4.1) pha chain -
					Bacillus stearothermophilus
3085	2	310	80	gi|1354211	PET112-like protein [Bacillus subtilis]	86	86	231
3847	1	1	228	gi|296464	ATPase [Lactococcus lactis]	86	63	228
4487	1	240	4	gi|1022726	unknown [Staphylococcus haemolyticus]	86	73	237
4583	1	187	2	gi|1022725	unknown [Staphylococcus haemolyticus]	86	79	186
25	5	4287	5039	gi|1502421	3-ketoacyl-acyl carrier protein reductase [Bacillus subtilis]	85	64	753
56	21	29395	28163	gi|1408507	pyrimidine nucleoside transport protein [Bacillus subtilis]	85	69	1233
68	2	332	1192	gi|467376	unknown [Bacillus subtilis]	85	74	861
73	2	880	1707	gi|142992	glycerol kinase (glpK) (EC 2.7.1.30) [Bacillus subtilis] pir|B45868|B45868	85	72	828
					glycerol kinase (EC 2.7.1.30) - Bacillus subtilis sp|P18157|GLPK_BACSU
					GLYCEROL KINASE (EC 2.7.1.30) (ATP: GLYCEROL-PHOSPHOTRANSFERASE)
					(GLYCEROKINASE) (GK).
106	4	1505	3490	gi|143766	(thrSv) (EC 6.1.1.3) [Bacillus subtilis]	85	74	1986
128	2	1153	2202	gi|311924	glycerladehyde-3-phosphate dehydrogenase [Clostridium pasteurianum]	85	75	1050
					pir|S34254|S34254 glyceraldehyde-3-phosphate dehydrogenase (EC .2.1.12) -
					Clostridium pasteurianum
129	4	5252	4038	gi|1064807	ORTHININE AMINOTRANSFERASE [Bacillus subtilis]	85	73	1215
138	6	3475	5673	gi|1072419	glcB gene product [Staphylococcus carnosus]	85	74	2199
189	1	2	169	gi|467385	unknown [Bacillus subtilis]	85	65	168
205	15	8106	7588	gi|1044981	ribosomal protein S5 [Bacillus subtilis]	85	75	519
205	20	10596	10264	pir|A02819|R5BS	ribosomal protein L24 - Bacillus stearothermophilus	85	72	333
220	6	6101	5712	gi|48980	secA gene product [Bacillus subtilis]	85	66	390
231	4	3159	1441	gi|1002520	MutS [Bacillus subtilis]	85	70	1719
243	9	8013	8783	gi|414011	ipa-87r gene product [Bacillus subtilis]	85	72	771
249	2	3186	478	gi|1405454	aconitase [Bacillus subtilis]	85	73	2709
302	1	140	475	gi|40173	homolog of E. coli ribosomal protein L21 [Bacillus subtilis]	85	72	336
					ir|S18439|S18439 Ribosomal protein L21 - Bacillus subtilis
					p|P26908|RL21_BACSU 50S RIBOSOMAL PROTEIN L21 [BL20].
333	1	2968	491	gi|442360	ClpC adenosine triphosphatase [Bacillus subtilis]	85	69	2478
364	6	6082	8196	gi|871784	Clp-like ATP-dependent protease binding subunit [Bos taurus]	85	68	2115
448	2	1339	686	gi|405134	acetate kinase [Bacillus subtilis]	85	68	654
747	1	853	455	gi|1373157	orf-X; hypothetical protein; Method: conceptual translation supplied by	85	73	399
					author [Bacillus subtilis]
886	2	159	467	gi|541768	hemin permease [Yersinia enterocolitica]	85	55	309
1089	1	606	4	pir|B47154|B471	signal recognition particle 54K chain homolog Ffh - Bacillus subtilis	85	71	603
1163	1	409	2	gi|304155	diaminopimelate decarboxylase [Bacillus methanolicus] sp|P41023|DCDA_BACMT	85	62	408
					DIAMINOPIMELATE DECARBOXYLASE (EC 4.1.1.20) DAP DECARBOXYLASE].
1924	1	251	15	gi|215098	excisionase [Bacteriophage 154a]	85	73	237
2932	1	390	4	gi|1041099	Pyruvate Kinase [Bacillus licheniformis]	85	71	387
3030	1	3	275	gi|42370	pyruvate formate-lyase [AA 1-760] [Escherichia coli] ir|S01788|S01788	85	74	273
					formate C-acetyltransferase (EC 2.3.1.54) - Escherichia coli
3111	1	299	3	gi|63568	limb deformity protein [Gallus gallus]	85	85	297
3778	1	316	2	gi|391840	beta-subunit of HDT [Pseudomonas fragi]	85	67	315
3835	1	1	387	gi|1204472	type I restriction enzyme ECOR124/3 I M protein [Haemophilus influenzae]	85	56	387
4042	1	3	386	gi|18178	formare acetyltransferase [Chlamydomonas reinhardtii] ir|S24997|S24997	85	70	384
					formate C-acetyltransferase (EC 2.3.1.54) - Chlamydomonas reinhardtii
4053	1	35	340	gi|1204472	type I restriction enzyme ECOR124/3 I M protein [Haemophilus influenzae]	85	56	306
4108	1	2	181	gi|1072418	glcA gene product [Staphylococcus carnosus]	85	61	180
4300	1	330	85	gi|151932	fructose enzyme II [Rhodobacter capsulatus]	85	59	246
4392	1	355	83	gi|1022725	unknown [Staphylococcus haemolyticus]	85	74	273
4408	1	2	235	gi|871784	Clp-like ATP-dependent protease binding subunit [Bos taurus]	85	62	234
4430	1	291	4	gi|1009366	Respiratory nitrate reductase [Bacillus subtilis]	85	68	288
4555	1	2	253	gi|450688	hsdM gene of EcoprrI gene product [Escherichia coli] pir|S38437|S38437 hsdM	85	52	252
					protein - Escherichia coli pir|S09629|S09629 hypothetical protein A -
					Escherichia coli (SUB 40-520)
4611	1	242	3	gi|1256635	dihydroxy-acid dehydratase [Bacillus subtilis]	85	65	240
4	10	10061	10591	gi|46982	fosB gene product [Staphylococcus epidermidis]	84	68	531
13	2	1172	996	gi|142450	ahrC protein [Bacillus subtilis]	84	56	177
16	4	1803	4652	gi|1277198	DNA repair protein [Deinococcus radiodurans]	84	67	2850
22	3	1128	721	gi|511069	UreF [Staphylococcus xylosus]	84	73	408
23	7	5055	5306	gi|603320	Yer082p [Saccharomyces cerevisiae]	84	61	252
53	11	11145	10693	gi|1303948	YqiW [Bacillus subtilis]	84	68	453
53	12	12770	11481	gi|142613	branched chain alpha-keto acid dehydrogenase E2 [Bacillus subtilis]	84	71	1290
					gi|1303944 BfmBB [Bacillus subtilis]
70	1	982	632	gi|46647	ORF (repE) [Staphylococcus aureus]	84	68	351
73	4	2512	4311	gi|142993	glycerol-3-phosphate dehydrogenase (glpD) (EC 1.1.99.5) [Bacillus subtilis]	84	74	1800
98	7	4324	6096	gi|467427	methionyl-tRNA synthetase [Bacillus subtilis]	84	66	1773
100	9	8680	7859	gi|1340128	ORF1 [Staphylococcus aureus]	84	78	822
117	3	1934	3208	gi|1237019	Srb [Bacillus subtilis]	84	68	1275
148	6	4720	5670	gi|467462	cysteine synthetase A [Bacillus subtilis]	84	69	951
152	4	2064	2456	gi|143377	pyruvate decarboxylase (E-1) alpha subunit [Bacillus subtilis]	84	70	393
					pir|B36718|DEBSPA pyruvate dehydrogenase (lipoamide) (EC 1.2.4.1) lpha
					chain - Bacillus subtilis
169	7	3634	3861	gi|1001342	hypothetical protein [Synechocystis sp.]	84	66	228
171	4	2657	2322	gi|517475	D-amino acid transaminase [Staphylococcus haemolyticus]	84	71	336
186	6	6216	5491	gi|467475	unknown [Bacillus subtilis]	84	70	726
205	9	5692	5123	gi|216340	ORF for adenylate kinase [Bacillus subtilis]	84	71	570
224	2	915	1391	gi|288269	beta-fructofuranosidase [Staphylococcus xylosus]	84	70	477
251	1	92	388	gi|1303790	YqeI [Bacillus subtilis]	84	65	297
282	3	1526	2836	gi|143040	glutamate-1-semialdehyde 2,1-aminotransferase [Bacillus subtilis]	84	75	1311
					pir|D42728|D42728 glutamate-1-semialdehyde 2,1-aminomutase (EC.4.3.8) -
					Bacillus subtilis
307	5	2959	2780	gi|1070014	protein-dependent [Bacillus subtilis]	84	62	180
320	4	2343	4229	gi|143390	carbamyl phosphate synthetase [Bacillus subtilis]	84	70	1887
372	1	3	296	gi|1022725	unknown [Staphylococcus haemolyticus]	84	70	294
413	2	1341	481	gi|1256146	YbbQ [Bacillus subtilis]	84	65	861
439	1	3	392	gi|1046173	osmotically inducible protein [Mycoplasma genitalium]	84	53	390
461	3	1362	2270	gi|40211	threonine synthase (thrC) (AA 1-352) [Bacillus subtilis] ir|A25364|A25364	84	69	909
					threonine synthase (EC 4.2.99.2) - Bacillus subtilis
487	1	3	299	gi|1144531	integrin-like protein alpha Intlp [Candida albicans]	84	46	297
491	2	624	905	pir|S08564|R3BS	ribosomal protein S9 - Bacillus stearothermophilus	84	69	282
491	3	836	1033	pir|S08564|R3BS	ribosomal protein S9 - Bacillus stearothermophilus	84	77	198
548	1	3	341	gi|431231	uracil permease [Bacillus caldolyticus]	84	74	339
728	2	1748	795	gi|912445	DNA polymerase [Bacillus caldotenax]	84	68	954
769	1	3	257	gi|1510953	cobalamin biosynthesis protein N [Methanococcus jannaschii]	84	38	255
954	1	156	4	gi|1405454	aconitase [Bacillus subtilis]	84	57	153
957	1	3	395	gi|143402	recombination protein (ttg start codon) [Bacillus subtilis] gi|1303923 RecN	84	68	393
					[Bacillus subtilis]
975	1	3	452	gi|885934	ClpB [Synechococcus sp.]	84	70	450
1585	1	3	257	gi|510140	ligoendopeptidase F [Lactococcus lactis]	84	56	255
2954	1	3	323	gi|603769	HutU protein, urocanase [Bacillus subtilis]	84	73	321
2996	1	348	46	gi|18178	formate acetyltransferase [Chlamydomonas reinhardtii] ir|S24997|S24997	84	65	303
					formate C-acetyltransferase (EC 2.3.1.54) - Chlamydomonas reinhardtii
3766	1	375	13	gi|517205	67 kDa Myosin-crossreactive streptococcal antigen [Streptococcus yogenes]	84	72	363
4022	1	2	169	gi|1146206	glutamate dehydrogenase [Bacillus subtilis]	84	54	168
4058	1	312	4	gi|151932	fructose enzyme II [Rhodobacter capsulatus]	84	71	309
4108	2	106	351	gi|1072418	glcA gene product [Staphylococcus carnosus]	84	77	246
4183	1	3	308	gi|603769	HutU protein, urocanase [Bacillus subtilis]	84	72	306
4726	1	55	234	gi|146208	glutamate synthase large subunit (EC 2.6.1.53) [Escherichia coli]	84	73	180
					pir|A29617|A29617 glutamate synthase (NADPH) (EC 1.4.1.13) large hain -
					Escherichia coli
22	4	1576	1109	gi|393297	urease accessory protein [Bacillus sp.]	83	64	468
53	13	13745	12768	gi|142612	branched chain alpha-keto acid dehydrogenase E1-beta [Bacillus subtilis]	83	68	978
57	16	12872	12387	gi|143132	lactate dehydrogenase (AC 1.1.1.27) [Bacillus caldolyticus]	83	66	486
					pir|B29704|B29704 L-lactate dehydrogenase (EC 1.1.1.27) - Bacillus
					aldolyticus
66	3	2274	1429	gi|1303894	YqhM [Bacillus subtilis]	83	63	846
66	5	4643	3168	gi|1212730	YqhK [Bacillus subtilis]	83	68	1476
70	3	1523	1182	gi|44095	replication initiator protein [Listeria monocytogenes]	83	73	342
90	1	377	1429	gi|155571	alcohol dehydrogenase I (adhA) (EC 1.1.1.1) [Zymomonas mobilis]	83	70	1053
					pir|A35260|A35260 alcohol dehydrogenase (EC 1.1.1.1) I - Zymomonas obilis
95	2	708	2162	gi|506381	phospho-beta-glucosidase [Bacillus subtilis]	83	70	1455
137	1	68	694	gi|467391	initiation protein of replicaton [Bacillus subtilis]	83	77	627
140	4	2742	2275	gi|634107	kdpB [Escherichia coli]	83	65	468
142	3	2989	2510	gi|1212776	lumazine synthase (b-subunit) [Bacillus amyloliquefaciens]	83	69	480
161	12	5749	6696	gi|903307	ORF75 [Bacillus subtilis]	83	64	948
164	9	9880	11070	gi|49316	ORF2 gene product [Bacillus subtilis]	83	66	1191
164	14	14148	14546	gi|580902	ORF6 gene product [Bacillus subtilis]	83	60	399
170	2	2467	1790	gi|520844	orf4 [Bacillus subtilis]	83	64	678
186	2	1370	711	gi|289284	cysteinyl-tRNA synthetase [Bacillus subtilis]	83	72	660
205	14	7607	7392	gi|216337	ORF for L30 ribosomal protein [Bacillus subtilis]	83	74	216
237	6	3683	4540	gi|1510488	imidazoleglycerol-phosphate synthase (cyclase) [Methanococcus jannaschii]	83	60	858
301	1	638	291	gi|467419	unknown [Bacillus subtilis]	83	65	348
302	4	1421	2743	gi|508979	GTP-binding protein [Bacillus subtilis]	83	68	1323
321	4	3571	3209	gi|39844	fumarase (citG) (aa 1-462) [Bacillus subtilis]	83	68	363
367	1	2	352	gi|1039479	ORFU [Lactococcus lactis]	83	54	351
387	1	3	662	gi|806281	DNA polymerase I [Bacillus stearothermophilus]	83	70	660
527	2	916	1566	gi|396259	protease [Staphylococcus epidermidis]	83	67	651
533	1	179	3	gi|142455	alanine dehydrogenase (EC 1.4.1.1) [Bacillus stearothermophilus]	83	66	177
					pir|B34261|B34261 alanine dehydrogenase (EC 1.4.1.1) - Bacillus
					stearothermophilus
536	4	1438	1259	gi|143366	adenylosuccinate lyase (PUR-B) [Bacillus subtilis] pir|C29326|WZBSDS	83	67	180
					adenylosuccinate lyase (EC 4.3.2.2) - Bacillus subtilis
652	1	2	859	gi|520753	DNA topoisomerase I [Bacillus subtilis]	83	72	858
774	2	200	361	gi|1522665	M. jannaschii predicted coding region MJECL28 [Methanococcus jannaschii]	83	58	162
897	1	120	296	gi|1064807	ORTHININE AMINOTRANSFERASE [Bacillus subtilis]	83	76	177
1213	1	3	491	gi|289288	lexA [Bacillus subtilis]	83	67	489
2529	1	150	4	gi|143786	tryptophanyl-tRNA synthetase (EC 6.1.1.2) [Bacillus subtilis]	83	69	147
					pir|JT0481|YWBS tryptophan - tRNA ligase (EC 6.1.1.2) - Bacillus subtilis
2973	1	326	3	gi|1109687	ProZ [Bacillus subtilis]	83	58	324
3009	1	366	4	gi|882532	ORF_o294 [Escherichia coli]	83	65	363
3035	2	45	305	gi|950062	hypothetical yeast protein 1 [Mycoplasma capricolum] pir|S48578|S48578	83	59	261
					hypothetical protein - Mycoplasma capricolum SGC3) (fragment)
3906	1	67	309	gi|1353197	thioredoxin reductase [Eubacterium acidaminophilum]	83	61	243
4458	1	271	2	gi|397526	clumping factor [Staphylococcus aureus]	83	78	270
4570	1	223	2	gi|1022726	unknown [Staphylococcus haemolyticus]	83	74	222
4654	1	97	261	gi|1072419	glcB gene product [Staphylococcus carnosus]	83	79	165
16	2	295	1191	gi|153854	uvs402 protein [Streptococcus pneumoniae]	82	67	897
16	3	1193	1798	gi|153854	uvs402 protein [Streptococcus pneumoniae]	82	70	606
38	12	8724	7804	gi|1204400	N-acetylneuraminate lyase [Haemophilus influenzae]	82	58	921
42	4	988	2019	gi|841192	catalase [Bacteroides fragilis]	82	70	1032
51	6	2590	3489	gi|143607	sporulation protein [Bacillus subtilis]	82	69	900
56	11	12270	13925	gi|39431	oligo-1,6-glucosidase [Bacillus cereus]	82	60	1656
56	15	17673	18014	gi|467410	unknown [Bacillus subtilis]	82	66	342
61	2	881	3313	gi|143148	transfer RNA-Leu synthetase [Bacillus subtilis]	82	70	2433
82	7	9162	11318	gi|48240	elongation factor G (AA 1-691) [Thermus aquaticus thermophilus]	82	64	2157
					ir|S15928|EFTWG translation elongation factor G - Thermus aquaticus
					p|P13551|EFG_THETH ELONGATION FACTOR G (EF-G).
85	2	3260	1050	gi|143369	phosphoribosylformyl glycinamidine synthetase II (PUR-Q) [Bacillus subtilis]	82	66	2211
102	6	3662	5380	gi|1256635	dihydroxy-acid dehydratase [Bacillus subtilis|	82	65	1719
117	4	3242	3493	pir|A47154|A471	orf1 5′ of Ffh - Bacillus subtilis	82	53	252
128	6	4377	5933	gi|460258	phosphoglycerate mutase [Bacillus subtilis]	82	66	1557
129	2	1229	2182	gi|403373	glycerophosphoryl diester phosphodiesterase [Bacillus subtilis]	82	62	954
					pir|S37251|S37251 glycerophosphoryl diester phosphodiesterase -Bacillus
					subtilis
170	1	2	1441	gi|1377831	unknown [Bacillus subtilis]	82	67	1440
177	1	3	1094	gi|467386	thiophen and furan oxidation [Bacillus subtilis]	82	65	1092
184	4	3572	4039	gi|153566	ORF (19 K protein) [Enterococcus faecalis]	82	59	468
189	8	4225	3995	gi|1001878	CspL protein [Listeria monocytogenes]	82	73	231
206	19	20707	20048	gi|473916	lipopeptide antibiotics iturin A [Bacillus subtilis]sp|P39144|LP14_BACSU	82	50	660
					LIPOPEPTIDE ANTIBIOTICS ITURIN A AND SURFACTIN IOSYNTHESIS PROTEIN.
221	2	805	1722	gi|517205	67 kDa Myosin-crossreactive streptococcal antigen [Streptococcus yogenes]	82	63	918
223	4	3651	3436	gi|439619	[Salmonella typhimurium IS200 insertion sequence from SARA17, artial.],	82	69	216
					gene product [Salmonella typhimurium]
260	3	4296	3385	gi|1161381	IcaB [Staphylococcus epidermidis]	82	61	912
315	3	2855	846	gi|143397	quinol oxidase [Bacillus subtilis]	82	67	2010
321	10	7945	7370	gi|142981	ORF5; This ORF includes a region (aa23-103) containing a potential ron-	82	62	576
					sulphur centre homologous to a region of Rhodospirillum rubrum nd
					Chromatium vinosum; putative [Bacillus stearothermophilus]
					pir|PQ0299|PQ0299 hypothetical protein 5 (gldA 3′ region) -
331	3	1055	1342	gi|436574	ribosomal protein L1 [Bacillus subtilis]	82	71	288
370	2	262	618	gi|1303793	YqeL [Bacillus subtilis]	82	59	357
404	4	3053	4024	gi|1303821	YqfE [Bacillus subtilis]	82	68	972
405	4	3073	1706	gi|1303913	YqhX [Bacillus subtilis]	82	67	1368
436	3	2864	1632	gi|149521	tryptophan synthase beta subunit [Lactococcus lactis]pir|S35129|S35129	82	67	1233
					tryptophan synthase (EC 4.2.1.20) beta chain - Lactococcus lactis subsp.
					lactis
441	4	2573	1752	gi|142952	glyceraldehyde-3-phosphate dehydrogenase [Bacillus tearothermophilus]	82	67	822
444	12	10415	11227	gi|1204354	spore germination and vegetative growth protein [Haemophilus influenzae]	82	67	813
446	1	3	191	gi|143387	aspartate transcarbamylase [Bacillus subtilis]	82	66	189
462	3	1007	1210	gi|142521	deoxyribodipyrimidine photolyase [Bacillus subtilis] pir|A37192|A37192 uvrB	82	64	204
					protein - Bacillus subtilis sp|P14951|UVRC_BACSU EXCINUCLEASE ABC SUBUNIT C.
537	1	784	8	gi|853767	UDP-N-acetylglucosamine 1-carboxyvinyltransferase [Bacillus subtilis]	82	61	777
680	2	407	700	gi|426472	secE gene product [Staphylococcus carnosus]	82	69	294
724	2	386	207	gi|143373	phosphoribosyl aminoimidazole carboxy formyl ormyltransferase/inosine	82	68	180
					monophosphate cyclohydrolase (PUR-H(J)) Bacillus subtilis)
763	1	213	4	gi|467458	cell division protein [Bacillus subtilis]	82	35	210
818	1	283	2	gi|1064787	function unknown [Bacillus subtilis]	82	69	282
858	1	175	1176	gi|143043	uroporphyrinogen decarboxylase [Bacillus subtilis] pir|B47045|B47045	82	71	1002
					uroporphyrinogen decarboxylase (EC 4.1.1.37) - Bacillus subtilis
895	1	3	599	gi|1027507	ATP binding protein [Borrelia burgdorferi]	82	72	597
939	1	10	399	gi|143795	transfer RNA-Tyr synthetase [Bacillus subtilis]	82	60	390
961	1	1	306	gi|577647	gamma-hemolysin [Staphylococcus aureus]	82	69	306
1192	1	155	3	gi|146974	NH3-dependent NAD synthetase [Escherichia coli]	82	71	153
1317	1	49	375	gi|407908	EIIscr [Staphylococcus xylosus]	82	72	327
1341	1	1	150	gi|39962	ribosomal protein L35 (AA 1-66) [Bacillus stearothermophilus]	82	68	150
					ir|S05347|R5BS35 ribosomal protein L35 - Bacillus earothermophilus
2990	2	349	131	gi|534855	ATPase subunit epsilon [Bacillus stearothermophilus]sp|P42009|ATPE_BACST	82	47	219
					ATP SYNTHASE EPSILON CHAIN (EC 3.6.1.34).
3024	1	45	224	gi|467402	unknown [Bacillus subtilis]	82	64	180
3045	1	139	2	gi|467335	ribosomal protein L9 [Bacillus subtilis]	82	60	138
3045	2	400	242	gi|467335	ribosomal protein L9 [Bacillus subtilis]	82	82	159
3091	1	238	2	gi|499335	secA protein [Staphylococcus carnosus]	82	78	237
3107	1	210	4	gi|546918	orfY 3′ of comK [Bacillus subtilis, E26, Peptide Partial, 140 aa]	82	64	207
					pir|S43612|S43612 hypothetical protein Y - Bacillus subtilis
					sp|P40398|YHXD_BACSU HYPOTHETICAL PROTEIN IN COMK 3′ REGION (ORFY)
					FRAGMENT).
4332	1	2	319	gi|42086	nitrate reductase alpha subunit [Escherichia coli] p|P09152|NARG_ECOLI	82	75	318
					RESPIRATORY NITRATE REDUCTASE 1 ALPHA CHAIN (EC 7.99.4). (SUB 2-1247)
23	3	2574	1873	gi|1199573	spsB [Sphingomonas sp.]	81	64	702
42	1	321	4	gi|466778	lysine specific permease [Escherichia coli]	81	59	318
48	5	4051	4350	gi|1045937	M. genitalium predicted coding region MG246 [Mycoplasma genitalium]	81	62	300
51	4	1578	2579	pir|S16649|S166	dciAC protein - Bacillus subtilis	81	55	1002
53	2	364	1494	gi|1303961	YqjJ [Bacillus subtilis]	81	67	1131
53	8	7971	6523	gi|146930	6-phosphogluconate dehydrogenase [Escherichia coli]	81	66	1449
54	9	10119	9481	gi|143016	permease [Bacillus subtilis]	81	65	639
54	10	11786	10212	gi|143015	gluconate kinase [Bacillus subtilis]	81	64	1575
57	17	13366	12749	pir|A25805|A258	L-lactate dehydrogenase (EC 1.1.1.27) - Bacillus subtilis	81	74	618
81	2	2217	1726	gi|1222302	NifU-related protein [Haemophilus influenzae]	81	54	492
86	1	374	3	gi|414017	ipa-93d gene product [Bacillus subtilis]	81	70	372
103	6	4861	3284	gi|971342	nitrate reductase beta subunit [Bacillus subtilis] sp|P42176|NARH_BACSU	81	64	1578
					NITRATE REDUCTASE BETA CHAIN (EC 1.7.99.4).
120	15	10845	12338	gi|1524392	GbsA [Bacillus subtilis]	81	67	1494
128	5	3676	4413	gi|143319	triose phosphate isomerase [Bacillus megaterium]	81	64	738
131	9	9280	8252	gi|299163	alanine dehydrogenase [Bacillus subtilis]	81	68	1029
143	6	5471	4854	gi|439619	[Salmonella typhimurium IS200 insertion sequence from SARA17, artial.],	81	61	618
					gene product [Salmonella typhimurium]
169	1	43	825	gi|897795	30S ribosomal protein [Pediococcus acidilactici] sp|P49668|RS2_PEDAC 30S	81	65	783
					RIBOSOMAL PROTEN S2.
230	1	226	2	gi|1125826	short region of weak similarity to tyrosine-protein kinase receptors in a	81	54	225
					fibronectin type III-like domain [Caenorhabditis elegans]
233	5	2000	2677	gi|467404	unknown [Bacillus subtilis]	81	63	678
241	2	2149	1217	gi|16510	succinate - CoA ligase (GDP-forming) [Arabidopsis thaliana] ir|S30579|S30579	81	69	933
					succinate—CoA ligase (GDP-forming) (EC 6.2.1.4) pha chain - Arabidopsis
					thaliana (fragment)
256	1	1	981	pir|S09411|S094	spoIIIE protein - [Bacillus subtilis]	81	65	981
259	3	2691	1630	sp|P28367|RF2_B	PROBABLE PEPTIDE CHAIN RELEASE FACTOR 2 (RF-2) (FRAGMENT).	81	65	1062
275	2	1728	3581	gi|726480	L-glutamine-n-fructose-6-phosphate amidotransferase [Bacillus subtilis]	81	68	1854
285	1	735	4	gi|1204844	H. influenzae predicted coding region HI0594 [Haemophilus influenzae]	81	63	732
296	1	99	1406	gi|467328	adenylosuccinate synthetase [Bacillus subtilis]	81	67	1308
302	9	5590	5889	gi|147485	queA [Escherichia coli]	81	64	300
317	2	1137	1376	gi|154961	resolvase [Transposon Tn917]	81	51	240
343	2	1034	1342	gi|405955	yeeD [Escherichia coli]	81	60	309
360	2	1404	2471	gi|1204570	aspartyl-tRNA synthetase [Haemophilus influenzae]	81	67	1068
364	5	5706	5161	gi|1204652	methylated-DNA-protein-cysteine methyltransferase [Haemophilus influenzae]	81	63	546
372	2	1135	563	gi|467416	unknown [Bacillus subtilis]	81	65	573
392	1	43	603	pir|S09411|S094	spoIIIE protein - Bacillus subtilis	81	65	561
404	9	5252	6154	gi|606745	Bex [Bacillus subtilis]	81	65	903
426	2	1119	511	gi|39453	Manganese superoxide dismutase [Bacillus caldotenax] ir|S22053|S22053	81	66	609
					superoxide dismutase (EC 1.15.1.1) (Mn) - Bacillus ldotenax
480	7	5653	5889	pir|C37083|C370	hypothetical protein II (ompH 3′ region) - Salmonella typhimurium	81	57	237
					[fragment]
625	3	1105	2070	gi|1262360	protein kinase PknB [Mycobacterium leprae]	81	56	966
754	2	504	1064	gi|1303902	YqhU [Bacillus subtilis]	81	71	561
842	1	86	430	gi|1405446	transketolase [Bacillus subtilis]	81	68	345
953	1	400	2	gi|1205429	dipeptide transport ATP-binding protein [Haemophilus influenzae]	81	57	399
961	2	252	401	gi|487686	synergohymenotropic toxin [Staphylococcus intermedius] pir|S44944|S44944	81	72	150
					synergohymenotropic toxin - Staphylococcus intermedius
1035	1	1	189	gi|1046138	M. genitalium predicted coding region MG423 [Mycoplasma genitalium]	81	43	189
1280	1	449	228	gi|559164	helicase [Autographa californica nuclear polyhedrosis virus]	81	43	222
					sp|P24307|V143_NPVAC HELICASE.
3371	1	68	241	gi|1322245	mevalonate pyrophosphate decarboxylase [Rattus norvegicus]	81	62	174
3715	1	239	3	gi|537137	ORF_f388 [Escherichia coli]	81	58	237
3908	1	2	325	gi|439619	[Salmonella typhimurium IS200 insertion sequence from SARA17, artial.],	81	68	324
					gene product [Salmonella typhimurium]
3940	1	3	401	gi|296464	ATPase [Lactococcus lactis]	81	69	399
3954	1	1	318	gi|1224069	amidase [Moraxella catarrhalis]	81	68	318
4049	1	170	3	gi|603768	HutI protein, imidazolone-5-propionate hydrolase [Bacillus subtilis]	81	68	168
					gi|603768 HutI protein, imidazolone-5-propionate hydrolase Bacillus
					subtilis ]
4209	1	1	324	gi|403373	glycerophosphoryl diester phosphodiesterase [Bacillus subtilis]	81	58	324
					pir|S37251|S37251 glycerophosphoryl diester phosphodiesterase - Bacillus
					subtilis
4371	1	322	17	gi|216677	indolepyruvate decarboxylase [Enterobacter cloacae] pir|S16013|S16013	81	72	306
					indolepyruvate decarboxylase (EC 4.1.1.—) - Enterobacter cloacae
4387	1	19	228	gi|460689	TVG [Thermoactinomyces vulgaris]	81	59	210
4391	1	306	31	gi|1524193	unknown [Mycobacterium tuberculosis]	81	67	276
4425	1	3	341	gi|143015	gluconate kinase [Bacillus subtilis]	81	66	339
9	1	847	101	gi|1064786	function unknown [Bacillus subtilis]	80	62	747
17	1	311	78	gi|559164	helicase [Autographa californica nuclear polyhedrosis virus]	80	40	234
					sp|P24307|V143_NPVAC HELICASE.
45	2	1159	2448	gi|1109684	ProV [Bacillus subtilis]	80	63	1290
45	5	4032	4733	gi|1109687	ProZ [Bacillus subtilis]	80	55	702
54	8	9502	8738	gi|563952	gluconate permease [Bacillus licheniformis]	80	62	765
62	12	7545	6238	gi|854655	Na/H antiporter system [Bacillus alcalophilus]	80	62	1308
62	14	8087	8683	gi|559713	ORF [Homo sapiens]	80	68	597
67	16	13781	14122	gi|305002	ORF_f356 [Escherichia coli]	80	65	342
70	13	10296	9097	gi|1303995	YqkN [Bacillus subtilis]	80	64	1200
98	9	6336	7130	gi|467428	unknown [Bacillus subtilis]	80	68	795
98	10	7294	7833	gi|467430	unknown [Bacillus subtilis]	80	64	540
98	11	7820	8737	gi|467431	high level kasgamycin resistance [Bacillus subtilis]	80	61	918
109	16	14154	14813	gi|580875	ipa-57d gene product [Bacillus subtilis]	80	63	660
112	15	14294	16636	gi|1072361	pyruvate-formate-lyase [Clostridium pasteurianum]	80	65	2343
139	1	726	4	gi|506699	CapC [Staphylococcus aureus]	80	58	723
139	2	1448	717	gi|506698	CapB [Staphylococcus aureus]	80	59	732
174	4	2870	2469	gi|1146242	aspartate 1-decarboxylase [Bacillus subtilis]	80	61	402
177	3	2102	2842	gi|467385	unknown [Bacillus subtilis]	80	70	741
184	6	5912	5700	gi|161953	85-kDa surface antigen [Trypanosoma cruzi]	80	46	213
186	4	3875	2382	gi|289282	glutamyl-tRNA synthetase [Bacillus subtilis]	80	65	1494
205	30	15140	14484	gi|40103	ribosomal protein L4 [Bacillus stearothermophilus]	80	66	657
207	1	140	1315	gi|460259	enolase [Bacillus subtilis]	80	67	1176
211	3	1078	1590	gi|410131	ORFX7 [Bacillus subtilis]	80	61	513
235	2	1962	2255	gi|143797	valyl-tRNA synthetase [Bacillus stearothermophilus] sp|P11931|SYV_BACST	80	55	294
					VALYL-TRNA SYNTHETASE (EC 6.1.1.9) VALINE-TRNA LIGASE) (VALRS).
239	1	1	1263	gi|143000	proton glutamate symport protein [Bacillus stearothermophilus]	80	59	1263
					pir|S26247|S26247 glutamate/aspartate transport protein - Bacillus
					stearothermophilus
272	5	2461	2198	gi|709993	hypothetical protein [Bacillus subtilis]	80	54	264
301	3	1111	776	gi|467418	unknown [Bacillus subtilis]	80	58	336
310	4	4501	3305	gi|1177686	acuC gene product [Staphylococcus xylosus]	80	67	1197
310	6	5258	7006	gi|348053	acetyl-CoA synthetase [Bacillus subtilis]	80	67	1749
310	7	7410	9113	gi|1103865	formyl-tetrahydrofolate synthetase [Streptococcus mutans]	80	67	1704
325	3	1114	1389	gi|310325	outer capsid protein [Rotavirus sp.]	80	40	276
337	1	636	4	gi|537049	ORF_o470 [Escherichia coli]	80	55	633
374	2	929	1228	gi|1405448	YneF [Bacillus subtilis]	80	70	300
375	5	3062	3331	gi|467448	unknown [Bacillus subtilis]	80	68	270
388	1	267	587	gi|1064791	function unknown [Bacillus subtilis]	80	65	321
394	1	9	659	gi|304976	matches PS00017: ATP_GTP_A and PS00301: EFACTOR_GTP; similar to longation	80	65	651
					factor G, TetM/Tet0 tetracycline-resistance proteins Escherichia coli]
456	1	625	1263	gi|1146183	putative [Bacillus subtilis]	80	65	639
475	1	1	654	gi|288269	beta-fructofuranosidase [Staphylococcus xylosus]	80	66	654
544	2	1449	2240	gi|529754	speC [Streptococcus pyogenes]	80	50	792
622	4	1623	1871	gi|1483545	unknown [Mycobacterium tuberculosis]	80	65	249
719	1	1	1257	gi|1064791	function unknown [Bacillus subtilis]	80	68	1257
739	1	107	838	gi|666983	putative ATP binding subunit [Bacillus subtilis]	80	61	732
745	2	414	247	gi|1511600	coenzyme PQQ synthesis protein III [Methanococcus jannaschii]	80	61	168
822	1	17	679	gi|410141	ORFX17 [Bacillus subtilis]	80	68	663
827	2	836	681	gi|1205301	leukotoxin secretion ATP-binding protein [Haemophilus influenzae]	80	54	156
1044	1	3	149	gi|60632	vp2 [Marburg virus]	80	55	147
1220	2	413	255	pir|A61072|EPSG	gallidermin precursor - Staphylococcus gallinarum	80	74	159
2519	1	75	275	gi|147556	dpj [Escherichia coli]	80	45	201
2947	1	279	55	gi|1184680	polynucleotide phosphorylase [Bacillus subtilis]	80	62	225
3120	1	2	226	gi|517205	67 kDa Myosin-crossreactive streptococcal antigen [Streptococcus yogenes]	80	65	225
3191	1	148	2	gi|151259	HMG-CoA reductase (EC 1.1.1.88) [Pseudomonas mevalonii] pir|A44756|A44756	80	59	147
					hydroxymethylglutaryl-CoA reductase (EC 1.1.1.88) Pseudomonas sp.
3560	2	285	434	gi|217130	photosystem I core protein B [Synechococcus vulcanus]	80	70	150
3655	1	47	346	gi|415855	deoxyribose aldolase [Mycoplasma hominis]	80	56	300
3658	2	324	584	gi|551531	2-nitropropane dioxygenase [Williopsis saturnus]	80	54	261
3769	1	400	2	gi|1339950	large subunit of NADH-dependent glutamate synthase [Plectonema boryanum]	80	68	399
3781	1	348	4	gi|166412	NADH-glutamate synthase [Medicago sativa]	80	62	345
3988	1	48	287	gi|1204696	fructose-permease IIBC component [Haemophilus influenzae]	80	69	240
4030	1	287	3	gi|1009366	Respiratory nitrate reductase [Bacillus subtilis]	80	60	285
4092	1	275	3	gi|1370207	orf6 [Lactobacillus sake]	80	69	273
4103	1	342	4	gi|39956	IIGlc [Bacillus subtilis]	80	65	339
4231	1	348	4	gi|289287	UDP-glucose pyrophosphorylase [Bacillus subtilis]	80	65	345
4265	1	299	3	gi|603768	HutI protein, imidazolone-5-propionate hydrolase [Bacillus subtilis]	80	63	297
					gi|603768 HutI protein, imidazolone-5-propionate hydrolase Bacillus
					subtilis ]
4504	1	250	2	gi|1339950	large subunit of NADH-dependent glutamate synthase [Plectonema boryanum]	80	68	249
2	6	5998	6798	gi|535351	codY [Bacillus subtilis]	79	63	801
4	7	7051	5807	gi|603768	HutI protein, imidazolone-5-propionate hydrolase [Bacillus subtilis]	79	64	1245
					gi|603768 HutI protein, imidazolone-5-propionate hydrolase Bacillus
					subtilis ]
25	6	5273	5515	pir|A36728|A367	acyl carrier protein - Rhizobium meliloti	79	65	243
59	2	1173	1424	gi|147923	threonine dehydratase 2 (EC 4.2.1.16) [Escherichia coli]	79	75	252
60	1	1	204	gi|666115	orf1 upstream of glucose kinase [Staphylococcus xylosus]pir|S52351|S52351	79	60	204
					hypothetical protein 1 - Staphylococcus xylosus
81	1	1590	178	gi|466882	pps1; B1496_C2_189 [Mycobacterium leprae]	79	64	1413
85	7	6505	5987	gi|143364	phosphoribosyl aminoimidazole carboxylase I (PUR-E) [Bacillus subtilis]	79	60	519
89	6	4554	3448	gi|144906	product homologous to E. coli thioredoxin reductase: J. Biol. Chem. 1988)	79	35	1107
					263: 9015-9019, and to F52a protein of alkyl hydroperoxide eductase from
					S. typhimurium : J.Biol.Chem. (1990) 265: 10535-10540; pen reading frame A
					[Clostridium pasteurianum]
102	11	7489	8571	gi|143093	ketol-acid reductoisomerase [Bacillus subtilis] sp|P37253|ILVC_BACSU KETOL-	79	64	1083
					ACID REDUCTOISOMERASE (EC 1.1.1.86) ACETOHYDROXY-ACID ISOMEROREDUCTASE)
					(ALPHA-KETO-BETA-HYDROXYLACIL EDUCTOISOMERASE).
102	14	11190	12563	gi|149428	putative [Lactococcus lactis]	79	65	1374
127	9	7792	9372	gi|458688	PrfC/RF3 [Dichelobacter nodosus]	79	68	1581
139	3	1983	1426	gi|506697	CapA [Staphylococcus aureus]	79	55	558
144	2	1156	668	gi|1498296	peptide methionine sulfoxide reductase [Streptococcus pneumoniae]	79	47	489
148	2	529	1098	gi|467457	hypoxanthine-guanine phosphoribosyltransferase [Bacillus subtilis]	79	59	570
					gi|467457 hypoxanthine-guanine phosphoribosyltransferase [Bacillus
					subtilis ]
150	1	591	217	gi|755602	unknown [Bacillus subtilis]	79	61	375
176	1	587	135	gi|297874	fructose-bisphosphate aldolase [Staphylococcus carnosus] pir|A49943|A49943	79	65	453
					fructose-bisphosphate aldolase (EC 4.1.2.13) - Staphylococcus carnosus
					(strain TM300)
186	7	6874	6164	gi|1314298	ORF5; putative Sms protein; similar to Sms proteins from Haemophilus	79	64	711
					influenzae and Escherichia coli [Listeria monocytogenes]
205	16	8498	8109	gi|1044980	ribosomal protein L18 [Bacillus subtilis]	79	70	390
211	1	1	519	gi|1303994	YqkM [Bacillus subtilis]	79	62	519
223	2	2801	1419	gi|488430	alcohol dehydrogenase 2 [Entamoeba histolytica]	79	60	1383
243	8	7896	6877	gi|580883	ipa-88d gene product [Bacillus subtilis]	79	60	1020
279	4	3721	4329	gi|413930	ipa-6d gene product [Bacillus subtilis]	79	59	609
300	1	11	1393	gi|403372	glycerol 3-phosphate permease [Bacillus subtilis]	79	62	1383
307	3	1935	940	gi|950062	hypothetical yeast protein 1 [Mycoplasma capricolum] pir|S48578|S48578	79	60	996
					hypothetical protein - Mycoplasma capricolum SGC3) (fragment)
352	6	8886	7666	gi|216854	P47K [Pseudomonas chlororaphis]	79	59	1221
412	1	578	3	gi|143177	putative [Bacillus subtilis]	79	51	576
481	3	621	1124	gi|786163	Ribosomal Protein L10 [Bacillus subtilis]	79	66	504
516	1	352	2	gi|805090	NisF [Lactococcus lactis]	79	48	351
525	2	1426	395	gi|143371	phosphoribosyl aminoimidazole synthetase (PUR-M) [Bacillus subtilis]	79	61	1032
					pir|H29326|AJBSCL phosphoribosylformylglycinamidine cyclo-ligase EC
					6.3.3.1) - Bacillus subtilis
538	4	2825	2202	gi|1370207	orf6 [Lactobacillus sake]	79	67	624
570	1	2	421	gi|476160	arginine permease substrate-binding subunit [Listeria monocytogenes]	79	61	420
645	8	2663	3241	gi|153898	transport protein [Salmonella typhimurium]	79	62	579
683	1	75	374	gi|1064795	function unknown [Bacillus subtilis]	79	62	300
816	3	3987	3274	gi|1407784	orf-1; novel antigen [Staphylococcus aureus]	79	62	714
2929	1	3	401	gi|1524397	glycine betaine transporter OpuD [Bacillus subtilis]	79	61	399
2937	1	202	47	pir|S52915|S529	nitrate reductase alpha chain - Bacillus subtilis (fragment)	79	58	156
2940	1	385	2	gi|149429	putative [Lactococcus lactis]	79	72	384
2946	1	286	2	gi|143267	2-oxoglutarate dehydrogenase (odhA; EC 1.2.4.2) [Bacillus subtilis]	79	61	285
2999	1	3	212	gi|710020	nitrite reductase (nirB) [Bacillus subtilis]	79	59	210
3022	1	332	150	gi|450686	3-phosphoglycerate kinase [Thermotoga maritima]	79	61	183
3064	1	3	314	gi|1204436	pyruvate formate-lyase [Haemophilus influenzae]	79	60	312
3083	1	2	220	gi|1149662	hypD gene product [Clostridium perfringens]	79	56	219
3126	1	411	121	gi|1339950	large subunit of NADH-dependent glutamate synthase [Plectonema boryanum]	79	55	291
3181	1	326	45	gi|1339950	large subunit of NADH-dependent glutamate synthase [Plectonema boryanum]	79	59	282
3345	1	3	476	gi|871784	Clp-like ATP-dependent protease binding subunit [Bos taurus]	79	63	474
3718	1	270	4	pir|C36889|C368	leuB protein, inactive - Lactococcus lactis subsp. lactis (strain IL1403)	79	71	267
3724	2	159	401	gi|1009366	Respiratory nitrate reductase [Bacillus subtilis]	79	64	243
3836	1	312	16	gi|1524193	unknown [Mycobacterium tuberculosis]	79	65	297
3941	1	2	334	gi|415855	deoxyribose aldolase [Mycoplasma hominis]	79	54	333
4113	1	3	341	gi|143015	gluconate kinase [Bacillus subtilis]	79	63	339
4501	1	209	12	gi|1022726	unknown [Staphylococcus haemolyticus]	79	66	198
4612	1	2	238	gi|460689	TVG [Thermoactinomyces vulgaris]	79	58	237
2	1	2	1213	gi|520753	DNA topoisomerase I [Bacillus subtilis]	78	64	1212
8	2	1220	174	gi|216151	DNA polymerase (gene L; ttg start codon) [Bacteriophage SP02] gi|579197	78	72	1047
					SP02 DNA polymerase (aa 1-648) [Bacteriophage SP02] pir|A21498|DJBPS2 DNA-
					directed DNA polymerase (EC 2.7.7.7) - phage P02
9	2	1089	838	gi|1064787	function unknown [Bacillus subtilis]	78	57	252
32	8	6803	7702	gi|146974	NH3-dependent NAD synthetase [Escherichia coli]	78	63	900
36	4	2941	3138	gi|290503	glutamate permease [Escherichia coli]	78	53	198
53	15	16221	14758	gi|1303941	YqiV [Bacillus subtilis]	78	58	1464
57	14	10520	12067	gi|1072418	glcA gene product [Staphylococcus carnosus]	78	65	1548
66	7	5812	4826	gi|1212729	YqhJ [Bacillus subtilis]	78	67	987
67	4	4029	4376	gi|466612	nikA [Escherichia coli]	78	71	348
91	9	10058	10942	gi|467380	stage 0 sporultion [Bacillus subtilis]	78	50	885
102	12	8574	10130	gi|149426	putative [Lactococcus lactis]	78	61	1557
112	6	3540	4463	gi|854234	cymG gene product [Klebsiella oxytoca]	78	56	924
124	2	1061	234	gi|405622	unknown [Bacillus subtilis]	78	60	828
130	3	1805	2260	gi|1256636	putative [Bacillus subtilis]	78	71	456
133	1	377	3	gi|168060	lamB [Emericella nidulans]	78	59	375
166	4	6163	5201	gi|451216	Mannosephosphate Isomerase [Streptococcus mutans]	78	63	963
186	1	795	4	gi|289284	cysteinyl-tRNA synthetase [Bacillus subtilis]	78	63	792
195	4	2315	1881	gi|1353874	unknown [Rhodobacter capsulatus]	78	58	435
199	3	3623	2967	gi|143525	succinate dehydrogenase cytochrome b-558 subunit [Bacillus subtilis]	78	57	657
					pir|A29843|DEBSSC succinate dehydrogenase (EC 1.3.99.1) cytochrome 558 -
					Bacillus subtilis
199	4	5557	3905	gi|142521	deoxyribodipyrimidine photolyase [Bacillus subtilis] pir|A37192|A37192 uvrB	78	62	1653
					protein - Bacillus subtilis sp|P14951|UVRC_BACSU EXCINUCLEASE ABC SUBUNIT
					C.
223	3	3523	3215	gi|439596	[Escherichia coli IS200 insertion sequence from ECOR63, partial.), ene	78	47	309
					product [Escherichia coli]
299	4	1865	2149	gi|467439	temperature sensitive cell division [Bacillus subtilis]	78	62	285
321	9	7315	6896	gi|142979	ORF3 is homologous to an ORF downstream of the spoT gene of E. coli; RF3	78	55	420
					[Bacillus stearothermophilus]
352	4	3714	3944	gi|349050	actin 1 [Pneumocystis carinii]	78	42	231
352	5	6093	4594	gi|903587	NADH dehydrogenase subunit 5 [Bacillus subtilis] sp|P39755|NDHF_BACSU NADH	78	58	1500
					DEHYDROGENASE SUBUNIT 5 (EC 1.6.5.3) NADH-UBIQUINONE OXIDOREDUCTASE CHAIN
					5).
376	1	2	583	gi|551693	dethiobiotin synthase [Bacillus sphaericus]	78	34	582
424	2	1595	1768	gi|1524117	alpha-acetolactate decarboxylase [Lactococcus lactis]	78	68	174
450	1	988	62	gi|1030068	NAD(P)H oxidoreductase, isoflavone reductase homologue [Solanum tuberosum]	78	63	927
558	1	562	362	gi|1511588	bifunctional protein [Methanococcus jannaschii]	78	60	201
670	3	1152	1589	gi|1122759	unknown [Bacillus subtilis]	78	64	438
714	1	64	732	gi|143460	37 kd minor sigma factor (rpoF, sigB; ttg start codon) [Bacillus subtilis]	78	57	669
814	1	3	368	gi|1377833	unknown [Bacillus subtilis]	78	59	366
981	1	692	3	gi|143802	GerC2 [Bacillus subtilis]	78	64	690
995	2	727	476	gi|296947	uridine kinase [Escherichia coli]	78	64	252
1045	1	3	401	gi|1407784	orf-1; novel antigen [Staphylococcus aureus]	78	61	399
1163	2	186	4	gi|410117	diaminopimelate decarboxylase [Bacillus subtilis]	78	54	183
2191	1	399	4	gi|215098	excisionase [Bacteriophage 154a]	78	65	396
2933	1	2	181	gi|1204436	pyruvate formate-lyase [Haemophilus influenzae]	78	73	180
3041	2	129	317	gi|624632	GltL [Escherichia coli]	78	53	189
3581	1	105	401	gi|763186	3-ketoacyl-coA thiolase [Saccharomyces cerevisiae]	78	55	297
3709	1	3	230	gi|460689	TVG [Thermoactinomyces vulgaris]	78	58	228
3974	1	265	2	gi|558839	unknown [Bacillus subtilis]	78	65	264
3980	1	3	401	gi|39956	IIGlc [Bacillus subtilis]	78	62	399
4056	1	354	61	gi|1256635	dihydroxy-acid dehydratase [Bacillus subtilis]	78	55	294
4114	1	316	2	pir|S09372|S093	hypothetical protein - Trypanosoma brucei	78	62	315
4185	1	3	179	gi|1339950	large subunit of NADH-dependent glutamate synthase [Plectonema boryanum]	78	58	177
4235	1	329	3	gi|558839	unknown [Bacillus subtilis]	78	60	327
4352	1	302	63	gi|603768	HutI protein, imidazolone-5-propionate hydrolase [Bacillus subtilis]	78	63	240
					gi|603768 HutI protein, imidazolone-5-propionate hydrolase Bacillus
					subtilis]
4368	1	307	2	gi|1353678	heavy-metal transporting P-type ATPase [Proteus mirabilis]	78	59	306
4461	1	216	4	gi|1276841	glutamate synthase (GOGAT) [Porphyra purpurea]	78	36	213
4530	1	238	2	gi|39956	IIGlc [Bacillus subtilis]	78	65	237
3	2	2073	1177	gi|1109684	ProV [Bacillus subtilis]	77	56	897
12	2	1965	1504	gi|467335	ribosomal protein L9 [Bacillus subtilis]	77	59	462
27	1	2	388	gi|1212728	YqhI [Bacillus subtilis]	77	63	387
39	2	590	1252	gi|40054	phenylalanyl-tRNA synthetase beta subunit (AA 1-804) [Bacillus subtilis]	77	60	663
42	6	2704	2931	gi|606241	30S ribosomal subunit protein S14 [Escherichia coli] sp|P02370|RS14_ECOLI	77	65	228
					30S RIBOSOMAL PROTEIN S14. (SUB 2-101)
46	18	15459	16622	gi|297798	mitochondrial formate dehydrogenase precursor [Solanum tuberosum]	77	55	1164
					pir|JQ2272|JQ2272 formate dehydrogenase (EC 1.2.1.2) precursor,
					itochondrial - potato
100	4	4002	3442	gi|1340128	ORF1 [Staphylococcus aureus]	77	54	561
102	8	5378	5713	gi|1311482	acetolactate synthase [Thermus aquaticus]	77	57	336
109	7	4742	5383	gi|710637	Unknown [Bacillus subtilis]	77	56	642
117	1	2	1228	gi|1237015	ORF4 [Bacillus subtilis]	77	53	1227
124	10	7688	7053	gi|405819	thymidine kinase [Bacillus subtilis]	77	63	636
147	3	985	824	gi|849027	hypothetical 15.9-kDa protein [Bacillus subtilis]	77	37	162
152	10	7354	7953	gi|1205583	spermidine/putrescine transport ATP-binding protein [Haemophilus	77	55	600
					influenzae ]
169	2	1004	1282	gi|473825	‘elongation factor EF-Ts’ [Escherichia coli]	77	58	279
184	2	380	1147	gi|216314	esterase [Bacillus stearothermophilus]	77	60	768
189	7	3296	3868	gi|853809	ORF3 [Clostridium perfringens]	77	48	573
193	1	132	290	gi|1303788	YqeH [Bacillus subtilis]	77	54	159
195	8	8414	8088	gi|1499620	M. jannaschii predicted coding region MJ0798 [Methanococcus jannaschii]	77	44	327
205	8	5204	4980	gi|216340	ORF for adenylate kinase [Bacillus subtilis]	77	61	225
205	29	14502	14209	gi|786155	Ribosomal Protein L23 [Bacillus subtilis]	77	62	294
211	5	1908	2084	gi|410132	ORFX8 [Bacillus subtilis]	77	47	177
217	5	3478	4416	gi|496254	fibronectin/fibrinogen-binding protein [Streptococcus pyogenes]	77	54	939
232	1	267	998	gi|1407784	orf-1; novel antigen [Staphylococcus aureus]	77	57	732
233	2	1346	873	gi|467408	unknown [Bacillus subtilis]	77	61	474
243	3	2299	1937	gi|516155	unconventional myosin [Sus scrofa]	77	32	363
299	1	68	769	gi|467436	unknown [Bacillus subtilis]	77	54	702
301	4	1283	1098	gi|950071	ATP-bind. pyrimidine kinase [Mycoplasma capricolum] pir|S48605|S48605	77	48	186
					hypothetical protein - Mycoplasma capricolum SGC3) (fragment)
302	5	2741	3211	gi|508980	pheB [Bacillus subtilis]	77	57	471
302	7	3835	4863	gi|147783	ruvB protein [Escherichia coli]	77	60	1029
307	9	4797	4192	gi|1070015	protein-dependent [Bacillus subtilis]	77	60	606
312	1	99	1391	gi|143165	malic enzyme (EC 1.1.1.38) [Bacillus stearothermophilus] pir|A33307|DEBSXS	77	62	1293
					malate dehydrogenase oxaloacetate-decarboxylating) (EC 1.1.1.38) -
					Bacillus tearothermophilus
312	2	1541	2443	gi|1399855	carboxyltransferase beta subunit [Synechococcus PCC7942]	77	58	903
321	5	4596	3526	gi|39844	fumarase (citG) (aa 1-462) [Bacillus subtilis]	77	65	1071
354	1	47	568	gi|1154634	YmaB [Bacillus subtilis]	77	57	522
365	1	2	1021	gi|143374	phosphoribosyl glycinamide synthetase (PUR-D; gtg start codon) Bacillus	77	62	1020
					subtilis ]
374	1	1	708	gi|1405446	transketolase [Bacillus subtilis]	77	61	708
385	1	565	2	gi|533099	endonuclease III [Bacillus subtilis]	77	63	564
392	2	594	1940	gi|556014	UDP-N-acetyl muramate-alanine ligase [Bacillus subtilis]	77	65	1347
					sp|P40778|MURC_BACSU UDP-N-ACETYLMURAMATE-ALANINE LIGASE (EC .3.2.8)
					(UDP-N-ACETYLMURANOYL-L-ALANINE SYNTHETASE) (FRAGMENT).
405	5	3570	3061	gi|1303912	YqhW [Bacillus subtilis]	77	64	510
487	4	1302	1472	gi|432427	ORF1 gene product (Acinetobacter calcoaceticus)	77	48	171
522	1	2	562	pir|A01179|SYBS	tyrosine-tRNA ligase (EC 6.1.1.1) - Bacillus stearothermophilus	77	63	561
523	2	1351	1115	gi|1387979	44% identity over 302 residues with hypothetical protein from Synechocystis	77	48	237
					sp, accession D64006_CD; expression induced by environmental stress; some
					similarity to glycosyl transferases; two potential membrane-spanning
					helices [Bacillus subtil
536	2	612	241	gi|143366	adenylosuccinate lyase (PUR-B) [Bacillus subtilis] pir|C29326|WZBSDS	77	61	372
					adenylosuccinate lyase (EC 4.3.2.2) - Bacillus subtilis
548	2	339	872	gi|143387	aspartate transcarbamylase [Bacillus subtilis]	77	56	534
597	1	2	481	gi|904198	hypothetical protein [Bacillus subtilis]	77	33	480
633	2	1313	879	gi|387577	ORF1A [Bacillus subtilis]	77	64	435
642	1	85	360	gi|46971	epiP gene product [Staphylococcus epidermidis]	77	61	276
659	1	125	1219	gi|1072381	glutamyl-aminopeptidase [Lactococcus lactis]	77	62	1095
670	4	1587	1820	gi|1122760	unknown [Bacillus subtilis]	77	58	234
789	1	2	391	gi|1377823	aminopeptidase [Bacillus subtilis]	77	65	390
815	1	10	573	gi|1303861	YqgN [Bacillus subtilis]	77	49	564
899	1	1	225	gi|1204844	H. influenzae predicted coding region HI0594 [Haemophilus influenzae]	77	55	225
1083	1	3	188	gi|460828	B969 [Saccharomyces cerevisiae]	77	66	186
1942	1	209	3	gi|160047	p101/acidic basic repeat antigen [Plasmodium falciparum] pir|A29232|A29232	77	38	207
					101 K malaria antigen precursor - Plasmodium alciparum (strain Camp)
2559	1	1	171	gi|1499034	M. jannaschii predicted coding region MJ0255 [Methanococcus jannaschii]	77	61	171
2933	2	243	401	gi|42370	pyruvate formate-lyase (AA 1-760) [Escherichia coli] ir|S01788|S01788	77	72	159
					formate C-acetyltransferase (EC 2.3.1.54) - Echerichia coli
2966	1	56	292	gi|1524397	glycine betaine transporter OpuD [Bacillus subtilis]	77	45	237
2976	1	309	4	gi|40003	oxoglutarate dehydrogenase (NADP+) [Bacillus subtilis] p|P23129|ODO1_BACSU	77	60	306
					2-OXOGLUTARATE DEHYDROGENASE E1 COMPONENT (EC 2.4.2) (ALPHA-KETOGLUTARATE
					DEHYDROGENASE).
2979	2	400	122	gi|1204354	spore germination and vegetative growth protein [Haemophilus influenzae]	77	61	279
2988	1	377	153	gi|438465	Probable operon with orfF. Possible alternative initiation codon, ases	77	55	225
					2151-2153. Homology with acetyltransferases.; putative Bacillus subtilis]
2990	1	167	3	gi|142562	ATP synthase epsilon subunit [Bacillus megaterium] pir|B28599|PWBSEM H+−	77	63	165
					transporting ATP synthase (EC 3.6.1.34) psilon chain - Bacillus megaterium
3032	1	3	389	gi|488430	alcohol dehydrogenase 2 [Entamoeba histolytica]	77	56	387
3057	1	1	195	gi|468764	mocR gene product (Rhizobium meliloti)	77	50	195
4008	1	400	74	gi|603768	HutI protein, imidazolone-5-propionate hydrolase [Bacillus subtilis]	77	52	327
					gi|603768 HutI protein, imidazolone-5-propionate hydrolase Bacillus
					subtilis ]
4048	1	386	69	gi|216278	gramicidin S synthetase 1 [Bacillus brevis]	77	55	318
4110	1	3	368	pir|S52915|S529	nitrate reductase alpha chain - Bacillus subtilis (fragment)	77	61	366
4115	1	1	348	gi|517205	67 kDa Myosin-crossreactive streptococcal antigen [Streptococcus yogenes]	77	65	348
4225	1	297	4	gi|1322245	mevalonate pyrophosphate decarboxylase [Rattus norvegicus]	77	60	294
4611	2	327	160	gi|508979	GTP-binding protein [Bacillus subtilis]	77	57	168
4668	1	182	3	pir|S52915|S529	nitrate reductase alpha chain - Bacillus subtilis (fragment)	77	61	180
25	1	2	1627	gi|1150620	MmsA [Streptococcus pneumoniae]	76	58	1626
38	5	1488	2537	pir|A43577|A435	regulatory protein pfoR - Clostridium perfringens	76	57	1050
52	5	2962	4041	gi|1161061	dioxygenase [Methylobacterium extorquens]	76	62	1080
56	20	27389	27955	gi|467402	unknown [Bacillus subtilis]	76	56	567
57	15	12046	12219	gi|1206040	weak similarity to keratin [Caenorhabditis elegans]	76	40	174
91	2	1062	2261	gi|475715	acetyl coenzyme A acetyltransferase (thiolase) [Clostridium cetobutylicum]	76	57	1200
98	2	818	1624	gi|467422	unknown [Bacillus subtilis]	76	62	807
98	5	2965	3228	gi|897793	y98 gene product [Pediococcus acidilactici]	76	52	264
98	8	5922	6326	gi|467427	methionyl-tRNA synthetase [Bacillus subtilis]	76	53	405
104	3	1322	1885	gi|216151	DNA polymerase (gene L; ttg start codon) [Bacteriophage SPO2] gi|579197	76	63	564
					SPO2 DNA polymerase (aa 1-648) [Bacteriophage SPO2) pir|A21498|DJBPS2 DNA-
					directed DNA polymerase (EC 2.7.7.7) - phage PO2
124	9	7055	5976	gi|853776	peptide chain release factor 1 [Bacillus subtilis] pir|S55437|S55437	76	58	1080
					peptide chain release factor 1 - Bacillus subtilis
164	5	2832	3311	gi|1204976	prolyl-tRNA synthetase [Haemophilus influenzae]	76	53	480
168	2	1841	1065	gi|1177253	putative ATP-binding protein of ABC-type [Bacillus subtilis]	76	58	777
189	2	163	888	gi|467384	unknown [Bacillus subtilis]	76	63	726
235	3	2253	3518	gi|142936	folyl-polyglutamate synthetase [Bacillus subtilis] pir|B40646|B40646 folC -	76	53	1266
					Bacillus subtilis
236	1	335	925	gi|1146197	putative [Bacillus subtilis]	76	54	591
237	8	5323	5541	gi|1279261	F13G3.6 [Caenorhabditis elegans]	76	47	219
263	5	4585	3680	gi|1510348	dihydrodipicolinate synthase [Methanococcus jannaschii]	76	49	906
304	3	1051	1794	gi|666982	putative membrane spanning subunit [Bacillus subtilis]pir|S52382|S52382	76	60	744
					probable membrane spanning protein - Bacillus subtilis
312	4	3611	4624	gi|143312	6-phospho-1-fructokinase (gtg start codon; EC 2.7.1.11) [Bacillus	76	56	1014
					tearothermophilus)
343	1	2	1036	gi|405956	yeeE [Escherichia coli]	76	59	1035
347	1	409	1701	gi|396304	acetylornithine deacetylase [Escherichia coli]	76	72	1293
358	1	672	1907	gi|1146215	39.0% identity to the Escherichia coli S1 ribosomal protein; putative	76	58	1236
					[Bacillus subtilis]
371	1	1	222	gi|537084	alternate gene name mgt; CG Site No. 497 [Escherichia coli]	76	61	222
					pir|S56468|S56468 mgtA protein - Escherichia coli
379	4	4331	4858	gi|143268	dihydrolipoamide transsuccinylase (odhB; EC 2.3.1.61) [Bacillus subtilis]	76	61	528
404	5	4022	4492	gi|1303823	YqfG [Bacillus subtilis]	76	60	471
411	1	2	307	gi|486025	ORF YKL027w [Saccharomyces cerevisiae]	76	55	306
472	3	2854	1352	gi|1405464	AlsT [Bacillus subtilis]	76	57	1503
546	1	273	995	gi|153821	streptococcal pyrogenic exotoxin type C (speC) precursor Streptococcus	76	36	723
					pyogenes]
588	1	557	60	gi|1002520	MutS [Bacillus subtilis]	76	61	498
591	1	16	735	gi|885934	ClpB [Synechococcus sp.]	76	44	720
602	2	175	798	gi|1486422	OppD homologue [Rhizobium sp.]	76	52	624
619	2	290	33	gi|330613	major capsid protein [Human cytomegalovirus]	76	47	258
660	4	2568	3302	gi|904199	hypothetical protein [Bacillus subtilis]	76	55	735
677	1	228	4	gi|40177	spoOF gene product [Bacillus subtilis]	76	58	225
962	1	24	206	gi|142443	adenylosuccinate synthetase [Bacillus subtilis]sp|P29726|PURA_BACSU	76	67	183
					ADENYLOSUCCINATE SYNTHETASE (EC 6.3.4.4) IMP —ASPARTATE LIGASE).
978	1	580	2	gi|1511333	M. jannaschii predicted coding region MJ1322 [Methanococcus jannaschii]	76	56	579
997	1	244	2	gi|467154	No definition line found [Mycobacterium leprae]	76	38	243
1563	1	266	3	gi|1303984	YqkG [Bacillus subtilis]	76	52	264
2184	1	182	3	gi|506706	CapJ [Staphylococcus aureus]	76	38	180
2572	1	1	387	gi|153898	transport protein [Salmonella typhimurium]	76	65	387
2942	1	29	400	gi|710020	nitrite reductase (nirB) [Bacillus subtilis]	76	59	372
2957	1	216	55	gi|1511251	hypothetical protein (SP: P42404) [Methanococcus janneschii]	76	47	162
2980	1	279	4	gi|1405464	AlsT [Bacillus subtilis]	76	53	276
3015	1	326	3	gi|408115	ornithine acetyltransferase [Bacillus subtilis]	76	61	324
3124	1	13	174	gi|882705	ORF_o401 (Escherichia coli)	76	65	162
3179	1	3	161	gi|168477	ferredoxin-dependent glutamate synthase [Zea mays]pir|A38596|A38596	76	53	159
					glutamate synthase (ferredoxin) (EC 1.4.7.1)- maize
3789	1	2	379	gi|39956	IIGlc [Bacillus subtilis)	76	55	378
3892	1	3	314	gi|1510398	ferripyochelin binding protein [Methanococcus jannaschii]	76	52	312
3928	1	400	2	gi|143016	permease [Bacillus subtilis]	76	59	399
4159	1	386	15	sp|P80544|MRSP—	METHICILLIN-RESISTANT SURFACE PROTEIN (FRAGMENTS)	76	66	372
4204	1	17	331	gi|29646	ATPase [Lactococcus lactis]	76	56	315
4398	1	249	4	gi|987255	Menkes disease gene [Homo sapiens]	76	48	246
4506	1	2	313	gi|216746	(D-lactate dehydrogenase [Lactobacillus plantarum]	76	47	312
4546	1	247	17	gi|1339950	large subunit of NADH-dependent glutamate synthase [Plectonema boryanum]	76	61	231
4596	1	191	3	gi|560027	cellulose synthase [Acetobacter xylinum]	76	70	189
4	5	4337	3417	gi|882532	ORF_o294 [Escherichia coli]	75	59	921
6	1	164	952	gi|40960	OTCase [Escherichia coli]	75	56	789
12	3	3944	1953	gi|467336	unknown [Bacillus subtilis]	75	57	1992
23	18	17310	16348	gi|1296433	0-acetylserine sulfhydrylase B [Alcaligenes eutrophus]	75	55	963
25	3	2356	3393	gi|1502419	PlsX [Bacillus subtilis]	75	56	1038
36	8	5765	6037	gi|1256517	unknown [Schizosaccharomyces pombe]	75	45	273
46	13	11186	12058	gi|48972	nitrate transporter [Synechococcus sp.]	75	46	873
51	7	3474	3677	gi|143607	sporulation protein [Bacillus subtilis]	75	61	204
53	16	16590	16330	gi|143402	(recombination protein (ttg start codon) [Bacillus subtilis] gi|1303923 RecN	75	51	261
					[Bacillus subtilis]
74	3	2568	1564	gi|1204847	ornithine carbamoyltransferase [Haemophilus influenzae]	75	61	1005
85	3	3930	3232	gi|143368	phosphoribosylformyl glycinamidine synthetase I (PUR-L; gtg start odon)	75	63	699
					[Bacillus subtilis]
85	5	4878	4168	gi|143367	phosphoribosyl aminoidazole succinocarboxamide synthetase (PUR-C; tg start	75	55	711
					codon) [Bacillus subtilis]
85	8	6625	7530	gi|1303916	YqiA [Bacillus subtilis]	75	53	906
87	3	2340	3590	gi|1064813	homologous to sp: PHOR_BACSU [Bacillus subtilis]	75	56	1251
87	6	6084	6896	gi|1064810	function unknown [Bacillus subtilis]	75	61	813
108	2	1503	1162	gi|1001824	hypothetical protein [Synechocystis sp.]	75	51	342
110	3	1748	3727	gi|1147593	putative ppGpp synthetase [Streptomyces coelicolor]	75	55	1980
110	7	4353	5252	gi|1177251	clwD gene product [Bacillus subtilis]	75	75	900
120	14	10649	10032	gi|1524394	ORF-2 upstream of gbsAB operon [Bacillus subtilis]	75	55	618
121	5	2050	4221	gi|1154632	NrdE [Bacillus subtilis]	75	54	2172
124	1	143	3	gi|405622	unknown [Bacillus subtilis]	75	56	141
128	1	81	1139	gi|143316	(gap) gene products [Bacillus megaterium]	75	48	1059
130	8	5760	5903	gi|1256654	54.8% identity with Neisseria gonorrhoeae regulatory protein PilB; putative	75	62	144
					[Bacillus subtilis]
136	2	3185	1890	gi|467403	seryl-tRNA synthetase [Bacillus subtilis]	75	54	1296
161	10	5439	5798	gi|1001195	hypothetical protein [Synechocystis sp.]	75	55	360
172	4	2995	2171	gi|755153	ATP-binding protein [Bacillus subtilis]	75	52	825
179	1	1107	190	gi|143037	porphobilinogen deaminase [Bacillus subtilis]	75	58	918
195	10	9374	9219	sp|P25745|YCFB—	HYPOTHETICAL PROTEIN IN PURB 5′ REGION (ORF-15) (FRAGMENT)	75	60	156
200	4	2605	4596	gi|142440	ATP-dependent nuclease [Bacillus subtilis]	75	56	1992
206	3	5620	4340	gi|1256135	YbbF [Bacillus subtilis]	75	53	1281
216	2	159	389	gi|1052800	unknown [Schizosaccharomyces pombe]	75	58	231
229	1	29	847	gi|1205958	branched chain aa transport system II carrier protein [Haemophilus	75	49	819
					influenzae ]
230	2	518	1714	gi|971337	nitrite extrusion protein [Bacillus subtilis]	75	53	1197
231	1	1122	4	gi|1002521	MutL [Bacillus subtilis]	75	54	1119
233	3	1314	1859	gi|467405	unknown [Bacillus subtilis]	75	59	546
269	1	164	3	gi|1511246	methyl coenzyme M reductase system, component A2 [Methanococcus jannaschii]	75	50	162
292	1	772	155	gi|1511604	M. jannaschii predicted coding region MJ1651 [Methanococcus jannaschii]	75	46	618
304	4	1773	2261	gi|1205328	surfactin [Haemophilus influenzae]	75	55	489
312	3	2437	3387	gi|285621	undefined open reading frame [Bacillus stearothermophilus]	75	62	951
312	5	4622	6403	gi|1041097	Pyruvate Kinase [Bacillus psychrophilus]	75	57	1782
319	1	353	877	gi|1212728	YqhI [Bacillus subtilis]	75	54	525
320	5	4321	5031	gi|1070361	OMP decarboxylase [Lactococcus lactis]	75	56	711
320	6	5010	5642	gi|143394	OMP-PRPP transferase [Bacillus subtilis]	75	60	633
337	4	1519	2088	gi|487433	citrate synthase II [Bacillus subtilis]	75	58	570
394	2	669	1271	gi|304976	matches PS00017: ATP_GTP_A and PS00301: EFACTOR_GTP; similar to longation	75	51	603
					factor G, TetM/TetO tetracycline-resistance proteins Escherichia coli]
423	1	127	570	gi|1183839	unknown [Pseudomonas aeruginosa]	75	59	444
433	2	1603	1929	gi|149211	acetolactate synthase [Klebsiella pneumoniae]	75	63	327
446	2	176	1540	gi|312441	dihydroorotase [Bacillus caldolyticus]	75	62	1365
486	1	249	4	gi|1149682	potF gene product [Clostridium perfringens]	75	55	246
496	1	3	794	gi|143582	spoIIIEA protein [Bacillus subtilis]	75	59	792
498	2	824	1504	gi|143328	phoP protein (put.); putative [Bacillus subtilis]	75	47	681
499	2	1061	1624	gi|1387979	44% identity over 302 residues with hypothetical protein from Synechocystis	75	51	564
					sp, accession D64006_CD; expression induced by environmental stress; some
					similarity to glycosyl transferases; two potential membrane-spanning
					helices [Bacillus subtil
568	1	453	265	pir|JC4110|JC41	triacylglycerol lipase (EC 3.1.1.3) 2 - Mycoplasma mycoides subsp. mycoides	75	50	189
					(SGC3)
613	2	233	36	gi|330993	tegument protein [Saimiriine herpesvirus 2]	75	75	198
621	1	1	525	gi|529754	speC [Streptococcus pyogenes]	75	43	525
642	5	1809	2474	gi|1176401	EpiG [Staphylococcus epidermidis]	75	51	666
646	2	454	657	gi|172442	ribonuclease P [Saccharomyces cerevisiae]	75	37	204
657	1	3	347	gi|882541	ORF_o236 [Escherichia coli]	75	47	345
750	1	832	2	gi|46971	epiP gene product [Staphylococcus epidermidis]	75	57	831
754	1	2	481	gi|1303901	YqhT [Bacillus subtilis]	75	57	480
763	2	393	223	gi|1205145	multidrug resistance protein [Haemophilus influenzae]	75	51	171
775	1	482	3	pir|B36889|B368	leuA protein, inactive - Lactococcus lactis subsp. lactis (strain IL1403)	75	63	480
793	1	1	180	gi|143316	[gap] gene products [Bacillus megaterium]	75	57	180
800	1	160	2	gi|509411	NFRA protein [Azorhizobium caulinodans]	75	34	159
811	1	560	3	gi|143434	Rho Factor [Bacillus subtilis]	75	60	558
940	1	329	165	gi|1276985	arginase [Bacillus caldovelox]	75	50	165
971	2	37	252	gi|1001373	hypothetical protein [Synechocystis sp.]	75	58	216
1059	1	232	80	gi|726480	L-glutamine-D-fructose-6-phosphate amidotransferase [Bacillus subtilis]	75	67	153
1109	2	219	374	gi|143331	alkaline phosphatase regulatory protein [Bacillus subtilis]	75	53	156
					pir|A27650|A27650 regulatory protein phoR - Bacillus subtilis
					sp|P23545|PHOR_BACSU ALKALINE PHOSPHATASE SYNTHESIS SENSOR PROTEIN HOR (EC
					2.7.3.—).
1268	1	137	3	gi|304135	ornithine acetyltransferase [Bacillus stearothermophilus]	75	63	135
					sp|Q07908|ARGJ_BACST GLUTAMATE N-ACETYLTRANSFERASE (EC 2.3.1.35) ORNITHINE
					ACETYLTRANSFERASE) (ORNITHINE TRANSACETYLASE) (OATASE)/MINO-ACID
					ACETYLTRANSFERASE (EC 2.3.1.1) (N-ACETYLGLUTAMATE YNTHA
1500	1	163	2	gi|1205488	excinuclease ABC subunit B [Haemophilus influenzae]	75	57	162
1529	1	400	2	gi|1002521	MutL [Bacillus subtilis]	75	54	399
3010	1	387	4	gi|1204435	pyruvate formate-lyase activating enzyme [Haemophilus influenzae]	75	54	384
3105	1	1	180	gi|1041097	Pyruvate Kinase [Bacillus psychrophilus]	75	57	180
3117	1	45	212	gi|899317	peptide synthetase module [Microcystis aeruginosa]pir|S49111|S49111	75	42	168
					probable amino acid activating domain - Microcystis aeruginosa (fragment)
					(SUB 144-528)
3139	2	139	345	gi|145294	adenine phosphoribosyl-transferase [Escherichia coli]	75	66	207
3880	1	310	2	gi|1009366	Respiratory nitrate reductase [Bacillus subtilis]	75	58	309
3911	1	48	401	gi|433991	ATP synthase subunit beta [Bacillus subtilis]	75	68	354
3957	1	2	379	pir|D36889|D368	3-isopropylmalate dehydratase (EC 4.2.1.33) chain leuC - Lactococcus lactis	75	65	378
					subsp. lactis (strain IL1403)
4005	1	5	259	gi|216746	D-lactate dehydrogenase [Lactobacillus plantarum]	75	48	255
4080	1	73	333	gi|415855	deoxyribose aldolase [Mycoplasma hominis]	75	59	261
4111	1	1	339	gi|149435	putative [Lactococcus lactis]	75	57	339
4136	1	303	4	gi|450688	hsdM gene of EcoprrI gene product [Escherichia coli] pir|S38437|S38437 hsdM	75	56	300
					protein - Escherichia coli pir|S09629|S09629 hypothetical protein A -
					Escherichia coli (SUB 40-520)
4144	1	336	4	gi|48972	nitrate transporter [Synechococcus sp.]	75	49	333
4237	1	374	84	gi|1339950	large subunit of NADH-dependent glutamate synthase [Plectonema boryanum]	75	55	291
4306	2	73	318	gi|294260	major surface glycoprotein [Pneumocystis carinii]	75	68	246
4343	1	359	3	gi|1204652	methylated-DNA-protein-cysteine methyltransferase [Haemophilus influenzae]	75	52	357
4552	1	312	4	gi|296464	ATPase [Lactococcus lactis]	75	55	309
38	9	5776	6126	gi|443793	NupC [Escherichia coli]	74	50	351
50	8	6221	5532	gi|1239988	hypothetical protein [Bacillus subtilis]	74	55	690
56	9	10770	12221	gi|1000451	TreP [Bacillus subtilis]	74	57	1452
64	2	1622	978	gi|41015	aspartate-tRNA ligase [Escherichia coli]	74	57	645
66	6	4848	4633	gi|1212729	YqhJ [Bacillus subtilis]	74	47	216
67	18	14334	14897	gi|1510631	endoglucanase [Methanococcus jannaschii]	74	52	564
102	15	12561	13136	gi|149429	putative [Lactococcus lactis]	74	67	576
102	16	13121	14419	gi|149435	putative [Lactococcus lactis]	74	57	1299
108	4	3902	2931	gi|39478	ATP binding protein of transport ATPases [Bacillus firmus] ir|S15486|S15486	74	59	972
					ATP-binding protein - Bacillus firmus p|P26946|YATR_BACFI HYPOTHETICAL
					ATP-BINDING TRANSPORT PROTEIN.
116	5	7093	5612	gi|1205430	dipeptide transport system permease protein [Haemophilus influenzae	74	49	1482
120	7	4342	4803	gi|146970	ribonucleoside triphosphate reductase [Escherichia coli] pir|A47331|A47331	74	58	462
					anaerobic ribonucleotide reductase - Escherichia coli
121	7	5961	6581	gi|1107528	ttg start [Campylobacter coli]	74	51	621
128	3	2320	3531	gi|143318	phosphoglycerate kinase [Bacillus megaterium]	74	57	1212
130	7	5237	5791	gi|1256653	DNA-binding protein [Bacillus subtilis]	74	60	555
136	3	5150	3555	gi|143076	histidase [Bacillus subtilis]	74	58	1596
145	2	664	1368	gi|407773	devA gene product [Anabaena sp.]	74	45	705
152	1	277	2	gi|1377833	unknown [Bacillus subtilis]	74	54	276
164	10	11064	11375	gi|580900	ORF3 gene product [Bacillus subtilis]	74	52	312
175	2	2624	2139	gi|642656	unknown [Rhizobium meliloti]	74	34	486
175	9	5612	5160	gi|854656	Na/H antiporter system ORF2 [Bacillus alcalophilus]	74	46	453
195	11	10339	9332	gi|1204430	hypothetical protein (SP: P25745) [Haemophilus influenzae]	74	55	1008
205	17	9059	8499	gi|1044979	ribosomal protein L6 [Bacillus subtilis]	74	64	561
236	7	5574	6710	gi|1146207	putative [Bacillus subtilis]	74	63	1137
241	3	3334	2147	gi|694121	malate thiokinase [Methylobacterium extorquens]	74	52	1188
246	6	2799	2293	gi|467374	single strand DNA binding protein [Bacillus subtilis]	74	64	507
249	4	5313	4075	gi|1524397	glycine betaine transporter OpuD [Bacillus subtilis]	74	55	1239
261	7	4081	3773	gi|809542	CbrB protein [Erwinia chrysanthemi]	74	42	309
278	6	4665	3616	gi|1204872	ATP-binding protein [Haemophilus influenzae]	74	54	1050
309	1	666	112	gi|1205579	hypothetical protein (GB: U14003_302) [Haemophilus influenzae]	74	53	555
315	2	862	251	gi|143398	quinol oxidase [Bacillus subtilis]	74	57	612
320	1	1	1065	gi|143389	glutaminase of carbamyl phosphate synthetase [Bacillus subtilis]	74	60	1065
					pir|E39845|E39845 carbamoyl-phosphate synthase glutamine-hydrolyzing) (EC
					6.3.5.5), pyrimidine-repressible, small hain - Bacillus subtilis
380	2	382	1128	gi|534857	ATPase subunit a [Bacillus stearothermophilus]	74	56	747
405	2	1311	880	gi|1303915	YqhZ [Bacillus subtilis]	74	65	432
433	5	2503	3270	gi|473902	alpha-acetolactate synthase [Lactococcus lactis]	74	56	768
452	1	1	942	gi|413982	ipa-58r gene product [Bacillus subtilis]	74	52	942
461	1	3	1193	gi|558494	homoserine dehydrogenase [Bacillus subtilis]	74	51	1191
461	2	1174	1407	gi|40211	threonine synthase (thrC) (AA 1-352) [Bacillus subtilis] ir|A25364|A25364	74	56	234
					threonine synthase (EC 4.2.99.2) - Bacillus subtilis
462	2	402	734	gi|142520	thioredoxin [Bacillus subtilis]	74	62	333
478	1	320	66	gi|1499005	glycyl-tRNA synthetase [Methanococcus jannaschii]	74	52	255
501	2	739	1740	gi|217040	acid glycoprotein [Streptococcus pyogenes]	74	58	1002
551	2	2791	1499	gi|143040	glutamate-1-semialdehyde 2,1-aminotransferase [Bacillus subtilis]	74	51	1293
					pir|D42728|D42728 glutamate-1-semialdehyde 2,1-aminomutase (EC .4.3.8) -
					Bacillus subtilis
573	1	1	477	gi|1006605	hypothetical protein [Synechocystis sp.]	74	45	477
596	2	1298	816	gi|1303853	YqgF [Bacillus subtilis]	74	55	483
618	2	1758	592	gi|1146237	21.4% of identity to trans-acting transcription factor of Sacharomyces	74	55	1167
					cerevisiae; 25% of identity to sucrose synthase of Zee mays; putative
					[Bacillus subtilis]
659	2	1269	1595	gi|1072380	ORF3 [Lactococcus lactis]	74	62	327
724	1	188	3	gi|143374	phosphoribosyl glycinamide synthetase (PUR-D; gtg start codon) Bacillus	74	58	186
					subtilis ]
743	2	604	1209	gi|153833	ORF1; putative [Streptococcus parasanguis]	74	50	606
836	1	2	259	gi|143458	ORF V [Bacillus subtilis]	74	47	258
989	2	443	724	gi|1303994	YqkM [Bacillus subtilis]	74	46	282
1106	1	1	492	gi|46970	epiD gene product [Staphylococcus epidermidis]	74	54	492
1135	2	373	528	gi|413948	ipa-24d gene product [Bacillus subtilis]	74	48	156
1234	1	452	87	gi|495245	recJ gene product [Erwinia chrysanthemi]	74	36	366
2586	1	2	238	gi|1149701	sbcC gene product [Clostridium perfringens]	74	62	237
2959	1	400	2	gi|1405454	aconitase [Bacillus subtilis]	74	60	399
2962	1	363	76	gi|450686	3-phosphoglycerate kinase [Thermotoga maritima]	74	58	288
2983	1	3	191	gi|1303893	YqhL [Bacillus subtilis]	74	56	189
3018	1	2	223	gi|143040	glutamate-1-semialdehyde 2,1-aminotransferase [Bacillus subtilis]	74	56	222
					pir|D42728|D42728 glutamate-1-semialdehyde 2,1-aminomutase (EC .4.3.8) -
					Bacillus' subtilis
3038	1	256	2	pir|S52915|S529	nitrate reductase alpha chain - Bacillus subtilis (fragment)	74	57	255
3062	1	189	4	gi|1107528	ttg start [Campylobacter coli]	74	51	186
4035	1	184	360	gi|1022725	unknown [Staphylococcus haemolyticus]	74	64	177
4045	1	305	3	gi|1510977	M. jannaachii predicted coding region MJ0938 [Methanococcus jannaschii]	74	41	303
4283	1	304	137	gi|520844	orf4 [Bacillus subtilis]	74	58	168
4449	1	3	221	gi|580910	peptide-synthetase ORF1 [Bacillus subtilis]	74	54	219
4587	1	231	4	gi|1370207	orf6 [Lactobacillus sake]	74	59	228
4603	1	29	214	gi|146208	glutamate synthase large subunit (EC 2.6.1.53) [Escherichia coli]	74	60	186
					pir|A29617|A29617 glutamate synthase (NADPH) (EC 1.4.1.13) large hain-
					Escherichia coli
4670	1	184	2	gi|1256135	YbbF [Bacillus subtilis]	74	61	183
5	10	7162	6371	gi|143727	putative [Bacillus subtilis]	73	42	792
11	2	1372	290	gi|166338	dihydroorotate dehydrogenase [Agrocybe aegerita]	73	55	1083
14	1	1020	16	gi|143373	phosphoribosyl aminoimidazole carboxy formyl ormyltransferase/inosine	73	54	1005
					monophosphate cyclohydrolase (PUR-H(J)) Bacillus subtilis]
23	5	4635	3844	gi|1468939	meso-2,3-butanediol dehydrogenase (D-acetoin forming) [Klebsiella	73	58	792
					pneumoniae]
23	17	16360	15341	gi|297060	ornithine cyclodeaminase [Rhizobium meliloti]	73	37	1020
29	2	692	1273	gi|467442	stage V sporulation [Bacillus subtilis]	73	54	582
31	5	4914	3361	gi|414000	ipa-76d gene product [Bacillus subtilis]	73	55	1554
37	8	7402	6146	gi|1429259	pepT gene product [Bacillus subtilis]	73	59	1257
37	9	7562	7386	gi|168367	alpha-isopropylmalate isomerase (put.); putative [Rhizomucor ircinelloides]	73	52	177
38	7	3931	4896	gi|405885	yeiN [Escherichia coli]	73	58	966
44	6	4238	3435	gi|580895	unknown [Bacillus subtilis]	73	53	804
44	11	7767	8306	gi|42009	moaB gene product [Eacherichia coli]	73	50	540
45	3	2439	3080	gi|1109685	ProW [Bacillus subtilis]	73	47	642
54	13	13794	13552	gi|413931	ipa-7d gene product [Bacillus subtilis]	73	61	243
59	4	1430	2248	gi|147923	threonine dehydratase 2 (EC 4.2.1.16) [Escherichia coli]	73	53	819
65	1	730	2	gi|677944	AppF [Bacillus subtilis]	73	56	729
80	2	860	345	gi|580932	murD gene product [Bacillus subtilis]	73	53	516
102	13	10124	11179	gi|580891	3-isopropylmalate dehydrogenase (AA 1-365) [Bacillus subtilis]	73	55	1056
					pir|A26522|A26522 3-isopropylmalate dehydrogenase (EC 1.1.1.85) - Bacillus
					subtilis
109	2	2600	1707	gi|1510849	M. jannaschii predicted coding region MJ0775 [Methanococcus jannaschii]	73	40	894
120	8	4782	5756	gi|146970	ribonucleoside triphosphate reductase [Escherichia coli] pir|A47331|A47331	73	56	975
					anaerobic ribonucleotide reductase - Escherichia coli
120	9	5726	6223	gi|1204333	anaerobic ribonucleoside-triphosphate reductase [Haemophilus influenzae]	73	62	498
132	5	4151	4363	gi|871048	HPSR2 - heavy chain potential motor protein [Giardia inrestinalis]	73	43	213
140	6	4324	2696	gi|634107	kdpB [Eacherichia coli]	73	59	1629
142	6	5939	4918	gi|410125	ribG gene product [Bacillus subtilis]	73	57	1122
149	4	1717	1568	gi|460892	heparin binding protein-44, HBP-44 [mice, Peptide, 360 aa]	73	53	150
					pir|JX0281|JX0281 heparin-binding protein-44 precursor - mouse gi|220434
					ORF [Mus musculus] (SUB 2-360)
158	1	1	1431	gi|882504	ORF_f560 [Eacherichia coli]	73	57	1431
174	6	4525	3698	gi|1146240	ketopantoate hydroxymethyltransferase [Bacillus subtilis]	73	55	828
175	8	5178	4819	gi|854657	Na/H antiporter system ORF3 [Bacillus alcalophilus)	73	56	360
186	5	5493	4393	gi|467477	unknown [Bacillus subtilis]	73	48	1101
249	6	5729	5175	gi|1524397	glycine betaine transporter OpuD [Bacillus subtilis]	73	56	555
265	4	1873	2280	gi|39848	U3 [Bacillus subtilis]	73	41	408
270	1	328	582	gi|780461	220 kDa polyprotein [African swine fever virus]	73	53	255
278	4	3618	2953	gi|1208965	hypothetical 23.3 kd protein [Eacherichia coli]	73	49	666
279	3	3593	2202	gi|1185288	isochorismate synthase [Bacillus subtilis]	73	58	1392
291	4	1207	1575	gi|1511440	glutamine - fructose-6-phosphate transaminase (Methanococcus jannaschii)	73	63	369
299	2	735	1166	gi|467437	unknown [Bacillus subtilis]	73	58	432
299	5	2050	3234	gi|467439	temperature sensitive cell division [Bacillus subtilis]	73	53	1185
334	1	728	219	gi|536655	ORF YBR244w [Saccharomyces cerevisise]	73	43	510
336	2	1036	245	gi|790943	urea amidolyase [Bacillus subtilis]	73	51	792
374	3	1389	1874	gi|1405451	YneJ [Bacillus subtilis]	73	55	486
433	4	1916	2554	gi|473902	alpha-aceholactate synthase [Lactococcus lactis]	73	54	639
509	2	1028	261	gi|467483	unknown [Bacillus subtilis]	73	56	768
513	1	918	127	gi|1146220	NAD+ dependent glycerol-3-phosphate dehydrogenase [Bacillus subtilis]	73	56	792
533	2	239	733	gi|1510605	hypothetical protein (SP: P42297) [Methanococcus jannaschii]	73	44	495
546	2	1148	2815	gi|41748	hsdM protein (AA 1-520) [Eacherichia coli]	73	52	1668
549	1	382	2	gi|1314847	CinA [Bacillus subtilis]	73	57	381
567	1	675	4	gi|410137	ORFX13 [Bacillus subtilis]	73	58	672
716	2	654	1112	gi|1256623	exodeoxyribonuclease [Bacillus subtilis]	73	56	459
772	1	3	677	gi|142010	Shows 70.2% similarity and 48.6% identity to the EnvM protein of almonella	73	57	675
					typhimurium [Anabaena sp.]
774	1	3	209	gi|409286	bmrU [Bacillus subtilis]	73	52	207
782	1	1	402	gi|143320	[gap] gene products [Bacillus megaterium]	73	56	402
789	2	451	762	gi|1063246	low homology to P14 protein of Heamophilus influenzar and 14.2 kDa protein	73	56	312
					of Escherichia coli [Bacillus subtilis]
796	1	3	911	gi|853754	ABC transporter [Bacillus subtilis]	73	58	909
806	3	949	689	gi|143786	tryptophanyl-tRNA synthetase (EC 6.1.1.2) [Bacillus subtilis]	73	51	261
					pir|JT0481|YWBS tryptophan-tRNA ligase (EC 6.1.1.2) - Bacillus subtilis
816	2	3097	1355	gi|41748	hsdM protein (AA 1-520) [Escherichia coli]	73	52	1743
839	1	400	2	gi|886906	argininosuccinate synthetase [Streptomyces clavuligerus] pir|S57659|S57659	73	59	399
					argininosuccinate synthase (EC 6.3.4.5) - treptomyces clavuligerus
857	1	3	290	gi|348052	acetoin utilization protein [Bacillus subtilis]	73	50	288
1008	1	398	6	gi|40100	rodC (tag3) polypeptide (AA 1-746) [Bacillus subtilis] ir|S06049|S06049	73	41	393
					rodC protein - Bacillus subtilis p|P13485|TAGF_BACSU TECHOIC ACID
					BIOSYNTHESIS PROTEIN F.
1018	1	1	213	gi|529357	No definition line found [Caenorhabditis elegans] sp|P46975|STT3_CAEEL	73	53	213
					OLIGOSACCHARYL TRANSFERASE STT3 SUBUNIT OMOLOG.
1033	1	3	491	gi|142706	comG1 gene product [Bacillus subtilis]	73	51	489
1174	1	204	13	gi|1149513	alpha3a subunit of laminin 5 [Homo sapiens]	73	60	192
1175	1	329	3	gi|473817	‘ORF’ [Escherichia coli]	73	57	327
1187	1	3	209	gi|580870	ipa-37d qoxA gene product [Bacillus subtilis]	73	52	207
1206	1	72	245	gi|144816	formyltetrahydrofolate synthetase (FTHFS) (ttg start codon) (EC .3.4.3)	73	43	174
					[Moorella thermoacetica]
1454	1	241	59	gi|1213253	unknown [Schizosaccharomyces pombe]	73	53	183
1469	1	260	3	gi|1303787	YqeG [Bacillus subtilis]	73	55	258
1761	1	189	4	gi|9135	Mst26Aa gene product [Drosophila simulans]	73	34	186
1849	1	243	19	gi|162307	DNA topoisomerase II [Trypanosoma cruzi]	73	60	225
2055	1	2	400	gi|559381	P47K protein [Rhodococcus erythropolis]	73	34	399
2556	1	2	244	gi|145925	fecB [Escherichia coli]	73	62	243
2947	2	400	251	gi|1184680	polynucleotide phosphorylase [Bacillus subtilis]	73	51	150
2956	1	375	4	gi|143397	quinol oxidase [Bacillus subtilis]	73	58	372
3037	1	329	3	gi|143091	acetolactate synthase [Bacillus subtilis]	73	55	327
3115	1	194	3	gi|323866	overlapping out-of-phase protein [Eggplant mosaic virus]	73	53	192
					sp|P20129|V70K_EPMV 70 KD PROTEIN.
3603	2	527	354	gi|1439521	glutaryl-CoA dehydrogenase precursor [Mus musculus]	73	48	174
3743	1	400	2	gi|450688	hsdM gene of EcoprrI gene product [Escherichia coli]pir|S38437|S38437 hsdM	73	54	399
					protein - Escherichia coli pir|S09629|S09629 hypothetical protein A -
					Escherichia coli (SUB 40-520)
3752	1	359	78	gi|1524193	unknown (Mycobacterium tuberculosis]	73	59	282
3852	1	2	181	gi|216746	D-lactate dehydrogenase [Lactobacillus plantarum]	73	68	180
3914	1	239	3	pir|S13490|S134	Hydroxymethylglutaryl-CoA synthase (EC 4.1.3.5) - Chicken (fragment)	73	53	237
3914	2	343	116	gi|528991	unknown [Bacillus subtilis]	73	38	228
4069	1	2	316	gi|40003	oxoglutarate dehydrogenase (NADP+) [Bacillus subtilis] p|P23129|OD01_BACSU	73	55	315
					2-OXOGLUTARATE DEHYDROGENASE E1 COMPONENT (EC 2.4.2) (ALPHA-KETOGLUTARATE
					DEHYDROGENASE).
4165	1	365	15	gi|1439521	glutaryl-CoA dehydrogenase precursor [Mus musculus]	73	48	351
4196	1	1	177	gi|809660	deoxyribose-phosphate aldolase [Bacillus subtilis] pir|S49455|S49455	73	60	177
					deoxyribose-phosphate aldolase (EC 4.1.2.4) - Bacillus subtilis
4202	1	378	184	gi|528991	unknown [Bacillus subtilis)	73	38	195
4314	1	2	193	gi|436797	N-acyl-L-amino acid amidohydrolase [Bacillus stearothermophilus]	73	47	192
					sp|P37112|AMA_BACST N-ACYL-L-AMINO ACID AMIDOHYDROLASE (EC .5.1.14)
					(AMINOACYLASE).
4393	1	3	263	gi|216267	ORF2 [Bacillus megaterium)	73	47	261
35	2	903	1973	gi|1146196	phosphoglycerate dehydrogenase [Bacillus subtilis]	72	53	1071
38	22	17877	16660	gi|602031	similar to trimethylamine DH [Mycoplasma capricolum] pir|S49950|S49950	72	54	1218
					probable trimethylamine dehydrogenase (EC .5.99.7) - Mycoplasma capricolum
					(SGC3) (fragment)
38	23	18134	19162	gi|413968	ipa-44d gene product [Bacillus subtilis]	72	54	1029
44	19	11895	12953	gi|516272	unknown [Bacillus subtilis]	72	49	1059
48	7	6248	7117	gi|43499	pyruvate synthase [Halobacterium halobium)	72	49	870
50	7	5691	4819	gi|1205399	proton glutamate symport protein [Haemophilus influenzae]	72	53	873
53	9	9259	7997	gi|1303956	YqjE [Bacillus subtilis]	72	52	1263
56	23	29549	29995	gi|467471	unknown [Bacillus subtilis]	72	47	447
69	4	4123	2948	gi|1354775	pfoS/R [Treponema pallidum]	72	46	1176
69	5	4377	4982	gi|904198	hypothetical protein [Bacillus subtilis]	72	43	606
73	1	2	856	gi|142997	glycerol uptake facilitator [Bacillus subtilis]	72	59	855
98	13	9371	10258	gi|467435	unknown [Bacillus subtilis]	72	50	888
127	1	1	1593	gi|217144	alanine carrier protein [thermophilic bacterium PS3] pir|A45111|A45111	72	56	1593
					alanine transport protein - thermophilic acterium PS-3
131	1	2600	3	gi|153952	polymerase III polymerase subunit (dnaE) [Salmonella typhimurium]	72	53	2598
					pir|A45915|A45915 DNA-directed DNA polymerase (EC 2.7.7.7) III lpha chain -
					Salmonella typhimurium
141	4	1040	1978	gi|1405446	transketolase [Bacillus subtilis]	72	54	939
149	8	2535	2251	gi|606234	secY [Escherichia coli]	72	44	285
149	17	5245	5018	gi|1304472	DNA polymerase [Unidentified phycodnavirus clone OTU4]	72	55	228
154	1	1	210	gi|1205620	ferritin like protein [Haemophilus influenzae]	72	40	210
155	1	1320	433	gi|391610	farnesyl diphosphate synthase [Bacillus stearothermophilus]	72	57	888
					pir|JX0257|JX0257 geranyltranstransferase (EC 2.5.1.10) - Bacillus
					stearothermophilus
180	1	2	328	gi|433630	A180 [Saccharomyces cerevisiae]	72	62	327
184	3	1145	3553	gi|1205110	virulence associated protein homolog [Haemophilus influenzae]	72	49	2409
195	2	1279	635	gi|1001730	hypothetical protein [Synechocystis sp.]	72	45	645
206	13	14646	15869	gi|1064807	ORTHININE AMINOTRANSFERASE [Bacillus subtilis]	72	50	1224
209	2	462	932	gi|1204666	hypothetical protein (GB: X73124_53) [Haemophilus influenzae]	72	60	471
215	2	522	280	gi|881513	insulin receptor homolog [Drosophila melanogaster] pir|S57245|S57245	72	63	243
					insulin receptor homolog - fruit fly (Drosophila elanogaster) (SUB 46-
					2146)
224	1	2	790	gi|949974	sucrose repressor [Staphylococcus xylosus]	72	54	789
233	1	765	4	gi|1408493	homologous to SwissProt: YIDA_ECOLI hypothetical protein [Bacillus subtilis]	72	52	762
240	1	220	1485	gi|537049	ORF_o470 [Escherichia coli]	72	52	1266
245	1	3	1340	gi|1204578	hypothetical protein (GB: U06949_1) [Haemophilus influenzae]	72	46	1338
259	2	1245	382	gi|1340128	ORF1 [Staphylococcus aureus]	72	59	864
304	2	285	1094	gi|1205330	glutamine-binding periplasmic protein [Haemophilus influenzae]	72	52	810
307	10	5039	4752	gi|1070015	protein-dependent [Bacillus subtilis]	72	53	288
315	1	260	3	gi|143399	quinol oxidase [Bacillus subtilis]	72	55	258
316	11	9308	8994	gi|1204445	hypothetical protein (SP: P27857) [Haemophilus influenzae]	72	52	315
337	3	926	1609	gi|487433	citrate synthase II [Bacillus subtilis]	72	55	684
364	7	10493	8448	gi|1510643	ferrous iron transport protein B [Methanococcus jannaschii]	72	53	2046
409	2	340	1263	gi|1402944	orfRM1 gene product [Bacillus subtilis]	72	49	924
441	3	1590	1003	gi|312379	highly conserved among eubacteria [Clostridium acetobutylicum]	72	48	588
					pir|S34312|S34312 hypothetical protein V - Clostridium cetobutylicum
453	6	2505	2356	pir|S00601|BXSA	antibacterial protein 3 - Staphylococcus haemolyticus	72	70	150
460	1	2	625	gi|1016162	ABC transporter subunit [Cyanophora paradoxa]	72	51	624
463	1	1628	3	gi|666014	The polymorphysm (RFLP) of this gene is associated with usceptibility to	72	60	1626
					essential hypertension. The SA gene product has light homology to acetyl-
					CoA synthetase [Homo sapiens]
480	4	3047	3466	gi|433992	ATP synthase subunit epsilon [Bacillus subtilis]	72	53	420
502	1	586	86	gi|310859	ORF2 [synechococcus sp.]	72	50	501
519	1	81	1184	gi|1303704	YrkE [Bacillus subtilis]	72	54	1104
559	1	3	746	gi|1107530	ceuD gene product [Campylobacter coli]	72	56	744
575	1	573	4	gi|1303866	Yqgs [Bacillus subtilis]	72	56	570
671	1	2	592	gi|1204497	protein-export membrane protein [Haemophilus influenzae]	72	44	591
679	2	295	1251	gi|563258	virulence-associated protein E [Dichelobacter nodosus]	72	52	957
687	2	295	957	gi|1146214	44% identical amino acids with the Escherichia coli smba supress; putative	72	49	663
					[Bacillus subtilis]
837	1	1	435	gi|1146183	putative [Bacillus subtilis]	72	54	435
868	1	150	788	gi|1377842	unknown [Bacillus subtilis]	72	55	639
922	1	130	432	gi|1088269	unknown protein [Azotobacter vinelandii]	72	58	303
941	1	2	238	gi|153929	NADPH-sulfite reducatase flavoprotein component [Salmonella yphimurium]	72	49	237
980	1	421	2	gi|853767	UDP-N-acetylglucosamine 1-carboxyvinyltransferase [Bacillus subtilis]	72	59	420
1209	1	213	43	gi|144735	neurotoxin type B [Clostridium botulinum]	72	44	171
1469	2	474	277	gi|1205458	hypothetical protein (GB: D26562_47) [Haemophilus influenzae]	72	63	198
1956	1	365	3	gi|154409	hexosephosphate transport protein [Salmonella typhimurium]	72	44	363
					pir|B41853|B41853 hexose phosphate transport system regulatory rotein uhpB -
					salmonella typhimurium
2101	1	3	401	gi|1303950	YqiY [Bacillus subtilis]	72	50	399
2503	1	399	229	gi|149713	formate dehydrogenase [Methanobacterium formicicum] pir|A42712|A42712	72	56	171
					formate dehydrogenase (EC 1.2.1.2) - Methanobacterium formicicum
2967	1	3	155	gi|1212729	YqhJ [Bacillus subtilis]	72	46	153
3004	1	185	3	gi|665999	hypothetical protein [Bacillus subtilis]	72	55	183
3109	1	141	4	gi|413968	ipa-44d gene product [Bacillus subtilis]	72	45	138
3171	1	3	287	gi|515938	glutamate synthase (ferredoxin) [Synechocystis sp.] pir|S46957|S46957	72	52	285
					glutamate synthase (ferredoxin) (EC 1.4.7.1) - Synechocystis sp.
3771	1	26	367	gi|1408501	homologous to N-acyl-L-amino acid amidohydrolase of Bacillus	72	63	342
					stearothermophilus [Bacillus subtilis]
3951	1	1	222	gi|1500409	M. jannaschii predicted coding region MJ1519 [Methanococcus jannaschii]	72	38	222
4190	1	362	3	gi|39956	IIGlc [Bacillus subtilis]	72	57	360
4444	1	3	347	gi|1009366	Respiratory nitrate reductase [Bacillus subtilis]	72	55	345
6	2	931	1200	gi|537095	ornithine carbamoyltransferase [Escherichia coli]	71	55	270
11	15	10859	10368	gi|532309	25 kDa protein [Escherichia coli]	71	47	492
19	2	1248	2435	gi|1244574	D-alanine; D-alanine ligase [Enterococcus hirae]	71	52	1188
21	2	898	1488	gi|149629	anthranilate synthase component 2 [Leptospira biflexa] pir|C32840|C32840	71	45	591
					anthranilate synthase (EC 4.1.3.27) component II Leptospira biflexa
34	1	1	567	gi|1303983	YqkF [Bacillus subtilis]	71	59	567
37	3	2806	2420	gi|1209681	glutamate-rich protein [Bacillus firmus]	71	50	387
38	18	12250	12462	gi|927645	arginyl endopeptidase [Porphyromonas gingivalis]	71	50	213
39	3	1246	4431	pir|S09411|S094	spoIIIE protein - Bacillus subtilis	71	49	3186
53	14	14760	13750	gi|142611	branched chain alpha-keto acid dehydrogenase E1-alpha [Bacillus subtilis]	71	58	1011
54	11	12625	11789	gi|143014	gnt repressor [Bacillus subtilis]	71	46	837
57	7	5860	4568	gi|508175	EIIC domain of PTS-dependent Gat transport and phosphorylation Escherichia	71	48	1293
					coli]
57	18	13897	14334	gi|1063247	high homology to flavohemoprotein (Haemoglobin-like protein) of Alcaligenes	71	56	438
					eutrophus and Saccharomyces cerevisiae [Bacillus subtilis]
62	16	9831	10955	gi|1303926	YgiG [Bacillus subtilis]	71	54	1125
70	12	8505	8966	gi|147198	phnE protein [Escherichia coli]	71	38	462
86	5	2089	1784	gi|904205	hypothetical protein [Bacillus subtilis]	71	51	306
96	7	7601	8269	gi|709991	hypothetical protein [Bacillus subtilis]	71	49	669
100	6	4822	5931	gi|1060848	Opine dehydrogenase [Arthrobacter sp.]	71	45	1110
103	1	532	2	gi|143089	iep protein [Bacillus subtilis]	71	41	531
109	18	15312	15695	gi|413985	ipa-61d gene product [Bacillus subtilis]	71	57	384
113	1	316	2	gi|663254	probable protein kinase [Saccharomyces cerevisiae]	71	57	315
114	5	5603	4608	gi|143156	membrane bound protein [Bacillus subtilis]	71	40	996
133	2	1723	359	gi|1303913	YqhX [Bacillus subtilis]	71	53	1365
149	19	5895	5455	gi|529650	G40P [Bacteriophage SPP1]	71	51	441
154	5	3087	2539	gi|425488	repressor protein [Streptococcus sobrinus]	71	47	549
164	11	11354	11689	gi|49318	ORF4 gene product [Bacillus subtilis]	71	52	336
169	5	1936	2745	gi|1403403	unknown [Mycobacterium tuberculosis]	71	56	810
193	2	272	1234	gi|1303788	YqeH [Bacillus subtilis]	71	49	963
205	1	895	47	gi|1215694	GlnQ [Mycoplasma pneumoniae]	71	46	849
233	4	1849	2022	gi|633732	ORF1 [Campylobacter jejuni]	71	50	174
237	7	4501	5169	gi|149384	HisIE [Lactococcus lactis]	71	54	669
272	4	2273	1698	gi|709993	hypothetical protein [Bacillus subtilis]	71	48	576
274	2	618	1496	gi|143035	NAD(P)H: glutamyl-transfer RNA reductase [Bacillus subtilis]	71	53	879
					pir|A35252|A35252 5-aminolevulinate synthase (EC 2.3.1.37) - Bacillus
					subtilis
276	5	2720	2091	gi|303562	ORF210 [Escherichia coli]	71	50	630
287	1	136	660	gi|310634	20 kDa protein [Streptococcus gordonii]	71	53	525
288	6	2771	2220	gi|1256625	putative [Bacillus subtilis]	71	47	552
301	6	2461	1430	gi|467417	similar to lysine decarboxylase [Bacillus subtilis]	71	57	1032
306	4	5222	3837	gi|1256618	transport protein [Bacillus subtilis]	71	56	1386
307	2	925	314	gi|602683	orfC [Mycoplasma capricolum]	71	45	612
310	5	5146	4499	gi|348052	acetoin utilization protein [Bacillus subtilis]	71	51	648
322	1	2	1303	gi|1001819	hypothetical protein [Synechocystis sp.]	71	46	1302
333	4	3995	3819	gi|467473	unknown [Bacillus subtilis]	71	57	177
350	2	548	922	gi|551879	ORF 1 [Lactococcus lactis]	71	55	375
375	4	1860	3071	gi|467447	unknown [Bacillus subtilis]	71	57	1212
380	5	1560	2102	gi|142557	ATP synthase b subunit [Bacillus megaterium]	71	43	543
414	2	251	637	gi|580904	homologous to E. coli rnpA [Bacillus subtilis]	71	49	387
424	1	335	1354	gi|581305	L-lactate dehydrogenase [Lactobacillus plantarum]	71	57	1020
436	4	3270	2839	pir|PN0501|PN05	phosphoribosylanthranilate isomerase (EC 5.3.1.24) - Bacillus subtilis	71	66	432
					[fragment]
482	1	3	1280	gi|410142	ORFX18 [Bacillus subtilis]	71	49	1278
525	3	1844	1416	gi|143370	Phosphoribosylpyrophosphate amidotransferase [PUR-F; EC 2.4.2.14] Bacillus	71	56	429
					subtilis ]
529	4	2047	1355	gi|606150	ORF_f309 [Escherichia coli]	71	43	693
563	1	22	969	gi|1237015	ORF4 [Bacillus subtilis]	71	53	948
581	1	255	4	gi|1301730	T25G3.2 [Caenorhabditis elegans]	71	47	252
612	2	913	758	gi|153968	fimbriae Z [Salmonella typhimurium]	71	55	156
613	1	1	654	gi|466778	lysine specific permease [Escherichia coli]	71	50	654
618	1	623	3	gi|1146238	poly(A) polymerase [Bacillus subtilis]	71	52	621
630	1	586	2	gi|1486243	unknown [Bacillus subtilis]	71	53	585
691	1	641	156	gi|289260	comE ORF1 [Bacillus subtilis]	71	51	486
694	2	149	427	gi|12971	NADH dehydrogenase subunit V (AA 1-605) [Gallus gallus] ir|s10197|S10197	71	47	279
					NADH dehydrogenase (ubiquinone) (EC 1.6.5.3) chain - chicken mitochondrion
					(SGC1)
715	2	169	777	gi|1303830	YqfL [Bacillus subtilis]	71	53	609
746	2	970	467	gi|1377843	unknown [Bacillus subtilis]	71	52	504
748	1	802	167	gi|1405459	YneS [Bacillus subtilis]	71	49	636
753	1	524	30	gi|1510389	M. jannaschii predicted coding region MJ0296 [Methanococcus jannaschii]	71	53	495
761	1	3	215	gi|475972	pentafunctional enzyme [Pneumocystis carinii]	71	47	213
783	1	703	203	gi|536655	ORF YBR244w [Saccharomyces cerevisiae]	71	52	501
800	3	987	682	gi|1204326	tRNA delta (2)-isopentenylpyrophosphate transferase [Haemophilus influenzae]	71	48	306
806	1	116	286	gi|1419075	cbiM gene product [Methanobacterium thermoautotrophicum]	71	50	171
931	1	488	3	gi|893358	PgsA [Bacillus subtilis]	71	56	486
1041	1	2	262	gi|1408507	pyrimidine nucleoside transport protein [Bacillus subtilis]	71	45	261
1070	1	2	172	gi|709993	hypothetical protein [Bacillus subtilis]	71	46	171
1176	1	57	365	gi|151259	HMG-CoA reductase (EC 1.1.1.88) [Pseudomonas mevalonii] pir|A44756|A44756	71	49	309
					hydroxymethylglutaryl-CoA reductase (EC 1.1.1.88) Pseudomonas sp.
1181	1	184	2	gi|46971	epiP gene product [Staphylococcus epidermidis]	71	50	183
1281	1	3	290	gi|153016	ORF 419 protein [Staphylococcus aureus]	71	50	288
1348	1	229	2	gi|602683	orfc [Mycoplasma capricolum]	71	48	228
2002	1	379	2	gi|1008177	ORF YJL046w [Saccharomyces cerevisiae]	71	48	378
2119	1	2	217	gi|1046088	arginyl-tRNA synthetase [Mycoplasma genitalium]	71	50	216
2418	1	3	320	gi|1499771	M. jannaschii predicted coding region MJ0936 [Methanococcus jannaschii]	71	57	318
2961	1	2	187	gi|312443	carbamoyl-phosphate synthase (glutamine-hydrolysing) [Bacillus aldolyticus]	71	57	186
2999	2	67	306	gi|710020	nitrite reductase (nirB) [Bacillus subtilis]	71	43	240
3033	1	2	184	gi|1262335	YmaA [Bacillus subtilis]	71	57	183
3584	1	3	338	gi|401716	beta-isopropylmalate dehydrogenase [Neurospora crassa]	71	55	336
3715	2	399	55	gi|563952	gluconate permease [Bacillus licheniformis]	71	59	345
3785	1	387	4	gi|47382	acyl-CoA-dehydrogenase [Streptomyces purpurascens]	71	57	384
3875	1	272	3	gi|1001541	hypothetical protein [Synechocystis sp.]	71	38	270
4135	1	320	3	gi|142695	S-adenosyl-L-methionine: uroporphyrinogen III methyltransferase Bacillus	71	52	318
					megaterium]
4249	1	63	239	gi|1205363	deoxyribose aldolase [Haemophilus influenzae]	71	63	177
4508	1	267	4	gi|1197667	vitellogenin [Anolis pulchellus]	71	46	264
1976	1	237	22	gi|9806	lysine-rich aspartic acid-rich protein [Plasmodium chabaudi]	56	33	216
					r|S22183|S22183 lysine/aspartic acid-rich protein - Plasmodiom baudi
2161	1	2	400	gi|1237015	ORF4 [Bacillus subtilis]	56	27	399
2958	1	183	4	gi|466685	No definition line found [Escherichia coli]	56	26	180
2979	1	212	3	gi|1204354	spore germination and vegetative growth protein [Haemophilus infiuenzae]	56	40	210
2994	2	326	126	gi|836646	phosphoribosylformimino-praic ketoisomerase [Rhodobacter phaeroides]	56	29	201
3026	1	179	328	gi|143306	penicllin V amidase [Bacillus sphaericus]	56	30	150
3189	1	146	3	gi|1166604	Similar to aldehyde dehydrogenase [Caenorhabditis elegans]	56	37	144
3770	1	63	401	gi|1129145	acetyl-CoA C-acyltransferase [Mangifera indica]	56	43	339
4054	2	361	2	gi|1205355	Na+/H+ antiporter [Haemophilus influenzae]	56	31	360
4145	1	1	324	gi|726095	long-chain acyl-CoA dehydrogenase [Mus musculus]	56	36	324
4200	1	254	3	gi|155588	glucose-fructose oxidoreductase [Zymomonas mobilis|pir|A42289|A42289	56	40	252
					glucose-fructose oxidoreductase (EC 1.1.—.—) recursor - Zymomonas mobilis
4273	1	355	35	gi|308861	GTG start codon [Lactococcus lactis]	56	33	321
1	3	3436	2777	gi|5341	Putative orF YCLX8c, len: 192 [Saccharomyces cerevisiae] r|S53591|S53591	55	25	660
					hypothetical protein - yeast (Saccharomyces evisiae)
11	12	8505	7633	gi|216773	haloacetate dehalogenase H-1 [Moraxella sp.]	55	32	873
12	4	4534	3935	gi|467337	unknown [Bacillus subtilis]	55	26	600
19	5	5404	5844	gi|1001719	hypothetical protein [Synechocystis sp.]	55	25	441
23	13	12339	10591	gi|474190	iucA gene product [Escherichia coli]	55	30	1749
32	7	5368	6888	gi|1340096	unknown [Mycobacterium tuberculosis]	55	37	1521
34	3	1808	1047	gi|1303968	YqjQ [Bacillus subtilis]	55	39	762
34	5	3412	2864	gi|1303962	Yqjk [Bacillus subtilis]	55	33	549
36	1	647	3	gi|606045	ORF_o118 [Escherichia coli]	55	27	645
36	6	5243	4266	gi|1001341	hypothetical protein [Synechocystis sp.]	55	31	978
47	3	3054	3821	gi|1001819	hypothetical protein [Synechocystis sp.]	55	21	768
49	1	1127	189	gi|403373	glycerophosphoryl diester phosphodiesterase [Bacillus subtilis]	55	36	939
					pir|S37251|S37251 glycerophosphoryl diester phosphodiesterase - Bacillus
					subtilis
67	11	8966	9565	gi|153053	norA1199 protein [Staphylococcus aureus]	55	23	600
75	3	881	1273	gi|41698	L-histidinol: NAD+ oxidoreductase (EC 1.1.1.23) (aa 1-434) Escherichia coli)	55	33	393
82	9	14194	13001	gi|1136221	carboxypeptidase [Sulfolobus solfataricus]	55	35	1194
87	4	3517	4917	gi|1064812	function unknown [Bacillus subtilis]	55	26	1401
88	2	1172	1636	gi|882463	protein-N(pi)-phosphohistldine-sugar phosphotransferase [Escherichia coli]	55	35	465
92	1	127	516	gi|1377832	unknown [Bacillus subtilis]	55	36	390
100	2	836	2035	gi|1370274	zeaxanthin epoxidase [Nicotiana plumbaginifolia]	55	36	1200
100	5	4658	4179	gi|396660	unknown open reading frame [Buchnera aphidicola]	55	29	480
108	3	2986	1706	gi|1499866	M. jannaschii predicted coding region MJ1024 [Methanococcus jannaschli]	55	31	1281
114	3	1834	1052	gi|1511367	formate dehydrogenase, alpha subunit [Methanococcus jannaschii]	55	29	783
144	3	1476	1147	gi|1100787	unkown [Saccharomyces cerevisiae]	55	35	330
165	5	5508	4804	gi|1045884	M. genitalium predicted coding region MG199 [Hycoplasma genitalium]	55	27	705
189	5	2205	2576	gi|142569	ATP synthase a subunit [Bacillus firmus]	55	35	372
191	6	6857	4578	gi|559411	B0272.3 [Caenorhabditis elegans]	55	39	2280
194	2	364	636	gi|1145768	K7 kinesin-like protein [Dictyostelium discoideum]	55	34	273
209	4	1335	1676	gi|473357	thi4 gene product [Schizosaccharomyces pombe]	55	35	342
211	2	1145	597	gi|410130	ORFX6 [Bacillus subtilis]	55	37	549
213	2	644	1372	gi|633692	TrsA [Yersinia enterocolitica]	55	28	729
214	7	4144	5481	gi|1001793	hypothetical protein [Synechocystis sp.]	55	30	1338
221	7	9197	6921	gi|466520	pocR [Salmonella typhimurium]	55	32	2277
233	8	4817	3726	gi|1237063	unknown [Mycobacterium tuberculosis]	55	38	1092
236	4	1375	2340	gi|1146199	putative [Bacillus subtilis]	55	32	966
243	2	380	1885	gi|459907	mercuric reductase (Plasmid pI258]	55	29	1506
258	1	394	2	gi|455006	orf6 [Rhodococcus fascians]	55	36	393
281	1	126	938	gi|1408493	homologous to SwissProt: YIDA_ECOLI hypothetical protein [Bacillus subtilis]	55	35	813
316	3	1323	2102	gi|1486447	LuxA homologue [Rhizobium sp.]	55	30	780
326	5	2744	2520	gi|1296824	proline iminopeptidase [Lactobacillus helveticus]	55	36	225
351	2	1429	536	gi|1204820	hydrogen peroxide-inducible activator [Haemophilus influenzae]	55	28	894
353	4	2197	2412	gi|1272475	chitin synthase [Emericella nidulans]	55	50	216
380	1	14	379	gi|142554	ATP synthase i subunit [Bacillus megaterium]	55	37	366
383	1	232	2	gi|289272	ferrichrome-binding protein [Bacillus subtilis]	55	36	231
386	1	3	938	gi|1510251	DNA helicase, putative [Methanococcus jannaschii]	55	30	936
410	2	1208	1891	gi|1205144	multidrug resistance protein [Haemophilus influenzae]	55	27	684
483	2	411	833	gi|413934	ipa-10r gene product [Bacillus subtilis]	55	26	423
529	3	1433	1089	gi|606150	ORF_f309 [Escherichia coli]	55	33	345
555	1	585	82	gi|143407	para-aminobenzoic acid synthase, component I (pab) [Bacillus subtilis]	55	28	504
565	1	202	2	gi|1223961	CDP-tyvelose epimerase [Yersinia pseudotuberculosis]	55	41	201
582	1	452	153	gi|1256643	20.2% identity with NADH dehydrogenase of the Leishmania major	55	36	300
					mitochondrion; putative [Bacillus subtilis]
645	5	2057	1854	gi|210824	fusion protein F [Bovine respiratory syncytial virus] pir|JQ1481|VGNZBA	55	25	204
					fusion glycoprotein precursor - bovine espiratory syncytial virus (strain
					A51908)
672	2	957	2216	gi|1511333	M. jannaschii predicted coding region MJ1322 [Methanococcus jannaschii]	55	36	1260
730	1	479	3	gi|537007	ORF_f379 [Escherichia coli]	55	30	477
737	1	945	31	gi|536963	CG Site No. 18166 [Escherichia coli]	55	30	915
742	2	228	572	gi|304160	product unknown [Bacillus subtilis]	55	38	345
817	2	903	595	gi|1136289	histidine kinase A [Dictyostelium discoideum]	55	29	309
819	1	355	128	gi|558073	polymorphic antigen [Plasmodium falciparum]	55	22	228
832	2	724	296	gi|40367	ORFC [Clostridium acetobutylicum]	55	32	429
840	1	386	3	gi|1205875	pseudouridylate synthase I [Haemophilus influenzae]	55	39	384
1021	1	23	529	gi|48563	beta-lactamase [Yersinia enterocolitica]	55	38	507
1026	1	60	335	gi|47804	Opp C (AA1-301) [Salmonella typhimurium]	55	26	276
1525	1	1	282	gi|1477533	sarA [Staphylococcus aureus]	55	29	282
1814	2	224	985	gi|1046078	M. genitalium predicted coding region MG369 [Mycoplasma genitalium]	55	38	762
3254	1	254	81	gi|413968	ipa-44d gene product [Bacillus subtilis]	55	30	174
3695	1	345	4	gi|216773	haloacetate dehalogenase H-1 [Moraxella sp.]	55	32	342
3721	1	1	312	gi|42029	ORF1 gene product [Escherichia coli]	55	31	312
3799	1	3	272	gi|42029	ORF1 gene product [Escherichia coli]	55	38	270
3889	1	22	423	gi|1129145	acetyl-CoA C-acyltransferase [Mangifera indica]	55	45	402
3916	1	2	385	gi|529754	speC [Streptococcus pyogenes]	55	38	384
3945	1	4	198	gi|476252	phase 1 flagellin [Salmonella enterica]	55	36	195
4074	1	246	4	gi|42029	ORF1 gene product [Escherichia coli]	55	38	243
4184	1	2	343	gi|1524267	unknown [Hycobacterium tuberculosis]	55	28	342
4284	1	14	208	gi|1100774	ferredoxin-dependent glutamate synthase [Synechocystis sp.]	55	36	195
4457	2	378	112	gi|180189	cerebellar-degeneration-related antigen (CDR34) [Homo sapiens] gi|182737	55	38	267
					cerebellar degeneration-associated protein [Homo sapiens]
					pir|A29770|A29770 cerebellar degeneration-related protein - human
4514	1	2	244	gi|216773	haloacetate dehalogenase H-1 [Moraxella sp.]	55	32	243
4599	1	217	2	gi|1129145	acetyl-CoA C-acyltransferase [Mangifera indica]	55	42	216
4606	1	210	4	gi|386120	myosin alpha heavy chain (S2 subfragment) [rabbits, masseter, eptide	55	27	207
					Partial, 234 aa]
5	8	4932	4516	gi|536069	ORF YBL047c [Saccharomyces cerevisiae]	54	27	417
12	7	6165	5164	gi|1205504	homoserine acetyltransferase [Haemophilus influenzae]	54	30	1002
23	16	15326	13566	gi|474192	iucC gene product [Escherichia coli]	54	31	1761
35	1	2	979	gi|48054	small subunit of soluble hydrogenase (AA 1-384) [Synechococcus sp.]	54	36	978
					ir|S06919|HQYCSS soluble hydrogenase (EC 1.12.—.—) small chain -
					nechococcus sp. (PCC 6716)
37	11	8667	7897	gi|537207	ORF_f277 [Escherichia coli]	54	38	771
37	12	8165	8332	gi|1160967	palmitoyl-protein thioesterase [Homo sapiens]	54	37	168
46	15	13025	13804	gi|438473	protein is hydrophobic, with homology to E. coli ProW; putative Bacillus	54	28	780
					subtilis ]
56	2	203	736	gi|1256139	YbbJ [Bacillus subtilis]	54	34	534
57	13	10179	9241	gi|1151248	inosine-uridine preferring nucleoside hydrolase [Crithidia fasciculata]	54	32	939
66	2	516	1133	gi|1335781	Cap [Drosophila melanogaster]	54	29	618
70	10	8116	8646	gi|1399823	PhoE [Rhizobium meliloti]	54	31	531
70	15	11801	11046	sp|P02983|TCR_S	TETRACYCLINE RESISTANCE PROTEIN.	54	29	756
87	5	4915	5706	gi|1064811	function unknown [Bacillus subtilis]	54	33	792
92	4	2289	1573	gi|1205366	oligopeptide transport ATP-binding protein [Haemophilus influenzae]	54	33	717
103	2	1556	516	gi|710495	protein kinase [Bacillus brevis]	54	33	1041
105	2	2095	605	gi|143727	putative [Bacillus subtilis]	54	30	1491
112	4	2337	2732	gi|153724	MalC [Streptococcus pneumoniae]	54	41	396
127	2	1720	2493	gi|144297	acetyl esterase (XynC) [Caldocellum saccharolyticum] pir|B37202|B37202	54	34	774
					acetylesterase (EC 3.1.1.6) (XynC) - Caldocellum accharolyticum
138	5	1600	3306	gi|42473	pyruvate oxidase [Escherichia coli]	54	36	1707
152	2	525	1172	gi|1377834	unknown [Bacillus subtilis]	54	23	648
161	9	4831	5469	gi|903305	ORF73 [Bacillus subtilis]	54	28	639
161	13	6694	7251	gi|1511039	phosphate transport system regulatory protein [Methanococcus jannaschii]	54	32	558
164	6	3263	4543	gi|1204976	prolyl-tRNA synthetase [Haemophilus influenzae]	54	34	1281
164	20	21602	22243	gi|143582	spoIIIEA protein [Bacillus subtilis]	54	32	642
171	6	4250	2817	gi|436965	[malA] gene products [Bacillus stearothermophilus] pir|S43914|S43914	54	37	1434
					hypothetical protein 1 - Bacillus stearothermophilus
206	18	19208	19720	gi|1240016	R09E10.3 [Caenorhabditis elegans]	54	38	513
218	2	1090	1905	gi|467378	unknown [Bacillus subtilis]	54	26	816
220	1	663	4	gi|1353761	myosin II heavy chain [Naegleria fowleri]	54	22	660
220	13	12655	13059	pir|S00485|S004	gene 11-1 protein precursor - Plasmodium falciparum (fragments)	54	35	405
221	3	2030	3709	gi|1303813	YqeW [Bacillus subtilis]	54	34	1680
272	7	4219	3383	gi|62964	arylamine N-acetyltransferase (AA 1-290) [Gallus gallus] ir|S06652|XYCHY3	54	33	837
					arylamine N-acetyltransferase (EC 2.3.1.5) (clone NAT-3) - chicken
316	7	4141	4701	gi|682769	mccE gene product [Escherichia coli]	54	31	561
316	10	6994	8742	gi|413951	ipa-27d gene product [Bacillus subtilis]	54	28	1749
338	3	2214	1051	gi|490328	LORF F [unidentified]	54	28	1164
341	4	3201	3614	gi|171959	myosin-like protein [Saccharomyces cerevisiae]	54	25	414
346	1	912	4	gi|396400	similar to eukaryotic Na+/H+ exchangers [Escherichia coli]	54	34	909
					sp|P32703|YJCE_ECOLI HYPOTHETICAL 60.5 KD PROTEIN IN SOXR-ACS NTERGENIC
					REGION (0549).
348	2	623	1351	gi|537109	ORF_f343a [Escherichia coli]	54	34	729
378	2	1007	1942	sp|P02983|TCR_S	TETRACYCLINE RESISTANCE PROTEIN	54	31	936
408	6	4351	5301	gi|474190	iucA gene product [Escherichia coli]	54	29	951
444	9	7934	8854	gi|216267	ORF2 [Bacillus megaterium]	54	32	921
463	2	2229	1741	gi|304160	product unknown [Bacillus subtilis]	54	50	489
502	2	1133	570	gi|1205015	hypothetical protein (SP: P10120) [Haemophilus influenzae]	54	38	564
505	6	5357	4452	gi|1500558	2-hydroxyhepta-2,4-diene-1,7-dioate isomerase [Methanococcus jannaschii]	54	41	906
550	1	1522	308	gi|40100	rodC (tag3) polypeptide (AA 1-746) [Bacillus subtilis] ir|S06049|S06049	54	35	1215
					rodC protein - Bacillus subtilis p|P13485|TAGF_BACSU TECHOIC ACID
					BIOSYNTHESIS PROTEIN F.
551	5	3305	4279	gi|950197	unknown [Corynebacterium glutamicum]	54	34	975
558	2	958	560	gi|485090	No definition line found [Caenorhabditis elegans]	54	32	399
580	1	91	936	gi|331906	fused envelope glycoprotein precursor [Friend spleen focus-forming irus]	54	45	846
603	3	554	757	gi|1323423	ORF YGR234w [Saccharomyces cerevisiae]	54	36	204
617	1	25	249	gi|219959	ornithine transcarbamylase [Homo sapiens]	54	40	225
622	3	1097	1480	gi|1303873	YqgZ [Bacillus subtilis]	54	25	384
623	1	3	404	gi|1063250	low homology to P20 protein of Bacillus lichiniformis and bleomycin	54	45	402
					acetyltransferase of Streptomyces verticillus [Bacillus subtilis]
689	1	1011	475	gi|552446	NADH dehydrogenase subunit 4 [Apis mellifera ligustica]pir|S52968|S52968	54	30	537
					NADH dehydrogenase chain 4 - honeybee itochondrion (SGC4)
725	2	686	1441	gi|987096	sensory protein kinase [Streptomyces hygroscopicus]	54	26	756
956	1	1	249	pir|S30782|S307	integrin homolog - yeast [Saccharomyces cerevisiae]	54	24	249
978	2	859	581	gi|1301994	ORF YNL091w [Saccharomyces cerevisiae]	54	33	279
1314	1	3	281	gi|1001108	hypothetical protein [Synechocystis sp.]	54	33	279
2450	1	1	228	gi|1045057	ch-TOG [Homo sapiens]	54	32	228
2934	1	1	387	gi|580870	ipa-37d qoxA gene product [Bacillus subtilis]	54	36	387
2970	1	251	3	sp|P37348|YECE—	HYPOTHETICAL PROTEIN IN ASPS 5′REGION (FRAGMENT).	54	42	249
3002	1	1	309	gi|44027	Tma protein [Lactococcus lactis]	54	33	309
3561	1	9	464	gi|151259	HMG-CoA reductase (EC 1.1.1.88) [Pseudomonas mevalonii] pir|A44756|A44756	54	35	456
					hydroxymethylglutaryl-CoA reductase (EC 1.1.1.88) Pseudomonas sp.
3572	1	72	401	gi|450688	hsdM gene of EcoprrI gene product [Escherichia coli] pir|S38437|S38437 hsdM	54	36	330
					protein - Escherichia coli pir|S09629|S09629 hypothetical protein A -
					Escherichia coli (SUB 40-520)
3829	1	400	2	gi|1322245	mevalonate pyrophosphate decarboxylase [Rattus norvegicus]	54	29	399
3909	1	1	273	gi|29865	CENP-E [Homo sapiens]	54	30	273
3921	1	3	209	pir|S24325|S243	glucan 1,4-beta-glucosidase (EC 3.2.1.74) - Pseudomonas fluorescens subsp.	54	34	207
					cellulosa
4438	1	285	4	gi|1196657	unknown protein [Mycoplasma pneumoniae]	54	30	282
4459	1	3	272	gi|1046081	hypothetical protein (GB: D26185_10) [Mycoplasma genitalium]	54	38	270
4564	1	3	221	gi|216267	ORF2 [Bacillus megaterium]	54	38	219
23	12	10685	8832	gi|474192	iucC gene product [Escherichia coli]	53	35	1854
23	14	13579	12317	gi|42029	ORF1 gene product [Escherichia coli]	53	32	1263
24	3	3940	3440	gi|1369947	c2 gene product [Bacteriophage B1]	53	36	501
26	4	3818	4618	gi|1486247	unknown [Bacillus subtilis]	53	37	801
38	6	2856	3998	gi|405880	yeil [Escherichia coli]	53	40	1143
38	10	7806	6232	gi|1399954	thyroid sodium/iodide symporter NIS [Rattus norvegicus]	53	29	1575
56	10	12100	11876	pir|A54592|A545	110k actin filament-associated protein - chicken	53	32	225
57	6	4583	4119	pir|A00341|DEZP	alcohol dehydrogenase (EC 1.1.1.1) - fission yeast [Schizosaccharomyces	53	39	465
					pombe ]
57	12	8932	7349	gi|1480429	putative transcriptional regulator [Bacillus stearothermophilus]	53	30	1584
67	12	9496	10218	gi|1511555	quinolone resistance norA protein protein [Methanococcus jannaschii]	53	31	723
69	3	2382	1639	gi|1087017	arabinogalactan-protein, AGP [Nicotiana alata, cell-suspension culture	53	30	744
					filtrate, Peptide, 461 aa]
79	1	3	1031	gi|1523802	glucanase [Anabaena variabilis]	53	32	1029
80	1	338	3	gi|452428	ATPase 3 [Plasmodium falciparum]	53	36	336
88	4	1910	2524	gi|537034	ORF_o488 [Escherichia coli]	53	25	615
88	5	2467	3282	gi|537034	ORF_o488 [Escherichia coli]	53	29	816
92	8	5505	5140	gi|399598	amphotropic murine retrovirus receptor [Rattus norvegicus]	53	33	366
94	5	3239	2061	gi|173038	tropomyosin (TPM1) [Saccharomyces cerevisiae]	53	25	1179
99	5	4207	5433	sp|P28246|BCR_E	BICYCLOMYCIN RESISTANCE PROTEIN (SULFONAMIDE RESISTANCE PROTEIN)	53	30	1227
120	3	1639	2262	gi|576655	ORF1 [Vibrio anguillarum]	53	35	624
120	11	7257	8897	gi|1524397	glycine betaine transporter OpuD [Bacillus subtilis]	53	33	1641
127	6	5685	4477	gi|1256630	putative [Bacillus subtilis]	53	32	1209
147	2	255	557	gi|581648	epiB gene product [Staphylococcus epidermidis]	53	34	303
158	4	4256	3807	gi|151004	mucoidy regulatory protein AlgR [Pseudomonas aeruginosa] pir|A32802|A32802	53	32	450
					regulatory protein algR —Pseudomonas aeruginosa sp|P26275|ALGR_PSEAE
					POSITIVE ALGINATE BIOSYNTHESIS REGULATORY ROTEIN.
171	7	5421	5125	gi|1510669	hypothetical protein (GP: D64044_18) [Methanococcus jannaschii]	53	34	297
191	9	11483	9879	gi|298085	acetoacetate decarboxylase [Clostridium acetobutylicum] pir|B49346|B49346	53	31	1605
					butyrate—acetoacetate CoA-transferase (EC .8.3.9) small chain -
					Clostridium acetobutylicum sp|P33752|CTFA_CLOAB BUTYRATE-ACETOACETATE COA-
					TRANSFERASE SUBUNIT (EC 2.8.3.9) (COAT A)
203	5	3763	4326	gi|143456	rpoE protein (ttg start codon) [Bacillus subtilis]	53	29	564
206	17	18204	18971	gi|304136	acetylglutamate kinase [Bacillus stearothermophilus] sp|Q07905|ARGB_BACST	53	36	768
					ACETYLGLUTAMATE KINASE (EC 2.7.2.8) (NAG INASE) (AGK) (N-ACETYL-L-
					GLUTAMATE 5-PHOSPHOTRANSFERASE).
212	10	4021	4221	gi|9878	protein kinase [Plasmodium falciparum]	53	28	201
231	2	1350	1120	gi|537506	paramyosin [Dirofilaria immitis]	53	34	231
272	6	2719	3249	pir|A33141|A331	hypothetical protein (gtfD 3′ region) - Streptococcus mutans	53	34	531
308	3	927	2576	gi|606292	ORF_o696 [Escherichia coli]	53	33	1650
320	7	5645	5884	gi|160596	RNA polymerase III largest subunit [Plasmodium falciparum]	53	33	240
					sp|P27625|RPC1_PLAFA DNA-DIRECTED RNA POLYMERASE III LARGEST UBUNIT (EC
					2.7.7.6).
327	1	218	901	gi|854601	unknown [Schizosaccharomyces pombe]	53	31	684
341	2	212	2500	gi|633732	ORF1 [Campylobacter jejuni]	53	31	2289
351	1	383	3	sp|P31675|YABM—	HYPOTHETICAL 42.7 KD PROTEIN IN TBPA-LEUD INTERGENIC REGION (ORF104).	53	32	381
433	7	4731	4375	gi|1001961	MHC class II analog [Staphylococcus aureus]	53	30	357
454	2	980	720	pir|A60328|A603	40K cell wall protein precursor (sr 5′ region) - Streptococcus mutans	53	27	261
					(strain OMZ175, serotype f)
470	4	1123	1761	gi|516826	rat GCP360 [Rattus rattus]	53	30	639
483	1	217	2	gi|1480429	putative transcriptional regulator [Bacillus stearothermophilus]	53	33	216
544	1	516	1259	gi|46587	ORF 1 (AA 1-121) (1 is 2nd base in codon) [Staphylococcus aureus]	53	38	744
					ir|S15765|S15765 hypothetical protein 1 (hlb 5′ region) - Staphylococcus
					aureus (fragment)
558	10	3754	3551	gi|15140	res gene [Bacteriophage P1]	53	32	204
603	2	339	620	gi|507738	Hmp [Vibrio parahaemolyticus]	53	26	282
693	1	941	213	gi|153123	toxic shock syndrome toxin-1 precursor [Staphylococcus aureus]	53	38	729
					pir|A24606|XCSAS1 toxic shock syndrome toxin-1 precursor - Staphylococcus
					aureus
766	1	2	673	gi|687600	orfA2; orfA2 forms an operon with orfA1 [Listeria monocytogenes]	53	43	672
781	1	335	3	gi|1204551	pilin biogenesis protein [Haemophilus influenzae]	53	26	333
801	1	3	545	gi|1279400	SapA protein [Escherichia coli]	53	25	543
803	1	2	910	gi|695278	lipase-like enzyme [Alcaligenes eutrophus]	53	30	909
872	1	590	3	gi|298032	EF [Streptococcus suis]	53	30	588
910	1	2	184	gi|1044936	unknown [Schizosaccharomyces pombe]	53	29	183
943	1	399	4	gi|290508	similar to unidentified ORF near 47 minutes [Escherichia coli]	53	30	396
					sp|P31436|YICK_ECOLI HYPOTHETICAL 43.5 KD PROTEIN IN SELC-NLPA NTERGENIC
					REGION.
988	1	504	4	gi|142441	ORF 3; putative [Bacillus subtilis]	53	28	501
1064	1	3	434	gi|305080	myosin heavy chain [Entamoeba histolytica]	53	26	432
1366	1	3	452	gi|308852	transmembrane protein [Lactococcus lactis]	53	33	450
1758	1	397	2	gi|1001774	hypothetical protein [Synechocystis sp.]	53	30	396
1897	1	1	447	gi|1303949	YqiX [Bacillus subtilis]	53	27	447
2381	1	400	2	gi|1146243	22.4% identity with Escherichia coli DNA-damage inducible protein ...;	53	37	399
					putative [Bacillus subtilis]
3537	1	1	327	gi|450688	hsdM gene of EcoprrI gene product [Escherichia coli] pir|S38437|S38437 hsdM	53	35	327
					protein - Escherichia coli pir|S09629|S09629 hypothetical protein A -
					Escherichia coli [SUB 40-520]
3747	2	137	397	gi|1477486	transposase [Burkholderia cepacia]	53	53	261
11	5	3049	3441	gi|868224	No definition line found [Caenorhabditis elegans]	52	33	393
15	5	2205	2369	gi|215966	G41 protein (gtg start codon) [Bacteriophage T4]	52	34	165
19	3	2429	3808	gi|1205379	UDP-murnac-pentapeptide synthetase [Haemophilus influenzae]	52	31	1380
24	1	3462	4	gi|579124	predicted 86.4 kd protein; 52 Kd observed [Mycobacteriophage 15]	52	32	3459
					pir|S30971|S30971 gene 26 protein - Mycobacterium phage L5
					sp|Q05233|VG26_BPML5 MINOR TAIL PROTEIN GP26. (SUB 2-837)
37	5	3015	3935	gi|1500543	P115 protein [Methanococcus jannaschii]	52	25	921
38	13	8795	9703	gi|46851	glucose kinase [Streptomyces coelicolor]	52	29	909
44	16	10617	11066	gi|42012	moaE gene product [Escherichia coli]	52	36	450
46	1	3	521	gi|1040957	NADH dehydrogenase subunit 6 [Anopheles trinkae]	52	25	519
51	10	5531	6280	gi|388269	traC [Plasmid pAD1]	52	32	750
56	5	2826	1684	gi|181949	endothelial differentiation protein (edg-1) [Homo sapiens]	52	23	1143
					pir|A35300|A35300 G protein-coupled receptor edg-1 - human
					sp|P21453|EDG1_HUMAN PROBABLE G PROTEIN-COUPLED RECEPTOR EDG-1.
57	5	4173	3496	gi|304153	sorbitol dehydrogenase [Bacillus subtilis]	52	27	678
62	5	2870	2376	gi|1072399	phaE gene product [Rhizobium meliloti]	52	25	495
62	6	3651	2857	gi|46485	NADH dehydrogenase [Synechococcus PCC7942]	52	27	795
67	14	11355	12962	gi|1511365	glutamate synthase (NADPH), subunit alpha [Methanococcus jannaschii]	52	30	1608
67	21	16935	18158	gi|1204393	hypothetical protein (SP: P31122) [Haemophilus influenzae]	52	25	1224
70	4	1997	1809	gi|7227	cytoplasmic dynein heavy chain [Dictyostelium discoldeum]r|A44357|A44357	52	36	189
					dynein heavy chain, cytosolic - slime mold Dictyostelium discoideum)
96	10	10005	10664	gi|1408485	B65G gene product [Bacillus subtilis]	52	26	660
103	5	3351	2716	gi|1009368	Respiratory nitrate reductase [Bacillus subtilis]	52	42	636
109	3	3350	2598	gi|699274	lmbE gene product [Mycobacterium leprae]	52	39	753
109	19	15732	17300	gi|1526981	amino acid permease YeeF like protein [Salmonella typhimurium]	52	30	1569
121	3	981	550	gi|732931	unknown [Saccharomyces cerevisiae]	52	32	432
125	3	865	1680	gi|1296975	puT gene product [Porphyromonas gingivalis]	52	38	816
130	2	659	1807	gi|1256634	25.8% identity over 120 aa with the Synenococcus sp. MpeV protein; putative	52	36	1149
					[Bacillus subtilis]
149	1	583	2	gi|1225943	PBSX terminase [Bacillus subtilis]	52	33	582
149	14	4415	4143	gi|1510368	M. jannaschii predicted coding region MJ0272 [Methanococcus jannaschii]	52	35	273
167	1	216	1001	gi|146025	cell division protein [Escherichia coli]	52	43	786
188	1	120	1256	gi|474915	orf 337; translated orf similarity to SW: BCR_ECOLI bicyclomycin esistance	52	26	1137
					protein of Escherichia coli [Coxiella burnetii] pir|S44207|S44207
					hypothetical protein 337 - Coxiella burnetii (SUB -338)
195	9	8760	8359	gi|3028	mitochondrial outer membrane 72K protein [Neurospora crassa]	52	25	402
					r|A36682|A36682 72K mitochondrial outer membrane protein - Neurospora crassa
200	3	2065	2607	gi|142439	ATP-dependent nuclease [Bacillus subtilis]	52	35	543
203	4	2776	3684	gi|303698	BltD [Bacillus subtilis]	52	25	909
227	8	5250	5651	gi|305080	myosin heavy chain [Entamoeba histolytica]	52	24	402
242	1	21	1424	gi|1060877	EmrY [Escherichia coli]	52	32	1404
249	5	4526	4753	pir|C37222|C372	cytochrome P450 1A1, hepatic - dog (fragment)	52	23	228
255	1	1055	3	gi|143290	penicillin-binding protein [Bacillus subtills]	52	28	1053
276	7	3664	3365	gi|1001610	hypothetical protein [Synechocystis sp.]	52	30	300
276	8	4055	3654	gi|416235	orf L3 [Mycoplasma capricolum]	52	26	402
289	2	1449	1042	gi|150900	GTP phosphohydrolase [Proteus vulgaris]	52	34	408
325	1	1	279	gi|1204874	polypeptide deformylase (formylmethionine deformylase) [Haemophilus	52	33	279
					influenzae ]
340	1	1010	3	gi|1215695	peptide transport system protein SapF homolog; SapF homolog [Mycoplasma	52	33	1008
					pneumoniae ]
375	3	340	1878	gi|467446	similar to SpoVB [Bacillus subtilis]	52	28	1539
424	4	3262	2420	gi|1478239	unknown [Mycobacterium tuberculosis]	52	34	843
430	1	3	575	pir|A42606|A426	orfA 5′ to orf405 - Saccharopolyspora erythraea (fragment)	52	28	573
444	4	3712	2696	gi|1408494	homologous to penicillin acylase [Bacillus subtilis]	52	31	1017
465	1	903	4	gi|143331	alkaline phosphatase regulatory protein [Bacillus subtilis]	52	36	900
					pir|A27650|A27650 regulatory protein phoR - Bacillus subtilis
					sp|P23545|PHOR_BACSU ALKALINE PHOSPHATASE SYNTHESIS SENSOR PROTEIN HOR (EC
					2.7.3.—)
469	5	4169	3633	gi|755152	highly hydrophobic integral membrane protein [Bacillus subtilis]	52	32	537
					sp|P42953|TAGG_BACSU TEICHOIC ACID TRANSLOCATION PERMEASE PROTEIN AGG.
495	1	633	4	gi|1204607	transcription activator [Haemophilus influenzae]	52	25	630
505	7	5762	5520	gi|142440	ATP-dependent nuclease [Bacillus subtilis]	52	28	243
517	2	1162	1614	gi|166162	Bacteriophage phi-11 int gene activator [Staphylococcus acteriophage phi	52	35	453
					11]
543	2	444	1295	gi|1215693	putative orf; GT9_orf434 [Mycoplasma pneumoniae]	52	25	852
586	1	1	336	gi|581648	epiB gene product [Staphylococcus epidermidis]	52	36	336
773	1	426	4	gi|1279769	FdhC [Methanobacterium thermofomicicum]	52	30	423
1120	2	100	330	gi|142439	ATP-dependent nuclease [Bacillus subtilis]	52	35	231
1614	1	347	3	gi|289262	comE ORF3 [Bacillus subtilis]	52	28	345
2495	1	1	324	gi|216151	DNA polymerase (gene L; ttg start codon) [Bacteriophage SP02] gi|579197	52	34	324
					SP02 DNA polymerase (aa 1-648) [Bacteriophage SPO2] pir|A21498|DJBPS2 DNA-
					directed DNA polymerase (EC 2.7.7.7) - phage PO2
2931	1	285	4	gi|1256136	YbbG [Bacillus subtilis]	52	30	282
2943	1	320	63	gi|41713	hisA ORF (AA 1-245) [Escherichia coli]	52	35	258
2993	1	295	2	gi|298032	EF [Streptococcus suis]	52	34	294
3667	1	307	2	gi|849025	hypothetical 64.7-kDa protein [Bacillus subtilis]	52	36	306
3944	1	260	42	gi|1218040	BAA [Bacillus licheniformis]	52	36	219
3954	2	347	81	gi|854064	U87 [Human herpesvirus 6]	52	50	267
3986	1	90	401	gi|1205919	Na+ and Cl− dependent gamma-aminobutryic acid transporter [Haemophilus	52	33	312
					influenzae ]
4002	1	3	389	gi|40003	oxoglutarate dehydrogenase (NADP+) [Bacillus subtilis] p|P23129|ODO1_BACSU	52	42	387
					2-OXOGLUTARATE DEHYDROGENASE E1 COMPONENT (EC 2.4.2) (ALPHA-KETOGLUTARATE
					DEHYDROGENASE).
4020	1	1	249	gi|159388	ornithine decarboxylase [Leishmania donovani]	52	47	249
4098	1	220	2	gi|409795	No definition line found [Escherichia coli]	52	32	219
4248	1	3	212	gi|965077	Adr6p [Seccharomyces cerevisiae]	52	40	210
7	1	3	575	gi|895747	putative cel operon regulator [Bacillus subtilis]	51	28	573
21	4	2479	3276	gi|1510962	indole-3-glycerol phosphate synthase [Methanococcus jannaschii]	51	32	798
22	9	5301	5966	gi|1303933	YqiN [Bacillus subtilis]	51	25	666
43	3	1283	1050	gi|1519460	Srp1 [Schizosaccharomyces pombe]	51	31	234
44	17	11042	11305	gi|42011	moaD gene product [Escherichia coli]	51	35	264
51	11	6453	6731	gi|495471	vacuolating toxin [Helicobacter pylori]	51	37	279
52	4	2537	2995	gi|1256652	25% identity to the E. coli regulatory protein MprA; putative [Bacillus	51	32	459
					subtilis]
57	10	6843	6355	gi|508173	EIIA domain of PTS-dependent Gat transport and phosphorylation Escherichia	51	32	489
					coli]
59	1	29	1111	gi|299163	alanine dehydrogenase [Bacillus subtilis]	51	33	1083
67	20	15791	16576	gi|1510977	M. jannaschii predicted coding region MJ0938 [Methanococcus jannaschii]	51	24	786
69	2	1218	877	gi|467359	unknown [Bacillus subtilis]	51	34	342
71	1	3	1196	gi|298032	EF [Streptococcus suis]	51	32	1194
78	2	176	3	gi|1161242	proliferating cell nuclear antigen [Styela clava]	51	28	174
99	4	3357	4040	gi|642795	TFIID subunit TAFII55 [Homo sapiens]	51	25	684
109	1	1428	4	gi|580920	rodD (gtaA) polypeptide (AA 1-673) [Bacillus subtilis] pir|S06048|S06048	51	27	1425
					probable rodD protein - Bacillus subtilis sp|P13484|TAGE_BACSU PROBABLE
					POLY (GLYCEROL-PHOSPHATE) LPHA-GLUCOSYLTRANSFERASE (EC 2.4.1.52) (TECHOIC
					ACID BIOSYNTHESIS ROTEIN E)
109	9	6007	6693	gi|1204815	hypothetical protein (SP: P32662) [Haemophilus influenzae]	51	23	687
112	3	1066	2352	pir|S05330|S053	maltose-binding protein precursor - Enterobacter aerogenes	51	42	1287
112	13	12855	11278	gi|405857	yehU [Escherichia coli]	51	29	1578
114	9	8967	8209	gi|435098	orf1 [Mycoplasma capricolum]	51	30	759
115	1	1	912	gi|1431110	ORF YDL085w [Saccharomyces cerevisiae]	51	25	912
127	10	9647	10477	gi|1204314	H. influenzae predicted coding region HI0056 [Haemophilus influenzae]	51	37	831
152	9	6814	7356	gi|431929	MunI regulatory protein [Mycoplasma sp.]	51	38	543
154	2	575	1153	gi|1237044	unknown [Mycobacterium tuberculosis]	51	36	579
154	7	5634	4681	gi|409286	bmrU [Bacillus subtilis]	51	27	954
171	8	6236	5529	gi|1205484	hypothetical protein (SP: P33918) [Haemophilus influenzae]	51	32	708
184	1	1	291	gi|466886	B1496_C3_206 [Mycobacterium leprae]	51	33	291
212	5	1501	2139	pir|A45605|A456	mature-parasite-infected erythrocyte surface antigen MESA - Plasmodium	51	23	639
					falciparum
228	2	707	1378	gi|8204	nuclear protein [Drosophila melanogaster]	51	27	672
236	8	7481	6825	gi|49272	Asparaginase [Bacillus licheniformis]	51	31	657
243	4	3546	2455	gi|1511102	melvalonate kinase [Methanococcus jannaschii]	51	29	1092
257	4	3373	3206	gi|1204579	H. influenzae predicted coding region HI0326 [Haemophilus influenzae]	51	22	168
258	3	1609	821	gi|160299	glutamic acid-rich protein [Plasmodium falciparum] pir|A54514|A54514	51	34	789
					glutamic acid-rich protein precursor - Plasmodium falciparum
265	5	2419	3591	gi|580841	F1 [Bacillus subtilis]	51	32	1173
298	2	518	748	gi|1336162	SCPB [Streptococcus agalactiae|	51	34	231
316	9	5817	7049	gi|413953	ipa-29d gene product [Bacillus subtilis]	51	39	1233
332	2	2057	339	gi|1209012	mutS [Thermus aquaticus thermophilus]	51	26	1719
364	4	3816	4991	gi|528991	unknown [Bacillus subtilis]	51	32	1176
440	2	448	684	gi|2819	transferase (GAL10) (AA 1-687) [Kluyveromyces lactis] r|S01407|XUVKG	51	32	237
					UDPglucose 4-epimerase (EC 5.1.3.2) - yeast uyveromyces marxianus var.
					lactis)
495	2	1177	1001	gi|297861	protease G [Erwinia chrysanthemi]	51	41	177
495	3	1718	1149	gi|1513317	serine rich protein [Entamoeba histolytica]	51	25	570
506	1	421	2	gi|455320	cII protein [Bacteriophage P4]	51	33	420
600	1	983	492	gi|587532	orf, len: 201, CAI: 0.16 [Saccharomyces cerevisiae] pir|S48818|S48818	51	30	492
					hypothetical protein - yeast (Saccharomyces erevisiae)
607	3	479	934	gi|1511524	hypothetical protein (SP: P37002) [Methanococcus jannaschii]	51	40	456
686	2	127	600	gi|493017	endocarditis specific antigen [Enterococcus faecalis]	51	30	474
726	1	33	230	gi|1353851	unknown [Prochlorococcus marinus]	51	45	198
861	1	176	652	gi|410145	dehydroquinate dehydratase [Bacillus subtilis]	51	34	477
869	1	393	4	gi|40100	rodC (tag3) polypeptide (AA 1-746) [Bacillus subtilis] ir|S06049|S06049	51	23	390
					rodC protein - Bacillus subtilis p|P13485|TAGF_BACSU TECHOIC ACID
					BIOSYNTHESIS PROTEIN F.
1003	1	322	2	gi|1279707	hypothetical phosphoglycerate mutase [Saccharomyces cerevisiae]	51	39	321
1046	2	624	382	gi|510257	glycosyltransferase [Escherichia coli]	51	29	243
1467	1	352	2	gi|1511175	M. jannaschii predicted coding region MJ1177 [Methanococcus jannaschii]	51	32	351
2558	1	230	3	sp|P10582|DPOM—	DNA POLYMERASE (EC 2.7.7.7) (S-1 DNA ORF 3).	51	26	228
3003	1	399	19	gi|809543	CbrC protein [Erwinia chrysanthemi]	51	27	381
3604	1	1	399	pir|JC4210|JC42	3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) - mouse	51	37	399
3732	1	2	316	gi|145906	acyl-CoA synthetase [Escherichia coli]	51	33	315
3791	1	2	274	gi|1061351	semaphorin III family homolog [Homo sapiens]	51	37	273
3995	1	46	336	gi|216346	surfactin synthetase [Bacillus subtilis]	51	38	291
4193	1	307	2	gi|42749	ribosomal protein L12 (AA 1-179) [Escherichia coli] ir|S04776|XXECPL	51	25	306
					peptide N-acetyltransferase rimL (EC 2.3.1.—) - Echerichia coli
4539	1	185	3	gi|1408494	homologous to penicillin acylase [Bacillus subtilis]	51	40	183
4562	1	239	36	gi|1458280	coded for by C. elegans cDNA cm01e7; Similar to hydroxymethylglutaryl-CoA	51	35	204
					synthase [Caenorhabditis elegans]
1	4	3576	4859	gi|559160	GRAIL score: null; cap site and late promoter motifs present pstream;	50	44	1284
					putative [Autographa californica nuclear polyhedrosis irus]
11	7	4044	5165	gi|1146207	putative [Bacillus subtilis]	50	35	1122
11	13	9496	8483	gi|1208451	hypothetical protein [Synechocystis sp.]	50	39	1014
19	1	1018	2	gi|413966	ipa-42d gene product [Bacillus subtilis]	50	29	1017
20	11	8407	8228	gi|1323159	ORF YGR103w [Saccharomyces cerevisiae]	50	28	180
24	5	4824	4240	gi|496280	structural protein [Bacteriophage Tuc2009]	50	29	585
34	4	1926	2759	gi|1303966	Yqj0 [Bacillus subtilis]	50	36	834
38	30	22865	23440	gi|1072179	Similar to dihydroflavonol-4-reductase (maize, petunia, tomato)	50	32	576
					[Caenorhabditis elegans]
47	2	1705	2976	gi|153015	FemA protein [Staphylococcus aureus]	50	29	1272
56	13	15290	15841	gi|606096	ORF_f167; end overlaps end of o100 by 14 bases; start overlaps f174, ther	50	30	552
					starts possible [Escherichia coli]
57	1	1077	19	gi|640922	xylitol dehydrogenase (unidentified hemiascomycete)	50	29	1059
58	2	628	1761	gi|143725	putative [Bacillus subtilis]	50	29	1134
88	6	3884	3375	gi|1072179	Similar to dihydroflavonol-4-reductase (maize, petunia, tomato)	50	32	510
					[Caenorhabditis elegans]
89	5	3356	3012	gi|1276658	ORF174 gene product [Porphyra purpurea]	50	25	345
141	1	3	239	gi|476024	carbamoyl phosphate synthetase II [Plasmodium falciparum]	50	33	237
151	1	186	626	gi|1403441	unknown [Mycobacterium tuberculosis]	50	35	441
166	7	9623	8181	gi|895747	putative cel operon regulator [Bacillus subtilis]	50	32	1443
201	6	5096	4908	gi|160229	circumsporozoite protein [Plasmodium reichenowi]	50	42	189
206	22	29555	28326	gi|1052754	LmrP integral membrane protein [Lactococcus lactis]	50	24	1230
211	4	1523	1927	gi|410131	ORFX7 [Bacillus subtilis]	50	29	405
214	4	2411	3295	sp|P37348|YECE—	HYPOTHETICAL PROTEIN IN ASPS 5′ REGION (FRAGMENT)	50	37	885
228	7	4406	3744	gi|313580	envelope protein [Human immunodeficiency virus type 1] pir|S35835|S35835	50	35	663
					envelope protein - human immunodeficiency virus type 1 (fragment) (SUB 1-
					77)
272	2	1723	398	gi|1408485	B65G gene product [Bacillus subtilis]	50	22	1326
273	2	984	352	gi|984186	phosphoglycerate mutase [Saccharomyces cerevisiae]	50	28	633
328	2	1605	703	gi|148896	lipoprotein [Haemophilus influenzae]	50	26	903
332	4	3802	2135	gi|1526547	DNA polymerase family X [Thermus aquaticus]	50	27	1668
342	5	3473	3931	gi|456562	G-box binding factor [Dictyostelium discoideum]	50	35	459
352	1	741	4	gi|288301	ORF2 gene product [Bacillus megaterium]	50	29	738
408	7	5299	5523	gi|11665	ORF2136 [Marchantia polymorpha]	50	27	225
420	3	650	1825	gi|757842	UDP-sugar hydrolase [Escherichia coli]	50	30	1176
464	1	1	591	gi|487282	Na+ -ATPase subunit J [Enterococcus hirae]	50	29	591
472	2	864	310	gi|551875	Bg1R [Lactococcus lactis]	50	23	555
520	1	23	541	gi|567036	CapE [Staphylococcus aureus]	50	27	519
529	1	6	410	gi|1256652	25% identity to the E. coli regulatory protein MprA; putative [Bacillus	50	34	405
					subtilis ]
534	5	6059	4392	gi|295671	selected as a weak suppressor of a mutant of the subunit AC40 of DNA	50	18	1668
					ependant RNA polymerase I and III [Saccharomyces cerevisiae]
647	1	1497	4	gi|405568	TraI protein shares sequence similarity with a family of opoisomerases	50	31	1494
					[Plasmid pSK41]
664	3	711	289	gi|410007	leukocidin F component [Staphylococcus aureus, MRSA No. 4, Peptide, 23 aa]	50	32	423
678	1	1	627	gi|298032	EF [Streptococcus suis]	50	29	627
755	3	947	1171	gi|150572	cytochrome c1 precursor (EC 1.10.2.2) [Paracoccus denitrificans] gi|45465	50	37	225
					cytochrome c1 (AA 1-450) [Paracoccus denitrificans] pir|C29413|C29413
					ubiquinol - cytochrome-c reductase (EC 1.10.2.2) ytochrome c1 precursor -
					Paracoccus denitrificans sp|P13627|CY1
827	1	683	3	gi|142020	heterocyst differentiation protein [Anabaena sp.]	50	21	681
892	1	3	752	gi|1408485	B65G gene product [Bacillus subtilis]	50	27	750
910	2	438	887	gi|1204727	tyrosine-specific transport protein [Haemophilus influenzae]	50	25	450
933	1	524	760	gi|1205451	cell division inhibitor [Haemophilus influenzae]	50	32	237
973	1	236	48	gi|886947	orf3 gene product [Saccharomyces cerevisiae]	50	40	189
1009	1	429	205	gi|153727	M protein [group G streptococcus]	50	28	225
1027	1	257	3	gi|413934	ipa-10r gene product [Bacillus subtilis]	50	25	255
1153	2	326	96	gi|773676	nccA [Alcaligenes xylosoxydans]	50	36	231
1222	1	400	2	gi|1408485	B65G gene product [Bacillus subtilis]	50	21	399
1350	1	399	106	gi|289272	ferrichrome-binding protein [Bacillus subtilis]	50	32	294
2945	1	184	2	gi|171704	hexaprenyl pyrophosphate synthetase (COQ1) [Saccharomyces erevisiae]	50	34	183
2968	2	804	4	gi|397526	clumping factor [Staphylococcus aureus]	50	33	801
2998	2	394	131	gi|495696	F54E7.3 gene product [Caenorhabditis elegans]	50	40	264
3046	2	306	106	pir|S13819|S138	acyl carrier protein - Anabaena variabilis (fragment)	50	32	201
3063	1	275	3	gi|474190	iucA gene product [Escherichia coli]	50	29	273
3174	1	3	146	gi|151900	alcohol dehydrogenase [Rhodobacter sphaeroides]	50	31	144
3792	1	314	3	gi|1001423	hypothetical protein [Synechocystis sp.]	50	35	312
3800	1	2	262	gi|144733	NAD-dependent beta-hydroxybutyryl coenzyme A dehydrogenase Clostridium	50	28	261
					acetobutylicum]
3946	1	188	3	gi|576765	cytochrome b [Myrmecia pilosula]	50	38	186
3984	1	291	4	sp|P37348|YECE—	HYPOTHETICAL PROTEIN IN ASPS 5′ REGION (FRAGMENT).	50	37	288
37	10	7885	7520	gi|1204367	hypothetical protein (GB: U14003_278) [Haemophilus influenzae]	49	30	366
46	16	13802	14848	gi|466860	acd: B1308_F1_34 [Mycobacterium leprae]	49	24	1047
59	5	2267	3601	gi|606304	ORF_o462 [Escherichia coli]	49	27	1335
112	18	17884	18615	gi|559502	ND4 protein (AA 1-409) [Caenorhabditis elegans]	49	25	732
138	9	6973	7902	gi|303953	esterase [Acinetobacter calcoaceticus]	49	29	930
217	6	4401	5138	gi|496254	fibronectin/fibrinogen-blnding protein [Streptococcus pyogenes]	49	31	738
220	12	11803	12657	gi|397526	clumping factor [Staphylococcus aureus]	49	31	855
228	4	1842	2492	pir|S23692|S236	hypothetical protein 9 - Plasmodium falciparum	49	24	651
268	1	2614	212	gi|143047	ORFB [Bacillus subtilis]	49	26	2403
271	2	1164	1373	gi|1001257	hypothetical protein [Synechocystis sp.]	49	38	210
300	3	3180	2020	gi|1510796	hypothetical protein (GP: X91006_2) [Methanococcus jannaschii]	49	26	1161
381	1	1142	3	gi|396301	matches PS00041: Bacterial regulatory proteins, araC family ignature	49	29	1140
					[Escherichia coli]
466	1	3	947	gi|1303863	YqgP [Bacillus subtilis]	49	26	945
666	1	191	3	gi|633112	ORF1 [Streptococcus sobrinus]	49	29	189
670	2	403	1014	gi|1122758	unknown [Bacillus subtilis]	49	32	612
709	1	795	157	gi|143830	xpaC [Bacillus subtilis]	49	29	639
831	1	473	3	gi|401786	phosphomannomutase [Mycoplasma pirum]	49	29	471
1052	1	213	4	gi|1303799	YqeN [Bacillus subtilis]	49	21	210
1800	1	172	2	gi|216300	peptidoglycan synthesis enzyme [Bacillus subtilis] sp|P37585|MURG_BACSU	49	28	171
					MURG PROTEIN UPD-N-ACETYLGLUCOSAMINE—N-ACETYLMURAMYL-
					PENTAPEPTIDE) PYROPHOSPHORYL-UNDECAPRENOL N-ACETYLGLUCOSAMINE RANSFERASE).
2430	1	2	376	sp|P27434|YFGA—	HYPOTHETICAL 36.2 KD PROTEIN IN NDK-GCPE INTERGENIC REGION.	49	26	375
3096	1	273	4	gi|516360	surfactin synthetase [Bacillus subtilis]	49	25	270
32	4	3100	2429	gi|1217963	hepatocyte nuclear factor 4 gamma (HNF4gamma) [Homo sapiens]	48	36	672
38	1	1	609	gi|1205790	H. influenzae predicted coding region HI1555 [Haemophilus influenzae]	48	28	609
45	6	5021	6427	gi|1524267	unknown [Mycobacterium tuberculosis]	48	20	1407
59	14	16346	31096	gi|1197336	Lmp3 protein [Mycoplasma hominis]	48	28	14751
61	1	3	608	gi|1511555	quinolone resistance norA protein protein [Methanococcus jannaschii]	48	30	606
61	3	3311	3646	gi|1303893	YqhL [Bacillus subtilis]	48	29	336
114	1	98	415	gi|671708	su(s) homolog; similar to Drosophila melanogaster suppressor of able	48	25	318
					(su(s)) protein, Swiss-Prot Accession Number P22293 Drosophila virilis)
121	1	610	89	gi|1314584	unknown [Sphingomonas S88]	48	29	522
136	1	1280	546	gi|1205968	H. influenzae predicted coding region HI1738 [Haemophilus influenzae]	48	23	735
171	10	8220	9557	gi|1208454	hypothetical protein [Synechocystis sp.]	48	34	1338
175	1	1814	3	gi|396400	similar to eukaryotic Na+/H+ exchangers [Escherichia coli]	48	29	1812
					sp|P32703|YJCE_ECOLI HYPOTHETICAL 60.5 KD PROTEIN IN SOXR-ACS NTERGENIC
					REGION (O549).
194	1	2	385	gi|1510493	M. jannaschii predicted coding region MJ0419 [Methanococcus jannaschii]	48	25	384
197	1	452	3	gi|1045714	spermidine/putrescine transport ATP-binding protein [Mycoplasma genitalium]	48	25	450
203	1	1	396	gi|940288	protein localized in the nucleoli of pea nuclei; ORF; putative Pisum	48	29	396
					sativum]
204	1	698	33	gi|529202	No definition line found [Caenorhabditis elegans]	48	25	666
206	20	27760	20705	gi|511490	gramicidin S synthetase 2 [Bacillus brevis]	48	27	7056
212	1	2	166	gi|295899	nucleolin [Xenopus laevis]	48	34	165
220	10	11426	10200	gi|44073	SecY protein [Lactococcus lactis]	48	23	1227
243	6	5491	4532	gi|1184118	mevalonate kinase [Methanobacterium thermoautotrophicum]	48	30	960
264	4	3308	1182	gi|1015903	ORF YJR151c [Saccharomyces cerevisiae]	48	26	2127
441	1	768	4	gi|142863	replication initiation protein [Bacillus subtilis] pir|B26580|B26580	48	23	765
					replication initiation protein - Bacillus subtilis
444	5	3898	5298	gi|145836	putative [Escherichia coli]	48	24	1401
484	2	388	1110	gi|146551	transmembrane protein (kdpD) [Escherichia coli]	48	18	723
542	3	1425	2000	pir|S28969|S289	N-carbamoylsarcosine amidohydrolase (EC 3.5.1.59) - Arthrobacter sp.	48	27	576
566	1	3	1019	gi|153490	tetracenomycin C resistance and export protein [Streptomyces laucescens]	48	24	1017
611	1	2	730	gi|1103507	unknown [Schizosaccharomyces pombe]	48	38	729
624	1	665	75	gi|144859	ORF B [Clostridium perfringens]	48	26	591
846	1	508	2	gi|537506	paramyosin [Dirofilaria immitis]	48	27	507
1020	1	66	950	gi|1499876	magnesium and cobalt transport protein [Methanococcus jannaschii]	48	30	885
1227	1	1	174	gi|493730	lipoxygenase [Pisum sativum]	48	35	174
1266	1	1	405	gi|882452	ORF_f211; alternate name yggA; orf5 of X14436 [Escherichia coli] gi|41425	48	24	405
					ORF5 (AA 1-197) [Escherichia coli] (SUB 15-211)
2071	1	381	55	gi|1408486	HS74A gene product [Bacillus subtilis]	48	25	327
2398	1	233	3	gi|1500401	reverse gyrase [Methanococcus jannaschii]	48	40	231
2425	1	246	16	pir|H48563|H485	G1 protein - fowlpox virus (strain HP444) (fragment)	48	40	231
2432	1	225	4	gi|1353703	Trio [Homo sapiens]	48	33	222
2453	1	399	4	gi|142850	division initiation protein [Bacillus subtilis]	48	29	396
2998	1	236	3	gi|577569	PepV [Lactobacillus delbrueckii]	48	31	234
3042	1	14	280	gi|945219	mucin [Homo sapiens]	48	35	267
3686	1	1	405	gi|145836	putative [Escherichia coli]	48	25	405
4027	2	301	110	pir|S51177|S511	trans-activator protein - Equine infectious anemia virus	48	32	192
4	2	2232	823	gi|1303989	YqkI [Bacillus subtilis]	47	24	1410
24	2	599	1084	gi|540083	PC4-1 gene product [Bradysia hygida]	47	28	486
36	10	6925	6326	gi|1209223	esterase [Acinetobacter lwoffii]	47	26	600
43	2	196	1884	gi|1403455	unknown [Mycobacterium tuberculosis]	47	27	1689
44	22	15108	14098	gi|1511555	quinolone resistance norA protein protein [Methanococcus jannaschii]	47	31	1011
69	7	6710	6279	gi|438466	Possible operon with orfG. Hydrophilic, no homologue in the atabase;	47	29	432
					putative [Bacillus subtilis]
81	4	4279	3536	gi|466882	ppsl; B1496_C2_189 [Mycobacterium leprae]	47	24	744
120	12	8863	8591	gi|927340	D9509.27p; CAI: 0.12 [Saccharomyces cerevisiae]	47	38	273
142	1	1174	326	gi|486143	ORF YKL094w [Saccharomyces cerevisiae]	47	32	849
168	1	1093	8	gi|1177254	hypothetical EcsB protein [Bacillus subtilis]	47	29	1086
263	1	943	2	gi|142822	D-alanine racemase cds [Bacillus subtilis]	47	34	942
279	1	561	13	gi|516608	2 predicted membrane helices, homology with B. subtilis men Orf3 Rowland	47	31	549
					et. al. unpublished Accession number M74183), approximately 1 minutes on
					updated Rudd map; putative [Escherichia coli] sp|P37355|YFBB_ECOLI
					HYPOTHETICAL 26.7 KD PROTEIN IN MEND-MENB
345	2	1676	732	gi|1204835	hippuricase [Haemophilus influenzae]	47	28	945
389	2	152	400	gi|456562	G-box binding factor [Dictyostelium discoideum]	47	32	249
391	1	1	831	gi|1420856	myo-inositol transporter [Schizosaccharomyces pombe]	47	19	831
404	3	2072	2773	gi|1255425	C33G8.2 gene product [Caenorhabditis elegans]	47	17	702
529	5	2145	3107	gi|1303973	YqjV [Bacillus subtilis]	47	29	963
565	2	1257	193	gi|142824	processing protease [Bacillus subtilis]	47	28	1065
654	1	483	4	gi|243353	ORF 5′ of ECRF3 [herpesvirus saimiri HVS, host-squirrel monkey, eptide, 407	47	23	480
					aa]
692	1	115	633	gi|150756	40 kDa protein [Plasmid pJM1]	47	25	519
765	1	819	4	gi|1256621	26.7% of identity in 165 aa to a Thermophilic bacterium hypothetical	47	28	816
					protein 6; putative [Bacillus subtilis]
825	2	211	1023	gi|397526	clumping factor [Staphylococcus aureus]	47	32	813
914	1	1	615	gi|558073	polymorphic antigen [Plasmodium falciparum]	47	29	615
1076	1	1	753	gi|1147557	Aspartate aminotransferase [Bacillus circulans]	47	33	753
1351	1	398	3	gi|755153	ATP-binding protein [Bacillus subtilis]	47	20	396
4192	1	3	293	gi|145836	putative [Escherichia coli]	47	24	291
5	6	4361	4014	gi|305080	myosin heavy chain [Entamoeba histolytica]	46	30	348
11	4	2777	3058	gi|603639	Ye1040p [Saccharomyces cerevisiae]	46	28	282
46	11	10300	10082	gi|1246901	ATP-dependent DNA ligase [Candida albicans]	46	28	219
61	4	3941	7930	gi|298032	EF [Streptococcus suis]	46	35	3990
132	4	4093	3158	gi|1511057	hypothetical protein SP: P45869 [Methanococcus jannaschii]	46	25	936
170	4	3652	2585	pir|S51910|S519	G4 protein - sauroleishmania tarentolae	46	26	1068
191	7	8284	7025	gi|1041334	F54D5.7 [Caenorhabditis elegans]	46	25	1260
253	1	1	396	gi|1204449	dihydrolipoamide acetyltransferase [Haemophilus influenzae]	46	35	396
264	3	437	973	gi|180189	cerebellar-degeneration-related antigen (CDR34) [Homo sapiens] gi|182737	46	29	537
					cerebellar degeneration-associated protein [Homo sapiens]
					pir|A29770|A29770 cerebellar degeneration-related protein - human
273	1	285	85	gi|607573	envelope glycoprotein C2V3 region [Human immunodeficiency virus type]	46	35	201
350	1	3	563	gi|537052	ORF_E286 [Escherichia coli]	46	35	561
384	1	2	862	gi|1221884	(urea?) amidolyase [Haemophilus influenzae]	46	31	861
410	4	1876	2490	gi|1110518	proton antiporter efflux pump [Mycobacterium smegmatis]	46	24	615
432	1	1455	247	gi|1197634	orf4; putative transporter; Method: conceptual translation supplied by	46	27	1209
					author [Mycobacterium smegmatis]
458	1	1211	3	gi|15470	portal protein [Bacteriophage SPP1]	46	30	1209
517	5	2477	4192	gi|1523812	orf5 [Bacteriophage A2]	46	23	1716
540	3	1285	1058	gi|215635	pacA [Bacteriophage P1]	46	30	228
587	2	649	1242	gi|537148	ORF_f181 [Escherichia coli]	46	29	594
1218	1	391	35	gi|1205456	single-stranded-DNA-specific exonuclease [Haemophilus influenzae]	46	30	357
3685	1	1	402	gi|450688	hsdM gene of EcoprrI gene product [Escherichia coli] pir|S38437|S38437 hsdM	46	33	402
					protein - Escherichia coli pir|S09629|S09629 hypothetical protein A -
					Escherichia coli (SUB 40-520)
4176	1	338	3	gi|951460	FIM-C.1 gene product [Xenopus laevis]	46	31	336
37	7	4813	5922	gi|606064	ORF_f408 [Escherichia coli]	45	24	1110
38	16	11699	12004	gi|452192	protein tyrosine phosphatase (PTP-BAS, type 2) [Homo sapiens]	45	24	306
87	2	1748	2407	gi|1064813	homologous to sp: PHOR_BACSU [Bacillus subtilis]	45	23	660
103	12	13385	12588	gi|1001307	hypothetical protein [Synechocystis sp.]	45	22	798
112	14	13811	12831	gi|1204389	H. influenzae predicted coding region HI0131 [Haemophilus influenzae]	45	23	981
145	4	3461	2439	gi|220578	open reading frame [Mus musculus]	45	20	1023
170	6	4965	3601	gi|238657	AppC = cytochrome d oxidase, subunit I homolog [Escherichia coli, K12,	45	27	1365
					eptide, 514 aa]
206	2	4346	3462	gi|1222056	aminotransferase [Haemophilus influenzae]	45	27	885
228	1	60	716	gi|160299	glutamic acid-rich protein [Plasmodium falciparum] pir|A54514|A54514	45	23	657
					glutamic acid-rich protein precursor - Plasmodium alciparum
288	1	2	1015	gi|1255425	C33G8.2 gene product [Caenorhabditis elegans]	45	23	1014
313	3	3128	1917	gi|581140	NADH dehydrogenase [Escherichia coli]	45	30	1212
332	1	459	4	gi|870966	F47A4.2 [Caenorhabditis elegans]	45	20	456
344	1	3	221	gi|171225	kinesin-related protein [Saccharomyces cerevisiae]	45	26	219
441	2	1073	645	gi|142863	replication initiation protein [Bacillus subtilis] pir|B26580|B26580	45	27	429
					replication initiation protein - Bacillus subtilis
672	1	2	982	gi|1511334	M. jannaschii predicted coding region MJ1323 [Methanococcus jannaschii]	45	22	981
763	3	851	357	gi|606180	ORF_f310 [Escherichia coli]	45	24	495
886	3	379	846	gi|726426	similar to protein kinases and C. elegans proteins F37C12.8 and 37C12.5	45	30	468
					[Caenorhabditis elegans]
948	1	3	473	gi|156400	myosin heavy chain (isozyme unc-54) [Caenorhabditis elegans]	45	25	471
					pir|A93958|MWKW myosin heavy chain B - Caenorhabditis elegans
					sp|P02566|MYSB_CAEEL MYOSIN HEAVY CHAIN B (MHC B).
1158	1	2	376	gi|441155	ransmission-blocking target antigen [Plasmodium falciparum]	45	35	375
2551	1	4	285	gi|1276705	ORF287 gene product [Porphyra purpurea]	45	28	282
3967	1	42	374	gi|976025	MrsA [Escherichia coli]	45	28	333
52	7	5846	4761	gi|467378	unknown [Bacillus subtilis]	44	22	1086
138	8	6475	6849	gi|173028	thioredoxin II [Saccharomyces cerevisiae]	44	28	375
221	5	5617	4202	gi|153490	tetracenomycin C resistance and export protein [Streptomyces laucescens]	44	21	1416
252	2	1122	913	gi|1204989	hypothetical protein (GB: U00022_9) [Haemophilus influenzae]	44	30	210
263	2	2093	921	gi|1136221	carboxypeptidase [Sulfolobus solfataricus]	44	26	1173
365	4	3524	2085	gi|1296822	orf1 gene product [Lactobacillus helveticus]	44	31	1440
543	3	1315	1833	gi|1063250	low homology to P20 protein of Bacillus lichiniformis and bleomycin	44	24	519
					acetyltransferase of Streptomyces verticillus [Bacillus subtilis]
544	4	3942	4892	gi|951460	FIM-C.1 gene product [Xenopus laevis]	44	32	951
792	1	613	2	gi|205680	high molecular weight neurofilament [Rattus norveglcus]	44	28	612
44	18	11303	11911	gi|1511614	molybdopterin-guanine dinucleotide biosynthesis protein A [Methanococcus	43	27	609
					jannaschii ]
59	8	3665	5128	gi|153490	tetracenomycin C resistance and export protein [Streptomyces laucescens]	43	21	1464
59	10	5536	7527	gi|153022	lipase Staphylococcus epidermidis]	43	22	1992
99	1	681	16	gi|1419051	unknown [Mycobacterium tuberculosis]	43	21	666
310	8	9402	12134	gi|397526	clumping factor [Staphylococcus aureus]	43	21	2733
432	3	2303	1824	pir|A60540|A605	sporozoite surface protein 2 - Plasmodium yoelii (fragment)	43	29	480
519	3	2547	3122	sp|Q06530|DHSU—	SULFIDE DEHYDROGENASE (FLAVOCYTOCHROME C) FLAVOPROTEIN CHAIN PRECURSOR (EC	43	23	576
					1.8.2.—) (FC) (FCSD).
4	13	12053	13321	gi|295671	selected as a weak suppressor of a mutant of the subunit AC40 of DNA	42	18	1269
					ependant RNA polymerase I and III [Saccharomyces cerevisiae]
94	2	1091	414	gi|501027	ORF2 [Trypanosoma brucei]	42	31	678
127	4	4550	3309	gi|42029	ORF1 gene product [Escherichia coli]	42	21	1242
297	3	1036	557	gi|142790	ORF1; putative [Bacillus firmus]	42	25	480
344	6	3525	2953	gi|40320	ORF 2 (AA 1-203) [Bacillus thuringiensis]	42	30	573
512	1	1115	63	gi|405957	yeeF [Escherichia coli]	42	23	1053
631	1	1223	12	gi|580920	rodD (gtaA) polypeptide (AA 1-673) [Bacillus subtilis] pir|S06048|S06048	42	24	1212
					probable rodD protein - Bacillus subtilis sp|P13484|TAGE_BACSU PROBABLE
					POLY(GLYCEROL-PHOSPHATE) LPHA-GLUCOSYLTRANSFERASE (EC 2.4.1.52) (TECHOIC
					ACID BIOSYNTHESIS ROTEIN E).
685	3	1739	1119	gi|1303784	YqeD [Bacillus subtilis]	42	19	621
4132	1	395	3	gi|1022910	protein tyrosine phosphatase [Dictyostelium discoideum]	42	25	393
86	2	884	393	gi|309506	spermidine/spermine N1-acetyltransferase [Mus saxicola] pir|S43430|S43430	41	30	492
					spermidine/spermine N1-acetyltransferase - spiny ouse (Mus saxicola)
191	12	14075	13353	gi|1124957	orf4 gene product [Methanosarcina barkeri]	41	22	723
212	6	2150	3127	gi|15873	observed 35.2 Kd protein [Mycobacteriophage 15]	41	26	978
213	3	1263	2000	gi|633692	TrsA [Yersinia enterocolitica]	41	18	738
408	4	2625	3386	gi|1197634	orf4; putative transporter; Method: conceptual translation supplied by	41	24	762
					author [Mycobacterium smegmatis]
542	1	3	1103	gi|457146	rhoptry protein [Plasmodium, yoelii]	41	21	1101
924	1	2	475	pir|JH0148|JH01	nucleolin - rat	41	30	474
1562	1	1	402	gi|552184	asparagine-rich antigen Pfa35-2 [Plasmodium falciparum] pir|S27826|S27826	40	20	402
					asparagine-rich antigen Pfa35-2 - Plasmodium alciparum (fragment)
2395	1	261	4	pir|S42251|S422	hypothetical protein 5 - fowlpox virus	40	18	258
4077	1	3	305	gi|1055055	coded for by C. elegans cDNA yk37g1.5; coded for by C. elegans cDNA	39	21	303
					yk5c9.5; coded for by C. elegans cDNA yk1a9.5; alternatively spliced form
					of F52C9.8b [Caenorhabditis elegans]
958	1	503	3	gi|1255425	C33G8.2 gene product [Caenorhabditis elegans]	37	25	501
59	12	8294	10636	gi|535260	STARP antigen [Plasmodium reichenowi]	36	24	2343
63	5	3550	8079	gi|298032	EF [Streptococcus suis]	36	19	4530
544	3	2507	3601	gi|1015903	ORF YJR151c [Saccharomyces cerevisiae]	35	22	1095
63	4	1949	3574	gi|552195	circumsporozoite protein (Plasmodium falciparum) sp|P05691|CSP_PLAFL	32	27	1626
					CIRCUMSPOROZOITE PROTEIN (CS) (FRAGMENT).

[0290]

TABLE 3
S. aureus - Putative coding regions of
novel proteins not similar to known proteins
	Contig	ORF	Start	Stop
	ID	ID	(nt)	(nt)
	4	1	692	150
	4	3	1712	2278
	4	4	3032	2361
	4	14	12585	12097
	5	2	1601	663
	5	3	1532	1771
	5	7	4550	4359
	5	9	6422	4905
	5	12	8547	8383
	6	4	1982	1605
	8	1	176	3
	11	8	5144	5983
	11	9	5968	6498
	11	10	6284	6096
	11	16	10954	11271
	12	5	4942	4532
	12	6	4596	4862
	15	3	1650	1405
	16	10	10835	10407
	18	2	917	741
	20	9	7764	6403
	20	10	8230	7889
	20	12	8803	8405
	20	13	10470	8782
	23	1	339	4
	23	6	5485	4832
	23	8	5942	5508
	23	9	6881	6111
	23	15	12618	12830
	24	4	4185	3814
	24	6	5241	4840
	25	2	1824	2402
	31	2	505	849
	31	3	1177	1524
	31	4	2454	3005
	32	2	765	1388
	32	9	7952	8575
	32	10	8591	8728
	32	11	9379	9020
	32	12	10087	9377
	34	2	1049	783
	36	7	5226	5801
	36	11	7261	6947
	36	12	7424	7621
	37	4	2964	2770
	38	2	980	375
	38	11	6425	6868
	38	20	16371	15760
	38	26	20253	20804
	38	27	20722	21264
	39	1	1	627
	40	1	404	3
	43	1	428	60
	44	4	2324	1974
	44	5	2484	3263
	44	14	10129	9671
	44	20	13536	13348
	44	21	13596	13994
	45	7	6297	6019
	46	8	6365	6520
	46	12	10449	10976
	46	17	15032	15424
	47	1	288	1079
	48	9	7620	7778
	50	1	962	312
	50	2	1316	1011
	51	1	370	2
	51	5	2245	1970
	53	1	287	132
	53	7	6319	5933
	54	7	8709	8404
	55	1	326	60
	55	3	786	520
	56	1	1	261
	56	3	1228	905
	56	4	1560	1150
	56	17	18712	18332
	57	4	3521	3348
	57	8	5436	5822
	58	9	8553	8221
	59	3	1366	1509
	59	6	2802	2578
	59	7	3570	3370
	59	9	4563	4180
	59	11	7518	8378
	59	13	10401	16403
	62	2	1521	346
	62	11	5440	5757
	63	1	1	336
	67	1	900	1781
	67	2	1774	2610
	67	3	2591	3904
	67	8	6955	6800
	68	1	78	326
	70	6	5199	3637
	70	11	8645	8355
	77	3	1192	794
	79	2	1228	947
	79	3	1411	1791
	83	1	2	403
	85	9	8300	8653
	85	10	8781	8593
	86	3	1232	1038
	87	8	9187	9366
	88	3	1620	1922
	89	1	3	161
	89	7	4878	4714
	91	1	550	2
	91	3	3141	2344
	92	2	449	928
	92	3	1467	976
	92	9	5638	6024
	94	1	332	3
	94	3	1813	1181
	94	4	2197	1811
	96	11	10601	11050
	99	6	4523	4374
	99	7	4784	4554
	100	8	7287	6916
	102	7	4368	4039
	103	3	2035	1574
	104	1	2	694
	104	2	699	1277
	105	1	693	151
	105	3	2655	2077
	106	1	3	221
	106	3	1209	1355
	107	1	542	3
	109	4	3651	3277
	109	13	11625	11996
	109	14	11981	12268
	109	20	17401	17688
	110	1	2	760
	114	10	8764	9384
	116	1	1	309
	116	3	4462	2651
	116	8	9976	8903
	116	9	10158	10003
	120	5	3320	2937
	120	6	3869	3468
	120	13	9290	9844
	121	2	417	569
	126	3	818	546
	127	3	2648	3196
	127	5	4084	4395
	131	6	6438	6103
	132	2	715	1695
	134	1	2	667
	135	2	258	4
	135	3	729	334
	138	1	3	152
	138	7	6008	6463
	140	1	1032	4
	140	2	1513	1007
	140	5	2387	2743
	142	2	1360	2388
	142	7	7586	6342
	143	7	6502	5714
	144	1	640	53
	146	1	2	511
	146	3	502	1350
	146	4	2540	1407
	146	5	2874	3071
	147	1	1	339
	149	11	3615	3274
	149	12	3785	3534
	149	13	4145	3783
	149	15	4610	4413
	149	16	5049	4603
	149	18	5491	5243
	149	21	7054	6692
	149	23	8521	7826
	149	24	9106	8531
	149	25	9897	9115
	150	2	1587	871
	154	3	1508	1221
	154	8	6398	6210
	154	14	12147	11590
	154	15	12803	12075
	156	1	315	593
	157	3	1183	2232
	158	2	1064	657
	159	3	452	808
	161	2	876	1808
	161	6	4279	3905
	161	7	4540	4277
	161	8	4717	4538
	161	11	5638	5459
	163	2	840	76
	163	5	2344	1892
	163	7	2647	2342
	163	9	4905	5132
	164	3	1147	956
	166	3	4854	4495
	168	4	2500	2868
	168	5	3595	4158
	170	3	2517	2777
	171	2	1450	623
	171	11	11125	9674
	172	1	3	278
	172	2	1149	358
	173	1	708	127
	173	5	6114	5227
	174	2	593	1105
	175	3	2552	2890
	175	5	3335	2850
	175	7	4342	4506
	182	4	4986	4495
	184	5	5702	5361
	188	2	1210	1755
	188	4	2647	2994
	189	6	2614	3039
	190	3	1998	2564
	191	1	1	153
	191	2	669	388
	191	10	11786	13039
	191	11	12363	11824
	192	1	91	426
	195	3	1932	1558
	195	5	2606	2313
	198	2	1016	1591
	201	1	170	625
	203	2	783	1466
	206	6	7815	6700
	206	12	13636	13325
	206	21	27960	27712
	212	2	170	817
	212	3	796	1167
	212	7	3128	3436
	212	9	3749	4075
	213	1	1	705
	214	2	570	64
	214	6	3738	3412
	214	9	6600	6995
	214	10	7469	7074
	217	1	965	3
	218	1	178	657
	218	3	1776	2156
	220	2	1369	887
	220	3	2262	1273
	220	7	7208	6141
	220	8	8661	7078
	220	9	10216	8636
	221	4	2613	2131
	221	9	10757	10086
	226	1	3	659
	226	2	1459	722
	226	3	1476	1961
	227	1	2	487
	227	2	460	975
	227	4	1855	2121
	227	5	2052	2345
	227	6	3768	2776
	227	9	5591	6367
	228	5	2503	2877
	228	6	2846	3526
	233	7	3762	3580
	236	2	579	349
	238	2	1391	807
	239	2	905	393
	241	5	4334	4173
	242	2	1363	1049
	243	1	127	576
	244	1	647	3
	244	2	1962	889
	245	2	1258	902
	246	1	69	215
	246	4	738	1733
	249	3	3712	3518
	250	1	249	4
	254	1	1	156
	256	2	956	1144
	257	3	3227	2754
	260	4	4580	4254
	261	4	2196	2606
	261	6	3214	3681
	264	2	155	439
	264	5	4533	3814
	264	6	4739	5107
	267	2	931	539
	268	4	4700	4260
	272	1	446	30
	272	3	1200	1439
	272	9	4691	4909
	272	10	6035	5601
	276	4	1746	1901
	278	1	224	553
	278	5	3299	3448
	278	7	4849	5127
	285	2	551	736
	288	3	1756	1950
	288	5	2055	2276
	289	1	1055	3
	290	2	1932	1630
	291	2	332	622
	291	5	1545	2051
	295	3	1349	1092
	295	4	2141	1554
	295	5	2220	2762
	297	2	465	142
	298	1	2	205
	300	2	1928	1476
	301	7	2624	2454
	304	1	3	194
	306	1	109	654
	306	5	4036	4257
	307	1	339	4
	307	8	3645	3995
	308	1	1	654
	308	2	599	78
	308	4	2332	2021
	313	2	1919	1524
	314	1	10	702
	316	2	982	1341
	316	6	2758	3165
	317	1	2	1114
	317	3	3458	2346
	321	6	5217	4789
	321	7	6140	5961
	321	8	6794	6138
	322	2	543	259
	326	2	165	1112
	326	3	1117	1467
	328	1	469	2
	328	5	3276	3100
	329	1	3	719
	329	2	781	1212
	329	3	1471	1833
	330	1	289	2
	330	3	1447	1623
	332	3	2204	2055
	332	7	4971	5138
	333	2	3128	2961
	335	1	433	2
	337	2	95	526
	340	2	1356	1054
	341	1	3	281
	341	3	2476	3192
	341	5	3618	3944
	341	6	3929	4558
	344	5	2889	2581
	345	1	768	4
	346	2	221	592
	350	3	1410	1598
	352	2	1765	1352
	352	3	4596	1876
	352	7	7967	8404
	352	8	8906	9247
	352	9	9854	9537
	359	1	1	546
	362	1	3	656
	364	2	1808	1458
	364	8	10714	10454
	365	2	1313	1014
	365	5	4090	3500
	365	7	4980	6239
	366	3	520	1719
	367	3	906	1085
	368	1	494	240
	375	1	2	136
	380	3	1097	843
	389	1	1	276
	390	1	2	877
	390	2	1373	1549
	391	2	560	369
	395	1	197	3
	396	1	1068	4
	398	3	1141	938
	399	1	178	669
	401	3	566	847
	402	2	100	465
	404	8	5370	5179
	408	2	2269	1031
	408	3	2672	2469
	408	5	3524	4423
	410	3	1890	1669
	413	1	488	96
	416	1	320	33
	416	2	578	847
	416	3	1590	985
	417	1	3	179
	417	2	161	616
	420	2	513	238
	422	2	357	677
	431	2	856	1407
	432	2	446	1084
	433	1	1	417
	433	3	2033	1755
	434	1	535	128
	434	2	1235	381
	440	1	1	450
	442	2	1269	3320
	443	3	1520	1167
	444	1	1	696
	444	7	6366	5971
	451	1	614	288
	453	2	636	376
	453	8	3833	4786
	453	9	4512	4306
	453	10	4731	4525
	455	1	219	4
	455	2	472	930
	459	1	265	687
	462	1	2	247
	466	2	907	320
	467	1	349	44
	468	1	2	250
	469	1	925	362
	469	3	2386	3372
	469	4	3464	3706
	470	1	77	538
	470	6	3694	3290
	470	7	5686	5042
	470	9	7351	8181
	470	10	8175	9773
	471	1	500	60
	471	2	1017	472
	476	1	70	267
	477	1	2	760
	477	3	1764	2081
	477	4	2066	2332
	480	5	4016	4261
	481	2	480	4
	486	3	613	774
	487	6	1795	2112
	488	1	359	3
	492	1	127	675
	493	1	2	520
	493	2	496	1242
	502	3	1149	1571
	504	1	346	2
	505	5	4150	3734
	511	2	1232	723
	512	2	583	747
	515	1	609	812
	517	4	2179	2511
	520	4	2097	2360
	520	6	3669	3430
	527	1	1	498
	528	1	335	33
	529	2	1104	529
	530	7	5298	5534
	536	1	156	4
	538	1	736	110
	538	3	2203	2880
	538	5	3121	2711
	538	6	3731	3114
	540	1	664	332
	540	2	1031	567
	541	1	89	433
	541	2	432	145
	542	2	1048	1272
	545	2	734	456
	551	1	1129	113
	555	2	704	516
	558	3	1154	951
	558	4	1458	1156
	558	5	1821	1537
	558	6	2020	1874
	558	7	2322	2008
	558	8	2802	2551
	558	9	3453	2920
	560	1	475	921
	565	3	1485	1264
	571	1	156	4
	571	3	994	1206
	577	1	2	199
	577	2	163	453
	579	1	1	477
	579	2	1200	616
	583	1	996	4
	585	1	539	132
	587	1	22	573
	588	2	1372	848
	588	3	1554	1366
	590	1	47	334
	592	2	1141	827
	593	1	2	775
	593	2	817	1122
	595	1	87	890
	596	3	1435	1277
	602	1	8	169
	603	5	1071	1469
	606	1	322	768
	607	5	1226	1008
	610	1	541	53
	612	1	3	500
	616	1	650	309
	617	2	491	246
	622	1	36	347
	625	4	2046	2549
	627	1	67	210
	628	1	452	3
	631	3	4004	3219
	634	1	759	70
	636	1	189	368
	636	2	1063	197
	637	2	1994	1665
	638	1	227	1081
	639	1	261	4
	639	2	811	245
	641	1	118	444
	642	3	1331	1047
	642	4	1847	1434
	643	1	3	608
	645	4	1534	1758
	645	6	2025	2321
	645	7	2488	2036
	648	1	2	1045
	660	1	77	601
	660	2	576	872
	661	1	961	197
	664	2	89	304
	667	1	3	413
	668	1	1	330
	671	2	516	220
	673	1	3	338
	674	2	584	303
	679	1	1	237
	679	3	1589	1906
	688	1	835	434
	688	2	1077	802
	694	1	3	143
	696	2	432	46
	706	1	224	81
	709	3	1183	1449
	711	1	3	908
	715	1	3	167
	716	1	2	637
	721	1	133	570
	722	1	383	3
	723	1	829	2
	723	2	1112	726
	727	1	2	472
	729	1	268	441
	731	1	130	828
	735	1	2	214
	736	1	3	782
	738	1	2	298
	742	1	3	230
	745	3	780	412
	748	2	282	464
	749	1	344	3
	751	1	452	3
	755	1	97	522
	755	2	520	918
	758	2	400	137
	764	2	746	459
	767	1	1	405
	768	1	2	373
	771	1	534	10
	778	1	902	69
	785	1	1023	256
	787	1	631	2
	791	1	3	224
	799	1	15	260
	804	1	304	711
	805	1	3	680
	808	1	219	842
	810	1	1112	3
	810	2	1442	1110
	812	1	38	979
	817	1	358	2
	818	2	487	1104
	819	2	1032	535
	819	3	1419	1090
	820	1	195	1064
	828	1	255	4
	829	1	48	800
	830	1	291	4
	832	1	298	2
	835	1	320	796
	840	3	491	709
	845	1	457	2
	850	2	303	449
	853	1	359	3
	860	1	2	256
	864	1	18	410
	864	2	383	715
	864	6	1676	1828
	870	1	1	588
	873	1	454	2
	875	1	294	4
	877	1	1020	379
	878	1	544	107
	879	1	785	3
	881	1	1	243
	882	1	389	604
	890	1	2	508
	905	1	398	3
	906	1	544	236
	912	1	188	3
	913	1	3	290
	913	2	547	2
	915	1	6	161
	915	2	169	402
	921	1	126	386
	927	1	808	38
	928	1	2	385
	929	1	2	400
	932	1	2	400
	934	1	1	384
	936	1	528	4
	937	1	2	616
	945	1	220	645
	945	2	649	1242
	946	1	950	198
	949	1	1	270
	951	1	3	362
	955	1	3	143
	960	1	400	77
	963	1	1	162
	965	1	346	2
	966	1	606	133
	969	1	3	302
	971	1	12	170
	974	1	161	3
	976	1	348	4
	977	1	2	211
	982	1	982	38
	984	1	296	3
	987	1	3	467
	993	1	1	525
	994	1	549	178
	1004	1	318	79
	1014	1	313	2
	1015	1	2	463
	1016	1	145	2
	1019	1	660	115
	1022	1	474	109
	1024	1	299	3
	1024	2	276	431
	1030	1	338	3
	1032	1	179	3
	1040	1	399	4
	1043	1	3	269
	1044	2	115	399
	1047	1	1	159
	1051	1	354	4
	1051	2	733	233
	1063	1	2	400
	1069	1	2	148
	1069	2	533	297
	1075	1	399	91
	1077	1	97	405
	1081	1	58	438
	1086	1	1	384
	1087	2	246	431
	1088	1	3	374
	1096	1	238	2
	1098	1	509	3
	1100	1	511	2
	1100	2	1158	796
	1101	1	353	3
	1102	1	194	3
	1107	1	2	580
	1114	1	3	422
	1115	1	2	268
	1119	1	22	267
	1129	1	40	342
	1132	1	181	2
	1133	1	376	143
	1144	1	225	4
	1147	1	280	2
	1153	1	1	153
	1154	1	3	818
	1159	1	1	330
	1161	1	186	31
	1164	1	254	81
	1171	1	19	240
	1171	2	108	299
	1183	1	2	379
	1195	1	179	3
	1196	1	1	189
	1200	1	33	197
	1203	2	129	464
	1222	2	105	401
	1232	1	1	387
	1240	1	2	175
	1247	1	311	102
	1271	1	221	30
	1286	1	2	595
	1295	1	1	165
	1306	1	185	3
	1314	2	158	631
	1316	1	58	570
	1359	1	193	2
	1370	1	1	402
	1371	1	1	345
	1374	1	357	4
	1378	1	2	400
	1392	1	3	413
	1411	1	202	432
	1433	1	167	3
	1450	1	2	256
	1453	1	149	3
	1471	1	398	75
	1477	1	639	409
	1502	1	399	4
	1518	1	126	449
	1534	1	143	3
	1546	1	3	401
	1547	1	255	4
	1583	1	3	350
	1587	1	3	563
	1602	2	170	679
	1629	1	1	402
	1665	1	235	2
	1760	1	314	3
	1762	1	3	200
	1876	2	119	286
	1895	1	2	379
	1931	1	400	2
	1976	2	383	51
	2055	2	252	401
	2056	1	167	3
	2150	1	263	3
	2157	1	399	4
	2164	1	283	2
	2175	1	218	400
	2212	1	331	170
	2338	1	367	2
	2342	1	3	167
	2352	1	166	2
	2352	2	398	174
	2355	1	47	352
	2356	1	341	3
	2359	1	152	3
	2421	1	150	4
	2422	1	306	43
	2443	1	263	99
	2454	1	3	158
	2463	1	253	2
	2485	1	3	374
	2557	1	246	4
	2575	1	2	355
	2582	1	3	284
	2607	1	1	294
	2930	1	17	400
	2939	1	242	18
	2944	1	3	359
	2945	2	399	97
	2952	1	2	190
	2953	1	399	61
	2964	1	166	2
	2969	1	144	4
	2977	1	2	373
	2981	2	334	167
	2986	1	7	279
	2991	1	363	118
	2995	1	1	321
	3007	1	191	39
	3017	1	308	48
	3018	2	136	351
	3025	1	197	3
	3040	1	180	4
	3046	1	185	3
	3049	1	278	3
	3050	1	3	314
	3052	1	253	2
	3065	1	2	157
	3070	1	190	23
	3075	1	222	4
	3080	1	1	285
	3092	1	162	4
	3093	1	250	89
	3100	1	52	237
	3103	1	47	298
	3118	1	174	4
	3123	1	2	145
	3127	1	1	147
	3138	1	169	2
	3142	1	203	18
	3144	1	386	108
	3151	1	170	3
	3155	2	202	384
	3168	1	12	176
	3205	1	145	2
	3282	1	1	150
	3303	2	239	400
	3371	2	211	399
	3558	1	2	148
	3558	2	36	401
	3568	1	377	3
	3595	1	380	3
	3618	1	2	238
	3618	2	130	402
	3622	1	86	358
	3622	2	398	132
	3642	1	439	2
	3649	1	398	15
	3651	1	314	3
	3664	1	467	637
	3674	1	55	402
	3677	1	311	3
	3704	1	1	402
	3726	1	269	3
	3765	1	256	2
	3779	1	357	160
	3794	1	135	4
	3794	2	377	87
	3796	2	375	112
	3801	1	262	50
	3806	1	298	143
	3807	1	42	389
	3815	1	400	2
	3827	1	3	320
	3842	1	392	3
	3853	1	399	127
	3855	1	1	324
	3857	1	2	235
	3861	1	297	4
	3865	1	399	103
	3897	1	3	173
	3897	2	143	400
	3898	2	225	401
	3921	2	103	342
	3927	1	70	375
	3930	1	76	234
	3946	2	382	113
	3951	2	105	377
	3965	1	344	42
	3973	1	400	5
	3981	1	3	311
	3998	1	3	356
	4001	1	296	111
	4003	1	90	335
	4018	1	2	259
	4018	2	186	401
	4021	1	1	345
	4043	1	3	344
	4054	1	3	344
	4066	1	1	150
	4070	1	1	324
	4072	2	187	390
	4073	1	1	285
	4077	2	127	372
	4083	1	3	359
	4090	1	27	368
	4101	1	103	297
	4105	1	1	306
	4107	1	286	2
	4119	1	339	49
	4121	1	372	4
	4123	1	3	230
	4127	1	3	341
	4128	1	2	331
	4130	1	415	62
	4146	1	97	381
	4157	1	3	206
	4186	1	254	3
	4224	1	256	2
	4239	1	1	348
	4242	1	356	3
	4252	1	296	3
	4253	1	1	174
	4256	1	323	78
	4258	2	334	170
	4267	1	144	4
	4271	1	2	304
	4287	1	163	23
	4289	1	319	167
	4302	1	153	305
	4304	1	1	186
	4304	2	96	314
	4306	1	2	151
	4318	1	289	2
	4322	1	5	148
	4331	1	221	3
	4331	2	364	200
	4338	1	399	70
	4346	1	277	83
	4367	2	117	311
	4373	1	2	268
	4381	1	326	78
	4384	1	309	4
	4397	1	9	311
	4402	1	1	249
	4403	1	328	50
	4406	1	3	317
	4411	1	2	280
	4411	2	398	99
	4412	1	2	364
	4418	1	3	230
	4424	1	398	195
	4443	1	215	3
	4471	1	323	3
	4478	1	271	2
	4482	1	50	289
	4489	1	302	3
	4491	1	12	206
	4495	1	3	179
	4496	1	252	4
	4500	1	130	306
	4511	1	248	3
	4518	1	1	246
	4526	1	241	2
	4527	1	2	163
	4532	1	3	239
	4542	1	11	175
	4567	1	36	200
	4573	1	1	231
	4578	1	322	2
	4619	1	1	180
	4620	1	176	3
	4662	1	1	246
	4669	1	2	157
	4680	1	28	183
	4690	1	174	4

[0291]

Claims

1. An isolated polynucleotide comprising a nucleic acid fragment of the Staphylococcus aureus genome, wherein said fragment consists of the nucleotide sequence of any one of SEQ ID NOS: 1-5,191 as depicted in Tables 2 and 3.

2. A vector comprising the polynucleotide of claim 1.

3. An organism which has been altered to contain the polynucleotide of claim 1.

4. An isolated polypeptide encoded by any one of the fragments of the Staphylococcus aureus genome of SEQ ID NOS: 1-5,191 and depicted in Tables 2 and 3.

5. An antibody which specifically binds the polypeptide of claim 4.

6. An isolated polynucleotide encoding the polypeptide of claim 4.

7. A vector comprising the polynucleotide of claim 6.

8. An organism which has been altered to contain the polynucleotide of claim 6.

9. A method for producing a polypeptide in a host cell comprising the steps of: (a) incubating a host containing a heterologous nucleic acid molecule whose nucleotide sequence consists of the polynucleotide of claim 6 under conditions where said heterologous nucleic acid molecule is expressed to produce said polypeptide, and (b) isolating said polypeptide.

10. An isolated polypeptide comprising an amino acid sequence identical to a Staphylococcus aureus polypeptide amino acid sequence selected from the group consisting of SEQ ID NOS: 5,192 to 5,255.