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Publication numberUS20040043037 A1
Publication typeApplication
Application numberUS 10/329,624
Publication dateMar 4, 2004
Filing dateDec 27, 2002
Priority dateJan 5, 1996
Also published asUS6593114
Publication number10329624, 329624, US 2004/0043037 A1, US 2004/043037 A1, US 20040043037 A1, US 20040043037A1, US 2004043037 A1, US 2004043037A1, US-A1-20040043037, US-A1-2004043037, US2004/0043037A1, US2004/043037A1, US20040043037 A1, US20040043037A1, US2004043037 A1, US2004043037A1
InventorsCharles Kunsch, Gil Choi, Steven Barash, Patrick Dillon, Michael Fannon, Craig Rosen
Original AssigneeHuman Genome Sciences, Inc.
Export CitationBiBTeX, EndNote, RefMan
External Links: USPTO, USPTO Assignment, Espacenet
Staphylococcus aureus polynucleotides and sequences
US 20040043037 A1
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.
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Claims(10)
What is claimed is:
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.
Description
CROSS REFERENCE TO RELATED APPLICATIONS

[0001] This application is a divisional of and claims priority under 35 U.S.C. 120 to U.S. application Ser. No. 08/956,171, filed Oct. 20, 1997, which is a continuation-in-part of and claims priority under 35 U.S.C. 120 to U.S. application Ser. No. 08/781,986, filed Jan. 3, 1997, which is a non-provisional of and claims benefit under 35 U.S.C. 119(e) of U.S. Provisional Application No. 60/009,861, filed Jan. 5, 1996.

REFERENCE TO A SEQUENCE LISTING PROVIDED ON COMPACT DISC

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

FIELD OF THE INVENTION

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

BACKGROUND OF THE INVENTION

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

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

[0006] Human Health and S. Aureus

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

[0008] Burns

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

[0010] Cellulitis

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

[0012] Eyelid Infections

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

[0014] Food Poisoning

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

[0016] Joint Infections

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

[0018] Osteomyelitis

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

[0020] Skin Infections

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

[0022] Surgical Wound Infections

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

[0024] Scalded Skin Syndrome

[0025]S. aureus is responsible for “scalded skin syndrome” (also called toxic epidermal necrosis, Ritter'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 2.5109 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 1109 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 29 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 2 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