Nucleic acid and amino acid sequences relating to Staphylococcus epidermidis for diagnostics and therapeutics

Information

  • Patent Grant
  • 7608450
  • Patent Number
    7,608,450
  • Date Filed
    Monday, August 22, 2005
    19 years ago
  • Date Issued
    Tuesday, October 27, 2009
    15 years ago
Abstract
The invention provides isolated polypeptide and nucleic acid sequences derived from Staphylococcus epidermidis that are useful in diagnosis and therapy of pathological conditions; antibodies against the polypeptides; and methods for the production of the polypeptides. The invention also provides methods for the detection, prevention and treatment of pathological conditions resulting from bacterial infection.
Description
REFERENCE TO A SEQUENCE LISTING

The Sequence Listing which accompanies this application on one compact disk and which contains SEQ ID NOS: 1-5676 is incorporated herein by reference in their entirety.


FIELD OF THE INVENTION

The invention relates to isolated nucleic acids and polypeptides derived from Staphylococcus epidermidis that are useful as molecular targets for diagnostics, prophylaxis and treatment of pathological conditions, as well as materials and methods for the diagnosis, prevention, and amelioration of pathological conditions resulting from bacterial infection.


BACKGROUND OF THE INVENTION


Staphylococcus epidermidis (S. epidermidis) is a species of staphylococcal bacteria that are Gram-positive, nonmotile, nonpigmented and coagulase-negative cocci, which are mainly found on the skin and mucous membrane of warm-blooded animals. Their large numbers and ubiquitous distribution result in frequent contamination of specimens collected from or through the skin, making these organisms amongst the most frequently isolated in the clinical laboratory. In the past, S. epidermidis was rarely the cause of significant infections, but with the increasing use of implanted catheters and prosthetic devices, it has emerged as an important agent of hospital-acquired infections and has been recognized as a true pathogen (Lowy and Hammer, 1983, Ann Inten Med, 99: 834-9; Blum and Rodvold, 1987, Clin Pharm, 6: 464-75; Hamory, Parisi et al., 1987, Am J Infect Control, 15:59-74). S. epidermidis is a major cause of infection of indwelling foreign devices such as, orthopedic devices, intravenous catheters, prosthetic heart valves, central nervous system shunts, and peritoneal dialysis catheters (Blum and Rodvold, 1987, Clin Pharm, 6: 464-75; Archer, 1988, J Antimicrob Chemother, 21 Suppl C: 133-8)(Lowy and Hammer, 1983, Ann Intern Med, 99: 834-9; Hamory, Parisi et al., Staphylococcus 1987, Am J Infect Control, 15: 59-74). In addition S. epidermidis is a common cause of postoperative wound infections, bacteremia of immunosuppressed patients, intensive-care unit patients and premature newborns (MacLowry, 1983, Am J Med, 75: 2-6) (Eykyn, 1988, Lancet, 1: 100-4). According to a national survey (Centers for Disease Control, 1981:7) S. epidermidis caused 8.9% of primary nosocomial bacteremias.


Treatment of S. epidermidis infections remains difficult because of the occult nature, association with foreign bodies, and frequent resistance to antimicrobial agents. Ordinarily, S. epidermidis is an organism with low virulence, however breaks in host defense caused by surgery, catheter placement, prosthesis insertion or immuno-suppression is prerequisite for infection. The presence of foreign bodies itself facilitates infection by protecting the organism from elimination by host defenses or antimicrobial therapy (Lowy and Hammer, 1983, Ann Intern Med, 99: 834-9). Furthermore, S. epidermidis due to its ability to produce extracellular polysaccharide material or slime, may be uniquely adapted to adhere to smooth surfaces such as plastics or metal. Slime producing strains of S. epidermidis appear to be more pathogenic than non-slime producing strains (Christensen, Simpson et al., 1983, Infect Immun, 40: 407-10; Peters and Pulverer, 1984, J Antimicrob Chemother, 14 Suppl D: 67-71; Gallimore, Gagnon et al., 1991, J Infect Dis, 164: 1220-3). This property and many factors are involved in the pathogenesis of device associated infections. Despite the increased recognition as a pathogen, S. epidermidis infections are difficult to diagnose. Differentiating clinically important from clinically unimportant bacterial isolates of S. epidermidis is difficult because of the high rate of contamination.


Although laboratory isolates of S. epidermidis have generally been susceptible to semisynthetic penicillins (methicillin, nafcillin, oxacillin), cephalosporins, amino-glycosides, vancomycin and rafampin, recent clinical isolates have had an increased resistance. Recent reports (Karchmer, 1985, Am J Med, 78: 116-27; Karchmer, 1991, J Hosp Infect, 18 Suppl A: 355-66) show that 83% of S. epidermidis isolates from patients with prosthetic valve endocarditis are methicillin resistant and 32% are gentamicin resistant as well. Multi-drug resistant staphylococci have emerged in the midst of high level use of penicillin and aminoglycosides (Centers for Disease Control and Prevention, 1993 MMWR 42:597; and S. Handwerger et al., 1993, Clin Infect Dis 16:750).


The use of antibiotics for therapeutics and prophylactic purposes, promotes the selection of resistant organisms and the spread of antibiotic resistance genes among bacteria. Previous studies have shown that virtually all staphylococci carry some antibiotic resistance genes on naturally occurring extrachromosomal mobile genetic elements, such as the plasmids. Survey and analysis of plasmids in clinical isolates of S. epidermidis have shown that more that 80% of isolates carry plasmids and in several cases more than one plasmid (Archer et al., 1982, Infect Immmun, 35:627-632; Kloos et al., 1981, Can J Microbiol, 27:271-278; Moller, 1988, J Hosp Infect 12:19-27). Though the most important forms of resistance has been the inactivation of antibiotics, particularly penicillins and cephalosporins, recent clinical isolates have resistance to one or more of the following antibiotics, methicillin, tetracycline, erythromycin, gentamycin, kanamycin and chloramphenicol. In fact due to the wide spread occurrence of plasmids and their involvement in antibiotic resistance, plasmid profiling has been used as an epidemiological reagent to study nosocomial infections. This invention relates to isolated nucleic acids and polypeptides derived from S. epidermidis plasmids that are useful as molecular targets for diagnosis, prophylaxis and treatment of pathological conditions, as well as materials and methods for the diagnosis, prevention, and amelioration of pathological conditions resulting from bacterial infection.


These concerns point to the need for diagnostic tools and therapeutics aimed at proper identification of strain and eradication of virulence. The design of vaccines that will limit the spread of infection and halt transfer of resistance factors is very desirable.


SUMMARY OF THE INVENTION

The present invention fulfills the need for diagnostic tools and therapeutics by providing bacterial-specific compositions and methods for detecting, treating, and preventing bacterial infection, in particular S. epidermidis infection.


The present invention encompasses isolated nucleic acids and polypeptides derived from S. epidermidis that are useful as reagents for diagnosis of bacterial disease, components of effective antibacterial vaccines, and/or as targets for antibacterial drugs including anti-S. epidermidis drugs. They can also be used to detect the presence of S. epidermidis and other Staphylococcus species in a sample; and in screening compounds for the ability to interfere with the S. epidermidis life cycle or to inhibit S. epidermidis infection. They also has use as biocontrol agents for plants.


More specifically, this invention features compositions of nucleic acids corresponding to entire coding sequences of S. epidermidis proteins, including surface or secreted proteins or parts thereof, nucleic acids capable of binding mRNA from S. epidermidis proteins to block protein translation, and methods for producing S. epidermidis proteins or parts thereof using peptide synthesis and recombinant DNA techniques. This invention also features antibodies and nucleic acids useful as probes to detect S. epidermidis infection. In addition, vaccine compositions and methods for the protection or treatment of infection by S. epidermidis are within the scope of this invention.


The nucleotide sequences provided in SEQ ID NO: 1-SEQ ID NO: 2837, a fragment thereof, or a nucleotide sequence at least 99.5% identical to SEQ ID NO: 1-SEQ ID NO: 2837 may be “provided” in a variety of medias 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., the nucleotide sequence provided in SEQ ID NO: 1-SEQ ID NO: 2837, a fragment thereof, or a nucleotide sequence at least 99.5% identical to a sequence contained within SEQ ID NO: 1-SEQ ID NO: 2837. Uses for and methods for providing nucleotide sequences in a variety of media is well known in the art (see e.g., EPO Publication No. EP 0 756 006).


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 media 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 media, 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 person skilled in the art can readily appreciate how any of the presently known computer readable media can be used to create a manufacture comprising computer readable media having recorded thereon a nucleotide sequence of the present invention.


As used herein, “recorded” refers to a process for storing information on computer readable media. A person skilled in the art can readily adopt any of the presently known methods for recording information on computer readable media to generate manufactures comprising the nucleotide sequence information of the present invention.


A variety of data storage structures are available to a person skilled in the art for creating a computer readable media 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 media. 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 person skilled in the art can readily adapt any number of data processor structuring formats (e.g. text file or database) in order to obtain computer readable media having recorded thereon the nucleotide sequence information of the present invention.


By providing the nucleotide sequence of SEQ ID NO: 1-SEQ ID NO: 2837, a fragment thereof, or a nucleotide sequence at least 99.5% identical to SEQ ID NO: 1-SEQ ID NO: 2837 in computer readable form, a person skilled in the art can routinely access the coding sequence information for a variety of purposes. Computer software is publicly available which allows a person skilled in the art to access sequence information provided in a computer readable media. Examples of such computer software include programs of the “Staden Package”, “DNA Star”, “MacVector”, GCG “Wisconsin Package” (Genetics Computer Group, Madison, Wis.) and “NCBI Toolbox” (National Center For Biotechnology Information).


Computer algorithms enable the identification of S. epidermidis open reading frames (ORFs) within SEQ ID NO: 1-SEQ ID NO: 2837 which contain homology to ORFs or proteins from other organisms. Examples of such similarity-search algorithms include the BLAST [Altschul et al., J. Mol. Biol. 215:403-410 (1990)] and Smith-Waterman [Smith and Waterman (1981) Advances in Applied Mathematics, 2:482-489] search algorithms. These algorithms are utilized on computer systems as exemplified below. The ORFs so identified represent protein encoding fragments within the S. epidermidis genome and are useful in producing commercially important proteins such as enzymes used in fermentation reactions and in the production of commercially useful metabolites.


The present invention further provides systems, particularly computer-based systems, which contain the sequence information described herein. Such systems are designed to identify commercially important fragments of the S. epidermidis genome. 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 person skilled in the artcan readily appreciate that any one of the currently available computer-based systems is suitable for use in the present invention. 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. 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.


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 S. epidermidis genome which are similar to, or “match”, a particular target sequence or target motif. A variety of known algorithms are known in the art and have been disclosed publicly, and a variety of commercially available software for conducting homology-based similarity searches are available and can be used in the computer-based systems of the present invention. Examples of such software includes, but is not limited to, FASTA (GCG Wisconsin Package), Bic_SW (Compugen Bioccelerator), BLASTN2, BLASTP2, BLASTX2 (NCBI) and Motifs (GCG). A person skilled in the art 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.


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 person skilled in the art 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 many genes are longer than 500 amino acids, or 1.5 kb in length, and that commercially important fragments of the S. epidermidis genome, such as sequence fragments involved in gene expression and protein processing, will often be shorter than 30 nucleotides.


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 specific functional domain or three-dimensional configuration which is formed upon the folding of the target polypeptide. There are a variety of target motifs known in the art. Protein target motifs include, but are not limited to, enzymatic active sites, membrane-spanning regions, and signal sequences. Nucleic acid target motifs include, but are not limited to, promoter sequences, hairpin structures and inducible expression elements (protein binding sequences).


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 S. epidermidis genome possessing varying degrees of homology to the target sequence or target motif. Such presentation provides a person skilled in the art 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.


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 S. epidermidis genome. In the present examples, implementing software which implement the BLASTP2 and bic_SW algorithms (Altschul et al., J. Mol. Biol. 215:403-410 (1990); Compugen Biocellerator) was used to identify open reading frames within the S. epidermidis genome. A person skilled in the art 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.


The invention features S. epidermidis polypeptides, preferably a substantially pure preparation of a S. epidermidis polypeptide, or a recombinant S. epidermidis polypeptide. In preferred embodiments: the polypeptide has biological activity; the polypeptide has an amino acid sequence at least 60%, 70%, 80%, 90%, 95%, 98%, or 99% identical to an amino acid sequence of the invention contained in the Sequence Listing, preferably it has about 65% sequence identity with an amino acid sequence of the invention contained in the Sequence Listing, and most preferably it has about 92% to about 99% sequence identity with an amino acid sequence of the invention contained in the Sequence Listing; the polypeptide has an amino acid sequence essentially the same as an amino acid sequence of the invention contained in the Sequence Listing; the polypeptide is at least 5, 10, 20, 50, 100, or 150 amino acid residues in length; the polypeptide includes at least 5, preferably at least 10, more preferably at least 20, more preferably at least 50, 100, or 150 contiguous amino acid residues of the invention contained in the Sequence Listing. In yet another preferred embodiment, the amino acid sequence which differs in sequence identity by about 7% to about 8% from the S. epidermidis amino acid sequences of the invention contained in the Sequence Listing is also encompassed by the invention.


In preferred embodiments: the S. epidermidis polypeptide is encoded by a nucleic acid of the invention contained in the Sequence Listing, or by a nucleic acid having at least 60%, 70%, 80%, 90%, 95%, 98%, or 99% homology with a nucleic acid of the invention contained in the Sequence Listing.


In a preferred embodiment, the subject S. epidermidis polypeptide differs in amino acid sequence at 1, 2, 3, 5, 10 or more residues from a sequence of the invention contained in the Sequence Listing. The differences, however, are such that the S. epidermidis polypeptide exhibits a S. epidermidis biological activity, e.g., the S. epidermidis polypeptide retains a biological activity of a naturally occurring S. epidermidis enzyme.


In preferred embodiments, the polypeptide includes all or a fragment of an amino acid sequence of the invention contained in the Sequence Listing; fused, in reading frame, to additional amino acid residues, preferably to residues encoded by genomic DNA 5′ or 3′ to the genomic DNA which encodes a sequence of the invention contained in the Sequence Listing.


In yet other preferred embodiments, the S. epidermidis polypeptide is a recombinant fusion protein having a first S. epidermidis polypeptide portion and a second polypeptide portion, e.g., a second polypeptide portion having an amino acid sequence unrelated to S. epidermidis. The second polypeptide portion can be, e.g., any of glutathione-S-transferase, a DNA binding domain, or a polymerase activating domain. In preferred embodiment the fusion protein can be used in a two-hybrid assay.


Polypeptides of the invention include those which arise as a result of alternative transcription events, alternative RNA splicing events, and alternative translational and postranslational events.


In a preferred embodiment, the encoded S. epidermidis polypeptide differs (e.g., by amino acid substitution, addition or deletion of at least one amino acid residue) in amino acid sequence at 1, 2, 3, 5, 10 or more residues, from a sequence of the invention contained in the Sequence Listing. The differences, however, are such that: the S. epidermidis encoded polypeptide exhibits a S. epidermidis biological activity, e.g., the encoded S. epidermidis enzyme retains a biological activity of a naturally occurring S. epidermidis.


In preferred embodiments, the encoded polypeptide includes all or a fragment of an amino acid sequence of the invention contained in the Sequence Listing; fused, in reading frame, to additional amino acid residues, preferably to residues encoded by genomic DNA 5′ or 3′ to the genomic DNA which encodes a sequence of the invention contained in the Sequence Listing.


The S. epidermidis strain, from which the nucleotide sequences have been sequenced, was deposited on Jul. 10, 1997 in the American Type Culture Collection (ATCC #55998) as strain 18972.


Included in the invention are: allelic variations; natural mutants; induced mutants; proteins encoded by DNA that hybridize under high or low stringency conditions to a nucleic acid which encodes a polypeptide of the invention contained in the Sequence Listing (for definitions of high and low stringency see Current Protocols in Molecular Biology, John Wiley & Sons, New York, 1989, 6.3.1-6.3.6, hereby incorporated by reference); and, polypeptides specifically bound by antisera to S. epidermidis polypeptides, especially by antisera to an active site or binding domain of S. epidermidis polypeptide. The invention also includes fragments, preferably biologically active fragments. These and other polypeptides are also referred to herein as S. epidermidis polypeptide analogs or variants.


The invention further provides nucleic acids, e.g., RNA or DNA, encoding a polypeptide of the invention. This includes double stranded nucleic acids as well as coding and antisense single strands.


In preferred embodiments, the subject S. epidermidis nucleic acid will include a transcriptional regulatory sequence, e.g. at least one of a transcriptional promoter or transcriptional enhancer sequence, operably linked to the S. epidermidis gene sequence, e.g., to render the S. epidermidis gene sequence suitable for expression in a recombinant host cell.


In yet a further preferred embodiment, the nucleic acid which encodes a S. epidermidis polypeptide of the invention, hybridizes under stringent conditions to a nucleic acid probe corresponding to at least 8 consecutive nucleotides of the invention contained in the Sequence Listing; more preferably to at least 12 consecutive nucleotides of the invention contained in the Sequence Listing; more preferably to at least 20 consecutive nucleotides of the invention contained in the Sequence Listing; more preferably to at least 40 consecutive nucleotides of the invention contained in the Sequence Listing.


In another aspect, the invention provides a substantially pure nucleic acid having a nucleotide sequence which encodes a S. epidermidis polypeptide. In preferred embodiments: the encoded polypeptide has biological activity; the encoded polypeptide has an amino acid sequence at least 60%, 70%, 80%, 90%, 95%, 98%, or 99% homologous to an amino acid sequence of the invention contained in the Sequence Listing; the encoded polypeptide has an amino acid sequence essentially the same as an amino acid sequence of the invention contained in the Sequence Listing; the encoded polypeptide is at least 5, 10, 20, 50, 100, or 150 amino acids in length; the encoded polypeptide comprises at least 5, preferably at least 10, more preferably at least 20, more preferably at least 50, 100, or 150 contiguous amino acids of the invention contained in the Sequence Listing.


In another aspect, the invention encompasses: a vector including a nucleic acid which encodes a S. epidermidis polypeptide or a S. epidermidis polypeptide variant as described herein; a host cell transfected with the vector; and a method of producing a recombinant S. epidermidis polypeptide or S. epidermidis polypeptide variant; including culturing the cell, e.g. in a cell culture medium, and isolating a S. epidermidis or S. epidermidis polypeptide variant, e.g., from the cell or from the cell culture medium.


One embodiment of the invention is directed to substantially isolated nucleic acids. Nucleic acids of the invention include sequences comprising at least about 8 nucleotides in length, more preferably at least about 12 nucleotides in length, even more preferably at least about 15-20 nucleotides in length, that correspond to a subsequence of any one of SEQ ID NO: 1-SEQ ID NO: 2837 or complements thereof. Alternatively, the nucleic acids comprise sequences contained within any ORF (open reading frame), including a complete protein-coding sequence, of which any of SEQ ID NO: 1-SEQ ID NO: 2837 forms a part. The invention encompasses sequence-conservative variants and function-conservative variants of these sequences. The nucleic acids may be DNA, RNA, DNA/RNA duplexes, protein-nucleic acid (PNA), or derivatives thereof.


In another aspect, the invention features, a purified recombinant nucleic acid having at least 50%, 60%, 70%, 80%, 90%, 95%, 98%, or 99% homology with a sequence of the invention contained in the Sequence Listing


The invention also encompasses recombinant DNA (including DNA cloning and expression vectors) comprising these S. epidermidis-derived sequences; host cells comprising such DNA, including fungal, bacterial, yeast, plant, insect, and mammalian host cells; and methods for producing expression products comprising RNA and polypeptides encoded by the S. epidermidis sequences. These methods are carried out by incubating a host cell comprising a S. epidermidis-derived nucleic acid sequence under conditions in which the sequence is expressed. The host cell may be native or recombinant. The polypeptides can be obtained by (a) harvesting the incubated cells to produce a cell fraction and a medium fraction; and (b) recovering the S. epidermidis polypeptide from the cell fraction, the medium fraction, or both. The polypeptides can also be made by in vitro translation.


In another aspect, the invention features nucleic acids capable of binding mRNA of S. epidermidis. Such nucleic acid is capable of acting as antisense nucleic acid to control the translation of mRNA of S. epidermidis. A further aspect features a nucleic acid which is capable of binding specifically to a S. epidermidis nucleic acid. These nucleic acids are also referred to herein as complements and have utility as probes and as capture reagents.


In another aspect, the invention features an expression system comprising an open reading frame corresponding to S. epidermidis nucleic acid. The nucleic acid further comprises a control sequence compatible with an intended host. The expression system is useful for making polypeptides corresponding to S. epidermidis nucleic acid.


In another aspect, the invention encompasses: a vector including a nucleic acid which encodes a S. epidermidis polypeptide or a S. epidermidis polypeptide variant as described herein; a host cell transfected with the vector; and a method of producing a recombinant S. epidermidis polypeptide or S. epidermidis polypeptide variant; including culturing the cell, e.g., in a cell culture medium, and isolating the S. epidermidis or S. epidermidis polypeptide variant, e.g., from the cell or from the cell culture medium.


In yet another embodiment of the invention encompasses reagents for detecting bacterial infection, including S. epidermidis infection, which comprise at least one S. epidermidis-derived nucleic acid defined by any one of SEQ ID NO: 1-SEQ ID NO: 2837, or sequence-conservative or function-conservative variants thereof. Alternatively, the diagnostic reagents comprise polypeptide sequences that are contained within any open reading frames (ORFs), including complete protein-coding sequences, contained within any of SEQ ID NO: 1-SEQ ID NO: 2837, or polypeptide sequences contained within any of SEQ ID NO: 2838-SEQ ID NO: 5674, or polypeptides of which any of the above sequences forms a part, or antibodies directed against any of the above peptide sequences or function-conservative variants and/or fragments thereof.


The invention further provides antibodies, preferably monoclonal antibodies, which specifically bind to the polypeptides of the invention. Methods are also provided for producing antibodies in a host animal. The methods of the invention comprise immunizing an animal with at least one S. epidermidis-derived immunogenic component, wherein the immunogenic component comprises one or more of the polypeptides encoded by any one of SEQ ID NO: 1-SEQ ID NO: 2837 or sequence-conservative or function-conservative variants thereof; or polypeptides that are contained within any ORFs, including complete protein-coding sequences, of which any of SEQ ID NO: 1-SEQ ID NO: 2837 forms a part; or polypeptide sequences contained within any of SEQ ID NO: 2838-SEQ ID NO: 5674, or polypeptides of which any of SEQ ID NO: 2838-SEQ ID NO: 5674 forms a part. Host animals include any warm blooded animal, including without limitation mammals and birds. Such antibodies have utility as reagents for immunoassays to evaluate the abundance and distribution of S. epidermidis-specific antigens.


In yet another aspect, the invention provides diagnostic methods for detecting S. epidermidis antigenic components or anti-S. epidermidis antibodies in a sample. S. epidermidis antigenic components are detected by a process comprising: (i) contacting a sample suspected to contain a bacterial antigenic component with a bacterial-specific antibody, under conditions in which a stable antigen-antibody complex can form between the antibody and bacterial antigenic components in the sample; and (ii) detecting any antigen-antibody complex formed in step (i), wherein detection of an antigen-antibody complex indicates the presence of at least one bacterial antigenic component in the sample. In different embodiments of this method, the antibodies used are directed against a sequence encoded by any of SEQ ID NO: 1-SEQ ID NO: 2837 or sequence-conservative or function-conservative variants thereof, or against a polypeptide sequence contained in any of SEQ ID NO: 2838-SEQ ID NO: 5674 or function-conservative variants thereof.


In yet another aspect, the invention provides a method for detecting antibacterial-specific antibodies in a sample, which comprises: (i) contacting a sample suspected to contain antibacterial-specific antibodies with a S. epidermidis antigenic component, under conditions in which a stable antigen-antibody complex can form between the S. epidermidis antigenic component and antibacterial antibodies in the sample; and (ii) detecting any antigen-antibody complex formed in step (i), wherein detection of an antigen-antibody complex indicates the presence of antibacterial antibodies in the sample. In different embodiments of this method, the antigenic component is encoded by a sequence contained in any of SEQ ID NO: 1-SEQ ID NO: 2837 or sequence-conservative and function-conservative variants thereof, or is a polypeptide sequence contained in any of SEQ ID NO: 2838-SEQ ID NO: 5674 or function-conservative variants thereof.


In another aspect, the invention features a method of generating vaccines for immunizing an individual against S. epidermidis. The method includes: immunizing a subject with a S. epidermidis polypeptide, e.g., a surface or secreted polypeptide, or a combination of such peptides or active portion(s) thereof, and a pharmaceutically acceptable carrier. Such vaccines have therapeutic and prophylactic utilities.


In another aspect, the invention features a method of evaluating a compound, e.g. a polypeptide, e.g., a fragment of a host cell polypeptide, for the ability to bind a S. epidermidis polypeptide. The method includes: contacting the Staphylococcus compound with a S. epidermidis polypeptide and determining if the compound binds or otherwise interacts with a S. epidermidis polypeptide. Compounds which bind S. epidermidis are candidates as activators or inhibitors of the bacterial life cycle. These assays can be performed in vitro or in vivo.


In another aspect, the invention features a method of evaluating a compound, e.g. a polypeptide, e.g., a fragment of a host cell polypeptide, for the ability to bind a S. epidermidis nucleic acid, e.g., DNA or RNA. The method includes: contacting the Staphylococcus compound with a S. epidermidis nucleic acid and determining if the compound binds or otherwise interacts with a S. epidermidis polypeptide. Compounds which bind S. epidermidis are candidates as activators or inhibitors of the bacterial life cycle. These assays can be performed in vitro or in vivo.


A particularly preferred embodiment of the invention is directed to a method of screening test compounds for anti-bacterial activity, which method comprises: selecting as a target a bacterial specific sequence, which sequence is essential to the viability of a bacterial species; contacting a test compound with said target sequence; and selecting those test compounds which bind to said target sequence as potential anti-bacterial candidates. In one embodiment, the target sequence selected is specific to a single species, or even a single strain, i.e., the S. epidermidis 18972. In a second embodiment, the target sequence is common to at least two species of bacteria. In a third embodiment, the target sequence is common to a family of bacteria. The target sequence may be a nucleic acid sequence or a polypeptide sequence. Methods employing sequences common to more than one species of microorganism may be used to screen candidates for broad spectrum anti-bacterial activity.


The invention also provides methods for preventing or treating disease caused by certain bacteria, including S. epidermidis, which are carried out by administering to an animal in need of such treatment, in particular a warm-blooded vertebrate, including but not limited to birds and mammals, a compound that specifically inhibits or interferes with the function of a bacterial polypeptide or nucleic acid. In a particularly preferred embodiment, the mammal to be treated is human.







DETAILED DESCRIPTION OF THE INVENTION

The sequences of the present invention include the specific nucleic acid and amino acid sequences set forth in the Sequence Listing that forms a part of the present specification, and which are designated SEQ ID NO: 1-SEQ ID NO: 5674. Use of the terms “SEQ ID NO: 1-SEQ ID NO: 2837,” “SEQ ID NO: 2838-SEQ ID NO: 5674,” and “the sequences depicted in Table 2”, etc., is intended, for convenience, to refer to each individual SEQ ID NO individually, and is not intended to refer to the genus of these sequences. In other words, it is a shorthand for listing all of these sequences individually. The invention encompasses each sequence individually, as well as any combination thereof.


Definitions


“Nucleic acid” or “polynucleotide” as used herein refers to purine- and pyrimidine-containing polymers of any length, either polyribonucleotides or polydeoxyribonucleotides or mixed polyribo-polydeoxyribo nucleotides. This includes single- and double-stranded molecules, i.e., DNA-DNA, DNA-RNA and RNA-RNA hybrids, as well as “protein nucleic acids” (PNA) formed by conjugating bases to an amino acid backbone. This also includes nucleic acids containing modified bases.


A nucleic acid or polypeptide sequence that is “derived from” a designated sequence refers to a sequence that corresponds to a region of the designated sequence. For nucleic acid sequences, this encompasses sequences that are homologous or complementary to the sequence, as well as “sequence-conservative variants” and “function-conservative variants.” For polypeptide sequences, this encompasses “function-conservative variants.” Sequence-conservative variants are those in which a change of one or more nucleotides in a given codon position results in no alteration in the amino acid encoded at that position. Function-conservative variants are those in which a given amino acid residue in a polypeptide has been changed without altering the overall conformation and function of the native polypeptide, including, but not limited to, replacement of an amino acid with one having similar physico-chemical properties (such as, for example, acidic, basic, hydrophobic, and the like): “Function-conservative” variants also include any polypeptides that have the ability to elicit antibodies specific to a designated polypeptide.


An “S. epidermidis-derived” nucleic acid or polypeptide sequence may or may not be present in other bacterial species, and may or may not be present in all S. epidermidis strains. This term is intended to refer to the source from which the sequence was originally isolated. Thus, a S. epidermidis-derived polypeptide, as used herein, may be used, e.g., as a target to screen for a broad spectrum antibacterial agent, to search for homologous proteins in other species of bacteria or in eukaryotic organisms such as fungi and humans, etc.


A purified or isolated polypeptide or a substantially pure preparation of a polypeptide are used interchangeably herein and, as used herein, mean a polypeptide that has been separated from other proteins, lipids, and nucleic acids with which it naturally occurs. Preferably, the polypeptide is also separated from substances, e.g., antibodies or gel matrix, e.g., polyacrylamide, which are used to purify it. Preferably, the polypeptide constitutes at least 10, 20, 50 70, 80 or 95% dry weight of the purified preparation. Preferably, the preparation contains: sufficient polypeptide to allow protein sequencing; at least 1, 10, or 100 mg of the polypeptide.


A purified preparation of cells refers to, in the case of plant or animal cells, an in vitro preparation of cells and not an entire intact plant or animal. In the case of cultured cells or microbial cells, it consists of a preparation of at least 10% and more preferably 50% of the subject cells.


A purified or isolated or a substantially pure nucleic acid, e.g., a substantially pure DNA, (are terms used interchangeably herein) is a nucleic acid which is one or both of the following: not immediately contiguous with both of the coding sequences with which it is immediately contiguous (i.e., one at the 5′ end and one at the 3′ end) in the naturally-occurring genome of the organism from which the nucleic acid is derived; or which is substantially free of a nucleic acid with which it occurs in the organism from which the nucleic acid is derived. The term includes, for example, a recombinant DNA which is incorporated into a vector, e.g., into an autonomously replicating plasmid or virus, or into the genomic DNA of a prokaryote or eukaryote, or which exists as a separate molecule (e.g., a cDNA or a genomic DNA fragment produced by PCR or restriction endonuclease treatment) independent of other DNA sequences. Substantially pure DNA also includes a recombinant DNA which is part of a hybrid gene encoding additional S. epidermidis DNA sequence.


A “contig” as used herein is a nucleic acid representing a continuous stretch of genomic sequence of an organism.


An “open reading frame”, also referred to herein as ORF, is a region of nucleic acid which encodes a polypeptide. This region may represent a portion of a coding sequence or a total sequence and can be determined from a stop to stop codon or from a start to stop codon.


As used herein, a “coding sequence” is a nucleic acid which is transcribed into messenger RNA and/or translated into a polypeptide when placed under the control of appropriate regulatory sequences. The boundaries of the coding sequence are determined by a translation start codon at the five prime terminus and a translation stop code at the three prime terminus. A coding sequence can include but is not limited to messenger. RNA, synthetic DNA, and recombinant nucleic acid sequences.


A “complement” of a nucleic acid as used herein refers to an anti-parallel or antisense sequence that participates in Watson-Crick base-pairing with the original sequence.


A “gene product” is a protein or structural RNA which is specifically encoded by a gene.


As used herein, the term “probe” refers to a nucleic acid, peptide or other chemical entity which specifically binds to a molecule of interest. Probes are often associated with or capable of associating with a label. A label is a chemical moiety capable of detection. Typical labels comprise dyes, radioisotopes, luminescent and chemiluminescent moieties, fluorophores, enzymes, precipitating agents, amplification sequences, and the like. Similarly, a nucleic acid, peptide or other chemical entity which specifically binds to a molecule of interest and immobilizes such molecule is referred herein as a “capture ligand”. Capture ligands are typically associated with or capable of associating with a support such as nitro-cellulose, glass, nylon membranes, beads, particles and the like. The specificity of hybridization is dependent on conditions such as the base pair composition of the nucleotides, and the temperature and salt concentration of the reaction. These conditions are readily discernable to one of ordinary skill in the art using routine experimentation.


“Homologous” refers to the sequence similarity or sequence identity between two polypeptides or between two nucleic acid molecules. When a position in both of the two compared sequences is occupied by the same base or amino acid monomer subunit, e.g., if a position in each of two DNA molecules is occupied by adenine, then the molecules are homologous at that position. The percent of homology between two sequences is a function of the number of matching or homologous positions shared by the two sequences divided by the number of positions compared×100. For example, if 6 of 10 of the positions in two sequences are matched or homologous then the two sequences are 60% homologous. By way of example, the DNA sequences ATTGCC and TATGGC share 50% homology. Generally, a comparison is made when two sequences are aligned to give maximum homology.


Nucleic acids are hybridizable to each other when at least one strand of a nucleic acid can anneal to the other nucleic acid under defined stringency conditions. Stringency of hybridization is determined by: (a) the temperature at which hybridization and/or washing is performed; and (b) the ionic strength and polarity of the hybridization and washing solutions. Hybridization requires that the two nucleic acids contain complementary sequences; depending on the stringency of hybridization, however, mismatches may be tolerated. Typically, hybridization of two sequences at high stringency (such as, for example, in a solution of 0.5×SSC, at 65° C.) requires that the sequences be essentially completely homologous. Conditions of intermediate stringency (such as, for example, 2×SSC at 65° C.) and low stringency (such as, for example 2×SSC at 55° C.), require correspondingly less overall complementarity between the hybridizing sequences. (1×SSC is 0.15 M NaCl, 0.015 M Na citrate).


The terms peptides, proteins, and polypeptides are used interchangeably herein.


As used herein, the term “surface protein” refers to all surface accessible proteins, e.g. inner and outer membrane proteins, proteins adhering to the cell wall, and secreted proteins.


A polypeptide has S. epidermidis biological activity if it has one, two and preferably more of the following properties: (1) if when expressed in the course of a S. epidermidis infection, it can promote, or mediate the attachment of S. epidermidis to a cell; (2) it has an enzymatic activity, structural or regulatory function characteristic of a S. epidermidis protein; (3) or the gene which encodes it can rescue a lethal mutation in a S. epidermidis gene. A polypeptide has biological activity if it is an antagonist, agonist, or super-agonist of a polypeptide having one of the above-listed properties.


A biologically active fragment or analog is one having an in vivo or in vitro activity which is characteristic of the S. epidermidis polypeptides of the invention contained in the Sequence Listing, or of other naturally occurring S. epidermidis polypeptides, e.g., one or more of the biological activities described herein. Especially preferred are fragments which exist in vivo, e.g., fragments which arise from post transcriptional processing or which arise from translation of alternatively spliced RNA's. Fragments include those expressed in native or endogenous cells as well as those made in expression systems, e.g., in CHO (Chinese Hamster Ovary) cells. Because peptides such as S. epidermidis polypeptides often exhibit a range of physiological properties and because such properties may be attributable to different portions of the molecule, a useful S. epidermidis fragment or S. epidermidis analog is one which exhibits a biological activity in any biological assay for S. epidermidis activity. Most preferably the fragment or analog possesses 10%, preferably 40%, more preferably 60%, 70%, 80% or 90% or greater of the activity of S. epidermidis, in any in vivo or in vitro assay.


Analogs can differ from naturally occurring S. epidermidis polypeptides in amino acid sequence or in ways that do not involve sequence, or both. Non-sequence modifications include changes in acetylation, methylation, phosphorylation, carboxylation, or glycosylation. Preferred analogs include S. epidermidis polypeptides (or biologically active fragments thereof) whose sequences differ from the wild-type sequence by one or more conservative amino acid substitutions or by one or more non-conservative amino acid substitutions, deletions, or insertions which do not substantially diminish the biological activity of the S. epidermidis polypeptide. Conservative substitutions typically include the substitution of one amino acid for another with similar characteristics, e.g., substitutions within the following groups: valine, glycine; glycine, alanine; valine, isoleucine, leucine; aspartic acid, glutamic acid; asparagine, glutamine; serine, threonine; lysine, arginine; and phenylalanine, tyrosine. Other conservative substitutions can be made in view of the table below.









TABLE 1







CONSERVATIVE AMINO ACID REPLACEMENTS









For Amino




Acid
Code
Replace with any of





Alanine
A
D-Ala, Gly, beta-Ala, L-Cys, D-Cys


Arginine
R
D-Arg, Lys, D-Lys, homo-Arg, D-homo-Arg,




Met, Ile, D-Met, D-Ile, Orn, D-Orn


Asparagine
N
D-Asn, Asp, D-Asp, Glu, D-Glu, Gln, D-Gln


Aspartic Acid
D
D-Asp, D-Asn, Asn, Glu, D-Glu, Gln, D-Gln


Cysteine
C
D-Cys, S-Me-Cys, Met, D-Met, Thr, D-Thr


Glutamine
Q
D-Gln, Asn, D-Asn, Glu, D-Glu, Asp, D-Asp


Glutamic Acid
E
D-Glu, D-Asp, Asp, Asn, D-Asn, Gln, D-Gln


Glycine
G
Ala, D-Ala, Pro, D-Pro, β-Ala, Acp


Isoleucine
I
D-Ile, Val, D-Val, Leu, D-Leu, Met, D-Met


Leucine
L
D-Leu, Val, D-Val, Leu, D-Leu, Met, D-Met


Lysine
K
D-Lys, Arg, D-Arg, homo-Arg, D-homo-Arg,




Met, D-Met, Ile, D-Ile, Orn, D-Orn


Methionine
M
D-Met, S-Me-Cys, Ile, D-Ile, Leu, D-Leu, Val,




D-Val


Phenylalanine
F
D-Phe, Tyr, D-Thr, L-Dopa, His, D-His, Trp,




D-Trp, Trans-3,4, or 5-phenylproline, cis-3,4, or




5-phenylproline


Proline
P
D-Pro, L-I-thioazolidine-4-carboxylic acid, D-or




L-1-oxazolidine-4-carboxylic acid


Serine
S
D-Ser, Thr, D-Thr, allo-Thr, Met, D-Met,




Met(O), D-Met(O), L-Cys, D-Cys


Threonine
T
D-Thr, Ser, D-Ser, allo-Thr, Met, D-Met,




Met(O), D-Met(O), Val, D-Val


Tyrosine
Y
D-Tyr, Phe, D-Phe, L-Dopa, His, D-His


Valine
V
D-Val, Leu, D-Leu, Ile, D-Ile, Met, D-Met









Other analogs within the invention are those with modifications which increase peptide stability; such analogs may contain, for example, one or more non-peptide bonds (which replace the peptide bonds) in the peptide sequence. Also included are: analogs that include residues other than naturally occurring L-amino acids, e.g., D-amino acids or non-naturally occurring or synthetic amino acids, e.g., β or γ amino acids; and cyclic analogs.


As used herein, the term “fragment”, as applied to a S. epidermidis analog, will ordinarily be at least about 20 residues, more typically at least about 40 residues, preferably at least about 60 residues in length. Fragments of S. epidermidis polypeptides can be generated by methods known to those skilled in the art. The ability of a Staphylococcus fragment to exhibit a biological activity of S. epidermidis polypeptide can be assessed by methods known to those skilled in the art as described herein. Also included are S. epidermidis polypeptides containing residues that are not required for biological activity of the peptide or that result from alternative mRNA splicing or alternative protein processing events.


An “immunogenic component” as used herein is a moiety, such as a S. epidermidis polypeptide, analog or fragment thereof, that is capable of eliciting a humoral and/or cellular immune response in a host animal.


An “antigenic component” as used herein is a moiety, such as a S. epidermidis polypeptide, analog or fragment thereof, that is capable of binding to a specific antibody with sufficiently high affinity to form a detectable antigen-antibody complex.


The term “antibody” as used herein is intended to include fragments thereof which are specifically reactive with S. epidermidis polypeptides.


As used herein, the term “cell-specific promoter” means a DNA sequence that serves as a promoter, i.e., regulates expression of a selected DNA sequence operably linked to the promoter, and which effects expression of the selected DNA sequence in specific cells of a tissue. The term also covers so-called “leaky” promoters, which regulate expression of a selected DNA primarily in one tissue, but cause expression in other tissues as well.


Misexpression, as used herein, refers to a non-wild type pattern of gene expression. It includes: expression at non-wild type levels, i.e., over or under expression; a pattern of expression that differs from wild type in terms of the time or stage at which the gene is expressed, e.g., increased or decreased expression (as compared with wild type) at a predetermined developmental period or stage; a pattern of expression that differs from wild type in terms of increased expression (as compared with wild type) in a predetermined cell type or tissue type; a pattern of expression that differs from wild type in terms of the splicing size, amino acid sequence, post-translational modification, or biological activity of the expressed polypeptide; a pattern of expression that differs from wild type in terms of the effect of an environmental stimulus or extracellular stimulus on expression of the gene, e.g., a pattern of increased or decreased expression (as compared with wild type) in the presence of an increase or decrease in the strength of the stimulus.


As used herein, “host cells” and other such terms denoting microorganisms or higher eukaryotic cell lines cultured as unicellular entities refers to cells which can become or have been used as recipients for a recombinant vector or other transfer DNA, and include the progeny of the original cell which has been transfected. It is understood by individuals skilled in the art that the progeny of a single parental cell may not necessarily be completely identical in genomic or total DNA compliment to the original parent, due to accident or deliberate mutation.


As used herein, the term “control sequence” refers to a nucleic acid having a base sequence which is recognized by the host organism to effect the expression of encoded sequences to which they are ligated. The nature of such control sequences differs depending upon the host organism; in prokaryotes, such control sequences generally include a promoter, ribosomal binding site, terminators, and in some cases operators; in eukaryotes, generally such control sequences include promoters, terminators and in some instances, enhancers. The term control sequence is intended to include at a minimum, all components whose presence is necessary for expression, and may also include additional components whose presence is advantageous, for example, leader sequences.


As used herein, the term “operably linked” refers to sequences joined or ligated to function in their intended manner. For example, a control sequence is operably linked to coding sequence by ligation in such a way that expression of the coding sequence is achieved under conditions compatible with the control sequence and host cell.


The “metabolism” of a substance, as used herein, means any aspect of the expression, function, action, or regulation of the substance. The metabolism of a substance includes modifications, e.g., covalent or non-covalent modifications of the substance. The metabolism of a substance includes modifications, e.g., covalent or non-covalent modification, the substance induces in other substances. The metabolism of a substance also includes changes in the distribution of the substance. The metabolism of a substance includes changes the substance induces in the distribution of other substances.


A “sample” as used herein refers to a biological sample, such as, for example, tissue or fluid isloated from an individual (including without limitation plasma, serum, cerebrospinal fluid, lymph, tears, saliva and tissue sections) or from in vitro cell culture constituents, as well as samples from the environment.


Technical and scientific terms used herein have the meanings commonly understood by one of ordinary skill in the art to which the present invention pertains, unless otherwise defined. Reference is made herein to various methodologies known to those of skill in the art. Publications and other materials setting forth such known methodologies to which reference is made are incorporated herein by reference in their entireties as though set forth in full. The practice of the invention will employ, unless otherwise indicated, conventional techniques of chemistry, molecular biology, microbiology, recombinant DNA, and immunology, which are within the skill of the art. Such techniques are explained fully in the literature. See e.g., Sambrook, Fritsch, and Maniatis, Molecular Cloning; Laboratory Manual 2nd ed. (1989); DNA Cloning, Volumes I and II (D. N Glover ed. 1985); Oligonucleotide Synthesis (M. J. Gait ed, 1984); Nucleic Acid Hybridization (B. D. Hames & S. J. Higgins eds. 1984); the series, Methods in Enzymoloqy (Academic Press, Inc.), particularly Vol. 154 and Vol. 155 (Wu and Grossman, eds.); PCR-A Practical Approach (McPherson, Quirke, and Taylor, eds., 1991); Immunology, 2d Edition, 1989, Roitt et al., C. V. Mosby Company, and New York; Advanced Immunology, 2d Edition, 1991, Male et al., Grower Medical Publishing, New York.; DNA Cloning: A Practical Approach, Volumes I and II, 1985 (D. N. Glover ed.); Oligonucleotide Synthesis, 1984, (M. L. Gait ed); Transcription and Translation, 1984 (Hames and Higgins eds.); Animal Cell Culture, 1986 (R. I. Freshney ed.); Immobilized Cells and Enzymes, 1986 (IRL Press); Perbal, 1984, A Practical Guide to Molecular Cloning; and Gene Transfer Vectors for Mammalian Cells, 1987 (J. H. Miller and M. P. Calos eds., Cold Spring Harbor Laboratory);


Any suitable materials and/or methods known to those of skill can be utilized in carrying out the present invention: however preferred materials and/or methods are described. Materials, reagents and the like to which reference is made in the following description and examples are obtainable from commercial sources, unless otherwise noted.



S. epidermidis Genomic Sequence


This invention provides nucleotide sequences of the genome of S. epidermidis which thus comprises a DNA sequence library of S. epidermidis genomic DNA. The detailed description that follows provides nucleotide sequences of S. epidermidis, and also describes how the sequences were obtained and how ORFs and protein-coding sequences were identified. Also described are methods of using the disclosed S. epidermidis sequences in methods including diagnostic and therapeutic applications. Furthermore, the library can be used as a database for identification and comparison of medically important sequences in this and other strains of S. epidermidis.


To determine the genomic sequence of S. epidermidis, DNA from strain 18972 of S. epidermidis was isolated after Zymolyase digestion, sodium dodecyl sulfate lysis, potassium acetate precipitation, phenol:chloroform extractionand ethanol precipitation (Soll, D. R., T. Srikantha and S. R. Lockhart: Characterizing Developmentally Regulated Genes in S. epidermidis. In Microbial Genome Methods. K. W. Adolph, editor. CRC Press. New York. p 17-37.). DNA was sheared hydrodynamically using an HPLC (Oefner, et. al., 1996) to an insert size of 2000-3000 bp. After size fractionation by gel electrophoresis the fragments were blunt-ended, ligated to adapter oligonucleotides and cloned into the pGTC (Thomann) vector to construct a “shotgun” subclone library


DNA sequencing was achieved using established ABI sequencing methods on ABI377 automated DNA sequencers. The cloning and sequencing procedures are described in more detail in the Exemplification.


Individual sequence reads were assembled using PHRAP (P. Green, Abstracts of DOE Human Genome Program Contractor-Grantee Workshop V, January 1996, p. 157). The average contig length was about 3-4 kb.


All subsequent steps were based on sequencing by ABI377 automated DNA sequencing methods. The cloning and sequencing procedures are described in more detail in the Exemplification.


A variety of approaches are used to order the contigs so as to obtain a continuous sequence representing the entire S. epidermidis genome. Synthetic oligonucleotides are designed that are complementary to sequences at the end of each contig. These oligonucleotides may be hybridized to libaries of S. epidermidis genomic DNA in, for example, lambda phage vectors or plasmid vectors to identify clones that contain sequences corresponding to the junctional regions between individual contigs. Such clones are then used to isolate template DNA and the same oligonucleotides are used as primers in polymerase chain reaction (PCR) to amplify junctional fragments, the nucleotide sequence of which is then determined.


The S. epidermidis sequences were analyzed for the presence of open reading frames (ORFs) comprising at least 180 nucleotides. As a result of the analysis of ORFs based on stop-to-stop codon reads, it should be understood that these ORFs may not correspond to the ORF of a naturally-occurring S. epidermidis polypeptide. These ORFs may contain start codons which indicate the initiation of protein synthesis of a naturally-occurring S. epidermidis polypeptide. Such start codons within the ORFs provided herein were identified by those of ordinary skill in the relevant art, and the resulting ORF and the encoded S. epidermidis polypeptide is within the scope of this invention. For example, within the ORFs a codon such as AUG or GUG (encoding methionine or valine) which is part of the initiation signal for protein synthesis were identified and the portion of an ORF to corresponding to a naturally-occurring S. epidermidis polypeptide was recognized. The predicted coding regions were defined by evaluating the coding potential of such sequences with the program GENEMARK™ (Borodovsky and Mclninch, 1993, Comp. 17:123).


Each predicted ORF amino acid sequence was compared with all sequences found in current GENBANK, SWISS-PROT, and PIR databases using the BLAST algorithm. BLAST identifies local alignments occurring by chance between the ORF sequence and the sequence in the databank (Altschal et al., 1990, L Mol. Biol. 215:403-410). Homologous ORFs (probabilities less than 10−5 by chance) and ORF's that are probably non-homologous (probabilities greater than 10−5 by chance) but have good codon usage were identified. Both homologous, sequences and non-homologous sequences with good codon usage, are likely to encode proteins and are encompassed by the invention.



S. epidermidis Nucleic Acids


The present invention provides a library of S. epidermidis-derived nucleic acid sequences. The libraries provide probes, primers, and markers which are used as markers in epidemiological studies. The present invention also provides a library of S. epidermidis-derived nucleic acid sequences which comprise or encode targets for therapeutic drugs.


The nucleic acids of this invention may be obtained directly from the DNA of the above referenced S. epidermidis strain by using the polymerase chain reaction (PCR). See “PCR, A Practical Approach” (McPherson, Quirke, and Taylor, eds., IRL Press, Oxford, UK, 1991) for details about the PCR. High fidelity PCRisused to ensure a faithful DNA copy prior to expression. In addition, the authenticity of amplified products is verified by conventional sequencing methods. Clones carrying the desired sequences described in this invention may also be obtained by screening the libraries by means of the PCR or by hybridization of synthetic oligonucleotide probes to filter lifts of the library colonies or plaques as known in the art (see, e.g., Sambrook et al., Molecular Cloning, A Laboratory Manual 2nd edition, 1989, Cold Spring Harbor Press, NY).


It is also possible to obtain nucleic acids encoding S. epidermidis polypeptides from a cDNA library in accordance with protocols herein described. A cDNA encoding a S. epidermidis polypeptide can be obtained by isolating total mRNA from an appropriate strain. Double stranded cDNAs can then be prepared from the total mRNA. Subsequently, the cDNAs can be inserted into a suitable plasmid or viral (e.g., bacteriophage) vector using any one of a number of known techniques. Genes encoding S. epidermidis polypeptides can also be cloned using established polymerase chain reaction techniques in accordance with the nucleotide sequence information provided by the invention. The nucleic acids of the invention can be DNA or RNA. Preferred nucleic acids of the invention are contained in the Sequence Listing.


The nucleic acids of the invention can also be chemically synthesized using standard techniques. Various methods of chemically synthesizing polydeoxynucleotides are known, including solid-phase synthesis which, like peptide synthesis, has been fully automated in commercially available DNA synthesizers (See e.g., Itakura et al. U.S. Pat. No. 4,598,049; Caruthers et al. U.S. Pat. No. 4,458,066; and Itakura U.S. Pat. Nos. 4,401,796 and 4,373,071, incorporated by reference herein).


In another example, DNA can be chemically synthesized using, e.g., the phosphoramidite solid support method of Matteucci et al., 1981, J. Am. Chem. Soc. 103:3185, the method of Yoo et al., 1989, J. Biol. Chem. 764:17078, or other well known methods. This can be done by sequentially linking a series of oligonucleotide cassettes comprising pairs of synthetic oligonucleotides, as described below.


Nucleic acids isolated or synthesized in accordance with features of the present invention are useful, by way of example, without limitation, as probes, primers, capture ligands, antisense genes and for developing expression systems for the synthesis of proteins and peptides corresponding to such sequences. As probes, primers, capture ligands and antisense agents, the nucleic acid normally consists of all or part (approximately twenty or more nucleotides for specificity as well as the ability to form stable hybridization products) of the nucleic acids of the invention contained in the Sequence Listing. These uses are described in further detail below.


Probes


A nucleic acid isolated or synthesized in accordance with the sequence of the invention contained in the Sequence Listing can be used as a probe to specifically detect S. epidermidis. With the sequence information set forth in the present application, sequences of twenty or more nucleotides are identified which provide the desired inclusivity and exclusivity with respect to S. epidermidis, and extraneous nucleic acids likely to be encountered during hybridization conditions. More preferably, the sequence will comprise at least twenty to thirty nucleotides to convey stability to the hybridization product formed between the probe and the intended target molecules.


Sequences larger than 1000 nucleotides in length are difficult to synthesize but can be generated by recombinant DNA techniques. Individuals skilled in the art will readily recognize that the nucleic acids, for use as probes, can be provided with a label to facilitate detection of a hybridization product.


Nucleic acid isolated and synthesized in accordance with the sequence of the invention contained in the Sequence Listing can also be useful as probes to detect homologous regions (especially homologous genes) of other Staphylococcus species using appropriate stringency hybridization conditions as described herein.


Capture Ligand


For use as a capture ligand, the nucleic acid selected in the manner described above with respect to probes, can be readily associated with a support. The manner in which nucleic acid is associated with supports is well known. Nucleic acid having twenty or more nucleotides in a sequence of the invention contained in the Sequence Listing have utility to separate S. epidermidis nucleic acid from one strain from the nucleic acid of other another strain as well as from other organisms. Nucleic acid having twenty or more nucleotides in a sequence of the invention contained in the Sequence Listing can also have utility to separate other Staphylococcus species from each other and from other organisms. Preferably, the sequence will comprise at least twenty nucleotides to convey stability to the hybridization product formed between the probe and the intended target molecules. Sequences larger than 1000 nucleotides in length are difficult to synthesize but can be generated by recombinant DNA techniques.


Primers


Nucleic acid isolated or synthesized in accordance with the sequences described herein have utility as primers for the amplification of S. epidermidis nucleic acid. These nucleic acids may also have utility as primers for the amplification of nucleic acids in other Staphylococcus species. With respect to polymerase chain reaction (PCR) techniques, nucleic acid sequences of ≧10-15 nucleotides of the invention contained in the Sequence Listing have utility in conjunction with suitable enzymes and reagents to create copies of S. epidermidis nucleic acid. More preferably, the sequence will comprise twenty or more nucleotides to convey stability to the hybridization product formed between the primer and the intended target molecules. Binding conditions of primers greater than 100 nucleotides are more difficult to control to obtain specificity. High fidelity PCR can be used to ensure a faithful DNA copy prior to expression. In addition, amplified products can be checked by conventional sequencing methods.


The copies can be used in diagnostic assays to detect specific sequences, including genes from S. epidermidis and/or other Staphylococcus species. The copies can also be incorporated into cloning and expression vectors to generate polypeptides corresponding to the nucleic acid synthesized by PCR, as is described in greater detail herein.


The nucleic acids of the present invention find use as templates for the recombinant production of S. epidermidis-derived peptides or polypeptides


Antisense


Nucleic acid or nucleic acid-hybridizing derivatives isolated or synthesized in accordance with the sequences described herein have utility as antisense agents to prevent the expression of S. epidermidis genes. These sequences also have utility as antisense agents to prevent expression of genes of other Staphylococcus species.


In one embodiment, nucleic acid or derivatives corresponding to S. epidermidis nucleic acids is loaded into a suitable carrier such as a liposome or bacteriophage for introduction into bacterial cells. For example, a nucleic acid having twenty or more nucleotides is capable of binding to bacteria nucleic acid or bacteria messenger RNA. Preferably, the antisense nucleic acid is comprised of 20 or more nucleotides to provide necessary stability of a hybridization product of non-naturally occurring nucleic acid and bacterial nucleic acid and/or bacterial messenger RNA. Nucleic acid having a sequence greater than 1000 nucleotides in length is difficult to synthesize but can be generated by recombinant DNA techniques. Methods for loading antisense nucleic acid in liposomes is known in the art as exemplified by U.S. Pat. No. 4,241,046 issued Dec. 23, 1980 to Papahadjopoulos et al.


The present invention encompasses isolated polypeptides and nucleic acids derived from S. epidermidis that are useful as reagents for diagnosis of bacterial infection, components of effective anti-bacterial vaccines, and/or as targets for anti-bacterial drugs, including anti-S. epidermidis drugs.


Expression of S. epidermidis Nucleic Acids


Table 2, which is appended herewith and which forms part of the present specification, provides a list of open reading frames (ORFs) in both strands and a putative identification of the particular function of a polypeptide which is encoded by each ORF, based on the homology match (determined by the BLAST algorithm) of the predicted polypeptide with known proteins encoded by ORFs in other organisms. An ORF is a region of nucleic acid which encodes a polypeptide. This region may represent a portion of a coding sequence or a total sequence and was determined from stop to stop codons. The first column contains a designation for the contig from which each ORF was identified (numbered arbitrarily). Each contig represents a continuous stretch of the genomic sequence of the organism. The second column lists the ORF designation. The third and fourth columns list the SEQ ID numbers for the nucleic acid and amino acid sequences corresponding to each ORF, respectively. The fifth and sixth columns list the length of the nucleic acid and the length of the amino acid, respectively. The nucleotide sequence corresponding to each ORF designation begins at the first nucleotide immediately following a stop codon and ends at the nucleotide immediately preceding the next downstream stop codon in the same reading frame. It will be recognized by one skilled in the art that the natural translation initiation sites will correspond to ATG, GTG, or TTG codons located within the ORFs. The natural initiation sites depend not only on the sequence of a start codon but also on the context of the DNA sequence adjacent to the start codon. Usually, a recognizable ribosome binding site is found within 20 nucleotides upstream from the initiation codon. In some cases where genes are translationally coupled and coordinately expressed together in “operons”, ribosome binding sites are not present, but the initiation codon of a downstream gene may occur very close to, or overlap, the stop codon of the an upstream gene in the same operon. The correct start codons can be generally identified without undue experimentation because only a few codons need be tested. It is recognized that the translational machinery in bacteria initiates all polypeptide chains with the amino acid methionine, regardless of the sequence of the start codon. In some cases, polypeptides are post-translationally modified, resulting in an N-terminal amino acid other than methionine in vivo. The seventh and eighth columns provide metrics for assessing the likelihood of the homology match (determined by the BLASTP2 algorithm), as is known in the art, to the genes indicated in the eleventh column when the designated ORF was compared against a non-redundant comprehensive protein database. Specifically, the seventh column represents the “Blast Score” for the match (a higher score is a better match), and the eighth column represents the “P-value” for the match (the probability that such a match can have occurred by chance; the lower the value, the more likely the match is valid). If a BLASTP2 score of less than 46 was obtained, no value is reported in the table the “P-value”. Column nine, Subject Taxonomy,” provides the name of the organism that was identified as having the closest homology match. The tenth column, “Subject Name,” provides where available, either a public database accession number or our own sequence name. The eleventh column provides, where available, the Swissprot accession number (SP), the locus name (LN), the Organism (OR), Source of variant (SR), E. C. number (EC), the gene name (GN), the product name (PN), the Function Description (FN), Left End (LE), Right End (RE), Coding Direction (DI), and the description (DE) or notes (NT) for each ORF. Information that is not preceded by a code designation in the eleventh column represents a description of the ORF. This information allows one of ordinary skill in the art to determine a potential use for each identified coding sequence and, as a result, allows use of the polypeptides of the present invention for commercial and industrial purposes.


Using the information provided in SEQ ID NO: 1-SEQ ID NO: 2837 and in Table 2 together with routine cloning and sequencing methods, one of ordinary skill in the art will be able to clone and sequence all the nucleic acid fragments of interest including open reading frames (ORFs) encoding a large variety proteins of S. epidermidis.


Nucleic acid isolated or synthesized in accordance with the sequences described herein have utility to generate polypeptides. The nucleic acid of the invention exemplified in SEQ ID NO: 1-SEQ ID NO: 2837 and in Table 2 or fragments of said nucleic acid encoding active portions of S. epidermidis polypeptides can be cloned into suitable vectors or used to isolate nucleic acid. The isolated nucleic acid is combined with suitable DNA linkers and cloned into a suitable vector.


The function of a specific gene or operon can be ascertained by expression in a bacterial strain under conditions where the activity of the gene product(s) specified by the gene or operon in question can be specifically measured. Alternatively, a gene product may be produced in large quantities in an expressing strain for use as an antigen, an industrial reagent, for structural studies, etc. This expression can be accomplished in a mutant strain which lacks the activity of the gene to be tested, or in a strain that does not produce the same gene product(s). This includes, but is not limited to, Eucaryotic species such as the yeast Saccharomyces cerevisiae, Methanobacterium strains or other Archaea, and Eubacteria such as E. coli, B. Subtilis, S. Aureus, S. Pneumonia or Pseudomonas putida. In some cases the expression host will utilize the natural S. epidermidis promoter whereas in others, it will be necessary to drive the gene with a promoter sequence derived from the expressing organism (e.g., an E. coli beta-galactosidase promoter for expression in E. coli).


To express a gene product using the natural S. epidermidis promoter, a procedure such as the following can be used. A restriction fragment containing the gene of interest, together with its associated natural promoter element and regulatory sequences (identified using the DNA sequence data) is cloned into an appropriate recombinant plasmid containing an origin of replication that functions in the host organism and an appropriate selectable marker. This can be accomplished by a number of procedures known to those skilled in the art. It is most preferably done by cutting the plasmid and the fragment to be cloned with the same restriction enzyme to produce compatible ends that can be ligated to join the two pieces together. The recombinant plasmid is introduced into the host organism by, for example, electroporation and cells containing the recombinant plasmid are identified by selection for the marker on the plasmid. Expression of the desired gene product is detected using an assay specific for that gene product.


In the case of a gene that requires a different promoter, the body of the gene (coding sequence) is specifically excised and cloned into an appropriate expression plasmid. This subcloning can be done by several methods, but is most easily accomplished by PCR amplification of a specific fragment and ligation into an expression plasmid after treating the PCR product with a restriction enzyme or exonuclease to create suitable ends for cloning.


A suitable host cell for expression of a gene can be any procaryotic or eucaryotic cell. Suitable methods for transforming host cells can be found in Sambrook et al. (Molecular Cloning: A Laboratory Manual, 2nd Edition, Cold Spring Harbor Laboratory press (1989)), and other laboratory textbooks.


For example, a host cell transfected with a nucleic acid vector directing expression of a nucleotide sequence encoding a S. epidermidis polypeptide can be cultured under appropriate conditions to allow expression of the polypeptide to occur. Suitable media for cell culture are well known in the art. Polypeptides of the invention can be isolated from cell culture medium, host cells, or both using techniques known in the art for purifying proteins including ion-exchange chromatography, gel filtration chromatography, ultrafiltration, electrophoresis, and immunoaffinity purification with antibodies specific for such polypeptides. Additionally, in many situations, polypeptides can be produced by chemical cleavage of a native protein (e.g., tryptic digestion) and the cleavage products can then be purified by standard techniques.


In the case of membrane bound proteins, these can be isolated from a host cell by contacting a membrane-associated protein fraction with a detergent forming a solubilized complex, where the membrane-associated protein is no longer entirely embedded in the membrane fraction and is solubilized at least to an extent which allows it to be chromatographically isolated from the membrane fraction. Chromatographic techniques which can be used in the final purification step are known in the art and include hydrophobic interaction, lectin affinity, ion exchange, dye affinity and immunoaffinity.


One strategy to maximize recombinant S. epidermidis peptide expression in E. coli is to express the protein in a host bacteria with an impaired capacity to proteolytically cleave the recombinant protein (Gottesman, S., Gene Expression Technology: Methods in Enzymology 185, Academic Press, San Diego, Calif. (1990) 119-128). Another strategy would be to alter the nucleic acid encoding a S. epidermidis peptide to be inserted into an expression vector so that the individual codons for each amino acid would be those preferentially utilized in highly expressed E. coli proteins (Wada et al., (1992) Nuc. Acids Res. 20:2111-2118). Such alteration of nucleic acids of the invention can be carried out by standard DNA synthesis techniques.


The nucleic acids of the invention can also be chemically synthesized using standard techniques. Various methods of chemically synthesizing polydeoxynucleotides are known, including solid-phase synthesis which, like peptide synthesis, has been fully automated in commercially available DNA synthesizers (See, e.g., Itakura et al. U.S. Pat. No. 4,598,049; Caruthers et al. U.S. Pat. No. 4,458,066; and Itakura U.S. Pat. Nos. 4,401,796 and 4,373,071, incorporated by reference herein).


The present invention provides a library of S. epidermidis-derived nucleic acid sequences. The libraries provide probes, primers, and markers which can be used as markers in epidemiological studies. The present invention also provides a library of S. epidermidis-derived nucleic acid sequences which comprise or encode targets for therapeutic drugs.


Nucleic acids comprising any of the sequences disclosed herein or sub-sequences thereof can be prepared by standard methods using the nucleic acid sequence information provided in SEQ ID NO: 1-SEQ ID NO: 2837. For example, DNA can be chemically synthesized using, e.g., the phosphoramidite solid support method of Matteucci et al., 1981, J. Am. Chem. Soc. 103:3185, the method of Yoo et al., 1989, J. Biol. Chem. 764:17078, or other well known methods. This can be done by sequentially linking a series of oligonucleotide cassettes comprising pairs of synthetic oligonucleotides, as described below.


Of course, due to the degeneracy of the genetic code, many different nucleotide sequences can encode polypeptides having the amino acid sequences defined by SEQ ID NO: 2838-SEQ ID NO: 5674 or sub-sequences thereof. The codons can be selected for optimal expression in prokaryotic or eukaryotic systems. Such degenerate variants are also encompassed by this invention.


Insertion of nucleic acids (typically DNAs) encoding the polypeptides of the invention into a vector is easily accomplished when the termini of both the DNAs and the vector comprise compatible restriction sites. If this cannot be done, it may be necessary to modify the termini of the DNAs and/or vector by digesting back single-stranded DNA overhangs generated by restriction endonuclease cleavage to produce blunt ends, or to achieve the same result by filling in the single-stranded termini with an appropriate DNA polymerase.


Alternatively, any site desired may be produced, e.g., by ligating nucleotide sequences (linkers) onto the termini. Such linkers may comprise specific oligonucleotide sequences that define desired restriction sites. Restriction sites can also be generated by the use of the polymerase chain reaction (PCR). See, e.g., Saiki et al., 1988, Science 239:48. The cleaved vector and the DNA fragments may also be modified if required by homopolymeric tailing.


The nucleic acids of the invention may be isolated directly from cells. Alternatively, the polymerase chain reaction (PCR) method can be used to produce the nucleic acids of the invention, using either chemically synthesized strands or genomic material as templates. Primers used for PCR can be synthesized using the sequence information provided herein and can further be designed to introduce appropriate new restriction sites, if desirable, to facilitate incorporation into a given vector for recombinant expression.


The nucleic acids of the present invention may be flanked by natural S. epidermidis regulatory sequences, or may be associated with heterologous sequences, including promoters, enhancers, response elements, signal sequences, polyadenylation sequences, introns, 5′- and 3′-noncoding regions, and the like. The nucleic acids may also be modified by many means known in the art. Non-limiting examples of such modifications include methylation, “caps”, substitution of one or more of the naturally occurring nucleotides with an analog, internucleotide modifications such as, for example, those with uncharged linkages (e.g., methyl phosphonates, phosphotriesters, phosphoroamidates, carbamates, etc.) and with charged linkages (e.g., phosphorothioates, phosphorodithioates, etc.). Nucleic acids may contain one or more additional covalently linked moieties, such as, for example, proteins (e.g., nucleases, toxins, antibodies, signal peptides, poly-L-lysine, etc.), intercalators (e.g., acridine, psoralen, etc.), chelators (e.g., metals, radioactive metals, iron, oxidative metals, etc.), and alkylators. PNAs are also included. The nucleic acid may be derivatized by formation of a methyl or ethyl phosphotriester or an alkyl phosphoramidate linkage. Furthermore, the nucleic acid sequences of the present invention may also be modified with a label capable of providing a detectable signal, either directly or indirectly. Exemplary labels include radioisotopes, fluorescent molecules, biotin, and the like.


The invention also provides nucleic acid vectors comprising the disclosed S. epidermidis-derived sequences or derivatives or fragments thereof. A large number of vectors, including plasmid and bacterial vectors, have been described for replication and/or expression in a variety of eukaryotic and prokaryotic hosts, and may be used for cloning or protein expression.


The encoded S. epidermidis polypeptides may be expressed by using many known vectors, such as pUC plasmids, pET plasmids (Novagen, Inc., Madison, Wis.), or pRSET or pREP (Invitrogen, San Diego, Calif.), and many appropriate host cells, using methods disclosed or cited herein or otherwise known to those skilled in the relevant art. The particular choice of vector/host is not critical to the practice of the invention.


Recombinant cloning vectors will often include one or more replication systems for cloning or expression, one or more markers for selection in the host, e.g. antibiotic resistance, and one or more expression cassettes. The inserted S. epidermidis coding sequences may be synthesized by standard methods, isolated from natural sources, or prepared as hybrids, etc. Ligation of the S. epidermidis coding sequences to transcriptional regulatory elements and/or to other amino acid coding sequences may be achieved by known methods. Suitable host cells may be transformed/transfected/infected as appropriate by any suitable method including electroporation, CaCl2 mediated DNA uptake, bacterial infection, microinjection, microprojectile, or other established methods.


Appropriate host cells include bacteria, archebacteria, fungi, especially yeast, and plant and animal cells, especially mammalian cells. Of particular interest are S. epidermidis, E. coli, B. Subtilis, Saccharomyces cerevisiae, Saccharomyces carlsbergensis, Schizosaccharomyces pombi, SF9 cells, C129 cells, 293 cells, Neurospora, and CHO cells, COS cells, HeLa cells, and immortalized mammalian myeloid and lymphoid cell lines. Preferred replication systems include M13, ColE1, SV40, baculovirus, lambda, adenovirus, and the like. A large number of transcription initiation and termination regulatory regions have been isolated and shown to be effective in the transcription and translation of heterologous proteins in the various hosts. Examples of these regions, methods of isolation, manner of manipulation, etc. are known in the art. Under appropriate expression conditions, host cells can be used as a source of recombinantly produced S. epidermidis-derived peptides and polypeptides.


Advantageously, vectors may also include a transcription regulatory element (i.e., a promoter) operably linked to the S. epidermidis portion. The promoter may optionally contain operator portions and/or ribosome binding sites. Non-limiting examples of bacterial promoters compatible with E. coli include: b-lactamase (penicillinase) promoter; lactose promoter; tryptophan (trp) promoter; araBAD (arabinose) operon promoter; lambda-derived P1 promoter and N gene ribosome binding site; and the hybrid tac promoter derived from sequences of the trp and lac UV5 promoters. Non-limiting examples of yeast promoters include 3-phosphoglycerate kinase promoter, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) promoter, galactokinase (GAL1) promoter, galactoepimerase promoter, and alcohol dehydrogenase (ADH) promoter. Suitable promoters for mammalian cells include without limitation viral promoters such as that from Simian Virus 40 (SV40), Rous sarcoma virus (RSV), adenovirus (ADV), and bovine papilloma virus (BPV). Mammalian cells may also require terminator sequences, polyA addition sequences and enhancer sequences to increase expression. Sequences which cause amplification of the gene may also be desirable. Furthermore, sequences that facilitate secretion of the recombinant product from cells, including, but not limited to, bacteria, yeast, and animal cells, such as secretory signal sequences and/or prohormone pro region sequences, may also be included. These sequences are well described in the art.


Nucleic acids encoding wild-type or variant S. epidermidis-derived polypeptides may also be introduced into cells by recombination events. For example, such a sequence can be introduced into a cell, and thereby effect homologous recombination at the site of an endogenous gene or a sequence with substantial identity to the gene. Other recombination-based methods such as nonhomologous recombinations or deletion of endogenous genes by homologous recombination may also be used.


The nucleic acids of the present invention find use as templates for the recombinant production of S. epidermidis-derived peptides or polypeptides.


Identification and use of S. epidermidis Nucleic Acid Sequences


The disclosed S. epidermidis polypeptide and nucleic acid sequences, or other sequences that are contained within ORFs, including complete protein-coding sequences, of which any of the disclosed S. epidermidis-specific sequences forms a part, are useful as target components for diagnosis and/or treatment of S. epidermidis-caused infection


It will be understood that the sequence of an entire protein-coding sequence of which each disclosed nucleic acid sequence forms a part can be isolated and identified based on each disclosed sequence. This can be achieved, for example, by using an isolated nucleic acid encoding the disclosed sequence, or fragments thereof, to prime a sequencing reaction with genomic S. epidermidis DNA as template; this is followed by sequencing the amplified product. The isolated nucleic acid encoding the disclosed sequence, or fragments thereof, can also be hybridized to S. epidermidis genomic libraries to identify clones containing additional complete segments of the protein-coding sequence of which the shorter sequence forms a part. Then, the entire protein-coding sequence, or fragments thereof, or nucleic acids encoding all or part of the sequence, or sequence-conservative or function-conservative variants thereof, may be employed in practicing the present invention.


Preferred sequences are those that are useful in diagnostic and/or therapeutic applications. Diagnostic applications include without limitation nucleic-acid-based and antibody-based methods for detecting bacterial infection. Therapeutic applications include without limitation vaccines, passive immunotherapy, and drug treatments directed against gene products that are both unique to bacteria and essential for growth and/or replication of bacteria.


Identification of Nucleic Acids Encoding Vaccine Components and Targets for Agents Effective Against S. epidermidis


The disclosed S. epidermidis genome sequence includes segments that direct the synthesis of ribonucleic acids and polypeptides, as well as origins of replication, promoters, other types of regulatory sequences, and intergenic nucleic acids. The invention encompasses nucleic acids encoding immunogenic components of vaccines and targets for agents effective against S. epidermidis. Identification of said immunogenic components involved in the determination of the function of the disclosed sequences, which can be achieved using a variety of approaches. Non-limiting examples of these approaches are described briefly below.


Homology to Known Sequences


Computer-assisted comparison of the disclosed S. epidermidis sequences with previously reported sequences present in publicly available databases is useful for identifying functional S. epidermidis nucleic acid and polypeptide sequences. It will be understood that protein-coding sequences, for example, may be compared as a whole, and that a high degree of sequence homology between two proteins (such as, for example, >80-90%) at the amino acid level indicates that the two proteins also possess some degree of functional homology, such as, for example, among enzymes involved in metabolism, DNA synthesis, or cell wall synthesis, and proteins involved in transport, cell division, etc. In addition, many structural features of particular protein classes have been identified and correlate with specific consensus sequences, such as, for example, binding domains for nucleotides, DNA, metal ions, and other small molecules; sites for covalent modifications such as phosphorylation, acylation, and the like; sites of protein:protein interactions, etc. These consensus sequences may be quite short and thus may represent only a fraction of the entire protein-coding sequence. Identification of such a feature in a S. epidermidis sequence is therefore useful in determining the function of the encoded protein and identifying useful targets of antibacterial drugs.


Of particular relevance to the present invention are structural features that are common to secretory, transmembrane, and surface proteins, including secretion signal peptides and hydrophobic transmembrane domains. S. epidermidis proteins identified as containing putative signal sequences and/or transmembrane domains are useful as immunogenic components of vaccines.


Targets for therapeutic drugs according to the invention include, but are not limited to, polypeptides of the invention, whether unique to S. epidermidis or not, that are essential for growth and/or viability of S. epidermidis under at least one growth condition. Polypeptides essential for growth and/or viability can be determined by examining the effect of deleting and/or disrupting the genes, i.e., by so-called gene “knockout”. Alternatively, genetic footprinting can be used (Smith et al., 1995, Proc. Natl. Acad. Sci. USA 92:5479-6433; Published International Application WO 94/26933; U.S. Pat. No. 5,612,180). Still other methods for assessing essentiality includes the ability to isolate conditional lethal mutations in the specific gene (e.g., temperature sensitive mutations). Other useful targets for therapeutic drugs, which include polypeptides that are not essential for growth or viability per se but lead to loss of viability of the cell, can be used to target therapeutic agents to cells.


Strain-Specific Sequences


Because of the evolutionary relationship between different S. epidermidis strains, it is believed that the presently disclosed S. epidermidis sequences are useful for identifying, and/or discriminating between, previously known and new S. epidermidis strains. It is believed that other S. epidermidis strains will exhibit at least 70% sequence homology with the presently disclosed sequence. Systematic and routine analyses of DNA sequences derived from samples containing S. epidermidis strains, and comparison with the present sequence allows for the identification of sequences that can be used to discriminate between strains, as well as those that are common to all S. epidermidis strains. In one embodiment, the invention provides nucleic acids, including probes, and peptide and polypeptide sequences that discriminate between different strains of S. epidermidis. Strain-specific components can also be identified functionally by their ability to elicit or react with antibodies that selectively recognize one or more S. epidermidis strains.


In another embodiment, the invention provides nucleic acids, including probes, and peptide and polypeptide sequences that are common to all S. epidermidis strains but are not found in other bacterial species.



S. epidermidis Polypeptides


This invention encompasses isolated S. epidermidis polypeptides encoded by the disclosed S. epidermidis genomic sequences, including the polypeptides of the invention contained in the Sequence Listing. Polypeptides of the invention are preferably at least 5 amino acid residues in length. Using the DNA sequence information provided herein, the amino acid sequences of the polypeptides encompassed by the invention can be deduced using methods well-known in the art. It will be understood that the sequence of an entire nucleic acid encoding a S. epidermidis polypeptide can be isolated and identified based on an ORF that encodes only a fragment of the cognate protein-coding region. This can be achieved, for example, by using the isolated nucleic acid encoding the ORF, or fragments thereof, to prime a polymerase chain reaction with genomic S. epidermidis DNA as template; this is followed by sequencing the amplified product.


The polypeptides of the present invention, including function-conservative variants of the disclosed ORFs, may be isolated from wild-type or mutant S. epidermidis cells, or from heterologous organisms or cells (including, but not limited to, bacteria, fungi, insect, plant, and mammalian cells) including S. epidermidis into which a S. epidermidis-derived protein-coding sequence has been introduced and expressed. Furthermore, the polypeptides may be part of recombinant fusion proteins.



S. epidermidis polypeptides of the invention can be chemically synthesized using commercially automated procedures such as those referenced herein, including, without limitation, exclusive solid phase synthesis, partial solid phase methods, fragment condensation or classical solution synthesis. The polypeptides are preferably prepared by solid phase peptide synthesis as described by Merrifield, 1963, J. Am. Chem. Soc. 85:2149. The synthesis is carried out with amino acids that are protected at the alpha-amino terminus. Trifunctional amino acids with labile side-chains are also protected with suitable groups to prevent undesired chemical reactions from occurring during the assembly of the polypeptides. The alpha-amino protecting group is selectively removed to allow subsequent reaction to take place at the amino-terminus. The conditions for the removal of the alpha-amino protecting group do not remove the side-chain protecting groups.


Methods for polypeptide purification are well-known in the art, including, without limitation, preparative disc-gel electrophoresis, isoelectric focusing, HPLC, reversed-phase HPLC, gel filtration, ion exchange and partition chromatography, and countercurrent distribution. For some purposes, it is preferable to produce the polypeptide in a recombinant system in which the S. epidermidis protein contains an additional sequence tag that facilitates purification, such as, but not limited to, a polyhistidine sequence. The polypeptide can then be purified from a crude lysate of the host cell by chromatography on an appropriate solid-phase matrix. Alternatively, antibodies produced against a S. epidermidis protein or against peptides derived therefrom can be used as purification reagents. Other purification methods are possible.


The present invention also encompasses derivatives and homologues of S. epidermidis-encoded polypeptides. For some purposes, nucleic acid sequences encoding the peptides may be altered by substitutions, additions, or deletions that provide for functionally equivalent molecules, i.e., function-conservative variants. For example, one or more amino acid residues within the sequence can be substituted by another amino acid of similar properties, such as, for example, positively charged amino acids (arginine, lysine, and histidine); negatively charged amino acids (aspartate and glutamate); polar neutral amino acids; and non-polar amino acids.


The isolated polypeptides may be modified by, for example, phosphorylation, sulfation, acylation, or other protein modifications. They may also be modified with a label capable of providing a detectable signal, either directly or indirectly, including, but not limited to, radioisotopes and fluorescent compounds.


To identify S. epidermidis-derived polypeptides for use in the present invention, essentially the complete genomic sequence of a Staphyolococcus epidermidis isolate was analyzed. While, in very rare instances, a nucleic acid sequencing error may be revealed, resolving a rare sequencing error is well within the art, and such an occurrence will not prevent one skilled in the art from practicing the invention.


Also encompassed are any S. epidermidis polypeptide sequences that are contained within the open reading frames (ORFs), including complete protein-coding sequences, of which any of SEQ ID NO: 2838-SEQ ID NQ: 5674 forms a part. Table 2, which is appended herewith and which forms part of the present specification, provides a putative identification of the particular function of a polypeptide which is encoded by each ORF, based on the homology match (determined by the BLAST algorithm) of the predicted polypeptide with known proteins encoded by ORFs in other organisms. As a result, one skilled in the art can use the polypeptides of the present invention for commercial and industrial purposes consistent with the type of putative identification of the polypeptide.


The present invention provides a library of S. epidermidis-derived polypeptide sequences, and a corresponding library of nucleic acid sequences encoding the polypeptides, wherein the polypeptides themselves, or polypeptides contained within ORFs of which they form a part, comprise sequences that are contemplated for use as components of vaccines. Non-limiting examples of such sequences are listed by SEQ ID NO in Table 2, which is appended herewith and which forms part of the present specification.


The present invention also provides a library of S. epidermidis-derived polypeptide sequences, and a corresponding library of nucleic acid sequences encoding the polypeptides, wherein the polypeptides themselves, or polypeptides contained within ORFs of which they form a part, comprise sequences lacking homology to any known prokaryotic or eukaryotic sequences. Such libraries provide probes, primers, and markers which can be used to diagnose S. epidermidis infection, including use as markers in epidemiological studies. Non-limiting examples of such sequences are listed by SEQ ID NO in Table 2, which is appended The present invention also provides a library of S. epidermidis-derived polypeptide sequences, and a corresponding library of nucleic acid sequences encoding the polypeptides, wherein the polypeptides themselves, or polypeptides contained within ORFs of which they form a part, comprise targets for therapeutic drugs.


Specific Example: Determination of Staphylococcus Protein Antigens for Antibody and Vaccine Development


The selection of Staphylococcus protein antigens for vaccine development can be derived from the nucleic acids encoding S. epidermidis polypeptides. First, the ORF's can be analyzed for homology to other known exported or membrane proteins and analyzed using the discriminant analysis described by Klein, et al. (Klein, P., Kanehsia, M., and DeLisi, C. (1985) Biochimica et Biophysica Acta 815, 468-476) for predicting exported and membrane proteins.


Homology searches can be performed using the BLAST algorithm contained in the Wisconsin Sequence Analysis Package (Genetics Computer Group, University Research Park, 575 Science Drive, Madison, Wis. 53711) to compare each predicted ORF amino acid sequence with all sequences found in the current GenBank, SWISS-PROT and PIR databases. BLAST searches for local alignments between the ORF and the databank sequences and reports a probability score which indicates the probability of finding this sequence by chance in the database. ORF's with significant homology (e.g. probabilities lower than 1×10−6 that the homology is only due to random chance) to membrane or exported proteins represent protein antigens for vaccine development. Possible functions can be provided to S. epidermidis genes based on sequence homology to genes cloned in other organisms.


Discriminant analysis (Klein, et al. supra) can be used to examine the ORF amino acid sequences. This algorithm uses the intrinsic information contained in the ORF amino acid sequence and compares it to information derived from the properties of known membrane and exported proteins. This comparison predicts which proteins will be exported, membrane associated or cytoplasmic. ORF amino acid sequences identified as exported or membrane associated by this algorithm are likely protein antigens for vaccine development.


Production of Fragments and Analogs of S. epidermidis Nucleic Acids and Polypeptides


Based on the discovery of the S. epidermidis gene products of the invention provided in the Sequence Listing, one skilled in the art can alter the disclosed structure of S. epidermidis genes, e.g., by producing fragments or analogs, and test the newly produced structures for activity. Examples of techniques known to those skilled in the relevant art which allow the production and testing of fragments and analogs are discussed below. These, or analogous methods can be used to make and screen libraries of polypeptides, e.g., libraries of random peptides or libraries of fragments or analogs of cellular proteins for the ability to bind S. epidermidis polypeptides. Such screens are useful for the identification of inhibitors of S. epidermidis.


Generation of Fragments


Fragments of a protein can be produced in several ways, e.g., recombinantly, by proteolytic digestion, or by chemical synthesis. Internal or terminal fragments of a polypeptide can be generated by removing one or more nucleotides from one end (for a terminal fragment) or both ends (for an internal fragment) of a nucleic acid which encodes the polypeptide. Expression of the mutagenized DNA produces polypeptide fragments. Digestion with “end-nibbling” endonucleases can thus generate DNAs which encode an array of fragments. DNAs which encode fragments of a protein can also be generated by random shearing, restriction digestion or a combination of the above-discussed methods.


Fragments can also be chemically synthesized using techniques known in the art such as conventional Merrifield solid phase f-Moc or t-Boc chemistry. For example, peptides of the present invention may be arbitrarily divided into fragments of desired length with no overlap of the fragments, or divided into overlapping fragments of a desired length.


Alteration of Nucleic Acids and Polypeptides: Random Methods


Amino acid sequence variants of a protein can be prepared by random mutagenesis of DNA which encodes a protein or a particular domain or region of a protein. Useful methods include PCR mutagenesis and saturation mutagenesis. A library of random amino acid sequence variants can also be generated by the synthesis of a set of degenerate oligonucleotide sequences. (Methods for screening proteins in a library of variants are elsewhere herein).


PCR Mutagenesis


In PCR mutagenesis, reduced Taq polymerase fidelity is used to introduce random mutations into a cloned fragment of DNA (Leung et al., 1989, Technique 1:11-15). The DNA region to be mutagenized is amplified using the polymerase chain reaction (PCR) under conditions that reduce the fidelity of DNA synthesis by Taq DNA polymerase, e.g., by using a dGTP/dATP ratio of five and adding Mn2+ to the PCR reaction. The pool of amplified DNA fragments are inserted into appropriate cloning vectors to provide random mutant libraries.


Saturation Mutagenesis


Saturation mutagenesis allows for the rapid introduction of a large number of single base substitutions into cloned DNA fragments (Mayers et al., 1985, Science 229:242). This technique includes generation of mutations, e.g., by chemical treatment or irradiation of single-stranded DNA in vitro, and synthesis of a complimentary DNA strand. The mutation frequency can be modulated by modulating the severity of the treatment, and essentially all possible base substitutions can be obtained. Because this procedure does not involve a genetic selection for mutant fragments both neutral substitutions, as well as those that alter function, are obtained. The distribution of point mutations is not biased toward conserved sequence elements.


Degenerate Oligonucleotides


A library of homologs can also be generated from a set of degenerate oligonucleotide sequences. Chemical synthesis of a degenerate sequences can be carried out in an automatic DNA synthesizer, and the synthetic genes then ligated into an appropriate expression vector. The synthesis of degenerate oligonucleotides is known in the art (see for example, Narang, S A (1983) Tetrahedron 39:3; Itakura et al. (1981) Recombinant DNA, Proc 3rd Cleveland Sympos. Macromolecules, ed. A G Walton, Amsterdam: Elsevier pp273-289; Itakura et al. (1984) Annu. Rev. Biochem. 53:323; Itakura et al. (1984) Science 198:1056; Ike et al. (1983) Nucleic Acid Res. 11:477. Such techniques have been employed in the directed evolution of other proteins (see, for example, Scott et al. (1990) Science 249:386-390; Roberts et al. (1992) PNAS 89:2429-2433; Devlin et al. (1990) Science 249: 404-406; Cwirla et al. (1990) PNAS 87: 6378-6382; as well as U.S. Pat. Nos. 5,223,409, 5,198,346, and 5,096,815).


Alteration of Nucleic Acids and Polypeptides: Methods for Directed Mutagenesis


Non-random or directed, mutagenesis techniques can be used to provide specific sequences or mutations in specific regions. These techniques can be used to create variants which include, e.g., deletions, insertions, or substitutions, of residues of the known amino acid sequence of a protein. The sites for mutation can be modified individually or in series, e.g., by (1) substituting first with conserved amino acids and then with more radical choices depending upon results achieved, (2) deleting the target residue, or (3) inserting residues of the same or a different class adjacent to the located site, or combinations of options 1-3.


Alanine Scanning Mutagenesis


Alanine scanning mutagenesis is a useful method for identification of certain residues or regions of the desired protein that are preferred locations or domains for mutagenesis, Cunningham and Wells (Science 244:1081-1085, 1989). In alanine scanning, a residue or group of target residues are identified (e.g., charged residues such as Arg, Asp, His, Lys, and Glu) and replaced by a neutral or negatively charged amino acid (most preferably alanine or polyalanine). Replacement of an amino acid can affect the interaction of the amino acids with the surrounding aqueous environment in or outside the cell. Those domains demonstrating functional sensitivity to the substitutions are then refined by introducing further or other variants at or for the sites of substitution. Thus, while the site for introducing an amino acid sequence variation is predetermined, the nature of the mutation per se need not be predetermined. For example, to optimize the performance of a mutation at a given site, alanine scanning or random mutagenesis may be conducted at the target codon or region and the expressed desired protein subunit variants are screened for the optimal combination of desired activity.


Oligonucleotide-Mediated Mutagenesis


Oligonucleotide-mediated mutagenesis is a useful method for preparing substitution, deletion, and insertion variants of DNA, see, e.g., Adelman et al., (DNA 2:183, 1983). Briefly, the desired DNA is altered by hybridizing an oligonucleotide encoding a mutation to a DNA template, where the template is the single-stranded form of a plasmid or bacteriophage containing the unaltered or native DNA sequence of the desired protein. After hybridization, a DNA polymerase is used to synthesize an entire second complementary strand of the template that will thus incorporate the oligonucleotide primer, and will code for the selected alteration in the desired protein DNA. Generally, oligonucleotides of at least 25 nucleotides in length are used. An optimal oligonucleotide will have 12 to 15 nucleotides that are completely complementary to the template on either side of the nucleotide(s) coding for the mutation. This ensures that the oligonucleotide will hybridize properly to the single-stranded DNA template molecule. The oligonucleotides are readily synthesized using techniques known in the art such as that described by Crea et al: (Proc. Natl. Acad. Sci. USA, 75: 5765[1978]).


Cassette Mutagenesis


Another method for preparing variants, cassette mutagenesis, is based on the technique described by Wells et al. (Gene, 34:315[1985]). The starting material is a plasmid (or other vector) which includes the protein subunit DNA to be mutated. The codon(s) in the protein subunit DNA to be mutated are identified. There must be a unique restriction endonuclease site on each side of the identified mutation site(s). If no such restriction sites exist, they may be generated using the above-described oligonucleotide-mediated mutagenesis method to introduce them at appropriate locations in the desired protein subunit DNA. After the restriction sites have been introduced into the plasmid, the plasmid is cut at these sites to linearize it. A double-stranded oligonucleotide encoding the sequence of the DNA between the restriction sites but containing the desired mutation(s) is synthesized using standard procedures. The two strands are synthesized separately and then hybridized together using standard techniques. This double-stranded oligonucleotide is referred to as the cassette. This cassette is designed to have 3′ and 5′ ends that are comparable with the ends of the linearized plasmid, such that it can be directly ligated to the plasmid. This plasmid now contains the mutated desired protein subunit DNA sequence.


Combinatorial Mutagenesis


Combinatorial mutagenesis can also be used to generate mutants (Ladner et al., WO 88/06630). In this method, the amino acid sequences for a group of homologs or other related proteins are aligned, preferably to promote the highest homology possible. All of the amino acids which appear at a given position of the aligned sequences can be selected to create a degenerate set of combinatorial sequences. The variegated library of variants is generated by combinatorial mutagenesis at the nucleic acid level, and is encoded by a variegated gene library. For example, a mixture of synthetic oligonucleotides can be enzymatically ligated into gene sequences such that the degenerate set of potential sequences are expressible as individual peptides, or alternatively, as a set of larger fusion proteins containing the set of degenerate sequences.


Other Modifications of S. epidermidis Nucleic Acids and Polypeptides


It is possible to modify the structure of a S. epidermidis polypeptide for such purposes as increasing solubility, enhancing stability (e.g., shelf life ex vivo and resistance to proteolytic degradation in vivo). A modified S. epidermidis protein or peptide can be produced in which the amino acid sequence has been altered, such as by amino acid substitution, deletion, or addition as described herein.


An S. epidermidis peptide can also be modified by substitution of cysteine residues preferably with alanine, serine, threonine, leucine or glutamic acid residues to minimize dimerization via disulfide linkages. In addition, amino acid side chains of fragments of the protein of the invention can be chemically modified. Another modification is cyclization of the peptide.


In order to enhance stability and/or reactivity, a S. epidermidis polypeptide can be modified to incorporate one or more polymorphisms in the amino acid sequence of the protein resulting from any natural allelic variation. Additionally, D-amino acids, non-natural amino acids, or non-amino acid analogs can be substituted or added to produce a modified protein within the scope of this invention. Furthermore, an S. epidermidis polypeptide can be modified using polyethylene glycol (PEG) according to the method of A. Sehon and co-workers (Wie et al., supra) to produce a protein conjugated with PEG. In addition, PEG can be added during chemical synthesis of the protein. Other modifications of S. epidermidis proteins include reduction/alkylation (Tarr, Methods of Protein Microcharacterization, J. E. Silver ed., Humana Press, Clifton N.J. 155-1194 (1986)); acylation (Tarr, supra); chemical coupling to an appropriate carrier (Mishell and Shiigi, eds, Selected Methods in Cellular Immunology, W H Freeman, San Francisco, Calif. (1980), U.S. Pat. No. 4,939,239; or mild formalin treatment (Marsh, (1971) Int. Arch. of Allergy and Appl. Immunol., 41: 199-215).


To facilitate purification and potentially increase solubility of a S. epidermidis protein or peptide, it is possible to add an amino acid fusion moiety to the peptide backbone. For example, hexa-histidine can be added to the protein for purification by immobilized metal ion affinity chromatography (Hochuli, E. et al., (1988) Bio/Technology, 6: 1321-1325). In addition, to facilitate isolation of peptides free of irrelevant sequences, specific endoprotease cleavage sites can be introduced between the sequences of the fusion moiety and the peptide.


To potentially aid proper antigen processing of epitopes within an S. epidermidis polypeptide, canonical protease sensitive sites can be engineered between regions, each comprising at least one epitope via recombinant or synthetic methods. For example, charged amino acid pairs, such as KK or RR, can be introduced between regions within a protein or fragment during recombinant construction thereof. The resulting peptide can be rendered sensitive to cleavage by cathepsin and/or other trypsin-like enzymes which would generate portions of the protein containing one or more epitopes. In addition, such charged amino acid residues can result in an increase in the solubility of the peptide.


Primary Methods for Screening Polypeptides and Analogs


Various techniques are known in the art for screening generated mutant gene products. Techniques for screening large gene libraries often include cloning the gene library into replicable expression vectors, transforming appropriate cells with the resulting library of vectors, and expressing the genes under conditions in which detection of a desired activity, e.g., in this case, binding to S. epidermidis polypeptide or an interacting protein, facilitates relatively easy isolation of the vector encoding the gene whose product was detected. Each of the techniques described below is amenable to high through-put analysis for screening large numbers of sequences created, e.g., by random mutagenesis techniques.


Two Hybrid Systems


Two hybrid assays such as the system described below (as with the other screening methods described herein), can be used to identify polypeptides, e.g., fragments or analogs of a naturally-occurring S. epidermidis polypeptide, e.g., of cellular proteins, or of randomly generated polypeptides which bind to an S. epidermidis protein. (The S. epidermidis domain is used as the bait protein and the library of variants are expressed as prey fusion proteins.) In an analogous fashion, a two hybrid assay (as with the other screening methods described herein), can be used to find polypeptides which bind a S. epidermidis polypeptide.


Display Libraries


In one approach to screening assays, the Staphylococcus peptides are displayed on the surface of a cell or viral particle, and the ability of particular cells or viral particles to bind an appropriate receptor protein via the displayed product is detected in a “panning assay”. For example, the gene library can be cloned into the gene for a surface membrane protein of a bacterial cell, and the resulting fusion protein detected by panning (Ladner et al., WO 88/06630; Fuchs et al. (1991) Bio/Technology 9:1370-1371; and Goward et al. (1992) TIBS 18:136-140). In a similar fashion, a detectably labeled ligand can be used to score for potentially functional peptide homologs. Fluorescently labeled ligands, e.g., receptors, can be used to detect homologs which retain ligand-binding activity. The use of fluorescently labeled ligands, allows cells to be visually inspected and separated under a fluorescence microscope, or, where the morphology of the cell permits, to be separated by a fluorescence-activated cell sorter.


A gene library can be expressed as a fusion protein on the surface of a viral particle. For instance, in the filamentous phage system, foreign peptide sequences can be expressed on the surface of infectious phage, thereby conferring two significant benefits. First, since these phage can be applied to affinity matrices at concentrations well over 1013 phage per milliliter, a large number of phage can be screened at one time. Second, since each infectious phage displays a gene product on its surface, if a particular phage is recovered from an affinity matrix in low yield, the phage can be amplified by another round of infection. The group of almost identical E. coli filamentous phages, M13, fd., and fl, are most often used in phage display libraries. Either of the phage gIII or gVIII coat proteins can be used to generate fusion proteins without disrupting the ultimate packaging of the viral particle. Foreign epitopes can be expressed at the NH2-terminal end of pIII and phage bearing such epitopes recovered from a large excess of phage lacking this epitope (Ladner et al. PCT publication WO 90/02909; Garrard et al., PCT publication WO 92/09690; Marks et al. (1992) J. Biol. Chem. 267:16007-16010; Griffiths et al. (1993) EMBO J 12:725-734; Clackson et al. (1991) Nature 352:624-628; and Barbas et al. (1992) PNAS 89:4457-4461).


A common approach uses the maltose receptor of E. coli (the outer membrane protein, LamB) as a peptide fusion partner (Charbit et al. (1986) EMBO 5, 3029-3037). Oligonucleotides have been inserted into plasmids encoding the LamB gene to produce peptides fused into one of the extracellular loops of the protein. These peptides are available for binding to ligands, e.g., to antibodies, and can elicit an immune response when the cells are administered to animals. Other cell surface proteins, e.g., OmpA (Schorr et al. (1991) Vaccines 91, pp. 387-392), PhoE (Agterberg, et al. (1990) Gene 88, 37-45), and PAL (Fuchs et al. (1991) Bio/Tech 9, 1369-1372), as well as large bacterial surface structures have served as vehicles for peptide display. Peptides can be fused to pilin, a protein which polymerizes to form the pilus-a conduit for interbacterial exchange of genetic information (Thiry et al. (1989) Appl. Environ. Microbiol: 55, 984-993). Because of its role in interacting with other cells, the pilus provides a useful support for the presentation of peptides to the extracellular environment. Another large surface structure used for peptide display is the bacterial motive organ, the flagellum. Fusion of peptides to the subunit protein flagellin offers a dense array of many peptide copies on the host cells (Kuwajima et al. (1988) Bio/Tech. 6, 1080-1083). Surface proteins of other bacterial species have also served as peptide fusion partners. Examples include the Staphylococcus protein A and the outer membrane IgA protease of Neisseria (Hansson et al. (1992) J. Bacteriol. 174, 4239-4245 and Klauser et al. (1990) EMBO J. 9, 1991-1999).


In the filamentous phage systems and the LamB system described above, the physical link between the peptide and its encoding DNA occurs by the containment of the DNA within a particle (cell or phage) that carries the peptide on its surface. Capturing the peptide captures the particle and the DNA within. An alternative scheme uses the DNA-binding protein LacI to form a link between peptide and DNA (Cull et al. (1992) PNAS USA 89:1865-1869). This system uses a plasmid containing the LacI gene with an oligonucleotide cloning site at its 3′-end. Under the controlled induction by arabinose, a LacI-peptide fusion protein is produced. This fusion retains the natural ability of LacI to bind to a short DNA sequence known as LacO operator (LacO). By installing two copies of LacO on the expression plasmid, the LacI-peptide fusion binds tightly to the plasmid that encoded it. Because the plasmids in each cell contain only a single oligonucleotide sequence and each cell expresses only a single peptide sequence, the peptides become specifically and stablely associated with the DNA sequence that directed its synthesis. The cells of the library are gently lysed and the peptide-DNA complexes are exposed to a matrix of immobilized receptor to recover the complexes containing active peptides. The associated plasmid DNA is then reintroduced into cells for amplification and DNA sequencing to determine the identity of the peptide ligands. As a demonstration of the practical utility of the method, a large random library of dodecapeptides was made and selected on a monoclonal antibody raised against the opioid peptide dynorphin B. A cohort of peptides was recovered, all related by a consensus sequence corresponding to a six-residue portion of dynorphin B. (Cull et al. (1992) Proc. Natl. Acad. Sci. U.S.A. 89-1869)


This scheme, sometimes referred to as peptides-on-plasmids, differs in two important ways from the phage display methods. First, the peptides are attached to the C-terminus of the fusion protein, resulting in the display of the library members as peptides having free carboxy termini. Both of the filamentous phage coat proteins, pIII and pvIII, are anchored to the phage through their C-termini, and the guest peptides are placed into the outward-extending N-terminal domains. In some designs, the phage-displayed peptides are presented right at the amino terminus of the fusion protein. (Cwirla, et al. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 6378-6382) A second difference is the set of biological biases affecting the population of peptides actually present in the libraries. The LacI fusion molecules are confined to the cytoplasm of the host cells. The phage coat fusions are exposed briefly to the cytoplasm during translation but are rapidly secreted through the inner membrane into the periplasmic compartment, remaining anchored in the membrane by their C-terminal hydrophobic domains, with the N-termini, containing the peptides, protruding into the periplasm while awaiting assembly into phage particles. The peptides in the LacI and phage libraries may differ significantly as a result of their exposure to different proteolytic activities. The phage coat proteins require transport across the inner membrane and signal peptidase processing as a prelude to incorporation into phage. Certain peptides exert a deleterious effect on these processes and are underrepresented in the libraries (Gallop et al. (1994) J. Med. Chem. 37(9):1233-1251). These particular biases are not a factor in the LacI display system.


The number of small peptides available in recombinant random libraries is enormous. Libraries of 107-109 independent clones are routinely prepared. Libraries as large as 1011 recombinants have been created, but this size approaches the practical limit for clone libraries. This limitation in library size occurs at the step of transforming the DNA containing randomized segments into the host bacterial cells. To circumvent this limitation, an in vitro system based on the display of nascent peptides in polysome complexes has recently been developed. This display library method has the potential of producing libraries 3-6 orders of magnitude larger than the currently available phage/phagemid or plasmid libraries. Furthermore, the construction of the libraries, expression of the peptides, and screening, is done in an entirely cell-free format.


In one application of this method (Gallop et al. (1994) J. Med. Chem. 37(9):1233-1251), a molecular DNA library encoding 1012 decapeptides was constructed and the library expressed in an E. coli S30 in vitro coupled transcription/translation system. Conditions were chosen to stall the ribosomes on the mRNA, causing the accumulation of a substantial proportion of the RNA in polysomes and yielding complexes containing nascent peptides still linked to their encoding RNA. The polysomes are sufficiently robust to be affinity purified on immobilized receptors in much the same way as the more conventional recombinant peptide display libraries are screened. RNA from the bound complexes is recovered, converted to cDNA, and amplified by PCR to produce a template for the next round of synthesis and screening. The polysome display method can be coupled to the phage display system. Following several rounds of screening, cDNA from the enriched pool of polysomes was cloned into a phagemid vector. This vector serves as both a peptide expression vector, displaying peptides fused to the coat proteins, and as a DNA sequencing vector for peptide identification. By expressing the polysome-derived peptides on phage, one can either continue the affinity selection procedure in this format or assay the peptides on individual clones for binding activity in a phage ELISA, or for binding specificity in a completion phage ELISA (Barret, et al. (1992) Anal. Biochem 204,357-364). To identify the sequences of the active peptides one sequences the DNA produced by the phagemid host.


Secondary Screening of Polypeptides and Analogs


The high through-put assays described above can be followed by secondary screens in order to identify further biological activities which will, e.g., allow one skilled in the art to differentiate agonists from antagonists. The type of a secondary screen used will depend on the desired activity that needs to be tested. For example, an assay can be developed in which the ability to inhibit an interaction between a protein of interest and its respective ligand can be used to identify antagonists from a group of peptide fragments isolated though one of the primary screens described above.


Therefore, methods for generating fragments and analogs and testing them for activity are known in the art. Once the core sequence of interest is identified, it is routine for one skilled in the art to obtain analogs and fragments.


Peptide Mimetics of S. epidermidis Polypeptides


The invention also provides for reduction of the protein binding domains of the subject S. epidermidis polypeptides to generate mimetics, e.g. peptide or non-peptide agents. The peptide mimetics are able to disrupt binding of a polypeptide to its counter ligand, e.g., in the case of a S. epidermidis polypeptide binding to a naturally occurring ligand. The critical residues of a subject S. epidermidis polypeptide which are involved in molecular recognition of a polypeptide can be determined and used to generate S. epidermidis-derived peptidomimetics which competitively or noncompetitively inhibit binding of the S. epidermidis polypeptide with an interacting polypeptide (see, for example, European patent applications EP-412,762A and EP-B31,080A).


For example, scanning mutagenesis can be used to map the amino acid residues of a particular S. epidermidis polypeptide involved in binding an interacting polypeptide, peptidomimetic compounds (e.g. diazepine or isoquinoline derivatives) can be generated which mimic those residues in binding to an interacting polypeptide, and which therefore can inhibit binding of a S. epidermidis polypeptide to an interacting polypeptide and thereby interfere with the function of S. epidermidis polypeptide. For instance, non-hydrolyzable peptide analogs of such residues can be generated using benzodiazepine (e.g., see Freidinger et al. in Peptides: Chemistry and Biology, G. R Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988), azepine (e.g., see Huffman et al. in Peptides: Chemistry and Biology, G. R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988), substituted gama lactam rings (Garvey et al. in Peptides: Chemistry and Biology, G. R. Marshall ed., ESCOM Publisher: Leiden, Netherlands, 1988), keto-methylene pseudopeptides (Ewenson et al. (1986) J Med Chem 29:295; and Ewenson et al. in Peptides: Structure and Function (Proceedings of the 9th American Peptide Symposium) Pierce Chemical Co. Rockland, Ill., 1985), b-turn dipeptide cores (Nagai et al. (1985) Tetrahedron Lett 26:647; and Sato et al. (1986) J Chem Soc Perkin Trans 1:1231), and b-aminoalcohols (Gordon et al. (1985) Biochem Biophys Res Commun 126:419; and et al. (1986) Biochem Biophys Res Commun 134:71).


Vaccine Formulations for S. epidermidis Nucleic Acids and Polypeptides


This invention also features vaccine compositions for protection against infection by S. epidermidis or for treatment of S. epidermidis infection, a gram-positive spiral bacterium. In one embodiment, the vaccine compositions contain one or more immunogenic components such as a surface protein from S. epidermidis, or portion thereof, and a pharmaceutically acceptable carrier. Nucleic acids within the scope of the invention are exemplified by the nucleic acids of the invention contained in the Sequence Listing which encode S. epidermidis surface proteins. Any nucleic acid encoding an immunogenic S. epidermidis protein, or portion thereof, which is capable of expression in a cell, can be used in the present invention. These vaccines have therapeutic and prophylactic utilities.


One aspect of the invention provides a vaccine composition for protection against infection by S. epidermis which contains at least one immunogenic fragment of an S. epidermidis protein and a pharmaceutically acceptable carrier. Preferred fragments include peptides of at least about 10 amino acid residues in length, preferably about 10-20 amino acid residues in length, and more preferably about 12-16 amino acid residues in length.


Immunogenic components of the invention can be obtained, for example, by screening polypeptides recombinantly produced from the corresponding fragment of the nucleic acid encoding the full-length S. epidermidis protein. In addition, fragments can be chemically synthesized using techniques known in the art such as conventional Merrifield solid phase f-Moc or t-Boc chemistry.


In one embodiment, immunogenic components are identified by the ability of the peptide to stimulate T cells. Peptides which stimulate T cells, as determined by, for example, T cell proliferation or cytokine secretion are defined herein as comprising at least one T cell epitope. T cell epitopes are believed to be involved in initiation and perpetuation of the immune response to the protein allergen which is responsible for the clinical symptoms of allergy. These T cell epitopes are thought to trigger early events at the level of the T helper cell by binding to an appropriate HLA molecule on the surface of an antigen presenting cell, thereby stimulating the T cell subpopulation with the relevant T cell receptor for the epitope. These events lead to T cell proliferation, lymphokine secretion, local inflammatory reactions, recruitment of additional immune cells to the site of antigen/T cell interaction, and activation of the B cell cascade, leading to the production of antibodies. A T cell epitope is the basic element, or smallest unit of recognition by a T cell receptor, where the epitope comprises amino acids essential to receptor recognition (e.g., approximately 6 or 7 amino acid residues). Amino acid sequences which mimic those of the T cell epitopes are within the scope of this invention.


Screening immunogenic components can be accomplished using one or more of several different assays. For example, in vitro, peptide T cell stimulatory activity is assayed by contacting a peptide known or suspected of being immunogenic with an antigen presenting cell which presents appropriate MHC molecules in a T cell culture. Presentation of an immunogenic S. epidermidis peptide in association with appropriate MHC molecules to T cells in conjunction with the necessary co-stimulation has the effect of transmitting a signal to the T cell that induces the production of increased levels of cytokines, particularly of interleukin-2 and interleukin-4. The culture supernatant can be obtained and assayed for interleukin-2 or other known cytokines. For example, any one of several conventional assays for interleukin-2 can be employed, such as the assay described in Proc. Natl. Acad. Sci USA, 86: 1333 (1989) the pertinent portions of which are incorporated herein by reference. A kit for an assay for the production of interferon is also available from Genzyme Corporation (Cambridge, Mass.).


Alternatively, a common assay for T cell proliferation entails measuring tritiated thymidine incorporation. The proliferation of T cells can be measured in vitro by determining the amount of 3H-labeled thymidine incorporated into the replicating DNA of cultured cells. Therefore, the rate of DNA synthesis and, in turn, the rate of cell division can be quantified.


Vaccine compositions of the invention containing immunogenic components (e.g., S. epidermidis polypeptide or fragment thereof or nucleic acid encoding an S. epidermidis polypeptide or fragment thereof) preferably include a pharmaceutically acceptable carrier. The term “pharmaceutically acceptable carrier” refers to a carrier that does not cause an allergic reaction or other untoward effect in patients to whom it is administered. Suitable pharmaceutically acceptable carriers include, for example, one or more of water, saline, phosphate buffered saline, dextrose, glycerol, ethanol and the like, as well as combinations thereof. Pharmaceutically acceptable carriers may further comprise minor amounts of auxiliary substances such as wetting or emulsifying agents, preservatives or buffers, which enhance the shelf life or effectiveness of the antibody. For vaccines of the invention containing S. epidermidis polypeptides, the polypeptide is co-administered with a suitable adjuvant.


It will be apparent to those of skill in the art that the therapeutically effective amount of DNA or protein of this invention will depend, inter alia, upon the administration schedule, the unit dose of antibody administered, whether the protein or DNA is administered in combination with other therapeutic agents, the immune status and health of the patient, and the therapeutic activity of the particular protein or DNA.


Vaccine compositions are conventionally administered parenterally, e.g., by injection, either subcutaneously or intramuscularly. Methods for intramuscular immunization are described by Wolff et al. (1990) Science 247: 1465-1468 and by Sedegah et al. (1994) Immunology 91: 9866-9870. Other modes of administration include oral and pulmonary formulations, suppositories, and transdermal applications. Oral immunization is preferred over parenteral methods for inducing protection against infection by S. epidermidis. Cain et. al. (1993) Vaccine 11-637-642. Oral formulations include such normally employed excipients as, for example, pharmaceutical grades of mannitol, lactose, starch, magnesium stearate, sodium saccharine, cellulose, magnesium carbonate, and the like.


The vaccine compositions of the invention can include an adjuvant, including, but not limited to aluminum hydroxide; N-acetyl-muramyl-L-threonyl-D-isoglutamine (thr-MDP); N-acetyl-nor-muramyl-L-alanyl-D-isoglutamine (CGP 11637, referred to as nor-MDP); N-acetylmuramyl-L-alanyl-D-isoglutaminyl-L-alanine-2-(1′-2′-dipalmitoyl-sn-glycero-3-hydroxyphos-phoryloxy)-ethylamine (CGP 19835A, referred to a MTP-PE); RIBI, which contains three components from bacteria; monophosphoryl lipid A; trehalose dimycoloate; cell wall skeleton (MPL+TDM+CWS) in a 2% squalene/Tween 80 emulsion; and cholera toxin. Others which may be used are non-toxic derivatives of cholera toxin, including its B subunit, and/or conjugates or genetically engineered fusions of the S. epidermidis polypeptide with cholera toxin or its B subunit, procholeragenoid, fungal polysaccharides, including schizophyllan, muramyl dipeptide, muramyl dipeptide derivatives, phorbol esters, labile toxin of E. coli, non-S. epidermidis bacterial lysates, block polymers or saponins.


Other suitable delivery methods include biodegradable microcapsules or immuno-stimulating complexes (ISCOMs), cochleates, or liposomes, genetically engineered attenuated live vectors such as viruses or bacteria, and recombinant (chimeric) virus-like particles, e.g., bluetongue. The amount of adjuvant employed will depend on the type of adjuvant used. For example, when the mucosal adjuvant is cholera toxin, it is suitably used in an amount of 5 mg to 50 mg, for example 10 mg to 35 mg. When used in the form of microcapsules, the amount used will depend on the amount employed in the matrix of the microcapsule to achieve the desired dosage. The determination of this amount is within the skill of a person of ordinary skill in the art.


Carrier systems in humans may include enteric release capsules protecting the antigen from the acidic environment of the stomach, and including S. epidermidis polypeptide in an insoluble form as fusion proteins. Suitable carriers for the vaccines of the invention are enteric coated capsules and polylactide-glycolide microspheres. Suitable diluents are 0.2 N NaHCO3 and/or saline.


Vaccines of the invention can be administered as a primary prophylactic agent in adults or in children, as a secondary prevention, after successful eradication of S. epidermidis in an infected host, or as a therapeutic agent in the aim to induce an immune response in a susceptible host to prevent infection by S. epidermidis. The vaccines of the invention are administered in amounts readily determined by persons of ordinary skill in the art. Thus, for adults a suitable dosage will be in the range of 10 mg to 10 g, preferably 10 mg to 100 mg. A suitable dosage for adults will also be in the range of 5 mg to 500 mg. Similar dosage ranges will be applicable for children. Those skilled in the art will recognize that the optimal dose may be more or less depending upon the patient's body weight, disease, the route of administration, and other factors. Those skilled in the art will also recognize that appropriate dosage levels can be obtained based on results with known oral vaccines such as, for example, a vaccine based on an E. coli lysate (6 mg dose daily up to total of 540 mg) and with an enterotoxigenic E. coli purified antigen (4 doses of 1 mg) (Schulman et al., J. Urol. 150:917-921 (1993); Boedecker et al., American Gastroenterological Assoc. 999:A-222 (1993)). The number of doses will depend upon the disease, the formulation, and efficacy data from clinical trials. Without intending any limitation as to the course of treatment, the treatment can be administered over 3 to 8 doses for a primary immunization schedule over 1 month (Boedeker, American Gastroenterological Assoc. 888:A-222 (1993)).


In a preferred embodiment, a vaccine composition of the invention can be based on a killed whole E. coli preparation with an immunogenic fragment of a S. epidermidis protein of the invention expressed on its surface or it can be based on an E. coli lysate, wherein the killed E. coli acts as a carrier or an adjuvant.


It will be apparent to those skilled in the art that some of the vaccine compositions of the invention are useful only for preventing S. epidermidis infection, some are useful only for treating S. epidermidis infection, and some are useful for both preventing and treating S. epidermidis infection. In a preferred embodiment, the vaccine composition of the invention provides protection against S. epidermidis infection by stimulating humoral and/or cell-mediated immunity against S. epidermidis. It should be understood that amelioration of any of the symptoms of S. epidermidis infection is a desirable clinical goal, including a lessening of the dosage of medication used to treat S. epidermidis-caused disease, or an increase in the production of antibodies in the serum or mucous of patients.


Antibodies Reactive with S. epidermidis Polypeptides


The invention also includes antibodies specifically reactive with the subject S. epidermidis polypeptide. Anti-protein/anti-peptide antisera or monoclonal antibodies can be made by standard protocols (See, for example, Antibodies: A Laboratory Manual ed. by Harlow and Lane (Cold Spring Harbor Press: 1988)). A mammal such as a mouse, a hamster or rabbit can be immunized with an immunogenic form of the peptide. Techniques for conferring immunogenicity on a protein or peptide include conjugation to carriers or other techniques well known in the art. An immunogenic portion of the subject S. epidermidis polypeptide can be administered in the presence of adjuvant. The progress of immunization can be monitored by detection of antibody titers in plasma or serum. Standard ELISA or other immunoassays can be used with the immunogen as antigen to assess the levels of antibodies.


In a preferred embodiment, the subject antibodies are immunospecific for antigenic determinants of the S. epidermidis polypeptides of the invention, e.g. antigenic determinants of a polypeptide of the invention contained in the Sequence Listing, or a closely related human or non-human mammalian homolog (e.g., 90% homologous, more preferably at least 95% homologous). In yet a further preferred embodiment of the invention, the anti-S. epidermidis antibodies do not substantially cross react (i.e., react specifically) with a protein which is for example, less than 80% percent homologous to a sequence of the invention contained in the Sequence Listing. By “not substantially cross react”, it is meant that the antibody has a binding affinity for a non-homologous protein which is less than 10 percent, more preferably less than 5 percent, and even more preferably less than 1 percent, of the binding affinity for a protein of the invention contained in the Sequence Listing. In a most preferred embodiment, there is no cross-reactivity between bacterial and mammalian antigens.


The term antibody as used herein is intended to include fragments thereof which are also specifically reactive with S. epidermidis polypeptides. Antibodies can be fragmented using conventional techniques and the fragments screened for utility in the same manner as described above for whole antibodies. For example, F(ab′)2 fragments can be generated by treating antibody with pepsin. The resulting F(ab′)2 fragment can be treated to reduce disulfide bridges to produce Fab′ fragments. The antibody of the invention is further intended to include bispecific and chimeric molecules having an anti-S. epidermidis portion.


Both monoclonal and polyclonal antibodies (Ab) directed against S. epidermidis polypeptides or S. epidermidis polypeptide variants, and antibody fragments such as Fab′ and F(ab′)2, can be used to block the action of S. epidermidis polypeptide and allow the study of the role of a particular S. epidermidis polypeptide of the invention in aberrant or unwanted intracellular signaling, as well as the normal cellular function of the S. epidermidis and by microinjection of anti-S. epidermidis polypeptide antibodies of the present invention.


Antibodies which specifically bind S. epidermidis epitopes can also be used in immunohistochemical staining of tissue samples in order to evaluate the abundance and pattern of expression of S. epidermidis antigens. Anti-S. epidermidis polypeptide antibodies can be used diagnostically in immuno-precipitation and immuno-blotting to detect and evaluate S. epidermidis levels in tissue or bodily fluid as part of a clinical testing procedure. Likewise, the ability to monitor S. epidermidis polypeptide levels in an individual can allow determination of the efficacy of a given treatment regimen for an individual afflicted with such a disorder. The level of a S. epidermidis polypeptide can be measured in cells found in bodily fluid, such as in urine samples or can be measured in tissue, such as produced by gastric biopsy. Diagnostic assays using anti-S. epidermidis antibodies can include, for example, immunoassays designed to aid in early diagnosis of S. epidermidis infections. The present invention can also be used as a method of detecting antibodies contained in samples from individuals infected by this bacterium using specific S. epidermidis antigens.


Another application of anti-S. epidermidis polypeptide antibodies of the invention is in the immunological screening of cDNA libraries constructed in expression vectors such as λgt11, λgt18-23, λZAP, and λORF8. Messenger libraries of this type, having coding sequences inserted in the correct reading frame and orientation, can produce fusion proteins. For instance, λgt11 will produce fusion proteins whose amino termini consist of β-galactosidase amino acid sequences and whose carboxy termini consist of a foreign polypeptide. Antigenic epitopes of a subject S. epidermidis polypeptide can then be detected with antibodies, as, for example, reacting nitrocellulose filters lifted from infected plates with anti-S. epidermidis polypeptide antibodies Phage, scored by this assay, can then be isolated from the infected plate. Thus, the presence of S. epidermidis gene homologs can be detected and cloned from other species, and alternate isoforms (including splicing variants) can be detected and cloned.


Kits Containing Nucleic Acids, Polypeptides or Antibodies of the Invention


The nucleic acid, polypeptides and antibodies of the invention can be combined with other reagents and articles to form kits. Kits for diagnostic purposes typically comprise the nucleic acid, polypeptides or antibodies in vials or other suitable vessels. Kits typically comprise other reagents for performing hybridization reactions, polymerase chain reactions (PCR), or for reconstitution of lyophilized components, such as aqueous media, salts, buffers, and the like. Kits may also comprise reagents for sample processing such as detergents, chaotropic salts and the like. Kits may also comprise immobilization means such as particles, supports, wells, dipsticks and the like. Kits may also comprise labeling means such as dyes, developing reagents, radioisotopes, fluorescent agents, luminescent or chemiluminescent agents, enzymes, intercalating agents and the like. With the nucleic acid and amino acid sequence information provided herein, individuals skilled in art can readily assemble kits to serve their particular purpose. Kits further can include instructions for use.


Drug Screening Assays Using S. epidermidis Polypeptides


By making available purified and recombinant S. epidermidis polypeptides, the present invention provides assays which can be used to screen for drugs which are either agonists or antagonists of the normal cellular function, in this case, of the subject S. epidermidis polypeptides, or of their role in intracellular signaling. Such inhibitors or potentiators may be useful as new therapeutic agents to combat S. epidermidis infections in humans. A variety of assay formats will suffice and, in light of the present inventions, will be comprehended by the person skilled in the art.


In many drug screening programs which test libraries of compounds and natural extracts, high throughput assays are desirable in order to maximize the number of compounds surveyed in a given period of time. Assays which are performed in cell-free systems, such as may be derived with purified or semi-purified proteins, are often preferred as “primary” screens in that they can be generated to permit rapid development and relatively easy detection of an alteration in a molecular target which is mediated by a test compound. Moreover, the effects of cellular toxicity and/or bioavailability of the test compound can be generally ignored in the in vitro system, the assay instead being focused primarily on the effect of the drug on the molecular target as may be manifest in an alteration of binding affinity with other proteins or change in enzymatic properties of the molecular target. Accordingly, in an exemplary screening assay of the present invention, the compound of interest is contacted with an isolated and purified S. epidermidis polypeptide.


Screening assays can be constructed in vitro with a purified S. epidermidis polypeptide or fragment thereof, such as a S. epidermidis polypeptide having enzymatic activity, such that the activity of the polypeptide produces a detectable reaction product. The efficacy of the compound can be assessed by generating dose response curves from data obtained using various concentrations of the test compound. Moreover, a control assay can also be performed to provide a baseline for comparison. Suitable products include those with distinctive absorption, fluorescence, or chemi-luminescence properties, for example, because detection may be easily automated. A variety of synthetic or naturally occurring compounds can be tested in the assay to identify those which inhibit or potentiate the activity of the S. epidermidis polypeptide. Some of these active compounds may directly, or with chemical alterations to promote membrane permeability or solubility, also inhibit or potentiate the same activity (e.g., enzymatic activity) in whole, live S. epidermidis cells.


Overexpression Assays


Overexpression assays are based on the premise that overproduction of a protein would lead to a higher level of resistance to compounds that selectively interfere with the function of that protein. Overexpression assays may be used to identify compounds that interfere with the function of virtually any type of protein, including without limitation enzymes, receptors, DNA- or RNA-binding proteins, or any proteins that are directly or indirectly involved in regulating cell growth.


Typically, two bacterial strains are constructed. One contains a single copy of the gene of interest, and a second contains several copies of the same gene. Identification of useful inhibitory compounds of this type of assay is based on a comparison of the activity of a test compound in inhibiting growth and/or viability of the two strains. The method involves constructing a nucleic acid vector that directs high level expression of a particular target nucleic acid. The vectors are then transformed into host cells in single or multiple copies to produce strains that express low to moderate and high levels of protein encoding by the target sequence (strain A and B, respectively). Nucleic acid comprising sequences encoding the target gene can, of course, be directly integrated into the host cell.


Large numbers of compounds (or crude substances which may contain active compounds) are screened for their effect on the growth of the two strains. Agents which interfere with an unrelated target equally inhibit the growth of both strains. Agents which interfere with the function of the target at high concentration should inhibit the growth of both strains. It should be possible, however, to titrate out the inhibitory effect of the compound in the overexpressing strain. That is, if the compound is affecting the particular target that is being tested, it should be possible to inhibit the growth of strain A at a concentration of the compound that allows strain B to grow.


Alternatively, a bacterial strain is constructed that contains the gene of interest under the control of an inducible promoter. Identification of useful inhibitory agents using this type of assay is based on a comparison of the activity of a test compound in inhibiting growth and/or viability of this strain under both inducing and non-inducing conditions. The method involves constructing a nucleic acid vector that directs high-level expression of a particular target nucleic acid. The vector is then transformed into host cells that are grown under both non-inducing and inducing conditions (conditions A and B, respectively).


Large numbers of compounds (or crude substances which may contain active compounds) are screened for their effect on growth under these two conditions. Agents that interfere with the function of the target should inhibit growth under both conditions. It should be possible, however, to titrate out the inhibitory effect of the compound in the overexpressing strain. That is, if the compound is affecting the particular target that is being tested, it should be possible to inhibit growth under condition A at a concentration that allows the strain to grow under condition B.


Ligand-binding Assays


Many of the targets according to the invention have functions that have not yet been identified. Ligand-binding assays are useful to identify inhibitor compounds that interfere with the function of a particular target, even when that function is unknown. These assays are designed to detect binding of test compounds to particular targets. The detection may involve direct measurement of binding. Alternatively, indirect indications of binding may involve stabilization of protein structure or disruption of a biological function. Non-limiting examples of useful ligand-binding assays are detailed below.


A useful method for the detection and isolation of binding proteins is the Biomolecular Interaction Assay (BIAcore) system developed by Pharmacia Biosensor and described in the manufacturer's protocol (LKB Pharmacia, Sweden). The BIAcore system uses an affinity purified anti-GST antibody to immobilize GST-fusion proteins onto a sensor chip. The sensor utilizes surface plasmon resonance which is an optical phenomenon that detects changes in refractive indices. In accordance with the practice of the invention, a protein of interest is coated onto a chip and test compounds are passed over the chip. Binding is detected by a change in the refractive index (surface plasmon resonance).


A different type of ligand-binding assay involves scintillation proximity assays (SPA, described in U.S. Pat. No. 4,568,649).


Another type of ligand binding assay, also undergoing development, is based on the fact that proteins containing mitochondrial targeting signals are imported into isolated mitochondria in vitro (Hurt et al., 1985, Embo J. 4:2061-2068; Eilers and Schatz, Nature, 1986, 322:228-231). In a mitochondrial import assay, expression vectors are constructed in which nucleic acids encoding particular target proteins are inserted downstream of sequences encoding mitochondrial import signals. The chimeric proteins are synthesized and tested for their ability to be imported into isolated mitochondria in the absence and presence of test compounds. A test compound that binds to the target protein should inhibit its uptake into isolated mitochondria in vitro.


Another ligand-binding assay is the yeast two-hybrid system (Fields and Song, 1989, Nature 340:245-246). The yeast two-hybrid system takes advantage of the properties of the GAL4 protein of the yeast Saccharomyces cerevisiae. The GAL4 protein is a transcriptional activator required for the expression of genes encoding enzymes of galactose utilization. This protein consists of two separable and functionally essential domains: an N-terminal domain which binds to specific DNA sequences (UASG); and a C-terminal domain containing acidic regions, which is necessary to activate transcription. The native GAL4 protein, containing both domains, is a potent activator of transcription when yeast are grown on galactose media. The N-terminal domain binds to DNA in a sequence-specific manner but is unable to activate transcription. The C-terminal domain contains the activating regions but cannot activate transcription because it fails to be localized to UASG. In the two-hybrid system, a system of two hybrid proteins containing parts of GAL4: (1) a GAL4 DNA-binding domain fused to a protein ‘X’ and (2) a GAL4 activation region fused to a protein ‘Y’. If X and Y can form a protein-protein complex and reconstitute proximity of the GAL4 domains, transcription of a gene regulated by UASG occurs. Creation of two hybrid proteins, each containing one of the interacting proteins X and Y, allows the activation region of UASG to be brought to its normal site of action.


The binding assay described in Fodor et al., 1991, Science 251:767-773, which involves testing the binding affinity of test compounds for a plurality of defined polymers synthesized on a solid substrate, may also be useful.


Compounds which bind to the polypeptides of the invention are potentially useful as antibacterial agents for use in therapeutic compositions.


Pharmaceutical formulations suitable for antibacterial therapy comprise the antibacterial agent in conjunction with one or more biologically acceptable carriers. Suitable biologically acceptable carriers include, but are not limited to, phosphate-buffered saline, saline, deionized water, or the like. Preferred biologically acceptable carriers are physiologically or pharmaceutically acceptable carriers.


The antibacterial compositions include an antibacterial effective amount of active agent. Antibacterial effective amounts are those quantities of the antibacterial agents of the present invention that afford prophylactic protection against bacterial infections or which result in amelioration or cure of an existing bacterial infection. This antibacterial effective amount will depend upon the agent, the location and nature of the infection, and the particular host. The amount can be determined by experimentation known in the art, such as by establishing a matrix of dosages and frequencies and comparing a group of experimental units or subjects to each point in the matrix.


The antibacterial active agents or compositions can be formed into dosage unit forms, such as for example, creams, ointments, lotions, powders, liquids, tablets, capsules, suppositories, sprays, aerosols or the like. If the antibacterial composition is formulated into a dosage unit form, the dosage unit form may contain an antibacterial effective amount of active agent. Alternatively, the dosage unit form may include less than such an amount if multiple dosage unit forms or multiple dosages are to be used to administer a total dosage of the active agent. Dosage unit forms can include, in addition, one or more excipient(s), diluent(s), disintegrant(s), lubricant(s), plasticizer(s), colorant(s), dosage vehicle(s), absorption enhancer(s), stabilizer(s), bactericide(s), or the like.


For general information concerning formulations, see, e.g., Gilman et al. (eds.), 1990, Goodman and Gilman's: The Pharmacological Basis of Therapeutics, 8th ed., Pergamon Press; and Remington's Pharmaceutical Sciences, 17th ed., 1990, Mack Publishing Co., Easton, Pa.; Avis et al. (eds.), 1993, Pharmaceutical Dosage Forms: Parenteral Medications, Dekker, New York; Lieberman et al (eds.), 1990, Pharmaceutical Dosage Forms: Disperse Systems, Dekker, New York.


The antibacterial agents and compositions of the present invention are useful for preventing or treating S. epidermidis infections. Infection prevention methods incorporate a prophylactically effective amount of an antibacterial agent or composition. A prophylactically effective amount is an amount effective to prevent S. epidermidis infection and will depend upon the specific bacterial strain, the agent, and the host. These amounts can be determined experimentally by methods known in the art and as described above.



S. epidermidis infection treatment methods incorporate a therapeutically effective amount of an antibacterial agent or composition. A therapeutically effective amount is an amount sufficient to ameliorate or eliminate the infection. The prophylactically and/or therapeutically effective amounts can be administered in one administration or over repeated administrations. Therapeutic administration can be followed by prophylactic administration, once the initial bacterial infection has been resolved.


The antibacterial agents and compositions can be administered topically or systemically. Topical application is typically achieved by administration of creams, ointments, lotions, or sprays as described above. Systemic administration includes both oral and parental routes. Parental routes include, without limitation, subcutaneous, intramuscular, intraperitoneal, intravenous, transdermal, inhalation and intranasal administration.


EXEMPLIFICATION

Cloning and Sequencing S. epidermidis Genomic Sequence


This invention provides nucleotide sequences of the genome of S. epidermidis which thus comprises a DNA sequence library of S. epidermidis genomic DNA. The detailed description that follows provides nucleotide sequences of S. epidermidis, and also describes how the sequences were obtained and how ORFs (Open Reading Frames) and protein-coding sequences can be identified. Also described are methods of using the disclosed S. epidermidis sequences in methods including diagnostic and therapeutic applications. Furthermore, the library can be used as a database for identification and comparison of medically important sequences in this and other strains of S. epidermidis as well as other species of Staphylococcus.


Chromosomal DNA from strainl9804 of S. epidermidis was isolated after Zymolyase digestion, sodium dodecyl sulfate lysis, potassium acetate precipitation, phenol:chloroform extraction and ethanol precipitation (Soll, D. R., T. Srikantha and S. R. Lockhart: Characterizing Developmentally Regulated Genes in S. epidermidis. In Microbial Genome Methods. K. W. Adolph, editor. CRC Press. New York. p 17-37.). Genomic S. epidermidis DNA was hydrodynamically sheared in an HPLC and then separated on a standard 1% agarose gel. Fractions corresponding to 2500-3000 bp in length were excised from the gel and purified by the GeneClean procedure (Bio101, Inc.).


The purified DNA fragments were then blunt-ended using T4 DNA polymerase. The healed DNA was then ligated to unique BstXI-linker adapters (5′-GTCTTCACCACGGGG-3′ (SEQ ID NO: 5675) and 5′-GTGGTGAAGAC-3′ (SEQ ID NO: 5676) in 100-1000 fold molar excess). These linkers are complimentary to the BstXI-cut pGTC vector, while the overhang is not self-complimentary. Therefore, the linkers will not concatermerize nor will the cut-vector religate itself easily. The linker-adapted inserts were separated from the unincorporated linkers on a 1% agarose gel and purified using GeneClean. The linker-adapted inserts were then ligated to BstXI-cut vector to construct a “shotgun” sublclone libraries.


Only major modifications to the protocols are highlighted. Briefly, the library was then transformed into DH5á competent cells (Gibco/BRL, DH5á transformation protocol). It was assessed by plating onto antibiotic plates containing ampicillin and IPTG/Xgal. The plates were incubated overnight at 37° C. Transformants were then used for plating of clones and picking for sequencing. The cultures were grown overnight at 37° C. DNA was purified using a silica bead DNA preparation (Engelstein, 1996) method. In this manner, 25 μg of DNA was obtained per clone.


These purified DNA samples were then sequenced using primarily ABI dye-terminator chemistry. All subsequent steps were based on sequencing by ABI377 automated DNA sequencing methods. The ABI dye terminator sequence reads were run on ABI377 machines and the data was transferred to UNIX machines following lane tracking of the gels. Base calls and quality scores were determined using the program PHRED (Ewing et al., 1998, Genome Res. 8: 175-185; Ewing and Green, 1998, Genome Res. 8: 685-734). Reads were assembled using PHRAP (P. Green, Abstracts of DOE Human Genome Program Contractor-Grantee Workshop V, January 1996, p. 157) with default program parameters and quality scores. The initial assembly was done at 2.3-fold coverage and yielded 5821 contigs.


Finishing can follow the initial assembly. Missing mates (sequences from clones that only gave reads from one end of the Staphylococcus DNA inserted in the plasmid) can be identified and sequenced with ABI technology to allow the identification of additional overlapping contigs.


End-sequencing of randomly picked genomic lambda was also performed. Sequencing on a both sides was done for all lambda sequences. The lambda library backbone helped to verify the integrity of the assembly and allowed closure of some of the physical gaps. Primers for walking off the ends of contigs would be selected using pick_primer (a GTC program) near the ends of the clones to facilitate gap closure. These walks can be sequenced using the selected clones and primers. These data are then reassembled with PHRAP. Additional sequencing using PCR-generated templates and screened and/or unscreened lambda templates can be done in addition.


To identify S. epidermidis polypeptides the complete genomic sequence of S. epidermidis were analyzed essentially as follows: First, all possible stop-to-stop open reading frames (ORFS) greater than 180 nucleotides in all six reading frames were translated into amino acid sequences. Second, the identified ORFs were analyzed for homology to known (archeabacter, prokaryotic and eukaryotic) protein sequences. Third, the coding potential of non-homologous sequences were evaluated with the program GENEMARK™ (Borodovsky and Mclninch, 1993, Comp. Chem. 17:123).


EE341901427USIdentification, Cloning and Expression of S. epidermidis Nucleic Acids


Expression and purification of the S. epidermidis polypeptides of the invention can be performed essentially as outlined below.


To facilitate the cloning, expression and purification of membrane and secreted proteins from S. epidermidis, a gene expression system, such as the pET System (Novagen), for cloning and expression of recombinant proteins in E. coli is selected. Also, a DNA sequence encoding a peptide tag, the His-Tag, is fused to the 3′ end of DNA sequences of interest in order to facilitate purification of the recombinant protein products. The 3′ end is selected for fusion in order to avoid alteration of any 5′ terminal signal sequence.


PCR Amplification and Cloning of Nucleic Acids Containing ORF's Encoding Enzymes


Nucleic acids chosen (for example, from the nucleic acids set forth in SEQ ID NO: 1-SEQ ID NO: 2837) for cloning from the 18972 strain of S. epidermidis are prepared for amplification cloning by polymerase chain reaction (PCR). Synthetic oligonucleotide primers specific for the 5′ and 3′ ends of open reading frames (ORFs) are designed and purchased from GibcoBRL Life Technologies (Gaithersburg, N. Dak., USA). All forward primers (specific for the 5′ end of the sequence) are designed to include an NcoI cloning site at the extreme 5′ terminus. These primers are designed to permit initiation of protein translation at a methionine residue followed by a valine residue and the coding sequence for the remainder of the native S. epidermidis DNA sequence. All reverse primers (specific for the 3′ end of any S. epidermidis ORF) include a EcoRI site at the extreme 5′ trminus to permit cloning of each S. epidermidis sequence into the reading frame of the pET-28b. The pET-28b vector provides sequence encoding an additional 20 carboxy-terminal amino acids including six histidine residues (at the extreme C-terminus), which comprise the His-Tag.


Genomic DNA prepared from the 18972 strain of S. epidermidis is used as the source of template DNA for PCR amplification reactions (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994). To amplify a DNA sequence containing a S. epidermidis ORF, genomic DNA (50 nanograms) is introduced into a reaction vial containing 2 mM MgCl2, 1 micromolar synthetic oligonucleotide primers (forward and reverse primers) complementary to and flanking a defined S. epidermidis ORE, 0.2 mM of each deoxynucleotide triphosphate; dATP, dGTP, dCTP, dTTP and 2.5 units of heat stable DNA polymerase (Arnplitaq, Roche Molecular Systems, Inc., Branchburg, N.J., USA) in a final volume of 100 microliters.


Upon completion of thermal cycling reactions, each sample of amplified DNA is washed and purified using the Qiaquick Spin PCR purification kit (Qiagen, Gaithersburg, Md., USA). All amplified DNA samples are subjected to digestion with the restriction endonucleases, e.g., NcoI and EcoRI (New England BioLabs, Beverly, Mass., USA)(Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994). DNA samples are then subjected to electrophoresis on 1.0% NuSeive (FMC BioProducts, Rockland, Me. USA) agarose gels. DNA is visualized by exposure to ethidium bromide and long wave uv irradiation. DNA contained in slices isolated from the agarose gel is purified using the Bio 101 GeneClean Kit protocol (Bio 101 Vista, Calif., USA).


Cloning of S. epidermidis Nucleic Acids into an Expression Vector


The pET-28b vector is prepared for cloning by digestion with restriction endonucleases, e.g., NcoI and EcoRI (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994). The pET-28a vector, which encodes a His-Tag that can be fused to the 5′ end of an inserted gene, is prepared by digestion with appropriate restriction endonucleases.


Following digestion, DNA inserts are cloned (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994) into the previously digested pET-28b expression vector. Products of the ligation reaction are then used to transform the BL21 strain of E. coli (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994) as described below.


Transformation of Competent Bacteria with Recombinant Plasmids


Competent bacteria, E. coli strain BL21 or E. coli strain BL21(DE3), are transformed with recombinant pET expression plasmids carrying the cloned S. epidermidis sequences according to standard methods (Current Protocols in Molecular, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994). Briefly, 1 microliter of ligation reaction is mixed with 50 microliters of electrocompetent cells and subjected to a high voltage pulse, after which, samples are incubated in 0.45 milliliters SOC medium (0.5% yeast extract, 2.0% tryptone, 10 mM NaCl, 2.5 mM KCl, 10 mM MgCl2, 10 mM MgSO4 and 20, mM glucose) at 37° C. with shaking for 1 hour. Samples are then spread on LB agar plates containing 25 microgram/ml kanamycin sulfate for growth overnight. Transformed colonies of BL21 are then picked and analyzed to evaluate cloned inserts as described below.


Identification Of Recombinant Expression Vectors with S. epidermidis Nucleic Acids


Individual BL21 clones transformed with recombinant pET-28b S. epidermidis ORFs are analyzed by PCR amplification of the cloned inserts using the same forward and reverse primers, specific for each S. epidermidis sequence, that were used in the original PCR amplification cloning reactions. Successful amplification verifies the integration of the S. epidermidis sequences in the expression vector (Current Protocols in Molecular Biology, John Wiley and Sons, Inc., F. Ausubel et al., eds., 1994).


Isolation and Preparation of Nucleic Acids from Transformants


Individual clones of recombinant pET-28b vectors carrying properly cloned S. epidermidis ORFs are picked and incubated in 5 mls of LB broth plus 25 microgram/ml kanamycin sulfate overnight. The following day plasmid DNA is isolated and purified using the Qiagen plasmid purification protocol (Qiagen Inc., Chatsworth, Calif., USA).


Expression of Recombinant S. epidermidis Sequences in E. coli


The pET vector can be propagated in any E. coli K-12 strain e.g. HMS174, HB101, JM109, DH5, etc. for the purpose of cloning or plasmid preparation. Hosts for expression include E. coli strains containing a chromosomal copy of the gene for T7 RNA polymerase. These hosts are lysogens of bacteriophage DE3, a lambda derivative that carries the lacI gene, the lacUV5 promoter and the gene for T7 RNA polymerase. T7 RNA polymerase is induced by addition of isopropyl-B-D-thiogalactoside (IPTG), and the T7 RNA polymerase transcribes any target plasmid, such as pET-28b, carrying its gene of interest. Strains used include: BL21(DE3) (Studier, F. W., Rosenberg, A. H., Dunn, J. J., and Dubendorff, J. W. (1990) Meth. Enzymol. 185, 60-89).


To express recombinant S. epidermidis sequences, 50 nanograms of plasmid DNA isolated as described above is used to transform competent BL21 (DE3) bacteria as described above (provided by Novagen as part of the pET expression system kit). The lacZ gene (beta-galactosidase) is expressed in the pET-System as described for the S. epidermidis recombinant constructions. Transformed cells are cultured in SOC medium for 1 hour, and the culture is then plated on LB plates containing 25 micrograms/ml kanamycin sulfate. The following day, bacterial colonies are pooled and grown in LB medium containing kanamycin sulfate (25 micrograms/ml) to an optical density at 600 nM of 0.5 to 1.0 O.D. units, at which point, 1 millimolar IPTG was added to the culture for 3 hours to induce gene expression of the S. epidermidis recombinant DNA constructions.


After induction of gene expression with IPTG, bacteria are pelleted by centrifugation in a Sorvall RC-3B centrifuge at 3500×g for 15 minutes at 4° C. Pellets are resuspended in 50 milliliters of cold 10 mM Tris-HCl, pH 8.0, 0.1 M NaCl and 0.1 mM EDTA (STE buffer). Cells are then centrifuged at 2000×g for 20 min at 4° C. Wet pellets are weighed and frozen at −80° C. until ready for protein purification.


A variety of methodologies known in the art can be utilized to purify the isolated proteins. (Current Protocols in Protein Science, John Wiley and Sons, Inc., J. E. Coligan et al., eds., 1995). For example, the frozen cells may be thawed, resupended in buffer and ruptured by several passages through a small volume microfluidizer (Model M-110SOS, Microfluidics International Corporation, Newton, Mass.). The resultant homogenate may be centrifuged to yield a clear supernatant (crude extract) and following filtration the crude extract may be fractionated over columns. Fractions may be monitored by absorbance at OD280 nm. and peak fractions may analyzed by SDS-PAGE


The concentrations of purified protein preparations may be quantified spectrophotometrically using absorbance coefficients calculated from amino acid content (Perkins, S. J. 1986 Eur. J. Biochem. 157, 169-180). Protein concentrations are also measured by the method of Bradford, M. M. (1976) Anal. Biochem. 72, 248-254, and Lowy, O. H., Rosebrough, N., Farr, A. L. & Randall, R. J. (1951) J. Biol. Chem. 193, pages 265-275, using bovine serum albumin as a standard.


SDS-polyacrylamide gels of various concentrations may be purchased from BioRad (Hercules, Calif., USA), and stained with Coomassie blue. Molecular weight markers may include rabbit skeletal muscle myosin (200 kDa), E. coli (-galactosidase (116 kDa), rabbit muscle phosphorylase B (97.4 kDa), bovine serum albumin (66.2 kDa), ovalbumin (45 kDa), bovine carbonic anhydrase (31 kDa), soybean trypsin inhibitor (21.5 kDa), egg white lysozyme (14.4 kDa) and bovine aprotinin (6.5 kDa).


EQUIVALENTS

Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments and methods described herein. The specific embodiments described herein are offered by way of example only, and the invention is to limited only by the terms of the appended claims, along with the full scope of equivalents to which such claims are entitled.



















TABLE 2





Contig
Orf
ntID
aaID
nt Length
aa Length
Blast Score
Blast Probability
Subject Taxonomy
Subject Name
Subject Definition

























Contig001D
14634450_c1_1
1
2838
204
68







Contig001D
24225000_c3_3
2
2839
342
114
152
4.80E−11

Archaeoglobus

g2649613
AF0984ABC transporter, ATP-binding proteinArchaeoglobus fulgidus section











fulgidus


71 of 172 ofthe complete genome.similar to SP


Contig001D
801552_c2_2
3
2840
381
127


Contig002D
32204583_f2_4
4
2841
198
66


Contig002D
34101427_c3_13
5
2842
549
183
301
7.80E−27

Haemophilus

P44609
H10277hypotheticalHaemophilus influenzae from bases 308943 to 320513











influenzae


(section 29 of 163) of the complete genome.similar to SP


Contig002D
39113327_c2_11
6
2843
243
81


Contig003D
16972205_f1_1
7
2844
240
80
192
3.70E−14

Pseudomonas

g1778585
catCstationary-phase inducible catalase CPseudomonas putida stationary-phase











putida


inducible catalase C (catC)g ene, complete cds.


Contig003D
31817898_c3_14
8
2845
249
83


Contig003D
3220277_f1_2
9
2846
735
245


Contig003D
6773543_f3_5
10
2847
267
89


Contig004D
29339567_f3_3
11
2848
237
79


Contig005D
197187_f2_3
12
2849
324
108
252
1.20E−21

Haemophilus

P44862
H10754glucokinase regulatorHaemophilus influenzae from bases 809329 to











influenzae


819404 (section 74 of 163) of the complete genome.similar to SP


Contig005D
33214506_f1_1
13
2850
888
296
206
3.50E−15

Borrelia

g2689897
BBB07outer surface protein, putativeBorrelia burgdorferi plasmid











burgdorferi


cp26, complete plasmid sequence.similar to GB


Contig006D
14566626_f2_4
14
2851
228
76


Contig006D
15661656_c1_12
15
2852
186
62


Contig006D
16601688_c2_13
16
2853
1368
456
156
2.30E−08

Caenorhabditis

e229183
C11G6.3Caenorhabditis elegans cosmid C11G6, complete sequence.cDNA EST











elegans


CEESG55F comes from this gene


Contig006D
24476091_c1_11
17
2854
444
148
127
1.10E−07
Orf virus
g332564
ORF5 proteinOrf cirus homologue of retroviral pseudoprotease gene,












completecds.ORF5


Contig006D
24867191_c3_14
18
2855
267
89
108
1.60E−05

Caenorhabditis

e229183
C11G6.3Caenorhabditis elegans cosmid C11G6, complete sequence.cDNA EST











elegans


CEESG55F comes from this gene


Contig006D
34180317_c1_10
19
2856
357
119
169
7.00E−12

SACCHARO-

P36043
YKL201Chypothetical protein YKL201c64.6 KD PROTEIN IN TOR2-











MYCES


PAS1 INTERGENIC REGION











CEREVISIAE



Contig007D
1959693_c2_1
20
2857
195
65


Contig008D
2776391_f2_1
21
2858
207
69


Contig008D
4304683_c1_3
22
2859
396
132
571
1.90E−55
Plasmid pIM13
P13956
mlsmacrofide-lincosamide-streptogramin B-resistancePlasmid p1M13 (from













B.subtilis), complete genome, encoding apossible replication protein













andmacrolide-lincosamide-streptogramin B resistance protein, completecds.rRNA












(adenine-N6-)-methyltransferase


Contig008D
976035_c3_4
23
2860
405
135
662
4.40E−65

Staphylococcus

g2317796
rRNA N-6-methyltransferaseStaphylococcus chromogenes plasmid pPV141











chromogenes


erythromycin resistanceplasmid, rRNA N-6-methyltransferase (ermM) and












plasmid replicationprotein genes, complete cds.


Contig009D
2349191_f2_2
24
2861
321
107
149
7.90E−10

Acinetobacter sp.

g2352826
benKbenzoate transport proteinAcinetobacter sp. ADP1 ben










ADPI

operon and car operon, completesequence.


Contig009D
31770762_c2_5
25
2862
735
245


Contig009D
4S605468_c3_6
26
2863
312
104


Contig009D
9961566_f3_3
27
2864
819
273
947
2.70E−95
Plasmid pWW0
P23102
xylL 1,2-dihydroxycyclohexa-3,4-diene carboxylatePseudomonas putida plasmid












pWW0 meta operon, 5′ genes.


Contig010D
10980305_e3_12
28
2865
189
63


Contig010D
11075275_f3_7
29
2866
564
188


Contig010D
33614811_f1_1
30
2867
504
168
274
5.70E−24

Bacillus subtilis

g1934656
yrdOcation transport protein YrdOBacillus subtilis aminoglycoside 6-












adenylyltransferase (aadK) gene.partial cds, and YrdA (yrdA), YrdB (yrdB),












hypothetical protein YrdC (yrdC), YrdD (yrdD), hypothetical cytochrome P450












protein YrdE(yrdE), ribonuclease inhi


Contig010D
4968908_c2_11
31
2868
729
243
195
1.90E−14

Escherichia coli

P11585
relAGTP pyrophosphokinaseEscherichia coli K-12 MG1655 section 252 of 400 of












the completegenome.guanosine 3′,5′-bis(diphosphate) 3′-












pyrophosphatasef744; 99 pct identical to RELA_ECOLI SW


Contig011D
11724141_f2_4
32
2869
750
250
139
3.20E−07

Plasmodium vivax

g482894
circumsporozoite proteinPlasmodium vivax isolate SOL101 circumsporozoite












protein gene.partial cds.


Contig011D
22772930_c1_7
33
2870
357
119
114
1.60E−06

Homo sapiens

A60533
tumor-associated antigen DF3


Contig011D
26770911_f3_5
34
2871
852
284
328
1.10E−29

Mycobacterium

e319154
MT1376.03cunknownMycobacterium tuberculosis cosmid 1376.MT1376.03c,











tuberculosis


unknown, lcn


Contig013D
12542203_f2_1
35
2872
699
233


Contig014D
16254012_c2_18
36
2873
627
209
340
5.80E−31

Rhizobium

g1439550

Rhizobium leguminosarum bv. trifolii TfuA (tfuA), gene, completecds.ORF1;












leguminosarum


high similarity to members of the LysR










bv. trifolii


Contig014D
24020200_f3_13
37
2874
1044
348
620
1.20E−60

Bacillus subtilis

P42086
ypaQtransport proteinBacillus subtilis (YAC10-9 clone) DNA region between












the serA andkdg loci.26% of identity to the Bacillus caldolyticus uracil


Contig014D
26377261_S2_17
38
2875
624
208
122
6.30E−05

Oryciolagus

P16230
histidine-rich calcium-binding protein precursorRabbit histidine-rich calcium-











cuniculus


binding protein mRNA, complete cds.histidine-rich calcium-binding












protein


Contig014D
36581376_f2_9
39
2876
192
64


Contig015D
14109413_c2_14
40
2877
741
247
608
2.30E−59

Haemophilus

P44849
H1073sodium-dependent noradrenaline transporterHaemophilus influenzae from











influenzae


bases 788391 to 799271 (section 72 of 163) of the complete genome.similar to SP


Contig015D
26462913_c1_10
41
2878
183
61


Contig015D
29964176_f1_2
42
2879
279
93
210
3.40E−17

Synechocystis sp.

d1017357
msrApeptide methionine sulfoxide reductaseSynechocystis sp. PCC6803












complete genome, 1/27, 1-133859.ORF_ID


Contig015D
30257686_f3_6
43
2880
240
80


Contig015D
36020031_f3_8
44
2881
387
129


Contig015D
36441953_f1_3
45
2882
450
150
324
2.90E−29

Escherichia coli

g1790665
msrApeptide methionine sulfoxide reductaseEscherichia coli K-12 MG1655












section 383 of 400 of the completegenome,f212; 100 pct identical












amino acid sequence and


Contig015D
7036628_c1_11
46
2883
339
113


Contig016D
16507686_c2_9
47
2884
186
62


Contig016D
26853200_c1_8
48
2885
1287
429
263
3.90E−20

Escherichia coli

P23886
cydCTransport ATP-binding protein CydCEscherichia coli genomic












DNA.(19.9-20.2 min).unassigned ATP-binding cassette proteinsf573; 100 pct












identical to CYDC_ECOLI SW


Contig016D
286293_f3_7
49
2886
192
64


Contig017D
20423412_f3_4
50
2887
324
108


Contig017D
26580008_f3_3
51
2888
195
65


Contig061D
10556712_c3_208
52
2889
990
330
1667
1.40E−171

Staphylococcus

g1408063
mecRmethicillin-resistance proteinStaphylococcus aureus methicillin











aureus


resistance protein (mecR) geneand unknown ORF, complete cds.putative


Contig061D
10634800_c1_138
53
2890
966
322
143
2.00E−07

Bacillus subtilis

g2619048
yobVtranscription regulatorBacillus subtilis chromosome region between












terC and odhAB.similar to Mycobacterium tuberculosis hypothetical


Contig061D
10928_c2_207
54
2891
1242
414
240
6.90E−18

Rhodobacter

g3128293
hypothetical proteinRhodobacter capsulatus strain SB1003, partial











capsulatus


genome.


Contig061D
111500_c3_227
55
2892
546
182
101
1.60E−05

Listeria

g940753
iapinvasive associated proteinL.monocytogenes type 2 partial











monocytogenes


iap gene (strain 64.1.1).invades nonprofessional phagocytic cells


Contig061D
1379132_c1_133
56
2893
564
188
446
3.40E−42

Bacillus anthracis

g929972

Bacillus anthracis Weybridge A toxin plasmid pXO1 right invertedrepeat













element (WeyAR) bordering the toxin-encoding region, ORFAand ORFB












genes, complete cds.ORFB; similar to B. anthracis SterneL. element ORFB;


Contig061D
13828575_f1_15
57
2894
444
148
617
2.60E−60
Plasmid pl258
P30330
arsCarsenate reductasePlasmid pl258 arsenic resistance operon (arsRBC)












genes, completecds.protein-tyrosine-phosphatase, low molecular weight


Contig061D
1384628_f2_70
58
2895
1278
426
251
3.60E−19

Methanococcus

g1522674
MJECL41M. jannaschii predicted coding region MJECL41Methanococcus











jannaschii



jannaschii large extra-chromosomal element, completesequence.identified by













GeneMark; putative


Contig061D
13864680_c2_192
59
2896
384
128
247
4.10E−21

Bacillus subtilis

P45949
yqcJYqcJBacillus subtilis DNA, 283 Kb region containing skin element.similarity












to arsenical resistance operon


Contig061D
13912551_c1_141
60
2897
1695
565
149
8.20E−08

Streptococcus

g455528
hypothetical protein 2S.thermophilus bacteriophage viral DNA, orf1 and











thermophilus


orf2.ORF2











bacteriophage



Contig061D
14111687_c3_117
61
2898
225
75
104
2.80E−05

Rhizobium sp.

P55500
y4iQY4iQRhizobium sp. NGR234 plasmid pNGR234a, section 16 of 46 of










NGR234

thecomplete plasmid sequence.putative insertion sequence ATP-binding protein;


Contig061D
14460882_c3_254
62
2899
435
145
676
1.40E−66

Staphylococcus

g1022726
unknownStaphylococcus haemolyticus IS1272 ORF1 and ORF2 genes,











haemolyticus


completecds.ORF1


Contig061D
14532058_c3_221
63
2900
273
91
452
7.80E−43

Staphylococcus

g46600
putative transposaseS.aureus plasmid pSH6 DNA for insertion sequences











aureus


IS257-2, IS257-3 and IS256.


Contig061D
14578382_f1_12
64
2901
192
64


Contig061D
14719827_c3_244
65
2902
330
110


Contig061D
15632952_c1_145
66
2903
489
163


Contig061D
15788276_f3_111
67
2904
198
66


Contig061D
16601512_c1_146
68
2905
510
170


Contig061D
16688_c2_196
69
2906
216
72


Contig061D
16695311_f2_59
70
2907
693
231
1184
2.10E−120

Staphylococcus

P19380
putative transposaseS. aureus IS431mec gene associated with methicillin











aureus


resistance.putative transposase (AA 1-224)


Contig061D
16695311_f2_68
71
2908
693
231
1191
3.80E−121

Staphylococcus

P19380
putative transposaseS. aureus IS431mec gene associated with methicillin











aureus


resistance.putative transposase (AA 1-224)


Contig061D
16975082_c1_159
72
2909
306
102


Contig061D
19647213_c3_317
73
2910
342
114
157
1.40E−11

Bacillus subtilis

d1020073
ydcNtranscriptional regulator (phage-related) homolog ydcNBacillus subtilis












genome sequence, 148 kb sequence of the regionbetween 35 and 47












degree.PROBABLE REPRESSOR PROTEIN.


Contig061D
19719812_c1_165
74
2911
474
158
803
5.00E−80

Staphylococcus

P19380
putative transposaseS. aureus IS431mec gene associated with methicillin











aureus


resistance.putative transposase (AA 1-224)


Contig061D
19720462_f1_81
75
2912
1203
401
370
3.80E−34

Escherichia coli

P39381
yjihypothetical 41.4 kD protein in iadA-mcrDEscherichia coli K-12 MG1655












section 393 of 400 of the completegenome.f392; 100 pct identical












amino acid sequence and


Contig061D
20523253_c3_220
76
2913
252
84
447
2.60E−42

Staphylococcus

g46597
transposaseS.aureus plasmid pSH6 DNA for insertion sequences IS257-1











aureus


andIS256.


Contig061D
20585963_c3_213
77
2914
348
116
216
8.00E−18

Bacillus anthracis

g929966

Bacillus anthracis Weybridge A toxin plasmid pXO1 left invertedrepeat













element (WeyAL) bordering the toxin-encoding region, truncated ORFA and












truncated ORFB genes, complete cds.truncated ORFB due to a basepair












deletion; similar


Contig061D
20585963_c3_248
78
2915
906
302
647
1.70E−63

Bacillus anthracis

g929972

Bacillus anthracis Weybridge A toxin plasmid pXO1 right invertedrepeat













element (WeyAR) bordering the toxin-encoding region, ORFA and ORFB












genes, complete cds.ORFB; similar to B. anthracis SterneL element ORFB;


Contig061D
20964212_c3_233
79
2916
1692
564
344
1.10E−29
Bacteriophage
e155312
integraseBacteriophage TP901-1 ORF1,2 & 3.Orf1


Contig061D
2120265_c3_218
80
2917
870
290
151
5.10E−08

Synechocystis sp.

d1019159
hypothetical proteinSynechocystis sp. PCC6803 complete genome, 16/27,












1991550-2137258.ORF_ID


Contig061D
21521878_c1_130
81
2918
354
118
181
9.90E−13

Haemophilus

g1574743
H11285type I restriction enzyme ECOR124/3 R proteinHaemophilus











influenzae



influenzae from bases 1356902 to 1368850 (section 123 of 163) of the













complete genome.similar to SP


Contig061D
21651677_f1_44
82
2919
255
85


Contig061D
2209675_f1_28
83
2920
1470
490
465
3.30E−44

Petroselinum

Q06086
TryDC-2tyrosine decarboxylaseParsley tyrosine decarboxylase (TryDC-2)











crispum


mRNA, complete cds.aromatic-L-amino-acid decarboxylase


Contig061D
22537563_c1_149
84
2921
231
77


Contig061D
23437803_f3_91
85
2922
714
238
122
1.60E−06

Streptococcus

JH0364
hypothetical protein 176 (SAGP 5′ region)











pyogenes



Contig061D
23438876_f3_116
86
2923
258
86


Contig061D
23439193_c3_240
87
2924
495
165
453
6.10E−43

Bacillus subtilis

e1182558
ydhKhypothetical protein ydhKBacillus subtilis complete genome (section 4 of












21) membrane protein


Contig061D
23556577_f1_46
88
2925
324
108


Contig061D
235678_f2_53
89
2926
216
72
203
1.90E−16

Bacillus subtilis

g2529473
yokZYokZBacillus subtilis 168 region at 182 min containing the cge












genecluster.similar to the VanYB (D,D-carboxypeptidase) of


Contig061D
23610952_c2_206
90
2927
855
285
305
2.90E−27

Archacoglobus

g2648798
AF17531ysopholipaseArchaeoglobus fulgidus section 125 of 172 of the











fulgidus


complete genome.similar to GP


Contig061D
23632883_c1_151
91
2928
183
61


Contig061D
23634682_c2_171
92
2929
375
125


Contig061D
23635931_c1_155
93
2930
375
125
637
1.90E−62
Plasmid pl258
P08656
merthypothetical 15K protein (mer operon) Plasmid pl258 (from S.aureus












strain RN23 8325) mercury resistance(mer) operon encoding












mercuric reductase (merA), organomercuriallyase (merB), regulatory












protein (merR) and membrane transportprotein (merT), complet


Contig061D
23679765_f3_90
94
2931
1269
423
1182
3.40E−120

Lactobacillus sake

e1227704
arcAarginine deiminaseLactobacillus sake DNA encoding the arginine-












deiminase pathwaygenes.


Contig061D
23959802_f2_80
95
2932
210
70


Contig061D
24101587_f3_93
96
2933
339
113


Contig061D
24250010_c3_243
97
2934
225
75


Contig061D
24256550_c2_191
98
2935
258
86


Contig061D
24273442_f1_37
99
2936
384
128
142
5.50E−10

Bacillus subtilis

g2618844
yvlA YvlABacillus subtilis 300-304 degree genomic sequence.


Contig061D
24273442_f1_9
100
2937
384
128
144
3.40E−10

Bacillus subtilis

g2618844
yvlA YvlABacillus subtilis 300-304 degree genomic sequence.


Contig061D
24299037_c3_226
101
2938
255
85


Contig061D
24401712_c1_140
102
2939
1125
375


Contig061D
24407828_c3_222
103
2940
2013
671
136
7.70E−05

Plasmodium

g1041785
rhoptry proteinPlasmodium yoellii rhoptry protein gene, partial cds.











yoelii



Contig061D
24409452_c3_253
104
2941
432
144
132
6.30E−09

Methanococcus

Q57997
MJ0577conserved hypothetical proteinMethanococcus jannaschii section











jannaschii


48 of 150 of the complete genome.hypothetical protein b0607similar to SP


Contig061D
24414680_c1_150
105
2942
1287
429


Contig061D
24414818_f3_113
106
2943
441
147


Contig061D
24424092_c2_174
107
2944
522
174


Contig061D
24430392_c1_157
108
2945
681
227
1116
3.40E−113
Plasmid pl258
P08653
merBorganomercurial lysasePlasmid pl258 (from S.aureus strain RN23 8325)












mercury resistance(mer) operon eencoding mercuric reductase (merA),












organomercuriallyase (merB), regulatory protein (merR) and membrane












transportprotein (merT), complete cds.alkylmercu


Contig061D
24432662_c2_190
109
2946
969
323
304
8.70E−48

Escherichia coli

P36649
yacKhypothetical protein in speE-gcd intergenicEscherichia coli K-12 MG1655












section 11 of 400 of the completegenome.0516; 100 pct identifical












to 463 residues from


Contig061D
24486008_c2_194
110
2947
978
326


Contig061D
24641941_f3_94
111
2948
510
170


Contig061D
24650427_f3_110
112
2949
3126
1042
1653
1.90E−220

Haemophilus

g1574743
H11285type 1 restriction enzyme ECOR 124/3 proteinHaemonphilus











influenzae



influenzae frombases 1356902 to 1368850 (section 123 of 163) of the













complete genome.similar to SP


Contig061D
24783462_c2_173
113
2950
339
113


Contig061D
24797126_f1_40
114
2951
249
83


Contig061D
24812927_f2_50
115
2952
183
61


Contig061D
254527_c2_183
116
2953
186
62


Contig061D
25583568_f1_3
117
2954
363
121


Contig061D
25587802_c1_134
118
2955
777
259
114
8.50E−05

Borrelia

g2688190
BB0276flagellar biosynthesis protein (fliZ) Borrelia burgdorferi (section 23 of











burgdorferi


70) of the complete genome.similar to PID


Contig061D
26597010_f3_118
119
2956
186
62
103
2.40E−05

Rhizobium sp.

Q53200
y4uHY4uHRhizobium sp. NGR234 plasmid pNGR234a, section 36 of 46 of










NGR234

thecomplete plasmid sequence.putative insertion sequence ATP-binding protein


Contig061D
26759707_c1_143
120
2957
450
150
319
9.70E−29

Staphylococcus

A60450
hypothetical protein an155 (transposon attachment site)











aureus



Contig061D
2819632_f1_48
121
2958
387
129


Contig061D
2867812_c2_195
122
2959
213
71


Contig061D
2946092_c2_169
123
2960
435
145


Contig061D
30086682_c2_185
124
2961
732
244
1134
4.20E−115
Plasmid pl258
g459905
hypothetical 24K protein (mer operon) Plasmid pl258(from S.aureus












strain RN23 8325) mercury resistance(mer) operon encoding












mercuric reductase (merA), organomercuriallyase (merB), regulatory












protein (merR) and membrane transportprotein (merT), complete cd


Contig061D
30111718_c2_189
125
2962
2124
708
1980
6.20E−211

Enterococcus

P05425
copBATPaseEnterococcus hirae ATPase (copA) gene, complete cds; ATPase











hirae


(copB) gene, complete cds.Enterococcus Cu2+-transporting ATPaseputative


Contig061D
32148381_f3_112
126
2963
198
66


Contig061D
32226577_c3_236
127
2964
354
118
596
4.30E−58
Plasmid pl258
g459904
hypothetical 18K protein (mer operon) Plasmid pI258 (from S.aureus












strain RN23 8325) mercury resistance(mer) operon encoding












mercuric reductase (merA), organomercuriallyase (merB), regulatory












protein (merR) and membrane transportprotein (merT), complete.cd


Contig061D
33261588_c2_168
128
2965
690
230


Contig061D
33261637_c3_225
129
2966
543
181


Contig061D
3332776_f3_129
130
2967
228
76


Contig061D
33867212_f3_128
131
2968
339
113


Contig061D
34016880_12_89
132
2969
273
91
422
3.40E−39

Staphyloco

g46611
mccAPB2AS. aureus mccA gene for PBP2′ (penicillin binding protein











aureus


2′).PBP2′ (AA 1-668)


Contig061D
34631527_f1_8
133
2970
834
278
472
5.90E−45

Marinococcus

g2098612
putative transposaseMarinococcus halophilus L-2,4-diaminobutyric acid











halophilus


acetyltransferase (cctA) gene, L-2,4-diaminobutyric acid transaminase(cctB)












gene, ectoine synthase (cctC) gene, putative transposaseorfA gene, complete












cds, and putatuve transposase orf


Contig061D
35357833_f2_54
134
2971
519
373
473
4.60E−45

Escherichia coli

P37354
speGSpermidine N1-acetyltransferase (EC 2.3.1.57) E.coli genomic DNA,












Kohara clone #308(35.3-35.7 min.).ORF_1D


Contig061D
35334686_f2_87
135
2972
1733
573
1253
1.00E−127

Staphylococcus

g1022726
unknownStaphylococcus haemolyticus ISI272 ORF1 and ORF2 genes,











haemolyticus


completecds.ORF1


Contig061D
36135952_f2_85
136
2973
3650
550
463
5.30E−44
Bacteriophage
e155312
integraseBacteriophage TP901-1 ORF1,2 & 3.Orf1










TP901-1


Contig061D
36211052_c1_156
137
2974
1662
554
2755
1.00E−287
Plasmid p3258
P08663
merAmercuric reductasePlasmid pI258 (from S.aureus strain RN23 8325)












mercury resistance(mer) operon encoding mercuric reductase (merA)












organomercuriallyase (merB), regulatory protein (merR) and membrane












transportprotein (merT), complete cds.dihydrolipoam


Contig061D
36225427_f2_83
138
2975
635
205


Contig061D
36226501_c2_175
139
2976
891
297


Contig061D
36584652_c1_132
140
2977
339
113
300
1.00E−26

Bacillus anthracis

g929968

Bacillus anthracis Sterne toxin plasmid pXO1 right inverted repeatelement













(SterneR) bordering the toxin-encoding region, ORFA andtruncated ORFB












genes, complete cds.ORFA; similar to B. anthracis WeyAR element ORFA;


Contig061D
3913137_f2_62
141
2978
570
390
982
5.40E−99
PlasmidpI258
g459909
Plasmid pI258 (from S.aureus strain RN23 8325) mercury resistance(mer)












operon encoding mercuric reductase (merA), organomercuriallyase (merB),












regulatory protein (merR) and membrane transportprotein (merT), complete












cds.ORF1


Contig061D
3938802_f2_84
142
2979
1383
461
238
2.50E−17
Bacteriophage
e155312
integraseBacteriophage TP901-1 ORF1,2 & 3.Orf1










TP901-1


Contig061D
4022952_f1_29
143
2980
1515
505
1186
3.30E−140

Mycobacterium

e1173886
hsdMDNA methylaseMycobacterium tuberculosis sequence











tuberculosis


v002.MTV002.21c, hsdM, type1 restriction/modification


Contig061D
4025302_f3_97
144
2981
1293
431
1892
2.00E−195
Plasmid pI258
P30329
arsBarsenic efflux pump proteinPlasmid pI258 arsenic resistance operon












(arsRBC) genes, completecds.arsenical pump membrane protein


Contig061D
4098518_c2_184
145
2982
417
139
682
3.30E−67
Plasmid pI258
P22874
MERRhypothetical 16K protein (mer operon) Plasmid pI258 (from S.aureus












strain RN23 8325) mercury resistance(mer operon encoding












mercuric reductase (merA), organomercuriallyase (merB), regulatory












protein (merR) and membrane transportprotein (merT), complet


Contig061D
4120462_f2_52
146
2983
945
315
791
9.30E−79

Escherichia coli

Q46807
YQEAhypothetical protein b2874Escherichia coli K-12 MG1655












section 260 of 400 of the completegenome.carbamate kinaseo310;












This 310 aa ORF is 45 pct identical (21 gaps)


Contig061D
4196051_f1_14
147
2984
333
111
424
7.20E−40

Staphylococcus

A41902
arsRarsenical resistance operon repressorarsenical resistance operon











xylosus


repressor


Contig061D
4453165_c1_160
148
2985
537
179
202
1.50E−15

Escherichia coli

d1006123
‘ORF’Escherichia coli genome, 2.4-4.1 min region (110.917-193.643 bpfrom 0












min).‘copper resistance protein copA homology’


Contig061D
4485937_f1_2
149
2986
1044
348
1060
2.90E−107

Haemophilus

P44770
H10596ornithine carbamoyltransferase (arcB) Haemophilus influenzae from











influenzae


bases 614291 to 624841 (section 56 of 163) of the complete genome.ornithine












carbamoyltransferasesimilar to GB


Contig061D
448785_f3_114
150
2987
927
309
408
3.60E−38

Anthrobacter sp.

Q44311
soxRnegative regulatorAnthrobacter sp. gene for negative regulator, sarcosine












oxidase,transporter, creatinase, creatininase and transporter,complete cds.


Contig061D
4694677_c1_144
151
2988
324
108


Contigo61D
4697337_f3_115
152
2989
549
183
255
5.90E−22

Bacillus subtilis

g1934639
yrpB2-nitropropane dioxygenaseBacillus subtilis alcohol dehydrogenase (adhB)












gene, partial cdds,hydrothetical spore coat protein (yraF), hydrothetical spore












coatprotein (yraG), YraH (yraH), YraI (yraI), YraJ (yraJ), YraK (yraK), YraL












(yraL), chilosanase precu


Contig061D
4722338_c3_224
153
2990
234
78


Contig061D
4726555_c3_224
154
2991
474
158
183
2.50E−14

Bacillus subtilis

P17893
ahrCAhrCB.subtilis ahrC gene,encoding an arginine












repressor/activatorprotein.ahrC protein


Contigo61D
4866425_f2_82
155
2992
465
155
305
2.90E−27

Bacillus subtilis

g1934639
yrpB2-nitropropane dioxygenaseBacillus subtilis alcohol dehydrogenase (adhB)












gene, partial cds,hydrothetical spore coat protein (yraF), hypothetical spore












coatprotein (yraG), YraH (yraH), YraI (yraI), YraJ (yraJ), YraK (yraK), YraL












(yraL), chilosanase precu


Contig061D
4867343_c3_215
156
2993
2739
913
234
5.10E−16

Borrelia

g2688552
BB0632exodeoxyribinonuclease V, alpha chain (recD) Borrelia burgdorferi (section










burgdorferi

50 of 70) of the complete genome.similar to SP


Contig061D
492086_f3_124
157
2994
1824
608


Contig061D
4971051_c2_178
158
2995
825
275
181
1.10E−13

Lactococcus lactis

g1405404
abiGiAbiLactococcus lactis cremoris abortive infection proteins (abiGi











cremoris


andabiGii) genes, complete cds.


Contig061D
5133462_f3_122
159
2996
1530
510
119
1.60E05.

Saccharomyces

P47037
SCP160hypothetical proteinS.cerevisiae DNA for hypothetical proteins and











cercvisiae


esterase genes.ORF YJL074c


Contig061D
5292300_c2_167
160
2997
342
114


Contig061D
649141_f2_86
161
2998
567
189


Contig061D
6521882_f1_16
162
2999
195
65


Contig061D
6643751_c1_158
163
3000
270
90


Contig061D
6819462_f1_1
164
3001
1491
497
1230
2.80E−125

Clostridium

e242289
arcDarginine ornithine antiporterC.perfringens strain 13











perfringens


arcABDC, ahrC and colA genes.


Contig061D
6834501_c1_142
165
3002
231
77


Contig061D
6929627_c2_197
166
3003
1146
382
756
4.80E−75

Mycobacterium

e322878
MTC128.02calcohol dehydrogenaseMycobacterium











tuberculosis



tuberculosis cosmid 128.MTC128.02c, alcohol dehydrogenase, len



Contig061D
6929642_f1_4
167
3004
243
81


Contig061D
6929686_c2_205
168
3005
264
88
368
6.20E−34

Staphylococcus

g46597
transposaseS.aureus plasmid pSH6 DNA for insertion sequences IS257-1











aureus


andIS256.


Contig061D
862927_c3_251
169
3006
195
65


Contig061D
892142_f2_55
170
3007
198
66


Contig061D
917550_c1_163
171
3008
216
72
143
4.30E−10

Bacillus anthracis

g929968

Bacillus anthracis Sterne toxin plasmid pXO1 right inverted repeatelement













(SterneR) bordering the toxin-encoding region, ORFA and truncated ORFB












genes, complete cds.ORFA; similar to B. anthracis WeyAR element ORFA;


Contig061D
970250_c2_193
172
3009
912
304
446
3.40E−42

Methanobacterium

g2621989
MTH894conserved proteinMethanobacterium











thermo-



thermoautotrophicum from bases 808939 to 820180(section 71 of 148) of the












autotrophicum


complete genome.Function Code


Contig061D
970386_f1_27
173
3010
333
111
270
4.30E−23

Bacillus subtilis

e1184706
yxcCmetabolite transport protein homolog yxcCBacillus subtilis complete












genome (section 21 of 21) similar to metabolite transport protein


Contig061D
979178_c3_246
174
3011
243
81


Contig061D
9806332_f3_109
175
3012
450
150
237
7.70E−20

Pyrococcus

d1027703
PHAB011376aa long hypothetical dehydrogenasePyrococcus horikoshii











horikoshii


OT3 genomic DNA, 512441-547109 nt position(complementary strand),












clonecontains ATP/GTP-binding site motif A (P-loop);


Contig061D
9806692_c3_235
176
3013
1374
458
907
4.70E−91
Plasmid pI258
P08655
merRregulatory proteinPiasmid pI258 (from S.aureus strain RN23 8325)












mercury resistance(mer) operon encoding mercuric reductase (merA),












organomercuriallyase (merB), regulatory protein (merR) and membrane












transportprotein (merT), complete cds.


Contig140D
1385927_f3_8
177
3014
369
123


Contig140D
14882135_f2_4
178
3015
2112
704
167
1.30E−09

Escherichia coli

P10411
melRmelibiose operon regulatory proteinEscerichia coli K-12 MG1655












section 374 of 400 of the completegenome.arabinose operon












regulatory proteinf302; CG Site No. 18166


Contig140D
24110652_c2_10
179
3016
822
274
879
4.40E−88

Bacillus cereus

e1179988
gltTproton/sodium-glutamate symport proteinB.cereus partial gltT, aspA and












partial maoX genes.


Contig140D
25634627_f2_5
180
3017
468
156
290
1.10E−25

Bacillus subtilis

P80238
ydaGgeneral stress protein homolog ydaGBacillus subtilis genome sequence,












148 kb sequence of the regionbetween 35 and 47 degree.FUNCTION












UNKNOWN.


Contig140D
29352342_c3_12
181
3018
531
177
371
3.00E−34

Bacillus

P24943
gltPproton glutamate symport proteinBacillus stearothermophilus











stearothermophilus


proton glutamate symport protein (gltP) gene, complete cds.


Contig140D
32242200_f1_1
182
3019
378
126


Contig149D
22042187_c2_15
183
3020
1401
467
1065
8.60E−108

Klebsiella

g2735583
rbtTribitol transporter Klebsiella pneumoniae ribitol kinase (rbtK) and











pneumaniae


ribitol transporter(rbtT) genes, complete cds.RbtT


Contig149D
22947833_c1_12
184
3021
192
64


Contig149D
31877334_c2_14
185
3022
521
174
432
1.00E−40

Azorhizobium

g763062
AraC-like proteinA.caulinodans nodD gene.gtg start codon; homologous to











caulinodans


AraC family of


Contig149D
6938816_c3_17
186
3023
453
151


Contig150D
24645942_c1_12
187
3024
444
148
384
1.30E−35

Haemophilus

P44814
H10670hypotheticalHaemophilus influenzae from bases 712950 to 723016











influenzae


(section 65 of 163) of the complete genome.similar to GB


Contig150D
24713531_f2_5
188
3025
228
76


Contig150D
26377250_c2_14
189
3026
711
237
643
4.50E−63

Xanthomonas

d1012290
aminopeptidaseXanthomonas campestris DNA for aminopeptidase, complete cds.











campestris



Contig150D
29423955_c1_11
190
3027
183
61
90
5.20E−06

Pseudomonas

g2642342
pip1proline iminopeptidasePseudomonas putida inducible histidine transporter











putida


(hutT), imidazolone propionate hydrolase (hutI), and N-












formylglutamaleamidohydrolase (hutG) genes, complete cds; and












prolineiminopeptidase (pip1) gene, partial cds.


Contig150D
3179561_f1_2
191
3028
225
75


Contig150D
32697905_c3_16
192
3029
207
69


Contig150D
35207326_c1_13
193
3030
1191
397
1384
1.30E−141

Escherichia coli

d1015377
mdoGMdoG proteinEscherichia coli genomic DNA. (23.6-23.9 min).


Contig150D
35408180_f2_8
194
3031
261
87


Contig157D
10008513_c1_34
195
3032
2667
889
3361
0

Bacillus

A26738
valSvaline--tRNA ligase, valine-tRNA ligase











stearothermophilus



Contig157D
10720877_c2_39
196
3033
1329
443
1343
3.00E−137

Bacillus subtilis

e1184072
tigtrigger factor (prolyl isomerase) Bacillus subtilis complete












genome (section 15 of 21) alternate gene name


Contig157D
1211562_c3_48
197
3034
1269
423
1518
8.50E−156

Bacillus subtilis

P50866
clpXClpX proteinB.subtilis clpX gene.ATP-dependent protease


Contig157D
188388_c1_38
198
3035
333
111
110
5.70E−06

Bacillus subtilis

g142856
mreCMreC proteinBacillus subtilis orfA, orfB, mreB, mreC, mreD, minC, and












minDgenes, complete coding regions.


Contig157D
19707767_f3_22
199
3036
324
108


Contig157D
20348160_f3_20
200
3037
222
74


Contig157D
2352257_c3_46
201
3038
381
127
450
1.30E−42

Bacillus subtilis

P55873
rplTribosomal protein L20Bacillus subtilis complete genome (section 15 of












21) homology to rplT of Bacillus stearothermphilus;


Contig157D
23697141_c3_50
202
3039
930
310
1327
1.50E−135

Staphylococcus

g2589181
hemCporphobilinogen deaminaseStaphylococcus aureus











aureus


hemCDBL gene cluster


Contig157D
24240877_c1_36
203
3040
522
174


Contig157D
24665777_c3_45
204
3041
234
78
226
6.90E−19

Bacillus subtilis

e1184135
rpmlribosomal protein L35Bacillus subtilis complete genome (section 15 of












21) homology to rpml of Bacillus stearothermophilus;


Contig157D
24897312_c1_31
205
3042
186
62
255
5.90E−22

Staphylococcus

g632816
hemBporphobilinogen synthasehem B = porphobilinogen











aureus


synthase [Staphylococcus aureus, SA 1959, Genomic, 1087 ntThis sequence












comes from FIG. 3. Protein sequence


Contig157D
25554642_c3_47
206
3043
486
162
363
2.10E−33

Bacillus subtilis

P50619
ymaBYmaBB.subtilis cwlC, nrdE. nrdF ymA and ymB genes.no similarities,












cannot be inactivated


Contig157D
25596000_c1_30
207
3044
825
275
460
1.10E−43

Bacillus subtilis

P16645
hemXmembrane-bound proteinBacillus subtilis hemA XCDBL gene












cluster.unidentified gene product


Contig157D
2866255_f2_17
208
3045
264
88


Contig157D
31510_f2_12
209
3046
627
209
435
4.90E−41

Haemophilus

P44321
H10654DNA-3-methyladenine glycosidase 1 (tag1) Haemophilus











influenzae



influenzae from bases 690801 to 702086 (section 63 of 163) of the complete













genome.3-methyladenine DNA glycosylase lsimilar to SP


Contig157D
33395050_c3_49
210
3047
618
206
577
4.40E−56

Bacillus subtilis

P38424
ysxChypothetical proteinB.subtilis Ion gene for protease La.orfX


Contig157D
33517_c2_41
211
3048
1077
359
258
2.60E−21

Bacillus subtilis

e1183059
yhjNhypothetical proteinBacillus subtilis complete genome (section 6 of 21) TTG












start; Similarity to a hypothetical protein


Contig157D
34642092_c2_43
212
3049
1284
428
907
4.70E−91

Bacillus subtilis

Q05865
folCfolyl-polyglutamate synthetaseBacillus subtilis valyl tRNA












synthetase (valS) gene, 3′ end cds; folylpolyglutamate synthetase (folC) gene,












complete cds; comCgene, 5′ end cds.


Contig157D
3914012_c3_51
213
3050
690
230
710
3.60E−70

Staphylococcus

g2589182
hemDuroporphyrinogen III synthaseStaphylococcus aureus











aureus


hemCDBL gene cluster


Contig157D
4080443_c1_32
214
3053
3296
432
2041
3.20E−211

Staphylococcus

g2589184
hemLGSA-1-aminotransferaseStaphylococcus aureus











aureus


hemCDBL gene cluster


Contig157D
439183_f3_24
215
3052
297
99
208
5.60E−17

Bacillus subtilis

e1165375
ysoChypothetical proteinB.subtilis genomic sequence 89009bp.unknown












function; putative


Contig157D
500052_c1_35
216
3053
669
223
440
1.50E−41

Bacillus subtilis

Q02170
orfBDNA repair protein homolog ysxABacillus subtilis orfA, orfB, mreB,












mrcC, mreD, minC, and minDgenes, complete coding regions.homologous to













E. coli.radC gene product and to



Contig157D
5268775_c1_28
217
3054
960
320
138
7.10E−07

Bacillus subtilis

e1184073
ysoAhypothetical proteinBacillus subtilis complete genome (section 15 of












21) unknown function; putative


Contig157D
5860827_c1_29
218
3055
3347
449
1372
3.90E−139

Bacillus subtilis

P16618
hemANAD(P)HBacillus subtilis hemAXCDBL gene cluster.glutamyl-












tRNA reductaseThe product of this hemA gene is not an


Contig157D
6845382_f1_1
219
3056
239
73


Contig157D
806530_c2_44
220
3057
734
238
389
5.80E−15

Bacillus subtilis

P15378
comClate competence proteinBacillus subtilis late competence protein (comC)












gene, completecds.


Contig157D
820253_f3_25
221
3058
297
99
206
9.10E−17

Bacillus subtilis

e1165375
ysoChypothetical proteinB.subtilis genomic sequence 89009bp.unknown












function; putative


Contig157D
978562_c2_40
222
3059
861
287
3261
1.50E−128

Staphylococcus

P50915
hemBd-aminolevulinic acid dehydralaseStaphylococcus aureus











aureus


hemCDBL gene cluster


Contig200D
14900826_f3_4
223
3060
351
117
188
7.40E−15
artificial sequence
g2089
Synthetic E.coli ORF16/lacZ fusion protein, partial cds.ORF16-lacZ fusion












protein


Contig219D
2214217_f1_2
224
3061
1845
615
1438
2.60E−147

Bacillus subtilis

d1011961
yyeGtwo-component sensor histidine kinase [Yye homolog yycGBacillus













subtilis 36 kb sequence between gntZ and tmY genesencoding 34













ORFs.homologous to sp


Contig219D
24848452_f2_7
225
3062
792
264
223
1.40E−18

Bacillus subtilis

d1011959
yyclhypothetical protein yyclBacillus subtilis 36 kb sequence between gntZ and












tmY genesencoding 34 ORFs.


Contig219D
33337760_f1_1
226
3063
705
235
954
5.00E−96

Bacillus subtilis

P37478
yycFunknownB. subtilis DNA, 180 kilobase region of replication












origin.ompR proteinhomologous to sp


Contig219D
34417813_c1_3
227
3064
807
269
851
4.10E−85

Bacillus subtilis

d1011958
yycJhypothetical protein yycJBacillus subtilis 36 kb sequence between gntZ and












tmY genesencoding 34 ORFs.


Contig219D
4093937_f2_4
228
3065
192
64


Contig219D
7223587_f2_6
229
3066
1401
467
218
4.10E−15

Bacillus subtilis

d1011960
yycHBacillus subtilis 36 kb sequence between gntZ and tmY genesencoding












34 ORFs.


Contig241D
30569025_c3_20
230
3067
2541
847
290
1.40E−21

Caenorhabditis

g1166621
F35A5.1Carnorhabditis elegans cosmid F35A5.











elegans



Contig241D
36042152_c3_21
231
3068
1152
384
202
1.90E−13

Trypanosoma

g53036l
12 proteinT.brucci 12 mRNA for flagellar antigen.











brucci



Contig241D
36042152_c3_22
232
3069
408
136
102
9.60E−06

STAPHYLO-

P80544
METHICILLIN-RESITANT SURFACE PROTEIN(FRAGMENTS)











COCCUS AUREUS



Contig255D
12142768_c1_7
233
3070
300
100
110
3.50E−06

Pyrococcus

d1027343
PHBW016235aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA, 180023-216005 nt position, clone


Contig255D
12603166_c3_17
234
3071
303
101
100
1.60E−05

Pyrococcus

d1027339
PHBW012106aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA, 180023-216005 nt position, clone


Contig255D
14849093_f3_5
235
3072
294
98
127
2.10E−08
Mitochondrion
e138028
putative orf79.1C.crispus complete mitochondrial genome.unique orf











Chondrus crispus



Contig255D
14900826_f2_2
236
3073
351
117
188
7.40E−15
artificial sequence
g208931
Synthetic E.coli ORF16/lacZ fusion protein, partial cds.ORF16-lacZ fusion












protein


Contig255D
2379658_c2_10
237
3074
225
75


Contig255D
285808_c2_12
238
3075
225
75


Contig255D
3361326_f2_3
239
3076
207
69


Contig276D
14147177_c2_3
240
3077
366
122


Contig276D
23725442_c1_2
241
3078
411
137


Contig278D
194202_f3_8
242
3079
255
85


Contig278D
20587536_c2_13
243
3080
630
210
241
1.80E−20

Bacillus subtilis

P37467
xpaChydrolysis of 5-bromo-4-chloroindolyl phosphateB. subtilis DNA,












180 kilobase region of replication origin.


Contig278D
24615915_12_5
244
3081
240
80
275
4.40E−24

Staphylococcus

g2226349
cspCCspCStapgylococcus aureus CspC (cspC) gene, complete cds.similar to











aureus


major cold-shock protein


Contig278D
25423425_c3_16
245
3082
210
70


Contig278D
25428378_c3_15
246
3083
228
76


Contig278D
33470001_f2_4
247
3084
336
112
137
1.90E−09

Streptococcus

g2058543
putative DNA binding proteinStreptococcus gordonii RNA











gordonii


polymerase beta′ subunit (rpoC).putative DNA binding protein, putative ABC












transporter subunitComYA (comYA). putative ABC transporter subunit












ComYB (comYB) andComYC gene, complete cds, and ComYD gene,


Contig278D
35159452_12_3
248
3085
1302
434
1371
3.20E−140

Staphylococcus

g2315995
branched-chain amino acid carrier proteinStaphylococcus aureus branched-











aureus


chain amino acid carrier proteingene, complete cds.branched-chain amino acid












transporter


Contig278D
4718760_f3_9
249
3086
327
109


Contig278D
4796875_c2_12
250
3087
315
105
146
2.10E−10

Archaeoglobus

g2649785
AF0818acylphosphalase (acyP) Archaeoglobus fulgidus section 60











fulgidus


of 172 of the complete genome.similar to SP


Contig278D
6442787_c3_17
251
3088
1179
393
923
9.60E−93

Bacillus subtilis

P37535
yaaNunknownB. subtilis DNA, 180 kilobase region of replication












origin.similar to toxic cation resistance


Contig282D
1056314_1f_14
252
3089
345
115


Contig282D
1214635_c2_43
253
3090
387
129
202
2.40E−16

Bacillus subtilis

Q08429
kapBkinase-associated protein BBacillus subtilis putative aminotransferase (patB),












ATP-dependentprotein kinase B (kinB), kinase-associated protein B (kapB),












andKapD (kapD) genes, complete cds.second and last ORF of the kinB-












kapB operon;


Contig282D
14460932_f2_13
254
3091
294
98
451
1.00E−42

Staphylococcus

g1022726
unknownStaphylococcus haemolyticus IS1272 ORF1 and ORF2 genes,











haemolyticus


completecds.ORF1


Contig282D
14484553_f2_16
255
3092
1356
452
1726
7.70E−178

Bacillus

P13375
PGIAglucose-6-phosphate isomerase, ABacillus stearothermophilus pgiA gene











stearothermophilus


for phosphoglucoisomeraseisoenzyme A (EC 5.3.1.9).glucose-6-phosphate












isomerasephosphoglucose isomerase A (AA 1-449)


Contig282D
15041078_f2_9
256
3093
279
93
319
9.70E−29

Bacillus subtilis

e1184283
yuiFconserved hypothetical protein yuiFBacillus subtilis complete genome












(section 17 of 21) similar to hypothetical proteins


Contig282D
21571937_c3_48
257
3094
213
71


Contig282D
21646015_f3_24
258
3095
201
67
198
6.40E−16

Staphylococcus

g1022725
unknownStaphylococcus haemolyticus IS1272 ORF1 and ORF2 genes,











haemolyticus


completecds.ORF2


Contig282D
22136087_c2_95
259
3096
1512
504
1214
1.40E−123

Bacillus subtilis

e1184241
yufDNADH dehydrogenase (ubiquinone) homolog yufDBBacillus subtilis complete












genome (section 17 of 21) similar to NADH dehydrogenase (ubiquinone)


Contig282D
22462787_f1_8
260
3097
261
87
257
3.60E−22

Staphylococcus

g1595809
spsAtype-1 signal peptidase SpsAStaphylococcus aureus type-1 signal











aureus


peptidase SpsA (spsA) gene, andtype-I signal peptidase SpsB (spsB) gene,












complete cds.inactive signal peptidase homologue; protein lacks


Contig282D
23445958_f1_3
261
3098
243
81


Contig2S2D
23535910_f1_7
262
3099
603
201
358
7.10E−33

Bacillus subtilis

e1183050
yhjEhypothetical proteinBacillus subtilis complete genome (section 6 of












21) similar to hypothetical proteins from B. subtilis


Contig282D
23859843_f1_5
263
3100
393
131
212
2.10E−17

Bacillus subtilis

e1184217
yuglunknownBacillus subtilis complete genome (section 17 of 21) similar to












polyribonucleotide


Contig282D
23947132_f3_17
264
3101
378
126
269
1.90E−23

Bacillus

e291128
ComABB.licheniformis comAB gene.











lichenifomis



Contig282D
24644702_c1_33
265
3102
435
145
307
1.80E−27

Bacillus subtilis

e1184239
yufUunknownBacillus subtilis complete genome (section 17 of 21) similar to












Na+/H+ antiporter


Contig282D
24745437_f3_26
266
3103
1263
421
1659
9.70E−171

Bacillus subtilis

P50735
ypcAglutamate dehydrogenaseBacillus subtilis phosphoglycerate dehydrogenase












(serA), ypaA, ferredoxin (fer), ypbB, recS, ypbD, ypbE, ypbF, ypbG,












ypbH, glutamate dehydrogenase (ypcA), ypdA, ypdB, ypdC, spore cortexlytic












enzyme (sleB), ypeB, ypfA, ypfB, cytidi


Contig282D
26178400_f3_28
267
3104
186
62


Contig282D
26756252_c3_54
268
3105
2427
809
2158
1.30E−223

Bacillus subtilis

e1184238
yufTunknownBacillus subtilis complete genome (section 17 of 21) similar to












NADH dehydrogenase


Contig282D
29742890_f2_14
269
3106
189
63


Contig282D
31281253_f3_25
270
3107
1221
407
1513
2.90E−155

Bacillus subtilis

P38021
rocDorthinine aminotransferaseBacillus subtilis 36 kb sequence between gntZ and












tmY genesencoding 34 ORFs.


Contig282D
32689812_c2_46
271
3108
312
104
224
1.10E−18

Bacillus subtilis

e1184242
yufCunknownBacillus subtilis complete genome (section 17 of 21)


Contig282D
33397338_c3_55
272
3109
492
164
167
1.20E−12

Pyrococcus

d1028563
PHCC005174aa long hypothetical proteinPyrococcus horokoshii OT3











horikoshii


genomic DNA, 1300517-1338254 nt position, clone


Contig282D
34384380_c1_34
273
3110
333
111
278
2.10E−24

Bacillus subtilis

e1184240
yufVunknownBacillus subtilis complete genome (section 17 of 21) similar to












Na+/H+ antiporter


Contig282D
34617286_f2_12
274
3111
612
204
336
8.30E−40

Homo sapiens

d1008136
KIAA0073Human mRNA for KIAA0073 gene, partial cds. The ha1539












protein is related to cyclophilin.


Contig282D
36604587_c1_35
275
3112
1173
391


Contig282D
3985893_c3_53
276
3113
186
62


Contig282D
4100393_c3_47
277
3114
1215
405
1458
1.90E−149

Bacillus subtilis

g229324
argGarginine succinate synthaseBacillus subtilis rmB-dnaB genomic region.


Contig282D
48587_c3_49
278
3115
1062
354
729
3.50E−72

Bacillus subtilis

P37965
glpQglycerophosphoryl diester phosphodiesteraseB.subtilis glpT and












glpQ genes for glycerol 3-phosphate permeaseand glycerophosphoryl diester












phosphodiesterase.alternate gene name


Contig282D
5085003_c1_32
279
3116
1455
485
1439
2.00E−147

Bacillus subtilis

g229324
argHarginine succinate lyaseBacillus subtilis rmB-dnaB genomic region.


Contig282D
5114680_c3_56
280
3117
363
121
227
5.40E−19

Bacillus subtilis

e118424
yufBunknownBacillus subtilis complete genome (section 17 of 21) similar to












hypothetical proteins


Contig282D
6672886_f3_23
281
3118
1173
391
914
8.60E−92

Bacillus subtilis

P54524
yqiGYqiBacillus subtilis DNA, 283 Kb region containing skin element.similar to












NADH-dependent flavin oxidoreductase


Contig282D
783125_c3_52
282
3119
183
61


Contig296D
10031712_f2_60
283
3120
990
330
597
3.40E−58

Bacillus subtilis

P54538
yqjAYqjABacillus subtilis DNA, 283 Kb region containing skin element.


Contig296D
10312561_f1_26
284
3121
1236
412
996
1.80E−100

Bacillus subtilis

P38494
yplDunknownBacillus subtilis phosphoglycerate dehydrogenase (serA),












ypaA, ferredoxin (fer), ypbB, recS, ypbD, ypbE, ypbF, ypbG, ypbH, glutamate












dehydrogenase (ypcA), ypdA, ypdB, ypdC, spore cortexlytic enzyme (sleB),












ypcB, ypfA, ypfB, cytidine monophosphate


Contig296D
10334752_c3_311
285
3122
192
64


Contig296D
10642180_f3_143
286
3123
186
62


Contig296D
1070437_f1_37
287
3124
894
298
727
5.60E−72

Bacillus subtilis

P54161
ypcPexodeoxyribonucleaseBacillus subtilis (YAC10-9 clone) DNA region












between the serA andkdg loci.36.1% identity with 219 aa at the 5′ end of the


Contig296D
1229750_f1_8
288
3125
468
156
504
2.40E−48

Bacillus

e290687
argRarginine repressorB.stearothermophilus argR gene.











stearpthemophilus



Contig296D
1345752_c1_194
289
3126
945
315
720
3.10E−71

Bacillus subtilis

P54569
yqkFYqkFBacillus subtilis DNA, 283 Kb region containing skin












element.similar to hypothetical proteins


Contig296D
13853500_c2_221
290
3127
246
82


Contig296D
13876943_f1_46
291
3128
1488
496
882
2.10E−88

Bacillus subtilis

g2529476
orfRM1OrfRM1Bacillus subtilis 168 region at 182 min containing the cge












genecluster.similar to the E. coli Prc and carboxyl-terminal


Contig296D
14097011_f1_1
292
3129
612
204
522
3.00E−50

Bacillus

Q07908
argJornithine acetyltransferaseBacillus stearothermophilus ornithine











stearothermophilus


acetyltransferase (argJ) andacetylglutamate kinase (argB) genes,












complete cds's, argC gene, 3′end, and argD gene, 5′ end.also bears acetyl-CoA


Contig296D
16610088_f1_21
293
3130
393
131
217
6.20E−18

Bacillus subtilis

P50726
ypaAhypothetical protein ypaABacillus subtilis phosphoglycerate dehydrogenase












(serA), ypaA, ferredoxin (fer), ypbB, recS, ypbD, ypbE, ypbF, ypbG,












ypdA, ypdB, ypdC, spore cortexlytic enzyme (sleB), ypeB, ypfA, ypfB, cyti


Contig296D
16923383_f1_15
294
3131
339
113
156
2.60E−11

Bacillus subtilis

P54554
yqiQYqjBacillus subtilis DNA, 283 Kb region containing skin element.similar to












ketoacyl reductase


Contig296D
17002217_f1_16
295
3132
465
155
587
3.90E−57

Bacillus subtilis

P54574
yqkLYqkLBacillus subtilis DNA, 283 Kb region containing skin












element.similar to transcriptional regulator (Fur family)


Contig296D
187593_f2_77
296
3133
972
324
177
3.20E−12

Bacillus subtilis

P50728
ypbBhypothetical protein ypbBBacillus subtilis phosphoglycerate dehydrogenase












(serA), ypaA, ferredoxin (fer), ypbB, recS, ypbD, ypbE, ypbF, ypbG,












ypbH, glutamate dehydrogenase (ypcA), ypdA, ypdB, ypdC, spore cortexlytic












enzyme (sleB), ypeB, ypfA, ypfB, cyti


Contig296D
19567588_f3_136
297
3134
513
171
443
7.00E−42

Bacillus

P42015
ptsGPTS glucose-specific permeaseBacillus stearothermophilus XL











stearothermophilus


65-6 phosphoenolpyruvate-dependentphosphotransferase system












glucose-specific permease (ptsG′) gene, partial cds, HPr (ptsH), enzyme I












(pts1), and ptsT (ptsT) genes, complete cds, and wall asso


Contig296D
19567812_f3_135
298
3135
465
155
478
1.40E−45

Bacillus subtilis

P54155
yppQtranscriptional regulator (PilB family) homolog yppQBacillus subtilis












(YAC10-9 clone) DNA region between the serA andkdg loci.54.8% identity with













Neisseria gonorrhoeae



Contig296D
19804838_c2_224
299
3136
717
239
549
4.10E−53

Bacillus subtilis

P54163
ypdPconserved hypothetical protein ypdPBacillus subtilis (YAC10-9 clone)












DNA region between the serA andkdg loci.putative


Contig296D
20035967_f2_78
300
3137
1059
353
920
2.00E−92

Bacillus subtilis

g1146220
glyCNAD+ dependent glycerol-3-phosphateBacillus subtilis












phosphoglycerate dehydrogenase (serA), ypaA, ferredoxin (fer), ypbB, recS, ypbD,












ypbE, ypbF, ypbG, ypbH, glutamate dehydrogenase (ypcA), ypdA, ypdB,












ypdC, spore cortexlytic enzyme (sleB), ypeB, ypfA,


Contig296D
20485712_f3_137
301
3138
573
191


Contig296D
20507937_f3_124
302
3139
1317
439
1823
4.10E−188

Bacillus subtilis

P39772
asnSusparaginyl-tRNA synthetaseBacillus subtilis (clone












YAC15-6B) ypiABF genes, qcrABC genes, ypjABCDEFGHI genes, birA












gene, aspB gene, asnS gene, dnaD gene, nth gene and ypoC gene,












completecds's.41.4% of identity to the


Contig296D
20517135_f1_27
303
3140
315
105
361
340E−33

Bacillus

P02346
hubstDNA binding protein HUBacillus stearothermophilus gene for DNA











stearothermophilus


binding protein HU, complete cds.bacterial DNA-binding protein


Contig296D
20594688_f2_100
304
3141
1725
575
126
5.10E−08

Bacillus subtilis

P37966
lplAlysis proteinBacillus subtilis lysis protein (lplA) gene, complete cds.


Contig296D
20734677_f1_53
305
3142
774
258
277
2.70E−24

Escherichia coli

g1789829
glpRrepressor proteinEscherichia coli K-12 MG1655 section 308 of 400 of the












completegenome.f252; CG Site No. 688


Contig296D
2148387_f2_82
306
3143
1278
426
1794
4.80E−1.85

Staphylococcus

Q59803
aroCchorismate synthaseStaphylococcus aureus chorismate synthase (aroC) and











aureus


nucleosidediphosphate kinase (ndk) genes, complete cds,












dehydroauinatesynthase (aroB) and geranylgeranyl pyrophosphate synthetase












homolog(gerCC) genes, partial cds.5-enolpyruvynish


Contig296D
21501550_f1_48
307
3144
1116
372
917
4.10E−92

Bacillus subtilis

e1186380
msmXmultiple sugar-binding transport ATP-bindingBacillus subtilis complete












genome (section 20 of 21) alternate gene name


Contig296D
21537962_f2_86
308
3145
612
204
357
9.10E−33

Bacillus subtilis

P54392
ypjAhypothetical protein ypjABacillus subtilis (clone YAC15-6B) ypiABF












genes, qerABC genes,ypjABCDEFGHI genes, birA gene, panBCD genes, dinG












gene, ypmB gene, adpB gene, asnS gene, dnaD gene, nth gene and ypoC gene,












completecds's.putative


Contig296D
21674067_c1_151
309
3146
198
66


Contig296D
21678187_f3_131
310
3147
240
80


Contig296D
21730443_f2_67
311
3148
1332
444
904
9.90E−91

Bacillus subtilis

P37942
bfmBBbranched chain alpha-keto acid dehydrogenase E2Bacillus subtilis












branched chain alpha-keto acid dehydrogenaseE1-alpha, branched chain












alpha-keto acid dehydrogenase E1-beta, andbranched chain alpha-keto acid












dehydrogenase E2, complete cds.dihydrolipos


Contig296D
21756562_f3_127
312
3149
696
232
162
4.20E−12

Bacillus subtilis

e1182974
yheGhypothetical proteinBacillus subtilis complete genome (section 6 of












21) similar to calcium-binding protein


Contig296D
21914067_f3_142
313
3150
1416
472
532
2.60E−51

Lactococcus lactis

g2182835
llkinAhistidine kinase LlkinALactococcus lactis subsp.











cremoris


cremoris MG1363 histidine kinase (llkinA) gene complete cds.


Contig296D
21962762_f1_56
314
3151
732
244
615
4.20E−60

Bacillus subtilis

g143267

B.subtilis 2-oxoglutarate dehydrogenase (odhA) gene 3′ end,













anddihydrolipoamide transsuccinylase (odhB) gene, complete cds.2-












oxoglutarate dehydrogenase (odhA; EC 1.2.4.2)


Contig296D
23445266_f1_45
315
3152
567
189
579
2.70E−56

Bacillus subtilis

P54154
yppPDNA-binding proteinBacillus subtilis (YAC10-9 clone) DNA region












between the serA andkdg loci.42.4% identity with the Lycopersicon












esculentum


Contig296D
23625000_f3_110
316
3153
1683
561
2374
1.70E−246

Staphylococcus

g474177
malAalpha-D-1,4-glucosidaseS.xylosus malR gene malA gene.alpha-











xylosus


amylase core homology


Contig296D
23707890_f2_95
317
3154
240
80
123
5.70E−08

Bacillus subtilis

e1185439
yozEhypothetical protein yozEBacillus subtilis complete genome (section 11 of












21)


Contig296D
23836052_c1_195
318
3155
849
283
392
1.80E−36

Bacillus subtilis

P54552
yqjOYqjOBacillus subtilis DNA, 283 Kb region containing skin element.similar to












pyrroline-5-carboxylate reductase


Contig296D
23884692_f1_5
319
3156
366
122
217
6.20E−18

Bacillus subtilis

P54519
yqhYYqhYBacillus subtilis DNA, 283 Kb region containing skin












element.similar to hypothetical proteins from B. subtilis


Contig296D
23964011_c2_214
320
3157
195
65


Contig296D
24100715_f1_11
321
3158
1035
345
888
4.90E−89

Bacillus subtilis

P37940
bfmBAAbranched chain alpha-keto acid dehydrogenaseBacillus subtilis branched












chain alpha-keto acid dehydrogenaseE1-alpha, branched chain alpha-keto acid












dehydrogenase E1-beta, andbranched chain alpha-keto acid dehydrogenase E2,












complete cds.pyruvate dehyd


Contig296D
24104702_f2_93
322
3159
30549
10183
618
8.80E−55

Plasmodium

g1041785
rhoptry proteinPlasmodium yoelii rhoptry protein gene, partial cds.











yoelii



Contig296D
24226412_f2_73
323
3160
570
190
437
3.00E−41

Bacillus subtilis

P54570
yqkGYqkGBacillus subtilis DNA, 283 Kb region containing skin












element.similar to hypothetical proteins


Contig296D
24229515_f1_12
324
3161
1170
390
980
8.70E−99

Bacillus subtilis

P54542
yqjEYqjEBacillus subtilis DNA, 283 Kb region containing skin element.similar to












tripeptidase


Contig296D
24261692_f3_148
325
3162
1902
634
995
2.20E−100

Bacillus subtilis

g3169331
yojOYojOBacillus subtilis YojA (yojA), YojB (yojB), YojC (yojC), YojD (yojD),












YojE (yojE), YojF (yojF), YojG (yojG), YojH (yojH), YojI (yojI), YojJ (yojJ),












YojK (yojK), YojL (yojL), YojM (yojM), YojN (yojN), and YojO (yojO)












genes, complete cds; and OdhA (odh


Contig296D
24274192_c2_225
326
3163
417
139
204
1.50E−16

Enterococcus

P36921
ebsBcell wall enzymeEnterococcus faecalis pore forming, cell wall enzyme











faecalis


regulatory, and dehydroquinase homologue proteins












(ebsA, ebsB, ebsC and ebsD) genes, complete cds with repeat region.putative


Contig296D
24410300_f2_74
327
3164
759
253
686
1.20E−67

Bacillus subtilis

P35159
ypuLconserved hypothetical protein ypuLBacillus subtilis spoVA to serA












region.ORFX13


Contig296D
24480275_f3_138
328
3165
990
330
602
9.90E−59

Bacillus subtilis

c1182690
lplBtransmembrane lipoproteinBacillus subtilis complete genome (section 4 of












21)


Contig296D
24511676_f1 _57
329
3166
246
82
251
3.50E−21

Bacillis subtilis

P16263
odhB2-oxoglutarate dehydrogenase complexB.subtilis 2-oxoglutarate












dehydrogenase (odhA) gene 3′ end, anddihydrolipoamide transsuccinylase












(ddhB) gene, complete cds.dihydrolipoamide












acetyltransferasedihydrolipoamide transsuccinylase (odhB; EC


Contig296D
24650016_f1_34
330
3167
417
339
155
2.30E−11

Bacillus subtilis

P50839
ypsBhypothetical protein ypsBBacillus subtilis (clone YAC15-6B) ponA gene,












yppBCDEFG genes, ypqAE genes, yprAB genes, cotD gene, ypsABC genes,












maP gene, yptAgene, ypuA gene, kduDI genes, kdgRKAT genes, ypwA gene,












completecds's.putative


Contig296D
24650252_c2_235
331
3168
633
211
549
4.10E−53

Bacillus subtilis

P39792
yppBunknownBacillis subtilis (clone YAC15-6B) ponA gene, yppBCDEFG












genes, ypqAE genes, yprAB genes, cotD gene, ypsABC genes, rnaP gene,












yptAgene, ypuA gene, kduDI genes, kdgRKAT genes, ypwA gene,












completecds's.50.3% of identity to the 23.1 kD protein from


Contig296D
24797827_f3_144
332
3169
1857
619
1242
1.50E−326

Bacillus subtilis

P23129
odhAoxoglutarate dehydrogenase (NADP+) B. subtilis odhA gene for 2-












oxoglutarate dehydrogenase.alternate gene name


Contig296D
24800461_f1_55
333
3170
231
77
235
1.40E−18

Bacillus subtilis

P23129
odhAoxoglutarate dehydrogenase (NADP+) B. subtilis odhA gene for 2-












oxoglutarate dehydrogenase.alternate gene name


Contig296D
24807790_f2_63
334
3171
909
303
687
9.80E−68

Bacillus

Q08291
farnesyl diphosphate synthaseB. stearothermophilus DNA for farnesyl











stearothermophilus


diphosphate synthase.complete cds.


Contig296D
25598818_f1_9
335
3172
3692
564
1195
1.40E.121

Bacillus subtilis

P17894
recNRecNBacillus subtilis DNA.283 Kb region containing skin element.recN












proteinrecombination protein (ttg start codon)


Contig296D
25652217_f1_32
336
3173
348
116


Contig296D
26058467_f2_72
337
3174
213
71
119
7.60E−07

Caenorhabdisis

g861340
E04F6.7Caenorhabditis elegans cosmid E04F6.similar to ribitol dehydrogenase


Contig296D
26225463_f3_114
338
3175
741
247
821
6.20E−82

Bacillus subtilis

P35163
resDtwo-component response regulatorBacillus subtilis spoVA to serA












region.ompR proteinORFX17


Contig296D
26259657_f2_65
339
3176
1425
475
1155
2.50E−117

BACILLUS

P54533
BFMBCDEHYDROGENASE) (LPD-VAL)











SUBTILIS



Contig296D
26306713_f2_101
340
3177
932
304
580
2.10E−56

Thermoanaerobac-

g1255237
xynBXynBThermoanaerobacterium thermosulfurigenes endoxylanase











terium


precursor (XynA) and membrane component of an ABC transporter











thermosulfurigenes


(XynB) genes, complete cds and XynC (xynC) gene, partial cds.Description


Contig296D
26368950_f3_116
341
3178
1380
460
744
3.90E−76

Bacillus subtilis

P50729
recSDNA or RNA helicase, DNA-dependent ATPaseBacillus subtilis












phosphoglycerate dehydrogenase (serA), ypaA, ferrodoxin (fer), ypbB, recS, ypbD,












ypbE, ypbF, ypbG, ypbH, glutamate dehydrogenase (ypcA), ypdA, ypdB,












ypdC, spore cortexlytic enzyme (sleB), ypeB,


Contig296D
26384682_f1_85
342
3179
1248
416
561
2.20E−54

Bacillus subtilis

P54389
ypiA conserved hypothetical protein ypiABacillus subtilis (clone YAC15-6B)












ypiABF genes, qerABC genes, ypjABCDEFGHI genes, birA












genes, panBCD genes, dinG gene, ypmB gene, aspB gene, asnS gene, dnaD gene,












nth gene and ypoC gene, completecds's.putative


Contig296D
26597386_f2_68
343
3180
444
148
544
1.40E−52

Bacillus subtilis

P54534
yqiWYqiQBacillus subtilis DNA, 283 Kb region containing skin












element.similar to hypothetical proteins from B. subtilis


Contig296D
26600337_c3_304
344
3181
533
377
188
7.40E−15

Bacillus subtilis

P17617
ypuFhypothetical protein X6Bacillus subtilis spoVA to serA region.ORFX6


Contig296D
26754662_f1_25
345
3182
672
224
514
2.10E−49

Bacillus subtilis

P38493
cmkeytidine monophosphate kinaseBacillus subtilis phosphoglycerate












dehydrogenase (serA), ypaA, ferredoxin (fer), ypbB, recS, ypbD, ypbE, ypbF,












ypbG, ypbB, recS, ypbD, ypbE, ypbF, ypbG, ypbH, glutamate dehydrogenase












(ypcA), ypdA, ypdB, ypdC, spore cortexlytic enzyme (sleB), ypeB, ypfA,












ypfB, c


Contig296D
26774062_f3_119
346
3183
1332
444
1670
6.70E−172

Bacillus subtilis

P50743
yphCconserved hypothetical protein yphCBacillus subtilis phosphoglycerate












dehydrogenase (serA), ypaA, ferredoxin (fer), ypbB, recS, ypbD, ypbE, ypbF,












ypbG, ypbH, glutamate dehydrogenase (ypcA), ypdA, ypdB, ypdC, spore












cortexlytic enzyme (sleB), ypeB, ypfA,


Contig296D
2756288_f1_18
347
3184
183
61


Contig296D
29457167_f1_43
348
3185
546
182
854
2.00E−85

Staphylococcus

Q59908
dfrCdihydrofolate reductaseS.epidermidis thyF and dfrC











epidermadis


genes.type 1 dihydrofolate reductase homology


Contig296D
29532252_c2_223
349
3186
195
65


Contig296D
29570250_f3_113
350
3187
813
271
491
5.70E−47

Bacillus subtilis

P35154
ypuGconserved hypothetical protein ypuGBacillus subtilis spoVA to serA












region.ORFX7


Contig296D
30085926_c2_256
351
3188
1554
518
1534
1.70E−157

Bacillus subtilis

P54547
yqjJYqjJBacillus subtilis DNA, 283 Kb region containing skin element.similar to












glucose-6-phosphate 1-dehydrogenase


Contig296D
30682927_f3_145
352
3189
828
276
211
2.70E−l7

Bacillus subtilis

e1181488
ykcA YkcABacillus subtilis 168 56 kb DNA fragment between xlyA and












ykoR.putative dioxygenase


Contig296D
31306926_f3_140
353
3190
891
297
215
4.40E−16

Saccharomyccs

g609417
YLR361VYIr361cpSaccharomyces cerevisiae chromosome XII cosmid 8039.











cerevisiae



Contig296D
31525262_f1_6
354
3191
393
131
275
4.40E−24

Bacillus subtilis

P54520
yqhZYqhZBactillus subtilis DNA, 283 Kb region containing skin












element.similar to transcription termination


Contig296D
31799057_f1_17
355
3192
918
306
855
1.50E−85

Bacillus subtilis

P46352
ripXYqkMBacillus subtilis DNA, 283 Kb region containing skin












element.alternate gene name


Contig296D
3182261_c1_190
356
3193
210
70
190
4.50E−15

BACILLUS

P10245
ferredoxin [4Fe-4SFERREDOXINferredoxin 2[4Fe-4S











THERMOPRO-












TEOLYTICUS



Contig296D
32078568_f2_94
357
3194
969
323
1734
1.10E−178

Staphylococcus

P13954
thyEThyEStaphylococcus aureus multi-resistance plasmid pSK1 DNA











aureus


containingtransposon Tn4003.thymidylate synthaseethymidylate












synthetase (AA I-318)


Contig296D
33492927_f2_88
358
3195
705
235
358
7.10E−33

Bacillus subtilis

P39787
dnaDDnaD proteinBacillus subtilis (clone YAC15-6B) ypiABF genes












qcrABC genes, ypjABCDEFGHI genes, birA gene, panBCD genes, dinG gene,












ypmB gene, aspB gene, asnS gene, dnaD gene, nth gene and ypoC gene,












completecds's.


Contig296D
33543_f1_59
359
3196
246
82
272
1.30E−23

Bacillus subtilis

P16263
odhB2-oxoglutarate dehydrogenase complexB.subtilis 2-oxoglutarate












dehydrogenase (odhA) gene 3′ end, anddihydrolipoamide transsuccinylase












(odhB) gene, complete cds.dihydrolipoamide












acetyltransferasedihydrolipoamide transsuccinylase (odhB; EC


Contig296D
33646056_f2_75
360
3197
294
98
188
7.40E−15

Bacillus subtilis

P50726
ypaAhypothetical protein ypaA Bacillus subtilis phosphoglycerate dehydrogenase












(serA), ypaA, ferredoxin (fer), ypbB, recS, ypbD, ypbE, ypbF, ypbG,












ypbH, glutamate dehydrogenase (ypcA), ypdA, ypdB, ypdC, spore cortexlytic












enzyme (sleB), ypeB, ypfA, ypfB, cyti


Contig296D
34017062_f2_97
361
3198
1101
367
537
7.70E−52

Borrelia

g2688704
BB0767UDP-N-acetylglucosamine--N-acetylmuramyl-Borrelia burgdorferi











burgdorferi


(section 62 of 70) of the complete genome.similar to GB


Contig296D
34027217_f3_118
362
3199
999
333
986
2.00E−99

Bacillus subtilis

P50736
ypdAthioredoxin reductase homolog ypdABacillus subtilis phosphoglycerate












dehydrogenase (serA), ypaA, ferredoxin (fer), ypbB, recS, ypbD, ypbE, ypbF,












ypbG, ypbH, glutamate dehydrogenase (ypcA), ypdA, ypdB, ypdC, spore












cortexlytic enzyme (sleB), ypeB, ypfA, y


Contig296D
34415925_f3_106
363
3200
1134
378
905
7.70E−91

Bacillus subulis

P36839
argDN-acetylomithine aminotransferaseB.subtilis (168) DNA












for argC-F citrulline biosynthetic operon.


Contig296D
34430342_f1_29
364
3201
711
237
475
2.80E−45

Bacillus subtilis

e1184209
yugPunknownBacillus subtilis complete genome (section 17 of 21)


Contig296D
34432787_f2_87
365
3202
1221
407
672
3.80E−66

Bacillus subtilis

P42977
ypjlpoly(A) polymeraseBacillus subtilis (clone YAC15-6B) ypiABF genes,












qerABC genes, ypjABCDEFGHI genes, birA gene, panBCD genes, dinG gene,












ypmB gene, aspB gene, asnS gene, dnaD gene, nth gene and ypoC gene,












completecds's.38.9% of identical aminoacids with


Contig296D
35050_f1_38
366
3203
210
70


Contig296D
35370250_f3_146
367
3204
222
74
199
5.00E−16

Bacillus subtilis

e1185402
yozChypothetical protein yoz CBacillus subtilis complete genome (section 11 of












21)


Contig296D
35975878_f1_132
368
3205
282
94
162
2.00E−11

Bacillus subtilis

P54169
ypgRconserved hypothetical protein ypgRBacillus subtilis (YAC10-9 clone)












DNA region between the serA andkdg loci.25.8% identity over 120 aa with the













Synenococcus



Contig296D
36135875_f1_31
369
3206
1164
388
1034
1.70E−104

Bacillus subtilis

P42982
ypjHlipopolysaccharide biosynthesis-related pr homolog ypjHBacillus subtilis












(clone YAC15-6B) ypiABF genes, qcrABC genes, ypjABCDEFGHI genes,












birA gene, panBCD genes, dinG gene, ypmB gene, aspB gene, asnS gene, dnaD












gene, nth gene and ypoC gene completecds


Contig296D
3915886_f2_66
370
3207
3014
338
1156
2.00E−117

Bacillus subtilis

P37941
bfmBABbranched chain alpha-keto acid dehydrogenaseBacillus subtilis branched












chain alpha-keto acid dehydrogenaseE1-alpha, branched chain alpha-keto acid












dehydrogenase E1-beta, andbranched chain alpha-keto acid dehydrogenase E2,












complete cds.pyruvate dehyd


Contig296D
3944838_f1_44
371
3208
858
286
791
9.30E−79

Staphylococcus

g886711
ORF3unknownS.epidermidis thyF and dfrC genes.











epidermidis



Contig296D
4007343_f2_98
372
3209
627
209
302
6.10E−27

Bacillus

g288301
ORF2hypothetical protein 2B.megaterium cytochrome P450mcg.











megaterium


ORF1 and ORF2 genes.


Contig296D
4022203_f3_108
373
3210
1347
449
933
8.30E−94

Bacillus subtilis

P54521
yqiBYqiBBacillus subtilis DNA, 283 Kb region containing skin element.similar to












exodeoxyribonuclease VII (large


Contig296D
4086088_f1_2
374
3211
747
249
404
9.50E−38

Lactobacillus

e284231
argBacetylglutamate kinaseL.plantarum carA & ORF8 partial CDS, argC,J,B,D,F











plantarum


& ORF7. citrullinebiosynthetic operon.


Contig296D
4101018_f1_54
375
3212
669
223
507
1.20E−48

Bacillus subtilis

e1181525
ykoGYkoGBacillus subtilis 168 56 kb DNA fragment between xlyA and












ykoR.homologous to response regulators


Contig296D
4103377_f2_61
376
3213
615
205
498
1.00E−47

Lactobacillus

e284230
argJglutamate N-acetyltransferaseL.plantarum carA &











plantarum


ORF8 partial CDS, argC,J,B,D,F & ORF7 citrullinebiosynthetic operon.


Contig296D
4166443_c1_178
377
3214
2241
747
3168
0

Staphylococcus

g483534
penicillin-binding protein 2S.aureus DNA for penicillin-binding protein 2.











aureus



Contig296D
4336687_f1_42
378
3215
678
226
465
3.30E−44

Methanococcus

Q58206
MJ0796ABC transporter, ATP-binding proteinMethanococcus jannaschii section











jannaschii


66 of 150 of the complete genome.unassigned ATP-binding












cassette proteinssimilar to SP


Contig296D
4476577_f2_81
379
3216
480
160
627
2.20E−61

Staphylococcus

P50588
ndknucleoside diphosphate kinaseStaphylococcus aureus chorismate











aureus


synthase (arpC) and nucleosidediphosphate kinase (ndk)












genes, complete cds, dehydroauinatesynthase (aroB) and












geranylgeranyl pyrophosphate synthetase homolog(gerCC) genes, partial cds.ATP


Contig296D
4494143_f2_79
380
3217
588
196
105
7.30E−06

Micrococcus

d1026194
hexs-acomponent A of hexaprenyl diphosphate synthaseMicrococcus luteus











luteus


hexs-a, menG, hexs-b gene, complete cds.


Contig296D
4510443_f3_123
381
3218
2721
907
728
2.10E-100

Bacillus subtilis

P54394
dinGATP-dependent helicaseBacillus subtilis (clone YAC15-6B) ypiABF












genes, qcrABC genes, ypjABCDEFGHI genes, birA gene, panBCD genes, dinG












gene, ypmB gene, aspB gene, asnS gene, dnaD gene, nth gene and ypoC gene,












completecds's.224% identity with Escherichi


Contig296D
4570393_f2_83
382
3219
1074
358
617
2.60E−60

Bacillus subtilis

P31102
aroBAroBB.subtilis dbpA, mtr(A,b), gerC(1-3), ndk, cheR,












aro(B,E,F,H), trp(A-F), hisH, and tyrA genes, complete cds.


Contig296D
4689075_c1_196
383
3220
906
302
275
4.40E−24

Bacillus subtilis

d1020105
ydeEtranscriptional regulator (AraC/XylS famil) homolog












ydeEBacillus subtilis genome sequence, 148 kb sequence of the regionbetween 35












and 47 degree.PROBABLE HTH_ARAC_FAMILY OF TRANSCRIPTIONAL


Contig296D
4726643_f1_4
384
3221
1236
412
1459
1.50E−149

Bacillus subtilis

d1013248
accCYqhXBacillus subtilis DNA, 283 Kb region containing skin












element.alternate gene name


Contig296D
4860702_f1_33
385
3222
333
111


Contig296D
4860953_f2_84
386
3223
1311
437
1735
8.60E−179

Staphylococcus

Q05615
aroA3-phosphoshikimate-1-carboxyvinyltransferaseStaphylococcus











aureus



aureus dehydroquinate synthase (aroB) gene, 3′ endcds; 3-phosphoshikimate-1-













carboxvinyltransferase (aroA) gene, complete cds; ORF3, complete crs.


Contig296D
4900342_f3_147
387
3224
804
268
825
2.30E−82

Bacillus subtilis

g3169330
yojNYojNBacillus subtilis YojA (yojA), YojB (yojB), YojC (yojC), YojD (yojD),












YojE (yojE), YojF (yojF), YojG (yojG), YojH (yojH), YojI (yojI), YojJ (yojJ),












YojK (yojK), YojL (yojL), YojM (yojM), YojN (yojN), and YojO (yojO)












genes, complete cds; and OdhA (odh


Contig296D
4964202_f3_125
388
3225
675
225
719
4.00E−71

Bacillus subtilis

P39788
nthendonuclease IIIBacillus subtilis (clone YAC15-6B) ypiABF genes,












qcrABC genes, ypjABCDEFGHI genes, birA gene, panBCD genes, dinG gene,












ypmB gene, aspB gene, asnS gene, dnaD gene, nth gene and ypoC gene,












completecds's.46.2% of identity to the Escherichia


Contig296D
5116018_f1_7
389
3226
240
80
107
2.50E−06

Escherichia coli

g1786624
xseBexodeoxyribonuclease small subunitEscherichia coli K-12 MG1655












section 38 of 400 of the completegenome.f80; 100 pct identical












to EX7S_ECOLI SW


Contig296D
5118762_f1_52
390
3227
1332
444
495
2.20E−47

Bacillus subtilis

e1183083
yisQYisQBacillus subtilis complete genome (section 6 of 21) alternative gene












name


Contig296D
5131412_f1_20
391
3228
1776
592
886
8.00E−89

Bacillus subtilis

P35164
resEtwo-component sensor histidine kinaseBacillus subtilis spoVA to serA












region.ORFX18


Contig296D
5324137_f3_122
392
3229
987
329
497
1.30E−47

Bacillus subtilis

P42975
birAbiotin [acetyl-CoA-carboxylaseBacillus subtilis (clone












YAC15-6B) ypiABF genes, qcrABC genes, ypjABCDEFGHI genes, birA












gene, panBCD genes, dinG gene, ypmB gene, aspB gene, asnS gene, dnaD gene,












nth gene and ypoC gene, completecds's.26.7% identity to the


Contig296D
5367140_f2_96
393
3230
186
62


Contig296D
571932_f1_30
394
3231
393
131
352
3.10E−32

Bacillus subtilis

P42979
jojDunknownBacillus subtilis dihydropicolinate reductase (jojE) gene,












completecds; poly(A) polymerase (jojl) gene, complete cds; biotinacetyl-CoA-












carboxylase ligase (birA) gene, complete cds; jojC, jojD, jojF, jojG, jojH genes,












complete cds's.putative


Contig296D
587813_f2_62
395
3232
471
157
337
1.20E−30

Bacillus subtilis

d1013247
accBYqhWBacillus subtilis DNA, 283 Kb region containing skin












element.alternate gene name


Contig296D
5892177_c1_47
396
3233
186
62


Contig296D
6414213_c1_188
397
3234
981
327
446
3.40E−42

Bacillus

P30363
ansAAsparaginaseB.licheniformis ansA gene for asparaginase.the putative











licheniformis


protein shows similaties with


Contig296D
6438767_f3_117
398
3235
1404
468
268
7.70E−23

Staphylococcus

g1397239
ebpSelastin binding proteinStaphylococcus aureus elastin











aureus


binding protein (cbpS) gene, completecds.


Contig296D
6739462_f3_126
399
3236
624
208
415
6.50E−39

Bacillus subtilis

P50838
ypsAconserved hypothetical protein ypsABacillus subtilis (clone YAC15-6B)












ponA gene, yppBCDEFG genes, ypqAE genes, yprAB genes, cotD gene, ypsABC












genes, rnaP gene, yplA gene, ypuA gene, kduD1 genes, kdgRKAT genes, ypwA












gene, completecds's.putative


Contig296D
6821063_f1_58
400
3237
789
263
598
2.60E−58

Bacillus subtilis

P16263
odhB2-oxoglutarate dehydrogenase complexB.subtilis 2-oxoglutarate












dehydrogenase (odhA) gene 3′ end, anddihydrolipoamide transsuccinylase












(odhB) gene, complete cds.dihydrolipoamide acetyltransferasedihydrolipoamide












transsuccinylase (odhB; EC


Contig296D
6853417_f3_112
401
3238
924
308
668
1.00E−65

Bacillus subtilis

P54548
yqjKYqjKBacillus subtilis DNA, 283 Kb region containing skin element.similar to












hypothetical proteins


Contig296D
6855301_f1_40
402
3239
204
68
140
9.00E−10

Bacillus subtilis

P54165
ypeQhypothetical protein ypeQBacillus subtilis (YAC10-9 clone) DNA region












between the serA andkdg loci.putative


Contig296D
7226552_c1_191
403
3240
195
65


Contig296D
7242807_f2_70
404
3241
1425
475
1636
2.70E−168

Salmonella

P14062
gnd6-phosphogluconate dehydrogenaseS. enterica gnd gene for 6-











enterica


phosphogluconate dehydrogenase.phosphogluconate












dehydrogenase (decarboxylating)6-phosphogluconate dehydrogenase (AA 1-












468)


Contig296D
7320257_f1_36
405
3242
3456
1152
463
1.40E−39

Bacillus subtilis

P54159
ypbRRhypothetical protein ypbRBacillus subtilis (YAC10-9 clone) DNA region












between the serA andkdg loci.26.7% of identity in 165 as tp a Thermophilic


Contig296D
788937_f3_133
406
3243
468
156
395
8.60E−37

Bacillus subtilis

P54170
yphPconserved hypothetical protein yphPBacillus subtilis (YAC10-9 clone)












DNA region between the serA andkdg loci.putative


Contig296D
814052_f3_120
407
3244
777
259
857
9.40E−86

Micrococcus

d1026195
menG2-hexaprenyl-1,4-naphthoquinoneMicrococcus luteus hexs-











luteus


a, menG, hexs-b gene, complete cds.


Contig296D
863903_c1_150
408
3245
186
62


Contig296D
86669_f1_41
409
3246
1062
354
185
4.60E−12

Mycobacterium

e1246003
MTV030.16putative ABC-transporter transmembrane subunitMycobacterium











tuberculosis



tuberculosis sequence v030.MTV030.16, possible ABC-transporter













transmembrane


Contig296D
912757_f1_19
410
3247
552
184
307
1.80E−27

Bacillus subtilis

P35155
ypuHconserved hypothetical protein ypuHBacillus subtilis spoVA to serA












region.ORFX8


Contig296D
970275_f1_35
411
3248
1164
388
1150
8.40E−117

Bacillus subdlis

P50840
ypsCconserved hypothetical protein ypsCBacillus subtilis (clone YAC15-6B)












ponA gene, yppBCDRFG genes, ypqAE genes, yprAB genes, colD gene, ypsABC












genes, rnaP gene, yptAgene, ypuA gene, kduD1 genes, kdgRKAT genes, ypwA












gene, completecds's.putative


Contig296D
9783510_f2_60
412
3249
648
216
547
6.70E−53

Bacillus

Q07906
argCBacillus stearothermophilus ornithine acetyltransferase (argJ)











stearothermophilus


andacetylglutamate kinase (argB) genes, complete cds's, argC gene, 3′end, and












argD gene, 5′ end.


Contig296D
9922962_f128
413
3250
1074
358
718
5.10E−71

Bacillus subtilis

P31114
gerC3GerC3B.subtilis dbpA, mir(A,B), gerC(1-3), ndk, cheR,












aro(B,E,F,H), trp(A-F), hisH, and tyrA genes, complete cds.alternative gene name


Contig296D
9970327_f3_121
414
3251
564
188
114
1.20E−05

Bacillus subtilis

P54390
ypiBhypothetical protein ypiBBacillus subtilis (clone YAC15-6B) ypiABF












genes, qcrABC genes, ypjABCDEFGHI genes, birA gene, panBCD genes, dinG












gene, ypmB gene, aspB gene, asn5 gene, dnaD gene, nth gene and ypoC gene,












completecds's.putative


Contig310D
13961568_c3_96
415
3252
945
315
1007
1.20E−101

Staphylococcus

P11099
LACClacC proteinStaphylococcus aureus lacC and lacD genes.lacC











aureus


polypeptide (AA 1-310)


Contig310D
13871068_c2_66
416
3253
666
222
877
7.20E−88

Bacillus subtilis

g1165309
rpsCS3Bacillus subtilis ribosomal protein gene cluster, rpsJ, rplC,












rplD, rplW, rplB, rpsS, rplV and rpsC genes, complete cds, and rplP












gene, partial cds.ribosomal protein


Contig310D
13886593_c2_79
417
3254
252
84
96
4.10E−05

Laclocaccus laccis

g727435

Lactococcus lactis N5-(1-carboxyethyl)-L-ornithine synthase (ceo) gene, complete













cds.putative 6-kDa protein


Contig310D
1408450_f1_8
418
3255
564
188
304
8.30E−06

Pyrococcus

d1028868
PHLG013100aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA, 1534516-1552267 nl position(complementary strand), clone


Contig310D
14277217_c3_88
419
3256
516
172
626
2.80E−61

Bacillus subtilis

P21467
rpsEribosomal protein S5Bacillus subtilis ribosomal protein












(rplPNXEFROQ, rpmCDJ, rpsQNHEMK) genes, integral












membrane protein (secY) gene, adenylatekinase (adk) gene, methione












aminopeptidase (map) gene, inititation factor 1 (infA) gene, RNA polymerase alp


Contig310D
14312750_c1_57
420
3257
492
164
665
2.10E−65

Staphylococcus

Q00990
rplMribosomal protein L13S.carnosus rplM gene for ribosomal protein











carnosus


L13.Escherichia coli ribosomal protein L13


Contig310D
14346067_c2_77
421
3258
1023
341
288
1.90E−25

Vigna radiata

g1184121
auxin-induced proteinVigna radiata clone Mil-3 auxin-induced protein












mRNA, complete cds.


Contig310D
16829627_c3_90
422
3259
372
124
484
3.20E−46

Bacillus subtilis

g1044989
rpsMribosomal protein S13Bacillus subtilis ribosomal protein












(rplPNXEFROQ, rpmCDJ, rpsQNHEMK) genes, integral












membrane protein (secY) gene, adenylatekinase (sdk) gene, methionine












aminopeptidase (map) gene, inititation factor 1 (infA) gene, RNA polymerase al


Contig310D
16835333_c3_82
423
3260
840
280
1198
6.90E−122

Bacillus subtilis

g1165306
rplBL2Bacillus subtilis ribosomal protein gene cluster, rpsJ, rplC,












rplD, rplW, rplB, rpsS, rplV and rpsC genes, complete cds, and rplP












gene,partial cds.ribosomal protein


Contig310D
197127_f1_94
424
3261
1965
655
285
7.50E−22

Rhizobium sp.

P55706
y4xNY4xNRhizobiom sp. NGR234 plasmid pNGR234a, section 43 of 46 of










NGR234

thecomplete plasmid sequence.hypothetical 71 kd protein;












similar to Escherichia


Contig310D
19822151_c3_91
425
3262
372
124
433
8.00E−41

Bacillus subtilis

g142464
rplQribosomal protein L17B.subtilis initiation factor 1, ribosomal proteins B,












S13, S11, L17 and RNA polymerase alpha core protein genes, complete












cds.Escherichia coli ribosomal protein L17


Contig310D
21751063_c2_64
426
3263
579
193
621
9.60E−61

Bacillus

P28600
rplCribosomal protein L3B.stearothermophilus genes rplC and











stearothermophilus


rplD for robosomal proteins L3 and L4, respectively.Escherichia coli ribosomal












protein L3


Contig310D
21915941_c2_69
427
3264
372
124
571
1.90E−55

Bacillus subtilis

P12875
rplNribosomal protein L14Bacillus subtilis ribosomal protein












(rplPNXEFROQ, rpmCDJ, rpsQNHEMK) genes, integral












membrane protein (secY) gene, adenylatekinase (adk) gene, methionine












aminopeptidase (map) gene, inititation factor 1 (infA) gene, RNA polymerase al


Contig310D
22002318_c1_51
428
3265
330
110
390
2.90E−36

BACILLUS

P04455
RPLXribosomal protein L2450S RIBOSOMAL PROTEIN











STEARO-


L24Escherichia coli ribosomal protein L24











THERMOPHILUS



Contig310D
23572128_c1_53
429
3266
183
61
282
8.10E−25

Staphylococcus

g2078380
L30ribosomal protein L30Staphylococcus aureus NCTC 8325











aureus


ribosomal protein L30(L30),ribosomal protein L15 (L15) and SecY(secY)












genes, complete cds.


Contig310D
23572180_c1_55
430
3267
222
74
326
1.80E−29

Bacillus subtilis

g142459
infAinitiation factor 1B.subtilis initiation factor 1, ribosomal proteins B, S13, S11,












L17 and RNA polymerase alpha core protein genes, complete cds.


Contig310D
23573567_c3_85
431
3268
201
67
284
5.00E−25

Bacillus subtilis

P12878
rpsNribosomal protein L14Bacillus subtilis ribosomal protein












(rplPNXEFROQ, rpmCDJ,rpsQNHEMK) genes, integral












membrane protein (secY) gene, adenylatekinase (adk) gene, methionine












aminopeptidase (map) gene, inititation factor 1 (infA) gene, RNA polymerase al


Contig310D
23603450_c2_78
432
3269
585
195


Contig310D
23632750_c3_102
433
3270
525
175
726
7.20E−72

Staphylococcus

g874289
asp23alkaline shock protein 23asp23 = alkaline shock protein 23











aureus


{methicillin resistant}[Staphylococcus aureus, 912, Genomic, 1360 ntMethod


Contig310D
23634813_c1_58
434
3271
771
257
970
1.00E−97

Staphylococcus

P16644
LACRlacR repressorStaphylococcus aureus lac repressor (lacR) gene,











aureus


complete cds andlacA repressor (lacA), partial cds.


Contig310D
23683375_c1_59
435
3272
507
169
583
1.00E−56

Streptococcus

P26423
lacAgalactosidase acetyltransferaseSteptococcus mutans lac operon











mutans



Contig310D
23882135_c3_92
436
3273
873
291
665
2.10E−65

Bacillus subtilis

e1182078
ybxAunknownBacillus subtilis complete genome (section 1 of 21) alternate gene












name


Contig310D
24337750_c3_97
437
3274
981
327
1524
2.00E−156

Staphylococcus

P11100
LACDlacD proteinStaphylococcus aureus lacC and lacD genes.lacD











aureus


polypeptide (AA 1-326)


Contig310D
24397127_c3_98
438
3275
1776
592
2460
1.30E−255

Staphylococcus

P11162
LACEphosphotransferase system enzyme ll,, lactose-specific, factor











aureus


llS.aureus enzyme lll-lac (lacF), enzyme ll-lac (lacE), andphospho-beta-












galactosidase (lacG) genes, complete cds.enzyme ll-lac (lacE)


Contig310D
24402217_c1_56
439
3276
405
135
560
2.80E−54

Bacillus subtilis

P04969
rpsKribosomal protein S11B.subtilis initiation factor 1, ribosomal proteins B,












S13, S11, L17 and RNA polymerase alpha core proteins genes, complete












cds.Escherichia coli ribosomal protein S11ribosomal protein S11


Contig310D
24648312_f3_34
440
3277
747
249
905
7.70E−91

Staphylococcus

g845686

Staphylococcus aureus lac repressor (lacR) gene, complete cds andlacA












aureus


repressor (lacA), partial cds.ORF-27


Contig310D
24744040_c1_63
441
3278
1065
355


Contig310D
24806662_c2_67
442
3279
237
792
52
1.20E−21

Bacillus subtilis

P12873
rpmCribosomal protein L29Bacillus subtilis ribosomal protein












(rplPNXEFROQ, rpmCDJ, rpsQNHEMK) genes, integral












membrane protein (secY) gene, adenylatekinase (adk) gene, methionine












aminopeptidase (map) gene, inititation factor 1 (infA) gene, RNA polymerase al


Contig310D
25908568_c2_71
443
3280
453
151
706
9.50E−70

Staphylococcus

O06445
L15ribosomal protein L15Staphylococcus aureus NCTC 8325











aureus


ribosomal protein L30 (L30), ribosomal protein L15 (L15) and SecY (secY)












genes, complete cds.


Contig310D
26360036_c1_52
444
3281
387
129
429
2.10E−40

Bacillus subtilis

P46899
rplRribosomal protein L18Bacillus subtilis ribosomal protein












(rplPNXEFROQ, rpmCDJ, rpsQNHEMK) genes, integral












membrane protein (secY) gene, adenylatekinase (adk) gene, methionine












aminopeptidase (map) gene, inititation factor 1 (infA) gene, RNA polymerase al


Contig310D
26773450_c2_68
445
3282
285
95
380
3.30E−35

Bacillus subtilis

P12874
rpsQribosomal protein S17 (BS16) B.subtilis S10/spc operon rpmC,












rpsQ, rplN, rplX, rplE, rpsN genes.Escherichia coli ribosomal protein












S17S17 protein (AA 1-87)


Contig310D
26776678_c3_84
446
3283
372
124
431
1.30E−40

Bacillus

P23311
RPLVribosomal protein L22B.stearophilus gene for











stearothermophilus


ribosomal proteins L2, S19, L22, S3, and L16.Escherichia coli ribosomal protein












L22


Contig310D
2735801_c1_62
447
3284
1848
616
274
1.10E−20

Rhizobium sp.

P55706
y4xNY4xNRhizobium sp. NGR234 plasmid pNGR234a, section 43 of 46 of










NGR234

thecomplete plasmid sequence.hypothetical 71 kd protein;












similar to Escherichia


Contig310D
29328312_c3_83
448
3285
339
113
415
6.50E−39

Bacillus subtilis

d1009468
rpsSRibosomal Protein S19Bacillus subtilis genes for ribosomal proteins












L13, L4, L23, L2, S19, L22, S3 and L16, partial and complete cds.ribosomal












protein


Contig310D
30742165_c1_54
449
3286
1323
441
1919
2.70E−198

Staphylococcus

Q05217
secYsecY proteinS.carnosus secY gene.secY protein











carnosus



Contig310D
31377318_c2_65
450
3287
291
97
297
2.10E−26

Bacillus subtilis

P42924
rplWRibosomal Protein L23Bacillus subtilis genes for ribosomal proteins












L13, L4, L23, L2, S19, L22, S3 and L16, partial and complete cds.ribosomal












protein


Contig310D
3304562_c1_60
451
3288
366
122
411
1.70E−38

Staphylococcus

P02909
LACFS.aureus enzyme lll-lac (lacF), enzyme ll-lac (lacE), andphospho-beta-











aureus


galactosidase (lacG) genes, complete cds. enzyme lll-lac (lacF)


Contig310D
33437802_c3_89
452
3289
669
223
772
9.60E−77

Bacillus subtilis

P16304
adkadenylate kinaseBacillus subtilis ribosomal protein (rplPNXEFROQ,












rpmCDJ,rpsQNHEMK) genes, integral membrane protein (secY) gene,












adenylatekinase (adk) gene, methionine aminopeptidase (map) gene, inititation












factor t (infA) gene, RNA polymerase alpha (r


Contig310D
34017517_c3_93
453
3290
828
276
714
1.30E−70

Bacillus subtilis

e118201
ybaFhypothetical protein ybaFBacillus subtilis complete genome (section 1 of












21)


Contig310D
34188213_c3_86
454
3291
423
141
579
2.70E−56

Bacillus subtilis

g1044978
rpsHribosomal protein S8Bacillus subtilis ribosomal protein












(rplPNXEFROQ, rpmCDJ, rpsQNHEMK) genes, integral












membrane protein (secY) gene, adenylatekinase (adk) gene, methionine












aminopeptidase (map) gene, inititation factor 1 (infA) gene, RNA polymerase alp


Contig310D
34406562_c2_73
455
3292
867
289
644
3.50E−63

Bacillus subtilis

e1182079
ybaEunknownBacillus subtilis complete genome (section 1 of 21) similar to ABC












transporter (ATP-binding protein)


Contig310D
34647177_c3_87
456
3293
558
186
594
7.00E−58

Bacillus

g143419
ribosomal protein L6ribosomal protein L6B.stearothermophilus ribosomal











stearothermophilus


protein L6 gene, complete cds.


Contig310D
34651577_f2_15
457
3294
1047
349
502
3.90E−48

Bacillus subtilis

d1023111
yceBYceBBacillus subtilis genomic DNA, 22 to 25 degree region,












completecds.homologue of a hypothetical 36.6 kDa protein in


Contig310D
36135437_c3_81
458
3295
648
216
676
1.40E−66

Bacillus

P28601
rplDribosomal protein L4B.stearothermophilus genes rplC and











stearothermophilus


rplD for ribosomal proteins L3 and L4, respectively.Escherichia coli ribosomal












protein L4


Contig310D
36226575_c2_70
459
3296
558
186
766
4.20E−76

Bacillus subtilis

P12877
rplEribosomal protein L5Bacillus subtilis ribosomal protein (rplPNXEFROQ,












rpmCDJ, rpsQNHEMK) genes, integral membrane protein (secY) gene,












adenylatekinase (adk) gene, methionine aminopeptidase (map) gene, inititation












factor 1 (infA) gene, RNA polymerase alp


Contig310D
4165677_c3_94
460
3297
807
269
544
1.40E−52

Bacillus subtilis

e1182081
truApseudouridylate synthase IBacillus subtilis complete genome (section 1 of












21) alternatate gene name


Contig310D
4564036_c3_101
461
3298
1044
348
898
4.30E−90

Bacillus subtilis

e1182735
yfmJYfmJBacillus subtilis complete genome (section 5 of 21) similar to












quinone oxidoreductase


Contig310D
4694030_c3_103
462
3299
1236
412
311
6.80E−28

Mycobacterium

g2073532

Mycobacterium smegmatis catalase-peroxidase (katG), putativearabinosyl












smegmatis


transferase (embC, embA, embB), genes complete cds andputative propionyl-coA












carboxylase beta chain (pccB) genes, partialcds.orf7; hypothetical membrane












protein


Contig310D
4697262_c3_95
463
3300
540
180
806
2.40E−80

Streplococcus

D43258
galactose-6-phosphate isomerase subunit LacB











mutans



Contig310D
4714817_c2_76
464
3301
879
293


Contig310D
4879442_c2_75
465
3302
576
192
981
6.80E−99

Staphylococcus

P11175
LACGbeta-galactosidase,S.aureus enzyme lll-lac (lacF), enzyme ll-lac











aureus


(lacE), andphospho-beta-galactosidase (lacG) genes, complete












cds.Agrobacterium beta-glucosidasephospho-beta-galactosidase












(lacG)


Contig310D
4886592_c1_50
466
3303
450
150
614
5.30E−60

Bacillus subtilis

P14577
rplPribosomal protein L16Bacillus subtilis complete genome (section 1 of 21)


Contig310D
4897202_c2_72
467
3304
768
256
996
1.80E−100

Bacillus sp.

d1025104
rpoARNA polymerase alpha subunitBacillus sp. gene for initiation












factor IF-1, RNA polymerase alphasubunit and ribosomal proteins,












partial and complete cds.


Contig310D
4901712_c2_74
468
3305
408
136
496
1.70E−47

Bacillus subtilis

e1182083
rpslribosomal protein S9Bacillus subtilis complete genome (section 1 of 21)


Contig310D
55437_c3_99
469
3306
867
289
1458
1.90E−149

Staphylococcus

P11175
LACGbeta-galactosidase,S.aureus enzyme lll-lac (lacF), enzyme ll-lac











aureus


(lacE), andphospho-beta-galactosidase (lacG) genes, complete












cds.Agrobacterium beta-glucosidasephospho-beta-galactosidase (lacG)


Contig313D
10736002_c3_112
470
3307
1521
507
2313
4.90E−240

Staphylococcus

Q5363B
LySSlysyl-tRNA synthetaseStaphylococcus aureus lysyl-











aureus


tRNA synthetase gene, complete cds,transfer RNA (tRNA) genes, 5S












ribosomal RNA (5S rRNA) gene, 16Sribosomal RNA (16S rRNA) gene,












23S ribosomal RNA (23S rRNA) gene.


Contig313D
11210316_c3_106
471
3308
195
65
166
1.60E−12

Bacillus subtilis

P37557
ynbOunknownB. subtilis DNA, 180 kilobase region of replication












origin.similar to hypothetical proteins


Contig313D
12142768_f3_62
472
3309
300
100
110
3.50E−06

Pyrococcus

d1027343
PHBW016235aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA, 180023-216005 nt position, clone


Contig313D
12929625_c3_95
473
3310
810
270
819
1.00E−81

Bacillus subtilis

P37541
yaaTunknownB. subtilis DNA, 180 kilobase region of replication












origin.similar to signal peptidase ll


Contig313D
13759688_c3_93
474
3311
615
205
527
8.80E−51

Bacillus subtilis

P37537
tmkunknownB. subtilis DNA, 180 kilobase region of replication












origin.alternate gene name


Contig313D
14849093_c1_63
475
3312
321
107
123
5.70E−08
Mitochondrion
e138028
putative orf79.1C.crispus complete mitochondrial genome.unique orf











Chondrus crispus



Contig313D
16522641_f3_46
476
3313
597
199
202
2.40E−16

Pyrococcus

d1027803
PHCU002146aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA, 609561-620132 nt position,clonecontains prokaryotic












membrane lipoprotein lipid


Contig313D
16594202_c1_73
477
3314
480
160
383
1.60E−35

Bacillus subtilis

P29252
folk7,8-dihydro-6-hydroxymethylpterin-pyrophoshphokinB. subtilis DNA, 180












kilobase region of replication origin.2-amino-4-hydroxy-6-












hydroxymethylhydropteridine pyrophosphokinase


Contig313D
190875_f2_22
478
3315
210
70


Contig313D
194142_c3_101
479
3316
1386
462
1339
7.90E−137

Bacillus subtilis

d1005827
tms26temperature sensitive cell divisionB. subtilis DNA, 180 kilobase












region of replication origin.alternate gene name


Contig313D
211687_c2_87
480
3317
897
299
985
2.60E−99

Bacillus subtilis

P37565
yacCunknownB. subtilis DNA, 180 kilobase region of replication












origin.similar to hypothetical proteins


Contig313D
22694002_c2_86
481
3318
546
182
544
1.40E−52

Bacillus subtilis

P37472
hprthypoxanthine-guanine phosphoribosyltransferaseB. subtilis












DNA, 180 kilobase region of replication origin.hypoxanthine












phosphoribosyltransferase


Contig313D
23445130_c3_108
482
3319
417
139
134
3.40E−08

Bacillus subtilis

e1182000
yacAcell-cycle protein homolog yacABacillus subtilis complete genome












(section 1 of 21) similar to cell-cycle protein


Contig313D
23601702_c3_98
483
3320
891
297
919
2.50E−92

Bacillus subtilis

P37468
ksgAhigh level kasgamycin resistanceB. subtilis DNA, 180 kilobase region of












replication origin.rRNA (adenine-N6-)-methyltransferase


Contig313D
23631327_c2_79
484
3321
966
322
1225
9.50E−125

Corynebacterium

g2289093
prsPRPP synthetaseCorynebacterium ammoniagenes N-acetyl glucoseamine 1-











ammoniagenes


phosphateuridyltransferase (glmU) gene, partial cds, and PRPP-synthetase(prs)












gene, complete cds.


Contig313D
23642135_c3_94
485
3322
357
119
389
3.70E−36

Bacillus subtilis

P37538
yaaQunknownB. subtilis DNA, 180 kilobase region of replication












origin.similar to hypothetical proteins


Contig313D
23860952_c3_107
486
3323
882
294
267
1.00E−22

Bacillus subtilis

e1182000
yacAcell-cycle protein homolog yacABacillus subtilis complete genome












(section 1 of 21) similar to cell-cycle protein


Contig313D
24647936_c2_84
487
3324
408
136
161
5.40E−12

Bacillus subtilis

P37471
divlCunknownB. subtilis DNA, 180 kilobase region of replication origin.


Contig313D
24649092_c1_72
488
3325
378
126
351
3.90E−32

Staphylococcus

g1118003
folQdihydroneopterin aldolaseStaphylococcus haemolyticus











haemolyticus


cysteine synthase A (cysK) anddihydroneopterin aldolase (folQ)












genes, partial cds, anddihydropteroate synthase (folP) gene, complete












cds.DHNA


Contig313D
24663892_c2_80
489
3326
1881
627
1224
1.20E−124

Bacillus subtilis

P37474
mfdtranscription-repair coupling factorB. subtilis DNA, 180 kilobase region of












replication origin.


Contig313D
24790916_c3_109
490
3327
2106
702
2133
5.80E−221

Bacillus subtilis

P37476
ftsHcell division proteinB. subtilis DNA, 180 kilobase region of replication












origin.FtsH/SEC18/CDC48-type ATP-binding domain homology


Contig313D
25662965_c3_102
491
3328
729
243
463
5.30E−44

Bacillus subtilis

d1005829
cicexpressed at the end of exponential growyh underB. subtilis DNA, 180












kilobase region of replication origin.


Contig313D
26839660_c2_76
492
3329
855
285
655
2.40E−64

Bacillus subtilis

P37544
yabCunknownB. subtilis DNA, 180 kilobase region of replication












origin.similar to hypothetical proteins


Contig313D
2928502_c2_88
493
3330
960
320
1166
1.70E−118

Bacillus subtilis

d1005850
cysKeysteine synthetase AB. subtilis DNA, 180 kilobase region of replication












origin.threonine dehydratase


Contig313D
31446881_c1_64
494
3331
351
117
194
1.70E−15

Bacillus subtilis

P37542
yabAunknownB. subtilis DNA, 180 kilobase region of replication origin.


Contig313D
32615811_f1_17
495
3332
189
63


Contig313D
33225017_c1_68
496
3333
867
289
792
7.30E−79

Bacillus subtilis

P37551
purRunknownB. subtilis DNA, 180 kilobase region of replication












origin.alternate gene name


Contig313D
33313817_c3_100
497
3334
333
111
323
3.60E−29

Bacillus

P28016
spoVGspoVG proteinB.megaterium spoVG and lms genes.











megatenum



Contig313D
3361326_c3_90
498
3335
207
69


Contig313D
34001510_c1_67
499
3336
798
266
916
5.30E−92

Bacillus subtilis

P37545
yabDunknownB. subtilis DNA, 180 kilobase region of replication












origin.similar to hypothetical proteins


Contig313D
34428515_c3_99
500
3337
285
95
284
5.00E−25

Bacillus subtilis

P37466
vegunknownB. subtilis DNA, 180 kilobase region of replication origin.


Contig313D
34571011_c2_81
501
3338
1608
536
1712
2.40E−176

Bacillus subtilis

P37474
mfdtranscription-repair coupling factorB. subtilis DNA, 180 kilobase region of












replication origin


Contig313D
3553_c2_75
502
3339
972
324
382
2.00E−35

Bacillus subtilis

P37540
holBsimilar to B. subtilis DnaHB. subtilis DNA, 180 kilobase region of












replication origin.alternate gene name


Contig313D
3916087_c1_65
503
3340
261
87
243
1.10E−20

Bacillus subtilis

e1181968
yazA conserved hypothetical protein yazA Bacillus subtilis complete genome












(section 1 of 21) similar to hypothetical proteins


Contig313D
3937950_f3_43
504
3341
186
62


Contig313D
3938838_c3_111
505
3342
846
282
1087
4.00E−110

Staphylococcus

Q59919
folPdihydropteroate synthaseStaphylococcus haemolyticus











haemolyticus


cysteine synthase A (cysK) anddihydroneopterin aldolase (folQ)












genes, partial cds, anddihydropteroate synthase (folP) gene, complete












cds.DHPS


Contig313D
4723192_c3_103
506
3343
606
202
539
4.70E−52

Bacillus subtilis

P37470
spoVCstage V sporulationB. subtilis DNA, 180 kilobase region of replication












origin.thermosensitive mutant blocks spore coal formation


Contig313D
4775312_c2_85
507
3344
405
135
436
3.90E−41

Bacillus subtilis

P37560
yabRunknownB. subtilis DNA, 180 kilobase region of replication












origin.orf128; homologous to RNA binding domain of E. coli


Contig313D
4884625_c3_97
508
3345
549
183
445
4.30E−42

Bacillus subtilis

P37547
yabFunknownB. subtilis DNA, 180 kilobase region of replication












origin.similar to hypothetical protein


Contig313D
5344015_c2_83
509
3346
1281
427
849
6.60E−85

Bacillus subtilis

P37556
yabNunknownB. subtilis DNA, 180 kilobase region of replication origin.beta-












lactamase regulatory protein homologsimilar to hypothetical proteins


Contig313D
5367813_c2_74
510
3347
543
181
432
1.00E−40

Escherichia coli

P37354
speGSpermidine N1-acetyltransferase (EC 2.3.1.57) E. coli genomic DNA,












Kohara clone #308(35.3-35.7 min.) ORF_ID


Contig313D
6015842_c2_78
511
3348
900
300
750
2.10E−74

Bacillus subtilis

P37550
yabHunknownB. subtilis DNA, 180 kilobase region of replication












origin.similar to hypothetical proteins


Contig313D
6136562_c1_69
512
3349
402
134
361
3.40E−33

Bacillus subtilis

P37552
yabJunknownB. subtilis DNA, 180 kilobase region of replication












origin.hypothetical protein H10719similar to hypothetical proteins


Contig313D
6742943_c1_66
513
3350
1983
663
2292
8.10E−238

Bacillus subtilis

P37465
metSmethionyl-tRNA synthetaseB. subtilis DNA, 180 kilobase region of












replication origin.


Contig313D
761_c3_96
514
3351
750
250
543
2.90E−52

Bacillus subtills

P37543
yabBunknownB. subtilis DNA, 180 kilobase region of replication












origin.similar to hypothetical proteins


Contig313D
781880_f3_50
515
3352
339
113
114
2.40E−06

Schizosaccharo-

e317491
SPBC3D6.14cunknownS.pombe chromosome ll cosmid











myces pombe


c3D6.SPBC3D6.14c, unknown; partial; serine rich,


Contig313D
829800_c3_104
516
3353
1575
525
597
3.40E−58

Bacillus subtilis

P37555
yabMsimilar to SpoVBB. subtilis DNA, 180 kilobase region of replication












origin.similar to amino acid transporter


Contig313D
976638_c3_92
517
3354
1371
457
556
7.40E−54

Bacillus subtilis

P37536
yaaOsimilar to lysine decarboxylaseB. subtilis DNA, 180 kilobase region of












replication origin.similar to lysine decarboxylase


Contig315D
10657827_12_7
518
3355
1401
467
393
1.40E−36

Streptomyces

e304997
Sequence 6 from Patent WO9408014.unnamed protein product











pristinaespiralis



Contig315D
11756543_c1_18
519
3356
231
77


Contig315D
3207507_c3_32
520
3357
1245
415
3312
9.00E−113

Bacillus subtilis

d1020148
ydgFamino acid ABC transporter (permease) homolog ydgFBacillus













subtilis genome sequence, 148 kb sequence of the regionbetween 35 and 47













degree.PROBABLE AMINO ACID TRANSPORT PERMIASE.


Contig315D
157807_f2_10
521
3358
3584
528
3780
1.50E−183

Staphylococcus

e316580
CTORF585S.sciuri mecA gene, strain K11 (792).











sciuri



Contig315D
16048828_f1_3
522
3359
261
87


Contig315D
36410912_c1_20
523
3360
279
93


Contig315D
24251400_c1_23
524
3361
792
264
723
2.40E−71

Staphylococcus

g1854577
lytRStaphylococcus aureus lytS and lytR genes, complete cds.











aureus



Contig315D
25431558_c3_38
525
3362
705
235
855
1.50E−85

Staphylococcus

g1575026
lrgBlrgBStaphylococcus aureus holin-like protein LrgA (lrgA) and LrgB (lrgB)











aureus


genes, complete cds.LytSR-regulated gene; similar to E. coli yohK


Contig315D
25433452_c3_36
526
3363
1791
597
1867
8.90E−193

Staphylococcus

g862312
lytSStaphylococcus aureus lytS and lytR genes, complete cds.











aureus



Contig315D
25585932_f2_4
527
3364
276
92
249
2.50E−21

Bacillus subtilis

d1020109
ydelhypothetical protein ydelBacillus subtilis genome sequence, 148 kb












sequence of the regionbetween 35 and 47 degree.FUNCTION UNKNOWN.


Contig315D
26188837_f2_6
528
3365
975
325
838
9.70E−84

Bacillus subtilis

g2293449
opuBCcholine binding protein precursorBacillus subtilis choline












transport system including ATPase(opuBA), transmembrane protein












(opuBB), choline binding proteinprecursor (opuBC) and












transmembrane protein (opuBD) genes, completecds; and unknown gene.part o


Contig315D
26751887_f2_8
529
3366
954
318
297
2.10E−26

Aquifex aeolicus

g2984043
aq_ 1727putative proteinAquifex aeolicus section 85 of 109 of the complete












genome


Contig315D
2853433_c1_23
530
3367
195
65


Contig315D
30367767_c3_34
531
3368
1533
511
339
1.10E−30

Pyrococcus

d1027272
PHDC009273aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA, 124750-131579 nt position (complementary strand),












clonecontains soybean trypsin inhibitor (Kunitz)


Contig315D
34016937_f2_5
532
3369
1383
461
1178
9.10E−120

Bacillus subtilis

g2271389
opuCAATPaseBacillus subtilis osmoprotectant transport system OpuC












includingATPase (opuCA), transmembrane protein (opuCB),












osmoprotectantbinding protein precursor (opuCC) and transmembrane protein












(opuCD) genes, complete cds.OpuCA; part of the osmoprotectan


Contig315D
34273436_c1_19
533
3370
855
285
372
2.30E−34

Bacillus subtilis

P54544
yqjGYqiGBacillus subtilis DNA, 283 Kb region containing skin element.similar to












lipoprotein SpolllJ-like


Contig315D
34554692_c3_37
534
3371
474
158
403
1.20E−37

Staphylococcus

g1575025
lrgAbholin-like protein LrgAStaphylococcus aureus holin-like











aureus


protein LrgA (lrgA) and LrgB (lrgB) genes, complete cds.LytSR-regulated












gene; similar to E. coli yohJ


Contig315D
36134678_f1_2
535
3372
699
233
674
2.30E−66

Bacillus subtilis

g2271392
opuCDtransmembrane proteinBacillus subtilis osmoprotectant transport system












OpuC includingATPase (opuCA), transmembrane protein (opuCB),












osmoprotectantbinding protein precursor (opuCC) and transmembrane protein












(opuCD) genes, complete cds.OpuCD; part of th


Contig315D
36596878_f3_12
536
3373
351
117


Contig315D
3906718_c3_39
537
3374
1065
355
747
4.30E−74

Bacillus subtilis

d1023636
ydjLdehydrogenaseBacillus subtilis genomic DNA containing gutA to cotA












region, 48degree.putative


Contig315D
4725068_f1_1
538
3375
645
215
605
4.80E−59

Bacillus subtilis

g2271390
opuCBtransmembrane proteinBacillus subtilis osmoprotectant transport system












OpuC includingATPase (opuCA), transmembrane protein (opuCB),












osmoprotectantbinding protein precursor (opuCC) and transmembrane protein












(opuCD) genes, complete cds.OpuCB; part of th


Contig315D
7242128_f3_15
539
3376
345
115
352
3.10E−32

Staphylococcus

c314909
hypothetical proteinS.sciuri mecA gene & ORF's 450, 145 & 179.ORF450











sciuri



Contig315D
882143_f3_16
540
3377
255
85


Contig329D
10241287_c2_143
541
3378
663
221


Contig329D
1042202_c1_119
542
3379
1074
358
625
3.60E−61

Escherichia coli

P23861
potDSpermidine/putrescine-binding periplasmicEscherichia coli genomic












DNA.(25.1-25.5 min).f348; 100 pct identical to POTD_ECOLI SW


Contig329D
10579000_c2_154
543
3380
957
319
728
4.40E−72

Bacillus subtilis

P24009
ctaBCtaB proteinBacillus subtilis genomic DNA 23.9 kB fragment.putative


Contig329D
10928_c1_127
544
3381
1242
414
239
9.10E−18

Rhodobacter

g3128293
hypothetical proteinRhodobacter capsulatus strain SB1003, partial genome











capsulatus



Contig329D
10969052_c3_165
545
3382
1725
575
2602
1.20E−270

Staphylococcus

P51183
ptslphosphoenolpyruvate-protein phosphataseS.aureus ptsH and ptsl genes











aureus



Contig329D
1173177_f3_103
546
3383
1053
351
691
3.70E−68

Escherichia coli

P22564
yaaFhydrothetical 32.6 kD protein in lytB-dapBEscherichia coli K-12 MG1655












section 3 of 400 of the completegenome.o304; 100 pct indentical












to YAAF_ECOLI SW


Contig329D
1178828_c2_137
547
3384
705
235
642
5.70E−63

Bacillus subtilis

P12046
purCphosphoribosylaminoimidazole succinocarboxamideB.subtilis pur












operon encoding purine biosynthesis enzymes,












12genes.phosphoribosylaminoimidazolesuccinocarboxamide












synthasephosphoribosyl aminoidazole succinocarboxamide


Contig329D
1179542_c3_175
548
3385
222
74


Contig329D
13864213_f3_83
549
3386
234
78
186
1.20E−14

Bacillus subtilis

e1185044
ykzGhypothetical protein ykzGBacillus subtilis complete genome (section 8 of












21)


Contig329D
13866257_c1_124
550
3387
258
86
100
1.60E−05

Saccharomyces

e222102
SMFlunknown proteinS.cerevisiae 10.6 kbp fragment from chromosome











cerevisiac


XV.internal to SMFl


Contig329D
13869091_f2_68
551
3388
294
98
246
5.30E−21

Bacillus subtilis

P34959
QOXDquinol oxidaseBacillus subtilis AA3-600 quinol oxidase (QOXA,












QOXB, QOXC, QOXD) genes, complete cds.alternate gene name


Contig329D
14460882_c3_176
552
3389
240
80
321
5.90E−29

Staphylococcus

g1022726
unknownStaphylococcus haemolyticus IS1272 ORF1 and ORF2 genes,











haemolyticus


completecds.ORF1


Contig329D
14642135_c1_126
553
3390
1905
635
2456
3.40E−255

Bacillus subtilis

e1185067
ylaGGTP-binding elongation factor homolog ylaGBacillus subtilis complete












genome (section 8 of 21) similar to GTP-binding elongation factor


Contig329D
14650302_c1_110
554
3391
264
88
179
6.60E−14

Bacillus subtilis

P12049
yexAconserved hypothetical protein yexABacillus subtilis complete genome












(section 4 of 21) similar to hypothetical proteins


Contig329D
156502_f1_21
555
3392
243
81


Contig329D
19537562_f2_66
556
3393
198
66


Contig329D
19804703_c2_138
557
3394
747
249
696
1.10E−68

Bacillus subtilis

P12041
purLphosphoribosylformylglycinamidine synthetase llB,subtilis pur operon












encoding purine biosynthesis enzymes, 12genes.phosphoribosylformylglycin-












amidine synthase component lphosphoribosylformyl glycinamidine synthetase l


Contig329D
21648962_c3_163
558
3395
1827
609
1793
6.20E−185

Streptococcus

g517205
67 kDa Myosin-crossreactive streptococcalStreptococcus pyrogenes 42











pyogenes


KD protein (ORF1) gene and 67 KDMyosin-crossreactive streptococcal












antigen gene, complete cds.ORF2


Contig329D
21759653_f3_102
559
3396
609
203
552
2.00E−53

Bacillus subtilis

P34958
QOXCquinol oxidaseBacillus subtilis AA3-600 quinol oxidase (QOXA,












QOXB, QOXC, QOXD) genes, complete cds.cytochrome-c oxidase chain












lllalternate gene name


Contig329D
21915911_f1_24
560
3397
894
298
229
3.30E−19

Bacillus subtilis

e1181521
ykoCYkoCBacillus subtilis 168 56 kb DNA fragment between xlA and ykoR.


Contig329D
22775126_f2_59
561
3398
633
211
263
8.30E−23

Bacillus subtilis

e1181523
ykoEYkoEBacillus subtilis 168 56 kb DNA fragment between xlA and ykoR.


Contig329D
22931642_c2_132
562
3399
1224
408
1250
2.10E−127

Staphylococcus

d1024918
fmtFmtStaphylococcus aureus DNA for Fmt, complete cds.











aureus



Contig329D
23442177_f2_43
563
3400
669
223
429
2.10E−40

Bacillus subtilis

g1377842
yktBunknownBacillus subtilis ampS-nprE gene region.


Contig329D
23448838_f1_33
564
3401
873
291
786
3.20E−78

Bacillus subtilis

P54382
folDYqiABacillus subtilis DNA, 283 Kb region containing skin element.alternate












gene name


Contig329D
23459753_f3_78
565
3402
276
92


Contig329D
23532327_c2_145
566
3403
1113
371
1432
1.10E−l46

Bacillus

P21873
pdhApyruvate dehydrogenase (lipoamide) B. stearothermophilus pdhA,











stearothermophilus


pdhB, pdhC, pdhD genes for pyruvatedehydrogenase multienzyme












complex (E.C. numbers 1.2.4.1, 2.3.1.12, 1.8.1.4).pyruvate dehydrogenase












(lipoamide) alpha chainE1 alpha subunit


Contig329D
23695900_c2_139
567
3404
1551
517
1349
6.90E−138

Bacillus subtilis

P00497
purFphosphoribosylpyrophosphate amidotransferaseB.subtilis pur operon












encoding purine biosynthesis enzymes, 12genes.amidophosphoribosyltransferase












phosphoribosylpyrophosphate amidotransferase


Contig329D
23730340_c2_147
568
3405
1422
474
2270
1.70E−235

Staphylococcus

g48874
pdhDdihydrolipoamide dehydrogenaseS.aureus pdhB, pdhC and











aureus


pdhD genes for pyruvate decarboxylase, dihydrolipoamide












acetyltransferase and dihydrolipoamidedehydrogenase.dihydro












lipoamide dehydrogenase


Contig329D
23834680_c3_162
569
3406
210
70


Contig329D
24025253_f1_34
570
3407
321
107
198
1.10E−14

Clostridium

d1024701
chiBchitinase BClostridum paraputrificum gene for chitinase B,











paraputrificum


complete cds.


Contig329D
24256551_c3_160
571
3408
1071
357
938
2.50E−94

Bacillus subtilis

P12043
purMphosphoribosylaminoimidazole synthetaseB.subtilis pur operon encoding












purine biosynthesis enzymes, 12genes.phosphoribosylformylglycin-












amidine cyclo-ligasephosphoribosylaminoimidazole synthetase (PUR-M)


Contig329D
24314067_c1_129
572
3409
957
319
382
2.00E−35

Bacillus subtilis

e334771
ylbCYlbC proteinBacillus subtilis genomic DNA 23.9 kB fragment.similar












to hypothetical protein from B. subtilis


Contig329D
24415885_c1_128
573
3410
1227
409
651
6.40E−64

Bacillus subtilis

O07639
ylaOcell-division protein homolog ylaOBacillus subtilis complete genome












(section 8 of 21) similar to cell-division protein


Contig329D
24484828_c3_172
574
3411
552
184
169
7.60E−13

Methanobacterium

g2621742
MTH659epoxidaseMethanobacterium thermoautotrophicum from bases 587310











thermoauto-


to 597778 (section 52 of 148) of the complete genome.Function Code











trophicum



Contig329D
24485950_c1_122
575
3412
537
179


Contig329D
24610885_f3_69
576
3413
423
141


Contig329D
24642042_c1_131
577
3414
228
76
118
1.90E−07

Bacillus subtilis

e334782
ylbNYlbN proteinBacillus subtilis genomic DNA 23.9 kB fragment


Contig329D
24643836_c3_168
578
3415
633
211
227
5.40E−19

Bacillus subtilis

g1377834
ykrCunknownBacillus subtilis ampS-nprE gene region.similar to Orf5












encoded by GenBank Accession


Contig329D
24652178_c3_180
579
3416
477
159
174
2.20E−13

Bacillus subtilis

1185386
yozBconserved hypothetical protein yozBBacillus subtilis complete genome












(section 11 of 21) similar to hypothetical protein


Contig329D
24730340_c3_167
580
3417
672
224
731
2.10E−72

Bacillus subtilis

P39760
ykqBorf4Bacillus subtilis genes for ampS, mreBH, orf1, kinC, orf3, orf4












andorf5.similar to product of orf4 encoded by GenBank


Contig329D
24801713_c1_118
581
3418
1314
438
1906
6.50E−197

Staphylococcus

Q59B21
pdhCdihydrolipoamide acetyltransferaseS.aureus pdhB, pdhC











aureus


and pdhD genes for pyruvate decarboxylase, dehydrolipoamide












acetyltransferase and dihydrolipoamidedehydrogenase.dihydro












lipoamide acetyltransferase


Contig329D
24851577_c2_156
582
3419
564
188
405
7.50E−38

Bacillus subtilis

e334776
ylbHYlbH proteinBacillus subtilis genomic DNA 23.9 kB fragment.similar












to hypothetical proteins


Contig329D
25509640_c1_22
583
3420
240
80


Contig329D
25604677_c3_181
584
3421
450
150
322
4.70E−29

Bacillus subtilis

e334774
ylbFYlbF proteinBacillus subtilis genomic DNA 23.9 kB fragment.similar












to hypothetical proteins


Contig329D
25685000_c3_170
585
3422
903
303
1224
1.20E−124

Bacillus subtilis

g143378
pdhBpyruvate decarboxylase (E-1) beta subunitB.subtilis pyruvate












dehydrogenase complex genes, complete cds; PAL-related lipoprotein (slp) gene,












complete cds, lysinedecarboxylase (cad) gene, partial cds.similar to pyruvate












decarboxylase (E-1) beta


Contig329D
25939030_f2_53
586
3423
183
61


Contig329D 26354550_c3_183
587
3424
192
64


Contig329D
26828187_f3_74
588
3425
504
168
187
9.40E−15

Bacillus subtilis

e1185072
ylaLhypothetical protein ylaLBacillus subtilis complete genome (section 8 of












21)


Contig329D
2868785_f1_28
589
3426
339
113
99
8.50E−05

Vigna unguiculata

S54157
extensin-like protein


Contig329D
29319086_c3_182
590
3427
519
173
467
2.00E−44

Bacillus subtilis

e334777
ylblYlbl proteinBacillus subtilis genomic DNA 23.9 kB fragment.similar












to lipopolysaccharide core biosynthesis


Contig329D
29384818_c3_179
591
3428
3465
1155
3900
0

Bacillus subtilis

e1185076
pycApyrubate carboxylaseBacillus subtilis complete genome (section 8 of












21) alternate gene name


Contig329D
30663955_c2_136
592
3429
1152
384
767
3.30E−76

Bacillus subtilis

P12045
purKphosphoribosylaminoimidazole carboxylase llB. subtilis pur operon












encoding purine biosynthesis enzymes, 12 genes.phosphoribosylaminoimidazole












carboxylase carbon dioxide-fixation chainphosphoribosyl aminoimidazole












carboxylase ll


Contig329D
30745680_f2_67
593
3430
2007
669
2279
1.90E−236

Bacillus subtilis

P34956
QOXBquinol oxidaseBacillus subtilis AA3-600 quinol oxidase (QOXA,












QOXB, QOXC, QOXD) genes, complete cds.cytochrome-c oxidase chain












lalternate gene name


Contig329D
32242890_f2_51
594
3431
1701
567
1986
2.20E−205

Bacillus subtilis

Q45493
ykqCunknownBacillus subtilis ampS-nprE gene region.similar aminopeptidase












AMPS with Swiss-Prot


Contig329D
32756_f2_44
595
3432
1401
467
748
3.40E−74

Oryza saliva

g2231132
OsNramplintegral membrane proteinOryza Sativa integral membrane












protein (OsNramp) mRNA.putative


Contig329D
33153_c3_173
596
3433
900
300
451
1.00E−42

Borrelia

g2688563
BB0641spermidine/putrescine ABC transporter, permeaseBorrelia











burgdorferi



burgdorferi (section 51 of 70) of the complete genome.similar to GB



Contig329D
33594187_c2_151
597
3434
303
101
150
5.90E−10

Laciobacillus

g2668605
unknownLactobacillus rhamnosus 6-phospho-beta-glucosidase homolog











rhamnosus


gene, partial cds; GNTR transcriptional regulator homolog and surfacelocated












protein genes, complete cds.3.0E-ORF-1


Contig329D
34175686_c1_109
598
3435
513
171
502
3.90E−48

Bacillus subtilis

P12044
purEphosphoribosylaminoimidazole carboxylase 1B.subtilis pur operon












encoding purine biosynthesis enzymes, 12genes.phosphoribosylaminoimidazole












carboxylase catalytic chainphosphoribosyl aminoimidazole












carboxylase l


Contig329D
35272200_f2_49
599
3436
222
74
94
6.70E−05

Saccharomyces

g791116
ODP2unknownS.cerevisiae PMS1, TPM1, MKS1, MSK1, ODP2,











cerevisiae


YL9A & FKH2 genes.N2375, len


Contig329D
35947191_c3_114
600
3437
1155
385
149
5.30E−07
Kaposi's sarcoma-
g1633572
Kaposi's sarcoma-associated herpes-like virus ORF73 homolog gene, complete










associated herpes-

cds.Herpesvirus saimiri ORF73 homolog










like virus


Contig329D
36129451_c1_115
601
3438
288
96
408
3.60E−38

Staphylococcus

P23534
ptsHHistidine-containing protein (HPr) S.carnosus ptsH gene for histidine-











carnosus


containing protein (HPr).phosphotransferase system












phosphohistidine-containing protein


Contig329D
36142817_c2_148
602
3439
1149
383
925
5.90E−93

Borrelia

g2688562
BB0642spermidine/putrescine ABC transporter, Borrelia burgdorferi (section











burgdorferi


51 of 70) of the complete genome.similar to GB


Contig329D
36219187_c3_159
603
3440
2208
736
2062
1.90E−213

Bacillus subtilis

P12042
purQphosphoribosylformylglycinamidin c synthetase lB.subtilis pur operon












encoding purine biosynthesis enzymes, 12genes.phocphoribosylformylglycin-












amidine synthase component llphosphoribosylformyl glycinamidine












synthetase ll


Contig329D
36601687_c1_111
604
3441
1260
420
1016
1.30E−102

Bacillus subtilis

P12039
purDphosphoribosylglycinamide synthetaseBacillus subtilis












phosphoribosylaminoimidazolecarboxamideformyltransferase (purH-J)












gene, partial cds, phosphoribosylglycinamide












synthetase (purD), YecA (yecA), putativedenine deaminase (yecB), YecC












(yecC), and Yec


Contig329D
3945257_f3_101
605
3442
1176
392
738
3.80E−73

Bacillus subtilis

e1186316
qoxAcytochrome aa3 quinol oxidase (subunit 11) Bacillis subtilis complete












genome (section 20 of 21) alternate gene name


Contig329D
4103438_c2_155
606
3443
255
85
110
1.40E−06

Bacillus subtilis

e334775
ylbGYlbG proteinBacillus subtilis genomic DNA 23.9 kB fragment.similar












to hypothetical proteins


Contig329D
4300332_c1_114
607
3444
1329
443


Contig329D
4741010_c1_125
608
3445
846
282
650
8.10E−64

Bacillus subtilis

g1377843
yktCunknownBacillus subtilis ampS-nprE gene region.similar to E. coli












extragenic suppressor protein


Contig329D
4876542_f1_20
609
3446
633
211
551
2.50E−53

Bacillus subtilis

g1377833
ykrBunknownBacillus subtilis ampS-nprE gene region.similar to polypeptide












deformylase from Mycoplasma


Contig329D
4899187_f1_1
610
3447
1149
383
402
1.60E−37

Bacillus subtilis

e334781
ylbMYlbM proteinBacillus subtilis genomic DNA 23.9 kB fragment.similar












to hypothetical proteins


Contig329D
5117162_c2_144
611
3448
1023
341
517
1.00E−49

Bacillus subtilis

g2293292
ythBYthBBacillus subtilis rrnB-dnaB genomic region.similarity to NADH












dehydrogenases


Contig329D
5157963_f1_4
612
3449
939
313
219
3.10E−22

Bacillus subtilis

e1182963
yhdWhypothetical proteinBacillus subtilis complete genome (section 6 of












21) similar to glycerophosphodiester phosphodesterase


Contig329D
5974138_f3_77
613
3450
204
68


Contig329D
6023593_c2_152
614
3451
288
96
296
2.60E−26

Bacillus subtilis

e1185074
ylaNhypothetical protein ylaNBacillus subtilis complete genome (section 8 of












21)


Contig329D
6115700_f3_93
615
3452
1404
468
356
6.50E−64

Bacillus subtilis

e1181522
ykoDYkoDBacillus subtilis 168 56 kb DNA fragment between xlyA and












ykoR.homologous to cobalt transport ATP binding protein


Contig329D
1632762_f3_104
616
3453
222
74


Contig329D
6720452_c3_166
617
3454
1356
452
879
4.40E−88

Bacillus subtilis

g2293293
ythAYthABacillus subtilis rrnB-dnaB genomic region.similarity to cytochrome












oxidase D subunit I


Contig329D
6834687_c3_171
618
3455
309
103
209
4.40E−17

Bacillus subtilis

g1377841
yktAunknownBacillus subtilis ampS-nprE gene region.


Contig329D
7320465_c2_149
619
3456
831
277
525
1.40E−50

Borrelia

g2688564
BB0640spermidine/putrescine ABC transporter, permeaseBorrelia











burgdorferi



burdgorferi (section 51 of 70) of the complete genome.similar to GB



Contig329D
867176_c3_161
620
3457
1512
504
1090
1.90E−110

Aquifex acolicus

g2984204
purHphosphoribosylaminoimidazolecarboxamideAquifex aeolicus section 97 of












109 of the complete genome.


Contig329D
968785_f1_8
621
3458
939
313
749
2.60E−74

Bacillus

d1011770
ctaAheme O oxygenaseBacillus stearothermophilus genes for heme O











stearothermophilus


oxygenase andsynthetase and cytochtome c subunits II, I, III and IV,












completecds.


Contig329D
9925910_c2_140
622
3459
597
199
430
1.70E−40

Bacillus subtilis

P12040
purNphosphoribosylglycinamide formyltransferaseB.subtilis pur operon












encoding purine biosynthesis enzymes, 12genes.phosphoribosylglycinamide












formyltransferasephosphoribosyl glycinamide formyltransferase


Contig329D
9933463_c3_164
623
3460
1188
396
897
5.40E−90

Bacillus subtilis

P39587
ipa-19dconserved hypothetical protein ywbDB.subtilis genomic region (325 to












333).alternate gene name


Contig333D
10553125_f2_90
624
3461
810
270
335
1.30E−31

Gallus gallus

g211700
type X collagenChicken type X collagen gene.


Contig333D
10665903_c2_226
625
3462
378
126
151
4.90E−10

Escherichia coli

P37349
yegChypothetical protein in treA 5′regionEscherichia coli K-12 MG1655












section 108 of 400 of the completegenome.f473; 100 pct identical












to fragment YCGC_ECOLI SW


Contig333D
10828312_f3_133
626
3463
1617
539
272
9.80E−21

Bacillus subtilis

c1182674
yesMtwo-component sensor histidine kinase [Yes homolog yesMBacillus













subtilis complete genome (section 4 of 21) similar to two-component sensor













histidine kinase


Contig333D
1182765_c1_189
627
3464
7215
2405
2909
0

Bacillus

g2982196
bacCbacitracin synthetase 3Bacillus lichenifomis bacitracin synthetase











licheniformis


operon includingbacitracin synthetase 1 (bacA), 2 (bacB) and 3 (bacC)












genes, complete cds.peptide sythetase; BA3; BacC


Contig333D
11895058_c2_206
628
3465
939
313
164
4.20E−10

Enterococcus

g43338
sprEStaphylococcal serine proteinase homologueE.faecalis sprE gene for











faecalis


serine proteinase homologue.


Contig333D
12554627_c1_161
629
3466
216
72


Contig333D
1367200_f1_55
630
3467
624
208


Contig333D
1367202_c2_224
631
3468
963
321
516
9.30E−61

Escherichia call

g1787450
hypothetical protein b1200Escherichia coli K-12 MG1655 section 108 of 400 of












the comletegenome.f366; 35 pct identical (32 gaps) to 355 residues


Contig333D
1367340_c2_193
632
3469
843
281
250
8.20E−31

Streptococcus

e187587
oppDoligopeptidepermeaseS.pyogenes DNA for oppA, oppB, oppC, oppD,











pyogenes


oppF, and dacA genes.


Contig333D
13707008_f2_73
633
3470
231
77


Contig333D
1385962_c1_185
634
3471
984
328
1016
1.30E−102

Bacillus subtilis

P53557
bioBbiotin synthaseBacillus subtilis rrnB-dnaB genomic region.


Contig333D
1411400_f1_37
635
3472
390
130
131
8.10E−09

Caenorhabditis

g1051338
T04F8.8Caenorhabditis elegans cosmid T04F8, complete sequence,cDNA EST











elegans


yk121f1.5 comes from this gene


Contig333D
14492327_c2_222
636
3473
429
143
495
2.20E−47

Staphylococcus

Q03377
fosBfosfomycin resistance protein BS.epidermidis plasmid p1P1842 fosB











epidermidis


gene for FOSB.


Contig333D
14895212_c1_168
637
3474
822
274
5.10
5.60E−49

Bacillus subtilis

g143607
spo0KDsporulation proteinBacillus subtilis spo0K operon.


Contig333D
157625_c2_196
638
3475
930
310


Contig333D
162550_c1_174
639
3476
198
66


Contig333D
162578_c2_194
640
3477
984
328
338
9.40E−31

Bacillus subtilis

e1181925
ykuTYkuT proteinBacillus subtilis 29 kB DNA fragment from ykwC gene to cse15












gene.similar to hypothetical proteins


Contig333D
165902_c1_190
641
3478
627
209
185
1.50E−14

Bacillus subtilis

P39144
lpa-14lipopeptide antibiotics iturin AB. subtilis lpa-14 gene encoding lipopeptide












antibiotics iturin A


Contig333D
187561_c2_215
642
3479
879
293


Contig333D
119401_c1_150
643
3480
1512
504
1102
1.00E−111

Corynebacterium

e1286985
mqoL-malate dehydrogenase (acceptor) Corynebacterium glutamicum











glutamicum


DNA for L-Malate


Contig333D
19773387_f2_88
644
3481
1248
416


Contig333D
20585963_f2_97
645
3482
897
299
657
1.50E−64

Bacillus anthracis

g929972

Bacillus anthracis Weybridge A toxin plasmid pXO1 right invertedrepeat













element (WeyAR) bordering the toxin-encoding region, ORFAand ORFB












genes, complete cds.ORFB; similar to B. anthracis SterneL. element ORFB;


Contig333D
20704012_f3_135
646
3483
240
80


Contig333D
207876_f3_130
647
3484
513
171
113
3.20E−05

Mus musculus

d1000902
Mouse putative primordial protein transcript.open reading frame (251 AA)


Contig333D
20979688_c3_231
648
3485
786
262
369
4.90E−34

Escherichia coli

P33592
nikCNikCEscherichia coli K-12 MG1655 section 313 of 400 of the












completegenome.o277


Contig333D
212827_f2_62
649
3486
1482
494
429
2.10E−40

Bacillus subtilis

e1185986
yubDmultidrug resistance protein homolog yubDBacillus subtilis complete












genome (section 16 of 21) similar to multidrug resistance protein


Contig333D
22042337_c3_255
650
3487
1434
478
981
6.80E−99

Bacillus subtilis

e1182351
ycnBhomologue of multidrug resistance protein B, Bacillus subtilis complete












genome (section 3 of 21) similar to multidrug resistance protein


Contig333D
22664140_12_87
651
3488
1395
465
191
8.30E−12

Archacogiobus

g2650395
AF0246iron (11) transporter (feoB-1) Archaeoglobus fulgidus section 18 of











fulgidus


172 of the complete genome.similar to GB


Contig333D
22664550_c3_232
652
3489
663
221
275
4.40E−24

Escherichia coli

g1789891
nikEnikE proteinEscerichia coli K-12 MG1655 section 313 of 400 of the












completegenome.unassigned ATP-binding cassette proteinso268


Contig333D
22853432_c2_207
653
3490
384
128
152
2.00E−10

Sus scrofa

P18175
IVLinvolucrinPig involucrin gene, complete cds.involcrininvolcrin


Contig333D
23444425_c2_195
654
3491
846
282
362
2.70E−33

Bacillus subtilis

1183056
yhjKhypothetical proteinBacillus subtilis complete genome (section 6 of












21) similar to hypothetical proteins


Contig333D
23470290_c3_243
655
3492
915
305
496
1.70E−47

Bacillus firmus

g1813497
dppCdipeptide transporter protein dppCBacillus firmus dppABC operon,












dipeptide transporter protein dppAgene, partial cds, and dipeptide transporter












proteins dppB and dppCgenes, complete cds.


Contig333D
235837_c2_216
656
3493
1425
475


Contig333D
23601510_c2_223
657
3494
1137
379
911
1.80E−91

Bacillus

P32816
gldglycerol dehydrogenaseBacillus stearothermophilus glycerol











stearothermophilus


dehydrogenase (proposed gld) gene, complete cds.lactaldehyde reductase


Contig333D
23647750_f2_81
658
3495
201
67


Contig333D
23860307_c1_170
659
3496
1218
406
260
1.80E−20

Synechocystis sp.

d1018569
norAquinolene resistance protein NorASynechocystis sp. PCC6803












complete genome, 11/27, 1311235-1430418.ORF_ID


Contig333D
24000275_f2_64
660
3497
1026
342
1033
2.10E−104

Haemophilus

P44770
H10596ornithine carbamoyltransferase (arcB) Haemophilus influenzae from











influenzae


bases 614291 to 624841 (section 56 of 163) of the complete genome.ornithine












carbamoyltransferasesimilar to GB


Contig333D
24105393_c3_247
661
3498
768
256
648
1.30E−63

Streptococcus

g2952528
pflCpyruvate-formate lyase activating enzymeStreptococcus mutans YtqB











mulans


(ytqB) gene, partial cds; ABC transporter (abcX), putative permease












(perM), putative hemolysin (hlyX), pyruvate-formate lyase activating












enzyme (pflC), D-alanine-D-alanylcarrier protein 1


Contig333D
24225375_c3_236
662
3499
213
71
97
3.20E−05

Staphylococcus

g3212079
phenol soluble modulin beta IStaphylococcus epidermidis phenol











epidermidis


soluble modulin beta 1 and phenolsoluble modulin beta 2 genes,












complete cds.PSM beta 1


Contig333D
24407677_f2_61
663
3500
234
78


Contig333D
24650300_c2_219
664
3501
1365
455
1037
8.00E−105

Laccobacillus

P54104
bmQbranched-chain amino acid carrierL.delbrueckii brnQ gene for











delbrueckii


branched-chain amino acid carrier.


Contig333D
24664012_f1_35
665
3502
453
151


Contig333D
24711588_c3_256
666
3503
225
75


Contig333D
24884688_c3_230
667
3504
528
176
157
2.50E−12

Archaeoglobus

g2648784
AF1767dipeptide ABC transporter dipeptide-bindingArchaeoglobus











fulgidus



fulgidus section 126 of 172 of the complete genome.similar to GP



Contig333D
24886552_c1_164
668
3505
792
264
585
6.30E−57

Klebsiella

d1013772
budCmeso-2,3-butanediol dehydrogenase (D-acetoinKlebsiella











pneumonae



pneumoniae gene for meso-2,3-butanediol dehydrogenase (D-acetoin













forming), complete cds.


Contig333D
25395877_c1_42
669
3506
360
120
140
5.00E−09

Caenorhabditis

e1188061
F46B3.cCaenorhabditis elegans cosmid F46B3.complete sequence.protein











elegans


predicted using Genfinder; preliminary


Contig333D
25429665_c2_228
670
3507
1338
446
267
3.60E−21

Lactococcus lactis

g1052754
lmrPLmrP integral membrane proteinL.lactis DNA for LmrP gene.


Contig333D
25894687_c1_160
671
3508
243
81


Contig333D
26182681_c1_145
672
3509
528
176


Contig333D
26367135_c2_229
673
3510
1473
491
749
2.60E−74

Staphylococcus

g2981225
gehllipase precursorStaphylococcus epidermidis lipase precursor (gch1) gene,











epidermidis


completecds.


Contig333D
26369027_f1_53
674
3511
984
328
1350
5.40E−138

Bacillus subtilis

e1182793
yfjNHfjNBacillus subtilis complete genome (section 5 of 21) similar to












hypothetic proteins


Contig333D
26600936_f1_51
675
3512
513
171
373
1.80E−34

Haemophilus

P43984
H10318H. influenzae predicted coding region H1031Haemophilus influenzae











influenzae


from bases 345094 to 356754 (section 32 of 163) of the complete












genome.identified by GeneMark; putative. E. Koonin


Contig333D
26759430_c1_177
676
3513
978
326
872
2.40E−87

Bacillus subtilis

e1186069
opuCCglycine betaine/carnitine/choline ABCBacillus subtilis complete genome












(section 18 of 21) alternate gene name


Contig333D
26760076_f2_65
677
3514
1578
526
1550
3.50E−159

Haemophilus

P44023
H10594H influenzae predicted coding region H10594Haemophilus influenzae











influenzae


from bases 614291 to 624841 (section 56 of 163) of the complete












genome.identified by GeneMark; putative. E. Koonin


Contig333D
272593_c1_165
678
3515
879
293


Contig333D
2928437_c2_220
679
3516
921
307
375
1.10E−34

Archaeoglobus

g2649377
AF1210conserved hypothetical proteinArchaeoglobus fulgidus section











fulgidus


86 to 172 of the complete genome.similar to GP


Contig333D
2929718_c2_211
680
3517
1959
653
1384
1.30E−141

Staphylococcus

P10335
GEHtriacylglycerol lipase, S.aureus geh gene encoding lipase (glycerol ester











aureus


hydrolase).lipase precursor (geh; EC 3.1.1.3)


Contig333D
3003137_f1_31
681
3518
906
302
294
4.30E−26

Aquifex aeolicus

g2982874
cobWcobalamin synthesis related protein CobWAquifex aeolicus section7 of 109












of the complete genome.


Contig333D
30271882_c1_155
682
3519
720
240
268
2.50E−23
unidentified
g490316
bioDSynthetic (LOF1) bioD gene.


Contig333D
30351677_c1_147
683
3520
804
268


Contig333D
30742307_c3_250
684
3521
669
223
640
9.30E−63

Bacillus subtilis

g2271392
opuCDtransmembrane proteinBacillus subtilis osmoprotectant transport system












OpuC includingATPase (opuCA), transmembrane protein (opuCB),












osmoprotectantbinding protein precursor (opuCC) and transmembrane protein












(opuCD) genes, complete cds.OpuCD; part of th


Contig333D
3163552_c1_146
685
3522
963
321
326
1.80E−29

Pyrococcus

d1027921
PHCH021323aa long hypothetical oligopeptide transportPyrococcus











horikoshii



horikoshii OT3 genomic DNA, 695940-732858 nt position, clonesimilar to













Swiss_Prot


Contig333D
3174187_f1_35
686
3523
330
110


Contig333D
32615677_c3_239
687
3524
1035
345
510
5.60E−49

Bacillus subtilis

d1023108
ycdHYcdHBacillus subtilis genomic DNA, 22 to 25 degree region,












completecds.homologue of adhesion protein precursor of


Contig333D
32755_f1_22
688
3525
195
65


Contig333D
33479716_c1_163
689
3526
1401
467
409
2.80E−38

Mycobacterium

e264148
MTCY3G12.01unknownMycobacterium tuberculosis cosmid











tuberculosis


SCY03G12.MTCY3G12.01. len


Contig333D
34429837_f3_113
690
3527
948
316
769
2.00E−76

Escherichia coli

Q46807
YQEAhypothetical protein b2874Escherichia coli K-12 MG1655












section 260 of 400 of the completegenome.carbamate kinaseo310;












This 310 aa ORF is 45 pct identical (21 gaps)


Contig333D
34631527_f3_136
691
3528
336
112
304
3.80E−27

Bacillus anthracis

g929968

Bacillus anthracis Sterne toxin plasmid pXO1 right inverted repeatelement













(SterneR) bordering the toxin-encoding region, ORFA andtruncated ORFB












genes, complete cds.ORFA; similar to B. anthracis WeyAR element ORFA;


Contig333D
34642135_c1_183
692
3529
246
82


Contig333D
34657677_c1_154
693
3530
3552
1184
423
1.70E−38

Bombyx mori

g457769
CollagenB.mori mRNA for collagen.unassigned collagens


Contig333D
35312766_f1_5
694
3531
195
65


Contig333D
35331905_c1_153
695
3532
318
106


Contig333D
36135752_f3_128
696
3533
1128
376
172
1.40E−10

Bacillus subtilis

P50736
ypdAthioredoxin reductase homolog ypdABacillus subtilis phosphoglycerate












dehydrogenase (serA), ypaA, ferredoxin (fer), ypbB, recS, ypbD, ypbE, ypbF,












ypbG, ypbH, glutamate dehydrogenase (ypcA), ypdA, ypdB, ypdC, spore












cortexlytic enzyme (sleB), ypeB, ypfA, y


Contig333D
36601703_c2_213
697
3534
939
313
294
4.30E−26

Eschenichia coli

P33944
yojLyojL proteinEscherichia coli K12 MG1655 section 200 of 400 of the












completegenome.f351; Residues 1-121 are 100 pct identical to


Contig333D
3939215_f1_47
698
3535
984
328
377
6.90E−35

Serpulina

g2766193
periplasmic-iron-binding protein ShiBSerpulina hyodysenteriae shi











hyodysenteriae


operon, periplasmic-iron-bindingproteins ShiA and ShiB, putative ABC transporter












ShiC, and putativepermeases ShiD and ShiE genes, complete cds.


Contig333D
3948408_c1_178
699
3536
777
259
315
2.60E−28

Caldicellulosiruptor

P23553
XynCacetylxylosidaseCaldicellulosiruptor saccarolyticus putative transport











saccharolyticus


protein (XynG), putative transport protein (XynH), xylanase (XynF), xylanase












(XynE), xylanase (xynD), xylenase (XynA), acetylxylosidase (XynC) and












xylanase (XynB) genes, complete cds


Contig333D
3954382_c2_197
700
3537
195
65


Contig333D
4062925_f1_46
701
3538
393
131
103
6.40E−07

Lactococcus lactis

g2072447
epsJEpsJLactococcus lactis cremoris plasmid pNZ4000 insertion











cremoris


seqenceIS982 putative transposase gene and eps gene












cluster (epsRXABCDEFGHIJKL), complete cds.


Contig333D
4072680_f3_125
702
3539
774
258
311
6.80E−28

Bacillus subtilis

e1186097
yvfRhypothetical proteinBacillus subtilis complete genome (section 18 of












21) similar to ABC transporter (ATP-binding protein)


Contig333D
4094052_f2_76
703
3540
239
73


Contig333D
4301063_f3_138
704
3541
396
132


Contig333D
4103640_c3_240
705
3542
3054
3018
680
1.60E−66

Bacillus subtilis

P54524
yqiGYqiBacillus subtilis DNA, 283 Kb region containing skin element.similar to












NADH-dependent flavin oxidoreductase


Contig333D
429785_f2_79
706
3543
192
64


Contig333D
4705053_c3_237
707
3544
1221
407
454
4.80E−43

Haemophilus

P44422
H115537-keto-8-aminopetargonic acid synthetase (bioF) Haemophilus











influenzae



influenzae from bases 1615141 to 163152B (section 145 to 163) of the













complete genome.similar to GB


Contig333D
4765_f1_45
708
3545
321
307


Contig333D
4773518_c1_184
709
3546
885
295
563
1.30E−54

Streptococcus

e312302
lppCcytoplasmic membrane lipoproteinS.equisimilis gapC and lppC











equisimilis


genes.


Contig333D
4782963_c2_209
710
3547
1365
455
1105
5.00E−112

Aquifex aeolicus

g2982887
bioADAPA aminotransferaseAquifex aeolicus section 8 of 109 of the complete












genome.


Contig333D
4797177_c3_248
711
3548
588
196
308
1.40E−27

Synechocystis sp.

d1011096
hypothetical proteinSynechocystis sp. PCC6803 complete genome, 22/27,












2755703-2868766.ORF_ID


Contig333D
4798202_c1_159
712
3549
816
272


Contig333D
4859628_c1_148
713
3550
195
65


Contig333D
4867842_c1_175
714
3551
978
326
486
1.90E−46

Archacoglobus

g2649379
AF12063-hydroxacyl-CoA dehydrogenase (hbd-8) Archaeoglobus











fulgidus



fulgidius section 86 of 172 of the complete genome.similar to PID



Contig333D
4884812_f2_70
715
3552
1257
419
292
7.00E−26

Escherichia coli

P23908
argEacetylornithine deacetylaseEscherichia coli K-12












MG1655 section 360 of 400 of the completegenome.f383; 100 pct identical












to ARGE_ECOLI SW


Contig333D
4825063_c3_246
716
3553
2271
757
2671
5.60E−278

Escherichia coli

P09373
pflFormate C-acetyltransferaseEscherichia coli












genomic DNA. (20.3-20.7 min).f760; 100 pct identical to PFLB_ECOLI SW


Contig333D
4974093_c3_249
717
3554
504
168


Contig333D
5309785_c1_187
718
3555
255
85


Contig333D
5113413_c1_176
719
3556
642
214
579
2.70E−56

Bacillus subtilis

g2271390
opuCBtransmembrane proteinBacillus subtilis osmoprotectant transport system












OpuC includingATPase (opuCA), transmembrane protein (opuCB),












osmoprotectantbinding protein precursor (opuCC) and transmembrane protein












(opuCD) genes, complete cds.OpuCB; part of th


Contig333D
5360925_c2_205
720
3557
392
64


Contig333D
5389037_c1_356
721
3558
711
237
351
3.90E−32

Methanococcus

g1591935
MJ12976-carboxyhexanoate-CoA ligase (bioW)Methanococcus jannaschii section











jannaschii


112 of 150 of the complete genome.similar to GB


Contig333D
6056567_c2_225
722
3559
579
193
320
7.60E−29

Escherichia coli

g1787449
hypothetical protein b1199Escherichia coli K-12 MG1655 section 108 of 400 of












the completegenome.f210; 30 pct identical (16 gaps) to 181 residues


Contig333D
625262_c2_398
723
3560
228
76


Contig333D
6302217_c1_167
724
3561
948
316
541
2.90E−52

Escherichia coli

g1789888
nikBnickel transport system permease protein nikBEscherichia coli K-12












MG1655 section 313 of 400 of the completegenome.0314; 99 pct identical












amino acid sequence and


Contig333D
7072825_c2_302
725
3562
774
258
446
3.40E−42

Candida albicans

P87219
SOU1Sou1pCandida albicans Sou2p (SOU2), Sou1p (Sou1) and Vma8p












(VMA8) genes, complete cds.short-chain alcohol dehydrogenase homolog


Contig333D
800300_c2_208
726
3563
585
195
313
4.20E−28

Saimiri sciureus

e256400
anti-P.falciparum antigenic polypeptideDNA encoding anti-













P.falciparum antigen polypeptide.



Contig333D
814140_c2_204
727
3564
1422
474
1168
1.00E−118

Escherichia coli

P13408
uhpThexosephosphate transport proteinEscherichia coli K-12 MG1655












section 334 of 400 of the completegenome.hexose phosphate












transport protein uhpTf463; 99 pct identical amino acid sequence and


Contig333D
816878_c1_166
728
3565
1632
544
840
6.00E−84

Escherichia coli

P33590
nikAnickel-binding periplasmic protein precursorEscherichia coli K-12 MG1655












section 313 of 400 of the completegenome.dipeptide transport












protein524; 100 pct identical amino acid sequence and


Contig333D
822150_f1_54
729
3566
516
172


Contig333D
875765_c3_235
730
3567
210
70


Contig333D
969157_c2_191
731
3568
1026
342
203
9.30E−14

Eseherichia coli

P33590
nikAnickel-binding periplasmic protein precursorEscherichia coli K-12 MG1655












section 313 of 400 of the completegenome.dipeptide transport












protein524; 100 pct identical amino acid sequence and


Contig333D
9806718_c2_318
732
3569
762
254
417
4.00E−39

Escherichia coli

P37313
dppFdipeptide transport ATP-binding protein dppFEscherichia coli K-12












MG1655 section 321 of 400 of the completegenome.inner membrane












protein malKf334; 100 pct identical amino acid sequence and


Contig333D
984686_c2_221
733
3570
1221
407
1172
3.90E−119

Bacillus subtilis

g2271389
opuCAATPaseBacillus subtilis osmoprotectant transport system OpuC












includingATPase (opuCA), transmembrane protein (opuCB),












osmoprotectantbinding protein precursor (opuCC) and transmembrane protein












(opuCD) genes, complete cds.OpuCA; part of the osmoprotectan


Contig333D
9970167_f2_96
734
3571
861
287
219
2.40E−25

Bacillus subtilis

e1182675
yesNtwo-component response regulator [YesMBacillus subtilis complete genome












(section 4 of 21) similar to two-component response regulator [YesM


Contig334D
1017_f1_54
735
3572
255
85


Contig334D
10666068_c3_256
736
3573
330
110
196
1.00E−15

Bacillus subtilis

P25955
comG3ComGCBacillus subtilis (clone pED4) comG-(1,2,3,4,5,6,and 7) proteins












incomG operon, completecds.


Contig334D
10969050_c2_201
737
3574
1596
532
1815
2.90E−187

Bacillus subtilis

P37949
lepAYqeQBacillus subtilis DNA, 283 Kb region containing skin












element.alternate gene name


Contig334D
10970258_f1_122
738
3575
1011
337
1197
8.80E−122

Bacillus subtilis

e1183983
yrvNconserved hypothetical protein yrvNBacillus subtilis complete genome












(section 14 of 21) similar to hypothetical proteins


Contig334D
11194067_c3_240
739
3576
747
249
431
1.30E−40

Bacillus subtilis

P54458
yqeMYqeMBacillus subtilis DNA, 283 Kb region containing skin












element.similar to hypothetical proteins


Contig334D
11720090_c3_241
740
3577
525
175
588
3.00E−57

Staphylococcus

P45556
HRCAORF37Staphylococcus aureus genes for ORF37; HSP20; HSP70;











aureus


HSP40; ORF35, complete cds.


Contig334D
1218750_c1_150
741
3578
681
227
336
1.50E−30

Streptococcus

g3211753
celAcompetence proteinStreptococcus pneumoniae competence protein (celA)











pneumoniae


and competenceprotein (celB) genes, complete cds; and unknown gene.


Contig334D
136068_f3_99
742
3579
1404
468
1201
3.30E−122

Mycobacterium

e315164
glySGlySMycobacterium tuberculosis cosmid Y27.MTC27.23, glyS, len











tuberculosis



Contig334D
14259631_c1_135
743
3580
1068
356
1207
7.70E−123

Bacillus subtilis

e1184021
queAS-adenosylmethionine tRNA ribosyltransferaseBacillus subtilis












complete genome (section 15 of 21)


Contig334D
14508567_c3_230
744
3581
276
92
184
2.00E−14

Bacillus subtilis

e1184019
yrbFconserved hypothetical protein yrbFBacillus subtilis complete genome












(section 15 of 21) similar to hypothetical proteins


Contig334D
14881687_c3_254
745
3582
993
331
1448
2.20E−148

Staphylococcus

g666116
glkAglucose kinaseS.xylosus glucose kinase gene.











xylosus



Contig334D
15728386_c3_229
746
3583
1143
381
1542
2.40E−158

Bacillus subtilis

e1184020
tgttRNA-guanine transglycosylaseBacillus subtilis












complete genome (section 15 of 21)


Contig334D
16828175_c1_163
747
3584
606
202
800
1.00E−79

Bacillus subtilis

d1013186
sodAYqgDBacillus subtilis DNA, 283 Kb region containing skin












element. alternate gene name


Contig334D
189203_c3_243
748
3585
762
254
550
3.20E−53

Bacillus subtilis

P54461
yqeUYqeUBacillus subtilis DNA, 283 Kb region containing skin












element.similar to hypothetical proteins


Contig334D
19540931_c2_199
749
3586
2220
740
647
1.70E−63

Bacillus subtilis

P39695
COMEChypothetical protein 3 (comE operon) Bacillus subtilis comE operon












encoding ORF1, ORF2, ORF3 andReverse-ORF genes, complete cds.


Contig334D
20006377_c1_160
750
3587
732
244
432
1.00E−40

Bacillus subtilis

P54471
yqfNYqfNBacillus subtilis DNA, 283 Kb region containing skin












element.similar to hypothetical proteins


Contig334D
20791068_c3_235
751
3588
273
91


Contig334D
21667676_c1_139
752
3589
888
296
590
1.90E−57

Bacillus subtilis

e1184002
yrvMconserved hypothetical protein yrvMBacillus subtilis complete genome












(section 15 of 21) similar to hypothetical proteins


Contig334D
21759427_c1_170
753
3590
1350
450
196
7.20E−143

Bacillus subtilis

P54376
yqhJYqhJBacillus subtilis DNA, 283 Kb region containing skin element.similar to












glycine dehydrogenase


Contig334D
2195307_c1_167
754
3591
1095
365
348
8.20E−32

Bacillus subtilis

P25954
comG2ComGBBacillus subtilis (clone pED4) comG-(1,2,3,4,5,6,and 7) proteins












incomG operon, complete cds.


Contig334D
2227312_c1_38
755
3592
1782
594
2019
6.90E−209

Bacillus subtilis

e1184003
aspSaspartyl-tRNA synthetaseBacillus subtilis complete genome (section 15 of












21)


Contig334D
23470327_c3_253
756
3593
1461
487
446
3.40E−42

Staphylococcus

g666115
uglhypothetical protein IS.xylosus glucose kinase gene.orf1 upstream of











xylosus


glucose kinase


Contig334D
23470452_c2_193
757
3594
441
147
209
4.40E−27

Aquifex aeolicus

g2983771
accBbiotin carboxyl carrier proteinAquifex aeolicus section 68 of












109 of the complete genome.


Contig334D
23476676_c3_246
758
3595
369
123
227
5.40E−19

Bacillus subtilis

g902055
dgkdiacylglycerol kinaseBacillus subtilis PhoH (phoH) gene, partial cds,












diacylglycerolkinase (dgk) gene, complete cds, and cytidine deaminase












(cdd) gene, partial cds.


Contig334D
23595137_c2_195
759
3596
558
186
522
3.00E−50

Bacillus subtilis

P54452
yqeGYqeGBacillus subtilis DNA, 283 Kb region containing skin












element.similar to hypothetical proteins


Contig334D
23642942_c2_209
760
3597
696
232
132
2.10E−06

Caenorhabditis

g1255425
C33G8.2Caenorhabditis elegans cosmid C33G8.











elegans



Contig334D
23703452_c2_224
761
3598
1509
503
1808
1.60E−186

Bacillus subtilis

P54377
yqhKYqhKBacillus subtilis DNA, 283 Kb region containing skin












element.similar to glycine dehydrogenase


Contig334D
2381885_c1_145
762
3599
1272
424
1066
6.70E−108

Bacillus subtilis

e1182373
ycsGbranched chain amino acids transporter homolog yesGBacillus












sibtilis complete genome (section 3 of 21) alternate gene name


Contig334D
23850302_c3_234
763
3600
2694
898
2695
1.60E−280

Bacillus subtilis

e1183970
alaSalanyl-tRNA syntheraseBacillus subtilis complete genome (section 14 of












21)


Contig334D
24042212_c1_168
764
3601
498
166


Contig334D
24071068_f3_91
765
3602
399
133
308
1.40E−27

Bacillus subtilis

P54510
yqhLYqhLBacillus subtilis DNA, 283 Kb region containing skin












element.similar to hypothetical proteins


Contig334D
24094090_c1_144
766
3603
957
319
927
3.60E−93

Bacillus subtilis

e1183965
yrrNproteinase homolog yrrNBacillus subtilis complete genome (section 14 of












21) similar to protease


Contig334D
24229805_c3_238
767
3604
1386
462
1133
5.30E−115

Bacillus subtilis

d1013248
accCYqhXBacillus subtilis DNA, 283 Kb region containing skin












element.alternate gene name


Contig334D
24260061_c3_226
768
3605
348
116
214
1.30E−17

Bacillus subtilis

P26942
ysxBconserved hypothetical protein ysxBB.subtilis spolVFA. spolVFB, L20.












orfX and L24 genes.ORF X


Contig334D
24275927_f2_76
769
3606
189
63


Contig334D
24306263_c2_322
770
3607
297
99


Contig334D
24470317_c2_208
771
3608
1020
340
1246
5.70E−127

Bacillus subtilis

P54466
yqfAYqfABacillus subtilis DNA, 283 Kb region containing skin element.


Contig334D
24486330_c1_142
772
3609
693
231
1321
5.90E−29

Bacillus subtilis

e1183978
yrrBconserved hypothetical protein yrrBBacillus subtilis complete genome












(section 14 of 21) similar to hypothetical proteins


Contig334D
24610877_c2_223
773
3610
519
173
226
6.90E−19

Lactococcus lactis

P43906
aroKshikimate kinaseL.lactis tyrA, aroA, aroK and phcA genes.shikimate kinase


Contig334D
24640937_c3_257
774
3611
498
166


Contig334D
24658562_f3_121
775
3612
276
92
233
4.00E−19

Bacillus subtilis

e1183983
yrvNconserved hypothetical protein yrvNBacillus subtilis complete genome












(section 14 of 21) similar to hypothetical proteins


Contig334D
24823311_c1_169
776
3613
210
70


Contig334D
24886587_c2_186
777
3614
2448
816
1981
1.90E−207

Bacillus subtilis

e1183977
yrrCconjugation transfer protein homolog trrBacillus subtilis complete












genome (section 14 of 21) similar to conjugation transfer protein


Contig334D
25413126_f2_62
778
3615
189
63


Contig334D
2542188_c2_218
779
3616
270
90


Contig334D
25502217_c2_176
780
3617
615
205
410
2.20E−38

Bacillus subtilis

e1184023
ruvAHolliday junction DNA helicaseBacillus subtilis complete












genome (section 15 of 21)


Contig334D
25595186_c2_188
781
3618
651
217
736
6.30E−73

Bacillus subtilis

e1183963
udkuridine kinaseBacillus subtilis complete genome (section 14 of 21)


Contig334D
25672337_c2_213
782
3619
780
260
367
7.90E−34

Bacillus subtilis

P42095
yqxNYqflBacillus subtilis DNA, 283 Kb region containing skin element.alternate












gene name


Contig334D
25680218_c3_244
783
3620
726
242
425
5.70E−40

Bacillus subtilis

P54465
yqeZYqeZBacillus subtilis DNA, 283 Kb region containing skin element.


Contig334D
26203942_c1_158
784
3621
630
210
636
2.50E−62

Bacillus subtilis

e1185791
yqzBconserved hypothetical protein yqzBBacillus subtilis complete genome












(section 13 of 21) similar to hypothetical proteins


Contig334D
26209425_c2_216
785
3622
1068
356
1672
4.10E−172

Staphylococcus

P26766
plaCsigma factorS.aureus sigma factor (plaC) gene, complete cds.transcription











aureus


initiation factor sigma 43


Contig334D
26212501_c1_162
786
3623
852
284
454
4.80E−43

Bacillus subtilis

d1023110
yceAYceABacillus subtilis genomic DNA, 22 to 25 degree region,












completecds.homologue of a hypothetical 32.8 kDa protein in


Contig334D
26251577_c1_149
787
3624
354
118
372
2.30E−34

Bacillus subtilis

P54457
yqeLYqeLBacillus subtilis DNA, 283 Kb region containing skin












element.similar to hypothetical proteins


Contig334D
26754750_c2_185
788
3625
1164
388
895
8.90E−90

Bacillus subtilis

e1183981
yrvONifS protein homolog homolog yrvOBacillus subtilis complete genome












(section 14 if 21) similar to NifS protein homolog


Contig334D
26772135_c1_151
789
3626
996
332
555
9.50E−54

Bacillus subtilis

P54459
yqeNYqeNBacillus subtilis DNA, 283 Kb region containing skin












element.similar to hypothetical proteins


Contig334D
29468751_c1_172
790
3627
1173
391
855
1.50E−85

Bacillus subtilis

P54518
yqhTYqhTBacillus subtilis DNA, 283 Kb region containing skin












element.similar to Xaa-Pro dipeptidase


Contig334D
29494055_c2_206
791
3628
942
314
1248
3.50E−127

Staphylococcus

P45557
PRMAORF35Staphylococcus aureus genes for ORF37; HSP20; HSP70;











aureus


HSP40; ORF35, complete cds.


Contig334D
29845127_c2_190
792
3629
636
212
588
3.00E−57

Clostridium

e303881
putative transposaseC.perfringens uapC, cpc, and nadC genes.











perfringens



Contig334D
29958512_c3_236
793
3630
372
124
181
4.10E−14

Bacillus subtilis

e1183968
yrzBhypothetical protein yrzBBacillus subtilis complete genome (section 14 of












21)


Contig334D
30366652_c3_232
794
3631
897
299
1137
2.00E−115

Staphylococcus

g2580435
lytHN-acetylmuramoyl-L-alanine amidaseStaphylococcus aureus gene for











aureus


histidyl-tRNA synthetase, ppGpphydrolase, lytic enzyme, complete












cds.partially similar to the LytC protein of Bacillus


Contig334D
3125378_c2_219
795
3632
2097
699
1425
6.10E−146

Bacillus subtilis

P54488
pbpAYqgFBacillus subtilis DNA, 283 Kb region containing skin












element.alternate gene name


Contig334D
31527312_c3_251
796
3633
438
146
700
4.10E−69

Staphylococcus

P54204
FurS.epidermidis genes fur and sod (partial).putative











epidermidis



Contig334D
32212_c2_181
797
3634
1317
439
1921
1.70E−198

Staphylococcus

g2550436
hisShistidyl-tRNA synthetaseStaphylococcus aureus gene











aureus


for histidyl-tRNA synthetase, ppGpphydrolase, lytic enzyme, complete












cds.putative; similar to the hisS gene of E.coli


Contig334D
32244050_c2_198
798
3635
465
155
550
3.20E−53

Bacillus subtilis

P32393
comEBComEBBacillus subtilis comE operon encoding ORF1, ORF2, ORF3












andReverse-ORF genes, complete cds.alternate gene name


Contig334D
32422015_c2_215
799
3636
1803
601
2059
4.00E−213

Staphylococcus

O05338
dnaGStaphylococcus aureus DNA for sigma70 operon, complete cds.











aureus



Contig334D
32459627_c1_166
800
3637
630
210
403
1.20E−37

Bacillus subtilis

P54501
ypgXYqgXBacillus subtilis DNA, 283 Kb region containing skin












element.similar to hypothetical proteins


Contig334D
33409385_c2_225
801
3638
852
284
917
4.10E−92

Bacillus subtilis

e1185721
yqhMconserved hypothetical protein yqhMBacillus subtilis complete genome












(section 13 of 21) similar to hypothetical proteins from B. subtilis


Contig334D
33711505_c1_147
802
3639
357
119
316
2.00E−28

Bacillus subtilis

P54454
yqelYqelBacillus subtilis DNA, 283 Kb region containing skin element.similar to












dihydrodipicolinate reductase


Contig334D
34002212_c1_143
803
3640
447
149
437
3.00E−41

Bacillus subtilis

c1183969
yrrKconserved hypothetical protein yrrKBacillus subtilis complete genome












(section 14 of 21) similar to hypothetical proteins


Contig334D
34021937_c1_161
804
3641
822
274
432
1.00E−40

Methanobacterium

g2621685
MTH605ABC transporterMethanobacterium











thermoauto-



thermoautotrophicum from bases 535779 to 549251 (section 48 of 148) of the












trophicum


complete genome.Function Code


Contig334D
34166088_c2_173
805
3642
321
107
382
2.00E−35

Bacillus subtilis

P26908
L20ribosomal protein L21 (BL20)B.subtilis spolVFA, spolVFB,












L20, orfX and L24 genes.Escherichia coli ribosomal protein L21homolog of













E.coli ribosomal protein L21



Contig334D
34181643_c1_146
806
3643
702
234
579
2.70E−56

Escherichia coli

P24247
pfsPfs proteinEscherichia coli K-12 MG1655 section 15 of 400 of the












completegenome.f232; 100 pct identical to PFS_ECOLI SW


Contig334D
34376512_f1_80
807
3644
1080
360
814
3.40E−81

Bacillus subtilis

d1020093
yddNconserved hypothetical protein yddNBacillus subtilis genome sequence,












148 kb sequence of the regionbetween 35 and 47 degree.SIMILAR TO












ALKANAL MONOOXYGENASE ALPHA CHAIN.


Contig334D
34417217_c2_189
808
3645
492
164
531
3.30E−51

Bacillus subtilis

e118394
greAtranscription elongation factorBacillus subtilis complete genome












(section 14 of 21)


Contig334D
34610925_c2_204
809
3646
1851
617
2792
8.50E−291

Staphylococcus

P45554
DNAKHSP70Staphylococcus aureus genes for ORF37; HSP20; HSP70;











aureus


HSP40; ORF35, complete cds.


Contig334D
34642127_f2_57
810
3647
237
79


Contig334D
35319157_c1_154
811
3648
675
225
724
1.20E−71

Staphylococcus

P45553
GRPEHSP20Staphylococcus aureus genes for ORF37; HSP20; HSP70;











aureus


HSP40; ORF35, complete cds.


Contig334D
35334680_c2_187
812
3649
699
233
377
6.90E−35

Bacillus subtilis

e1183966
yrrMcaffeoyl-CoA O-methyltransferase homolog yrrMBacillus subtilis complete












genome (section 14 of 21) similar to caffeoyl-CoA O-methyltransferase


Contig334D
35343875_c3_328
813
3650
1026
342
1044
1.40E−105

Eseherichia coli

P08577
ruvBHolliday junction DNA helicase RuvB.E.coli genomic DNA, Kohara












clone #337 (41.9-42.3 min.).ruvB proteinORF_ID


Contig334D
35444067_c3_248
814
3651
837
279
1206
9.80E−123

Staphylococcus

d1020251
orf30Staphylococcus aureus DNA for sigma70 operon, complete cds.











aureus



Contig334D
35975077_c3_250
815
3652
891
297
1175
1.90E−119

Bacillus subtilis

P54476
yqfSYqfSBacillus subtilis DNA, 283 Kb region containing skin element.similar to












endonuclease IV


Contig334D
36125057_c3_149
816
3653
1368
456
1039
4.90E−105

Bacillus subtilis

P54475
yqfRYqfRBacillus subtilis DNA, 283 Kb region containing skin element.similar to












ATP-dependent RNA helicase


Contig334D
36225626_c2_180
817
3654
537
179
839
7.60E−84

Staphylococcus

g2580432
aptadenine phosphoribosyltransferaseStaphylococcus











aureus



aureus gene for histidyl-tRNA synthetase, ppGpphydrolase, lytic













enzyme, complete cds.putative; similar to the api gene of E.coli


Contig334D
36573502_c3_231
818
3655
2211
737
3507
0

Staphylococcus

g2580433
relppGpp hydrolaseStaphylococcus aureus gene for histidyl-tRNA











aureus


synthetase, ppGpphydrolase, lytic enzyme, complete cds.putative; similar












to the relA and spoT genes of


Contig334D
3916011_c2_214
819
3656
207
69


Contig334D
3916578_c1_137
820
3657
501
167
619
1.60E−60

Staphylococcus

g2580434

Staphylococcus aureus gene for histidyl-tRNA synthetase, ppGpphydrolase, lytic












aureus


enzyme, complete cds.ORF1


Contig334D
3941262_c1_153
821
3658
465
155
609
1.80E−59

Bacillus subtilis

P37949
lepAYqeQBacillus subtilis DNA, 283 Kb region containing skin












element.alternate gene name


Contig334D
3945937_c2_207
822
3659
1371
457
1764
7.30E−182

Bacillus subtilis

P54462
yqeVYqeVBacillus subtilis DNA, 283 Kb region containing skin












element.similar to hypothetical proteins


Contig334D
4015702_c2_211
823
3660
468
156
416
5.10E−39

Bacillus subtilis

P46347
yqfGYqfGBacillus subtilis DNA, 283 Kb region containing skin












element.similar to hypothetical proteins


Contig334D
4023415_f3_125
824
3661
240
80


Contig334D
41088_c3_255
825
3662
987
329
517
1.00E−49

Bacillus subtilis

P25953
comG1ComGABacillus subtilis (clone pED4) comG-(1,2,3,4,5,6,and 7) proteins












incomG operon, complete cds.late competence gene


Contig334D
4152203_c2_174
826
3663
300
100
426
4.40E−40

Bacillus subtilis

P05657
rpmA1.27 ribsomal proteinBacillus subtilis ribosomal protein L27 gene,












upstream of spo0Blocus, complete cds.Escherichia coli ribosomal protein












L27polypeptide homologous to E. coli ribosomal protein


Contig334D
4172025_c2_991
827
3664
744
248
456
1.30E−45

Bacillus subtilis

P42967
ycsJurea amidolysaseBacillus subtilis genome around 39 degree region












encoding 17 ORFs, complete cds.similar to allophanate hydrolase


Contig334D
4176557_c3_237
828
3665
1302
434
1676
1.50E−172

Bacillus subtilis

e1183964
yrrOproteinase homolog yrrOBacillus subtilis complete genome (section 14 of












21) similar to protease


Contig334D
42132_f1_51
829
3666
288
96


Contig334D
4556693_c1_141
830
3667
1131
377
1158
1.20E−117

Bacillus subtilis

e1183979
yrrAconserved hypothetical protein yrrABacillus subtilis complete genome












(section 14 of 21) similar to hypothetical proteins


Contig334D
4406502_c1_157
831
3668
939
313
1033
2.10E−104

Bacillus subtilis

P42182
bexYqfHBacillus subtilis DNA, 283 Kb region containing skin element.similar to












Era, an essential small G-protein in E.


Contig334D
4459380_c2_178
832
3669
207
69


Contig334D
4492268_c2_203
833
3670
489
163
614
5.30E−60

Staphylococcus

P45556
HRCAORF37Staphylococcus aureus genes for ORF37; HSP20; HSP70;











aureus


HSP40; ORF35, complete cds.


Contig334D
4564137_c1_1
834
3671
633
211
125
2.60E−06

Borrelia

g466482
OspFouter surface protein FBorellia burgorferi outer surface protein F











burgdorferi


(OspF) gene, completecds.putative


Contig334D
4693812_c3_258
835
3672
1116
372
970
1.00E−97

Bacillus subtilis

P54378
yqhlYqhlBacillus subtilis DNA, 283 Kb region containing skin element.similar to












aminomethyltransferase


Contig334D
4704678_c1_165
836
3673
210
70
115
4.00E−07

Bacillus subtilis

P54494
yqgQYqgQBacillus subtilis DNA, 283 Kb region containing skin element.


Contig334D
4798143_c3_233
837
3674
432
144
305
2.90E−27

Bacillus subtilis

e1183982
yrzCconserved hypothetical protein yrzCBacillus subtilis complete genome












(section 14 of 21) similar to hypothetical proteins


Contig334D
4822177_c2_220
838
3675
330
110
476
2.20E−45

Staphylococcus

e147899
dglAS.xylosus glucose kinase gene.orf2 downstream of glucose kinase











xylosus



Contig334D
4859677_c2_210
839
3676
939
313
974
3.80E−98

Bacillus subtilis

P46343
phoHYqfEBacillus subtilis DNA, 283 Kb region containing skin












element.alternate gene name


Contig334D
4860942_c3_239
840
3677
594
198
356
1.20E−32

Bacillus subtilis

P54455
yqeJYqeJBacillus subtilis DNA, 283 Kb region containing skin element.similar to












hypothetical proteins


Contig334D
4884675_c2_217
841
3678
1104
368
612
8.70E−60

Bacillus subtilis

e1185784
yqfOconserved hypothetical protein yqfOBacillus subtilis complete genome












(section 13 of 21) similar to hypothetical proteins


Contig334D
4892200_c2_196
842
3679
1101
367
1012
3.50E−102

Bacillus subtilis

P54453
yqeHYqeHBacillus subtilis DNA, 283 Kb regioni containing skin












element.similar to hypothetical proteins


Contig334D
4892942_c2_194
843
3680
768
256
660
7.10E−65

Bordetella

g2290993
unknownBordetella pertussis D-3-phosphoglycerate dehydrogenase











pertussis


homolog (serA) and Brg1 (brg1) genes, complete cds.orf7; similar to B. subtilis












YcsF


Contig334D
4900381_c2_179
844
3681
2298
766
1335
2.10E−136

Bacillus subtilis

e1184010
yrvEsingle-strand DNA-specific exonuclease homolog yrvEBacillus












subtilis complete genome (section 15 of 21) similar to single-strand DNA-specific












exonuclease


Contig334D
4939377_c2_175
845
3682
480
160
277
2.70E−24

Bacillus subtilis

P21204
phcBchorismate mutaseBacillus subtilis sporulation protein (spoOB), GTP-












binding protein(obg), phenylalanine biosynthesis associated protein (pheB),












andmonofunctional prephenate dehydratase (pheA) genes, complete cds.


Contig334D
5078786_c2_182
846
3683
189
63


Contig334D
5100002_c1_155
847
3684
285
95
268
2.50E−23

Bacillus subtilis

d1013149
rpsUYqeXBacillus subtilis DNA, 283 Kb region containing skin












element.alternate gene name


Contig334D
5115876_f1_4
848
3685
270
90


Contig334D
5136062_c2_197
849
3686
825
275
543
1.80E−52

Bacillus subtilis

P54374
aroDaroDBacillus subtilis DNA, 283 Kb region containing skin element.


Contig334D
5269011_c2_192
850
3687
1014
338
491
5.70E−47

Pyrococcus

d1028099
PHAF014331aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA, 886755-916062 nt position, clonesimilar to Swiss_Prot


Contig334D
5875257_c2_205
851
3688
1158
386
1741
2.00E−179

Staphylococcus

P45555
DNAJHSP40Staphylococcus aureus genes for ORF37; HSP20; HSP70;











aureus


HSP40; ORF35, complete cds.


Contig334D
6041018_c2_177
852
3689
2301
767
1547
7.20E−159

Bacillus subtilis

e1184013
secFprotein-export membrane proteinBacillus subtilis complete genome












(section 15 of 21)


Contig334D
6048177_c2_202
853
3690
1176
392
948
2.10E−95

Bacillus subtilis

d1013140
hemNYqeRBacillus subtilis DNA, 283 Kb region containing skin












element.alternate gene name


Contig334D
6058468_c2_212
854
3691
417
139
332
4.10E−30

Bacillus subtilis

P19079
cddCddBacillus subtilis DNA, 283 Kb region containing skin element.


Contig334D
6719077_c3_260
855
3692
558
186
700
4.10E−69

Bacillus subtilis

P49778
efpYqhUBacillus subtilis DNA 283 Kb region containing skin element.alternate












gene name


Contig334D
6759838_f1_24
856
3693
264
68
160
6.80E−12

Bacillus subtilis

d1013135
rpsTYqeOBacillus subtilis DNA, 283 Kb region containing skin element.alternate












gene name


Contig334D
6925012_c3_227
857
3694
1320
440
1527
9.50E−157

Bacillus subtilis

P20964
obgGTP-binding proteinBacillus subtilis sporulation protein (spoOB), GTP-












binding protein (obg), phenylalanine biosynthesis associated protein (pheB),












andmonofunctional prephenate dehydratase (pheA) genes, complete












cds.spo0B 3′-region GTP-binding proteinTh


Contig334D
7273457_c3_252
858
3695
570
190
299
1.30E−26

Streptococcus

d1029655

Streptococcus mutans gene for glucose-1-phosphateuridylyltransferase, complete












mutans


cds.hypothetical protein


Contig334D
812817_c1_148
859
3696
612
204
367
7.90E−34

Bacillus subtilis

P54456
yqeKYqeKBacillus subtilis DNA, 283 Kb region containing skin












element.similar to hypothetical proteins


Contig334D
820452_c1_171
860
3697
270
90
105
1.20E−05

Staphylococcus

g1022725
unknownStaphylococcus haemolyticus IS1272 ORF1 and ORF2 genes,











haemolyticus


completecds.ORF2


Contig336D
12690706_f1_1
861
3698
231
77


Contig336D
14552215_f1_2
862
3699
192
64


Contig336D
14901578_f1_5
863
3700
463
154
323
3.60E−29

Bacillus subtilis

d1020044
ydbOconserved hypothetical protein ydbOBacillus subtilis genome sequence,












148 kb sequence of the regionbetween 35 and 47 degree.FUNCTION












UNKNOWN, SIMILAR PRODUCT IN B. SUBTILIS


Contig336D
20413202_c3_14
864
3701
1152
384
961
9.00E−97

Escherichia coli

P23524
yhaDhypothetical 42.1 kD protein in mpB-sohAEscherichia coli K-12












MG1655 section 284 of 400 of the completegenome.f408; 100 pct identical












amino acid sequence and


Gontig336D
23600412_c2_12
865
3702
1242
414
546
8.50E−53

Bacillus subtilis

d1020154
ydgKbicyclomycin resistance protein homolog ydgKBacillus subtilis genome












sequence, 148 kb sequence of the regionbetween 35 and 47












degree.SIMILAR TO BICYCLOMYCIN RESISTANCE PROTEIN.


Contig336D
34585317_f3_8
866
3703
1491
497


Contig336D
4098518_c3_15
867
3704
711
237
121
4.90E−08

Plasmodium

P04931
Ag319asparagine-rich proteinPlasmodium falciparum











falciparum


asparagine-rich protein (ARP), partial cds.


Contig336D
4392767_f2_6
868
3705
435
145
145
2.70E−10

Actinobacillus

d1020420

Actinobacillus actinomycelemcomitans DNA for glycosyltransferase, lytic












actinomycetem-


transglycosylate, dTDP-4-rhamnose reductase, complete cds.unnamed protein











comitans


product


Contig337D
1180328_c3_35
869
3706
836
272
372
2.30E−34

Bacillus subtilis

g2293147
tyxMYtxMBacillus subtilis rrnB-dnaB genomic region.similarity with 2-












hydroxy-6-oxo-2,4-heptadienoate


Contig337D
11924012_c1_25
870
3707
225
75


Contig337D
13848387_f2_19
871
3708
240
80
131
8.10E−09

Syncchocystis sp.

d1011491
clpPhypothetical proteinSynechocystis sp. PCC6803 complete genome, 25/27












3138604-3270709.ORF_ID


Contig337D
16683437_c1_1
872
3709
1023
341
571
1.90E.55

Bacillus subtilis

e1184942
ykrPconserved hypothetical protein ykrPBacillus subtilis complete genomes












(section 8 of 21) similar to hypothetical proteins


Contig337D
20739037_c1_28
873
3710
426
142
690
4.70E−68

Staphylococcus

g2267243
putative transcriptional regulator AtlRStaphylococcus epidermidis











epidermidis


autolysin AtlE and putativetranscriptional regulator AtlR












genes, complete cds.


Contig337D
23524191_c1_24
874
3711
540
380
529
5.40E−51

Staphylococcus

g1022725
unknownStaphylococcus haemolyticus IS1272 ORF1 and ORF2 genes,











haemolyticus


completecds.ORF2


Contig337D
22703588_f2_16
875
3712
954
318
803
5.00E−80

Bacillus subtilis

P39582
ipa-6dhypothetical proteinB.subtilis genomic region (325 to 333).alternative












gene name


Contig337D
123625637_c2_30
876
3713
183
61


Contig337D
24072175_f3_20
877
3714
780
260
1321
6.40E−135

Staphylococcus

g2267239

Staphylococcus epidermidis autolysin AtlE and putativetranscriptional












epidermidis


regulator AtlR genes, complete cds.ORF1


Contig337D
24105342_c1_27
878
3715
831
277
1242
1.50E−126

Bacillus subtilis

g2293148
menBdihydroxynaphthoate synthaseBacillus subtilis rmB-dnaB












genomic region.


Contig337D
24416702_f2_9
879
3716
4008
1336
7001
0

Staphylococcus

g2267242
autolysin AtlEStaphylococcus epidermidis autolysin AtlE and











epidermidis


putativetranscriptional regulator AtlR genes, complete cds.primary attachment












to a polystyrene surface


Contig337D
26775637_c1_26
880
3717
1389
463
599
2.10E−58

Bacillus subtilis

P23973
menFisochorismate synthaseBacillus subtilis rmB-dnaB genomic regioin.based












on similarity to E. coli EntC, A. hydrophila


Contig337D
33710968_12_8
881
3718
453
151
742
1.40E−73

Staphylococcus

g2267241

Staphylococcus epidermidis autolysin AtlE and putativetranscriptional












epidermidis


regulator AltR genes, complete cds.ORF3


Contig337D
3394540_f2_17
882
3719
312
104


Contig337D
4181312_c2_31
883
3720
606
202


Contig337D
5115927_c2_32
884
3721
1680
560
340
1.10E−59

Synechocystis sp.

d1011017
menD2-succinyl-6-hydroxy-2, Synechocystis sp. PCC6803 complete












genome, 21/27, 2644795-2755702.ORF_ID


Contig337D
6688757_f2_7
885
3722
507
169
823
3.80E−82

Staphylococcus

g2267240

Staphylococcus epidermidis autolysin AtlE and putativetranscriptional












epidermidis


regulator AtlR genes, complete cds.ORF2


Contig337D
978436_f2_10
886
3723
1188
396
875
1.20E−87

Bacillus subtilis

C33496
hisC homolog


Contig338D
12142768_c3_17
887
3724
300
100
110
3.S0E−06

Pyrococcus

d1027343
PHBW016235aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA, 180023-216005 nt position, clone


Contig338D
12531558_c2_13
888
3725
351
117


Contig338D
14849093_f1_1
889
3726
294
98
127
2.10E−08
Mitochondrion
e138028
putative orf79.1C.crispus complete mitochondrial genome.unique orf











Chondrus crispus



Contig338D
23870801_f1_2
890
3727
240
80


Contig338D
30265640_f1_5
891
3728
1080
360
485
2.50E−46

Treponema

g1354775
pfoS/RpfoS/RTreponema pallidum methyl-accepting chemotaxis protein











pallidum


(mep-1)gene, complete cds, and potential regulatory molecule (pfoS/R) gene,












partial cds.potential regulatory molecule; pFoS/R-like


Contig338D
32680_f1_4
892
3729
936
312
776
3.60E−77

Staphylococcus

P04188
glutamyl endopeptidase, precursorStaphylococcus aureus V8











aureus


serine protease gene.staphylococcal serine proteinasepreproenzyme (AA −68












to 268)


Contig338D
3361326_f3_6
893
3730
207
69


Contig339D
10605337_c2_54
894
3731
747
249
706
9.50E−70

Bacillus subtilis

P39456
ORF3putative ATP binding subunitB.subtilis putative amino acid












transporter gene.inner membrane protein malKpotential ABC-transport system


Contig339D
1207938_c3_64
895
3732
828
276
250
2.00E−21

Bacillus subtilis

g1934611
yrhGformate dehydrogenaseBacillus subtilis cysteine synthase (yrhA),












cystathioninegamma-lysase (yrhB), YrhC (yrhC), YrhD (yrhD), formate












dehydrogenasechain A (yrhE), YrhF (yrhF), formate dehydrogenase (yrhG),












YrhH (yrhH), regulatory protein (yrhI), cytochro


Contig339D
13843910_c1_50
896
3733
216
72
258
3.20E−22

Staphylococcus

g2529402
narTnitrate transporterStaphylococcus carnosus nitrate transporter (narT) gene,











carnosus


completecds.NarT


Contig339D
14454083_f2_14
897
3734
471
157
259
2.20E−22

Bacillus subtilis

e1181515
ykmAYkmABacillus subtilis 168 56 kb DNA fragment between xlyA and












ykoR.simimlar to hypothetical proteins


Contig339D
15711457_f3_28
898
3735
201
67


Contig339D
164715_c3_66
899
3736
951
317
424
3.00E−42

Bacillus subtilis

P42437
nasBES-adenosyl-L-methionineBacillus subtilis DNA around narB region (nasB












operon and nasAgene).alternate gene name


Contig339D
20524067_c1_41
900
3737
639
213
231
2.00E−19

Bacillus subtilis

e1186036
yvgVconserved hypothetical protein yvgVBacillus subtilis complete genome












(section 18 of 21) similar to hypothetical proteins


Contig339D
22299205_c3_60
901
3738
312
104
152
1.20E−10

Bacillus subtilis

d1020044
ydbOconserved hypothetical protein ydbOBacillus subtilis genome sequence,












148 kb sequence of the regionbetween 35 and 47 degree.FUNCTION












UNKNOWN, SIMILAR PRODUCT IN B. SUBTILIS


Contig339D
22345265_f1_9
902
3739
189
63


Contig339D
24250177_c1_47
903
3740
714
238
159
8.70E−12

Bacillus subtilis

P42178
narJRespitory nitrate reductaseB.subtilis narGHJI












genes.gamma subunit


Contig339D
24353392_c2_57
904
3741
2409
803
2267
3.60E−235

Bacillus subtilis

P42435
nasBCsubunit of nitrite reductaseBacillus subtilis DNA around












narB region (nasB operon and nasAgene).alternate gene name


Contig339D
24416068_c1_43
905
3742
549
183
528
6.90E−51

Bacillus subtilis

g2293246
ytmlYtmlBacillus subtilis rrnB-dnaB genomic region.similar to a hypothetical












19 kD protein from B.


Contig339D
24648377_c3_71
906
3743
1146
382
1301
8.40E−133

Staphylococcus

g2529402
narTnitrate transporterStaphylococcus carnosus nitrate transporter (narT) gene,











carnosus


completecds.NarT


Contig339D
24855337_c2_59
907
3744
693
231
577
4.40E−56

Bacillus subtilis

P42177
narlnitrate reductase gamma subunitB.subtilis nar[G,H,I,J,K


Contig339D
29532827_f2_21
908
3745
243
81


Contig339D
3007827_c2_53
909
3746
789
263
605
4.80E−59

Bacillus subtilis

e1182313
yckKhomologue of glutamine-binding periplasmicBacillus subtilis complete












genome (section 2 of 21) similar to glutamine ABC transporter


Contig339D
34033563_c1_46
910
3747
327
109
261
1.40E−22

Bacillus subtilis

P42436
nasBDsubunit of nitrate reductaseBacillus subtilis DNA around












narB region (nasB operon and nasAgene).alternate gene name


Contig339D
34194002_c2_52
911
3748
711
237
657
1.50E−64

Zymomonas

P30798
pgrmphosphoglyceromutaseZymomonas mobilis phosphoglyceromutase (pgm)











mobilis


gene, complete cds, and 2-hydroxyacid dehydrogenase homologue (ddh) gene, 5′












end.phosphoglycerate mutase


Contig339D
34385012_f2_18
912
3749
1362
454
364
4.90E−40

Methanosarcina

e212291
orf4hypothetical protein 4M.barkeri fmdE, fmdF, fmdA, fmdC, fmdD, fmdB,











barkeri


orf4, orf3, orf2, andorf1 genes.


Contig339D
34430428_c2_56
913
3750
375
125


Contig339D
4069643_c3_63
914
3751
480
160


Contig339D
4100453_c3_70
915
3752
1044
348
329
8.40E−30

Bacillus brevis

P54663
degSprotein kinaseBacillus brevis protein kinase (degS) gene, complete












cds; transcriptional activator protein (degU) gene, complete cds.regulatory












protein degSputative


Contig339D
4720317_f2_20
916
3753
1257
419
1460
1.20E−149

Staphylococcusg

2072412
liflysostaphin immunity factorStaphylococcus simulans











simulans


lysostaphin (lss and lysostaphin immunityfactor (lif) genes, complete cds,












insertion seqence IS1293, complete sequence, and IS257-1 reansposase (tnp-












1) gene, completecds.similar to FcmA and FcmB of St


Contig339D
4737550_c3_65
917
3754
759
253
187
9.40E−15

Bacillus subtilis

e332188
ylnEYlnE proteinBacillus subtilis pyrE to YloA gene region.similar to












hypothetical proteins


Contig339D
4777217_c3_68
918
3755
1569
523
1883
1.80E−194

Bacillus subtilis

P42176
narHnitrate reductase beta subunitB.subtilis nar[G,H,I,J,K


Contig339D
4980378_c1_49
919
3756
537
179
328
1.10E−29

Bacillus subtilis

P13800
degUtranscriptional regulator of degradationB.subtilis icp gene encoding












a protease production enhancerprotein complete cds. and SacU enhancer protein












gene, 3′ end.regulatory protein comAiep protein


Contig339D
595260_c2_58
920
3757
3780
1260
4084
0

Bacillus subtilis

P42175
narGRespiratort nitrate reductaseB.subtilis narGHJI genes.alpha












subunit


Contig339D
6132893_c3_69
921
3758
462
154


Contig339D
7039051_c3_61
922
3759
750
250
585
6.30E−57

Bacillus subtilis

P42200
ORF2putative membrane spanning subunitB.subtilis putative amino acid












transporter gene.potential ABC-transport system


Contig339D
995300_f1_10
923
3760
204
68


Contig340D
10548383_f1_1
924
3761
237
79


Contig340D
1209417_c3_85
925
3762
1704
568
797
2.20E−79

Bacillus subtilis

P23545
phoRsignal transduction protein kinaseBacillus subtilis rrnB-dnaB












genomic region.


Contig340D
13001537_f3_53
926
3763
249
83


Contig340D
13722338_c3_78
927
3764
507
169
505
1.90E−48

Bacillus subtilis

g2293238
ytglYtglBacillus subtilis rrnB-dnaB genomic region.similarity to tagD












protein from V.cholerae


Contig340D
13723318_c3_80
928
3765
1149
383
1215
1.10E−123

Bacillus

P17557
alanine dehydrogenase, B.stearothermiphilus











stearothermophilus


alanine dehydrogenase gene complete cds.alanine dehydrogenasealanine












dehydrogenase (EC 1.4.1.1)


Contig340D
14877316_f1_19
929
3766
378
126
311
6.80E−28

Escherichia coli

d1016364
YKL069W, YKL340hypothetical protein b1832E.coli genomic DNA, Kohara












clone #335 (40.9-41.3 min.).ORF_ID


Contig340D
19770437_c2_69
930
3767
1332
444
1018
8.20E−103

Bacillus subtilis

g2293258
ytolYtolBacillus subtilis rrnB-dnaB genomic region.similarity with












hypothetical protein 3 from


Contig340D
20901713_c3_76
931
3768
1707
569
613
6.80E−60

Bacillus subtilis

g2293228
ytwPYtwPBacillus subtilis rrnB-dnaB genomic region.similarity to fcrA protein












precursor from


Contig340D
2115812_f2_38
932
3769
1113
371
843
2.90E−84

Bacillus subtilis

e1184976
ykvYXaa-Pro dipeptidase homolog ykvYBacillus subtilis complete genome












(section 8 of 21) similar to Xaa-Pro dipeptidase


Contig340D
21491462_c1_63
933
3770
1161
387
1188
7.90E−121

Bacillus subtilis

g2293267
citZcitrate synthase subunit llBacillus subtilis rrnB-dnaB genomic












region.alternate gene name


Contig340D
2189718_f3_46
934
3771
1371
457
1309
1.20E−133

Escherichia coli

P39312
cycAd-serine/d-alanine/glycine trransporterEscherichia coli K-12












MG1655 section 382 of 400 of the completegenome.o470; 100 pct identical












amino acid sequence and


Contig340D
22277327_c3_91
935
3772
1371
457
496
1.70E−47

Bacillus subtilis

P07908
dnaBDnaBBacillus subtilis rrnB-dnaB genomic region. The part of the protein












encoded by 634-693 binds to


Contig340D
23485443_c1_54
936
3773
1239
413
931
1.40E−93

Bacillus subtilis

g2293230
ytbJYtbJBacillus subtilis rrnB-dnaB genomic region.similar to hypothetical












protein MG372 from M.


Contig340D
23489090_c2_72
937
3774
1038
346
1033
2.10E−104

Bacillus subtilis

g2293264
pfk6-phosphofructokinase Bacillus subtilis rrnB-dnaB genomic region.


Contig340D
23555302_f2_40
938
3775
387
129


Contig340D
23603375_f2_37
939
3776
417
139
139
1.10E−09

Methanococcus

Q57997
MJ0577conserved hypothetical proteinMethanococcus jannaschii section











jannaschii


48 of 150 of the complete genome.hypothetical protein b0607similar to SP


Contig340D
23651567_c3_87
940
3777
888
296
387
4.30E−41

Thermus

d1025814
mutMThermus thermophilus MutM gene, complete cds.











thermophilus



Contig340D
24017890_c2_75
941
3778
1428
476
1242
1.50E−126

Escherichia coli

g1788480
lysPlysine-specific permeaseEscherichia coli K-12 MG1655 section 195 of 400 of












the completegenome.arginine permeasef489; 100 pct identical to












LYSP_ECOLI SW


Contig340D
24407577_c1_65
942
3779
738
246
833
3.30E−83

Bacillus subtilis

P13792
phoPB.subtilis phoP gene.


Contig340D
24407765_c1_55
943
3780
795
265
413
1.10E−38
Pseudomonas
P29942
hypothetical protein 9P.denitrificans cobN, cobO, cobP, cobQ, cobW, and











denitrificans’


ORF6-9 genes, complete cds.ORF9


Contig340D
24508552_c3_92
944
3781
1953
651
2471
8.80E−257

Bacillus subtilis

P18255
thrSthreonine tRNA synthetaseBacillus subtilis rrnB-dnaB genomic












region.threonine--tRNA ligase (thrSv) (EC 6.1.1.3)


Contig340D
24662915_c3_86
945
3782
2718
906
2572
1.70E−267

Bacillus subtilis

g2293272
polADNA-polymerase IBacillus subtilis rrnB-dnaB genomic region.


Contig340D
24726077_c3_89
946
3783
1026
342
1088
3.10E−110

Bacillus subtilis

g2293277
gapBglyceraldehyde-3-P-dehydrogenaseBacillus subtilis rrnB-












dnaB genomic region.


Contig340D
25398425_c2_67
947
3784
1167
389
731
2.10E−72

Bacillus subtilis

g2293229
nifS2NifS2Bacillus subtilis rrnB-dnaB genomic region.similar to R.sphaeroides












nitrogenase stabilizer


Contig340D
25667217_c3_88
948
3785
627
209
405
7.50E−38

Bacillus subtilis

g2293275
ytaGYtaGBacillus subtilis rrnB-dnaB genomic region.similar to hypothetical












protein H10890 from H.


Contig340D
26181551_c2_71
949
3786
948
316
1016
1.30E−102

Bacillus subtilis

g2293263
accAacetyl-CoA carboxylase subunitBacillus subtilis rrnB-dnaB












genomic region.


Contig340D
26188891_f1_7
950
3787
210
70


Contig340D
3140917_c3_83
951
3788
189
63


Contig340D
33209677_c2_70
952
3789
972
324
764
6.80E−76

Bacillus subtilis

g2293259
ytqlYtqlBacillus subtilis rrnB-dnaB genomic region.similarity to MGPA












protein from M.genitalium


Contig340D
33985077_c1_61
953
3790
1230
410
1529
5.B0E−157

Bacillus subtilis

g2293261
ytsJYtsJBacillus subtilis rrnB-dnaB genomic region.similarity to malate












dehydrogenase (NADP+) from


Contig340D
34177127_c1_62
954
3791
1806
602
1853
2.70E−191

Bacillus.

P51181
PYKPyruvate KinaseBacillus licheniformis gene for pyruvate kinase,











licheniformis


complete cds.pyruvate kinase


Contig340D
34181551_c2_74
955
3792
924
308
618
2.00E−60

Bacillus subtilis

P06567
dnaIDnaIBacillus subtilis rrnB-dnaB genomic region.44K dnaA protein












homologORF 311 (AA 1-311)


Contig340D
35360932_c3_79
956
3793
1278
426
1493
3.80E−153

Bacillus subtilis

P37877
ackAacetate kinaseBacillus subtilis rrnB-dnaB genomic region.acetate kinase


Contig340D
4459380_c1_57
957
3794
207
69


Contig340D
4693800_f2_39
958
3795
570
190
191
3.50E−15

Methanobacterium

g2621993
MTH898conserved proteinMethanobacterium











thermoautotro-



thermoautotrophicum from bases 808939 to 820180 (section 71 of 148) of the












phicum


complete genome.Function Code


Contig340D
5135265_c3_90
959
3796
504
168
434
6.30E−41

Bacillus subtilis

g2293279
ytcGYtcGBacillus subtilis rrnB-dnaB genomic region.similar to hypothetical












protein H10943 from H.


Contig340D
5882753_c3_84
960
3797
273
91


Contig340D
6125262_c2_73
961
3798
192
64


Contig340D
6906300_c2_68
962
3799
1014
338
519
6.20E−50

Bacillus subtilis

g2293239
ytxKYtxKBacillus subtilis rrnB-dnaB genomic region.similarity to












modification metilase Accl


Contig340D
7066588_c1_60
963
3800
320
1068
1849
4.20E−212

Bacillus subtilis

g2293260
dnaEDNA-polymerase III alpha-chainBacillus subtilis rrnB-dnaB












genomic region


Contig340D
7244012_c1_64
964
3801
1287
429
1768
2.70E−182

Bacillus israeli

e320380
isocitrate dehydrogenaseBacillus israeli isocitrate dehydrogenase gene.


Contig340D
803393_c3_81
965
3802
732
244
536
9.80E−52

Archaeoglobus

g2649315
AFI265conserved hypothetical proteinArchaeoglobus fulgidus section











fulgidus


90 of 172 of the complete genome.similar to GB


Contig340D
824086_c3_82
966
3803
882
294
859
5.80E−86

Bacillus subtilis

g2293262
yttlacetyl-CoA carboxylase subunitBacillus subtilis rrnB-dnaB












genomic region.similar to acetyl-CoA carboxylase


Contig341D
125880_f3_28
967
3804
309
103


Contig341D
13678452_c2_47
968
3805
1263
421
438
2.40E−41

Bacillus subtilis

P55340
ecsBhypothetical EcsB proteinB.subtilis ecsA, ecsB, and ecsC genes.alternate












gene name


Contig341D
14656327_c3_55
969
3806
624
208
799
1.30E−79

Staphylococcus

g1916729
cadDCadDStaphylococcus aureus plasmid pRW001, cadnium resistance











aureus


CadD (cadD) gene, complete cds.contains 5 transmembrane domains; confers low












level


Contig341D
16533442_c1_33
970
3807
522
174
546
8.50E−53

Bacillus subtilis

g1381681
cspRCspRBacillus subtilis methylase homolog (cspR) gene, complete












cds.methylase homolog


Contig341D
165908_f1_3
971
3808
507
1169
182
3.20E−14

Bacillus subtilis

P38049
yhgCHypothetical proteinBacillus subtilis penicillin-binding protein (pbpF)












gene, 5′ end.product unknown


Contig341D
19922162_c2_41
972
3809
1161
387
517
1.00E−49

Bacillus subtilis

e1182980
yhcBhypothetical proteinBacillus subtilis complete genome (section 6 of 21)


Contig341D
20706557_c2_43
973
3810
1254
418
592
1.10E−57

Bacillus subtilis

e1182993
yhaOhypothetical proteinBacillus subtilis complete genome (section 6 of












21) similar to hypothetical proteins


Contig341D
21645967_f1_7
974
3811
993
331
363
2.10E−33

Bacillus subtilis

P24327
prsA33kDa lipoproteinB.subtilis prsA gene for a 33kDa lipoprotein.See Swiss












Prot P24327


Contig341D
23694052_f3_27
975
3812
603
201


Contig341D
2380342_c1_36
976
3813
636
212
463
5.30E−44

Bacillus subtilis

e1182922
yhcZhypothetical proteinBacillus subtilis complete genome (section 5 of












21) similar to two-component response regulator [YhcY


Contig341D
24025463_c3_53
977
3814
2952
984
1357
9.80E−139

Staphylococcus

g710421
unknownStaphylococcus aureus cmp-binding-factor 1 (cbf1) and ORF X











aureus


genes, complete cds.ORF X


Contig341D
24120262_c1_32
978
3815
993
331
451
1.00E−42

Bacillus subtilis

P54536
yqiYYqiYBacillus subtilis DNA, 283 Kb region containing skin element.similar to












amino acid ABC transporter (permease)


Contig341D
24296943_f1_15
979
3816
261
87
93
8.60E−05

Pyrococcus

d1027256
PHBN033139a long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA, 85072-124749 nt position, clone


Contig341D
24490702_c3_51
980
3817
405
135


Contig341D
24744077_c1_34
981
3818
183
61


Contig341D
2538252_c3_56
982
3819
981
327
988
1.20E−99

Bacillus subtilis

P32396
hcmHferrochclataseBacillus subtilis penicillin binding protein 1A (ponA)












gene; uroporphyrinogen decarboxylase (hemE) gene; ferrochelatase (hemH) gene












complete cds, (hemY) gene, complete cds; ORFA, complete cds; ORFB 5′












end.alternate gene name


Contig341D
30114637_c2_39
983
3820
1167
389
1177
1.20E−119

Bacillus subtilis

e1182880
yhbAhypothetical 48.5 kd proteinBacillus subtilis complete genome












(section 5 of 21) alternate gene name


Contig341D
33647577_c1_35
984
3821
1386
462
1586
5.30E−163

Bacillus subtilis

e1249821
citGfumarase protein, CitGBacillus subtilis 42.7 kB DNA fragment from












yvsA to yvqA.


Contig341D
33831512_f3_30
985
3822
234
78


Contig341D
34272752_c2_94
986
3823
963
321
1413
1.10E−144

Staphylococcus

g710422
cbflcmp-binding-factor IStaphylococcus aureus cmp-binding-factor 1 (cbf1) and











aureus


ORF X genes, complete cds.


Contig341D
34617017_c2_46
987
3824
696
232
708
5.80E−70

Bacillus subtilis

P55339
ecsAputative ATP-binding protein of ABC-typeB.subtilis ccsA, ccsB, and












ccsC genes.alternate gene name


Contig341D
3906642_c2_50
988
3825
600
200
244
8.60E−21

Bacillus subtilis

d1020114
ydeNhypothetical protein ydeNBacillus subtilis genome sequence, 148 kb












sequence of the regionbetween 35 and 47 degree.FUNCTION UNKNOWN.


Contig341D
4073892_c2_49
989
3826
1458
486
1083
1.10E−109

Bacillus subtilis

P32397
hemYprotoporphyrinogen IX and coproporphyrinogen IIIBacillus subtilis












penicillin binding protein 1A (ponA) gene; uroporphyrinogen decarboxylase












(hemE) gene; ferrochelatase (hemH) gene complete cds, (hemY) gene, complete












cds; ORFA, complete cds; ORFB 5′ end.a


Contig341D
4173427_c1_37
990
3827
474
158


Contig341D
4345967_f3_25
991
3828
441
147
368
6.20E−34

Bacillus subtilis

e1183005
hitHit-like proteinBacillus subtilis complete genome (section 6 of












21) alternate gene name


Contig341D
4568761_c2_48
992
3829
1116
372
1257
3.90E−128

Bacillus subtilis

P32395
hemEuroporphrynogen decarboxylaseBacillus subtilis penicillin












binding protein 1A (ponA) gene; uroporphyrinogen decarboxylase












(hemE) gene; ferrochelatase (hemH) gene complete cds, (hemY) gene, complete












cds; ORFA, complete cds; ORFB 5′ cnd.see Swiss Prot P323


Contig341D
4876718_c3_52
993
3830
1143
381
810
9.00E−81

Bacillus subtilis

e1182921
yhcYhypothetical proteinBacillus subtilis complete genome (section 5 of












21) similar to two-component sensor histidine kinase


Contig341D
4882963_f1_10
994
3831
834
278
457
2.30E−43

Bacillus subtilis

P54604
yhcThypothetical proteinB.subtilis chromosomal DNA (region 75












degreesSimilarity to DRAP deaminase from Saccharomyces


Contig341D
5132078_c2_38
995
3832
729
243
752
1.30E−74

Archacoglobus

g2649950
AF0680glutamine ABC transporter, ATP binding proteinArchaeoglobus fulgidus











fulgidus


section 49 of 172 of the complete genome.similar to GB


Contig341D
6689717_c2_40
996
3833
615
205


Contig341D
6929651_c2_42
997
3834
366
122
289
1.50E−25

Bacillus subtilis

e1182981
yhcAhypothetical proteinBacillus subtilis complete genome (section 6 of 21)


Contig341D
817555_f3_26
998
3835
447
149


Contig342D
10193763_c1_46
999
3836
186
62


Contig342D
10360902_f1_6
1000
3837
183
61


Contig342D
1063753_c1_50
1001
3838
1374
458
2070
2.70E−214

Staphylococcus

g2271510
murDUDP-N-acetylmuramoyl-L-alanine Staphylococcus aureus UDP-N-











aureus


acetylmuramoyl-L-alanine MurD


Contig342D
11806512_f1_17
1002
3839
207
69


Contig342D
1209682_c1_41
1003
3840
2409
803
1984
3.50E−205

Bacillus subtilis

e1184112
pheTphenylalanyl-tRNA synthetase (beta subunit) Bacillus subtilis complete












genome (section 15 of 21) phenylalanyl-tRNA synthetase beta subunit


Contig342D
14644066_c1_47
1004
3841
189
63


Contig342D
14664012_f3_34
1005
3842
468
156
341
4.50E−31

Bacillus subtilis

e334785
ylbPYlbP proteinBacillus subtilis genomic DNA 23.9 kB fragment.


Contig342D
19957802_c3_73
1006
3843
1896
632
1972
6.60E−204

Bacillus subtilis

P14951
uvrBdeoxyribodipyrimidine photolyaseBacillus subtilis thioredoxin












(trx), uvrB and aspartokinase llgenes, complete cds.excinuclease ABC, chain












Calternate gene name


Contig342D
20502217_c2_64
1007
3844
1626
542
718
5.10E−71

Bacillus subtilis

e1185102
yliAhypothetical protein yllABacillus subtilis complete genome (section 8 of 21)


Contig342D
211677_c2_63
1008
3845
702
234
436
3.90E−41

Bacillus subtilis

e1182712
yfnBYfnBBacillus subtilis complete genome (section 4 of 21) similar to












hypothetical proteins


Contig342D
21656327_c3_78
1009
3846
936
1312
1464
4.50E−150

Staphylococcus

g2149891
yllCunknownStaphylococcus aureus strain ATCC 8325-4 cell wall/cell











aureus


divisionsgene cluster, yllB, yllC, yllD, pbpA, mraY, murD, div1B, ftsA andftsZ












genes, complete cds.


Contig342D
22542567_c1_40
1010
3847
759
253
562
1.70E−54

Bacillus subtilis

e1184114
ysgAhypothetical proteinBacillus subtilis complete genome (section 15 of












21) similar to rRNA methylase


Contig342D
23438887_c3_71
1011
3848
300
100
196
1.00E−15

Bacillus subtilis

e1184110
yshAhypothetical proteinBacillus subtilis complete genome (section 15 of












21) unknown function; putative


Contig342D
23572178_c1_43
1012
3849
846
282
1070
2.50E−108

Bacillus subtilis

g143527
sdhBsuccinate dehydrogenase (iron-sulfur protein) B.subtilis succinate












dehydrogenase complex encoding cyclochromeb-558 subunit, complete cds,












and flavoprotein subunit. 5′ end.iron-sulfur protein


Contig342D
24025467_c1_45
1013
3850
522
174
238
3.70E−20

Bacillus subtilis

P94559
ysnBhypothetical proteinBacillus subtilis complete genome (section 15 of












21) similar to hypothetical protein


Contig342D
24245437_c3_80
1014
3851
1005
335
1471
8.10E−151

Staphylococcus

d1023423
mraYMRAYStaphylococcus aureus genes for penicillin-binding protein 1,











aureus


MraY, MurD, partial and complete cds.


Contig342D
24330337_f1_15
1015
3852
957
319
555
9.50E−54

Bacillus subtilis

e1184111
ysgBhypothetical proteinBacillus subtilis complete genome (section 15 of












21) similar to hypothetical proteins


Contig342D
24642817_c1_44
1016
3853
810
270
1197
8.80E−122

Staphylococcus

P52974
dgaglutamate racemaseStaphylococcus haemolyticus Y176 glutamate racemase











haemolyticus


(dga) gene, complete cds.


Contig342D
25425202_c3_72
1017
3854
522
174
196
1.00E−15

Bacillus subtilis

e1184109
yshBhypothetical proteinBacillus subtilis complete genome (section 15 of












21) unknown function; putative


Contig342D
25475250_c2_61
1018
3855
1827
609
2503
3.60E−260

Bacillus subtilis

A27763
sdhAsuccinate dehydrogenase, flavoproteinfumarate reductase












flavoprotein


Contig342D
26597077_c1_51
1019
3856
1398
466
1113
7.00E−113

Staphylococcus

g2149896
div1Bcell division proteinStaphylococcus aureus strain











aureus


ATCC 8325-4 cell wall/cell divisiongene cluster, yllB, yllC, yllD, pdpA, mraY,












murD, div1B, flsA and flsZ genes, complete cds.


Contig342D
33651636_c2_58
1020
3857
1776
592
1528
7.40E−157

Bacillus subtilis

e1184108
yshChypothetical proteinBacillus subtilis complete genome (section 15 of












21) similar to DNA polymerase beta


Contig342D
34644125_c1_52
1021
3858
1170
390
1559
3.90E−160

Staphylococcus

g2149897
ftsAcell division proteinStaphylococcus aureus strain ATCC 8325-4 cell wall/cell











aureus


divisiongene cluster, yllB, yllC, yllD, pbpA, mraY, murD, div1B, ftsA and ftsZ












genes, complete cds.


Contig342D
34646937_c2_60
1022
3859
336
112
334
2.S0E−30

Bacillus subtilis

g142520
trxthioredoxinBacillus subtilis thioredoxin (trx), uvrB and aspartokinase












IIgenes, complete cds.thioredoxinputative


Contig342D
36147150_c3_75
1023
3860
609
203
492
4.50E−47

Bacillus subtilis

e1184085
ysnAhypothetical proteinBacillus subtilis complete genome (section 15 of












21) similar to hypothetical proteins


Contig342D
36520302_c1_48
1024
3861
189
63
250
2.00E−2l

Staphylococcus

O07319
yllBunknownStaphylococcus aureus strain ATCC 8325-4 cell wall/cell











aureus


divisiongene cluster, yllB, yllC, yllD, pbpA, mraY, murD, div1B, flsA andflsZ












genes, complete cds.


Contig342D
4067342_c2_57
1025
3862
1086
362
1267
3.40E−129

Bacillus subtilis

P17921
pheSphenylalanyl-tRNA synthetase (alpha subunit) Bacillus subtilis complete












genome (section 15 of 21) phenylalanyl-tRNA synthetase beta subunit


Contig342D
4306562_c3_77
1026
3863
306
102
469
1.20E−44

Staphylococcus

O07319
yllBunknownStaphylococcus aureus strain ATCC 8325-4 cell wall/cell











aureus


divisiongene cluster, yllB, yllC, yllD, pbpA, mraY, murD, div1B, flsA andflsZ












genes, complete cds.


Contig342D
4330275_c2_53
1027
3864
297
99
94
6.70E−05
Human
P06460
E5A proteinGenital human papillomavirus type 6b










papillomavirus

(HPV6b).papillomavirus E5 proteinopen reading frame E5a


Contig342D
4457788_c2_39
1028
3865
1716
572
266
7.40E−20

Plasmodium

g535260
STARP antigenP.reichenowi STARP gene for STARP antigen.











reichenowi



Contig342D
4532967_c2_59
1029
3866
2358
786
1882
2.30E−194

Bacillus subtilis

e1184107
yshDhypothetical proteinBacillus subtilis complete genome (section 15 of












21) similar to DNA mismatch repair protein


Contig342D
4696068_c3_69
1030
3867
186
62
237
4.70E−20

BACILLUS

P07840
RPMFribosomal protein BL3750S RIBOSOMAL PROTEIN L32











STEAROTHERMO-


(RIBOSOMAL PROTEIN 1) (BL37) Bacillus stearothermophilus











PHILUS


ribosomal protein BL37


Contig342D
4725415_c1_49
1031
3868
2337
779
3205
0

Staphylococcus

d1023422
pbpApenicillin-binding protein IStaphylococcus aureus genes for











aureus


penicillin-binding protein 1, MraY, MurD, partial and complete cds.


Contig342D
6131693_c3_79
1032
3869
414
138
574
9.20E−56

Staphylococcus

d1023421
yllDcell division proteinStaphylococcus aureus genes for penicillin-binding











aureus


protein 1, MraY, MurD, partial and complete cds.unnamed protein product


Contig342D
968811_c3_74
1033
3870
651
217
599
2.10E−58

Bacillus subtilis

P08064
sdhCsuccinate dehydrogenase (cytochrome b558B.subtilis succinate












dehydrogenase complex encoding cytochromeb-558 subunit, complete cds,












and flavoprotein subunit, 5′ end,succinate dehydrogenase cytochrome












dehydrogenase cytochrome b558succinate dehydrogenase












cytochrome b-558 subunit


Contig343D
10580443_c2_74
1034
3871
237
79
246
5.30E−21

Escherichia coli

P33014
yeeDhypothetical 8.1 kD protein in sbeB 3′regionE.coli genomic DNA, Kohara












clone #349 (44.6-45.0 min.).ORF_ID


Contig343D
1417338_c3_81
1035
3872
228
76


Contig343D
14493812_c2_71
1036
3873
465
155
289
1.50E−25

Bacillus subtilis

e1182570
ydiBconserved hypothetical protein ydiBBacillus subtilis complete genome












(section 4 of 21) similar to hypothetical proteins


Contig343D
146l637_f1_11
1037
3874
249
83
123
5.70E−08

Bacillus subtilis

P37252
ilvNacetolactate synthase small subunitBacillus subtilis ilvB, ilvN and












ilvC genes, complete ilv-leuoperon.acetolactate synthase












(acetohydroxy-acid synthase)


Contig343D
14849093_c1_45
1038
3875
294
98
127
2.10E−08
Mitochondrion
e138028
putative orf79.1C.crispus complete mitochondrial genome.unique orf











Chondrus crispus



Contig343D
14897837_f3_41
1039
3876
1275
425
1161
3.60E−128

LACTOCOCCUS

Q02145
ILVAprobable theonine dehydratase, DEAMINASE) threonine











LACTIS


dehydratase


Contig343D
16453328_f3_37
1040
3877
339
113
113
1.80E−05
Chloroplast
P12221
5S rRNAhypothetical protein 1068Liverwort Marchantia polymorpha











Marchantia


chloroplast genome DNA.ORF1068











polymorpha



Contig343D
1702_f1_2
1041
3878
522
374


Contig343D
19564128_c3_89
1042
3879
315
305


Contig343D
19564400_c3_92
1043
3880
321
107
113
6.50E−07.
Kinetoplast
g501027

Trypanosoma brucei EATRO 164 kinetoplast (CR4) mRNA, complete












Trypanosoma


cds.ORF2











brucei



Contig343D
20422318_f2_20
1044
3881
417
139
105
3.80E−05

Bacillus subtilis

e1183973
glnHglutamine ABC transporter (glutamine-bindingBacillus subtilis












complete genome (section 14 of 21)


Contig343D
22441907_c1_10
1045
3882
1869
623
1924
8.10E−199

Bacillus subtilis

P51785
ilvDdihydroxy-acid dehydrataseBacillus subtilis (YAC10-9 clone) DNA region












between the serA andkdg loci.51.0% identity with the Escherichia coli


Contig343D
22939705_c2_79
1046
3883
402
334


Contig343D
23478463_f2_31
1047
3884
1755
585
1667
1.40E−171

Bacillus subtilis

c1184080
ilvBacetolactate synthase (acetohydroxy-acidBacillus subtilis complete genome












(section 15 of 21) acetolactate synthase (acetohydroxy-acid synthase)


Contig343D
23626577_c1_62
1048
3885
210
70


Contig343D
23867325_f1_15
1049
3886
570
390
561
2.20E−54

Lactococcus lactis

Q02144
leuDLeuDLactococcus lactis unknown gene, partial cds, and HisC












(hisC), unknown, HisG (hisG), unknown, HisB (hisB), unknown, HisH (hish), HisA












(hisA), HisF (hisF), His1E (his1E), unknown, unknown, LeuA (leiA), LeuB












(leuB), LeuC (leuC), LeuD (leuD), unknown, I


Contig343D
24343813_c2_73
1050
3887
3119
373
1075
7.50E−109

Eseherichia coli

P33015
yeeEhypothetical 38.1 kD protein in sbcB 3′regionE.coli genomic DNA,












Kohara clone #349 (44.6-45.0 min.).ORF_ID


Contig343D
24640625_c3_91
1051
3888
960
320
954
5.00E−96

Staphylococcus

e264641
scrRsucrose repressorS.xylosus scrB and scrR genes.











xylosus



Contig343D
24642202_c3_94
1052
3889
648
216
822
4.80E−82

Staphylococcus

g2689554

Staphylococcus aureus toxic shock syndrome toxin-1 (tst), enterotoxin (ent),












aureus


and integrase (int) genes, complete cds.orf7


Contig343D
24646962_c2_78
1053
3890
210
70


Contig343D
24814812_f2_29
1054
3891
1950
650
1516
1.40E−155

Bacillus subtilis

e1182574
ydiFABC transporter (ATP-binding protein) homolog ydiFBacillus subtilis












complete genome (section 4 of 21) similar to ABC transporter (ATP-












binding protein


Contig343D
24823588_f1_14
1055
3892
1386
462
1633
5.50E−168

Lactococcus lactis

Q02142
leuCLeuCLactococcus lactis unknown gene, partial cds, and HisC












(hisC), unknown. HisG (hisG), unknown, HisB (hisB), unknown, HisH (hish), HisA












(hisA), HisF (hisF), His1E (his1E), unknown, unknown, LeuA (leuA), LeuB












(leuB), LeuC (leuC), LeuD (leuD), unknown, 1


Contig343D
25665687_c1_63
1056
3893
876
292
322
4.70E−29

Staphylococcus

g2689560

Staphylococcus aureus toxic shock syndrome toxin-1 (tst), enterotoxin (ent),












aureus


and integrase (int) genes, complete cds.orf13


Contig343D
25900300_c1_61
1057
3894
312
104
297
2.10E−26

Staphylococcus

g2689561

Staphylococcus aureus toxic shock syndrome toxin-1 (tst), enterotoxin (ent),












aureus


and integrase (int) genes, complete cds.orf14


Contig343D
26615912_c1_56
1058
3895
1479
493
1943
7.80E−201

Staphylococcus

Q05936
scrBbeta-fructofuranosidaseS.xylosus scrB and scrR genes.











xylosus



Contig343D
2866090_f1_1
1059
3896
1254
418
1250
2.10E−127

Staphylococcus

g2689564
intintegraseStaphylococcus aureus toxic shock syndrome toxin-1 (tst), enterotoxin











aureus


(ent), and integrase (int) genes, complete cds.similar to staphylococcal phage












integrase


Contig343D
31680342_f2_21
1060
3897
546
182
173
8.00E−12
Kaposi's sarcoma-
g1633572
Kaposi's sarcoma-associated herpes-like virus ORF73 homolog gene, complete










associated herpes-

cds.Herpesvirus saimiri ORF73 homolog










like virus


Contig343D
3361326_c3_82
1061
3898
207
69


Contig343D
34257878_f1_13
1062
3899
1065
355
894
1.10E−49

Lactococcus lactis

Q02143
leuBLeuBLactococcus lactis unknown gene, partial cds, and HisC












(hisC), unknown, HisG (hisG), unknown, HisB (hisB), unknown, HisH (hish), HisA












(hisA), HisF (hisF), His1E (his1E), unknown, unknown, LeuA (leuA), LeuB












(leuB), LeuC (leuC), LeuD (leuD), unknown, 1


Contig343D
34412750_c1_57
1063
3900
966
322
1031
3.40E−104

Staphylococcus

g46512
hypothetical protein 7S.aureus agrA, agrB and hld genes.orf7











aureus



Contig343D
35428187_c2_80
1064
3901
438
146


Contig343D
35598750_f2_19
1065
3902
849
283
112
3.30E−06

Streptococcus

g2897106
repressorStreptococcus thermophilus bacteriophage lysogeny module,











thermophilus


integrasehomolog (int), putative host cell surface-exposed lipoprotein, putative










bacteriophage TP-

metallo-proteinase, repressor, Cro-like regulatoryprotein, and P1-antirepressor










J34

homolog genes, complete cds.


Contig343D
36132937_c1_8
1066
3903
1641
547
273
8.00E−20

Streptococcus

P10564
hexAmismatch repair proteinS.pneumoniae mismatch repair











pneumoniae


protein (hexA) gene, complete cds.


Contig343D
36206502_c1_51
1067
3904
483
161
340
5.80E−31

Bacillus subtilis

e1182572
ydiDribosomal-protein-alanine N-acetyltransfer homolog ydiDBacillus













subtilis complete genome (section 4 of 21) similar to ribosomal-protein-alanine



Contig343D
36441292_f2_34
1068
3905
210
70
101
3.60E−05

Pyrococcus

d1027343
PHBW016235aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA, 180023-216005 nt position, clone


Contig343D
36601678_c3_33
1069
3906
1728
576


Contig343D
4707506_c3_90
1070
3907
1314
438
1156
2.00E−117

Bacillus subtilis

Q07429
nrgAmembrane-associated proteinBacillus subtilis operon












membrane-associated protein (nrgA). andPII-like protein (nrgB) genes,












complete cds.putative


Contig343D
4958387_c2_72
1071
3908
537
179
305
2.90E−27

Bacillus subtilis

e1182571
ydiCglycoprotein endopeptidase homolog ydiCBacillus subtilis complete












genome (section 4 of 21) similar to glycoprotein endopeptidase


Contig343D
5359438_c3_88
1072
3909
1107
369
1096
4.50E−111

Bacillus subtilis

e1182573
ydiEglycoprotein endopeptidase homolog ydiEBacillus subtilis complete












genome (section 4 of 21) similar to glycoprotein endopeptidase


Contig343D
5909428_c1_55
1073
3910
750
250
568
4.00E−55

Bacillus subtilis

e1182576
ydiHhypothetical protein ydiHBacillus subtilis complete genome (section 4 of












21)


Contig343D
860790_f2_32
1074
3911
1593
531
1391
2.40E−142

Lactococcus lactis

g2565151
leuALeuALactococcus lactis unknown gene, partial cds, and HisC












(hisC), unknown, HisG (hisG), unknown, HisB (hisB), unknown, HisH (hish).HisA












(hisA), HisF), His1E (his1E), unknown, unknown, LeuA (leuA), LeuB












(leuB), LeuC (leuC), LeuD (leuD), unknown, 1


Contig343D
9843800_f3_39
1075
3912
192
64


Contig343D
995451_f1_12
1076
3913
1020
340
1139
1.20E−115

Bacillus subtilis

P37253
ilyCketol-acid reductoisomeraseBacillus subtilis ilvB, ilvN and ilvC genes.












complete ilv-leuoperon.ketol-acid reductoisomerase (acetohydroxy-acid


Contig344D
10410638_c2_202
1077
3914
330
110
267
3.10E−23

Staphylococcus

g1595809
spsAtype-1 signal peptidase SpsAStaphylococcus aureus type-1 signal











aureus


peptidase SpsA (spsA) gene, andtype-I signal peptidase SpsB (spsB) gene,












complete cds.inactive signal peptidase homologue; protein lacks


Contig344D
10646950_c2_238
1078
3915
1221
407
1151
6.60E−117

Bacillus subtilis

g1934606
yrhBcystathionine gamma-lyaseBacillus subtilis cysteine synthase (yrhA),












cystathioninegamma-lyase (yrhB), YrhC (yrhC), YrhD (yrhD), formate












dehydrogenasechain A (yrhE). YrhF (yrhF), formate dehydrogenase (yrhG),












YrhH (yrhH), regulatory protein (yrh1), cyto


Contig344D
10760378_c1_200
1079
3916
210
70


Contig344D
10948587_c2_225
1080
3917
822
274
706
9.50E−70

Bacillus subtilis

e1183364
ykoYtoxic anion resistance protein homolog ykoYBacillus subtilis complete












genome (section 7 of 21) similar to toxic anion resistance protein


Contig344D
11062_f3_152
1081
3918
1128
376
218
1.70E−15

Rhodobacter

g3128293
hypothetical proteinRhodobacter capsulatus strain SB1003, partial











capsulatus


genome.


Contig344D
1171892_f3_142
1082
3919
261
87
110
2.50E−06
Kinetoplast Bodo
g3037018
ND5NADH dehydrogenase subunit 5Bodo saltans NADH dehydrogenase











saltans


subunit 5 (ND5) mRNA, kinetoplastgene encoding kinetoplast protein, partial












cds.partially edited mRNA


Contig344D
1178785_c1_198
1083
3920
939
313
731
2.10E−72

Bacillus subtilis

g1934605
yrhAcysteine synthaseBacillus subtilis cysteine synthase (yrhA),












cystathioninegamma-lyase (yrhB), YrhC (yrhC), YrhD (yrhD), formate












dehydrogenasechain A (yrhE), YrhF (yrhF), formate dehydrogenase (yrhG),












YrhH (yrhH), regulatory protein (yrhl), cytochrome P


Contig344D
11931540_f2_63
1084
3921
825
275
786
3.20E−78

Staphylococcus

e352090
transcriptional regulator from the LysR-typeStaphylococcus xylosus lacR, lacP,











xylosus


lacH genes and 2 ORF's.ORF1


Contig344D
12603166_f2_59
1085
3922
303
101
100
1.60E−05

Pyrococcus

d1027339
PHBW012106aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA, 180023-216005 nt position, clone


Contig344D
126068_f3_122
1086
3923
555
185
119
2.60E−06

Escherichia coli

P05530
MCBGmcbG proteinE. coli genes mcbE, mcbF and mcbG for microcin B17












immunity onwildtype plasmid pMccB17.McbG gene product (AA 1-187)


Contig344D
12681510_f2_100
1087
3924
825
275
702
2.50E−69

Bacillus subtilis

e261990
putative orfYitUB.subtilis nprB gene.similar to hypothetical proteins


Contig344D
12750290_c2_207
1088
3925
1122
374
1233
1.40E−125

Bacillus subtilis

e1183166
oppDoligopeptide ABC transporter (ATP bindingBacillus subtilis complete












genomc (section 7 of 21) alternate gene name


Contig344D
13089052_f2_80
1089
3926
240
80
112
8.30E−07

Staphylococcus

g295834
replication protein REPS.aureus plasmid pOX2000.ORF 154











aureus



Contig344D
13678300_c3_273
1090
3927
1233
411
1393
1.50E−142

Bacillus subtilis

e1182288
yciChomologues to nitrile hydratase regionBacillus subtilis complete genome












(section 2 of 21) similar to hypothetical proteins


Contig344D
14271068_f3_124
1091
3928
261
87


Contig344D
1445930_f1_16
1092
3929
621
207


Contig344D
14460882_c2_230
1093
3930
1695
565
1304
4.00E−133

Staphylococcus

g1022726
unknownStaphylococcus haemolyticus IS1272 ORF1 and ORF2 genes,











haemolyticus


completecds.ORF1


Contig344P
15022153_f3_135
1094
3931
389
63


Contig344D
15900305_f3_115
1095
3932
789
263


Contig344D
16196963_f1_13
1096
3933
392
64


Contig344D
16257665_f3_118
1097
3934
192
64


Contig344D
16283286_c1_197
1098
3935
1359
453
1059
3.70E−107

Bacillus subtilis

e1182948
yhdHhypothetical proteinBacillus subtilis complete genome (section 6 of












21) similar to sodium-dependent transporter


Contig344D
16832562_f3_150
1099
3936
804
268
320
3.70E−36

Bacillus subtilis

e1183175
yjbHhypothetical protein yjbHBacillus subtilis complete genome (section 7 of












21)


Contig344D
187683_c2_218
1100
3937
228
76
256
1.10E−23

Staphylococcus

P20384
B1N3Staphylococcus aureus plasmid p19789 DNA with binR and bin3











aureus


genes, derived from transposon TN552.bin3 product


Contig344D
19547938_c3_261
1101
3938
372
324
224
6.10E−18

LEUCONOSTOC

P11411
ZWFGLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE, (G6PD)











MESENTEROIDES



Contig344D
1960952_c3_249
1102
3939
906
302
575
7.20E−56

Bacillus subtilis

e1183077
yisKYisKBacillus subtilis complete genome (section 6 of 21) similar to 5-oxo












1,2,5-tricarboxilic-3-penten acid


Contig344D
19610442_f3_148
1103
3940
246
82
132
6.30E−09

Bacillus anthracis

g929968

Bacillus anthracis Sterne toxin plasmid pXO1 right inverted repeatelement













(SterneR) bordering the toxin-encoding region, ORFA andtruncated ORFB












genes, complete cds.ORFA; similar to B. anthracis WeyAR element ORFA;


Contig344D
19712762_c3_288
1104
3941
600
200
813
4.30E−81

Bacillus subtilis

P24277
recRrecombination proteinB. subtilis DNA, 180 kilobase region of replication












origin.alternate gene name


Contig344D
19790902_c3_257
1105
3942
813
271
919
2.50E−92

Bacillus subtilis

e1183181
yjbNconserved hypothetical protein yjbNBacillus subtilis complete genome












(section 7 of 21) similar to hypothetical proteins


Contig344D
19960162_c2_236
1106
3943
2631
877
1785
4.30E−184

Bacilius subtilis

e1182118
ybcDhypothetical protein ybcDBacillus subtilis complete genome (section 1 of












21)


Contig344D
20093_c1_190
1107
3944
306
102


Contig344D
20314005_c3_283
1108
3945
4590
1530
4186
0

Bacillus subtilis

e1183503
gltAglutamate synthase (large subunit)Bacillus subtilis complete












genome (section (section 10 of 21)


Contig344D
20517062_c3_252
1109
3946
1002
334
961
9.00E−97

Bacillus subtilis

e1183136
xjaX3-oxoacyl-acyl-carrier protein synthase homolog yjaXBacillus subtilis












complete genome (section 6 of 21) similar to 3-oxoacyl-acyl carrier protein


Contig344D
20602262_c2_245
1110
3947
543
181


Contig344D
20602263_c3_74
1111
3948
1512
504
1414
8.90E−145

Bacillus subtilis

P39755
ndhFNADH dehydrogenase subunit 5Bacillus subtilis NADH dehydrogenase












subunit 5 (ndhF) gene, complete cds.alternate gene name


Contig344D
2125903_f2_88
1112
3949
1239
413
197
5.20E−13

Pyrococcus

d1027783
PHLA010413aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA, 588982-607168 nt position, clone


Contig344D
2142316_f2_76
1113
3950
213
71


Contig344D
21525051_f1_11
1114
3951
309
103


Contig344D
21594202_f1_23
1115
3952
1176
392
591
1.50E−57

Bacillus subtilis

P54166
ypfPcell wall synthesis homolog ypfBacillus subtilis (YAC10-9 clone)












DNA region between the serA andkdg loci.putative


Contig344D
21753125_c3_253
1116
3953
1194
398
664
1.60E−79

Bacillus subtilis

e1181495
dppCDppCBacillus subtilis 168 56 kb DNA fragment between xlyA and












ykoR.alternate gene name


Contig344D
22305342_f2_75
1117
3954
543
181
156
5.20E−10
Kaposi's sarcoma
g1633572
Kaposi's sarcoma-associated herpes-like virus ORF73 homolog gene, complete










associated herpes-

cds.Herpesvirus saimiri ORF73 homolog










like virus


Contig344D
23484678_c2_346
1118
3955
1731
577
1263
9.00E−129

Bacillus subtilis

P09122
dnaHDNA polymerase III subunitB. subtilis DNA, 180 kilobase region of












replication origin.alternate gene name


Contig344D
23556500_f3_116
1119
3956
282
94


Contig344D
23634641_c2_206
1120
3957
1248
416
1475
3.10E−151

Bacillus subtilis

e1183137
yjaY3-oxoacyl-acyl-carrier protein synthase homolog yjaYBacillus subtilis












complete genome (section 6 of 21) similar to 3-oxoacyl-acyl-carrier protein


Contig344D
23678800_c1_172
1121
3958
399
133
395
8.60E−37

Bacillus subtilis

c261991
putative orfYitWB.subtilis nprB gene.similar to hypothetical proteins


Contig344D
23861318_f3_155
1122
3959
210
70


Contig344D
24016916_c3_285
1123
3960
1044
348
396
6.70E−37

Escherichia coli

P33019
yeiHhypothetical 36.9 kD protein in lysP-nfoEscherichia coli K-12 MG1655












section 195 of 400 of the completegenome.o349; 100 pct identical












to YEIH_ECOLI SW


Contig344D
24022191_f1_45
1124
3961
222
74
97
3.20E−05

Bacillus subtilis

e1183130
yjzDhypothetical protein yjzDBacillus subtilis complete genome (section 6 of












21) unnamed protein product


Contig344D
24024142_c3_260
1125
3962
315
105
93
8.60E−05

Bacillus firmus

g2654481
hypothetical 10.1 kDa proteinBacillus firmus hypothetical 34.0 kDa protein,












hypothetical 8.9 kDaprotein, hypothetical 10.1 kDa protein,












hypothetical 21.0 kDaprotein, putative thiosulfate sulfurtransferase, hypothetical












16.1 kDa transcriptional regulator an


Contig344D
24272337_f2_74
1126
3963
432
144


Contig344D
24391885_f2_65
1127
3964
183
61


Contig344D
24409428_c2_227
1128
3965
258
86
357
9.10E−33

Staphylococcus

g1731452
prerecombination proteinStaphylococcus aureus chloramphenicol resistance











aureus


plasmid pKH7, complete sequence.


Contig344D
24412517_c1_181
1129
3966
393
131
213
9.90E−17

Bacillus subtilis

P54547
yqjJYqjJBacillus subtilis DNA, 283 Kb region containing skin element.similar to












glucose-6-phosphate 1-dehydrogenase


Contig344D
24415632_c2_203
1130
3967
579
193
827
1.40E−82

Staphylococcus

g1595810
spsBtype-1 signal peptidase SpsBStaphylococcus aureus type-1 signal











aureus


peptidase SpsA (spsA) gene, andtype-1 signal peptidase SpsB (spsB) gene,












complete cds.signal peptidase, leader peptidase, serine


Contig344D
24646886_c1_185
1131
3968
1557
519
285
3.00E−22

Helicobacter

g2313187
HP01042′, 3p40 -cyclic-nucleotide 2′-phosphodiesteraseHelicobacter pylori











pylori


section 10 of 134 of the complete genome.similar to EGAD


Contig344D
24648412_c2_211
1132
3969
642
214
683
2.60E−67

Bacillus subtilis

e1183180
yjbMGTP pyrophosphokinase homolog yjbMBacillus subtilis complete genome












(section 7 of 21) similar to GTP pyrophosphokinase


Contig344D
24664802_c2_237
1133
3970
747
249
380
3.30E−35

Bacillus subtilis

e1186050
yvaKcarboxylesterase homolog yvaKBacillus subtilis complete genome












(section 18 of 21) similar to carboxylesterase


Contig344D
24804677_c1_187
1134
3971
366
122
117
1.20E−06

Pseudomonas

g2541936
Pseudomonas syringae phaseolotoxin operonORF6; similar to Pseudomonas











syringae



syringae fatty acid



Contig344D
25392826_f1_26
1135
3972
1146
382
557
5.80E−54

Bacillus subtilis

e1184257
yueFconserved hypothetical protein yueFBacillus subtilis complete genome












(section 17 of 21) similar to hypothetical proteins


Contig344D
25429512_c1_184
1136
3973
1392
464
1130
1.10E−114

Bacillus subtilis

e1184940
ykrMNa+-transporting ATP synthase homolog ykrMBacillus subtilis complete












genome (section 8 of 21) similar to Na+-transporting ATP synthase


Contig344D
25586693_c3_287
1137
3974
333
111
374
1.40E−34

Bacillus subtilis

P24281
yaaKunknownB.subtilis DNA, 180 kilobase region of replication












origin.ORF107


Contig344D
256468_c2_242
1138
3975
330
110


Contig344D
26212787_f2_91
1139
3976
612
204
308
1.40E−27

Bacillus subtilis

e1183178
yjbKhypothetical protein yjbKBacillus subtilis complete genome (section 7 of












21)


Contig344D
26377340_c3_256
1140
3977
999
333
208
3.90E−15

Lactococcus lactis

c257629
transcription factorL.lactis ORF, genes homologous to vsf-1 and pepF2 and gene












encodingprotein homologous to methyltransferase.weak homology with












vsf-1 gene (X73635)


Contig344D
26460887_c3_117
1141
3978
1524
508
366
5.90E−32

Bacillus subtilis

P13484
tagEUDP-glucoseBacillus subtilis rodC operon.rodD (gtaA) polypeptide (AA 1-












673)


Contig344D
26564012_c3_251
1142
3979
2616
872
2649
1.20E−275

Lactococcus lactis

g3150046
clpBClpB chaperone homologLactococcus lactis cremoris










subsp. cremoris

ClpB chaperone homolog (clpB) andphosphoribosylformylglycinamide












cyclo-ligase (pur5) genes, completecds; and phosphoribosylglycinamide












formyltransferase (pur3) gene, partial cds.


Contig344D
26604662_c3_259
1143
3980
630
210


Contig344D
26776562_c1_194
1144
3981
399
133


Contig344D
289802_f1_41
1145
3982
189
63


Contig344D
2922260_c1_178
1146
3983
384
128
174
2.20E−13

Bacillus subtilis

e1183179
yjbLhypothetical protein yjbLBacillus subtilis complete genome (section 7 of












21)


Contig344D
30265952_c3_280
1147
3984
387
129
118
1.90E−07

Methanobacterium

g2621161
MTH122mutator MulT related proteinMethanobacterium











thermoautotro-



thermoautotrophicum from bases 68653 to 79584 (section 7 of 148) of the












phicum


complete genome.Function Code


Contig344D
30664130_13_120
1148
3985
258
86


Contig344D
30682802_c1_196
1149
3986
261
87


Contig344D
32062875_c2_28
1150
3987
291
97
333
3.20E−30

Staphylococcus

g1731452
prerecombination proteinStaphylococcus aureus chloramphenicol resistance











aureus


plasmid pKH7, complete sequence.


Contig344D
32067937_f1_53
1151
3988
1365
455
1790
1.30E−184

Staphylococcus

g2792490
coenzyme A disulfide reductaseStaphylococcus aureus











aureus


coenzyme A disulfide reductase gene, completecds.CoADR; flavoenzyme












(FAD); single catalytic cysteine


Contig344D
32457312_c3_262
1152
3989
495
165
233
1.30E−19

Clostridiurn

e303881
putative transposaseC.perfringens uapC, cpe, and nadC genes.











perfringens



Contig344D
32635937_c2_224
1153
3990
1503
501
895
8.90E−90

Bacillus subtilis

Q03523
murEUDP-N-acetylmuramoylananine-D-glutamate-2,6-B.subtilis genes spoVD,












murE, mraY, murD.


Contig344D
33364067_c2_226
1154
3991
1782
594
542
2.30E−52

Streptococcus

g2109443
sphtraputative serine proteaseStreptococcus pneumoniae R801











pneumoniae


tRNA-Arg gene, partial sequence, andputative serine protease (sphtra).












SPSpoJ (spspoJ), initiatorprotein (spdnaa) and beta subunit of DNA












polymerase III (spdnan) genes, complete cds.SPHtra


Contig344D
33399055_c3_275
1155
3992
393
131
419
2.40E−39

Bacillus subtilis

e1182121
ybclhypothetical protein ybclBacillus subtilis complete genome (section 1 of












21)


Contig344D
3371067_c3_254
1156
3993
954
318
1033
2.10E−104

Bacillus subtilis

g143608
spo0KEsporulation proteinBacillus subtilis spo0K operon.inner membrane












protein malK


Contig344D
34062930_c2_229
1157
3994
273
91
290
1.10E−25
Plasmid pT181
P03864
Plasmid pT181, complete genome.Pre protein (plasmid recombination)


Contig344D
34073552_c3_266
1158
3995
1545
515
1235
8.30E−126

Dichelobacter

P39883
prfCPrfC/RF3Dichelobacter nodosus A198 LpsA (lpsA), putative peptide











nodosus


releasefactor 3 (prfC), and putative amino acid binding protein (aabA) genes,












complete cds.peptide release factor 3 (putative)


Contig344D
34163562_f2_89
1159
3996
486
162
329
8.40E−30

Bacillus subtilis

e209890
adhBNAD alcohol dehydrogenaseB.subtilis 23.9 kb












fragment from map position 233 degrees on thechromosome.


Contig344D
34407625_c1_189
1160
3997
354
118
587
3.90E−57

Staphylococcus

g1658281
CadXStaphylococcus lugdunensis strain 995 cadmium reisitance











lugdunensis


plasmidpLUG10, complete sequence.


Contig344D
34407888_c1_177
1161
3998
729
243
288
1.60E−37

Bacillus firmus

g2952027
mecAMccA homologBacillus firmus MecA homolog (mecA) and cardiolipin












synthase (cls) genes, complete cds.


Contig344D
35158177_c2_213
1162
3999
1407
469
855
1.50E−85

Bacillus subtilis

e1181529
ykoKYkoKBacillus subtilis 168 56 kb DNA fragment between xlyA and












ykoR.homologous to magnesium transporters


Contig344D
35937827_c3_264
1163
4000
510
170
343
2.80E−31

Bacillus subtilis

e1183205
yjcGhypothetical protein yjcGBacillus subtilis complete genome (section 7 of












21)


Contig344D
36134717_c2_208
1164
4001
1647
549
889
3.80E−89
Plasmid pADI
g388269
traCpheromone cAD1 binding protein precursorPlasmid pAD1 (from













Enterococcus faecalis strain



Contig344D
36227142_c2_240
1165
4002
993
331
409
2.80E−38

Bacillus subtilis

P54421
papQphosphatase-associated proteinBacillus subtilis phosphatase-












associated protein (papQ) gene, complete cds.Muralytic when cloned in E.coli;












lap60 homolog;


Contig344D
36229625_f2_81
1166
4003
204
68
195
1.30E−15

Bacillus subtilis

e1184971
ykvShypothetical protein ykvSBacillus subtilis complete genome (section 8 of












21)


Contig344D
36568828_c3_272
1167
4004
1050
350
984
3.30E−99

Clostridium

A43577
regulatory protein pfoR











perfringens



Contig344D
36593802_c3_278
1168
4005
867
289
454
4.80E−43

Pasteurella

Q08868
PLPAlipoproteinPasteurella haemolytica lipoprotein gene, complete











haemolytica


cds.lipoprotein-28precursor


Contig344D
36611062_c1_170
1169
4006
420
140
174
2.20E−13

Bacillus subtilis

e1183078
yisLYisLBacillus subtilis complete genome (section 6 of 21) putative


Contig344D
3944143_c1_188
1170
4007
627
209
971
7.80E−98

Staphylococcus

g1916729
cadDCadDStaphylococcus aureus plasmid pRW001, cadnium resistance











aureus


CadD (cadD) gene, complete cds.contains 5 transmembrane domains; confers low












level


Contig344D
3954718_c2_204
1171
4008
3489
1163
1331
5.60E−136

Bacillus subtilis

P23477
addAATP-dependent nucleaseBacillus subtilis ATP-dependent nuclease (addA)












and (addB), andopen reading frame 3, partial cds.TTG start; see ref[3


Contig344D
4019193_c2_219
1172
4009
783
261
749
2.60E−74

Bacillus subtilis

e1183192
yjbWenoyl-acyl-carrier protein reductase homolog yjbWBacillus subtilis












complete genome (section 7 of 21) similar to enoyl- acyl-carrier protein












reductase


Contig344D
4064818_c2_239
1173
4010
675
225
533
2.00E−51

Escherichia coli

P31547
yaeEhypothetical 23.3 kd proteinEscherichia coli K-12 MG1655












section 19 of 400 of the completegenome.f218; 100 pct identical












to YAEE_ECOLI SW


Contig344D
4070151_c3_248
1174
4011
447
149
165
2.00E−12

Bacillus subtilis

e1173495
AddAB.subtilis 54 kb genomic DNA fragment.


Contig344D
4080443_c2_214
1175
4012
1854
618
1574
9.90E−162

Bacillus subtilis

e1183184
yjbQNa+/H+ antiporter homolog yjbQBacillus subtilis complete genome












(section 7 of 21) similar to Na+/H+ antiporter


Contig344D
4082828_c1_195
1176
4013
702
234
207
7.10E−17

Helicobacter

g2313985
HP0851conserved hypothetical integral membraneHelicobacter pylori section 74











pylori


of 134 of the complete genome.similar to EGAD


Contig344D
4088962_c3_265
1177
4014
279
93


Contig344D
4094433_f3_154
1178
4015
999
333
1184
2.10E−120

Bacillus subtilis

P21656
trpStryptophanyl-tRNA synthetaseB.subtilis trpS gene encoding












tryptophanyl-tRNA synthetase, complete cds.tryptophan-tRNA












ligasetryptophanyl-tRNA synthetase (EC 6.1.1.2)


Contig344D
40957_c2_212
1179
4016
858
286
513
2.70E−49

Bacillus subtilis

e1183182
yjbOconserved hypothetical protein yjcHBacillus subtilis complete genome












(section 7 of 21) similar to hypothetical proteins


Contig344D
4173410_c3_263
1180
4017
792
264
485
2.50E−46

Bacillus subtilis

e1183206
yjcHhypothetical protein yjcHBacillus subtilis complete genome (section 7 of












21)


Contig344D
4322752_f3_121
1181
4018
207
69
93
8.60E−05

Pyrococcus

d1028459
PHAU021101aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA, 1195819-1238496 nt position, clone


Contig344D
4328468_c2_243
1182
4019
1473
491
1279
1.80E−130

Bacillus subtilis

e1183502
gltBglutamate synthase (small subunit) Bacillus subtilis complete












genome (section 10 of 21)


Contig344D
4344011_f3_104
1183
4020
252
84


Contig344D
4687518_c3_269
1184
4021
585
195
379
6.60E−14

Bacillus subtilis

P40396
comKcompetence transcription factor (CTF) Bacillus subtilis complete genome












(section 6 of 21) This sequence comes from FIG. 3.


Contig344D
4703512_c1_193
1185
4022
486
162
335
2.00E−30

Bacillus subtilis

e1184521
ywqNunknownBacillus subtilis complete genome (section 19 of 21) similar to












hypothetical proteins


Contig344D
4726010_C2_217
1186
4023
2304
768
1777
3.10E−183

Streptomyces

g1196907
drrCdaunorubicin resistance proteinStreptomyces peucetius











peucetius


daunorubicin resistance protein (drrC) gene, complete cds.


Contig344D
4781275_f1_29
1187
4024
249
83


Contig344D
4812675_c2_216
1188
4025
321
107
273
2.60E−23

Bacillus subtilis

P54547
yqjJYqjJBacillus subtilis DNA, 283 Kb region containing skin element.similar to












glucose-6-phosphate 1-dehydrogenase


Contig344D
4882806_c3_270
1189
4026
522
174
399
3.20E−37

Bacillus subtilis

e1183088
yisUYlsUBacillus subtilis complete genome (section 6 of 21) similar to












hypothetical proteins


Contig344D
5165711_f2_92
1190
4027
447
149
338
9.40E−31

Bacillus subtilis

e1183176
yjblhypothetical protein yjblBacillus subtilis complete genome (section 7 of












21)


Contig344D
5250258_c2_309
1191
4028
1839
613
1741
2.00E−179

Bacillus

d1014255
Pz-peptidaseBacillus licheniformis DNA for Pz-peptidase, complete cds.











licheniformis



Contig344D
5265643_f1_7
1192
4029
1122
374


Contig344D
5343760_c1_12
1193
4030
267
89


Contig344D
5860927_f1_14
1194
4031
189
63


Contig344D
6057943_c3_268
1195
4032
999
333
990
7.60E−100

Bacillus subtilis

e1183027
yhfJhypothetical proteinBacillus subtilis complete genome (section 6 of












21) similar to lipoate-protein ligase


Contig344D
6760887_f3_114
1196
4033
924
308
333
3.20E−30

Bacillus subtilis

P20668
gltCtranscriptional regulator (LysR family) Bacillus subtilis complete












genome (section 10 of 21)


Contig344D
6921877_c2_215
1197
4034
219
73
192
1.90E−14

Bacillus subtilis

P54547
yqjJYqjJBacillus subtilis DNA, 283 Kb region containing skin element.similar to












glucose-6-phosphate 1-dehydrogenase


Contig344D
7081712_f3_140
1198
4035
234
78


Contig344D
7145260_f2_93
1199
4036
243
81


Contig344D
7228438_c3_247
1200
4037
3231
1077
1793
6.20−185

Bacillus subtilis

P23478
addBATP-dependent nucleaseBacillus subtilis ATP-dependent nuclease (addA)












and (addB), andopen reading frame 3, partial cds.alternate gene name


Contig344D
7308375_c1_173
1201
4038
942
314
791
9.30E−79

Bacillus subtilis

e1183164
oppBoligopeptide ABC transporter (permease) Bacillus subtilis complete












genome (section 7 of 21) alternate gene name


Contig344D
782816_c2_205
1202
4039
1857
619
776
3.10E−116

Bacillus subtilis

g1934616
yrhLhypothetical protein YrhLBacillus subtilis cysteine synthase (yrhA),












crystathioninegama-lyase (yrhB), YrhC (yrhC), YrhD (yrhD), formate












dehydrogenasechain A (yrhE), YrhF (yrhF), formate dehydrogenase (yrhG),












YrhH (yrhH), regulatory protein (yrhI), cyto


Contig344D
819056_c1_55
1203
4040
189
63


Contig344D
859838_f2_98
1204
4041
384
128


Contig344D
984703_c3_277
1205
4042
1026
342
763
8.60E−76

Escherichia coli

P30750
abcATP-binding proteinEscherichia coli K-12 MG1655 section 19 of 400 of the












completegenome.malK protein homologyf343; 98 pct identical to fragment (231 aa)


Contig344D
985887_c1_175
1206
4043
435
145
570
2.40E−55

Bacillus subtilis

e1183170
yjbDconserved hypothetical protein yjbDBacillus subtilis complete genome












(section 7 of 21) similar to hypothetical proteins


Contig345D
12697136_c3_28
1207
4044
873
291
1519
6.70E−156

Staphylococcus

g1161381
icaBlcaBStaphylococcus epidermidis operon mediating intercellular adhesion











epidermidis



Contig345D
15126592_c1_19
1208
4045
1086
362
1831
5.80E−189

Staphylococcus

g1161382
icaClcaCStaphylococcus epidermidis operon mediating intercellular adhesion











epidermidis



Contig345D
23445387_f2_5
1209
4046
195
65


Contig345D
24406542_c1_18
1210
4047
339
113
513
2.70E−49

Staphylococcus

g2914128
icaDlcaDStaphylococcus epidermidis operon mediating intercellular adhesion











epidermidis



Contig345D
24421937_f2_6
1211
4048
1269
423
778
2.20E−77

Bacillus subtilis

e1182844
yfhlantibiotic resistance protein homolog yfhlBacillus subtilis complete genome












(section 5 of 21) similar to antibiotic resistance protein


Contig345D
25675155_c3_24
1212
4049
1521
507


Contig345D
33203385_f2_4
1213
4050
597
199
967
2.10E−97

Staphylococcus

g2978430
icaRlcaRStaphylococcus epidermidis operon mediating intercellular adhesion











epidermidis



Contig345D
35995316_c2_21
1214
4051
1257
419
2160
7.90E−224

Staphylococcus

g1161380
icaAlcaAStaphylococcus epidermidis operon mediating intercellular adhesion











epidermidis



Contig345D
4004643_c1_91
1215
4052
201
67


Contig345D
53413_c3_25
1216
4053
1602
534
424
7.20E−40

Helicobacter

g2313187
HP01042′, 3p40 -cyclic-nucleotide 2′-phosphodiesteraseHelicobacter pylori











pylori


section 10 of 134 of the complete genome.similar to EGAD


Contig345D
6350031_f1_1
1217
4054
2100
700
3598
0

Staphylococcus

g2981225
gehllipase precursorStaphylococcus epidermidis lipase precursor (gch1) gene,











epidermidis


completecds.


Contig346D
10317307_f1_38
1218
4055
267
89


Contig346D
10626525_f3_105
1219
4056
1023
341
810
9.00E−41

Bacillus subtilis

e1183034
yhfPhypothetical proteinBacillus subtilis complete genome (section 6 of












21) similar to hypothetical proteins


Contig346D
10662763_c1_136
1220
4057
1089
363
688
7.60E−68

Bacillus subtilis

Q06754
yacLunknownB.subtilis DNA, 180 kilobase region of replication












origin.similar to hypothetical proteins


Contig346D
10928_c1_131
1221
4058
1242
414
230
1.00E−16

Rhodobacter

g3128293
hypothetical proteinRhodobacter capsulatus strain SB1003, partial











capsulatus


genome.


Contig346D
10976625_c3_190
1222
4059
888
296
870
4.00E−87

Bacillus subtilis

e1183045
yhxDhypothetical proteinBacillus subtilis complete genome (section 6 of












21) similar to ribitol dehydrogenase


Contig346D
11114677_f3_87
1223
4060
204
68


Contig346D
11740778_f1_21
1224
4061
216
72


Contig346D
1207250_c1_122
1225
4062
480
160


Contig346D
13695125_c1_140
1226
4063
603
201
117
7.80E−06

Clostridium

g3025463
sigXSigXClostridium acetobutylicum pho-sigX gene region, phoP, phoR,











acetobutylicum


sigX, orf36, and orf18 gene, complete cds.proposed ECF subfamily RNA












polymerase sigmafactor


Contig346D
14644018_f3_98
1227
4064
969
323
324
2.90E−29

Staphylococcus

g2196513
epiHputative membrane proteinStaphylococcus epidermidis











epidermidis


plasmid pTue32 putative ABC transportersubunits (epiG), epiE), and












(epiF), putative membrane protein (epiH), EpiT′ (epiT′), and EpiT″ (epiT″) genes,












complete cds.EpiH


Contig346D
14656952_f1_24
1228
4065
633
211


Contig346D
15035952_f1_23
1229
4066
477
159


Contig346D
15117317_c3_176
1230
4067
2184
728
953
2.00E−102

Bacillus subtilis

P13485
tagFCDP-glycerolBacillus subtilis rodC operon.rodC (tag3) polypeptide (AA 1-












746)


Contig346D
15136562_c3_179
1231
4068
1500
500
1307
1.90E−133

Eschenichia coli

P33940
yojHyojH proteinE.coli genomic DNA, Kohara clone #373 (49.5-49.9












min.).ORF_ID


Contig346D
15804076_f2_61
1232
4069
1557
519
903
1.30E−90

Bacillus subtilis

P94524
araBL-ribulokinaseBacillus subtilis complete genome (section 15 of












21) homology to araB of Escherichia coli;identified on


Contig346D
15829135_c3_173
1233
4070
204
68
105
8.40E−06

Bacillus subtilis

e1182361
ycnlhypothetical protein ycnlBacillus subtilis complete genome (section 3 of












21)


Contig346D
16681687_c3_192
1234
4071
1029
343
694
1.80E−68

Bacillus subtilis

P37570
yaclunknownB. subtilis DNA, 180 kilobase region of replication












origin.similar to creatine kinase


Contig346D
16836012_c1_130
1235
4072
519
173


Contig346D
16972575_f2_48
1236
4073
186
62


Contig346D
174218_c2_153
1237
4074
1989
663
1225
9.50E−125

Bacillus subtilis

e1182890
yhcAmultidrug resistance protein homolog yhcABacillus subtilis′ complete












genome (section 5 of 21) similar to multidrug resistance protein


Contig346D
179653_c2_162
1238
4075
666
222


Contig346D
1970178_f1_19
1239
4076
219
73


Contig346D
19742962_c3_187
1240
4077
1026
342
267
3.10E−23

Acinetobacter

P05149
MROaldose 1-epimerase, Acinetobacter calcoaceticus gene for mutarotase (EC











calcoaceticus


5.1.3.3.).precursor (aa −20 to 381)


Contig346D
20500938_f3_100
1241
4078
228
76


Contig346D
20580443_c1_120
1242
4079
333
111
165
2.00E−12

Bacillus

P39044
Xgene X proteinB.sphaericus gene for ribosomal protein S14 homologue.











sphaericus



Contig346D
20897125_c2_155
1243
4080
975
325
504
2.40E−48

Bacillus subtilis

e1182790
yfjQYfjQBacillus subtilis complete genome (section 5 of 21) similar to












divalent cation transport protein


Contig346D
20980262_c1_135
1244
4081
2472
824
2959
0

Bacillus subtilis

P37571
mecBclpA/clpB familyB. subtilis DNA 180 kilobase region of replication












origin.ATP-dependent Clp proteinase chain Aalternate gene name


Contig346D
22277215_c1_15
1245
4082
1164
388
109
1.20E−05

Plasmodium

C44863
R45 antigen











falciparum



Contig346D
22455213_f2_68
1246
4083
687
229
411
1.70E−38

Thermotoga

g1575577
drrADNA-binding response regulatorThermotoga maritima DNA-











marilima


binding response regulator (drrA) and histidine protein kinase (hpkA)












genes, complete cds; thymidne/pyrimidine phosphorylase












homolog gene, partial cds.complete cds.DrrA; OmpR/PhoB subfamily












response


Contig346D
22689067_f2_54
1247
4084
1221
407
1218
5.30E−124

Bacillus subtilis

P39141
nupCpyrimidine nucleoside transport proteinBacillus subtilis genome sequence












between the iol and hui operon, partial and complete cds.


Contig346D
22867942_c3_188
1248
4085
711
237
411
1.70E−38

Pyrococcus

d1024727
PHAA004229aa long hypothetical ribose 5-phosphatePyrococcus horikoshii OT3











horikoshii


PHAA001-PHAA055 gene, complete cds.similar to PIR


Contig346D
22869687_c2_44
1249
4086
438
146
143
4.30E−10

Escherichia coli

g1788146
hypothetical protein b1841Escherichia coli K-12 MG1655 section 168 of 400 of












the completegenome.f124; This 124 aa ORF is 39 pct identical (6 gaps)


Contig346D
23556552_c3_174
1250
4087
405
135
123
5.70E−08
Chloroplast
P51192
ORF174hypothetical protein 174Porphyra purpyrea chloroplast











Porphyra purpurea


complete genome.


Contig346D
23601557_f2_58
1251
4088
201
67


Contig346D
23601577_f1_17
1252
4089
186
62


Contig346D
23704678_f3_95
1253
4090
216
72


Contig346D
23839193_c2_147
1254
4091
1614
538
1324
3.10E−135

Bacillus subtilis

e1182258
IclPL-lactate permeaseBacillus subtilis complete genome (section 2 of












21) alternate gene name


Contig346D
239234_f3_94
1255
4092
225
75


Contig346D
24267567_f2_65
1256
4093
645
215


Contig346D
24407327_c3_195
1257
4094
696
232
892
1.802−89

Bacillus subtilis

e1182036
rplAribosomal protein L1 (BL1) Bacillus subtilis complete genome (section 1 of












21)


Contig346D
24407827_c3_185
1258
4095
561
187


Contig346D
24412826_c2_161
1259
4096
963
321
286
3.00E−25

Klebsiella

P19452
HUTGK.aerogenes histidine utilization repressor C (hutC) gene,











aerogenes


completecds.histidine utilization repressor G


Contig346D
24415925_c2_154
1260
4097
903
301
282
8.10E−25

Acinetobacter

g1209223
estesteraseAcinebacter lwofii orf1 and esterase (est) gene, complete cds.











lwoffii



Contig346D
245953_c2_164
1261
4098
579
193
231
2.00E−19

Listeria

g1314295

Listeria monocytogenes ClpC ATP{dot over (a)}se (mec) gene, complete cds.ORF2;












monocytogenes


putative 19 kDa protein


Contig346D
24662825_c1_927
1262
4099
618
206
538
6.00E−52

Bacillus subtilis

e1184514
ywrFhypothetical protein ywrFBacillus subtilis complete genome (section 19 of












21)


Contig346D
2470010_c2_146
1263
4100
723
241
150
3.10E−08

Dicryoscelium

g2952545
DB10coronin binding proteinDicryostelium discoideum











discoideum


coronin binding protein (DB10) mRNA, complete cds.


Contig346D
24803386_c2_150
1264
4101
1080
360
215
2.00E−15

Mycobacterium

Q50735
MTCY9C4.05cunknownMycobacterium tuberculosis cosmid











tuberculosis


SCY09C4.MTCY9C4.05c, unknown,len


Contig346D
25527188_c3_189
1265
4102
1137
379
829
8.80E−83

Bacillus subtilis

g2293256
hipOputative hippurate hydrolaseBacillus subtilis rrnB-dnaB












genomic region.


Contig346D
25551640_c2_157
1266
4103
861
287


Contig346D
25579390_f3_101
1267
4104
1194
398
402
7.10E−37

Streptomyces

e1294490
SC1C3.12putative transferaseStreptomyces coelicolor











coelicolor


cosmid 1C3.SC1C3.12, possible transferase, len


Contig346D
25667753_c1_141
1268
4105
564
188
906
6.10E−91

Staphylococcus

P36264
nusGtranscription antitermination factor nusGS.carnosus secE, nusG and rplK











carnosus


genes.transcription antiterminatioin factor nusG


Contig346D
2620668_c3_194
1269
4106
210
70
278
2.10E−24

Staphylococcus

g2078376
secESecEStaphylococcus aureus NCTC 8325 SecE (secE), NusG (nusG) and











aureus


RplK (rplK) genes, complete cds.


Contig346D
26753588_f3_99
1270
4107
1383
461
344
2.20E−31

Bacillus subtilis

e1182343
yclKhomologue of alkaline phosphatase synthethesisBacillus subtilis complete












genomic (section 3 of 21) similar to two-component sensor histidine kinase


Contig346D
26854757_c2_167
1271
4108
660
220
9.75
3.00E−98

Staphylococcus

P77985
cysEserine O-acetyltransferaseS.xylosus cysE gene, genomic region.











xylosus



Contig346D
29565627_c1_108
1272
4109
879
293


Contig346D
31256916_c1_142
1273
4110
507
169
681
4.20E−67

Staphylococcus

P36254
rplKL11 proteinS.carnosus secE, nusG and rplK genes.Escherichia coli











carnosus


ribosomal protein L11


Contig346D
3134386_f1_2
1274
4111
228
76


Contig346D
34199202_c2_145
1275
4112
540
180
343
2.80E−31

Bacillus subtilis

e1184294
paiAtranscription regulatorBacillus subtilis complete genome (section 17 of












21)


Contig346D
34610667_c1_114
1276
4113
690
230
465
3.30E−44

Archaeoglobus

g2649576
AF1018ABC transporter, ATP-binding proteinArchaeoglobus fulgidus section











fulgidus


74 of 172 of the complete genome.similar to GB


Contig346D
35159528_c3_169
1277
4114
732
244
942
9.30E−95

Staphylococcus

P51184
scrAEllserS.xylosus scrA gene and unidentified open reading











xylosus


frames.phosphotransferase system sucrose-specific enzyme II, factor












IIORF2


Contig346D
35162800_c2_166
1278
4115
1506
502
1701
3.50E−175

Bacillus subtilis

P22250
gltXglutamyl-tRNA synthetaseB.subtilis DNA, 180 kilobase region of replication












origin.glutamate-tRNA ligase


Contig346D
36134715_c2_168
1279
4116
771
257
666
1.60E−65

Bacillus subtilis

Q06753
yacOunknownB.subtilis DNA, 180 kilobase region of replication












origin.similar to hypothetical proteins


Contig346D
36140963_f1_37
1280
4117
1431
477
226
1.60E−15

Bacillus subtilis

P13485
tagFCDP-glycerolBacillus subtilis rodC operon.rodC (tag3) polypeptide (AA 1-












746)


Contig346D
4062562_c3_186
1281
4118
183
61


Contig346D
4382062_f3_91
1282
4119
189
63


Contig346D
4496062_c1_109
1283
4120
345
115
168
9.70E−13

Bacillus subtilis

e1182361
ycnlhypothetical protein ycnlBacillus subtilis complete genome (section 3 of












21)


Contig346D
4687893_c2_156
1284
4121
1059
353
523
2.30E−50

Halobacterium sp.

g2822338

Halobacterium sp. NRC-1 plasmid pNRC100, complete plasmid











NRC-1

sequence.ORF H0660; similar to ORF in Sulfolobus


Contig346D
4727217_f3_93
1285
4122
402
134


Contig346D
4881588_c3_181
1286
4123
465
155
134
3.90E−09

Bacillus subtilis

d1020150
ydgGtranscriptional regulator (MarR family) homolog ydgGBacillus subtilis












genome sequence, 148 kb sequence of the regionbetween 35 and 47












degree.FUNCTION UNKNOWN.


Contig346D
5128587_f2_59
1287
4124
696
232
336
1.50E−30

Bacillus subtilis

e1182755
yflKYflKBacillus subtilis complete genome (section 5 of 21) similar to












hypothetical proteins


Contig346D
5283390_c3_182
1288
4125
1416
472
131
5.60E−05

Mycoplasma

g587472
Imp2M.hominis lmpl and lmp2 genes.











hominis



Contig346D
6149152_c2_165
1289
4126
1389
463
1543
1.90E−158

Bacillus subtilis

P37572
smunknownB. subtilis DNA, 180 kilobase region of replication












origin.alternate gene name


Contig346D
6443763_c1_138
1290
4127
408
136
298
1.60E−26

Bacillus subtilis

e1182028
yazCconserved hypothetical protein yazCBacillus subtilis complete genome












(section 1 of 21) similar to hypothetical proteins


Contig346D
661062_c3_193
1291
4128
1440
480
1568
4.30E−161

Bacillus subtilis

Q06752
cysScysteinyl-tRNA synthetaseB. subtilis DNA, 180 kilobase region of












replication origin.alternate gene name


Contig346D
6725707_c1_139
1292
4129
552
184
327
1.40E−29

Bacillus subtilis

P37574
yBCPunknownB. subtilis DNA, 180 kilobase region of replication












origin.similar to hypothetical proteins


Contig346D
6930462_c3_183
1293
4130
1227
409
634
4.00E−62

Bacillus subtilis

d1020154
ydgKbicyclomycin resistance protein homolog ydgKBacillus subtilis genome












sequence, 148 kb sequence of the regionbetween 35 and 47












degree.SIMILAR TO BICYCLOMYCIN RESISTANCE PROTEIN.


Contig346D
7229680_c3_191
1294
4131
492
164
377
6.90E−35

Bacillus subtilis

P37568
ctsRunknownB. subtilis DNA, 180 kilobase region of replication












origin.alternate gene name


Contig346D
7242812_f2_62
1295
4132
627
209
373
1.80E−34

Bacillus subtilis

e1186361
yxlJDNA-3-methyladenine glycosidase homolog yxlJBacillus subtilis complete












genome (section 20 of 21) similar to DNA-3-methyladenine glycosidase


Contig346D
804837_f3_106
1296
4133
963
321
342
3.50E−31

Laclococcus lactis

e327689
orfALactococcus lactis pfl gene (strain DB1341).


Contig346D
814838_c2_152
1297
4134
660
220
472
5.90E−45

Bacillus subtilis

e1182889
yhbJhypothetical protein yhbJBacillus subtilis complete genome (section 5 of












21)


Contig346D
837578_c2_163
1298
4135
1233
411
708
5.80E−70

Borrelia

g2688567
BB0637Na+/H+ antiporter (nhaC-1)Borrelia burgdorferi (section 51 of 70)











burgdorferi


of the complete genome.similar to GB


Contig346D
8568_c1_110
1299
4136
429
143


Contig346D
901515_c2_159
1300
4137
285
95


Contig346D
990952_f2_63
1301
4138
1209
403
732
1.70E−72

Helicobacter

g2314680
HP1506glutamate permease (gltS)Helicobacter pylori section 126 of











pylori


134 of the complete genome.sodium-glutamate symport carrier proteinsimilar












to EGAD


Contig346D
9924055_c1_137
1302
4139
216 72


Contig346D
9944132_f3_92
1303
4140
189
63


Contig347D
10657925_c1_52
1304
4141
948
316
573
1.20E−55

Bacillus subtilis

e1184303
thrBhomoserine kinaseBacillus subtilis complete genome (section 17 of












21) alternate gene name


Contig347D
10975428_f1_5
1305
4142
879
293


Contig347D
11212785_f3_33
1306
4243
213
71


Contig347D
12382052_c1_53
1307
4244
189
63


Contig347D
14901512_c1_49
1308
4145
552
184
500
6.40E−48

Staphylococcus

P43269
nucthemonucleaseS.intermedius nuc gene for thermonuclease.











intermedius



Contig347D
19953281_c1_51
1309
4146
1347
449
822
4.80E−82

Bacillus subtilis

P19582
homhomoserine dehydrogenaseBacillus subtilis homoserine dehydrogenase












(hom) gene, completecds, threonine synthase (thrC) gene, 5′ end of












cds.homoserine dehydrogenase


Contig347D
20370457_c3_71
1310
4147
183
61


Contig347D
20485875_c1_45
1311
4148
231
77


Contig347D
20745462_c2_56
1312
4149
1257
419
862
2.80E−86

Bacillus subtilis

g1750108
ynbAYnbABacillus subtilis SpoVK (spoVK), YnbA (ynbA), YnbB (ynbB),












GlnR (glnR), glutamine synthetase (glnA), YnaA (ynaA), YnaB (ynaB),












YnaC (ynaC), YnaD (ynaD), YnaE (ynaE), YnaF (ynaF), YnaG (ynaG),












YnaH( ynaH), YnaI (ynaI), YnaJ (ynaJ), xylan beta-1,4-xylo


Contig347D
21751938_f2_22
1313
4150
708
236
183
2.50E−14

Streptococcus

g2897104
putative host cell surface-exposed lipoproteinStreptococcus thermophilus











thermophilus


bacteriophage lysogeny module, integrasehomolog (int), putative host cell











bacteriophage TP-


surface-exposed lipoprotein, putative metallo-proteinase, repressor, Cro-like










J34

regulatoryprotein, and P1-antir


Contig347D
22539812_c2_57
1314
4151
1254
418
1290
1.20E−131

Bacillus subtilis

g1750109
ynbBYnbBBacillus subtilis SpoVK (spoVK), YnbA (ynbA), YnbB (ynbB),












GlnR (glnR), glutamine synthetase (glnA), YnaA (ynaA), YnaB (ynaB),












YnaC (ynaC), YnaD (ynaD), YnaE (ynaE), YnaF (ynaF), YnaG (ynaG),












YnaH (ynaH), YnaI (ynaI) YnaJ (ynaJ), xylan beta-1,4-xylo


Contig347D
23557807_f1_12
1315
4152
534
178
506
1.50E−48

Lactococcus lactis

e1172770
gpogluthatione peroxidaseLactococcus lactis carB and gpo genes.


Contig347D
24017127_c2_58
1316
4153
405
135
537
7.70E−52

Staphylococcus

g468509
glnRglutamine synthetase repressorS.aureus (bb270) glnA and











aureus


glnR genes.


Contig347D
24078753_c1_41
1317
4154
450
150
295
3.40E−26

Bacillus subtilis

e1183392
miaAtRNA isopentenylpyrophosphate transferaseBacillus subtilis complete












genome (section 10 of 21)


Contig347D
24352200_f2_21
1318
4155
1095
365
674
2.30E−66

Leishmania major

g2266911
L4171-60Leishmania major strain Freilin chromosome t cosmid clone












L4171.contains leucine zipper


Contig347D
24412811_c1_40
1319
4156
957
319
147
3.70E−11

Oryza saliva

g2801536
LPL1lysophospholipase homologOryza sativa lysophospholipase homolog












(LPL1) mRNA, complete cds.


Contig347D
24414187_c1_43
1320
4157
396
132


Contig347D
24495928_c2_60
1321
4158
210
70


Contig347D
24631637_c1_42
1322
4159
708
236
236
6.00E−20

Streptococcus

g2444107
ORF28Streptococcus thermophilus bacteriophage 01205 DNA sequence











thermophilus



Contig347D
24877312_f3_32
1323
4160
1392
464
1093
9.30E−111

Bacillus subtilis

g1182346
yclMhomologue of aspartokinase 2 alpha and betaBacillus subtilis complete












genome (section 3 of 21) similar to homoserine dehydrogenase


Contig347D
25449061_c2_64
1324
4161
249
83
191
3.50E−15

Bacillus subtilis

g2619014
yocGsensor regulatorBacillus subtilis chromosome region between terC and












odhAB.similar to B.subtilis Spo0A protein (267 aa)


Contig347D
25626625_c3_74
1325
4162
636
212


Contig347D
26205387_f1_2
1326
4163
336
112


Contig347D
26369016_c2_61
1327
4164
387
129
105
4.60E−06
Bacteriophage B1
e139437
b1 (sfp)scaffolding proteinBacteriophage TP901-1 genomic region.putative


Contig347D
29509442_c1_38
1328
4165
720
240
651
6.40E−64

Bacillus subtilis

P18156
glpFglycerol uptake facilitatorBacillus subtilis antiterminator regulatory protein












(glpP), glycerol uptake facilitator (glpF) genes, complete cds, glycerokinase












(glpK) gene; 5′ end.glycerol facilitator proteinputative


Contig347D
30355.313_c2_63
1329
4166
1113
371
382
2.00E−35

Bacillus subtilis

g2619013
yocFsensor kinaseBacillus subtilis chromosome region between terC and












odhAB.similar to B.subtilis DegS sensor kinase (385 aa)


Contig347D
34070261_c1_47
1330
4167
900
300
386
7.70E−36

Bacillus subtitis

e1186097
yvfRhypothetical proteinBacillus subtilis complete genome (section 18 of












21) similar to ABC transporter (ATP-binding protein)


Contig347D
34195135_c3_77
1331
4168
1104
368
1236
6.50E−126

Bacillus subtilis

P04990
thrCthreonine synthaseB. subtilis thrB and theC genes for homoserine kinase












and threoninesynthase (EC 2.7.1.39 and EC 4.2.99.2, respectively).threonine












dehydratasealternate gene name


Contig347D
36134401_c3_78
1332
4169
831
277
315
2.60E−28

Bacillus subtilis

P54947
yxeHconserved hypothetical protein yxeHBacillus subtilis complete genome












(section 21 of 21) similar to hypothetical proteins


Contig347D
4080342_c1_39
1333
4170
1515
505
1998
1.20E−206

Bacillus subtilis

P18157
glpKglycerol kinaseB.subtilis glycerol kinase (glpK) and glycerol-3-












phosphatedehydrogenase (glpD) genes, complete cds.xylulokinaseglycerol












kinase (glpK) (EC 2.7.1.30)


Contig347D
4891577_c3_69
1334
4171
582
194
453
6.10E−43

Bacillus subtilis

e1183392
miaAtRNA isopentenylpyrophosphate transferaseBacillus subtilis complete












genome (section 10 of 21)


Contig347D
5109625_c1_48
1335
4172
372
124
258
2.80E−22

Bacillus subtilis

e1186094
yvfUhypothetical proteinBacillus subtilis complete genome (section 18 of












21) similar to two-component response regulator [YvfT


Contig347D
5355012_c2_59
1336
4173
1359
453
2274
6.60E−236

Staphylococcus

Q59812
glnAglutamine synthetaseS.aureus (bb270) glnA and glnR genes.











aureus



Contig347D
5859568_f1_1
1337
4174
357
119
315
4.70E−28

ESCRERICHIA

P25737
LYSPLYSINE-SPECIFIC PERMEASE











COLI



Contig347D
6525_f2_13
1338
4175
1035
345
729
3.50E−72

Escherichia coli

g1788480
lysPlysine-specific permeaseEscherichia coli K-12 MG1655 section 195 of 400 of












the completegenome.arginine permeasef489; 100 pct identical to












LYSP_ECOLI SW


Contig347D
6641963_c1_46
1339
4176
1485
495
1302
6.60E−133

Bacillus subtilis

e1184565
ywnEUnknownBacillus subtilis complete genome (section 19 of 21) similar to












cardiolipin synthase


Contig347D
6929677_c2_55
1340
4177
258
86
187
9.40E−15

Bacillus subtilis

e1183393
ymaHhost factor-1 protein homolog ymaHBacillus subtilis complete genome












(section 10 of 21) similar to host factor-1 protein


Contig347D
869052_c3_68
1341
4178
1677
559
1700
4.40E−175

Bacillus subtilis

P18158
glpDglycerol-3-phosphate dehydrogenaseB.subtilis glycerol kinase












(glpK) and glycerol-3-phosphatedehydrogenase (glpD) genes,












complete cds.glycerol-3-phosphate dehydrogenase (glpD) (EC


Contig347D
9851507_f2_20
1342
4179
417
139


Contig347D
995967_c3_72
1343
4180
747
249
341
4.50E−31

Bacillus subtilis

e1186096
yvfShypothetical proteinBacillus subtilis complete genome (section 18 of












21) probable permease


Contig348D
10578392_f2_26
1344
4181
510
170
525
1.40E−50

Staphylococcus

g2735511
YwpF homologStaphylococcus carnosus (3R)-hydroxymyrostoyl acyl carrier











carnosus


prorteindehydrase homolog (fabZ) gene, partial cds, YwpF homolog.single-strand












binding protein homolog (ssb), SceD precursor (sceD), SceA precursor (sceA)












and SceE precursor (sceE) genes


Contig348D
10739063_c1_98
1345
4182
693
231
601
1.30E−58

Staphylococcus

g2735513
sceDSceD precursorStaphylococcus carnosus (3R)-hydroxymyristoyl acyl











carnosus


carrier proteindehydrase homolog (fabZ) gene, partial cds, YwpF homolog, single-












strand binding protein homolog (ssb), SceD precursor (sceD), ScA precursor












(sceA) and SceE precursor (sceE)


Contig348D
12111018_f3_64
1346
4183
426
142
174
2.20E−13

Azospirillum

g642965
carRA.brasilense carR gene.ORF2











brasilense



Contig348D
12142768_f1_23
1347
4184
300
100
110
3.50E−06

Pyrococcus

d1027343
PHBW016235aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA, 180023-216005 nt position, clone


Contig348D
1250_c3_151
1348
4185
714
238
644
3.50E−63

Staphylococcus

g2735516
tenATenA homologStaphylococcus carnosus (3R)-hydroxymyristoyl acyl











carnosus


carrier proteindehydrase homolog (fabZ) gene, partial cds, YwpF homolog, single-












strand binding protein homolog (ssb), SceE precursor (sceD), SceA precursor












(sceA) and SceE precursor (sceE) g


Contig348D
1292842_c2_110
1349
4186
672
224
397
5.30E−37

Bacillus subtilis

e1183028
yhfKhypothetical proteinBacillus subtilis complete genome (section 6 of












21) similar to hypothetical proteins


Contig348D
1366660_c3_136
1350
4187
1215
405
566
6.50E−55

Mycobacterium

e1251137
MTV016.15cputative aminohydrolaseMycobacterium











tuberculosis



tuberculosis sequence v016.MTV016.05c, lcn



Contig348D
13790952_c2_114
1351
4188
1194
398
1350
5.40E−138

Bacillus subtilis

d1013330
drmYqkNBacillus subtilis DNA, 283 Kb region containing skin element.alternate












gene name


Contig348D
1415877_c2_109
1352
4189
912
304
198
6.70E−16

Methanococcus

g1499745
MJ0912 conserved hypothetical proteinMethanococcus jannaschii section











jannaschii


77 of 150 of the complete genome.similar to GP


Contig348D
14225327_f1_15
1353
4190
1029
343
867
8.20E−87

Bacillus subtilis

g1934656
yrdOcation transport protein YrdOBacillus subtilis aminoglycoside 6-












adenylyltransferase (aadK) gene.partial cds, and YrdA (yrdA), YrdB (yrdB),












hypothetical protein YrdC (yrdC), YrdD (yrdD), hypothetical cytochrome P450












protein YrdE(yrdE), ribonuclease inhi


Contig348D
1438927_c1_85
1354
4191
1686
562
2118
2.20E−219

Bacillus subtilis

P13242
ctrACTP synthetaseBacillus subtilis spo0F, CTP synthetase (ctrA),












andfructose-bisphosphate aldolase (orfY-tsr) genes, complete cds.CTP












synthasealternate gene name


Contig348D
14849093_c3_129
1355
4192
294
98
127
2.10E−08
Mitochondrion
e138028
putative orf79.1C.crispus complete mitochondrial genome.unique orf











Chondrus crispus



Contig348D
16251305_c3_146
1356
4193
786
262
724
1.20E−71

Bacillus

P42010
ATPBATPase subunit aBacillus stearothermophilus genes for ATPase











stearothermophilus


subunits a and c, complete cds.


Contig348D
19739675_c3_141
1357
4194
636
212
638
1.50E−62

Bacillus subtilis

Q03221
tdkthymidine kinase Bacillus subtilis OrfR, 3′ end; OrfQ; transcriptional












terminator (rho) gene; ribosomal protein L31; thymidine kinase (tdk)












gene, complete cds.thymidine kinaseIncorrect sequence given in Quirk












cl al. citation.


Contig348D
20156686_c3_144
1358
4195
573
191
415
6.50E−39

Bacillus subtilis

P39157
ipc-33dUnknownB.subtilis spoll-R, glyC and upp genes.alternate gene name


Contig348D
20572255_f1_3
1359
4196
207
69


Contig348D
21517182_f3_73
1360
4197
375
125
233
1.30E−19

Bacillus subtilis

e1185384
yozAtranscriptional regulator (ArsR family) homolog yozA Bacillus subtilis












complete genome (section 11 of 21) similar to transcription regulator












(ArsR family)


Contig348D
21756937_c1_100
1361
4198
672
224
401
2.00E−37

Bacillus subtilis

P39594
ipa-26dthiamine-phosphate pyrophosphorylaseB.subtilis genomic












region (325 to 333).thiE proteinalternate gene name


Contig348D
22460882_c3_135
1362
4199
687
229
612
8.70E−60

Bacillus subtilis

e1191863
dradeoxyribose-phosphate aldolaseB.subtilis operon contg. dra












nupC and pdp genes.


Contig348D
23439002_c2_111
1363
4200
1404
468


Contig348D
23446887_f3_74
1364
4201
1155
385


Contig348D
23594057_c1_87
1365
4202
183
61


Contig348D
23595137_c3_134
1366
4203
501
167
423
9.20E−40

Bacillus subtilis

g2293159
ytkBstress- and starvation-induced gene controlled by sigma-B dpsBacillus













subtilis rrnB-dnaB genomic region.similarity to H11349 from H.














influenzae



Contig348D
23625008_c1_80
1367
4204
963
321
747
4.30E−74

Bacillus subtilis

e1182566
ydhSmannose-6-phosphate isomerase homolog ydhSBacillus subtilis complete












genome (section 4 of 21) similar to mannose-6-phosphate isomerase


Contig348D
23634678_c2_116
1368
4205
1194
398


Contig348D
23634702_c2_128
1369
4206
792
264
498
1.00E−47

Bacillus subtilis

P39593
ipa-25dhydroxyethylthiazole kinaseB.subtilis genomic region (325 to












333).hypothetical protein H10415alternate gene name


Contig348D
23651702_c1_78
1370
4207
870
290
255
5.90E−22

Bacillus subtilis

e1184491
ywtEconserved hypothetical protein ywtEBacillus subtilis complete genome












(section 19 of 21) similar to hypothetical proteins


Contig348D
2379658_f2_51
1371
4208
225
75


Contig348D
2383253_c2_103
1372
4209
399
133


Contig348D
24015687_c2_124
1373
4210
465
155
119
1.50E−07

thermophilic

P09354
H+-transporting ATP synthase, chain IThermophilic bacterium PS3 TF0F-1











bacterium PS3


operon for ATP synthase complex.1 protein (AA 1-127)


Contig348D
24074137_c3_139
1374
4211
1332
444
1360
4.70E−139

Bacillus subtilis

g143434
rhoRho FactorBacillus subtilis OrfR, 3′ end; OrfQ; transcriptional












terminator (rho) gene; ribosomal protein L31; thymidine kinase (tdk)












gene, complete cds.


Contig348D
24228411_c1_97
1375
4212
399
133
358
7.10E−33

Staphylococcus

g2735512
ssbsingle-strand binding protein homologStaphylococcus carnosus (3R)-











carnosus


hydroxymyristol acyl carrier proteindehydrase homolog (fabZ) gene,












partial cds, YwpF homolog, single-strand binding protein homolog (ssb), SceD












precursor (sceD), SceA precursor (sceA) and


Contig348D
24245327_c1_88
1376
4213
714
238
843
2.90E−84

Bacillus

e258331
uppuracil phosphoribosyltransferaseB.caldolyticus











caldolyticus


upp gene.


Config348D
24254202_c1_91
1377
4214
1512
504
2050
3.60E−212

Bacillus

P17674
ATPAAT synthase alpha subunitB.megaterium ATP synthase











megaterium


i, a, c, b, delta, alpha, gamma, beta andepsilon subunit gene, complete cds,












and ORF.H+-transporting ATP synthase alpha chain


Contig348D
24353427_c3_148
1378
4215
543
181
229
3.30E−19

Bacillus subtilis

P37811
alpHATP synthase subunit deltaB.subtilis (168) atpase genes for












ATP synthase subunits i, a, c, b, delta, alpha, gamma, beta, epsilon.


Contig348D
24392193_c1_79
1379
4216
204
68


Contig348D
24406260_c2_120
1380
4217
1296
432
1258
3.00E−128

Bacillus subtilis

P19670
murZUDP-N-acetylglucosamineB.subtilis












chromosomal DNA (region 320-321 degrees).alternate gene name


Contig348D
24415933_c2_112
1381
4218
435
145


Contig348D
24508563_c2_122
1382
4219
1092
364
1226
7.50E−125

Bacillus subtilis

P45872
prfApeptide chain release factor 1B.subtilis chromosomal DNA (region












320-321 degrees).translation releasing factorgtg start codon


Contig348D
24641687_c2_123
1383
4220
426
142
237
4.70E−20

Bacillus subtilis

P39155
ipc-31dUnknownB.subtilis spoll-R, glyC and upp genes.protein-tyrosine-












phosphatase, low molecular weightalternate gene name


Contig348D
24647558_c1_82
1384
4221
357
119


Contig348D
24665932_c3_142
1385
4222
840
280
477
1.70E−45

Bacillus subtilis

P45873
ywkEprotoporphyrinogen oxidase homolog ywkEB.subtilis chromosomal












DNA (region 320-321 degrees).product similar to E.coli PRFA2 protein


Contig348D
2541301_c3_149
1386
4223
351
117
180
5.20E−14

Bacillus subtilis

e1184584
ywzBhypothetical protein ywzBBacillus subtilis complete genome (section 19 of












21)


Contig348D
25422081_c3_132
1387
4224
204
68


Contig348D
26751542_f1_10
1388
4225
492
164
577
4.40E−56

Helicobacter

g2313188
HP0105conserved hypothetical proteinHelicobacter pylori section 10 of











pylori


134 of the complete genome.similar to EGAD


Contig348D
26757677_c2_106
1389
4226
1377
459
2163
3.80E−224

Staphylococcus

e283110
femDS.aureus femD gene.











aureus



Contig348D
29695252_c3_143
1390
4227
1098
366
665
2.10E−65

Bacillus subtilis

P39153
ipc-29dSimilar to Saccharomyces cerevisiae SUA5B.subtilis spoll-R, glyC












and upp genes.alternate gene name


Contig348D
29879407_c2_108
1391
4228
189
63


Contig348D
30682816_c1_90
1392
4229
537
179
376
8.80E−35

Bacillus

P20601
ATPFATP synthase b subunitB.megaterium ATP synthase











megaterium


i, a, c, b, delta, alpha, gamma, beta, andepsilon subunit genes, complete cds,












and ORF.H+-transporting ATP synthase chain 1


Contig348D
31637_c2_104
1393
4230
891
297
736
6.30E−73

Bacillus subtilis

d1020268
ybbPYbbPBacillus subtilis DNA for FeuB, FeuA, YbbB, YbbC, YbbD,












YbzA, YbbE, YbbF, YbbH, YbbI, YbbJ, YbbK, YbbL, YbbM, YbbP, complete












cds.alternate gene name


Contig348D
33412800_c2_118
1394
4231
882
294
135
1.00E−08

Bacillus subtilis

d1013033
btlDBltBacillus subtilis DNA, 283 Kb region containing skin element.alternate












gene name


Contig348D
3361326_c2_101
1395
4232
207
69


Contig348D
33673776_c2_121
1396
4233
297
99
296
2.60E−26

Bacillus subtilis

g2293155
ytiAYtiABacillus subtilis rrnB-dna-B genomic region.homology with the












ribosomal protein L31


Contig348D
33751260_c1_95
1397
4234
471
157
448
2.10E−42

Bacillus subtilis

e1184543
ywpBhydroxymyristoyl-(acyl carrier protein) de homolog ywpBBacillus












subtilis complete genome (section 19 of 21) similar to hydroxymyrisoyl-(acyl












carrier protein)


Contig348D
34387702_c2_105
1398
4235
936
312
328
1.20E−29

Bacillus subtilis

e1182109
ybbRhypothetical protein ybbRBacillus subtilis complete genome (section 1 of












21)


Contig348D
34589010_c1_81
1399
4236
246
82


Contig348D
34611067_f3_67
1400
4237
540
180
145
2.70E−30

Bacillus subtilis

P06629
ywjGhypothetical protein ywjGB.subtilis chromosomal DNA (region 320-321












degrees).


Contig348D
34615700_f2_41
1401
4238
819
273
155
2.30E−08

Caenorhabditis

g1293846
C42D8.3Caenorhabditis elegans cosmid C42D8.coded for by C. elegans cDNA











elegans


yk30b3.5; coded for by


Contig348D
34646926_f2_44
1402
4239
732
244
585
6.30E−57

Actinobacillus

g1732037
deoDpurine nucleoside phosphorylaseActinobacillus











pleuropneumoniae



pleuropneumoniea heat shock 10 protein GroES (mopB), heat-shock 60 protein













GroEL (mopA), purine nucleoside phosphorylase (deoD) genes, complete












cds, alcohol dehydrogenase (adhE) gene, partial cds.


Contig348D
35354656_f1_21
1403
4240
228
76


Contig348D
35647783_f1_19
1404
4241
690
230
181
4.10E−14

Pyrococcus

d1028033
PHLB002128aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA, 827700-833735 nt position (complementary strand), clone


Contig348D
36128785_c1_92
1405
4242
888
296
796
2.70E−79

Bacillus

P20602
ATPGATP synthase gamma subunitB.megaterium ATP synthase











megaterium


i, a, c, b, delta, alpha, gamma, beta andepsilon subunit genes, complete cds,












and ORF.H+-transporting ATP synthase gamma chain


Contig348D
36225052_c3_147
1406
4243
234
78
270
1.50E−23

Bacillus farmus

g142570
atpEATP synthase c subunitBacillus firmus ATP synthase a and c subunit












genes, 3′ end andcomplete cds.H+-transporting ATP synthase lipid-binding












proteinputative


Contig348D
4063202_c3_145
1407
4244
1239
413
1563
1.50E−160

Bacillus subtilis

P39148
glyCserine hydroxymethyltransferaseB.subtilis spoll












R,glyC and upp genes.glycine hydroxymethyltransferasealternate gene












name


Contig348D
40712_f2_45
1408
4245
216
72


Contig348D
4072135_c3_138
1409
4246
1467
489
870
4.00E−87

Mycobacterium

e304956
MTCY08D5.18aldehyde dehydrogenaseMycobacterium











tuberculosis



tuberculosis cosmid SCY08D5.MTCY08D5.18, aldehyde













dehydrogenase, len


Contig348D
4178218_c1_83
1410
4247
675
225


Contig348D
4728558_c2_107
1411
4248
1860
620
2088
3.40E−216

Bacillus subtilis

g726480
gcaAL-glutamine-D-fructose-6-phosphateBacillus subtilis L-glutamine












D-frutose-6-phosphateamidotransferase (gcaA) gene, complete cds.alternate gene












name


Contig348D
476567_c1_84
1412
4249
567
189
292
7.00E−26

Bacillus subtilis

P12464
rpoERNA polymerase delta subunitB.subtilis RNA polymerase delta












subunit (rpoE) gene, complete cds.DNA-directed RNA polymerase delta












chainrpoE protein (ttg start codon)


Contig348D
4901712_c1_93
1413
4250
1428
476
1999
9.10E−207

Bacillus subtilis

P37809
atpDATP synthase subunit betaB.subtilis (168) atpase genes for ATP synthase












subunits i, a, c, b, delta, alpha, gamma, beta, epsilon.H+-transporting ATP












synthase alpha chain


Contig348D
4962802_c2_113
1414
4251
1305
435
1545
1.20E−158

Bacillus subtilis

P39142
pdppyrimidine nucleoside phosphorylaseB.subtilis operon contg.












dra, nupC and pdp genes.


Contig348D
5078177_c1_89
1415
4252
1062
354
1169
8.20E−119

Staphylococcus

g1773355
cap5PCap5PStaphylococcus aureus capsule gene cluster Cap5A through











aureus


Cap5Pgenes, complete cds.putative N-actylglucosamine 2-epimerase


Contig348D
5131927_f1_17
1416
4253
210
70


Contig348D
5319213_c2_127
1417
4254
417
139
312
5.30E−28

Bacillus subtilis

P37812
atpCATP synthase subunit epsilonB.subtilis (168) atpase genes for












ATP synthase subunits i, a, c, b, delta, alpha, gamma, beta, epsilon.H+-












transporting ATP synthase epsilon chain


Contig348D
5895301_c1_99
1418
4255
948
316
603
7.80E−59

Haemophilus

P44697
H10416hypotheticalHaemophilus influenzae from bases 436488 to 446714











influenzae


(section 40 of 163) of the complete genome.similar to GB


Contig348D
6454635_c2_119
1419
4256
912
304
1173
3.10E−119

Bacillus subtilis

P13243
orfY-tsrfructose-bisphosphate aldolaseBacillus subtillis spo0F, CTP












synthetase (ctrA), andfructose-bisphosphate aldolase (orfY-tsr) genes,












complete cds.fructose-bisphosphate aldolase llalternate gene name


Contig348D
6906570_c1_94
1420
4257
1296
432
1429
2.30E−146

Bacillus subtilis

c276830
murAUDP-N-acerylglucosamineB.subtilis atpC gene.


Contig348D
992291_f2_46
1421
4258
186
62


Contig349D
1281557_c2_26
1422
4259
1131
377
899
3.30E−90

Bacillus subtilis

P96612
ddlAPROBABLE D-ALANINE--D-ALANINE LIGASE ABacillus subtilis












genome sequence, 148 kb sequence of the regionbetween 35 and 47 degree.


Contig349D
14555051_c3_42
1423
4260
471
157
409
2.80E−38

Bacillus subtilis

d1020070
ydcKconserved hypothetical protein ydcKBacillus subtilis genome sequence,












148 kb sequnce of the regionbetween 35 and 47 degree.FUNCTION UNKNOWN


Contig349D
19728433_f3_16
1424
4261
1215
405
691
3.70E−68

Bacillus subtilis

P39604
ipa-42dcell-division protein homolog ywcFB.subtilis genomic region (325 to












333).alternate gene name


Contig349D
20348453_c2_27
1425
4262
1587
529
1214
1.40E−123

Bacillus subtilis

d1020048
ydbRATP-dependent RNA helicase homolog ydbRBacillus subtilis genome












sequence, 148 kb sequence of the regionbetween 35 and 47 degree.ATP-












DEPENDENT RNA HELICASE DEAD HOMOLOG.


Contig349D
20569052_c1_19
1426
4263
327
109
198
6.40E−16

Bacillus subtilis

e1186040
yvgZconserved hypothetical protein yvgZBacillus subtilis complete genome












(section 18 of 21) similar to hypothetical proteins


Contig349D
2230303_f1_8
1427
4264
669
223
346
1.30E−31

Bacillus subtilis

P54168
ypgQconserved hypothetical protein ypgQBacillus subtilis (YAC10-9 clone)












DNA region between the serA andkdg loci.putative


Contig349D
22692137_c1_24
1428
4265
486
162
688
7.60E−68

Staphylococcus

e279934
rsbWS.aureus sigB gene.











aureus



Contig349D
23437803_c2_32
1429
4266
2187
729
1827
1.50E−188

Staphylococcus

e279936
ORF6S.aureus sigB gene.











aureus



Contig349D
23625387_c3_43
1430
4267
219
73


Contig349D
23711642_c3_40
1431
4268
1026
342
1445
4.60E−148

Staphylococcus

e284997
rsbUS.aureus rsbU, rsbV, rsbW & sigB genes.











aureus



Contig349D
24235952_c3_41
1432
4269
327
109
501
5.00E−48

Staphylococcus

e284998
rsbVS.aureus rsbU, rsbV, rsbW & sigB genes.











aureus



Contig349D
24625216_f1_7
1433
4270
186
62


Contig349D
24642963_c1_20
1434
4271
216
72


Contig349D
26173800_c3_37
1435
4272
186
62


Contig349D
26212756_f3_17
1436
4273
1488
496
1477
1.90E−151

Bacillus subtilis

d1184565
ywnEUnknownBacillus subtilis complete genome (section 19 of 21) similar to












cardiolipin synthase


Contig349D
26360260_c2_29
1437
4274
375
125
285
3.90E−25

Bacillus subtilis

d1020052
ydcBholo- acyl-carrier protein synthase homolog ydcBBacillus subtilis genome












sequence, 148 kb sequence of the regionbetween 35 and 47












degree.FUNCTION UNKNOWN, SIMILAR PRODUCT IN E. COLI AND


Contig349D
2775462_c3_38
1438
4275
522
174
171
4.70E−13

Bacillus subtilis

d1020049
ydbShypothetical protein ydbSBacillus subtilis genome sequence, 148 kb












sequence of the regionbetween 35 and 47 degree.FUNCTION UNKNOWN.


Contig349D
30587843_f3_14
1439
4276
276
92


Contig349D
33870312_c2_31
1440
4277
792
264
1213
1.80E−123

Staphylococcus

e279935
sigBsigma factor BS.aureus sigB gene.











aureus



Contig349D
34062928_c2_30
1441
4278
1083
361
659
9.10E−65

BACILLUS

P10724
DALALANINE RACEMASE,











STEAROTHERMO-












PHILUS



Contig349D
34181277_c1_22
1442
4279
501
167
153
3 80E−11

Bacillus subtilis

d1020049
ydbShypothetical protein ydbSBacillus subtilis genome sequence, 148 kb












sequence of the regionbetween 35 and 47 degree.FUNCTION UNKNOWN.


Contig349D
34250327_c3_39
1443
4280
363
121
540
3.70E−52

Staphylococcus

e279931
ORF1S.aureus sigB gene.











aureus



Contig349D
35196926_c1_18
1444
4281
837
279
417
4.00E−39

Bacillus subtilis

P54544
yqjGYqiGBacillus subtilis DNA, 283 Kb region containing skin element.similar to












lipoprotein SpolllJ-like


Contig349D
4869213_c2_28
1445
4282
1521
507
384
1.30E−35

Bacillus subtilis

d1020050
ydbThypothetical protein ydbTBacillus subtilis genome sequence, 148 kb












sequence of the regionbetween 35 and 47 degree.FUNCTION UNKNOWN.


Contig349D
582760_c1_23
1446
4283
207
69
108
2.20E−06

Staphylococcus

c284995

S.aureus rsbU, rsbV, rsbW & sigB genes.ORF56












aureus



Contig349D
7240675_c1_21
1447
4284
1374
458
976
2.30E−98

Bacillus subtilis

d1020047
ydbQUDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-Bacillus subtilis genome












sequence, 148 kb sequence of the regionbetween 35 and 47












degree.PROBABLE UDP-N-ACETYLMURAMOYLALANYL-D-












GLUTAMYL-2,


Contig350D
1046885_f1_7
1448
4285
2217
739
1356
3.30E−338

Acinetobacter

e245927
ppkpolyphosphate kinaseA.calcoaceticus ADP1, cysD, cobQ, sodM, syk, rubA,











calcoaceticus


rubB, estB, ORF1, ppk, mtkA, ORF2 and ORF3 genes.putative; transcription of












ppk is induced by


Contig350D
10585432_c3_371
1449
4286
591
197
171
1.90E−18

Bacillus subtilis

P54422
ggtgamma-glutamyltranspeptidaseBacillus subtilis












gamma-glutamyltranspeptidase (ggt) gene, completecds.alternate gene name


Contig350D
10601625_c3_502
1450
4287
231
77


Contig350D
1063552_f3_217
1451
4288
390
330


Contig350D
1074177_c2_464
1452
4289
825
275
417
4.00E−39

Escherichia coli

g1787043
hypothetical protein b0822Escherichia coli K-12 MG1655 section 74 of 400 of












the completegenome.f271; This 271 aa ORF is 24 pct identical (16 gaps)


Contig350D
10756925_f1_54
1453
4290
1566
522
793
5.70E−79

Bacillus subtilis

d1020925
YfnABacillus subtilis genomic DNA 69-70 degree region, partialsequence.


Contig350D
10954327_f3_230
1454
4293
203
67


Contig350D
10973385_c1_343
1455
4292
312
104


Contig350D
11063801_f1_105
1456
4293
225
75


Contig350D
115761_c3_541
1457
4294
1458
486
799
3.30E−79

Synechocystis sp.

d1018310
glgPhypothetical proteinSynechocyctis sp. PCC6803 complete genome, 9/27,












1056467-1188885.ORF_ID


Contig350D
117350_f1_38
1458
4295
1333
437
288
1.50E−33

Caenorhabditis

C55729
hydroxymethylglutaryl-CoA synthase homolog











elegans



Contig350D
1173130_c1_366
1459
4296
2091
697
2663
4.00E−277

Staphylococcus

Q57071
glcAphosphotransferase system enzyme II,, glucose-specific, factor











carnosus


IIAS.carnosus glcA gene and glcB gene.phosphotransferase system N-












acetylglucosamine-specific enzyme II


Contig350D
1178593_f3_221
1460
4297
1590
530
3527
9.50E−157

Bacillus subtilis

c1182639
yerDYerD proteinBacillus subtilis complete genome (section 4 of












21) similar to glutamate synthase (ferredoxin)


Contig350D
1180292_c1_369
1461
4298
1164
388
1050
3.30E−106

Bacillus subtilis

c1184496
ywsCcapsular polyglutamate biosynthesis homolog ywsCBacillus













subtilis complete genome (section 19 of 21) similar to capsular polyglutamate













biosynthesis


Contig350D
11855463_c1_340
1462
4299
747
249
791
9.30E−79

Bacillus subtilis

e332183
cysHputative phospho-adenylylsulphateBacillus subtilis pyrE to












yloA gene region.


Contig350D
119633_f1_2
1463
4300
1389
463
494
2.80E−47

Bacillus subtilis

g1762126
estBintracellular esterase BBacillus subtilis putative orf1 unknown protein,












putativetranscriptional regulative (slr), and intracellular esterase B (estB) genes,












complete cds.EstB; esterase of the serine-hydrolase family


Contig350D
1230437_c1_364
1464
4301
408
136
201
3.10E−16

Bacillus subtilis

P39591
ipa-23rhypothetical proteinB.subtilis genomic region (325 to 333).alternate












gene name


Contig350D
1281627_c3_569
1465
4302
1293
431
1106
3.90E−112

Bacillus subtilis

c1185127
ylmBacetylornithine deactylase homolog ylmBBacillus subtilis complete












genome (section 9 of 21) similar to acetylornithine deactylase


Contig350D
1298202_f2_204
1466
4303
3986
662
1779
1.90E−183

Bacillus subtilis

e1183221
yjdDfructose phosphotransferase system enzyme homolog yjdDBacillus subtilis












complete genome (section 7 of 21) similar to fructose phosphotransferase












system


Contig350D
13089086_c1_337
1467
4304
1035
345
120
2.50E−05

Bacillus firmus

g1813493
hydrophobic proteinBacillus firmus putative hydrophobic protein gene,












partial cds.similar to Bacillus subtilis putative protein


Contig350D
1351687_c1_360
1468
4305
906
302
739
3.00E−73

Staphylococcus

g1644433
ddhD-specific D-2-hydroxyacid dehydrogenaseStaphylococcus aureus D-











aureus


specific D-2-hydroxyacid dehydrogenase (ddh) gene, complete












cds.36.7 kDa protein; similar to NAD+-linked D-LDH,


Contig350D
1359635_f3_303
1469
4306
471
157
297
2.10E−26

Bacillus subtilis

e1181514
yklAYklABacillus subtilis 168 56 kb DNA fragment between xlyA and












ykoR.homologous to OsmC from Escherichia coli


Contig350D
1366012_c1_96
1470
4307
213
71


Contig350D
1376926_c3_490
1471
4308
849
283
438
2.40E−41

Pseudomonas

g3127079
ptxCPtxCPseudomonas stutzeri Orf117 (orf117), Orf86 (orf86) genes,











stutzeri


completecds; and ptxABCDE operon, partial sequence.putative inner












membrane component of


Contig350D
13835462_c3_504
1472
4309
1449
483
1161
5.80E−118

Clostridium

e242289
arcDarginine ornithine antiporterC.perfringens strain 13











perfringens


arcABDC, ahrC and colA genes.


Contig350D
13869827_f3_244
1473
4310
2385
795
2176
1.60E−225

Bacillus subtilis

e1186038
yvgXheavy metal-transporting ATPase homolog yvgXBacillus subtilis complete












genome (section 18 of 21) similar to heavy metal-transporting ATPase


Contig350D
14460882_c3_531
1474
4311
210
70
264
6.50E−23

Staphylococcus

g1022726
unknownStaphylococcus haemolyticus IS1272 ORF1 and ORF2 genes,











haemolyticus


completecds.ORF1


Contig350D
14495712_c1_393
1475
4312
297
99
103
1.20E−05

Synechocystis sp.

d1019027
hypothetical proteinSynechocystis sp. PCC6803 complete genome, 15/27,












1848242-1991549.ORF_ID


Contig350D
14534387_f3_299
1476
4313
225
75


Contig350D
14626432_c2_398
1477
4314
2421
807
1387
6.50E−142

Staphylococcus

O06446
secASecAStaphylococcus aureus NCTC 8325 SecA (secA) gene, complete cds.











aureus



Contig350D
14644037_c3_512
1478
4315
1575
525
401
2.40E−40

Escherichia coli

g1787094
hypothetical protein b0869Escherichia coli K-12 MG1655 section 78 of 400 of












the completegenome.f486; This 486 aa ORF is 21 pct identical (13 gaps)


Contig350D
14650312_c3_505
1479
4316
1170
390
281
1.00E−24

Bacillus subtilis

e1184494
ywtBcapsular polyglutamate biosynthesis homolog ywtBBacillus













subtilis complete genome (section 19 of 21) similar to capsular polyglutamate













biosynthesis


Contig350D
14720378_c3_499
1480
4317
726
242
292
7.00E−26

Aquifex aeolicus

g2983456
aq_928putative proteinAquifex aeolicus section 46 of 109 of the complete












genome


Contig350D
14729702_c2_402
1481
4318
2031
677
266
2.20E−19

Mus musculus

e1288122
DSPPdentin sialophosphoproteinMus musculus DSPP gene.


Contig350D
14742887_c2_418
1482
4319
606
202


Contig350D
14742937_c1_336
1483
4320
1203
401


Contig350D
14879667_c2_440
1484
4321
867
289
735
8.00E−73

Bacillus subtilis

P52998
panCpantothenate synthetaseBacillus subtilis (clone YAC15-6B) ypiABF












genes, qcrABC genes, ypjABCDEFGHI genes, bitA gene, panBCD genes, dinG












gene, ypmB gene, aspB gene, asnS gene, dnaD gene, nth gene and ypoC gene,












completecds's.40.8% of identity to the Esch


Contig350D
14880051_f1_20
1485
4322
1971
657
2450
1.50E−254

Bacillus subtilis

d1011939
yydEfructose-1,6-bisphosphataseBacillus subtilis 36 kb sequence between gnt2 and












trnY genesencoding 34 ORFs.alternate gene name


Contig350D
14881250_f3_234
1486
4323
999
333
1407
4.90E−144

Staphylococcus

g1644433
ddhD-specific D-2-hydroxyacid dehydrogenaseStaphylococcus aureus D-











aureus


specific D-2-hydroxyacid dehydrogenase (ddh) gene, complete












cds.36.7 kDa protein; similar to NAD+-linked D-LDH,


Contig350D
14881908_c1_353
1487
4324
213
71


Contig350D
14931501_c2_444
1488
4325
1062
354
608
2.30E−59

Treponema

g1354775
pfoS/RpfoS/RTreponema pallidum methyl-accepting chemotaxis protein











pallidum


(mep-1)gene, complete cds, and potential regulatory molecule (pfoS/R) gene,












partial cds.potential regulatory molecule; pFoS/R-like


Contig350D
14961631_f1_32
1489
4326
198
66


Contig350D
14979713_c1_391
1490
4327
483
161
251
1.60E−21

Listeria

P33385
ORFZListeria monocytogenes lecithinase, lactate dehydrogenase











monocytogenes


(actA) gene complete cds, (plcB) gene complete cds, (ldh) gene












completecds.ORFZ


Contig350D
158411_c3_534
1491
4328
993
331
880
3.40E−88

Bacillus subtilis

A25805
L-lactate dehydrogenase, L-lactate dehydrogenase


Contig350D
15914762_f1_63
1492
4329
579
193
534
1.60E−51

Bacillus subtilis

g1524394
yuaCconserved hypothetical protein yuaCBacillus subtilis gbsAB operon












glycine betaine aldehydedehydrogenase GbsA, alcohol dehydrogenase GbsB












genes, complete cds.ORF-2 upstream of gbsAB operon


Contig350D
16798125_c2_473
1493
4330
441
147
154
2.20E−l0

Bacillus subtilis

P42237
ycbEglucarate dehydrataseBacillus subtilis DNA around 20 degrees region












of chromosomecontaining yckA-T genes.similar to glucarate transporter


Contig350D
16838207_f1_22
1494
4331
288
96
175
1.80E−13

Escherichia coli

P39274
yjdJhypothetical 10.5 kD protein in dcub-lysuEscherichia coli K-12 MG1655












section 375 of 400 of the completegenome.090a; 100 pct identical












amino acid sequence and


Contig350D
17010952_c3_550
1495
4332
864
288
639
1.20E−62

Bacillus subtilis

e1186383
yxkDconserved hypothetical protein yxkDBacillus subtilis complete genome












(section 20 of 21) similar to hypothetical proteins


Contig350D
179010_c3_547
1496
4333
546
182
344
2.20E−31

Haemophilus

P44687
H10402methylaled-DNA--protein-cysteineHaemophilus influenzae from











influenzae


bases 413366 to 426435 (section 38 of 163) of the complete












genome.methylated-DNA--protein-cysteine S-methyltransferase












homologysimilar to SP


Contig350D
19531436_c3_516
1497
4334
357
119
96
7 30E−05

Methanococcus

Q57859
MJ0416M. jannaschii predicted coding region MJ0416Methanococcus











jannaschii



jannaschii section 35 of 150 of the complete genome.hypothetical protein;













identified by GeneMark;


Contig350D
19562805_c3_546
1498
4335
213
71


Contig350D
19564702_c1_339
1499
4336
477
159
397
5.30E−37

Nicotiana

P30708
glutathione peroxidase homologN.sylvestris mRNA for 6P229











sylvestris


polypeptide homologous to animalglutathione peroxidases,glutathione












peroxidasehomologous to animal glutathione peroxidases


Contig350D
19585877_c1_349
1500
4337
1212
404
834
2.60E−83

Bacillus subtilis

e1183009
yhaAaminoacylase homolog yhaABacillus subtilis complete genome












(section 6 of 21) similar to aminoacylase


Contig350D
19720642_c2_407
1501
4338
1296
432
253
3.40E−21

Bacillus subtilis

g2529465
yokPYokPBacillus subtilis 168 region at 182 min containing the cge












genecluster.similar to the succinyl-diaminopimelate


Contig350D
197312_c2_447
1502
4339
873
291
813
4.30E−81

Bacillus subtilis

e1182946
yhdFhypothetical proteinBacillus subtilis complete genome (section 6 of












21) similar to glucose 1-dehydrogenase


Contig350D
19929586_c3_560
1503
4340
198
66


Contig350D
20317_c2_413
1504
4341
2088
696
431
7.00E−38

Bacillus subtilis

P13485
tagFCDP-glycerolBacillus subtilis rodC operon.rodC (tag3) polypeptide (AA 1-












746)


Contig350D
20335260_c1_344
1505
4342
1881
627
1711
3.00E−176

Escherichia coli

g1790686
nrdDanacrobic ribonucleoside-triphosphate reductaseEscherichia coli K-












12 MG1655 section 385 of 400 of the completegenome.oxygen-sensitive












ribonucleoside-triphosphate reductasef712; 99 pct identical amino












acid sequence and


Contig350D
20360885_f3_226
1506
4343
1683
561
906
6.10E−91

Bacillus subtilis

e1182920
yhxBhypothetical proteinBacillus subtilis complete genome (section 5 of












21) similar to phosphomannomutase


Contig350D
20433135_c3_549
1507
4344
801
267
151
1.10E−10

Enterococcus

d1011987
orf8ORF8Enterococcus faecalis plasmid pY117 genes for BacA, BacB,











faecalis


ORF3, ORF4, ORF5, ORF6, ORF7, ORF8, ORF9, ORF10, ORF11, partial












cds.


Contig350D
20507625_c3_487
1508
4345
1011
1337
244
8.60E−21

Pseudomonas

g3127078
ptxBPtxBPseudomonas stutzeri Orf117 (orf117), Orf86 (orf86) genes,











stutzeri


completecds; and ptxABCDE operon, partial sequence.putative binding protein












component of


Contig350D
20509637_c3_538
1509
4346
1335
445
218
6.70E−15

Bacillus subtilis

e1186076
yvbJhypothetical protein yvbJBacillus subtilis complete genome (section 18 of












21)


Contig350D
20509637_c3_564
1510
4347
1545
515
1655
2.60E−170

Bacillus

P46834
gntKgluconate kinaseBacillus licheniformis DNA for hypothetical











licheniformis


protein and Gntproteins.xylulokinase


Contig350D
20589568_c1_317
1511
4348
1557
519
282
9.50E−22

Bacillus subtilis

P13484
tagEUDP-glucoseBacillus subtilis rodC operon.rodD (gtaA) polypeptide (AA 1-












673)


Contig350D
2068937_f3_282
1512
4349
1539
513
1041
3.00E−105

Bacillus subtilis

e1182553
phoBalkaline phosphatase lllBacillus subtilis complete genome (section 4 of












21) alternate gene name


Contig350D
20822287_c1_386
1513
4350
684
228
563
1.30E−54

Bacillus subtilis

P10585
gntRgluconate operon repressorBacillus subtilis genomic DNA, 36 kb region












between gnt and ioloperons.PROSITE; PS00043; HTH_GNTR_FAMILY; see












SWISS_PROT


Contig350D
210885_f2_169
1514
4351
222
74


Contig350D
2113952_f2_214
1515
4352
2835
945
183
1.50E−11

Vigna unguiculata

S54157
extensin-like protein


Contig350D
2136712_c3_574
1516
4353
1197
399
469
1.20E−44

Bacillus subtilis

e1182559
ydhLchloramphenicol resistance protein homolog ydhLBacillus subtilis complete












genome (section 4 of 21) similar to chloramphenicol resistance protein


Contig350D
21515707_f3_242
1517
4354
198
66


Contig350D
21517012_c2_412
1518
4355
411
137
289
1.50E−25

Bacillus subtilis

g2318065
yeeEYeeEBacillus subtilis strain 168 trpC2 YefA (yefA) gene, partial cds, and












YefB (yefB), YefC (yefC), YeeA (yeeA), YeeB (yeeB), YeeC (yeeC),












YeeD (yeeD), YeeE (yeeE) and YeeF (yeeF) genes, completecds.


Contig350D
21604040_c1_361
1519
4356
2028
676
1295
3.60E−132

Methanacoccus

Q57986
MJ0566ferrous iron transport protein B (feoB) Methanococcus jannaschii section











jannaschii


47 of 150 of the complete genome.similar to SP


Contig350D
21664126_c2_409
1520
4357
1083
361
1134
4.20E−115

Lactobacillus sake

c1227705
arcBornithine transcarbarnoylaseLactobacillus sake












DNA encoding the arginine-deiminase pathwaygenes


Contig350D
21687963_c1_328
1521
4358
477
159
184
2.00E−14

Bacillus subtilis

P17893
ahrCAhrCB.subtilis ahrC gene,encoding an arginine












repressor/activatorprotein.ahrC protein


Contig350D
21759718_f1_41
1522
4359
297
99


Contig350D
21774087_c3_539
1523
4360
732
244
336
1.50E−30

Haemophilus

P44068
H1088H. influenzae predicted coding region H10882Haemophilus influenzae











influenzae


from bases 932179 to 942337 (section 85 of 163) of the complete












genome.identified by GeneMark; putative


Contig350D
22380343_f2_206
1524
4361
1983
661
363
1.90E−30

Enterococcus

P37710
bacterial cell wall hydrolaseStreptococcus faecalis bacterial











faecalis


cell wall hydrolase gene, completecds.


Contig350D
2242136_c3_506
1525
4362
684
228
583
1.00E−56

Clostridium

e303881
putative transposaseC.perfringens uapC, cpc, and nadC genes.











perfringens



Contig350D
22460302_c1_357
1526
4363
756
252
334
2.50E−30

Staphylococcus

g2735514
sceASceA precursorStaphylococcus carnosus (3R)-hydroxymyristoyl acyl











carnosus


carrier proteindehydrase homolog (fabZ) gene, partial cds, YwpF homolog; single-












strand binding protein homolog (ssb), SceD precursor (sceD), SceA precursor












(sceA) and SceE precursor (sceE)


Contig350D
23438751_f2_120
1527
4364
228
76


Contig350D
23468942_f1_5
1528
4365
1101
367
928
2.80E−93

Bacillus subtilis

e1184131
ysdChypothetical proteinBacillus subtilis complete genome (section 15 of












21) similar to endo-1,4-beta-glucanase


Contig350D
23476503_f3_297
1529
4366
189
63


Contig350D
23476702_c1_354
1530
4367
882
294
595
5.50E−58

Bacillus subtilis

P39592
ipa-24dhypothetical proteinB.subtilis genomic region (325 to 333).alternate












gene name


Contig350D
23479702_c3_509
1531
4368
273
91


Contig350D
23480467_c1_375
1532
4369
912
304
862
2.80E−86

Bacillus subtilis

e1185177
ylpAputative Yhap proteinBacillus subtilis complete genome (section 9 of












21) similar to L-serine dehydratase


Contig350D
23556338_c1_384
1533
4370
303
101
170
6.00E−13

Bacillus subtilis

e1182354
ycnEconserved hypothetical protein ycnEBacillus subtilis complete genome












(section 3 of 21) similar to hypothetical proteins


Contig350D
23593800_c1_352
1534
4371
942
314
141
7.00E−08

Bacillus subtilis

d1020110
ydeJhypothetical protein ydeJBacillus subtilis genome sequence, 148 kb












sequencce of the regionbetween 35 and 47 degree.FUNCTION UNKNOWN.


Contig350D
23600752_f1_50
1535
4372
240
80


Contig350D
23602015_c2_485
1536
4373
687
229
374
1.40E−34

Escherichia coli

P77279
YBBLhypothetical protein b0490Escherichia coli K-12 MG1655












section 45 of 400 of the completegenome.malK protein












homologyo225; This 225 aa ORF is 32 pct identical (7 gaps)


Contig350D
23604052_f1_47
1537
4374
318
106


Contig350D
23631311_c2_454
1538
4375
297
99


Contig350D
23636343_c1_314
1539
4376
813
271
409
2.80E−38

Escherichia coli

P16683
PHNEphnE proteinE.coli psiD locus containing alkylphosphonate uptake












(phn) genes A through Q, complete cds.phnE proteinphnE protein


Contig350D
23642942_c3_525
1540
4377
231
77


Contig350D
23649187_c3_507
1541
4378
2637
879
209
1.30E−12

Plasmodium

g1151158
repeat organellar proteinPlasmodium chabaudi repeat orrganellar protein gene.











chabaudi


complete cds.ROPE


Contig350D
23672518_f1_232
1542
4379
1011
337
529
5.40E−51

Bacillus subtilis

e1185017
moeBmolybdopterin biosynthesis proteinBacillus subtilis complete genome












(section 8 of 21)


Contig350D
23680300_f1_87
1543
4380
948
316


Contig350D
23694162_f2_175
1544
4381
219
73


Contig350D
23868887_c2_458
1545
4382
189
63


Contig350D
24015687_c1_347
1546
4383
1521
507
1701
3.50E−175

Bacillus subtilis

P71016
gbsAGbsABacillus subtilis gbsAB operon, glycine betaine












aldehydedehydrogenase GbsA, alcohol dehydrogenase GbsB genes, complete












cds.glycine betaine aldehyde dehydrogenase


Contig350D
24022177_c1_387
1547
4384
1389
463
1499
8.80E−154

Bacillus subtilis

P12012
gntPgluconate permeaseBacillus subtilis genomic DNA; 36 kb region between gnt












and ioloperons.homologs are found in E. coli and H. influenzae;


Contig350D
24087760_c1_519
1548
4385
903
301
665
2.10E−65

Bacillus subtilis

g2293257
ytnMYtnMBacillus subtilis rrnB-dnaB genomic region.similar to a hypothetical












protein


Contig350D
24101701_c1_351
1549
4386
1542
514
1186
1.30E−120

Corynebacterium

e1286985
mqoL-malate dehydrogenase (acceptor) Corynebacterium glutamicum











glutamicum


DNA for L-Malate


Contig350D
24220260_c3_537
1550
4387
1056
352


Contig350D
24220290_f2_132
1551
4388
1482
494
935
5.10E−94

Escherichia coli

d1015750
aldAAldehyde dehydrogenase (NAD+) (EC 1.2.1.3) E.coli genomic DNA,












Kohara clone #269 (31.8-32.1 min.).ORF_ID


Contig350D
24226577_c3_563
1552
4389
834
278
153
7.90E−11

Bacillus sp.

P22853
merRunknown proteinBacillus sp. mercury resistance (merA) gene,












complete cds.ORF1; putative


Contig350D
24261062_c2_421
1553
4390
1773
591
1994
3.20E−206

Bacillus subtilis

e1186031
yvgQsulfite reductase homolog yvgQBacillus subtilis complete genome












(section 18 of 21) similar to sulfite reductase


Contig350D
24273375_c3_523
1554
4391
600
200
282
2.40E−24

Escherichia coli

g1788102
hypothetical protein b1801Escherichia coli K-12 MG1655 section 164 of 400 of












the completegenome.o481; UUG start; 29 pct identical (3 gaps) to 447


Contig350D
24304712_f1_80
1555
4392
1674
558
1008
9.40E−102

Enterobacter

P23234
IPDCindolepyrubate decarboxylase, E. cloacae gene for indolepyruvate











cloacae


decarboxylase.thiamine pyrophosphate-binding domain homologyindolepyruvate












decarboxylase


Contig350D
24337791_c3_515
1556
4393
1113
371


Contig350D
24337807_c1_341
1557
4394
1890
630
1795
3.80E−185

Bacillus subtilis

e1186032
yvgRsulfite reductase homolog yvgRBacillus subtilis complete genome












(section 18 of 21) similar to sulfite reductase


Contig350D
24338217_c3_521
1558
4395
597
199
259
2.20E−22

Haemophilus

P45080
HI1155anaerobic ribonucleoside-triphosphate reductaseHaemophilus











influenzae



influenzae from bases 1218795 to 1228832 (section 110 of 163) of the













complete genome.similar to SP


Contig350D
24351562_f3_298
1559
4396
255
85


Contig350D
24353390_c2_479
1560
4397
696
232
421
1.50E−39

Synechocystis sp.

d1011336
hypothetical proteinSynechocystis sp. PCC6803 complete genome, 24/27,












3002966-3138603.ribitol dehydrogenaseORF_ID


Contig350D
24406952_c1_330
1561
4398
447
149
188
7.40E−15

Rhodobacter

P31078
petPprotein of unknown functionR.capsulatus petP, petR, and











capsulatus


fbcF genes.part of the pctPR operon in front of fbc operon


Contig350D
24407875_c3_524
1562
4399
753
251
350
5.00E−32

Escherichia coli

d1016320
Probable carnitine transporter E.coli genomic DNA, Kohara clone #332 (40.4-












40.7 min.).ORF_ID


Contig350D
24415887_c2_431
1563
4400
927
309


Contig350D
24429663_c1_332
1564
4401
933
311
326
1.80E−29

Bacillus subtilis

P42422
B65Ehypothetical proteinBacillus subtilis 15 kb chromosome segment












contains the iol operon.homologous to sensor protein BvgC, His protein


Contig350D
24432327_c2_437
1565
4402
1665
555
1633
5.50E−168

Laccococcus lactis

g473902
alsalpha-acetolactate synthaseLactococcus lactis alpha-












acetolactate synthase (als) gene, completecds.


Contig350D
24500300_c2_423
1566
4403
1206
402
1208
6.00E−123

Bacillus subtilis

e332185
ylnBputative sulfate adenylyltransferaseBacillus subtilis pyrE












to yloA gene region.similar to sulfate adenylyltransferase


Contig350D
245443_c1_374
1567
4404
696
232
375
1.10E−34

Bacillus subtilis

e1185176
yloWputative YhaQ proteinBacillus subtilis complete genome (section 9 of












21) similar to phosphoglycerate dehydrogenase


Contig350D
24611567_c2_459
1568
4405
1074
358
478
1.40E−45

Bacillus anthracis

d1003632
depORFBacillus anthracis plasmid pTE702 dep gene for ORF, complete












cds.


Contig350D
24617262_c1_355
1569
4406
825
275
690
4.70E−68

Bacillus subtilis

P52996
panBketopantoate hydroxymethyltransferaseBacillus













subtilis (clone YAC15-6B) ypiABF genes, qcrABC genes, ypjABCDEFGHI













genes, bitA gene, panBCD genes, dinG gene, ypmB gene, aspB gene, asnS gene,












dnaD gene, nth gene and ypoC gene, completecds's.47.1% of identi


Contig350D
24641932_c2_417
1570
4407
672
224
476
2.20E−45

Bacillus subtulis

e1186160
yvcPhypothetical proteinBacillus subtilis complete genome (section 18 of












21) similar to two-component response regulator [YveQ


Contig350D
24643930_c3_548
1571
4408
696
232
399
3.20E−37

Escherichia coli

P33373
yohKyohK proteinEscherichia coli K-12 MG1655 sectioin 193 of 400 of the












completegenome.yohK proteino231; residues 10295 are 100 pct identical to aa


Contig350D
24646963_c1_338
1572
4409
1350
450
1703
2.10E−175

Staphylococcus

e315090
ORF454S.sciuri mecA1 gene, strain K3 (MM2).











sciuri



Contig350D
24648502_c3_526
1573
4410
468
156
228
4.30E−19

Bacillus subtilis

P38049
yhgCHypothetical proteinBacillus subtilis penicillin-binding protein (pbpF)












gene, 5′ end.product unknown


Contig350D
24665957_c3_551
1574
4411
1494
498
1335
2.10E−136

Bacillus subtilis

P39211
xylBxylulose kinaseBacillus subtilis SpoVK (spoVK), YnbA (ynbA), TnbB












(ynbB), GlnR (glnR), glutamine synthetase (glnA), YnaA (ynaA), YnaB












(ynaB), YnaC (ynaC), YnaD (ynaD), YnaE (ynaE), YnaF (ynaF), YnaG












(ynaG), YnaH (ynaH), YnaI (ynaI), YnaJ (ynaJ), xylan be


Contig350D
24722175_c1_370
1575
4412
1101
367
353
2.40E−32

Bacillus subtilis

e1184494
ywtBcapsular polyglutamate biosynthesis homolog ywtBBacillus













subtilis complete genome (section 19 of 21) similar to capsular polyglutamate













biosynthesis


Contig350D
24730438_c2_461
1576
4413
420
140
276
3.50E−24

Haemophilus

P44734
H10501high affinity ribose transport protein (rbsD) Haemophilus influenzae











influenzae


from bases 515922 to 527487 (section 47 of 63) of the complete genome.similar to












GB


Contig350D
24797140_c2_474
1577
4414
900
300
145
6.10E−08

PSEUDOMONAS

P22862
ARYLESTERASE, (ARYL-ESTER HYDROLASE)











FLUORESCENS



Contig350D
24814838_c2_443
1578
4415
870
290
350
5.00E−32

Synechocystis sp.

d1019435
hypothetical proteinSynechocystis sp. PCC6803 complete genome, 26/27,












3270710-3418851.ORF_ID


Contig350D
24817202_c1_358
1579
4416
1809
603
799
1.90E−116

Bacillus subtilis

g1934616
yrhLhypothetical protein YrhLBacillus subtilis cysteine synthase (yrhA),












crystathioninegama-lyase (yrhB), YrhC (yrhC), YrhD (yrhD), formate












dehydrogenasechain A (yrhE), YrhF (yrhF), formate dehydrogenase (yrhG),












YrhH (yrhH), regulatory protein (yrhI), cyto


Contig350D
250178_c3_555
1580
4417
234
78


Contig350D
2507950_f1_43
1581
4418
216
72


Contig350D
25398426_f1_48
1582
4419
198
66


Contig350D
25429700_c2_395
1583
4420
1356
452
130
1.80E−05

Schistosoma

g454844

Schistosoma mansoni p48 eggshell protein gene, complete cds.ORF3












mansoni



Contig350D
25578215_c3_518
1584
4421
543
181
483
4.00E−46

Staphylococcus

e316582
ORF141S.sciuri mecA gene, strain K11 (792).











sciuri



Contig350D
2557962_f2_172
1585
4422
1377
459
953
6.30E−96

Enterococcus

P37061
noxNADH oxidaseS.faecalis nox gene for NADH oxidase.











faecalis



Contig350D
25600015_c3_527
1586
4423
1632
544
1561
2.40E−160

Bacillus subtilis

g2293232
ytcIYtcIBacillus subtilis rrnB-dnaB genomic region.putative acetate CoA-












ligase


Contig350D
25961087_f1_23
1587
4424
813
271
399
3.20E−37

Bacillus subtilis

P54721
yfiEunknownBacillus subtilis complete genome (section 5 of 21) similar to












hypothetical proteins from B. subtilis


Contig350D
26179777_c1_379
1588
4425
1818
606
522
3.00E−50

Synechocystis sp.

d1011128
hypothetical proteinSynechocystis sp. PCC6803 complete genome, 22/27,












2755703-2868766.ORF_ID


Contig350D
26353411_c1_316
1589
4426
576
192


Contig350D
26380265_c3_503
1590
4427
1263
421
1190
4.90E−121

Lactobacillus sake

e1227704
arcAarginine deiminaseLactobacillus sake DNA encoding the arginine-












deiminase pathwaygenes.


Contig350D
26383512_c1_356
1591
4428
1398
466
1195
1.40E−121

Bacillus subtilis

d1020148
ydgFamino acid ABC transporter (permease) homolog ydgFBacillus













subtilis genome sequence, 148 kb sequence of the regionbetween 35 and 47













degree.PROBABLE AMINO ACID TRANSPORT PERMIASE.


Contig350D
26571937_f2_128
1592
4429
789
263
838
9.70E−84

Bacillus subtilis

e1183189
yjbTthiamin biosynthesis homolog yjbTBacillus subtilis complete genome












(section 7 of 21) similar to thiamin biosynthesis


Contig350D
26595641_f2_129
1593
4430
621
207
416
5.10E−39

Lactococcus lactis

Q48630
aplalkaline phosphatase like proteinL.lactis (MG 1363) apl gene for












alkaline phosphatase like protein.


Contig350D
26605001_c3_571
1594
4431
825
275
686
1.20E−67

Bacillus subtilis

P46331
yxbGprobable oxidoreductaseBacillus subtilis genomic DNA, 36 kb region












between gnt and ioloperons.conserved universally


Contig350D
26672512_c1_377
1595
4432
192
64


Contig350D
273452_c2_452
1596
4433
1278
426
800
1.00E−79

Archaeoglobus

g2648815
AF17363-hydroxy-3-methylglutaryl-coenzyme A reductaseArchaeoglobus











fulgidus



fulgidus section 124 of 172 of the complete genome.similar to SP



Contig350D
2739050_c2_453
1597
4434
927
309
583
1.00E−56

Bacillus subtilis

P39592
ipa-24dhypothetical proteinB.subtilis genomic region (325 to 333).alternate












gene name


Contig350D
2739561_f1_14
1598
4435
1440
480
1505
2.00E−154

Bacillus subtilis

P37948
glpTglycerol 3-phosphate permeaseB.subtilis glpT and glpQ genes












for glycerol 3-phosphate permeaseand glycerophophoryl diester












phosphodiesterase.hexose phosphate transport protein uhpTalternate gene












name


Contig350D
2760930_f1_21
1599
4436
189
63


Contig350D
2790936_f2_305
1600
4437
954
318
834
2.60E−83

Streptococcus

Q59935
pmiMannosephosphate IsomeraseS.mutans pmi gene for











mutans


mannosephosphate isomerase (complete cds) andscrK gene for fructokinase












(partial cds).


Contig350D
2823562_c3_533
1601
4438
1365
455
909
2.90E−91

Pyrococcus

d1028608
PHCC050438aa hypothetical aminotransferasePyrococcus horikoshii











horikoshii


OT3 genomic DNA, 1300517-1338254 ni position, clonecontains












aminotransferases class-111


Contig350D
2867961_c2_469
1602
4439
963
321
410
2.20E−38

Bacillus subtilis

d1023108
ycdHYcdHBacillus subtilis genomic DNA, 22 to 25 degree region,












completecds.homologue of adhesion protein precursor of


Contig350D
29352312_c3_514
1603
4440
765
255
617
2.60E−60

Bacillus subtilis

P42423
B65Fhypothetical proteinBacillus subtilis 15 kb chromosome segment












contains the iol operon.homologous to cell division protein FtsE of E.


Contig350D
29400332_c1_385
1604
4441
417
139
309
1.10E−27

Bacillus subtilis

d1020028
ydaThypothetical protein ydaTBacillus subtilis genome sequence, 148 kb












sequence of the regionibetween 35 and 47 degree.FUNCTION UNKNOWN.


Contig350D
29695327_c3_517
1605
4442
750
250


Contig350D
30133562_c1_318
1606
4443
1191
397
306
2.30E−27

Bacillus subtilis

P37498
yybFunknownB. subtilis DNA, 180 kilobase region of replication












origin similar to antibiotic resistance protein


Contig350D
30470325_c3_561
1607
4444
1953
651
425
6.80E−38

Bacillus subtilis

e1186043
yvaCconserved hypothetical protein yvaCBacillus subtilis complete genome












(section 18 of 21) similar to hypothetical proteins


Contig350D
30651577_c3_552
1608
4445
612
204


Contig350D
31693_c2_410
1609
4446
699
233
128
6.00E−08

Streptococcus

JH0364
hypothetical protein 176 (SAGP 5′ region)











pyogenes



Contig350D
31720942_12_200
1610
4447
576
192


Contig350D
32221012_c1_383
1611
4448
471
157
114
7.60E−06

Homo sapiens

g2062692
NPT4sodium phosphate transporterHuman sodium phosphate












transporter (NPT4) mRNA, complete cds.


Contig350D
32664093_f2_127
1612
4449
627
209
142
5.50E−10

Aquifex aeolicus

g2983767
thiEIthiamine phosphate synthaseAquifex aeolicus section 68 of












109 of the complete genome.


Contig350D
33211092_f3_256
1613
4450
471
157


Contig350D
33241093_c2_448
1614
4451
1557
519
1634
4.30E−168

Bacillus subtilis

e1182273
ycgN68% identity protein loBacillus subtilis complete genome (section 2 of












21) similar to 1-pyrroline-5-carboxylate dehydrogenase


Contig350D
33242842_c1_388
1615
4452
2871
957
315
1.70E−24

Saccharomyccs

g914990
YDR332WYdr332wpSaccharomyces cerevisiae chromosome IV cosmid











cerevisiae


9798.Similar to DEAD box family helicases


Contig350D
33359381_c2_402
1616
4453
210
70


Contig350D
33391337_c2_484
1617
4454
864
288


Contig350D
33620176_c3_528
1618
4455
858
286
494
2.80E−47

Staphylococcus

d1020251
orf30Staphylococcus aureus DNA for sigma70 operon, complete cds.











aureus



Contig350D
3402312_c1_365
1619
4456
1761
587
1316
2.20E−134

Bacillus subtilis

d1020024
ydaPpyruvate oxidase homolog ydaPBacillus subtilis genome sequence,












148 kb sequence of the regionbetween 35 and 47 degree.SIMILAR TO












PYRUVATE OXIDASE AND ACETOLACTATE


Contig350D
34197318_f3_258
1620
4457
903
301
1117
2.70E−113

Staphylococcus

Q07159
fdafructose-bisphosphate aldolaseS.carnosus fda gene.











carnosus



Contig350D
34410843_c2_399
1621
4458
1431
477


Contig350D
34412952_c3_573
1622
4459
783
261
580
2.20E−56

Escherichia coli

P77307
YBBMhypothetical protein b0491Escherichia coli K-12 MG1655












section 45 of 400 of the completegenome.o268; This 268 aa ORF












is 27 pct identical (9 gaps)


Contig350D
34617937_f3_296
1623
4460
525
275
223
1.10E−17

Dictyosiclium

g2952545
DB10coronin binding proteinDicryostelium discoideum











discoideum


coronin binding protein (DB10) mRNA, complete cds.


Contig350D
34647150_c1_331
1624
4461
1356
452
274
1.40E−23

Litomosoides

g2570198
shp3microfilarial sheath protein SHP3Litomosoides sigmodontis











sigmodontis


microfilarial sheath proteins SHP3a (shp3a) and SHP3 (shp3) genes,












complete cds.structural protein; similar to shp3 genes from


Contig350D
35193950_c2_451
1625
4462
489
163


Contig350D
35317188_c2_396
1626
4463
6414
2138
1445
2.20E−149

Caenorhabditis

g1707247
K06A9.1Caenorhabditis elegans cosmid K06A9.partial CDS; coded for by C.











elegans


elegans cDNA yk50c7.5


Contig350D
35433438_f3_231
1627
4464
1137
379
420
1.90E−39

Bacillus subtilis

e1183187
yjbRsarcosine oxidase homolog yjbRBacillus subtilis complete genome












(section 7 of 21) similar to sarcosine oxidase


Contig350D
35993802_c2_397
1628
4465
1584 528


Contig350D
36127302_c2_476
1629
4466
888
296
1058
4.70E−107

Bacillus subtilis

Q05852
gtaBUDP-glucose pyrophosphorylaseBacillus subtilis UDP-












glucose pyrophosphorylase (gtaB) gene, complete cds.Escherichia coli UTP-glucose-1-phosphate












uridylyltransferasesimilar to UDP-glucose pyrophosphorylase of


Contig350D
36151692_c2_466
1630
4467
681
227
671
4.80E−66

Bacillus subtilis

e1182773
yfkOYfkOBacillus subtilis complete genome (section 5 of 21) similar to












NAD(P)H-flavin oxidoreductase


Contig350D
36205285_c2_411
1631
4468
780
260
284
5.00E−25

Caldicellulosiruptor

P23553
XynCacetylxylosidaseCaldicellulosiruptor saccarolyticus putative transport











saccharolyticus


protein (XynG), putative transport protein (XynH), xylanase (XynF), xylanase












(XynE), xylanase (xynD), xylenase (XynA), acetylxylosidase (XynC) and












xylanase (XynB) genes, complete cds


Contig350D
36225250_c2_408
1632
4469
1542
514
2622
8.70E−273

Staphylococcus

P43148
SepP1proteaseS.epidemis gene for protease.











epidermidis



Contig350D
36617832_c2_422
1633
4470
801
267
758
2.90E−75

Bacillus

P29928
COBAS-adenosyl-L-methioneBacillus megaterium S-adenosy-L-











megaterium


methioneATCC #1078


Contig350D
3909376_c2_394
1634
4471
396
132
244
8.60E−21

Helicobacter

g2314761
HP1576ABC transporter, ATP-binding protein (abc) Helicobacter pylori section











pylori


133 of 134 of the complete genome.malK protein homologysimilar












to EGAD


Contig350D
3910675_f3_293
1635
4472
234
78


Contig350D
3923842_c2_460
1636
4473
891
297
442
8.90E−42

Bacillus

P40419
hypothetical 30.5K chainB.megaterium glucose dehydrogenase (EC 1.1.1.47)











megaterium


and ORFs.ORF2


Contig350D
3941078_f1_19
1637
4474
324
108
110
1.40E−06

Bacillus subtilis

e1183188
yjbShypothetical protein yjbSBacillus subtilis complete genome (section 7 of












21)


Contig350D
3945818_f3_216
1638
4475
1485
495
1215
1.10E−123

Bacillus subtilis

e1182164
ybeCamino acid transporter homolog ybeCBacillus subtilis complete genome












(section 2 of 21) similar to amino acid transporter


Contig350D
3953400_f1_82
1639
4476
195
65


Contig350D
4003431_f2_195
1640
4477
204
68


Contig350D
4079552_f2_171
1641
4478
630
210


Contig350D
4079626_f1_88
1642
4479
192
64


Contig350D
4094703_c1_333
1643
4480
2022
674
224
3.10E−21

Bacillus subtilis

g2293178
ytsDYtsDBacillus subtilis rrnB-dnaB genomic regioin.similarity to NADH












dehydrogenase


Contig350D
40966_c3_495
1644
4481
1626
542


Contig350D
4100938_c2_472
1645
4482
534
178
291
1.60E−25

Bacillus subtilis

P42237
ycbEglucarate dehydrataseBacillus subtilis DNA around 20 degrees region












of chromosomecontaining yckA-T genes.similar to glucarate transporter


Contig350D
4148428_f2_112
1646
4483
1149
383.
528
6.90E−51

Alcaligenes

P14940
ADHalcohol dehydrogenase, A.eutrophus alcohol dehydrogenase (ADH) gene,











eutrophus


complete cds. alcohol dehydrogenasealcohol dehydrogenase












(EC 1.1.1.1)


Contig350D
4167842_f2_112
1647
4484
201
67


Contig350D
4303377_f2_142
1648
4485
270
90


Contig350D
4303927_c1_381
1649
4486
312
104


Contig350D
4329453_c1_367
1650
4487
336
112
220
3.00E−18

Bacillus subtilis

d1020138
ydfQthioredoxin homolog ydfQBacillus subtilis genome sequence, 148 kb












sequence of the regionbetween 35 and 47 degree.SIMILAR TO THIOREDOXIN.


Contig350D
4336088_c1_342
1651
4488
624
208
283
6.30E−25

Bacillus subtilis

e332189
ylnFYlnF proteinBacillus subtilis pyrE to yloA gene region.similar to uroporphyrin












III C-methyltransferase


Contig350D
4459375_f2_207
1652
4489
207
69


Contig350D
4491713_f2_113
1653
4490
1542
514
416
5.10E−39

Helicobacier

g2313368
HP0278guanosine pentaphosphate phosphohydrolaseHelicobacter pylori











pylori


section 24 of 134 of the complete genome.similar to EGAD


Contig350D
4574012_f1_46
1654
4491
1080
360
600
1.60E−58

Drosophila

JN0500
dhoddihydroorotate oxidase,, mitochondrialdihydroorotate oxidase











melanogaster



Contig350D
4662_f2_168
1655
4492
318
106


Contig350D
4687752_c1_359
1656
4493
1185
395
773
7.50E−77

Bacillus subtilis

e1184948
ykrVaspartate aminotransferase homolog ykrVBacillus subtilis complete genome












(section 8 of 21) similar to aspartate aminotransferase


Contig350D
4713377_f2_144
1657
4494
447
149


Contig350D
4719775_c3_562
1658
4495
744
248
434
6.30E−41

Bacillus subtilis

P39583
ipa-7dGTP-pyrophosphokinase homolog ywaCB.subtilis genomic region (325 to












333).alternate gene name


Contig350D
4723510_c2_430
1659
4496
2661
887
2374
1.70E−246

CLOSTR1DIUM

P22983
PPDKDIKINASE)











SYMBIOSUM



Contig350D
4727187_c2_403
1660
4497
2889
963
617
6.20E−58

Lactococcus lactis

P49022
pipLactococcus lactis pip and gerC2 genes, complete cds's, and rcggene, 5′












end of cds.GTG start codon


Contig350D
4787807_f3_218
1661
4498
210
70


Contig350D
4870907_f1_42
1662
4499
231
77


Contig350D
4876932_c2_416
1663
4500
249
83


Contig350D
4882893_c3_493
1664
4501
1209
403
241
2.40E−26

Aquifex aeolicus

g2982812
secYpreprotein translocase SecYAquifex aeolicus section 4 of 109 of the complete












genome.


Contig350D
4891002_c2_462
1665
4502
1116
372
671
4.80E−66

Clostridium

A43577
regulatory protein pfoR











perfringens



Contig350D
5117137_c2_457
1666
4503
459
153
499
8.20E−48

Bacillus subtilis

e1184495
ywtAcapsular polyglutamate biosynthesis homolog ywtABacillus













subtilis complete genome (section 19 of 21) similar to capsular polyglutamate













biosynthesis


Contig350D
5128425_f2_203
1667
4504
1878
626
477
1.70E−45

Bacillus subtilis

e1183220
yjdCtranscriptional antiterminator (BglG famil) homolog yjdCBacillus subtilis












complete genome (section 7 of 21) similar to transcriptional












antiterminator (BglG


Contig350D
5133562_f2_160
1668
4505
222
74
180
5.20E−14

Bacillus subtilis

e1186039
yvgYmercuric transport protein homolog yvgYBacillus subtilis complete genome












(section 18 of 21) similar to mercuric transport protein


Contig350D
5136002_c2_400
1669
4506
366
122
136
2.40E−09

Bacillus subtilis

g2618844
yvlA YvlABacillus subtilis 300-304 degree genomic sequence.


Contig350D
5250087_f2_213
1670
4507
783
261
152
3.40E−09

Mus musculus

d1000902
Mouse putative primordial protein transcript.open reading frame (251 AA)


Contig350D
5281568_f3_235
1671
4508
504
168
330
6.60E−30

Escherichia coli

d1015799
Phosphinothricin acetyltransferase (ECE.coli genomic DNA, Kohara clone












#273 (32.5-32.8 min.).ORF_ID


Contig350D
5290675_c3_536
1672
4509
405
135
411
1.70E−38

Bacillus subtilis

P52999
panDaspartate 1-decarboxylaseBacillus subtilis (clone YAC15-6B) ypiABF












genes, qcrABC genes, ypjABCDEFGHI genes, birA gene, panBCD genes, dinG












gene, ypmB gene, aspB gene, asnS gene, dnaD gene, nth gene and ypoC gene,












completecds's.48.3% of identity to the Es


Contig350D
5314077_c1_335
1673
4510
1593
531
1036
1.00E−104

Escherichia coli

P31448
yidKhypothetical 62.1 kD protein in ilvo-ibpdEscherichia coli K-12 MG1655












section 335 of 400 of the completegenome.f571; 100 pct identical












to YIDK_ECOLI SW


Contig350D
5369212_c3_567
1674
4511
1509
503
425
1.60E−39

Bacillus subtilis

P13484
tagEUDP-glucoseBacillus subtilis rodC operon.rodD (gtaA) polypeptide (AA 1-












673)


Contig350D
56693_c1_324
1675
4512
792
264
778
2.20E−77

Bos taurus

g2058476
acetoin reductaseBos taurus acetoin reductase mRNA, complete cds.similar












to acetoin reductase of Klebsiella


Contig350D
5915653_f2_197
1676
4513
183
61


Contig350D
6047827_c2_438
1677
4514
705
235
569
3.10E−55

Lactococcus lactis

g2565161
aldBAldBLactococcus lactis unknown gene, partial cds, and HisC












(hisC), unknown, HisG (hisG), unknown, HisB (hisB), unknown, HisH (hish), HisA












(hisA), HisF (hisF), His1E (his1E), unknown, unknown, LeuA (leuA), LeuB












(leuB), LeuC (leuC), LeuD (leuD), unknown, I


Contig350D
6070938_c1_348
1678
4515
1773
591
1342
3.80E−137

Escherichia coli

P17444
betAcholine dehydrogenaseEscherichia coli K-12 MG1655 section 28 of 400 of












the completegenome.alcohol oxidasef556; 100 pct identical to












BETA_ECOLI SW


Contig350D
6136050_c2_449
1679
4516
246
82


Contig350D
6136527_c2_424
1680
4517
615
205
618
2.00E−60

Bacillus subtilis

e332186
ylnCputative adenosine 5-phosphosulfate kinaseBacillus subtilis pyrE to yloA gene












region.similar to adenylylsulfate kinase


Contig350D
6369688_f2_125
1681
4518
935
305
119
2.90E−05

Methanococcus

Q57819
MJ0374lipoprotein B (lppB) Methanococcus jannaschii section











jannaschii


32 of 150 of the complete genome.similar to GB


Contig350D
6442202_f3_233
1682
4519
1050
350
330
8.70E−28

Bacillus subtilis

P37520
yyaDunknownB. subtilis DNA, 180 kilobase region of replication












origin.unnamed protein product


Contig350D
6678507_f3_267
1683
4520
207
69


Contig350D
6829812_c1_372
1684
4523
948
336
592
3.10E−57

Haemophilus

P44331
H10505ribokinase (rbsK) Haemophilus influenzae from bases 515922 to 527487











influenzae


(section 47 of 163) of the complete genome.ribokinasesimilar to GB


Contig350D
6837938_f1_103
1685
4522
3563
1187
198
3.80E−34

Homo sapiens

P51861
CDR1cerebellar degeneration-related proteinHuman cerebellar-degeneration-












related antigen (CDR34) gene, complete cds.cerebellar-degeneration-related












antigen (CDR34)


Contig350D
6844032_c3_522
1686
4523
1344
448
589
2.40E−57

Escherichia coli

P04539
dcuAanaerobic c4-dicarboxylate transporter dcuaEscherichia coli K-12












MG1655 section 376 of 400 of the completegenome.dicarboxylate












membrane-transporter protein Af433; 100 pct identical amino acid sequence












and


Contig350D
6928_c1_373
1687
4524
843
281


Contig350D
7227175_c3_508
1688
4525
189
63


Contig350D
7228517_c3_568
1689
4526
411
337
391
3.50E−15

Mycobacterium

e317133
mutTMutTMycobacterium tuberculosis cosmid 165.MTC165.27, mutT, len











tuberculosis



Contig350D
7234627_c1_389
1690
4527
230
70


Contig350D
7245377_c1_368
1691
4528
1002
334
258
2.80E−22

Acinetobacter

g1209223
estesteraseAcinebacter lwofii orf1 and esterase (est) gene, complete cds.











lwoffii



Contig350D
7301078_c3_488
1692
4529
465
155
340
5.80E−31

Pseudomonas

g3114664
htxDATPase component HtxDPseudomonas stutzeri putative











stutzeri


alpha-ketoglutarate-dependenthypophosphite dioxygenase












(htxA), binding protein component HcxB (htxB), inner membrane component












HtxC (htxC), ATPase component HtxD (htxD) inner membrane component












HtxE (h


Contig350D
787677_f2_152
1693
4530
483
161
246
5.30E−21

Staphylococcus

g2735506
SceBSceB precursorStaphylococcus carnosus N5, N10-











carnosus


methylenetetrahydromethanopterinreductase homolog, SceB precursor (sceB) and












putative transmembraneprotein genes, complete cds, and putative Na+/H+












antiporter NhaC (nhaC) gene, partial cds.major secret pro


Contig350D
823518_f1_35
1694
4531
225
75


Contig350D
860425_c3_553
1695
4532
258
86
106
3.60E−06

Paramecium

g624122
a56LParamecium bursaria Chlorella virus I, complete genome.contains type











bursaria Chlorella


I hydrophobic transmembrane region










virus I


Contig350D
86088_f2_21
1696
4533
369
123
154
3.00E−11

Staphylococcus

g2735504

Staphylococcus carnosus N5, N10-methylenetetrahydromethanopterinreductase












carnosus


homolog, SceB precursor (sceB) and putative transmembraneprotein genes,












complete cds, and putative Na+/H+ antiporter NhaC (nhaC) gene, partial












cds.Orf1


Contig350D
860917_f2_191
1697
4534
201
67


Contig350D
895253_c3_497
1698
4535
510
170
302
6.10E−27

Helicobacter

g2313314
HP0224 peptide methione sulfoxide reductase (msrA) Helicobacter pylori











pylori


section 20 of 134 of the complete genome.similar to EGAD


Contig350D
901377_c2_441
1699
4536
327
109


Contig350D
953142_f1_51
1700
4537
954
318
228
4.30E−19

Mycobacterium

Q50648
MTCY227.28cunknownMycobacterium tuberculosis cosmid











tuberculosis


Y227.MTCY227.28c, unknown, len


Contig350D
961562_c1_319
1701
4538
186
62


Contig350D
968800_c2_446
1702
4539
804
268
1031
3.40E−104

Staphylococcus

e244971

S.aureus orfs 1,2,3 & 4.ORF1












aureus



Contig350D
978965_c3_511
1703
4540
213
71


Contig350D
9875333_c1_376
1704
4541
1533
511
1134
4.20E−115

Vibrio cholerae

P23240
aldAaldehyde dehydrogenaseVibrio cholerae pathogenicity island, putative












transposase, aldehyde dehydrogenase (aldA), toxR-activated gene A












protein (tagA), putative inner membrane protein, and putative zincmetalloprotease












genes, complete cds; and toxR-activa


Contig351D
15055313_c3_16
1705
4542
444
148
726
7.20E−72

Staphylococcus

e1237897
ORF142hypothetical proteinStaphylococcus aureus mecA,











aureus


mecR1, mec1 genes and ORF168, ORF142, ORF44, ORF145 and












ORF224.ORF142


Contig351D
21644175_c3_12
1706
4543
273
91


Contig351D
24407812_c3_15
1707
4544
771
257
738
3.80E−73

Staphylococcus

g48713
hypothetical proteinS. aureus hypervariable region, 3′ to mecA











aureus


gene.orf145


Contig351D
29320127_c3_14
1708
4545
390
130
139
5.40E−09

Bacillus subtilis

P40830
pksGunknownBacillus subtilis W168 polyketide synthase (pksX and












pksorfx6) genes, complete cds.pksorfx2; similar to hamster


Contig351D
29300687_c3_11
1709
4546
1191
397


Contig351D
34016880_f2_3
1710
4547
2028
676
3469
0

Staphylococcus

g46994
mecApenicillin-binding protein mecA, low-affinityS. epidermidis mecA gene











epidermidis


for PBP2′ (penicillin binding protein 2′).PBP2′(AA 1-668)


Contig351D
6828125_c1_10
1711
4548
252
84


Contig351D
6929686_f1_1
1712
4549
693
231
1200
4.20E−122

Staphylococcus

P19380
putative transposaseS. aureus IS431mec gene associated with methicillin











aureus


resistance.putative transposase (AA 1-224)


Contig352D
10320337_c3_135
1713
4550
192
64


Contig352D
10359688_f3_74
1714
4551
198
66


Contig352D
1071002_f3_54
1715
4552
411
137


Contig352D
10727217_f1_23
1716
4553
270
90
212
2.10E−17

Bacillus subtilis

d1020027
ydaSconserved hypothetical protein ydaSBacillus subtilis genome sequence,












148 kb sequence of the regionbetween 35 and 47 degree.FUNCTION












UNKNOWN.


Contig352D
111592_c2_117
1717
4554
243
81


Contig352D
1205000_f1_12
1718
4555
555
185
314
3.30E−28

Bacillus subtilis

d1020012
ydaFacetyltransferase homolog ydaFBacillus subtilis genome sequence,












148 kb sequence of the regionbetween 35 and 47 degree.PROBABLE












ACETYLTRANSFERASE.


Contig352D
12536337_f2_38
1719
4556
327
109


Contig352D
134677_f2_45
1720
4557
1101
367
1373
2.00E−140

Bacillus subtilis

P37518
yyaFunknownB.subtilis DNA, 180 kilobase region of replication












origin.similar to hypothetical proteins


Contig352D
14220027_f3_55
1721
4558
1143
381
190
2.50E−12

Enterococcus

d1025733
bacGEnterococcus faecalis plasmid pPD1 bacA, bacB, bacC, bacD,











faecalis


bacE, bacF, bacG, bacH and bacI genes, complete cds.


Contig352D
14547556_f1_29
1722
4559
453
151


Contig352D
14728382_f1_21
1723
4560
300
100
336
1.50E−30

Bacillus subtilis

P21468
rpsFribosomal protein S6B. subtilis DNA, 180 kilobase region of replication












origin.Escherichia coli ribosomal protein S6


Contig352D
14881552_f1_14
1724
4561
216
72


Contig352D
15052318_f2_30
1725
4562
1395
465
1606
4.00E−165

Bacillus subtilis

P25811
tdhFthiophen and furan oxidationB. subtilis DNA, 180 kilobase region of












replication origin.homologous to E.coli 50 K


Contig352D
15752213_f1_5
1726
4563
270
90


Contig352D
16432963_c1_88
1727
4564
1116
372
972
6.10E−98

Bacillus subtilis

e1183207
yjclcysthionine gamma-synthase homolog yjclBacillus subtilis complete












genome (section 7 of 21) similar to cystathionine gamma-synthase


Contig352D
19548192_c3_136
1728
4565
765
255


Contig352D
1960300_f1_11
1729
4566
201
67


Contig352D
20517318_f1_7
1730
4567
1200
400
1171
5.00E−119

Thermoanaero-

e281310
thlAacetyl coenzyme A acetyltransferase (thiolase) C.thermosaccharolyticum etfB,











bacterium


etfA, hbd, thlA and actA genes.











thermosacchara-












lyticum



Contig352D
2148468_f2_34
1731
4568
2073
691
1498
1.10E−153

Staphylococcus

P10335
GEHtriacylglycerol lipase, S.aureus geh gene encoding lipase (glycerol ester











aureus


hydrolase).lipase precursor (geh; EC 3.1.1.3)


Contig352D
21506575_c1_85
1732
4569
897
299
1331
5.20E−30
Bacteriophage
e257764
LyslysinLactobacillus bacteriophage phigle DNA for Rorf162, Holin,










phigle

Lysin, and Rorf175 genes.gtg start codon


Contig352D
23462762_c3_128
1733
4570
1527
509
2298
1.90E−238

Staphylococcus

g1916317
ahpFalkyl hydroperoxide reductase subunit FStaphylococcus aureus alkyl











aureus


hydroperoxide reductase subunit C (aphC) and subunit F (aphF) genes,












complete cds.AhpF


Contig352D
23634786_f3_56
1734
4571
1200
400
692
2.90E−68

Enterococcus

d1025735
baclEnterococcus faecalis plasmid pPD1 bacA, bacB, bacC, bacD, bacE, bacF,











faecalis


bacG, bacH and bacI genes, complete cds.


Contig352D
23860812_f2_37
1735
4572
603
201
534
1.60E−51

Staphylococcus

g1595810
spsBtype-1 signal peptidase SpsBStaphylococcus aureus type-1 signal











aureus


peptidase SpsA (spsA) gene, andtype-1 signal peptidase SpsB (spsB) gene,












complete cds.signal peptidase, leader peptidase, serine


Contig352D
24220062_c3_129
1736
4573
285
95


Contig352D
24406338_c3_138
1737
4574
186
62


Contig352D
24431502_c3_137
1738
4575
846
282
297
2.10E−26

Archaeoglobus

g2649574
AF1021ABC transporter, ATP-binding proteinArchaeoglobus fulgidis section











fulgidus


74 of 172 of the complete genome.similar to GB


Contig352D
24647142_c2_116
1739
4576
645
215
575
7.20E−56

Staphylococcus

c352094
orf5hypothetical proteinStaphylococcus xylosus lacR, lacP, lacH genes and 2











xylosus


ORF's.


Contig352D
24665811_c3_127
1740
4577
486
162
166
1.60E−12

Anolis pulchellus

g1197667
vitellogeninAnolis pulchellus vitellogenin mRNA, partial cds.ApVtg5;












similar to chicken and Xenopus phosvitin


Contig352D
25548452_f1_20
1741
4578
915
305
354
1.90E−32

Bacillus subtilis

e1181925
ykuTYkuT proteinBacillus subtilis 29 kB DNA fragment from ykwC gene to cse15












gene.similar to hypothetical proteins


Contig352D
25554012_c2_109
1742
4579
213
71


Contig352D
25667767_c3_131
1743
4580
1191
397
907
4.70E−91

Bacillus subtilis

e1183208
yjcJcystathionine beta-lyase homolog yjcJBacillus subtilis complete genome












(section 7 of 21) similar to cystathionine beta-lyase


Contig352D
25679712_f3_59
1744
4581
660
220
153
1.40E−09

Schizosaccharo-

e317491
SPBC3D6.14cunknownS.pombe chromosome ll cosmid











myces pombe


c3D6.SPBC3D6.14c, unknown; partial; serine rich,


Contig352D
26198535_c3_133
1745
4582
765
255
117
7.10E−07

Mycobacterium

e1253947
MTV048.03hypothetical protein MTV048.03Mycobacterium tuberculosis











tuberculosis


sequence v048.MTV048.03, len


Contig352D
26214002_f3_64
1746
4583
870
290
627
2.20E−61

Bacillus subtilis

P26497
AF0818acylphosphalase (acyP) Archaeoglobus fulgidus section 60











fulgidus


of 172 of the complete genome.similar to SP


Contig352D
26365911_f1_3
1747
4584
561
187
203
1.90E−16

Bacillus subtilis

d1020119
ydeStranscriptional regulator (TetR/AcrR famil( homolog












ydeSBacillus subtilis genome sequence, 148 kb sequence of the regionbetween 35












and 47 degree.PROBABLE TRANSCRIPTIONAL REGULATOR,












SIMILAR TO


Contig352D
26600015_f1_1
1748
4585
354
118
280
1.30E−24

Bacillus subtilis

P25814
rnpAprotein component of ribonuclease PB. subtilis DNA, 180 kilobase region of












replication origin.


Contig352D
26756660_c2_121
1749
4586
651
217


Contig352D
2745462_c1_81
1750
4587
642
214


Contig352D
29860902_c3_132
1751
4588
2277
759
1816
2.20E−187

Bacillus subtilis

e1181518
metCMetCBacillus subtilis 168 56 kb DNA fragment between xlyA and ykoR.


Contig352D
30060255_f1_7
1752
4589
384
128


Contig352D
31443827_f2_46
1753
4590
510
170
563
1.30E−54

Bacillus subtilis

P37455
ssbsingle strand DNA binding proteinB. subtilis DNA, 180 kilobase region of












replication origin.single-stranded DNA-binding protein homology.


Contig352D
32062762_c2_123
1754
4591
183
61


Contig352D
32423410_c1_91
1755
4592
210
70
167
1.20E−12

Archeoglobus

g2648767
AF1793repressor proteinArchaeoglobus fulgidus section 128 of 172 of the











fulgidus


complete genome.similar to GB


Contig352D
3320317_f3_65
1756
4593
237
79
150
7.80E−11

Streptococcus

g2109447

Streptococcus pneumoniae R801 tRNA-Arg gene, partial sequence, andputative












pneumoniae


serine protease (sphtra), SPSpoJ (spspoJ), initiatorprotein (spdnaa) and












beta subunit of DNA polymerase III (spdnan) genes, complete cds.ORFX


Contig352D
33228180_f1_16
1757
4594
243
81


Contig352D
34180340_f2_33
1758
4595
711
237
609
1.80E−59

Enterococcus

d1025734
bacHEnterococcus faecalis plasmid pPD1 bacA, bacB, bacC, bacD,











faecalis


bacE, bacF, bacG, bacH and bacI genes, complete cds.


Contig352D
34182952_f3_58
1759
4596
402
134


Contig352D
34414012_f1_22
1760
4597
273
91
336
1.50E−30

Bacillus subtilis

d1005761
rpsRribosomal protein S18B. subtilis DNA, 180 kilobase region of replication












origin.Escherichia coli ribosomal protein S18


Contig352D
34414187_c1_82
1761
4598
399
133
152
4.80E−11

Bacillus subtilis

d1020108
ydeHhypothetical protein ydeHBacillus subtilis genome sequence, 148 kb












sequence of the regionbetween 35 and 47 degree.FUNCTION UNKNOWN.


Contig352D
34417552_f3_53
1762
4599
381
127


Contig352D
34580342_c1_94
1763
4600
771
257
802
6.40E−80

Bacillus subtilis

g2293177
ytsCtransporterBacillus subtilis rrnB-dnaB genomic region.similar to ABC












transporter (ATP-binding protein)


Contig352D
34643751_c1_79
1764
4601
591
197
910
2.30E−91

Staphylococcus

g1916316
ahpCalkyl hydroperoxide reductase subunit CStaphylococcus aureus alkyl











aureus


hydroperoxide reductase subunit C (aphC) and subunit F (aphF) genes,












complete cds.AphC


Contig352D
34664700_f2_32
1765
4602
861
287
617
2.60E−60

Bacillus subtilis

P37524
yyaADNA binding protein (probable) B. subtilis DNA, 180 kilobase region of












replication origin.unnamed protein product


Contig352D
35343807_f1_27
1766
4603
237
79


Contig352D
35978127_f3_73
1767
4604
777
259
559
3.60E−54

Bacillus subtilis

P39605
ipa-43dhypothetical proteinB.subtilis genomic region (325 to 333).alternate












gene name


Contig352D
36228126_f2_31
1768
4605
1896
632
2407
5.30E−250

Bacillus subtilis

P25812
gisAunknownB.subtilis DNA, 180 kilobase region of replication












origin.gidA proteinhomologous to E.coli gidA


Contig352D
36522507_c1_2
1769
4606
741
247
740
2.40E−73

Bacillus subtilis

P25813
gidBunknownB.subtilis DNA, 180 kilobase region of replication origin.gidB












proteinhomologous to E.coli gidB


Contig352D
4335750_c1_4
1770
4607
600
200
158
1.70E−11

Clostridium

g853809
hypothetical protein 3C.perfringens nanH gene & ORF1,2,3 & 4.ORF3











perfringens



Contig352D
4725385_c1_24
1771
4608
675
225
366
1.00E−33

Bacillus subtilis

e1183940
yrhPdihydrodipicolinate reductase homolog yrhPBacillus subtilis complete












genome (section 14 of 21) similar to dihydrodipicolinate reductase


Contig352D
4957943_f3_68
1772
4609
600
200
205
6.00E−16

Caenorhabditis

Q21122
K02B2.1Caenorhabditis elegans cosmid K02B2.Similar to 6-phosphofructo-2-











elegans


kinase.


Contig352D
5313316_c2_118
1773
4610
1413
471
245
6.90E−38

Sulfolobus

e283949
orf c01010sugar transporterS.solfataricus 100 kbp DNA fragment.











solfataricus



Contig352D
57217_c1_95
1774
4611
207
69


Contig352D
582777_c2_103
1775
4612
1476
492
1405
8.00E−144

Bacillus subtilis

P54596
yhcLhypothetical proteinB.subtilis chromosomal DNA (region 75












degreessimilarity to the proton/sodium-glutamate symport


Contig352D
6644537_c1_9
1776
4613
258
86


Contig352D
6715_c3_139
1777
4614
510
170


Contig352D
6728578_c2_120
1778
4615
1893
631
678
8.80E−67

Bacillus subtilis

g2293178
ytsDYtsDBacillus subtilis rrnB-dnaB genomic regioin.similarity to NADH












dehydrogenase


Contig352D
7297338_f1_15
1779
4616
213
71


Contig352D
9773385_c1_78
1780
4617
816
272
303
4.80E−27

Escherichia coli

g2695682
hpcG2-oxo-hept-4-ene-1,7-dioate hydrataseEscherichia coli 2-oxo-hept-4-












ene-1,7-dioate hydratase (hpcG) gene, section cds.OHED hydratase


Contig352D
9792842_c1_89
1781
4618
1851
617
1480
9.10E−152

Bacillus subtilis

e1183103
yitJYitJBacillus subtilis complete genome (section 6 of 21) similar to












hypothetical proteins


Contig352D
9854643_f2_52
1782
4619
237
79


Contig353D
11886592_f3_38
1783
4620
654
218
481
6.60E−46

Haemophilus

P44434
H10475phosphoribosyl-AMP cyclohydrolase (his1E) Haemophilus











influenzae



influenzae from bases 492332 to 505971 (section 45 of 163) of the complete













genome.hisl bifunctional enzymesimilar to SP


Contig353D
1207287_f3_36
1784
4621
621
207
365
1.30E−33

Laciococcus lactis

Q02129
hisGHisGLactococcus lactis unknown gene, partial cds, and HisC












(hisC), unknown, HisG (hisG), unknown, HisB (hisB), unknown, HisH (hish), HisA












(hisA), HisF (hisF), His1E (his1E), unknown, unknown, LeuA (leuA), LeuB












(leuB), LeuC (leuC), LeuD (leuD), unknown, I


Contig353D
14480312_f2_15
1785
4622
1308
436
588
3.00E−57

Bacillus subtilis

e1182798
acoCacetoin dehydrogenase E2 componentBacillus subtilis complete












genome (section 5 of 21) alternate gene name


Contig353D
14662577_f1_7
1786
4623
537
179


Contig353D
14725887_c2_53
1787
4624
183
61


Contig353D
14851551_c3_64
1788
4625
993
331
1143
4.70E−116

Lactococcus lactis

g2565150
unknownLactococcus lactis unknown gene, partial cds, and HisC












(hisC), unknown, HisG (hisG), unknown, HisB (hisB), unknown, HisH (hish), HisA












(hisA), HisF (hisF), His1E (his1E), unknown, unknown, LeuA (leuA), LeuB












(leuB), LeuC (leuC), LeuD (leuD), unknown, II


Contig353D
14851713_f3_27
1789
4626
966
322
941
1.20E−94

Bacilius subtilis

g2957146
acoATPP-dependent acetoin dehydrogenase, E1Bacillus subtilis












acetoin dehydrogenase enzyme system gene cluster, ribosomal protein L6-like












protein gene, partial cds, TPP-dependentacetoin dehydrogenase, E1












alpha-subunit (acoA), TPP-dependentacetoin dehydrogen


Contig353D
16689067_f2_23
1790
4627
597
199
470
9.70E−45

Lactococcus lactis

Q02134
hisBHisBLactococcus lactis unknown gene, partial cds, and HisC












(hisC), unknown, HisG (hisG), unknown, HisB (hisB), unknown, HisH (hish), HisA












(hisA), HisF (hisF), His1E (his1E), unknown, unknown, LeuA (leuA), LeuB












(leuB), LeuC (leuC), LeuD (leuD), unknown, I


Contig353D
21563751_c2_54
1791
4628
237
79


Contig353D
22656300_c1_41
1792
4629
1542
514
1225
9.50E−125

Escherichia coli

P33940
yojHyojH proteinE.coli genomic DNA, Kohara clone #373 (49.5-49.9












min.).ORF_ID


Contig353D
24070155_c1_40
1793
4630
495
165
279
1.70E−24

Bacillus subtilis

e1183223
yjdFhypothetical protein yjdFBacillus subtilis complete genome (section 7 of












21)


Contig353D
24269812_c3_62
1794
4631
627
209
210
3.40E—17

Helicobacter

g2314454
HP1286conserved hypothetical secreted proteinHelicobacter pylori section 111 of











pylori


134 of the complete genome.similar to EGAD


Contig353D
24640910_f3_28
1795
4632
519
173


Contig353D
24652312_c3_65
1796
4633
1617
539
1125
3.80E−114

Bacillus subtilis

P54417
opuDputative transporterBacillus subtilis rrnB-dnaB genomic region.alternate gene












name


Contig353D
24797900_f2_20
1797
4634
213
71


Contig353D
25510293_f2_12
1798
4635
972
324
877
7.20E−88

Bacillus subtilis

e1184489
ywtGmetabolite transport protein homolog ywtGBacillus subtilis complete












genome (section 19 of 21) similar to metabolite transport protein


Contig353D
25666427_c2_60
1799
4636
306
102


Contig353D
26385928_c1_46
1800
4637
1437
479
1441
1.20E−147

Bacillus subtilis

e1182747
yflSYflSBacillus subtilis complete genome (section 5 of 21) similar to 2-












oxoglutarate/malate translocator


Contig353D
26600425_c2_50
1801
4638
792
264
220
3.00E−18

Mus musculus

P50294
NATlartylamine N-acetyltransferaseMus musculus arylamine N-acetyltrasnferase












(NATl) gene, completecds.


Contig353D
266877_c1_39
1802
4639
450
150
285
3.90E−25

Bacillus subtilis

d1020015
ydalBacillus subtilis genome sequence, 148 kb sequence of the regionbetween 35












and 47 degree.PROBABLE TRANSCRIPTION REGULATOR,












SIMILAR TO LEU


Contig353D
26751431_f1_4
1803
4640
1062
354
1037
8.00E−105

Bacillus subtilis

g2245638
acoBTPP-dependent acetoin dehydrogenase, E1Bacillus subtilis












acetoin dehydrogenase enzyme system gene cluster, ribosomal protein L6-like












protein gene, partial cds, TPP-dependentacetoin dehydrogenase, E1












alpha-subunit (acoA), TPP-dependentacetoin dehydrogen


Contig353D
2819303_f1_2
1804
4641
363
121
192
2.80E−15

Pseudomonas

e308975
FC2.2hypothetical proteinP.fluorescens FC2.1, FC2.2, FC2.3c, FC2.4 and











fluorescens


FC2.5c open readingframes.similar to E. coli RarD (SP


Contig353D
3009382_f1_1
1805
4642
531
177


Contig353D
30360925_c1_47
1806
4643
642
214
204
1.60E−16

Haemophilus

P44658
H10357thiamine-repressed protein (nmtl) Haemophilus influenzae from











influenzae


bases 378525 to 389412 (sectioin 35 of 163) of the complete genome.similar to












GP


Contig353D
33988778_c1_43
1807
4644
660
220
636
2.50E−62

Staphylococcus

g790573
peppyrrolidone carboxyl peptidaseStaphylococcus aureus











aureus


pyrrolidone carboxyl peptidase (pep) gene, complete cds.pyrase


Contig353D
35449093_f3_35
1808
4645
831
277


Contig353D
36214052_c1_6
1809
4646
999
333
169
1.10E−10

Sulfolobus

P46218

Sulfolobus acidocaldarius RNA polymerase subunit homolog












acidocaldarius


gene, complete cds.homologous to Swiss-Prot Accession Number P20435


Contig353D
36228252_c1_11
1810
4647
777
259
678
8.80E−67

Bacillus subtilis

g2618870
hisFcyclaseBacillus subtilis 300-304 degree genomic sequence.HisF protein


Contig353D
36366326_f3_26
1811
4648
771
257
409
2.80E−38

Bacillus subtilis

g3169320
yojDYojDBacillus subtilis YojA (yojA), YojB (yojB), YojC (yojC), YojD (yojD),












YojE (yojE), YojF (yojF), YojG (yojG), YojH (yojH), YojI (yojI), YojJ (yojJ),












YojK (yojK), YojL (yojL), YojM (yojM), YojN (yojN), and YojO (yojO)












genes, complete cds; and OdhA (odh


Contig353D
4110712_f2_16
1812
4649
591
197


Contig353D
4719827_f1_8
1813
4650
417
139


Contig353D
4728187_f2_22
1814
4651
234
78


Contig353D
5203452_f1_10
1815
4652
579
193
398
4.10E−37

Lactococcus lactis

Q02132
hishHisHLactolacoccus lactisunknown gene, partial cds, and HisC












(hisC), unknown, HisG (hisG), unknown, HisB (hisB), unknown, HisH (hish), HisA












(hisA), HisF (hisF), His1E (his1E), unknown, unknown, LeuA (leuA), LeuB












(leuB), LeuC (leuC), LeuD (leuD), unknown, I


Contig353D
5963300_c1_45
1816
4653
504
168
114
7.40E−06

Pyrococcus

d1027672
PHCK021192aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA, 478722-509861 nt position, clone


Contig353D
651527_f2_24
1817
4654
732
244
359
5.60E−33

Synechocystis sp.

P74561
hisAphosphorybosilformimino-5-amino Synechocystis sp. PCC6803 complete












genome, 26/27, 3270710-3418851.ORF_ID


Contig353D
6745250_f3_30
1818
4655
207
69


Contig353D
7243832_f3_25
1819
4656
1722
574
249
2.00E−18

Methanococcus

g1500527
MJ1628M. jannaschii predicted coding region MJ1628Methanococcus











jannaschii



jannaschii section 145 of 150 of the complete genome.hypothetical protein;













identified by GeneMark;


Contig353D
784387_f1_3
1820
4657
1425
475
769
2.00E−76

Clostridium

g472330
dihydrolipoamide dehydrogenaseClostridium magnum











magnum


acoR gene, complete cds; TPP-dependent acetoindehydrogenase alpha












and beta subunit (acoAB) genes, complete cds; acoX genes,












dihydrolipoamide acetyltransferase (acoCL) genes, complete cds.


Contig353D
798838_f1_9
1821
4658
1260
420
845
1.80E−84

Aquifex aeolicus

g2983343
hisDhistidinol dehydrogenaseAquifex aeolicus section 39 of 109 of the












complete genome.


Contig354D
10240925_c3_196
1822
4659
252
84


Contig354D
10553827_c1_151
1823
4660
216
72
128
1.70E−08

Bacillus subtilis

e1182777
yfkKYfkKBacillus subtilis complete genome (section 5 of 21)


Contig354D
11125052_c2_173
1824
4661
1497
499
1715
1.10E−176

Bacillus subtilis

e1184252
yueKnicotinate phosphoribosyltransferase homolog












yueKBacillus subtilis complete genome (section 17 of 21) similar to nicotinate












phosphoribosyltransferase


Contig354D
11755317_c1_348
1825
4662
759
253
135
3.70E−07

Bacillus subtilis

e1249815
yvqFYvqF proteinBacillus subtilis 42.7 kB DNA fragment from yvsA to












yvcA.


Contig354D
117687_c2_175
1826
4663
1377
459
1704
1.70E−175

Bacillus subtilis

P12047
purBadenylosuccinate lyaseB.subtilis pur operon encoding purine biosynthesis












enzymes, 12 genes.fumarate hydratasedenylosuccinate lyase (PUR-B)


Contig354D
1214075_f2_59
1827
4664
507
169
309
1.10E−27

Haemophilus

P43707
H11384ferritin like protein (rsgA) Haemophilus influenzae from











influenzae


bases 1479577 to 1492547 (section 134 of 163) of the complete












genome.similar to SP


Contig354D
12603166_f2_51
1828
4665
303
101
300
1.60E−05

Pyrococcus

d1027339
PHBW012106aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA, 180023-216005 nt position, clone


Contig354D
1287557_f3_98
1829
4666
233
71


Contig354D
13678131_f2_83
1830
4667
840
280
299
1.30E−26

Bacillus subtilis

e1182580
ydiLhypothetical protein ydiLBacillus subtilis complete genome (section 4 of












21) transmembrane


Contig354D
1377337_c1_152
1831
4668
840
280
602
9.90E−59

Staphylococcus

g310603

Staphylococcys aureus DNA sequence encoding three ORFs, completecds;












aureus


prophage phi-11 sequence homology, 5′]flank.


Contig354D
13837927_c3_206
1832
4669
1155
385
623
9.60E−61

Staphylococcus

P06696
tnpAtnpA proteinStaphylococcus aureus transposon Tn554.(aa 1-361)











aureus



Contig354D
13851088_c1_128
1833
4670
1089
363
185
5.10E−14

Caenorhabditis

g1947171
E031H12.5Caernorhabditis elegans cosmid E03H12.coded for by C. elegans cDNA











elegans


yk170g3.5


Contig354D
1385927_c2_176
1834
4671
711
237
851
4.10E−85

Staphylococcus

Q53726
pcrApcrB proteinStaphylococcus aureus helicase required for T181 replication











aureus


(pcrA) gene, complete cds.


Contig354D
1414005_c2_191
1835
4672
579
193
324
2.90E−29

Bacillus subtilis

e1182857
ygaChypothetical 12.2 kd proteinBacillus subtilis complete genome












(section 5 of 21)


Contig354D
14581306_f2_76
1836
4673
303
101
115
4.00E−07

Bacillus subtilis

e1183598
yolDunknownBacillus subtilis complete genome (section 12 of 21) similar to












hypothetical proteins from B. subtilis


Contig354D
14714077_c2_177
1837
4674
1209
403
715
1.10E−70

Bacillus subtilis

e1182643
yerHYerH proteinBacillus sibtilis complete genome (section 4 of 21)


Contig354D
14883592_c2_168
1838
4675
2076
692
600
1.60E−58

Clostridium

g436133
hypothetical proteinC.butyricum transposon containing tbcC gene.product











bucyricum


is similar to TnpB of transposon Tn554 from


Contig354D
15041430_c3_220
1839
4676
249
83


Contig354D
15121077_c2_178
1840
4677
1476
492
1626
3.10E−167

Bacillussubtilis

e1182648
ycrMamidase homolog ycrMBacillus subtilis complete genome (section 4 of












21) alternate gene name


Contig354D
16219007_f2_74
1841
4678
921
307
1319
1.00E−134

Enterococcus

P00807
blaZbeta-lactamaseE.faecalis beta-lactamase mRNA, complete cds.beta-











faecalis


lactamase lbeta-lactamase (aa 1-281)


Contig354D
16677343_c2_162
1842
4679
447
149
111
1.10E−06

Methanococcus

Q57803
MJ0357M. jannaschii predicted coding region MJ0357Methanococcus











jannaschii



jannaschii section 31 of 150 of the complete genome.hypothetical protein;













identified by GeneMark;


Contig354D
16695300_f2_54
1843
4680
1113
371
586
4.90E−57

Bacillus subtilis

e1182859
ygaEhypothetical 40.7 kd proteinBacillus sibtilis complete genome (section 5 of












21)


Contig354D
19536693_c1_143
1844
4681
318
106
232
1.60E−19

Bacillus subtilis

g2589194
gatCGlu-tRNAGln amidotransferase subunit CBacillus subtilis Glu-tRNAGln












amidotransferase subunits C (gatC), A (gatA) and B (gatB) genes, complete












cds.similar to Synechocystis sp. hypothetical protein.


Contig354D
1958183_f3_119
1845
4682
648
216
943
7.30E−95

Staphylococcus

g2981297
agrB AgrStaphylococcus epidermidis agr system including response











epidemidis


regulator (agrA), histidine kinase (agrC), AgrD (agrD), AgrB (agrB) and












deltatoxin (hld) genes, complete cds.required for peptide pheromone












productioin; similar


Contig354D
1972278_f2_53
1846
4683
300
100
316
2.00E−28

Bacillus subtilis

e1182860
gsaBglutamate-1-semialdehyde aminotransferaseBacillus subtilis












complete genome (section 5 of 21)


Contig354D
1988811_c1_154
1847
4684
1083
361
779
1.70E−77

Bacillus subtilis

e1182852
yfhQYfhQBacillus subtilis complete genome (section 5 of 21) similar to A/G-












specific adenine glycosylase


Contig354D
19957567_c3_222
1848
4685
291
97
94
7.30E−05
Mitochondrion
g881925
NADH dehydrogenase subunit 6Cepaea nemoralis complete mitochondrial











Cepaea nemoralis


genome.followed by putative incomplete stop codon ‘TA’


Contig354D
20344411_c3_198
1849
4686
336
112
440
1.50E−41

Staphylococcus

P48227
hsp10heat shock protein 10Staphylococcus epidermidis 9759 heat











epidermidis


shock protein 10 (hsp10) andheat shock protein 60 (hsp60) genes, complete cds.


Contig354D
2037838_f1_29
1850
4687
249
83
122
7.30E−08

Pyrococcus

d1027966
PHAL02713aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA, 734966-774775 nt position, clone


Contig354D
20706500_f1_40
1851
4688
339
113
158
1.10E−11
Kinetoplast Bodo
g3037018
ND5NADH dehydrogenase subunit 5Bodo saltans NADH dehydrogenase











saltans


subunit 5 (ND5) mRNA, kinetoplastgene encoding kinetoplast protein, partial












cds.partially edited mRNA


Contig354D
20735686_f3_108
1852
4689
957
319
853
2.50E−85

Bacillus subtilis

P37487
yybQunknownB. subtilis DNA, 180 kilobase region of replication












origin.similar to hypothetical proteins


Contig354D
20881510_c3_199
1853
4690
492
164
213
1.70E−17

Bacillus subtilis

g2293169
ytrAtranscription regulatorBacillus subtilis rrnB-dnaB genomic












region.similar to transcriptional regulator (GntR family)


Contig354D
21616078_c2_174
1854
4691
192
64
135
3.00E−09

Bacillus subtilis

g2239294
yebGunknownBacillus subtilis CotA (cotA), GabP (gabP), YeaB (yeaB),












YeaC (yeaC), YebA (yebA), GMP synthetase (guaA) genes, complete cds,












andAIR carboxylase 1 (purE) gene, partial cds.yebG


Contig354D
21676433_c1_138
1855
4692
1137
379
192
2.80E−12

Streptomyces

e1292355
SC1A6.07chypothetical protein SC1A6.07cStreptomyces coelicolor











coelicolor


cosmid 1A6.SC1A6.07c, unknown, len


Contig354D
22289077_c3_203
1856
4693
546
182


Contig354D
23438461_c2_163
1857
4694
687
229


Contig354D
23495437_f1_39
1858
4695
1305
435
1004
2.50E−101

Bacillus circulans

e216734
aspATAspartate aminotransferaseB.circulans aspartate












aminotransferase gene.


Contig354D
23572125_c3_224
1859
4696
534
178
393
1.40E−36

Bacillus subtilis

P49851
YKHABacillus subtilis hmp DNA for 7 ORFs, complete cds.low homology to












P14 protein of Haemophilus


Contig354D
23595386_c2_193
1860
4697
627
209
271
1.20E−23

Bacillus subtilis

e1186156
yvcTglycerate dehydrogenase homolog yvcTBacillus subtilis complete genome












(section 18 of 21) similar to glycerate dehydrogenase


Contig354D
23629202_c2_170
1861
4698
381
127
598
2.60E−58

Staphylococcus

P18415
blalbeta-lactamase repressorS.aureus Tn552 transposable element.regulatory











aureus


protein blalblal protein (AA 1-126)


Contig354D
23672562_c2_161
1862
4699
297
99


Contig354D
23727212_f1_12
1863
4700
303
101


Contig354D
23727250_f2_72
1864
4701
1395
465
1167
1.30E−118

Bacillus subtilis

P39616
ipa-58raldehyde dehydrogenase homolog ywdHB.subtilis genomic region (325 to












333).alternate gene name


Contig354D
23850907_f3_116
1865
4702
201
67


Contig354D
24218791_f3_107
1866
4703
588
196
525
1.40E−50

Bacillus subtilis

e1184253
yueJpyrazinamidase/nicotinamidase homolog yueJBacillus subtilis complete












genome (section 17 of 21) similar to pyrazinamidase/nicotinamidase


Contig354D
24257827_c3_200
1867
4704
387
129


Contig354D
24353382_c1_127
1868
4705
1623
541
2592
1.30E−269

Staphylococcus

g535342
hsp60heat shock protein 60Staphylococcus epidermidis 9759 heat











epidermidis


shock protein 10 (hsp10) andheat shock protein 60 (hsp60) genes, complete cds.


Contig354D
24407787_c2_192
1869
4706
354
118


Contig354D
24415942_c3_305
1870
4707
840
280


Contig354D
24429688_c2_158
1871
4708
327
109


Contig354D
24885938_c1_140
1872
4709
642
214
302
6.10E−27

Bacillus subtilis

g2239293
yebFunknownBacillus subtilis CotA (cotA), GabP (gabP), YeaB (yeaB),












YeaC (yeaC), YebA (yebA), GMP synthetase (guaA) genes, complete cds,












andAIR carboxylase 1 (purE) gene, partial cds.ycbF


Contig354D
25428507_c2_182
1873
4710
576
192


Contig354D
25595387_f3_111
1874
4711
432
144
111
1.10E−06

Bacillus subtilis

e1183598
yolDunknownBacillus subtilis complete genome (section 12 of 21) similar to












hypothetical proteins from B. subtilis


Contig354D
25603388_f3_120
1875
4712
1293
431
2112
9.70E−219

Staphylococcus

g2981295
agrChistidine kinaseStaphylococcus epidermidis agr system including











epidermidis


response regulator (agrA), histidine kinase (agrC), AgrD (agrD), AgrB












(agrB) and deltatoxin (hld) genes, complete cds.AgrC; similar to S. aureus












and S. lugdunensis AgrC.


Contig354D
256265_c3_221
1876
4713
1092
364
538
6.00E−52

Bacillus subtilis

c1249816
yvqEYvqE proteinBacillus subtilis 42.7 kB DNA fragment from yvsA to












yvqA.similar to two-component sensor histidine kinase


Contig354D
25678438_c3_230
1877
4714
474
158
334
2.50E−30

Aquifex acolicus

g2983147
aq_495hypothetical proteinAquifex aeolicus section 24 of 109 of the












complete genome.


Contig354D
25781392_f3_97
1878
4715
1029
343
225
4.80E−17

Bacillus subtilis

e1182859
ygaEhypothetical 40.7 kd proteinBacillus sibtilis complete genome (section 5 of












21)


Contig354D
25790718_c3_211
1879
4716
315
105
349
6.40E−32

Bacillus subtilis

g2465565
yecDYecDBacillus subtilis phosphoribosylaminoimidazole-












carboxamideformyltransferase (purH-J) gene, partial












cds, phosphoribosylglycinamide synthetase (purD), YecA (yecA),












syntetase (purD), YecA (yecA), putativeadenine deaminase (yecB), YecC












(yecC), and YecD (yecD) genes, complete cds, and


Contig354D
26177163_c2_185
1880
4717
1272
424
971
7.80E−98

Bacillus subtilis

P39762
ampSaminopeptidaseBacillus subtilis ampS-nprE gene region.similar to ampS












gene with GenBank Accession Number


Contig354D
26209577_f2_69
1881
4718
1068
356
892
1.80E−89

Bacillus subtilis

e1182753
yflMYflMBacillus subtilis complete genome (section 5 of 21) similar to nitric-












oxide synthase


Contig354D
26212875_c1_130
1882
4719
318
106


Contig354D
26354787_c3_194
1883
4720
744
248


Contig354D
26593808_f1_5
1884
4721
981
327
753
9.90E−75

Bacillus subtilis

e1182851
yfhPYfhPBacillus subtilis complete genome (section 5 of 21)


Contig354D
26689703_c1_157
1885
4722
453
151
562
1.70E−54

Bacillus subtilis

e1182862
ygaGhypothetical 16.4 kd proteinBacillus subtilis complete genome












(section 5 of 21) similar to transcriptional regulator (Fur family)


Contig354D
26756500_c1_147
1886
4723
777
259
721
2.40E−71

Bacillus subtilis

e1182759
yflGYflGBacillus subtilis complete genome (section 5 of 21) similar to












methionine aminopeptidase


Contig354D
26757312_f2_58
1887
4724
1197
399
543
1.80E−52

Bacillus subtilis

e1182780
yfkHYfkHBacillus subtilis complete genome (section 5 of 21) similar to












transporter


Contig354D
2939187_f3_90
1888
4725
198
66


Contig354D
2992943_c2_166
1889
4726
624
208
324
2.90E−29

Bacillus subtilis

g2293170
ytrBtransporterBacillus subtilis rrnB-dnaB genomic region.similar to ABC












transporter (ATP-binding protein)


Contig354D
32037826_c2_180
1890
4727
1476
492
1119
1.60E−113

Bacillus subtilis

e1182653
yefARNA methyltransferase homolog yefABacillus subtilis complete genome












(section 4 of 21) alternate gene name


Contig354D
3251577_c1_141
1891
4728
2190
730
3095
0

Staphylococcus

Q53727
pcrAhelicaseStaphylococcus aureus helicase required for T181 replication











aureus


(pcrA) gene, complete cds.


Contig354D
32689162_f2_85
1892
4729
807
269
1384
1.30E−141

Staphylococcus

g2981299
orf5unknownStaphylococcus epidermidis agr system including











epidermidis


response regulator (agrA), histidine kinase (agrC), AgrD (agrD), AgrB












(agrB) and deltatoxin (hld) genes, complete cds.similar to S.aureus and S.













lugdunensis orf5



Contig354D
32696088_c3_228
1893
4730
3749
583
1899
3.60E−196

Bacillus subtilis

e1182858
ygaDunidentified transporter-ATP bindingBacillus subtilis complete












genome (section 5 of 21) similar to ABC transporter (ATP-binding protein)


Contig354D
33631292_c2_183
1894
4731
414
138


Contig354D
3392952_c2_160
1895
4732
591
197
195
1.30E−15
Bacteriophage
e247149
Rorf172Lactobacillus bacteriophage phigle complete genomic DNA.










phigle


Contig354D
34275325_c3_227
1896
4733
1521
507
238
4.20E−17

Bacillus subtilis

P42954
tagHATP-binding protienBacillus subtilis 168 highly hydrophobic integral












membrane protein (tagG) gene and ATP-binding protein (tagH) gene, complete












cds.


Contig354D
34383400_c1_133
1897
4734
582
394


Contig354D
34572177_c3_202
1898
4735
735
245
147
1.20E−08

Staphylococcus

g459263
membrane spanning protein (putative) S. epidermidis (968) genes for











epidermidis


potential ABC transpoerter andpotential membrane spanning protein.


Contig354D
34652177_c1_149
1899
4736
648
216
546
8.50E−53

Bacillus subtilis

e1249817
yvqCYvqC proteinBacillus subtilis 42.7 kB DNA fragment from yvsA to












yvqA.similar to two-component response regulator (YvqE


Contig354D
35443785_c3_219
1900
4737
207
69


Contig354D
35885_f2_78
1901
4738
504
168


Contig354D
36119093_c1_142
1902
4739
2003
667
2102
1.10E−217

Bacillus subtilis

e1182642
yerGDNA ligase homolog yerGBacillus subtilis complete genome (section 4 of












21) similar to DNA ligase


Contig354D
36195250_f2_70
1903
4740
822
274
375
1.10E−34

Methanococcus

Q58054
MJ0637chorismate mutase/prephenate dehydratase (pheA) Methanococcus











jannaschii



jannaschii section 53 of 150 of the complete genome.prephenate













dehydratase homologysimilar to SP


Contig354D
36219692_c1_145
1904
4741
561
187
133
2.00E−08

Streptococcus

d1003084
parrepressor proteinStreptococcus sobrinus gene for repressor protein of











sobrinus


surfaceprotein antigen gene (pag), complete cds. This ORF2 starts at the












GTG codon (position 1162)


Contig354D
36220000_c3_207
1905
4742
1047
349
557
5.80E−54

Bacillus subtilis

e1181502
ykgBYkgBBacillus subtilis 168 56 kb DNA fragment between xlyA and












ykoR.similar to hypothetical proteins


Contig354D
36367302_c1_123
1906
4743
564
188
122
2.30E−06

Methanococcus

Q57805
MJ0359M. jannaschii predicted coding region MJ0359Methanococcus











jannaschii



jannaschii section 31 of 150 of the complete genome.hypothetical protein;













identified by GeneMark;


Contig354D
36522175_f3_102
1907
4744
1557
519
2240
2.60E−232

Staphyiococcus

g2565311
putPhigh affinity proline permeaseStaphylococcuc aureus high











aureus


affinity proline permease (putP) gene, complete cds.


Contig354D
39077_f1_42
1908
4745
717
239
1223
1.60E−124

Staphylococcus

g2981294
agrAresponse regulatorStaphylococcus epidermidis agr system including











epidermidis


response regulator (agrA), histidine kinase (agrC), AgrD (agrD), AgrB












(agrB) and deltatoxin (hld) genes, complete cds.AgrA; similar to S. aureus












and S. lugdunensis AgrA


Contig354D
3939013_c3_225
1909
4746
210
70
109
1.70E−06

Bacillus subtilis

e1182787
yfjTYfjTBacillus subtilis complete genome (section 5 of 21)


Contig354D
3942015_c2_187
1910
4747
528
176
790
1.20E−78

Staphylococcus

g310602

Staphylococcus aureus DNA sequence encoding three ORFs, completecds;












aureus


prophage phi-11 sequence homology, 5′ flank.


Contig354D
4021888_c1_129
1911
4748
669
223


Contig354D
4062500_c3_197
1912
4749
1401
467
488
9.70E−46

Staphylococcus

g397526
clumping factorS.aureus gene for clumping factor.











aureus



Contig354D
4089763_f3_95
1913
4750
501
167
358
7.10E−33

Bacillus subtilis

e1182778
yfkJYfkJBacillus subtilis complete genome (section 5 of 21) similar to












protein-tyrosine phosphatase


Contig354D
4095277_c1_135
1914
4751
1827
609
2760
2.10E−287

Staphylococcus

g152966
blaR1gla regulator protein blaR1Staphylococcus aureus blaZ gene,











aureus


5′ end; blaR1 gene, complete cds; bla1 gene, complete csd; and binR gene, 5′












end.beta-lactamase OXA2 homology


Contig354D
4101517_f3_113
1915
4752
1068
356


Contig354D
4179637_c1_133
1916
4753
387
129
207
7.10E−17

Staphylococcus

P06698
tnpCpot. tnpC proteinStaphylococcus aureus transposon Tn554 (aa 1-125)











aureus



Contig354D
430325_c2_181
1917
4754
1383
461
522
3.00E−50

Synechocystis sp.

d1019130
hypothetical proteinSynechocystis sp. PCC6803 complete genome, 16/27,












1991550-2137258.ORF_ID


Contig354D
4689130_f1_43
1918
4755
306
102


Contig354D
4722265_c2_188
1919
4756
858
286
416
5.10E−39

Bacillus subtilis

e1182842
yfhGYfhGBacillus subtilis complete genome (section 5 of 21)


Contig354D
4726566_f1_18
1920
4757
582
194
155
2.30E−11

Aquifex acolicus

g2983450
dnaQDNA polymerase III epsilon subunitAquifex aeolicus section 46 of












109 of the complete genome.


Contig354D
4728377_f1_10
1921
4758
1146
382
544
1.40E−52

Bacillus subtilis

e1182785
yfkBYfkBBacillus subtilis complete genome (section 5 of 21)


Contig354D
4900443_c2_179
1922
4759
1440
480
2460
1.30E−255

Bacillus subtilis

Q45486
YZDDPET112-like proteinBacilus subtilis PET112-like protein gene,












complete cds.


Contig354D
5167268_c1_146
1923
4760
1080
360
613
6.80E−60

Escherichia coli

Q47155
dinPhypothetical protein DinPEscherichia coli K-12 MG1655












sectioin 21 of 400 of the completegenome.o351; 100 pct identical












to GB


Contig354D
5860052_f2_80
1924
4761
435
145
107
2.80E−06

Pyrococcus

d1028904
PHCY019133aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA, 1552268-1595600 nt position, clone


Contig354D
6053308_c3_210
1925
4762
903
301
815
2.70E−81

Escherichia coli

P18843
nadE, efg, ntrL_NH(3)-dependent NAD(+) synthetase (EC 6.3.5.1) E.coli












genomic DNA, Kohara clone #326 (39.1-39.4 min.).spore outgrowth factor












BORF_ID


Contig354D
6147252_c2_189
1926
4763
846
282
150
1.30E−08

Bacillus subtilis

P42953
tagGhighly hydrophobic integral membrane proteinBacillus subtilis 168












highly hydrophobic integral membrane protein (tagG) gene and ATP-binding












protein (tagH) gene, complete cds.


Contig354D
632661_c3_218
1927
4764
777
259
301
7.80E−27

Mycobacterium

e1264573
MTV025.06Ihypothetical protein MTV025.06IMycobacterium











tuberculosis



tuberculosis sequence v025.MTV025.061, len



Contig354D
6682627_c1_125
1928
4765
357
119
123
5.70E−08

Paramecium

g624123
a58LParamecium bursaria Chlorella virus 1, complete genome.contains Glu-,











bursaria Chlorella


Gln-rich regions










virus 1


Contig354D
6829687_c3_201
1929
4766
618
206
355
1.50E−32

Staphylococcus

g459256
stpCPotential ABC transporterS.aureus (RN4220) genes for potential ABC











aureus


transporter and potentialmembrane spanning protein.


Contig354D
6931261_c2_159
1930
4767
537
179
128
1.70E−08

Staphylococcus

g2689551

Staphylococcus aureus toxic shock syndrome toxin-1 (tst), enterotoxin (ent),












aureus


and integrase (int) genes, complete cds.orf4


Contig354D
7164087_c3_226
1931
4768
333
111
217
6.20E−18

Bacillus subtilis

e1182843
yfhHYfhHBacillus subtilis complete genome (section 5 of 21)


Contig354D
7207518_f1_41
1932
4769
375
125
151
6.10E−11
Glycine max
B27059
hypothetical protein 2


Contig354D
799188_f3_118
1933
4770
468
156
202
7.60E−15

Plasmodium

g9826
11-111-1 polypeptidePlasmodium falciparum 11-1 gene part 1.











falciparum



Contig354D
820325_f1_3
1934
4771
948
316
1131
8.70E−115

Bacillus subtilis

P71084
gsaBglutamate-1-semialdehyde aminotransferaseB.subtilis 25 kb












genomic DNA segment (from sspE to katA).


Contig354D
959635_12_55
1935
4772
294
98
98
7.30E−05

TRYPANOSOMA

P24499
MURF4ATP SYNTHASE A CHAIN, (PROTEIN 6)











BRUCEI












BRUCEI



Contig354D
979712_c2_169
1936
4773
1422
474


Contig354D
985678_c1_144
1937
4774
975
325
889
3.80E−89

Bacillus subtilis

e1182652
yerQconserved hypothetical protein yerQBacillus subtilis complete genome












(section 4 of 21) similar to hypothetical proteins


Contig354D
10972150_c3_125
1938
4775
2055
685
3024
0

Staphylococcus

d1025491
recGRecGStaphylococcus aureus recG gene, complete cds.











aureus



Contig355D
114626_f3_61
1939
4776
207
69


Contig355D
1204567_c2_904
1940
4777
750
250
481
6.60E−46

Bacillus subtilis

e1185167
yloOputative Ptc 1 proteinBacillus subtilis complete genome (section 9 of












21) similar to hypothetical proteins


Contig355D
1209638_c1_80
1941
4778
540
1180
1642
5.70E−63
Staphylococcus
P31024
lspprolipoprotein signal peptidaseStaphylococcus aureus











aureus


prolipoprotein signal peptidase (tsp) gene, complete cds.lipoprotein signal












peptidase


Contig355D
13720312_c3_119
1942
4779
240
80
117
2.50E−07

Bacillus subtilis

e1185160
yloHputative rpoZ proteinBacillus subtilis complete genome (section 9 of












21)


Contig355D
1376317_c2_98
1943
4780
564
188
481
6.60E−46

Lactobacillus

e199384
pyrRL.plantarum pyrimidine biosynthetical operon (pyrR, pyrB,











plantarum


pyrC, pyrAA, pyrAB, pyrD, pyrF, and pyrE) genes.


Contig355D
19557752_c1_81
1944
4781
912
304
844
2.30E−84

Bacillus subtilis

P05654
pyrBaspartate transcarbamylaseB.subtilis pyrB gene encoding aspartate












transcarbamoylase, completecds.ornithine












carbamoyltransferaseaspartate transcarbamoylase (EC 2.1.3.2)


Contig355D
209840_c1_10
1945
4782
195
65


Contig355D
2242938_c3_112
1946
4783
933
311
1055
9.80E−107

Bacillus subtilis

Q45480
YLYBBacillus subtilis signal peptidase ll (lsp) gene, complete cds, isoleucyl-












tRNA synthetase (ileS) and pyrR genes, partial cds.orf-X; hypothetical protein;












Method


Contig355D
22461078_c1_79
1947
4784
735
245
814
3.40E−81

Staphylococcus

g1314301
ORFunknownStaphylococcus aureus isoleucyl-tRNA synthetase (ileS)











aureus


gene, partial cds.


Contig355D
22462802_c3_120
1948
4785
1203
401
1070
2.50E−108

Bacillus subtilis

e1185161
ylolputative Dfp proteinBacillus subtilis complete genome (section 9 of












21) similar to pantothenate metabolism flavoprotein


Contig355D
23492327_c1_8
1949
4786
204
68
126
2.70E−08

Synechocystis sp.

d1011491
clpPhypothetical proteinSynechocystis sp. PCC6803 complete genome, 25/27












3138604-3270709.ORF_ID


Contig355D
23572253_c1_92
1950
4787
741
247
623
5.90E−61

Bacillus subtilis

e1185184
mcSribonuclease lllBacillus subtilis complete genome (section 9 of












21) alternate gene name


Contig355D
23632962_c2_97
1951
4788
810
270
270
1.50E−23

Bacillus subtilis

P54721
yfiEunknownBacillus subtilis complete genome (section 5 of 21) similar to












hypothetical proteins from B. subtilis


Contig355D
23642217_c1_88
1952
4789
648
216
396
6.70E−37

Bacillus subtilis

e1185171
yloSYloS proteinBacillus subtilis complete genome (section 9 of 21)


Contig355D
23647178_c2_106
1953
4790
633
211
398
4.10E−37

Bacillus subtilis

e1185179
ylpCYlpC proteinBacillus subtilis complete genome (section 9 of 21)


Contig355D
23650293_c1_85
1954
4791
627
209
693
2.30E−68

Bacillus subtilis

e1185159
yloDputative Gmk proteinBacillus subtilis complete genome (section 9 of












21) similar to guanylate kinase


Contig355D
2383603_c2_100
1955
4792
192
641
53
9.70E−10

Bacillus

P46537
PyrAbcarbamoyl-phosphate synthaseB.caldoyticus pyrimidine











caldolyticus


biosynthesis genes.carbamoyl-phosphate synthase (glutamine-hydrolyzing) large












chain


Contig355D
24240676_f3_62
1956
4793
246
82


Contig355D
24297217_c1_82
1957
4794
3114
1038
3756
0

Bacillus

P46537
PyrAbcarbamoyl-phosphate synthaseB.caldoyticus pyrimidine











caldolyticus


biosynthesis genes.carbamoyl-phosphate synthase (glutamine-hydrolyzing) large












chain


Contig355D
24355342_c1_95
1958
4795
1014
338
1265
5.50E−129

Bacillus subtilis

P37105
ffhsignal recognition particalBacillus subtilis complete genome (section 9 of












21)


Contig355D
24406291_c2_105
1959
4796
417
139
369
4.90E−34

Bacillus subtilis

e1185174
yloUputative Asp23 proteinBacillus subtilis complete genome (section 9 of












21) similar to alkaline-shock protein


Contig355D
24407327_c3_117
1960
4797
612
204
623
5.90E−61

Bacillus subtilis

A30492
pyrEorotate phosphoribosyltransferase, orotate












phosphoribosyltransferase


Contig355D
24407936_c2_103
1961
4798
1122
374
1380
3.60E−141

Bacillus subtilis

e1185166
yloNYloN proteinBacillus subtilis complete genome (section 9 of












21) similar to hypothetical proteins


Contig355D
24422077_c3_115
1962
4799
1101
367
1196
1.10E−121

Bacillus

P52557
PyrAacarbamoyl-phosphate synthaseB.caldolyticus pyrimmidine











caldolyticus


biosynthesis genes. carbamoyl-phosphate synthase (glutamine-hydrolyzing) small












chain homology


Contig355D
24424038_c1_89
1963
4800
1692
564
1538
6.50E−158

Bacillus subtilis

e1185175
yloVYloV proteinBacillus subtilis complete genome (section 9 of












21) similar to hypothetical proteins


Contig355D
24609637_c3_108
1964
4801
798
266
445
4.30E−42

Bacillus subtilis

e1185129
ylmDconserved hypothetical protein ylmDBacillus subtilis complete genome












(section 9 of 21) similar to hypothetical proteins


Contig355D
24632827_c1_86
1965
4802
963
321
1917
4.10E−92

Bacillus subtilis

e1185164
fmtmethionyl-tRNA formyltransferaseBacillus subtilis












complete genome (section 9 of 21) alternate gene name


Contig355D
24645025_c3_114
1966
4803
1284
428
1287
2.60E−131

Bacillus

P46538
PyrCdihydroorotaseB.caldolyticus pyrimidine biosynthesis genes.Bacillus











caldolyticus


dihydroorotase


Contig355D
24648412_c1_94
1967
4804
402
134
302
6.10E−27

Bacillus subtilis

P37104
ylxMORF1Bacillus subtilis complete genome (section 9 of 21) similar to












hypothetical proteins


Contig355D
25635962_c3_111
1968
4805
486
162
274
5.70E−24

Staphylococcus

e244971

S.aureus orfs 1,2,3 & 4.ORF1












aureus



Contig355D
25816552_c3_109
1969
4806
777
259
468
1.60E−44

Bacillus subtilis

g1518679
ylmHcell-division protein homolog ylmHBacillus subtilis minicell-












associated protein (divIVA) gene, complete cds, and isoleucyl-tRNA-












synthetase (ileS) gene, partialcds.orf


Contig355D
26423305_c1_78
1970
4807
336
112
226
6.90E−19

Bacillus subtilis

e1185132
ylmGconserved hypothetical protein ylmGBacillus subtilis complete genome












(section 9 of 21) similar to hypothetical proteins


Contig355D
26598402_c3_113
1971
4808
1314
438
1251
1.70E−127

Bacillus

P41006
pyrPuracil permeaseB.caldolyticus (DSM405) pyrR, pyrP and pyrB (partial)











caldolyticus


genes.


Contig355D
26614167_c1_91
1972
4809
240
80
238
3.70E−20

Bacillus subtilis

P80643
acpAacyl carrier proteinBacillus subtilis complete genome (section 9 of 21) acyl












carrier proteinalternate gene name


Contig355D
29320217_f2_32
1973
4810
207
69


Contig355D
30656300_c3_122
1974
4811
1353
451
912
1.40E−91

Bacillus subtilis

e1185165
yloMputative Fmu proteinBacillus subtilis complete genome (section 9 of












21) alternate gene name


Contig355D
3314128_f2_23
1975
4812
234
78


Contig355D
34017812_f3_63
1976
4813
1722
574
1369
5.20E−140

Bacillus subtilis

e332190
yloAputative fibronectin-binding proteinBacillus subtilis pyrE to yloA












gene region.protein A-like


Contig355D
34642213_c2_96
1977
4814
615
205
328
1.10E−29

Bacillus subtilis

e1185131
ylmFconserved hypothetical protein ylmFBacillus subtilis complete genome












(section 9 of 21) similar to hypothetical proteins


Contig355D
34650452_c1_83
1978
4815
225
75


Contig355D
35978392_c1_87
1979
4816
2007
669
949
1.70E−95

Bacillus subtilis

e1185168
yloPputative Pkn2 proteinBacillus subtilis complete genome (section 9 of












21) similar to protein kinase


Contig355D
36141893_c3_127
1980
4817
1248
416
1166
1.70E−118

Bacillus subtilis

e1185186
ftsYsignal recognition particle (docking protein) Bacillus subtilis somplete












genome (section 9 of 21) alternate gene name


Contig355D
3912890_f3_57
1981
4818
222
74
246
5.30E−21

BACILLUS

P23374
RPMBribosomal protein L2850S RIBOSOMAL PROTEIN L28











STEAROTHERMO-












PHILUS



Contig355D
4509661_c1_84
1982
4819
411
137


Contig355D
4725000_c1_93
1983
4820
3636
1212
2426
5.10E−252

Bacillus subtilis

e1185185
smcchromosome segregation SMC protein homolgBacillus subtilis complete












genome (section 9 of 21) alternate gene name


Contig355D
4741703_c2_102
1984
4821
2418
806
2153
4.40E−223

Bacillus subtilis

e1185162
priAprimosomal replication factor Y (primosomalBacillus subtilis complete












genome (section 9 of 21) alternate gene name


Contig355D
4875055_f1_3
1985
4822
225
75


Contig355D
4875452_c3_124
1986
4823
645
215
518
7.90E−50

Bacillus subtilis

e1185170
yloRputative CfxE proteinBacillus subtilis complete genome (section 9 of












21) similar to ribulose-5-phosphate 3-epimerase


Contig355D
4877203_c1_90
1987
4824
936
312
661
5.60E−65

Bacillus subtilis

e1185181
fabDmalonyl CoA-acyl carrier protein transacylaseBacillus subtilis complete












genome (section 9 of 21) alternate gene name


Contig355D
4970462_c2_107
1988
4825
750
250
837
1.20E−83

Bacillus subtilis

e1185182
fabG3-ketoacyl-acyl carrier protein reductaseBacillus subtilis complete












genome (section 9 of 21) alternate gene name


Contig355D
5096012_f3_64
1989
4826
231
77


Contig355D
5276712_c3_116
1990
4827
708
236
659
9.10E−65

Lactococcus lactis

P50924
pyrFOMP decarboxylaseL.lactis pyrD and pyrF genes.


Contig355D
5978453_c3_121
1991
4828
492
164
261
1.40E−22

Bacillus subtilis

P94462
defpolypeptide deformylaseB.subtilis priA, def, fmt, sun genes.alternate gene












name


Contig355D
6072125_c1_77
1992
4829
672
224
591
1.50E−57

Bacillus subtilis

e1185130
ylmEconserved hypothetical protein ylmEBacillus subtilis complete genome












(section 9 of 21) similar to hypothetical proteins


Contig355D
6149077_c3_123
1993
4830
891
297
708
5.80E−70

Bacillus subtilis

e1185169
yloQYloQ proteinBacillus subtilis complete genome (section 9 of












21) similar to hypothetical proteins


Contig355D
642_c3_110
1994
4831
2784
928
4356
0

Staphylococcus

P41972
ileSisoleucyl-tRNA synthetaseS.aureus gene for isoleucyl-tRNA synthetase











aureus



Contig355D
7225000_c3_126
1995
4832
1026
342
898
4.30E−90

Bacillus subtilis

e1185180
plsXputative PlsX proteinBacillus subtilis complete genome (section 9 of












21) alternate gene name


Contig355D
892141_f2_44
1996
4833
396
132
208
5.60E−17

Pyrococcus

d1027160
PHBC037103aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA, 1-37345 and 1737608-1738505nt position (complementary












strand), clone


Contig355D
990702_c1_76
1997
4834
1185
395
1801
8.70E−186

Staphylococcus

P45498
ftsZFtsZStaphylococcus aureus SA4 FtsZ (ftsZ) gene, complete cds.cell











aureus


division protein ftsZ


Contig355D
9954640_f3_67
1998
4835
228
76
117
2.50E−07

Enterococcus

g2196686
pyrAbpyrimidine biosynthesis protein AbEnterococcus faecalis plasmid pKV48











faecalis


pyrimidine biosynthesis proteinAb (pyrAb) gene, partial cds.


Contig356D
10719452_c2_53
1999
4836
684
228
371
3.00E−34

Bacillus subtilis

P54175
yplQhemolysin III homolog homolog yplQBacillus subtilis (YAC10-9 clone)












DNA region between the serA andkdg loci20.2% identity with NADH












dehydrogenase of the


Contig356D
10752342_c1_40
2000
4837
981
327
773
7.50E−77

Bacillus subtilis

e1182740
yfmEYfmEBacillus subtilis complete genome (section 5 of 21) similar to












ferrichrome ABC transporter (permease)


Contig356D
10928_c2_61
2001
4838
414
138


Contig356D
12142768_f2_12
2002
4839
300
100
110
3.50E−06

Pyrococcus

d1027343
PHBW016235aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA, 180023-216005 nt position, clone


Contig356D
12578885_f3_36
2003
4840
366
122


Contig356D
12603166_f3_28
2004
4841
303
101
110
1.40E−06

Pyrococcus

d1027339
PHBW012106aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA, 180023-216005 nt position, clone


Contig356D
1368046B_c1_43
2005
4842
1080
360
1133
5.30E−115

Bacillus subtilis

P50863
rec233unknownB.subtilis cwlD, rec223 and gerD genes.alternate gene name


Contig356D
14064055_c1_46
2006
4843
603
201
565
8.30E−55

Bacillus subtilis

P37528
yaaEunknownB.subtilis DNA, 180 kilobase region of replication












origin.similar to hypothetical proteins


Contig356D
14849093_c2_59
2007
4844
294
98
127
2.10E−08
Mitochondrion
e138028
putative orf79.1C.crispus complete mitochondrial genome.unique orf











Chondrus crispus



Contig356D
14900826_c2_58
2008
4845
351
117
188
7.40E−15
artificial sequence
g208931
Synthetic E.coli ORF16/lacZ fusion protein, partial cds.ORF16-lacZ fusion












protein


Contig356D
157750_c2_54
2009
4846
195
65


Contig356D
19730052_c3_66
2010
4847
1479
493
990
7.60E−100

Bacillus subtilis

e1182351
ycnBhomologue of multidrug resistance protein B, Bacillus subtilis complete












genome (section 3 of 21) similar to multidrug resistance protein


Contig356D
20363762_c2_52
2011
4848
1215
405
533
2.00E−51

Arabidopsis

g3033397
F19l3.25Arabidopsis thaliana chromosome I1 BAC F19l3 genomic











thaliana


sequence, complete sequence.unknown protein


Contig356D
23460931_f3_31
2012
4849
429
143


Contig356D
23642761_f2_18
2013
4850
228
76


Contig356D
2379658_f3_23
2014
4851
225
75


Contig356D
24244012_c2_51
2015
4852
546
182
280
1.30E−24

Bacillus subtilis

e1249789
yvsGYvsG proteinBacillus subtilis 42.7 kB DNA fragment from yvsA to












yvqA.similar to hypothetical proteins


Contig356D
24273450_f3_20
2016
4853
1365
455
749
2.60E−74

Bacillus subtilis

d1020112
ydcLtranscriptional regulator (GntR family)/homolog ydeLBacillus subtilis












genomic sequence, 148 kb sequence of the regionbetween 35 and 47












degree.SIMILAR TO THE RHIZOPINE CATABOLISM (MOCR) GENE OF


Contig356D
24339718_c1_42
2017
4854
483
161


Contig356D
24490930_c2_60
2018
4855
912
304
1220
3.20E−124

Bacillus subtilis

P37527
yaaDunknownB. subtilis DNA, 180 kilobase regioin of replication












origin.similar to hypothetical proteins


Contig356D
24641927_c3_63
2019
4856
1380
460
978
1.40E−98

Bacillus firmus

P30267
hypothetical protein AB.firmus ORF A and ORF B, complete cds.ORF A;












putative


Contig356D
24855303_c2_47
2020
4857
1047
349
784
5.10E−78

Bacillus subtilis

e1182741
yFmDYfmDBacillus subtilis complete genome (section 5 of 21) similar to












ferrichrome ABC transporter (permease)


Contig356D
277312_c3_65
2021
4858
1353
451
423
9.20E−40

Bacillus subtilis

e1184366
yusPmultidrug-efflux transporter homolog yusPBacillus subtilis complete












genome (section 17 of 21) similar to multidrug-efflux transporter


Contig356D
285808_f3_25
2022
4859
225
75


Contig356D
29376066_c3_62
2023
4860
183
61
109
8.70E−06

Bacillus subtilis

e1182742
yfmCYfmCBacillus subtilis complete genome (section 5 of 21) similar to












ferrichrome ABC transporter (binding


Contig356D
3361326_c1_44
2024
4861
207
69


Contig356D
35348182_f3_29
2025
4862
231
77


Contig356D
4100327_c1_6
2026
4863
360
120
133
5.00E−09

Bacillus subtilis

e1182694
yetGhypothetical protein yetGBacillus subtilis complete genome (section 4 of












21)


Contig356D
6854675_f2_17
2027
4864
279
93
119
1.50E−07

Bacillus subtilis

e1183408
ynzGhypothetical protein ynzGBacillus subtilis complete genome (section 4 of












21)


Contig356D
797308_f3_37
2028
4865
189
63


Contig357D
10439005_f2_28
2029
4866
516
172
143
4.30E−10

Pyrococcus

d1028459
PHAU021101aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA, 1195819-1238496 nt position, clone


Contig357D
11728376_c1_51
2030
4867
249
83
241
1.80E−20

Bacillus subtilis

e1184298
yuzBhypothetical protein yuzBBacillus subtilis complete genome (section 17 of












21)


Contig357D
14538202_c2_54
2031
4868
762
254
1034
1.70E−104

Bacillus subtilis

e1184349
yurYABC transporter (ATP-binding protein) homolog yurYBacillus subtilis












complete genome (section 17 of 21) similar to ABC transporter (ATP-












binding protein)


Contig357D
14970251_f3_29
2032
4869
294
98


Contig357D
2l68I702_c3_73
2033
4870
198
66
163
1.80E−11

Bacillus subtilis

e1184289
yumBNADH dehydrogenaseBacillus subtilis complete genome (section 17 of












21) similar to NADH dehydrogenase


Contig357D
21883512_c2_56
2034
4871
225
75


Contig357D
22462926_c3_68
2035
4872
783
261
669
7.90E−66

Bacillus subtilis

e1184308
yutFN-acetyl-glucosamine catabolism homolog yutFBacillus subtilis complete












genome (section 17 of 21) similar to N-acetyl-glucosamine catabolism


Contig357D
23475892_c3_67
2036
4873
1362
454
707
7.40E−70

Bacillus subtilis

e1184316
yunBconserved hypothetical protein yunDBacillus subtilis complete genome












(section 17 of 21) similar to hypothetical proteins


Contig357D
23728412_c2_53
2037
4874
699
233
726
7.20E−72

Bacillus subtilis

e1184352
yusBconserved hypothetical protein yusBBacillus subtilis complete genome












(section 17 of 21) similar to hypothetical proteins


Contig357D
24033567_c1_47
2038
4875
450
150
207
7.10E−17

Bacillus subtilis

e1184309
yutEhypothetical protein yetEBacillus subtilis complete genome (section 17 of












21)


Contig357D
24242285_c2_57
2039
4876
1056
352
414
8.30E−39

Borrelia

g2688091
BB0202hemolysin, putativeBorrelia burgdorferi (section 16 of 70) of the











burgdorferi


complete genome.similar to PID


Contig357D
24415930_f3_31
2040
4877
1068
356
977
1.80E−98

Bacillus subtilis

e1184299
yutJNADH dehydrogenase homolog yutJBacillus subtilis complete genome












(section 17 of 21) similar to NADH dehydrogenase


Contig357D
24803332_c1_40
2041
4878
840
280
712
2.20E−70

Bacillus subtilis

e1184351
yusAconserved hypothetical protein yusABacillus subtilis complete genome












(section 17 of 21) similar to hypothetical proteins


Contig357D
26190785_c1_41
2042
4879
1287
429
1408
3.90E−144

Bacillus subtilis

e1184347
yurWNifS protein homolog homolog yurWBacillus subtilis complete genome












(section 17 of 21) similar to NifS protein homolog


Contig357D
26360663_c2_63
2043
4880
1176
392
877
7.20E−88

Bacillus subtilis

e1184289
yumBNADH dehydrogenaseBacillus subtilis complete genome (section 17 of












21) similar to NADH dehydrogenase


Contig357D
26376077_c3_64
2044
4881
192
64
101
1.20E−05

Bacillus subtilis

e276829
ywmHunknownB.subtilis atpC gene.


Contig357D
26594050_c2_61
2045
4882
243
81
378
5.40E−35

Staphylococcus

d1013748
dltCD-alanyl carrier proteinStaphyloscoccus aureus gene for











aureus


unknown function and dlt operon dltA, dltB, dltC and dltD genes, complete












cds.Sequence homologous to the dltC genes of


Contig357D
30198587_f1_1
2046
4883
258
86
306
2.30E−27

Bacillus subtilis

e1184301
yutlNifU protein homolog homolog yutlBacillus subtilis complete genome












(section 17 of 21) similar to NifU protein homolog


Contig357D
30265692_c2_60
2047
4884
1050
350
675
1.80E−66

Pyrococcus

d1027703
PHAB011376aa long hypothetical dehydrogenasePyrococcus horikoshii











horikoshii


OT3 genomic DNA, 512441-547109 nt position(complementary strand),












clonecontains ATP/GTP-binding site motif A (P-loop);


Contig357D
31876563_c3_69
2048
4885
1239
413
1924
8.10E−199

Staphylococcus

d1013747
dltBhypothethecal membrane transporter Staphylococcus aureus gene











aureus


for unknown function and dlt operon dltA, dltB, dltC and dltD genes, complete












cds.Sequence homologous to the dltB genes of


Contig357D
33628441_f1_5
2049
4886
255
85


Contig357D
33645967_f2_19
2050
4887
282
94


Contig357D
34069680_c3_70
2051
4888
213
71


Contig357D
34242162_c2_55
2052
4889
489
163
529
5.40E−51

Bacillus subtilis

e1184346
yurVNifU protein homolog homolog yurVBacillus subtilis complete genome












(section 17 od 21) similar to Nifu protein homolog


Contig357D
34251887_c1_49
2053
4890
1266
422
1047
6.90E−106

Staphylococcus

d1013749
dltDeextramembranal proteinStaphylococcus aureus gene for











aureus


unkknown function and dlt operon dltA, dltB, dltC and dltD genes, complete












cds.putative


Contig357D
36563_c1_39
2054
4891
1074
358
908
3.70E−91

Bacillus subtilis

e1184353
yusCABC transporter (ATP-binding protein homolog yusCBacillus subtilis












complete genome (section 17 to 21) similar to ABC transporter (ATP-












binding protein)


Contig357D
3944001_c1_52
2055
4892
1524
508
684
2.00E−67

Bacillus subtilis

e1184284
yuiEleucyl aminopeptidase homolog yuiEBacillus subtilis complete genome












(section 17 of 21) similar to leucyl aminopeptidase


Contig357D
3948587_f3_37
2056
4893
873
291
295
3.40E−26

Borrelia

g2688692
BB0759B. burgdorferi predicted coding region BB0759Borrelia burgdorferi











burgdorferi


(section 61 of 70) of the complete genome.hypothetical protein; identified












by GeneMark;


Contig357D
14101643_c1_46
2057
4894
399
133
1304
3.80E−27

Bacillus subtilis

e1184310
yutDhypothetical protein yutDBacillus subtilis complete genome (section 17 of












21)


Contig357D
4330390_c2_58
2058
4895
876
292
787
2.50E−78

Bacillus subtilis

e1184318
yunFhypothetical protein yunFBacillus subtilis complete genome (section 17 of












21)


Contig357D
4687843_c1_50
2059
4896
330
110
242
1.40E−20

Bacillus subtilis

e1184300
yuzDhypothetical protein yuzDBacillus subtilis complete genome (section 17 of












21)


Contig357D
4709575_c1_42
2060
4897
354
118


Contig357D
5117793_c3_74
2061
4898
273
91
197
8.20E−16

Vibrio

P46231
ORF3Vibrio parahaemolyticus BB22 RNase T (rnt) gene and flagellar











parahaemolyticus


motorcomponent (motY) gene, complete cds.


Contig357D
6023915_c1_45
2062
4899
969
323
1144
3.60E−16

Bacillus subtilis

e1184312
yutBlipoic acid synthetase homolog yutBBacillus subtilis complete genome












(section 17 of 21) similar to lipoic acid synthetase


Contig357D
6057338_c2_59
2063
4900
840
280
622
7.50E−61

Bacillus subtilis

e1184317
yunEhypothetical protein yunEBacillus subtilis complete genome (section 17 of












21)


Contig357D
6423376_f1_13
2064
4901
197
66


Contig357D
6695968_c1_48
2065
4902
1470
490
1365
1.40E−139

Staphylococcus

d1013746
dltAD-alanine-D-alanyl carrier protein ligaseStaphylococcus aureus gene for











aureus


unknown function and dlt operon dltA, dltB, dltC and dltD genes, complete












cds.Sequence homologous to the dltA genes of


Contig357D
6836088_c3_65
2066
4903
1320
440
1260
1.90E−128

Bacillus subtilis

e1184348
yurXconserved hypothetical protein yurXBacillus subtilis complete genome












(section 17 of 21) similar to hypothetical proteins


Contig357D
6929512_c3_66
2067
4904
1416
472
2098
2.90E−217

Bacillus subtilis

e1184345
yurUconserved hypothetical protein yurUBacillus subtilis complete genome












(section 17 of 21) similar to hypothetical proteins


Contig357D
989010_c3_72
2068
4905
408
136
371
3.00E−34

Bacillus subtilis

e1184295
yutMconserved hypothetical protein yutMBacillus subtilis complete genome












(section 17 of 21) similar to hypothetical proteins


Contig358D
10025277_f1_12
2069
4906
396
132
101
3.70E−05

Aquifex aeolicus

g2982842
aq_106putative proteinAquifex aeolicus section 5 of 1009 of the complete genome


Contig358D
10553766_f3_73
2070
4907
195
65


Contig358D
1058463_c2_138
2071
4908
2121
707
2472
6.90E−257

Bacillus subtilis

P50849
pnpApolynucleotide phosphorylaseBacillus subtilis ribosomal












protein RpsO (prsO) gene, partial cds, and polynucleotide phosphorylase












(pnpA) gene, complete cds.alternative gene name


Contig358D
1074090_c3_146
2072
4909
906
302
697
8.50E−69

Bacillus subtilis

P39776
codVCodVBacillus subtilis JH642 dipeptide permease operon regulators












codV, vodW, codX, and codY genes, complete cds.


Contig358D
1183337_c1_110
2073
4910
447
149
303
4.80E−27

Bacillus subtilis

P32727
ORF2transcription terminatioin antitermination factor nusA












homologB.subtilis infB-nusA operon


Contig358D
11930317_c2_136
2074
4911
336
112
251
1.60E−21

Bacillus subtilis

P32729
ORF4hypothetical protein 2 (infB 5′ region) B.subtilis infB-nusA












operon.alternative gene name


Contig358D
19735887_c3_165
2075
4912
1581
527
1924
8.10E−199

Bacillus subtilis

e1185292
ymcBconserved hypothetical protein ymcBBacillus subtilis complete genome












(sectioin 9 of 21) similar to hypothetical proteins


Contig358D
20423127_c2_143
2076
4913
2676
892
2302
7.10E−239

Bacillus subtilis

e1185295
mutSDNA mismatch repair (recognition) mutSBacillus subtilis complete genome












(section 9 of 21)


Contig358D
20504512_c1_119
2077
4914
1758
586
685
3.40E−79

Halobacterium

g43498
ferredoxin oxidoreductaseH.haloboim gene for pyruvatealpha-subunit; pyruvate











halobium


synthase


Contig358D
205327_c1_106
2078
4915
1332
444
1679
7.40E−173

Bacillus subtilis

e1185204
gidglucose-inhibited division proteinBacillus subtilis complete genome












(section 9 of 21) alternate gene name


Contig358D
21912535_f2_56
2079
4916
420
140


Contig358D
22368803_c1_115
2080
4917
2397
799
1659
9.70E−171

Bacillus subtilis

P21458
spolllEDNA translocaseBacillus subtilis complete genome (section 9 of 21)


Contig358D
22444075_c2_127
2081
4918
873
291
381
2.60E−35

Bacillus subtilis

e1185202
smfDNA processing Smf protein homologBacillus subtilis complete












genome (section 9 of 21)


Contig358D
22470463_c2_142
2082
4919
810
270
881
2.70E−88

Bacillus subtilis

e1185288
ymdBconserved hypothetical protein ymdBBacillus subtilis complete genome












(section 9 of 21) similar to hypothetical proteins


Contig358D
22850885_c3_163
2083
4920
1596
532
1799
1.40E−185

Bacillus subtilis

e1185287
ymdAconserved hypothetical protein ymdABacillus subtilis complete genome












(section 9 of 21) similar to hypothetical proteins


Contig358D
23445463_c2_130
2084
4921
801
267
1002
4.10E−101

Bacillus subtilis

e1185240
rpsBribosomal protein S2Bacillus subtilis complete genome (section 9 of












21)


Contig358D
23472175_c2_137
2085
4922
417
139
360
4.40E−33

Bacillus subtilis

P32731
ORF6ribosome-binding factor AB.subtilis infB-nusA












operon.Escericia coli protein P15Balternate gene name


Contig358D
23554760_f1_6
2086
4923
255
85


Contig358D
23632758_c3_145
2087
4924
258
86


Contig358D
23633467_c1_113
2088
4925
987
329
659
9.10E−65

Bacillus subtilis

e269877
ribCFMN adenylyltransferaseB.subtilis ribC, rpsO and pnpA genes.riboflavin












kinase


Contig358D
23650250_c3_147
2089
4926
546
182
667
1.30E−65

Bacillus subtilis

P39070
codWCodWBacillus subtilis JH642 dipeptide permease operon regulators












codV, codW, codX, and codY genes, complete cds.alternate gene name


Contig358D
24033217_c1_112
2090
4927
930
310
720
3.10E−71

Bacillus subtilis

e1185257
truBtRNA pseudouridine 55 synthaseBacillus subtilis complete












genome (section 9 of 21) alternate gene name


Contig358D
24267941_c3_158
2091
4928
726
242
304
3.80E−27

Bacillus subtilis

e1185272
ymfCtranscriptional regulator (GntR family) homolog ymfCBacillus subtilis












complete genome (section 9 of 21) similar to transcriptional regulator












(GntR family)


Contig358D
24414818_c3_153
2092
4929
870
290
952
8.10E−96

Bacillus subtilis

e1185251
nusAtranscription termination nusABacillus subtilis complete genome












(section 9 of 21)


Contig358D
24492827_f2_63
2093
4930
2601
867
1069
3.20E−108

Bacillus subtilis

e1182850
yfhOYfhOBacillus subtilis complete genome (section 5 of 21)


Contig358D
24792776_c1_109
2094
4931
528
176
371
3.00E−34

Bacillus subtilis

P32726
ORF1protein P15A homologB.subtilis infB-nusA operon.nus operon 15K












proteinalternate gene name


Contig358D
24886550_c3_156
2095
4932
288
96
350
5.00E−32

Bacillus subtilis

e269878
rpsPribosomal protein S15B.subtilis ribC, rpsO and pnpA genes.


Contig358D
24886677_c2_134
2096
4933
1722
574
1885
1.10E−194

Bacillus subtilis

e1185248
proSprolyl-tRNA synthetaseBacillus subtilis complete genome (section 9 of












21)


Contig358D
24900332_c1_124
2097
4934
981
327
935
5.10E−94

Bacillus subtilis

P49850
mutLMutLBacillus subtilis spore coat protein (cotE) gene, partial cds,












andmismatch repair recognition proteins (mutS) and (mutL) genes, complete cds.


Contig358D
255B7942_c2_126
2098
4935
786
262
556
7.40E−54

Bacillus subtilis

e1185197
mhribonuclease HBacillus subtilis complete genome (section 9 of 21)


Contig358D
25665937_c2_132
2099
4936
558
186
841
4.70E−84

Staphylococcus

g2645713
frrribosome recycling factorStaphylococcus aureus ribosome











aureus


recycling factor (frr) gene, complete cds.


Contig358D
26257806_c2_144
2100
4937
984
328
707
7.40E−70

Bacillus subtilis

P49850
mutLMutLBacillus subtilis spore coat protein (cotE) gene, partial cds,












andmismatch repair recognition proteins (mutS) and (mutL) genes, complete cds.


Contig358D
26306257_c1_105
2101
4938
2073
691
2490
8.50E−259

Bacillus subtilis

P39814
topADNA topoisomerase IBacillus subtilis (smf) gene, 3′ end, DNA












topisomerase gene, completecds, (gid) gene, 5′ end.alternate gene name


Contig358D
26353417_c3_164
2102
4939
294
98
141
7.00E−10

Clostridium

g498839
hypothetical protein 2Clostridium perfringens JIR4025 extracellular toxin











perfringens


productionregulatory locus ORF1 and ORF3 genes, partial cds, and












ORF2, ORF10c, virR, virS, and ORF4 genes, complete cds.ORF2


Contig358D
26370703_c2_125
2103
4940
285
95


Contig358D
26460951_c1_108
2104
4941
792
264
917
4.10E−92

Bacillus subtilis

e1185242
smbAuridylate kinaseBacillus subtilis complete genome (section 9 of 21)


Contig358D
275427_c3_157
2105
4942
1722
574
1379
4.60E−141

Bacillus subtilis

e1185269
ymfAconserved hypothetical protein ymfABacillus subtilis complete genome












(section 9 of 21) similar to hypothetical proteins


Contig358D
30656317_c1_107
2106
4943
822
274
858
7.40E−86

Bacillus subtilis

P39779
codYCodYBacillus subtilis JH642 dipeptide permease operon regulators,












codV, codW, codX, and codY genes, complete cds.


Contig358D
31552_c3_166
2107
4944
522
174


Contig358D
31697151_c1_101
2108
4945
315
105
441
1.10E−41

Bacillus subtilis

e1185195
rplSribsomal protein L19Bacillus subtilis complete genome (section 9 of












21)


Contig358D
3257827_c1_116
2109
4946
705
235
356
1.20E−32

Bacillus subtilis

e1185278
ymfl3-oxoacyl-acyl-carrier protein reductase homolog ymflBacillus subtilis












complete genome (section 9 of 21) similar to 3-oxoacyl-acyl-carrier












protein


Contig358D
32611557_c2_131
2110
4947
294
98
316
2.00E−28

Bacillus subtilis

e1185241
tsfelongation factor TsBacillus subtilis complete genome (section 9 of 21)


Contig358D
33283167_c2_140
2111
4948
1338
446
967
2.10E−97

Bacillus subtilis

e1185277
ymfHprocessing proteinase homolog ymfHBacillus subtilis complete genome












(section 9 of 21) similar to processing protease


Contig358D
33800901_f2_41
2112
4949
318
106
127
2.10E−08

Leishmania

S51910
cryptogene protein G4











tarentolae



Contig358D
34571877_c3_159
2113
4950
1275
425
372
2.30E−34

Bacillus subtilis

e1185276
ymfGprocessing proteinase homolog ymfGBacillus subtilis complete genome












(section 9 of 21) similar to processing protease


Contig358D
34663177_c1_118
2114
4951
1167
389
641
1.70E−65

Bacillus subtilis

g1842440
cinACinABacillus subtilis tRNA-Ala, phosphatidylglycerophosphate












synthase (psgA) and CinA (cinA) genes. complete cds, and RecA (recA)












gene, partial cds.


Contig358D
35370318_c1_104
2115
4952
930
310
1274
6.10E−130

Bacillus subtilis

e1185201
sucDsuccinyl-CoA synthetase (alpha subunit) Bacillus subtilis complete












genome (section 9 of 21)


Contig358D
36220061_c2_129
2116
4953
1425
475
1399
3.50E−143

Bacillus subtilis

P39778
codXCodXBacillus subtilis JH642 dipeptide permease operon regulators,












codV, codW, codX, and codY genes, complete cds.alternate gene name


Contig358D
36225938_c1_103
2117
4954
1185
395
1557
6.30E−160

Bacillus subtilis

e1185200
sucCsuccinyl-CoA synthetase (beta subunit) Bacillus subtilis complete












genome (section 9 of 21)


Contig358D
40686_c3_152
2118
4955
4089
1363
6425
0

Staphylococcus

d1013849
DNA polymerase IIIStaphylococcus aureus DNA for DNA polymerase lll,











aureus


complete cds.


Contig358D
40938l8_c1_117
2119
4956
591
197
436
3.90E−41

Bacillus subtilis

P46322
pgs1APgsABacillus subtilis pgs1A gene for












phosphatidylglycerophosphatesynthase, complete cds.PgsA


Contig358D
4095286_c1_123
2120
4957
375
125
246
3.30E−21

Bacillus subtilis

e1185293
ymcAconserved hypothetical protein ymcABacillus subtilis complete genome












(section 9 of 21) similar to hypothetical proteins


Contig358D
4336536_c3_154
2121
4958
315
105
211
2.70E−17

Bacillus subtilis

P32728
ORF3conserved hypothetical protein ylxRB.subtilis infB-nusA












operon.alternate gene name


Contig358D
4425068_f3_100
2122
4959
2613
871
880
3.40E−88

Bacillus subtilis

e1182850
yfhOYfhOBacillus subtilis complete genome (section 5 of 21)


Contig358D
4572162_c2_133
2123
4960
1290
430
932
1.10E−93

Bacillus subtilis

e1185247
yluCconserved hypothetical protein yluCBacillus subtilis complete genome












(section 9 of 21) similar to hypothetical proteins


Contig358D
5195328_c3_161
2124
4961
393
131
142
1.90E−09

Bacillus subtilis

g1842438
unknownBacillus subtilis tRNA-Ala, phosphatidylglycerophosphate












synthase (pgsA) and CinA (cinA) genes, complete cds, and RecA (recA)












gene, partial cds.ORF307; hypothetical 34.7 kd protein


Contig358D
5198557_c3_149
2125
4962
801
267
691
3.70E−68

Bacillus subtilis

e1185244
yluAconserved hypothetical protein yluABacillus subtilis complete genome












(section 9 of 21) similar to hypothetical proteins


Contig358D
5212776_c1_102
2126
4963
867
289
839
7.60E−84

Bacillus subtilis

e1185196
ylqFconserved hypothetical protein ylqFBacillus subtilis complete genome












(section 9 of 21) similar to hypothetical proteins


Contig358D
6678140_c2_135
2127
4964
348
116
328
3.10E−28

Staphylococcus

g642270
DNA polymerase IIIS.aureus gene for DNA polymerase III











aureus



Contig358D
6688126_c3_162
2128
4965
1074
358
1661
6,00E−171

Staphylococcus

Q02350
recAStaphylococcus aureus recA gene, complete cds.putative











aureus



Contig358D
6837812_c3_150
2129
4966
786
262
611
1.10E−59

Bacillus subtilis

e1185245
cdsAphosphatidate cytidylyltransferaseBacillus subtilis












complete genome (section 9 of 21)


Contig358D
6933390_c3_167
2130
4967
552
184
402
1.60E−37

Bacillus subtilis

P30300
glpPregulatory proteinBacillus subtilis antiterminator regulatory protein












(glpP), glycerol uptake facilator (glpF) genes, complete cds. glycerolkinase












(glpK) gene, 5′ end.see EMBL M99611 and Swiss Prot P30300.


Contig358D
7064077_c3_155
2131
4968
2187
729
2508
1.10E−260

Bacillus subtilis

P17889
IF2translation initiation factor IF-2B.subtilis protein synthesis initiation












factor 2 (infB) gene, complete cds.translation initiation factor IF-












2protein synthesis initiation factor 2 (infB)


Contig358D
891700_c1_120
2132
4969
867
289
599
2.10E−58

Halobacterium

g43499
ferredoxin oxidoreductaseH.halobium gene for pyruvatepyruvate synthase beta











halobium


chainbeta-subunit; pyruvate synthase


Contig358D
9767263_c1_121
2133
4970
639
213
280
1.30E−24

Bacillus subtilis

e1185518
yoqZphage-related protein homolog yoqZBacillus subtilis complete genome












(section 11 of 21) similar to phage-related protein


Contig358D
9804202_c3_148
2134
4971
627
209
704
1.50E−69

Bacillus subtilis

e1185241
tsfelongation factor TsBacillus subtilis complete genome (section 9 of 21)


Contig358D
9807807_c3_160
2135
4972
873
291
522
3.00E−50

Bacillus subtilis

g1842437
unknownBacillus subtilis tRNA-Ala, phosphatidylglycerophosphate












synthase (pgsA) and CinA (cinA) genes, complete cds, and RecA (recA)












gene.partial cds.hypothetical 17.9 kDa protein; ORF158


Contig359D
10406642_f1_17
2136
4973
342
114
165
2.30E−12

Bacillus subtilis

P39756
narQunknownB.subtilis atpC gene.alternate gene name


Contig359D
1054640_f3_85
2137
4974
213
71
170
6.00E−13

Bacillus subtilis

P39756
narQunknownB.subtilis atpC gene.alternate gene name


Contig359D
10928_c1_113
2138
4975
1242
414
234
3.50E−17

Rhodobacter

g3128293
hypothetical proteinRhodobacter capsulatus strain SB1003, partial











capsulatus


genome.


Contig359D
1209800_c2_148
2139
4976
282
94


Contig359D
12588250_f1_40
2140
4977
198
66


Contig359D
12595175_f2_62
2141
4978
498
166
261
1.40E−22

Bacillus subtilis

P49856
ykkCYkkCBacillus subtilis hmp DNA for 7 ORFs, complete cds.unnamed












protein product


Contig359D
1261078_c1_111
2142
4979
579
193
471
7.60E−45

Bacillus subtilis

P42085
xptadenine phosphoribosyltransferaseBacillus













subtilis (YAC10-9 clone) DNA region between the serA andkdg loci27%













identity with E.coli adenine


Contig359D
1375308_c2_160
2143
4980
411
137
96
4.10E−05

Staphylococcus

g684950
sarAstaphylococcal accessory regulator AStapgylococcus aureus staphylococcal











aureus


accessory regulator A (sarA) gene, complete cds.


Contig359D
13849056_c1_120
2144
4981
279
93


Contig359D
14097586_f3_90
2145
4982
438
146
470
9.70E−45

Staphylococcus

P42874
ureBurease beta subunitS.xylosus gene for ureA, ureB, and ureC for











xylosus


urease gamma, beta and alpha subunits.urease 12K chain


Contig359D
14460882_f1_10
2146
4983
189
63
221
2.30E−18

Staphylococcus

g1022726
unknownStaphylococcus haemolyticus IS1272 ORF1 and ORF2 genes,











haemolyticus


completecds.ORF1


Contig359D
14549010_c2_158
2147
4984
666
222
185
1.50E−14

Bacillus subtilis

e1185016
mobAmolybdopterin-guanine dinucleotide biosynthesisBacillus subtilis












complete genome (section 8 of 21)


Contig359D
15033181_f3_109
2148
4985
444
148


Contig359D
19533567_f2_50
2149
4986
264
88


Contig359D
21611592_f3_102
2150
4987
369
123


Contig359D
21646015_f2_52
2151
4988
210
70
158
1.10E−11

Staphylococcus

g1022725
unknownStaphylococcus haemolyticus IS1272 ORF1 and ORF2 genes,











haemolyticus


completecds.ORF2


Contig359D
21675050_f3_100
2152
4989
360
120


Contig359D
21681561_f1_32
2153
4990
891
297
776
3.60E−77

Bacillus subtilis

e1182103
ybblconserved hypothetical protein ybblBacillus subtilis complete genome












(section 1 of 21) similar to hypothetical proteins


Contig359D
21776942_c1_116
2154
4991
642
214
855
1.50E−85

Bacillus subtilis

e1182158
ybxGamino acid permease homolog ybxGBacillus subtilis complete genome












(section 2 of 21) alternate gene name


Contig359D
2211433_f3_93
2155
4992
867
289
534
1.60E−51

Bacillus sp.

Q07400
UreDurease accessory proteinThermophilic Bacillus genes for












urease subunits and ureaseaccessory proteins, complete cds.


Contig359D
22290657_c3_177
2156
4993
387
129
157
1.40E−11

Staphylococcus

g684950
sarAstaphylococcal accessory regulator AStapgylococcus aureus staphylococcal











aureus


accessory regulator A (sarA) gene, complete cds.


Contig359D
22692177_c1_131
2157
4994
537
179
391
2.30E−36

Bacillus subtilis

g2293241
moaBputative molibdenum cofactor biosynthesisBacillus subtilis rrnB-dnaB












genomic region.


Contig359D
23538427_f2_73
2158
4995
309
103
132
6.80E−09

Pyrococcus

d1027429
PHCD003215aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA, 270845-299829 nt position, clonecontains prokaryotic












membrane lipoprotein lipid


Contig359D
23609628_c2_153
2159
4996
975
325
385
9.80E−36

Trypanosoma

g2645495
inosine-adenosine-guanosine-nucleosideTrypanosoma brucei brucei











brucei brucei


inosine-adenosine-guanosine-nucleosidehydrolase mRNA, complete












cds.N-ribohydrolase; 1AG-nucleoside hydrolase


Contig359D
23620260_c2_150
2160
4997
1107
369
334
2.50E−30

Arthrobactcr sp.

d1008736
opine dehydrogenaseArthrobacter sp. gene for opine dehydrogenase, complete












cds.


Contig359D
23631551_c3_183
2161
4998
792
264


Contig359D
23642167_f3_81
2162
4999
1218
406
611
1.10E−59

Bacillus subtilis

e1184551
ywoGunknown similar to quinolon resistance proteinBacillus subtilis












complete genome (section 19 of 21) similar to antibiotic resistance protein


Contig359D
23678262_c3_182
2163
5000
573
191
370
3.80E−34

Bacillus subtilis

e1183039
yhfUhypothetical proteinBacillus subtilis complete genome (section 6 of












21) similar to biotin biosynthesis


Contig359D
24104677_c2_143
2164
5001
1656
552
1619
1.70E−166

Bacillus subtilis

P54715
glvCphosphotransferase system (PTS) arbutin-likeBacillus subtilis complete












genome (section 5 of 21) alternate gene name


Contig359D
24234562_f2_75
2165
5002
222
74


Contig359D
24257012_c1_128
2166
5003
735
245
480
8.40E−46

Synechocyslis sp.

d1011427
ABC transporterSynechocystis sp. PCC6803 complete genome, 24/27,












3002966-3138603.unassigned ATP-binding cassette proteinsORF_ID


Contig359D
24314818_c2_159
2167
5004
1035
345
923
9.60E−93

Bacillus subtilis

P39757
narAMoaA-like proteinB.subtilis atpC gene.alternate gene name


Contig359D
24406577_c2_162
2168
5005
3156
1052
2317
1.80E−240

Bacillus subtilis

e1182651
yerPacriflavin resistance protein homolog yerPBacillus subtilis complete












genome (section 4 of 21) similar to acriflavin resistance protein


Contig359D
24431532_c1_135
2169
5006
1254
418
343
2.80E−31

Staphylococcus

e329240
femAStaphylococcus hominis femA gene.











hominis



Contig359D
24616251_12_63
2170
5007
696
232
139
2.20E−07

Streptomyces

g567887
dnrOputative repressorStreptomyces peucetius TDP-D-glucose-4,6-











peucetius


dehydratase (dnrM) gene, 3p40 p0 end, regulatory protein (dnrN) gene, complete












cds, and repressorprotein (dnrO) gene, complete cds.putative


Contig359D
24644008_c3_184
2171
5008
792
264
408
3.60E−38

Bacillus subillis

c1249786
yvgLputative molybdate binding protein YvgLBacillus subtilis 42.7 kB DNA












fragment from yvsA to yvsA.alternate gene name


Contig359D
24647292_c3_164
2172
5009
1275
425
1180
5.60E−120

Bacillus subtilis

P42086
ypaQtransport proteinBacillus subtilis (YAC10-9 clone) DNA region between












the serA andkdg loci.26% of identity to the Bacillus caldolyticus uracil


Contig359D
25430317_c1_132
2173
5010
492
164
215
1.00E−17

Bacillus subtilis

e1185019
mobBmolybdopterin-gunaine dinucleotide biosynthesisBacillus subtilis












complete genome (section 8 of 21)


Contig359D
25443838_c2_149
2174
5011
789
263
448
2.10E−42

Staphylococcus

d1023468
NAGStaphylococcus aureus DNA for N-acetyl-glucosaminidase, partialcds.











aureus



Contig359D
25554213_f1_20
2175
5012
627
209
943
7.30E−95

Staphylococcus

P42877
UREGUreGS.xylosus (C2a) UreF and UreG genes.











xylosus



Contig359D
25554675_f3_110
2176
5013
237
79


Contig359D
25582885_11_9
2177
5014
453
151
153
3.80E−11

Bacillus subtilis

e1184550
ywoHunknown, similar to cytolysin SlyA fromBacillus subtilis complete












genome (section 9 of 21) similar to transcriptional regulator (MarR family)


Contig359D
25679762_c1_119
2178
5015
831
277
374
1.40E−34

Bacillus subtilis

g1377843
yktCunknownBacillus subtilis ampS-nprE gene region.similar to E. coli












extragenic suppressor protein


Contig359D
26182800_c1_134
2179
5016
813
271


Contig359D
26375031_f1_2
2180
5017
195
65


Contig359D
26758426_c2_151
2181
5018
750
250
107
8.80E−06

Staphylococcus

g684950
sarAstaphylococcal accessory regulator AStapgylococcus aureus staphylococcal











aureus


accessory regulator A (sarA) gene, complete cds.


Contig359D
29494067_c3_167
2182
5019
213
71


Contig359D
29697752_c2_147
2183
5020
786
262
499
8.20E−48

Bacillus subtilis

Q02115
lytRmembrane bound proteinBacillus subtilis membrane bound protein (lytA












and lytR); amidaseenhancer (lytB); and amidase (lytC) genes, complete cds's.


Contig359D
3250075_f3_96
2184
5021
1008
336
705
1.20E−69

Pyrococcus

d1027703
PHAB011376aa long hypothetical dehydrogenasePyrococcus horikoshii











horikoshii


OT3 genomic DNA, 512441-547109 nt position(complementary strand),












clonecontains ATP/GTP-binding site motif A (P-loop);


Contig359D
33360910_f3_95
2185
5022
549
183
120
1.20E−07

Syncchocystis sp.

d1017705
hypothetical proteinSynechocystis sp. PCC6803 complete genome, 4/27,












402290-524345.ORF_ID


Contig359D
3371062_f1_3
2186
5023
333
111


Contig359D
3401887_c1_112
2187
5024
1485
495
1969
1.40E−203

Bacillus subtilis

d1005787
guaB1MP dehydrogenaseB.subtilis DNA, 180 kilobase region of replication












origin.1MP dehydrogenasealternate gene name


Contig359D
34192165_c1_26
2188
5025
345
115
264
6.50E−23

Bacillus subtilis

e1181510
ykkDYkkDBacillus subtilis 168 56 kb DNA fragment between xlyA and












ykoR.similar to chaperonin


Contig359D
34411552_f2_58
2189
5026
1722
574
2703
2.30E−281

Staphylococcus

P42873
ureCurease alpha subunitS.xylosus gene for ureA, ureB, and ureC genes for











xylosus


urease gamma, beta and alpha subunits.urease 62K chain


Contig359D
34431300_c2_146
2190
5027
774
258
139
2.40E−09

Enterococcus

d1011987
orf8ORF8Enterococcus faecalis plasmid pY117 genes for BacA, BacB,











faecalis


ORF3, ORF4, ORF5, ORF6, ORF7, ORF8, ORF9, ORF10, ORF11, partial












cds.


Contig359D
34617187_f2_69
2191
5028
207
69


Contig359D
35944052_c1_44
2192
5029
690
230


Contig359D
36113805_c1_117
2193
5030
750
250
775
4.60E−77

Bacillus subtilis

e1182158
ybxGamino acid permease homolog ybxGBacillus subtilis complete genome












(section 2 of 21) alternate gene name


Contig359D
36132792_c3_187
2194
5031
255
85
127
2.10E−08

Syncchocystis sp.

d1011104
hypothetical proteinSynechocystis sp. PCC6803 complete genome, 22/27,












2755703-2868766.ORF_ID


Contig359D
36134427_c1_115
2195
5032
657
219
251
1.60E−21

Bacillus subtilis

P54607
yhcWhypothetical proteinB.subtilis chromosomal DNA (region 75












degreessimilarity to phosphoglycolate phosphatase from


Contig359D
36147301_c3_165
2196
5033
237
79


Contig359D
36209660_f2_55
2197
5034
378
126


Contig359D
36225625_f1_22
2198
5035
795
265
1034
1.70E−104

Staphylococcus

c244971

S.aureus orfs 1,2,3 & 4.ORF1












aureus



Contig359D
36615903_c2_152
2199
5036
1164
388
1007
1.20E−101

Bacillus subtilis

d1020042
ydbMbutyryl-CoA dehydrogenase homolog ydbMBacillus subtilis genome












sequence, 148 kb sequence of the regionbetween 35 and 47












degree.SIMILAR TO ACYL-COA DEHYDROGENASE.


Contig359D
3947153_f3_92
2200
5037
456
152
482
5.20E−46

Bacillus sp.

Q07401
UreEurease accessory proteinThermophilic Bacillus genes for












urease subunits and ureaseaccessory proteins, complete cds.


Contig359D
4042327_c3_180
2201
5038
918
306
309
1.10E−27

Homo sapiens

g1322222
RACH1RACH1Human RACH1 (RACH1) mRNA, complete cds.


Contig359D
4086568_c3_176
2202
5039
1983
661
130
1.50E−07

Escherichia coli

P22539
soxSregulatory protein SoxSEscherichia coli K-12 MG1655 section 369 of 400 of












the completegenome.f107; 100 pct identical amino acid sequence and


Contig359D
4305342_c2_142
2203
5040
1557
519
2015
1.80E−208

Bacillus subtilis

g2239288
guaAGMP synthetaseBacillus subtilis CotA (cotA), GabP (gabP), YeaB












(yeaB), YeaC (yeaC), YebA (yebA), GMP synthetase (guaA) genes, complete












cds, and AlR carboxylase 1 (purE) gene, partial cds.alternate gene name


Contig359D
4459380_f1_39
2204
5041
207
69


Contig359D
4486693_f2_49
2205
5042
804
268
976
2.30E−98

Staphylococcus

e324856
gdhglucose-1-dehydrogenaseStaphylococcus xylosus gltA, gdh genes.











xylosus



Contig359D
4491450_f2_65
2206
5043
873
291
306
2.30E−27

Bacillus subtilis

d1020262
YbbHBacillus subtilis DNA for FeuB, FeuA, YbbB, YbbC, YbbD, YbzA,












YbbE, YbbF, YbbH, YbbI, YbbJ, YbbK, YbbL, YbbM, YbbP, complete cds.


Contig359D
4547163_f1_19
2207
5044
699
233
741
1.90E−73

Staphylococcus

P42876
UREFUreFS.xylosus (C2a) UreF and UreG genes.











xylosus



Contig359D
4569012_c1_35
2208
5045
588
196


Contig359D
4720928_f1_4
2209
5046
186
62


Contig359D
4800202_c1_129
2210
5047
621
207
384
1.30E−35

Helicobacter

g1800188
ORF37H. pylori chromosomal fragment ~38.5 kb, complete sequence.ORF37 -











pylori


similar to H. influenzae HitC - S72674; E.


Contig359D
4804153_c1_14
2211
5048
690
230
439
1.90E−41

Bacillus subtilis

e1182575
ydiGmolybdopterin precursor biosynthesis homolog ydiGBacillus













subtilis complete genome (section 4 of 21) similar to molybdopterin precursor













biosynthesis


Contig359D
4876675_f2_57
2212
5049
399
133
430
1.70E−40

Staphylococcus

P42875
ureAurease gamma subunitS.xylosus gene for ureA, ureB, and ureC genes for











xylosus


urease gamma, beta and alpha subunits.urease 11K chain


Contig359D
4884662_c3_171
2213
5050
1128
376
293
5.50E−26

Acinetobacter

g2271503
unknownAcinetobacter calcoaceticus ADP1 vanillate demethylase











calcoaceticus


region, vanillate demethylase (vanB) and vanillate demethylase (vanA) genes,












complete cds.similar to salicylate hydroxylase; ORF7


Contig359D
4976687_c1_137
2214
5051
924
308
192
1.60E−13

Methanobacterium

g2622492
MTH1382conserved proteinMethanobacterium











thermoauto-



thermoautotrophicum from bases 1243964 to 1257931 (section 107 of 148)












trophicum


of the complete genome.Function Code


Contig359D
5087556_c2_156
2215
5052
849
283
499
8.20E−48

Bacillus subtilis

e1185017
moeBmolybdopterin biosynthesis proteinBacillus subtilis complete genome












(section 8 of 21)


Contig359D
5113550_f2_64
2216
5053
1089
363
240
9.90E−19

Borrelia

g2689897
BBB07outer surface protein, putativeBorrelia burgdorferi plasmid











burgdorferi


cp26, complete plasmid sequence.similar to GB


Contig359D
5266018_f2_71
2217
5054
771
257
415
6.50E−39

Bacillus subtilis

P54717
yfiAunknownBacillus subtilis complete genome (section 5 of 21) similar to












hypothetical proteins


Contig359D
5898328_f2_48
2218
5055
864
288
1102
1.00E−111

Staphylococcus

e324855
gltAglucose uptake proteinStaphylococcus xylosus gltA, gdh











xylosus


genes.


Contig359D
6929676_c1_121
2219
5056
342
114


Contig359D
7031318_f2_67
2220
5057
339
113


Contig359D
7086677_c3_170
2221
5058
243
81


Contig359D
818812_c2_157
2222
5059
1287
429
1034
1.70E−104

Bacillus subtilis

e1185018
mooAmolybdopterin biosynthesis proteinBacillus subtilis complete genome












(section 8 of 21)


Contig359D
829761_c1_140
2223
5060
2172
724
1751
1.70E−180

Bacillus subtilis

d1020016
topBPROBABLE DNA TOPOISOMERASE IIIBacillus subtilis












genome sequence, 148 kb sequence of the regionbetween 35 and 47 degree


Contig359D
959427_f1_25
2224
5061
417
139
241
1.80E−20

Staphylococcus

g2735506
SceBSceB precursorStaphylococcus carnosus N5, N10-











carnosus


methylenetetrahydromethanopterinreductase homolog, SceB precursor (sceB) and












putative transmembraneprotein genes, complete cds, and putative Na+/H+












antiporter NhaC (nhaC) gene, partial cds.major secret pro


Contig359D
964077_c1_133
2225
5062
453
151
443
7.00E−42

Bacillus subtilis

e1185020
moaEmolybdopterin converting factor (subunit 2) Bacillus subtilis complete












genome (section 8 of 21)


Contig359D
975061_c3_173
2226
5063
1455
485
916
5.30E−92

Haemophilus

Q57007
H11107Na+/H+ antiporter (nhaC) Haemophilus influenzae from











influenzae


bases 1163012 to 1173282 (section 105 of 163) of the complete












genome.similar to GB


Contig359D
9928500_c1_130
2227
5064
261
87
229
3.30E−19

Bacillus subtilis

e1185017
moeBmolybdopterin biosynthesis proteinBacillus subtilis complete genome












(section 8 of 21)


Contig359D
9977318_f1_33
2228
5065
1437
479
700
4.10E−69

Escherichia coli

d1017042
IPA-49DPTS SYSTEM, SUCROSE-SPECIFIC IIBC COMPONENTE.coli












genomic DNA, Kohara clone #419 (54.7-55.1 min.).similar to [SwissProt












Accession Number P05306


Contig360D
10463_f3_80
2229
5066
504
168
315
2.60E−28

Bacillus subtilis

P40779
ytxGYtxGBacillus subtilis rrnB-dnaB genomic region.ORF1


Contig360D
1056693_f2_45
2230
5067
1101
367
774
5.90E−77

Bacillus subtilis

g2293210
ytoPYtoPBacillus subtilis rrnB-dnaB genomic regioin.similar to hypothatical












protein f356 from E. coli


Contig360D
116337_c1_90
2231
5068
627
209
199
5.00E−16

Lactococcus lactis

g3043872
transmembrane protein Tmp3Lactococcus lactis transmembrane












protein Tmp3 gene, partial cds.PBP1A homolog; identified as a fusion to a












signal


Contig360D
1203827_f2_34
2232
5069
639
213
475
2.80E−45

Actinobacilius

P50854
ribBriboflavin synthase alpha subunitActinobacillus pleuropneumoniae











pleuropneumoniae


riboflavin biosynthesis operon, riboflavin-specific deaminase (ribG), riboflavin












synthase alphasubunit (ribB), bifunctional GTP cyclohydraseII/3.4-












dihydroxy-2-butanone-4-phosphate synthas


Contig360D
1284381_f3_62
2233
5070
741
247
297
2.10E−26

Methanococcus

g1591624
MJ0960transaldolaseMethanococcus jannaschii section 81 of 150 of the











jannaschii


complete genome.Bacillus subtilis 23K phosphoprotein orfUsimilar to SP


Contig360D
13787912_f2_32
2234
5071
1524
508
118
1.40E−05

Escherichia coli

g1787957
hypothetical protein b1668Escherichia coli K-12 MG1655 section 152 of 400 of












the completegenome.o534; This 534 aa ORF is 38 pct identical (6 gaps)


Contig360D
13852187_c2_161
2235
5072
186
62
113
3.70E−06
Bacteriophage phi-
g758229
intintegraseBacteriophage phi-13 integrase gene.










13


Contig360D
14251933_c1_87
2236
5073
663
221
818
1.30E−81

Bacillus subtilis

g2293319
rpsDribosomal protein S4Bacillus subtilis rrnB-dnaB genomic












regioin.Escherichia coli ribosomal protein S4


Contig360D
14742937_f1_7
2237
5074
231
77


Contig36OD
14882928_f1_16
2238
5075
1098
366
1279
1.80E−130

Staphylococcus

e220317
aroAchorismate mutaseS.xylosus aroA, ccpA, acuC and acuA genes.











xylosus



Contig360D
14894807_c3_190
2239
5076
228
76


Contig360D
163151_f2_28
2240
5077
1248
416
1800
1.10E−185

Staphylococcus

P50307
S-adenisylmethionine synthetaseStaphylococcus aureus S-











aureus


adenosylmethionine synthetase gene, complete cds.SAM synthetase


Contig360D
16586012_c3_186
2241
5078
588
196
456
2.90E−43

Bacillus subtilis

g2293301
ytqBYtqBBacillus subtilis rrnB-dnaB genomic region.


Contig360D
16994043_c1_20
2242
5079
1128
376


Contig360D
191713_f2_39
2243
5080
11091
3697
562
3.80E−49

Homo sapiens

g405715
giantinH.sapiens giantin mRNA.giantina new 376 kD golgi complex outher












membrane protein


Contig360D
19565876_f3_76
2244
5081
201
67


Contig360D
19645900_c3_181
2245
5082
357
119
135
5.70E−09
mitochondrion
C30010
hypothetical ORF-6 protein











Leishmania












tarentolae



Contig360D
19742842_c1_4
2246
5083
849
283
776
3.60E−77

Bacillus subtilis

e1249784
yvgNputative reductase protein, YvgNBacillus subtilis 42.7 kB DNA












fragment from yvsA to yvqA.alternate gene name


Contig360D
1991325_c3_171
2247
5084
219
73


Contig360D
1992943_c1_136
2248
5085
747
249
104
1.90E−05

Plasmodium

g160225
CSPcircumsporozoite proteinPlasmodium yoelii











yoelii


circumsporozoite protein (CSP) gene, 5′ end.precursor


Contig360D
20834812_c3_194
2249
5086
306
102


Contig360D
2117077_c1_124
2250
5087
366
122
195
1.30E−15

Aquifex aeolicus

g2983116
aq_449hypothetical proteinAquifex aeolicus section 22 of 109 of the












complete genome.


Contig360D
2126250_c3_185
2251
5088
210
70


Contig360D
21522010_c3_193
2252
5089
1725
575
2393
1.60E−248

Staphylococcus

P51065
pckaphosphoenolpyruvate carboxykinaseStaphylococcus aureus











aureus


phosphoenolpyruvate carboxykinase (pcka) gene, complete cds.PEPCK;












homologue


Contig360D
22078331_c1_138
2253
5090
252
84


Contig360D
22391432_c1_137
2254
5091
525
175
288
1.90E−25
Bacteriophage phi-
g758229
intintegraseBacteriophage phi-13 integrase gene.










13


Contig360D
22459692_c2_157
2255
5092
201
67


Contig360D
23601713_12_35
2256
5093
1194
398
1108
2.40E−112

Bacillus

P51695
ribA3,4-dihydroxy-2-butanone 4-phosphate synthaseB.amyloliquefaciens











amyloliquefaciens


ribB, ribG, ribA, ribH & ribT genes.GTP cyclohydrolase II


Contig360D
2383253_f3_55
2257
5094
198
66


Contig360D
23984787_c1_17
2258
5095
1011
337
1404
1.00E−143

Staphylococcus

c220318
ccpAS.xylosus aroA, cppA, acuC and acuA genes.











xylosus



Contig360D
24020250_f3_63
2259
5096
882
294
551
5.40E−52

Staphylococcus

e1295630
aasAAS surface proteinStaphylococcus saprophyticus aas gene.











saprophyticus



Contig360D
24226543_f2_52
2260
5097
783
261
365
1.30E−33

Bacillus subtilis

e1182963
yhdWhypothetical proteinBacillus subtilis complete genome (section 6 of












21) similar to glycerophosphodiester phosphodesterase


Contig360D
24296925_c1_122
2261
5098
552
184
127
5.70E−08

Clostridium

e184374
P-21C.botulinum progenitor toxin complex genes.











botulinum



Contig360D
24334563_f1_11
2262
5099
453
151
109
2.00E−05

Pyrococcus

d1027404
PHBM041279aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA, 216006-259128 nt position, clonesimilar to PIR


Contig360D
24337750_f3_74
2263
5100
852
284
1238
4.00E−126

Staphylococcus

P54694
datD-amino acid transaminaseStaphylococcus











haemolyticus



haemolyticus Y176 D-amino acid transaminase (dat) gene, complete cds.



Contig360D
24417252_f2_37
2264
5101
1248
416
1036
1.00E−104

Bacillus subtilis

g2293179
yttBYttBBacillus subtilis rrnB-dnaB genomic region.similarity to tetracycline












resistance protein from


Contig360D
24609676_c1_6
2265
5102
471
157


Contig360D
24692338_f2_36
2266
5103
474
158
540
3.70E−52

Bacillus

Q44681
ribHlumazine synthase (b-subunit)B.amyloliquefaciens ribB, ribG,











amyloliquefaciens


ribA, ribH & ribT genes.


Contig360D
24720291_c3_189
2267
5104
498
166


Contig360D
24740701_f2_38
2268
5105
2508
836
3293
0

Bacillus subtilis

g2293181
leuSleucine tRNA synthetaseBacillus subtilis rrnB-dnaB genomic region.


Contig360D
24797177_f2_36
2269
5106
3534
1178
1450
1.40E−148

Bacillus subtilis

g2293215
ytpTYtpTBacillus subtilis rrnB-dnaB genomic region.strong similarity to FtsK












of E. coli and SpoIIIE of


Contig360D
24853437_f3_65
2270
5107
831
277
423
9.20E−40

Bacillus subtilis

g2293167
ytpAprobable lysophospholipaseBacillus subtilis rrnB-dnaB genomic












region.similar to lysophospholipase


Contig360D
2548537_f2_51
2271
5108
222
74


Contig360D
25665878_f3_72
2272
5109
1665
555
1014
2.20E−102

Bacillus subtilis

g2293198
ytgPYtgPBacillus subtilis rrnB-dnaB genomic region.similar to SpoVB protein












from B. subtilis


Contig360D
26175952_c1_121
2273
5110
258
86


Contig360D
26259686_c2_141
2274
5111
1242
414
801
8.10E−80

Bacillus subtilis

e1181491
ykdAYkdABacillus subtilis 168 56 kb DNA fragment between xlyA and












ykoR.putative serine protease, heat-shock inducible;


Contig360D
26567062_f3_58
2275
5112
792
264
428
2.70E−40

Bacillus subtilis

g2293162
ytmAputative peptidaseBacillus subtilis rrnB-dnaB genomic region.


Contig360D
26596062_c1_101
2276
5113
1284
428
1198
6.90E−122

Bacillus subtilis

g2293312
ytfPYtfPBacillus subtilis rrnB-dnaB genomic region.similarity to hypothetical












protein f400 from E.


Contig360D
2757633_f1_3
2277
5114
1494
498
1275
1.60E−164

Staphylococcus

Q53634
meneo-succinylbenzoic acid (OSB) CoA ligaseStaphylococcus aureus o-











aureus


succinylbenzoic acid CoA ligase (mene), and o-succinylbenzoic acid












synthetase (menc) genes, complete cds.


Contig360D
281531_c3_180
2278
5115
372
124
94
6.70E−05
Kinetoplast
g501027

Trypanosoma brucei EATRO 164 kinetoplast (CR4) mRNA, complete












Trypanosoma


cds.ORF2











brucei



Contig360D
2923202_12_50
2279
5116
1473
491
1202
2.60E−122

Vibrio Furnissii

g1732197
nagEPTS permease for N-acetylglucosamine and Vibrio furnissii












PTS permease for N-acetylglucosamine and glucose (nagE) gene, complete












cds.PTS enzyme IINag


Contig360D
29562552_c1_131
2280
5117
276
92
281
1.00E−24

Bacillus subtilis

g2293294
ytjAYtjABacillus subtilis rrnB-dnaB genomic region.similar to hypothetical












9.3 kD protein from P.


Contig360D
30079651_c3_164
2281
5118
1620
540
1135
3.30E−115

Bacillus subtilis

g1146196
scrAphosphoglycerate dehydrogenaseBacillus subtilis












phosphoglycerate dehydrogenase (serA), ypaA, ferredoxin (fer), ypbB, recS, ypbD,












ypbE, ypbF, ypbG, ypbH, glutamate dehydrogenase (ypcA), ypdA, ypdB,












ypdC, spore cortexlytic enzyme (sleB), ypcB, ypfA, ypfB,


Contig360D
30084402_c2_140
2282
5119
1188
396
716
8.30E−71

Synechococcus

P14776
soluble hydrogenase, small chainSynechococcus DNA for the small










sp.

subunit of soluble hydrogenase.serine--pyruvate aminotransferasesmall subunit












of soluble hydrogenase (AA 1-384)


Contig360D
30274187_c1_115
2283
5120
969
323
1317
1.70E−134

Bacillus subtilis

g2293302
y1qAYtqABacillus subtilis rrnB-dnaB genomic region.similarity to biotine












synthase from B.sphaericus


Contig360D
31256568_f3_86
2284
5121
201
67
114
5.10E−07

Pyrococcus

d1024740
PHAA016119aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


PHAA001-PHAA055 genes, complete cds.


Contig360D
3158502_f2_44
2285
5122
225
75
122
2.20E−07

Bacillus subtilis

g2293206
ytmPYtmPBacillus subtilis rrnB-dnaB genomic region.


Contig360D
33287515_c2_156
2286
5123
330
110


Contig360D
33360312_c3_168
2287
5124
420
140
295
1.30E−25

Streptococcus

e1284114
pbp1bpenicillin-binding protein 1bStreptococcus pneumoniae pbp1b











pneumoniae


gene, partial, beta-lactamresistant.


Contig360D
33630311_f3_73
2288
5125
1341
447
1001
5.20E−101

Bacillus

g436965
hypothetical protein 1Bacillus stearothermophilus maltose permease











stearothermophilus


(malA) gene, completecds.


Contig360D
3365887_12_43
2289
5126
630
210
501
5.00E−48

Bacillus subtilis

g2293206
ytmPYtmPBacillus subtilis rrnB-dnaB genomic region.


Contig360D
34178128_f2_30
2290
5127
216
72


Contig360D
34199077_f2_25
2291
5128
1017
339
864
1.70E−86

Staphylococcus

g1255260
menco-succinylbenzoic acid (OSB) synthetaseStaphylococcus aureus o-











aureus


succinylbenzoic acid CoA ligase (mene), and o-succinylbenzoic acid












synthetase (menc) genes. complete cds.


Contig360D
34415925_f3_75
2292
5129
654
218
540
3.70E−52

Bacillus subtilis

g2293207
ytmQYtmQBacillus subtilis rrnB-dnaB genomic region.similar to hypothetical












protein H10340 from H.


Contig360D
34429838_f2_26
2293
5130
483
161
261
1.40E−22

Bacillus subtilis

g2293161
ytkDYtkDBacillus subtilis rrnB-dnaB genomic region.


Contig360D
34610925_c2_139
2294
5131
462
154
274
5.70E−24

Bacillus subtilis

c1183387
ymaDconserved hypothetical protein ymaDBacillus subtilis complete genome












(section 10 of 21) similar to hypothetical proteins


Contig360D
4110882_c3_172
2295
5132
351
117


Contig360D
4183428_f1_15
2296
5133
1329
443
1966
2.90E−203

Staphylococcus

g2642659
murCUDP-N-acetylmuramoyl-L-alanine synthetaseStaphylococcus aureus UDP-N











aureus


acetylmuramoyl-L-alanine synthetase (murC) gene, complete












cds.MurC; UDP-N-acetylmuramate-alanine ligase


Contig360D
4296950_f1_2
2297
5134
198
66


Contig360D
4299175_f3_56
2298
5135
240
80


Contig360D
4502308_f3_83
2299
5136
636
212
502
3.90E−48

Bacillus subtilis

e1182955
yhdOhypothetical proteinBacillus subtilis complete genome (section 6 of












21) similar to 1-acylglycerol-3-phosphate


Contig360D
4697318_f3_77
2300
5137
867
289
671
4.80E−66

Bacillus subtilis

g2293212
ytpQYtpQBacillus subtilis rrnB-dnaB genomic region.


Contig360D
4776702_f3_67
2301
5138
312
104
164
2.60E−12

Bacillus subtilis

P54433
yrkFYrkFBacillus subtilis DNA, 283 Kb region containing skin element.similar to












hypothetical proteins from B.subtilis


Contig360D
4876300_f3_81
2302
5139
1695
565
1839
8.20E−190

Streptococcus

Q59925
fhsformyl-tetrahydrofolate synthetaseStreptococcus mutans formyl-











mutans


tetrahydrofolate synthetase (fhs) gene, complete cds.formyl-












tetrahydrofolate ligase; ATP-dependent


Contig360D
5081252_c3_191
2303
5140
360
120
199
5.00E−16

Aquifex aeolicus

g2983116
aq_449hypothetical proteinAquifex aeolicus section 22 of 109 of the












complete genome.


Contig360D
5355250_f2_49
2304
5141
1284
428
1343
3.00E−137

BACILLUS

P00952
TYRStyrosine--tRNA ligase, TYROSYL-TRNA SYNTHETASE, (TYROSINE--











STEAROTHERMO-


TRNA LIGASE) (TYRRS) tyrosine--tRNA ligase











PHILUS



Contig360D
551907_c1_134
2305
5142
708
236
183
2.50E−14

Streptococcus

g2897104
putative host cell surface-exposed lipoproteinStreptococcus thermophilus











thermophilus


bacteriophage lysogeny module, integrasehomolog (int), putative host cell










bacteriophage TP-

surface-exposed lipoprotein, putative metallo-proteinase, repressor, Cro-like










J34

regulatoryprotein, and P1-antir


Contig360D
572186_f2_47
2306
5143
1284
428
190
2.00E−11

Petromyzon

g632549
NF-180Petromyzon marinus neurofilament subunit NF-180 mRNA,











marinus


complete cds.180 kDa neurofilament subunit


Contig360D
5911592_f2_29
2307
5144
924
308


Contig360D
6070392_f2_42
2308
5145
708
236
415
6.50E−39

Haemophilus

P45124
H11243hypotheticalHaemophilus influenzae from bases 1311704 to











influenzae


1324184 (section 119 of 163) of the complete genome.similar to SP


Contig360D
6100150_f2_23
2309
5146
189
63


Contig360D
6317_c1_13
2310
5147
411
137
267
3.10E−23

Bacillus subtilis

g2293211
yrpPputative thioredoxinBacillus subtilis rrnB-dnaB genomic region.similar to












thioredoxin H1


Contig360D
785952_f1_14
2311
5148
567
189
552
2.00E−53

Bacillus subtilis

g2293213
ytpRYtpRBacillus subtilis rrnB-dnaB genomic region.similarity to












phenylalanine tRNA ligase of E. coli


Contig360D
82562_c1_116
2312
5149
1110
370
680
5.40E−67

Bacillus subtilis

e1182272
yegMproline oxidase homolog ycgMBacillus subtilis complete genome












(section 2 of 21) similar to proline oxidase


Contig360D
954768_f2_33
2313
5150
1053
351
611
1.10E−59

Bacillus subtilis

P17618
ribGriboflavin-specific deaminaseBacillus subtilis spoVA to












scrA region.ribG protein product (AA 1-361)


Contig360D
960012_f3_66
2314
5151
450
150
109
1.70E−06

Bacillus firmus

g2654484
hypothetical 16.1 kDa transcriptional regulatorBacillus firmus hypothetical












34.0 kDa protein, hypothetical 8.9 kDaprotein, hypothetical 10.1 kDa












protein, hypothetical 21.0 kDaprotein, putative thiosulfatte sulfurtransferase












hypothetical 16.1 kDa transcript


Contig360D
9845327_f3_60
2315
5152
192
64


Contig361D
11739752_c3_51
2316
5153
915
305
1172
3.90E−119

Staphylococcus

P49994
dnaA DnaAStaphylococcus aureus DNA for DnaA complete cds.











aureus



Contig361D
157500_c1_43
2317
5154
729
243
253
9.50E−22

Helicobacter

g2314496
HP1331conserved hypotheticalintegral membraneHelicobacter pylori section











pylori


112 of 134 of the complete genome.similar to EGAD


Contig361D
21660805_f1_8
2318
5155
1017
339
867
8.20E−87

Staphylococcus

g3044072
hlbbeta-hemolysinStaphylococcus schleiferi beta-hemolysin (hlb) gene,











schleiferi


partial cds.


Contig361D
22902302_c1_41
2319
5156
1407
469
2010
6.20E−208

Staphylococcus

P95689
serSseryl-trna synthetaseS.aureus serS gene.











aureus



Contig361D
23507_c1_40
2320
5157
2709
903
3998
0

Staphylococcus

d1001842
gyrADNA gyrase AStaphylococcus aureus genes for DNA gyrase A and B,











aureus


complete cds.


Contig361D
23704502_f1_14
2321
5158
267
89


Contig361D
24023300_c2_46
2322
5159
516
172
1760
1.80E−75

Staphylococcus

P49994
dnaA DnaAStaphylococcus aureus DNA for DnaA complete cds.











aureus



Contig361D
24645817_c2_50
2323
5160
453
151
461
8.70E−44

Bacillus

g143421
ribsomal protein L9ribosomal protein L9B.stearothermophilus ribosomal











stearothermophilus


protein L9 gene, complete cds.


Contig361D
24817142_c1_39
2324
5161
1947
649
3147
0

Staphylococcus

P20832
gyrBDNA gyraseS.aureus genes gyrB, gyrA and recF (partial).DNA











aureus


topoisonmerase (ATP-hydrolyzing) chain B


Contig361D
270890_c3_53
2325
5162
186
62


Contig361D
2931557_c3_52
2326
5163
1119
373
1692
3.10E−174

STAPHYLOCOC-

P29232
RECFrecF proteinRECF PROTEINrecF protein











CUS AUREUS



Contig361D
33244187_c3_57
2327
5164
1989
663
1592
1.20E−163

Bacillus subtilis

P37484
yybTunknownB. subtilis DNA, 180 kilobase region of replication origin


Contig361D
34004590_f3_31
2328
5165
291
97


Contig361D
34266582_c2_47
2329
5166
1158
386
1796
3.00E−185

STAPHYLOCOC-

P50029
DNANDNA-directed DNA polymerase, III beta chainDNA POLYMERASE III,











CUS AUREUS


BETA CHAIN, DNA-directed DNA polymerase III beta chain


Contig361D
35324092_c1_44
2330
5167
987
329
219
8.20E−28

Saccharomyces

P08465
MET2homoserine O-acetyltransferase, S.cerevisiae











cerevisiac


chromosome XIV reading frame ORF YNL277w.homoserine












acetyltransferaseORF YNL277w


Contig361D
35369052_c1_45
2331
5168
1404
468
1252
1.30E−127

Bacillus subtilis

P37469
dnaCreplicative DNA helicaseB.subtilis DNA, 180 kilobase region of replication












origin.


Contig361D
36359761_f3_36
2332
5169
840
280
581
1.70E−56

Streptococcus

P96051

Streptococcus thermophilus tetrahydrofolatedehydrogenase/cyclorolase












thermophilus


(folD), penicillin-binding protein 2b (pbp2b) and DNA repair and












recomination protein (recM) genes, complete cds.orf1091


Contig361D
41265_c3_58
2333
5170
1365
455
1593
9.60E−164

Bacillus subtilis

d1005716
purAadenylosuccinate synthetaseB. subtilis DNA, 180 kilobase region of












replication origin.adentlosuccinate synthase


Contig361D
4179680_c2_49
2334
5171
936
312
214
1.50E−16

Bacillus subtilis

P37485
yybSunknownB.subtilis DNA, 180 kilobase region of replication origin.


Contig361D
5190938_c3_56
2335
5172
471
357


Contig361D
6054512_f3_35
2336
5173
207
69


Contig361D
7031563_c1_38
2337
5174
243
81
358
7.10E−33

Staphylococcus

S54709
hypothetical protein 81











aureus



Contig362D
10195942_c1_98
2338
5175
636
232
253
9.50E−22

Thermotoga

Q56320
trpFphosphoribosyl anthranilate isomeraseT.maritima trpD, trpC, trpF,











maritima


trpB, and trpA genes.trpF homology


Contig362D
10667002_f1_14
2339
5176
189
63


Contig362D
31844802_c3_157
2340
5177
327
109


Contig362D
13087513_c2_112
2343
5178
3033
1011
547
1.30E−49

Aquifex aeolicus

g2983515
aq_1006hypothetical proteinAquifex aeolicus section 50 of 109 of the












complete genome.


Contig362D
3360958_c2_110
2342
5179
270
90
109
1.70E−06

Bacillus subtilis

e249647
yneJYneJB.subtilis DNA (26.2 kb feagment; 170 degree region).identical to












yoxt (from acc. no. X87845)


Contig362D
13678462_f3_61
2343
5180
564
188
303
4.80E−27

Synechococcus

P39665
sphXSphXSynechococcus sp. sphX gene for phosphate regulon SphX,










sp.



Contig362D
13845300_f1_1
2344
5181
309
103


Contig362D
13875216_c1_95
2345
5182
1023
341
895
8.90E−90

Staphylococcus

e1181777
glcTantiterminatorStaphylococcus carnosus glcT gene.











carnosus



Contig362D
34253643_f3_79
2346
5183
309
103
143
4.30E−30

Bacillus subtilis

e249654
yneRYneRB.subtilis DNA (26.2 kb feagment; 170 degree region)


Contig362D
14471938_c3_331
2347
5184
183
61
231
2.00E−39

BACILLUS

P23375
RPMGribosomal protein L3350S RIBOSOMAL PROTEIN











STEAROTHERMO-


L33Escherichia coli ribosomal protein











PHILUS



Contig362D
1461588_f3_62
2348
5185
942
314
712
2.20E−70

Archaeoglobus

g2649218
AF1357phosphate ABC transporter, permease proteinArchaeoglobus fulgidus











fulgidus


section 97 of 172 of the complete genome.similar to SP


Contig362D
14723387_c2_109
2349
5186
282
94
250
2.00E−21

Bacillus subtilis

P45708
yneFYneFB.subtilis DNA (26.2 kb fragment; 170 degree region).identical to












yoxG (from acc. no. X87845)


Contig362D
14850082_f3_64
2350
5187
933
311
880
3.40E−88

Bacillus subtilis

P46342
yqgKYqgKBacillus subtilis DNA, 283 Kb region containing skin












element.Similarity to phosphate transport protein (PstB) of


Contig362D
14876553_c3_146
2351
5188
996
332
570
2.40E−55

Enterococcus

g1147744
PSREnterococcus hirae psr gene, complete cds.











hirae



Contig362D
15084826_c3_136
2352
5189
300
100
268
2.50E−23

Bacillus subtilis

e249647
yneJYneJB.subtilis DNA (26.2 kb feagment; 170 degree region).identical to












yoxt (from acc. no. X87845)


Contig362D
15757712_f3_68
2353
5190
732
244
358
7.10E−33

Aquifex aeolicus

g2984331
abcT11ABC transporterAquifex aeolicus section 106 of 109 of the complete












genome


Contig362D
157875_c3_137
2354
5191
390
130


Contig362D
16205378_c2_123
2355
5192
243
81


Contig362D
16835388_f3_65
2356
5193
654
218
265
5.10E−23

Enterobacter

d1023735
phoUnegative regulatory protein of pho regulatonEnterobacter cloacae pstS, pstC,











cloacae


pstA, pstB and phoU genes, complete cds. The phoU gene is required for












chemotaxis to ward


Contig362D
19540678_c1_91
2357
5194
438
146
241
9.90E−20

Bacillus subtilis

P54417
opuDputative transporterBacillus subtilis rrnB-dnaB genomic region.alternate gene












name


Contig362D
19730438_c3_151
2358
5195
1272
424
2221
2.70E−230

Staphylococcus

g1815620
femBFEMBStaphylococcus epidermidis factor essential for methilcillinresistance











epidermidis


FEMB (femB) gene, complete cds.Factor essential for methicillin resistance


Contig362D
20312510_f2_38
2359
5196
1041
347
290
1.50E−48

Escherichia coli

d1015860
Dipeptide transport system permease proteinE.coli genomic DNA, Kohara












clone #278 (33.3-33.7 min.).ORF_ID


Contig362D
2040005_f2_56
2360
5197
810
270
691
3.70E−68

Bacillus subtilis

P31080
lexAtranscriptional regulatorBacillus subtilis lexA gene, 3′ end.alternate gene












name


Contig362D
20501250_c3_148
2361
5198
1029
343
551
2.50E−53

Methanococcus

Q57686
MJ0234anthranitate synthase component II(trpD)Methanococcus jannaschii











jannaschii


section 21 of 150 of the complete genome.trpD homologysimilar to GB


Contig362D
21643877_f1_4
2362
5199
954
338
687
9.80E−68

Archaeoglobus

g2649217
AF1358phosphate ABC transporter, permease proteinArchaeoglobus fulgidus











fulgidus


section 97 of 172 of the complete genome.similar to GB


Contig362D
22663932_f3_67
2363
5200
972
324
450
1.30E−42

Bacillus firmus

g1813497
dppCdipeptide transporter protein dppCBacillus firmus dppABC operon,












dipeptide transporter protein dppAgene, partial cds, and dipeptide transporter












proteins dppB and dppCgenes, complete cds.


Contig362D
23491077_c2_129
2364
5201
1266
422
1031
3.40E−104

Bacillus subtilis

g410117
lysAdiaminopimelate decarboxylaseBacillus subtilis spoVA to serA region.


Contig362D
23650343_c3_159
2365
5202
1167
389
527
8.80E−51

Pyrococcus

d1028137
PHAJ010387aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA, 922700-958423 nt position (complementary strand),












clonesimilar to Swiss_Prot


Contig362D
23671890_c2_117
2366
5203
1287
429
918
3.20E−92

Bacillus subtilis

e1183597
uvrXUV-damage repair proteinBacillus subtilis complete genome (section 12 of












21) alternate gene name


Contig362D
23673350_c3_333
2367
5204
1002
334
1329
9.10E−136

Bacillus subtilis

e1184292
yumDunknownBacillus subtilis complete genome (section 17 of 21) similar to












GMP reductase


Contig362D
23860952_f2_44
2368
5205
516
372
460
1.10E−43

Bacillus subtilis

P54154
yppPDNA-binding proteinBacillus subtilis (YAC10-9 clone) DNA region












between the serA andkdg loci.42.4% identity with the Lycopersicon












esculentum


Contig362D
23944052_c1_86
2369
5206
378
126
248
1.40E−20

Bacteroides

P45737
katBcatalaseBacteroides fragilis catalase (katB) gene, complete cds.catalase











fragilis



Contig362D
24225053_c3_134
2370
5207
318
106
202
2.40E−16

Bacillus subtilis

e1183447
ynzChypothetical protein ynzCBacillus subtilis complete genome (section 10 of












21)


Contig362D
24253466_c3_92
2371
5208
2745
915
3437
0

Bacillus subtilis

e249650
citBaconitaseB.subtilis DNA (26.2 kb fragment; 170 degree region).


Contig362D
24267942_c2_128
2372
5209
1089
363
300
1.00E−26

Bacillus subtilis

d1020054
alrALANINE RACEMASEBacillus subtilis genome sequence, 148 kb












sequence of the regioinbetween 35 and 47 degree.alternate gene name


Contig362D
24640925_c3_138
2373
5210
1272
424
1288
2.00E−131

Bacillus subillis

P54417
opuDputative transporterBacillus subtilis rrnB-dnaB genomic region.alternate gene












name


Contig362D
24647176_c3_152
2374
5211
771
257
120
3.10E—05

Bacillus subtilis

g1377832
ykrAunknownBacillus subtilis ampS-nprE gene region.similar in C-terminus












to partial sequence of orf1


Contig362D
24647182_c2_126
2375
5212
729
243
347
1.00E−31

Aquifex aeolicus

g2983426
dapBdihydrodipicolinate reductaseAquifex aeolicus section 45 of












109 of the complete genome.


Contig362D
24666043_c2_115
2376
5213
1233
411
866
1.10E−86

Bacillus subtilis

e1185989
yubAconserved hypothetical protein yubABacillus subtilis complete genome












(section 16 of 21) similar to hypothetical proteins


Contig362D
24744010_c3_132
2377
5214
273
91
347
1.00E−31

Bacillus subtilis

e1182877
yhzAribosomal protein S14 homolog yhzABacillus subtilis complete genome












(section 5 of 21) similar to ribosomal protein S14


Contig362D
24823377_f2_35
2378
5215
912
304
462
6.80E−44

Bacillus subtilis

e1183105
yitLhypothetical protein yitLBacillus subtilis complete genome (section 6 of












21)


Contig362D
25445253_c3_139
2379
5216
495
165
336
1.50E−30

Bacillus subtilis

e249652
ynePYnePB.subtilis DNA (26.2 kb fragment; 170 degree region).similar to












hypothetical proteins


Contig362D
25664512_c3_144
2380
5217
495
165
279
1.70E−24

Bacillus subtilis

e1182832
yfiWYfiWBacillus subtilis complete genome (section 5 of 21)


Contig362D
25977318_c1_94
2381
5218
2415
805
3470
0

Staphylococcus

d1011747
grlADNA topoisomerase IV GrlA subunitStaphylococcus aureus DNA for











aureus


DNA topoisimerase IV GrlB subunit, DNA topoisomerase IV GrlA












subunit, complete cds.


Contig362D
26210925_c3_135
2382
5219
2028
676
2097
3.80E−217

Bacillus subtilis

P45694
tktAtransketolaseB.subtilis DNA (26.2 kb fragment; 170 degree region).alternate












gene name


Contig362D
26213890_c3_130
2383
5220
699
233
757
3.70E−75

Streptomyces

e313391
catAcatalaseS.coelicolor catA gene.











coelicolor



Contig362D
26354837_c3_158
2384
5221
900
300
570
2.40E−55

Methanococcus

Q57695
MJ0244dihydrodipicolinate synthase (dapA) Methanococcus jannaschii section











jannaschii


22 of 150 of the complete genome.similar to GB


Contig362D
2931337_f1_6
2385
5222
780
260
352
3.10E−32

Pyrococcus

d1027923
PHCH023oligopeptide transport ATP-binding protein APPDPyrococcus











horikoshii



horikoshii OT3 genomic DNA, 695940-732858 nt position, clonecontains ABC













transporter family signature;


Contig362D
32812_c3_145
2386
5223
204
68


Contig362D
35187587_c1_97
2387
5224
588
196
370
3.80E−34

Thermotoga

S34747
anthranilate synthase, component liglutamine amidotransferase











maritima



Contig362D
35557787_c1_105
2388
5225
1275
425
787
2.50E−78

Bacillus subtilis

P08495
LYSCaspartokinase II alpha subunitBacillus subtilis thioredoxin (trx),












uvrB and aspartokinase IIgenes, complete cds.aspartate kinase homology


Contig362D
36142827_c2_122
2389
5226
1812
604
780
1.40E−77

Bacillus

d1014255
Pz-peptidaseBacillus licheniformis DNA for Pz-peptidase, complete cds.











licheniformis



Contig362D
36523462_c2_113
2390
5227
900
300
1439
2.00E−147

Staphylococcus

d1011744
grlBDNA topoisomerase IV GrlB subunitStaphylococcus aureus DNA for











aureus


DNA topoisomerase IV GrlB subunit, DNA topisomerase IV GrlA












subunit, complete cds.


Contig362D
3928177_c1_5
2391
5228
360
120


Contig362D
3937551_c2_125
2392
5229
999
333
803
5.00E−80

Aquifex aeolicus

g2984139
asdaspartate-semialdehyde dehydrogenaseAquifex aeolicus section












92 of 109 of the complete genome.


Contig362D
3961702_c2_120
2393
5230
1269
423
2249
2.90E−233

Staphylococcus

JC5325
femAmethicillin resistance factor FEMA











epidermidis



Contig362D
4025303_c3_149
2394
5231
792
264
450
1.30E−42

Lactococcus lactis

Q01999
trpCindoleglycerol phosphate synthaseL. lactis trpE, trpG, trpD, trpF, trpC, trpB












trpA genes, completecds.indole-3-glycerol-phosphate synthase


Contig362D
4062762_f3_82
2395
5232
405
135
508
9.10E−49

Staphylococcus

g3135292
mscLlarge conductance mechanosensitive











aureus


channelStaphylococcus aureus large conductance mechanosensitive












channel (mscL) gene, complete cds.MscL


Contig362D
4063802_c2_118
2396
5233
1497
499
808
1.80E−80

Lactococcus lactis

Q02001
trpEanthranitate synthase alpha subunitL. lactis trpE, trpG, trpD, trpF, trpC, trpB












trpA genes, completecds.anthranitate synthase component I


Contig362D
4089062_c2_111
2397
5234
1176
392
319
9.70E−29

Aquifex aeolicus

g2984155
sbcDATP-dependent dsDNA exonucleaseAquifex aeolicus section 93












of 109 of the complete genome.


Contig362D
4798453_c1_87
2398
5235
1026
342
242
2.70E−27

Bacillus subtilis

e334771
ylbCYlbC proteinBacillus subtilis genomic DNA 23.9 kB fragment.similar












to hypothetical protein from B. subtilis


Contig362D
4884675_c1_99
2399
5236
1212
404
1268
2.60E−129

Lactococcus lactis

Q01998
trpBtryptophan synthase beta subunitL. lactis trpE, trpG, trpD, trpF, trpC, trpB












trpA genes, completecds.tryptophan synthase beta chain


Contig362D
4890802_f1_12
2400
5237
1152
384
819
1.00E−81

Bacillus subtilis

g143815
tyrATyrAB.subtilis dbpA, mir (A,B). gerC (1-3), ndk, cheR,












aro (B,E,F,H), trp (A-F), hisH and tyrA genes, complete cds.


Contig362D
4964686_f2_42
2401
5238
204
68
195
1.30E−15

Bacillus subtilis

e267624
ywhBUnknown, highly similar to Pseudomas putidaB.subtilis thrZ












downstream chromosomal region.similar to 4-oxalocrotonate tautomerase


Contig362D
5109378_f3_78
2402
5239
615
205
469
1.20E−44

Bacillus subtilis

e249655
yneSYneSB.subtilis DNA (26.2 kb fragment; 170 degree region).similar to












hypothetical protein MG247 from


Contig362D
5120635_c2_108
2403
5240
240
80


Contig362D
6258588_c2_114
2404
5241
1470
490
1305
3.20E−133

Bacillus subtilis

Q45068
alsTAlsTB.subtilis DNA (26.2 kb fragment; 170 degree region).similar to












sodium/proton dependent alanine carrier


Contig362D
6416566_c1_93
2405
5242
1155
385
1755
6.50E−181

Staphylococcus

P50072
grlBDNA topoisomerase IV GrlB subunitStaphylococcus aureus DNA for











aureus


DNA topoisomerase IV GrlB subunit, DNA topoisomerase IV GrlA












subunit, complete cds.DNA topoisomerase (ATP-hydrolyzing) chain












Bunnamed protein product


Contig362D
6664127_c3_156
2406
5243
438
146


Contig362D
6818827_c1_104
2407
5244
1608
536
2088
3.40E−216

Bacillus subtilis

e1185033
ykpAABC transporter (ATP-binding protein) homolog ykpABacillus subtilis












complete genome (section 8 of 21) similar to ABC transporter (ATP-












binding protein)


Contig362D
6929652_c2_127
2408
5245
744
248
683
2.60E−67

Bacillus subtilis

e1181922
ykuQYkuQ proteinBacillus subtilis 29 kB DNA fragment from ykwC gene to esel5












gene.homologous to acetyltransferases


Contig362D
7203176_c2_119
2409
5246
801
267
426
4.40E−40

Methanococcus

Q60180
MJ1038tryptophan synthase alpha subunit (trpA) Methanococcus jannaschii











jannaschii


section 88 of 150 of the complete genome.tryptophan synthase alpha chain












homologysimilar to GB


Contig362D
7242250_c3_150
2410
5247
681
227
276
3.50E−24

Saccharomyces

g927800
TDR533CYdr533cpSaccharomyces cerevisiae chromosome IV cosmids











cerevisiae


8166, 9787, 9717, and lambda 3973.similar to Schizosaccharomyces













pombe hypothetical



Contig362D
837550_c3_143
2411
5248
246
82


Contig362D
970306_c2_106
2412
5249
642
214
776
3.60E−77

Vibrio fischeri

g3064126
katAcatalaseVibrio fischeri catalase (katA) gene, complete cds.


Contig362D
978450_c2_116
2413
5250
2049
683
965
3.40E−97

Bacillus subtilis

d1025380
YfiXBacillus subtilis DNA, genome sequence, 79 to 81 degree region.


Contig362D
9798180_c1_89
2414
5251
204
68


Contig362D
9814213_f2_36
2415
5252
471
157
232
1.60E−19

Archaeoglobus

g2649219
AF1356phosphate ABC transporter periplasmicArchaeoglobus fulgidus











fulgidus


section 97 of 172 of the complete genome.similar to PID


Contig363D
10667002_c2_258
2416
5253
207
69


Contig363D
10734838_c3_307
2417
5254
996
332
397
5.30E−37

Saccharomyces

P32377
ERG19diphosphomevalonate decarboxylaseS.cerevisiae ERG19











cerevisiae


gene.ORF YNR043w


Contig363D
10735832_c1_220
2418
5255
273
91


Contig363D
11032762_f3_148
2419
5256
327
109
160
6.80E−12

Bacteriophage

e244469
Bacteriophage SPP1 complete nucleotide sequence.gene 2.1











SPP1



Contig363D
117893_c3_318
2420
5257
426
142


Contig363D
1227250_f2_111
2421
5258
996
332
562
1.70E−54

Bacillus subtilis

P54948
yxelpenicillin amidase homolog yxclBacillus subtilis complete genome












(section 21 of 21) similar to penicillin amidase


Contig363D
12714833_c2_286
2422
5259
1218
406


Contig363D
12902217_f1_41
2423
5260
683
227
292
7.00E−26

Bacillus subtilis

g3169323
yojGYojGBacillus subtilis YojA (yojA), YojB (yojB), YojC (yojC), YojD (yojD),












YojE (yojE), YojF (yojF), YojG (yojG), YojH (yojH), YojI (yojI), YojJ (yojJ),












YojK (yojK), YojL (yojL), YojM (yojM), YojN (yojN), and YojO (yojO)












genes, complete cds; and OdhA (odh


Contig363D
134702_f3_164
2424
5261
834
278
673
3.00E−66

Bacillus subillis

P39610
ipa-52rhosphosphomethylpyrimidine kinaseB.subtilis genomic region (325 to












333).alternate gene name


Contig363D
13835930_c3_313
2425
5262
276
92


Contig363D
13876005_c2_250
2426
5263
339
113


Contig363D
14547143_c1_195
2427
5264
522
374
501
5.00E−48

Bacillus subtilis

P21335
yaaJunknownB.subtilis DNA, 180 kilobase region of replication












origin.ORF17 (AA 1-161)


Contig363D
14587817_f2_101
2428
5265
528
376


Contig363D
14647510_f1_7
2429
5266
255
85


Contig363D
14879688_c2_261
2430
5267
927
309
234
4.20E−26

Pyrococcus

d1028731
PHLE008335aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA, 1434542-1450104 nt position, clonecontains GHMP kinase












putative ATP-binding domain;


Contig363D
14882681_c1_216
2431
5268
210
70
99
2.00E−05

Streptococcus

g2897106
repressorStreptococcus thermophilus bacteriophage lysogeny module,











thermophilus


integrasehomolog (int), putative host cell surface-exposed lipoprotein, putative










bacteriophage TP-

metallo-proteinase, repressor, Cro-like regulatoryprotein, and P1-antirepressor










J34

homolog genes, complete cds.


Contig363D
14885260_c2_269
2432
5269
441
147
209
4.40E−17

Streptococcus

g2444132
ORF25Streptococcus thermophilus bacteriophage 01205 DNA











thermophilus


sequence.putative small subunit of the terminase


Contig363D
15735181_f3_134
2433
5270
204
68


Contig363D
15782160_c2_245
2434
5271
747
249
469
1.20E−44

Caenorhabditis

g1458327
F08F3.4Caenorhabditis elegans cosmid F08F3.











elegans



Contig363D
16054827_c3_320
2435
5272
357
119


Contig363D
16212803_c2_274
2436
5273
318
106
124
4.50E−08
Bacteriophage
e244843
15gene 15 proteinBacteriophage SPP1 complete nucleotide sequence.gene 15










SPP1


Contig363D
16413130_f3_170
2437
5274
246
82
135
2.00E−08

Saccharomyces

P32583
SRP40SRP40 proteinS.cerevisiae DNA of chromosome XI, right arm.ORF











cerevisiae


YKR412


Contig363D
16603427_c2_284
2438
5275
531
177


Contig363D
16798777_c3_291
2439
5276
3558
1186
5906
0

Staphylococcus

P47768
rpoBDNA-direction RNA polymerase beta chainS.aureus rplL. orf202,











aureus


rpoB(rif) and rpoC genes for ribosomalprotein L7/L12, hypothetical












protein ORF202, DNA-directed RNApolymerase beta & beta′












chains.DNA-directed RNA polymerase beta chain


Contig363D
19690876_c1_208
2440
5277
876
292
662
4.40E−65

Bacillus subtilis

P39648
ipa-90dhypothetical proteinB.subtilis genomic region (325 to 333).alternate












gene name


Contig363D
19695386_c3_315
2441
5278
771
257


Contig363D
20078287_f2_108
2442
5279
825
275
145
2.10E−07

Mycobacterium

e1264597
MTV025.085putative membrane proteinMycobacterium tuberculosis











tuberculosis


sequence v025.MTV025.085, len


Contig363D
20087752_f1_44
2443
5280
1506
502
397
2.10E−36

Bacillus subtilis

P13484
tagEUDP-glucoseBacillus subtilis rodC operon.rodD (gtaA) polypeptide (AA 1-












673)


Contig363D
20322153_c3_306
2444
5281
219
73


Contig363D
20331552_c3_296
2445
5282
996
332
447
2.60E−42

Methanobacterium

g2622612
MTH1495ornithine cyclodeaminaseMethanobacterium











thermoautotro-



thermoautotrophicum from bases 1349621 to 1362200 (section 116 of 148)












phicum


of the complete genome.Function Code


Contig363D
20511590_c2_340
2446
5283
384
128
414
8.30E−39

MICROCOCCUS

P02395
RPLLribosomal protein L7/L1250S RIBOSOMAL PROTEIN L7/L12











LUTEUS


(MA1/MA2)Eschericia coli ribosomal protein L12


Contig363D
20756260_c1_225
2447
5284
408
136


Contig363D
2131552_f3_132
2448
5285
378
126
118
1.10E−06

Plasmodium

P04929
histidine-rich proteinPlasmodium gene fragment for histidine-rich











lophurae


protein.plasmodium histidine-rich protein


Contig363D
21484465_c2_278
2449
5286
516
172


Contig363D
21598838_f2_109
2450
5287
465
155
155
6.00E−11

Haemophilus

P44520
H10108hypotheticalHaemophilus influenzae from bases 111654 to 122227











influenzae


(section 11 of 163) of the complete genome.similar to GB


Contig363D
21758468_c3_340
2451
5288
489
163
123
5.70E−08

Aquifex aeolicus

g2983204
rimlribosomal-protein-alanine acetyltransferaseAquifex aeolicus section












28 of 109 of the complete genome.


Contig363D
22069160_c3_294
2452
5289
393
131
623
5.90E−61

Staphylococcus

P48942
rpsLribosomal protein S12Staphylococcus aureus ribosomal











aureus


protein S12 (rpsL) gene, completecds, ribosomal protein S7 (rpsG) and ORF 1












genes, partial cds.


Contig363D
22272200_c1_229
2453
5290
939
313


Contig363D
22400261_c2_273
2454
5291
834
278
634
4.00E−62
Bacteriophage B1
e139438
mhpmajor head proteinBacteriophage TP901-1 genomic region.


Contig363D
22694377_c1_185
2455
5292
741
247
762
1.10E−75

Staphylococcus

g677850
ORF202hypothetical proteinS.aureus rplL, orf202, rpoB(rif) and rpoC genes











aureus


for ribosomalprotein L7/L12, hypothetical protein ORF202, DNA-












directed RNApolymerase beta & beta′ chains.


Contig363D
22773302_c1_232
2456
5293
1803
601
1371
3.20E−140

Staphylococcus

e286568
ply187cell wall hydrolase Ply187Staphylococcus phage 187 ply187










phage 187

and hol187 gene.


Contig363D
22790941_c2_277
2457
5294
543
181
143
4.30E−10
Bacteriophage
e244714
Bacteriophage SPP1 complete nucleotide sequence.gene 17.1










SPP1


Contig363D
23442135_c2_253
2458
5295
675
225
148
1.80E−09

Synechocystis sp.

d1018298
cbbZpphosphoglycolate phosphataseSynechocystis sp. PCC6803












complete genome, 9/27, 1056467-1188885.ORF_ID


Contig363D
23469213_c2_268
2459
5296
411
137


Contig363D
23477213_c2_260
2460
5297
1011
337
1085
6.50E−110

Bacillus subtilis

P39646
ipa-88dphosphotransacctylaseB.subtilis genomic region (325 to 333).alternate












gene name


Contig363D
23572178_c3_319
2461
5298
195
65


Contig363D
23601637_c1_193
2462
5299
816
272
374
1.40E−34

Haemophilus

g471234
CDP-rebitol pyrophosphorylaseH.influenzae DNA for











influenzae


serotype b capsulation locus.orf1


Contig363D
23603391_c3_328
2463
5300
294
98


Contig363D
23617140_c2_254
2464
5301
1404
468
441
5.00E−44

Bacillus subtilis

e1183038
yhfThypothetical proteinBacillus subtilis complete genome (section 6 of












21) similar to long-chain fatty-acid-CoA ligase


Contig363D
23712830_c1_213
2465
5302
489
163
225
8.80E−19

Streptococcus

g2352435

Streptococcus thermophilus bacteriophage Sfi21 DNA












thermophilus


replicationmodule.orf157










bacteriophage










Sfi21


Contig363D
23867125_f1_36
2466
5303
204
68


Contig363D
2392837_c1_226
2467
5304
426
142
226
6.90E−19
Bacteriophage
e244844
Bacteriophage SPP1 complete nucletide sequence.gene 16.1










SPP1


Contig363D
23992128_c2_282
2468
5305
222
74
114
5.10E−07

Staphylococcus

e286569
hol187holin protein Hol187Staphylococcus phage 187










phage 187

ply187 and hol187 genes.


Contig363D
24026077_c3_326
2469
5306
954
318
560
2.80E−54
Bacteriophage
e244838
7 gene 7 proteinBacteriophage SPP1 complete nucleotide sequence.gene 7










SPP1


Contig363D
24229837_c1_215
2470
5307
243
81
97
3.20E−05

Lactobacillus sake

g599850
orf1hypothetical protein (bacteriocin siaA 3′-region)L.sake sakecin A gene












cluster.


Contig363D
24258462_c3_335
2471
5308
336
112
200
3.90E−16

Lactococcus lactis

g928831
Bacteriophage BK5-T ORF′410, 3′ end pf cds, 20 ORFs, repressorprotein, and










phage BK5-T

Cro repressor protein genes, complete cds, ORF70′genes, 5′ end of cds.ORF95;












putative


Contig363D
24275342_c1_217
2472
5309
378
126


Contig363D
24328127_f3_135
2473
5310
204
68
154
2.10E−10

Escherichia coli

P77212
ykgCykgC proteinEscherichia coli K-12 MG1655 section 27 of 400 of the












completegenome.f450; 35 pct identical (29 gaps) to 430 residues of


Contig363D
24337800_c2_285
2474
5311
1386
462
223
6.90E−18

Staphylococcus

JC5470
hypothetical 29.1 K protein











aureus



Contig363D
2438878_f3_169
2475
5312
213
71
288
1.90E−25
Plasmid pl258
P30330
arsCarsenate reductasePlasmid pl258 arsenic resistance operon (arsRBC)












genes, completecds.protein-tyrosine-phosphatase, low molecular weight


Contig363D
24401462_c1_200
2476
5313
591
197
367
7.90E−34

Bacillus subtilis

P42404
yckFunknownBacillus subtilis DNA around 28 degrees region of












chromosomecontaining yckA-H genes.similar to hypothetical proteins


Contig363D
24414050_c3_301
2477
5314
2793
931
4374
0

Staphylococcus

e1296735
fibrinogen-binding proteinStaphylococcus epidermidis gene











epidermidis


encoding fibrinogen-bindingprotein complete CDS.


Contig363D
24415875_c3_297
2478
5315
300
100
129
1.40E−07

Caenorhabditis

g1458327
F08F3.4Caenorhabditis elegans cosmid F08F3.











elegans



Contig363D
24429643_c1_192
2479
5316
222
74


Contig363D
24491037_c1_218
2480
5317
495
165


Contig363D
24500387_c3_322
2481
5318
564
188


Contig363D
24617130_c2_241
2482
5319
3648
1216
5258
0

Staphylococcus

e187583
rpoCDNA-directed RNA polymeraseS.aureus DNA for rpoC











aureus


gene.B′ subunit


Contig363D
24648937_c1_203
2483
5320
657
219
626
2.80E−61

Bacillus subtilis

P39615
ipa-57duracil-DNA glycosylaseB.subtilis genomic region (325 to 333).uracil-DNA












glycosylasealternate gene name


Contig363D
24650332_c3_323
2484
5321
228
76


Contig363D
24650468_f2_103
2485
5322
1383
461
489
9.40E−47
Bacteriophage
e155312
integraseBacteriophage TP901-1 ORF1,2 & 3.Orf1










TP901-1


Contig363D
24667192_f1_42
2486
5323
183
61
201
1.40E−15
Plasmid pl258
P30329
arsBarsenic efflux pump proteinPlasmid pl258 arsenic resistance operon












(arsRBC) genes, completecds.arsenical pump membrane protein


Contig363D
24803462_f1_4
2487
5324
861
287
463
5.30E−44

Syncchocystis sp.

P73846
SLR1717hypothetical proteinSynechocystis sp. PCC6803












complete genome, 12/27, 1430419-1576592.ORF_ID


Contig363D
24823437_f2_102
2488
5325
495
165


Contig363D
24854637_c3_300
2489
5326
903
301
404
9.50E−38

Bacillus subtilis

e1184491
ywtEconserved hypothetical protein ywtEBacillus subtilis complete genome












(section 19 of 21) similar to hypothetical proteins


Contig363D
25438433_f2_81
2490
5327
420
140


Contig363D
25509692_c3_331
2491
5328
498
166
151
6.10E−11
Bacteriophage
e244846
Bacteriophage SPP1 complete nucleotide sequence.gene 17.5










SPP1


Contig363D
25578827_c2_242
2492
5329
261
87
334
2.50E−30

Staphylococcus

Q53602
unknownStaphylococcus aureus ribosomal protein S12 (rpsL) gene,











aureus


completecds, ribosomal protein S7 (rpsG) and ORF 1 genes, partial cds.ORF1


Contig363D
25579662_f1_52
2493
5330
1221
407
849
6.60E−85

Bacillus subtilis

e1183009
yhaAaminoacylase homolog yhaABacillus subtilis complete genome












(section 6 of 21) similar to aminoacylase


Contig363D
25660937_c3_339
2494
5331
498
166
175
2.90E−13

Bacillus subtilis

P46922
opuACglycine betaine-binding protein precursorBacillus subtilis ATPase












(opuAA), transmembrane protein (opuAB) andglycine betaine-binding












protein precursor (opuAC) genes, completecds.


Contig363D
26l73287_c3_329
2495
5332
363
121
103
7.50E−06
Bacteriophage
e244712
Bacteriophage SPP1 complete nucleotide sequence.gene 16










SPP1


Contig363D
26290912_f2_114
2496
5333
882
294
665
2.10E−65

Bacillus subtilis

e1182286
yciAconserved hypothetical protein yciABacillus subtilis complete genome












(section 2 of 21) similar to hypothetical proteins


Contig363D
26306568_c1_221
2497
5334
330
110


Contig363D
26350125_c2_265
2498
5335
252
84


Contig363D
26360327_c1_222
2499
5336
552
184
164
3.10E−22

Homo sapiens

P33316
DUTdeoxyuridine nucleotidohydrolaseHuman deoxyuridine












nucleotidohydrolase mRNA, complete cds.retroviral proteinaseDUT-N;












alternatively spliced; nuclear form of the


Contig363D
26369082_c2_267
2500
5337
252
84


Contig363D
26375952_c1_214
2501
5338
627
209
223
1.40E−18
Bacteriophage
e1254413
hypothetical proteinBacteriophage TP901-1 ORFs 1-12.ORF11










TP901-1


Contig363D
26569377_c3_304
2502
5339
639
213
625
3.60E−61

Bacillus subtilis

e1182298
yckGD-arabino 3-hexulose 6-phosphate formaldeh homolog yckGBacillus













subtilis complete genome (section 2 of 21) similar to D-arabino 3-hexulose 6-













phosphate


Contig363D
26734625_f3_156
2503
5340
351
117
210
3.40E−17

Streptococcus

e308969
orf127cl-like repressorStreptococcus thermophilus bacteriophage Sfi21 DNA;











thermophilus


lysogenymodule, 8141 bp.putative










bacteriophage










Sfi21


Contig363D
26772801_f3_157
2504
5341
504
168
127
2.30E−09

Dictyostelium

g467292
glutamine-asparagine rich proteinDictostellium discoideum AX3











discoideum


glutamine-aparagine rich proteingene, partial cds.


Contig363D
26839638_c1_236
2505
5342
1314
438
1429
2.30E−146

Bacillus subtilis

P39651
ywfOUnknownBacillus subtilis complete genome (section 20 of 21) alternate gene












name


Contig363D
27318_c2_290
2506
5343
1035
345
1198
6.90E−122

Zymonionas

P20368
ADHAalcohol dehydrogenase 1Z.mobilis alcohol dehydrgenase I











mobilis


(adhA) gene, complete cds.alcohol dehydrogenasealcohol dehydrogenase 1












(adhA) (EC 1.1.1.1)


Contig363D
276590_c3_309
2507
5344
375
125
279
1.70E−24

Bacillus subtilis

e1186261
ywzChypothetical protein ywzCBacillus subtilis complete genome (section 20 of












21)


Contig363D
2847887_f1_43
2508
5345
576
192
797
2.20E−79
Plasmid pl258
P30329
arsBarsenic efflux pump proteinPlasmid pI258 arsenic resistance operon












(arsRBC) genes, completecds.arsenical pump membrane protein


Contig363D
29694425_f3_172
2509
5346
852
284
418
3.10E−39

Bacillus subtilis

P51831
fabG3-ketoacyl-acyl carrier protein reductaseBacillus subtilis PlsX (plsX),












malonyl-CoAalso called 3-oxoacyl-acyl carrier protein


Contig363D
2995675_f2_60
2510
5347
252
84


Contig363D
30742332_c2_271
2511
5348
228
76


Contig363D
31334838_c3_341
2512
5349
519
173
544
1.40E−52

Bacillus subtilis

e267625
ywhDUnknownB.subtilis thrZ downstream chromosomal region.


Contig363D
31353377_c1_188
2513
5350
474
158
699
5.20E−69

Bacillus subtilis

e1182044
rpsGribosomal protein 57 (BS7) Bacillus subtilis complete genome (section 1 of












21)


Contig363D
32031437_c1_230
2514
5351
2706
902
1163
3.50E−118
Bacteriophage
P07537
12pre-neck appendage proteinBacteriophage PZA (from










PZA


B.subtilis), complete genome.phage PZA gene 12 protein



Contig363D
32595152_c1_231
2515
5352
402
134


Contig363D
3306563_c2_256
2516
5353
366
122


Contig363D
33235050_12_70
2517
5354
507
169


Contig363D
33414693_c3_308
2518
5355
1089
363
150
5.80E−16

Methanococcus

Q58487
MJ1087mevalonate kinaseMethanococcus jannaschii section











jannaschii


93 of 150 of the complete genome.similar to PID


Contig363D
33600035_c3_295
2519
5356
2118
706
2785
4.70E−290

Bacillus subtilis

e1182045
fuselongation factor GBacillus subtilis complete genome.similar (section 1 of 21)


Coniig363D
33756503_c3_311
2520
5357
210
70
125
3.50E−08

Lactobacillus

e1285113
orfBhypothetical proteinBacteriophage A2 rep, xis and int gene.











casei











bacteriophage A2


Contig363D
33786251_c2_287
2521
5358
246
82


Contig363D
33869193_c1_223
2522
5359
183
61
130
1.00E−08

Staphylococcus

Q03183
rinBBacteriophage phi-11 int gene activatorBacteriophage phi-11 rinA and










bacteriophage phi11

rin B genes, required for theactivatioin of Staphylococcal phage phi-11 int












expression.


Contig363D
34025066_c2_281
2523
5360
642
214
89
6.90E−07
Bacteriophage
e247172
Rorf232Lactobacillus bacteriophage phigle complete genomic DNA.










phigle


Contig363D
34242202_c3_317
2524
5361
270
90


Contig363D
34242202_f2_120
2525
5362
210
70


Contig363D
34407053_f3_128
2526
5363
783
261
564
1.10E−54

Synechocystis sp.

d1019442
hypothetical proteinSynechocystis sp. PCC6803 complete genome, 26/27,












3270710-3418851.ORF_ID


Contig363D
34609703_c3_324
2527
5364
198
66


Contig363D
34651555_c1_228
2528
5365
3123
1041
267
2.30E−24
Bacteriophage
e244718
Bacteriophage SPP1 complete nucleotide sequence.gene 18










SPP1


Contig363D
36054813_c2_264
2529
5366
387
129


Contig363D
36228563_c3_321
2530
5367
699
233


Contig363D
36521067_f2_112
2531
5368
204
68


Contig363D
3909643_f2_62
2532
5369
1197
399
654
3.10E−64

Synechocystis sp.

d1017466
hypothetical proteinSynechocystis sp. PCC6803 complete genome, 2/27,












133860-271599.ORF_ID


Contig363D
3912503_c2_259
2533
5370
1500
500
331
1.30E−28

Bacillus subtilis

e1182947
ydhGhypothetical proteinBacillus subtilis complete genome (section 6 of












21) similar to amino acid transporter


Contig363D
3961590_c1_201
2534
5371
1164
388
669
7.90E−66

Bacillus subtilis

e1183037
yhfShypothetical proteinBacillus subtilis complete genome (section 6 of












21) similar to acetyl-CoA C-acetyltransferase


Contig363D
39635_f1_30
2535
5372
1245
415
972
6.10E−98

Escherichia coli

P77212
ykgCykgC proteinEscherichia coli K-12 MG1655 section 27 of 400 of the












completegenome.f450; 35 pct identical (29 gaps) to 430 residues of


Contig363D
4031952_c1_184
2536
5373
501
167
545
1.10E−52

Bacillus subtilis

P42923
rplJRibosomal Protein L10Bacillus subtilis genes for ribosomal proteins L1,












L10 and L12, partial and complete cds.


Contig363D
4078518_f3_173
2537
5374
882
294
534
1.60E−51

Bacillus subtilis

P54950
yxeKmonooxygenase homolog yxeKBacillus subtilis complete genome












(section 21 of 21) similar to monooxygenase


Contig363D
4181527_c1_219
2538
5375
447
149


Contig363D
4181577_c3_316
2539
5376
1251
417
465
3.30E−44

Aquifex aeolicus

g2983861
dnaBreplicative DNA helicaseAquifex aeolicus section 74 of 109 of the












complete genome.


Contig363D
4329063_c2_243
2540
5377
1245
415
1759
2.50E−181

Bacillus subtilis

P33166
tufAelongation factor TuBacillus subtilis complete genome (section 1 of












21) translation elongation factor Tu


Contig363D
4398453_f1_49
2541
5378
477
159
279
3.70E−24

Chelatobacter

P54989
nmoANTA monooxygenerase component AChelatobacter heintzii NTA











heintzii


monooxygenase component B (nmoB), NTAmonooxygenase component A












(nmoA), regulatory protein (nmoR) andtransposase (nmoT) genes, complete












cds.


Contig363D
446062_c1_235
2542
5379
690
230
1165
2.20E−118

Staphylococcus

P19380
putative transposaseS. aureus IS431mec gene associated with methicillin











aureus


resistance.putative transposase (AA 1-224)


Contig363D
4725006_c3_334
2543
5380
537
179


Contig363D
4727203_c1_204
2544
5381
369
123


Contig363D
4735833_f1_46
2545
5382
711
237
464
4.20E−44

Bacillus subtilis

P37530
yaaGunknownB. subtilis DNA, 180 kilobase region of replication












origin.similar to deoxypurine kinase subunit


Contig363D
4741068_c3_327
2546
5383
609
203
210
3.40E−17
Bacteriophage
e247154
Rorf204 minor capsid proteinLactobacillus bacteriophage










phigle

phigle complete genomic DNA.


Contig363D
4741077_c3_314
2547
5384
687
229
238
3.70E−20
Bacleriophage
e247139
Rorf242Lactobacillus bacteriophage phigle complete genomic DNA.










phigle


Contig363D
4875756_f2_89
2548
5385
201
67


Contig363D
4876967_c1_196
2549
5386
579
193
168
9.70E−13

Bacillus subtilis

e1182923
yhdAhypothetical proteinBacillus subtilis complete genome (section 5 of












21) similar to hypothetical proteins


Contig363D
4882760_c3_345
2550
5387
183
61


Contig363D
4886075_f2_118
2551
5388
678
226
794
4.50E−79

Bacillus subtilis

P37529
yaaFunknownB. subtilis DNA, 180 kilobase region of replication












origin.similar to deoxypurine kinase subunit


Contig363D
4892127_c1_233
2552
5389
2706
902
1557
6.30E−160

Bacillus subtilis

d1020130
ydfJantibiotic transport-associated protein homolog ydfJBacillus subtilis












genome sequence, 148 kb sequence of the regionbetween 35 and 47












degree.PROBABLE TRANSPORT PROTEIN. SIMILAR TO ANTIBIOTIC


Contig363D
4901703_c1_191
2553
5390
510
170


Contig363D
4946962_c2_247
2554
5391
1068
356
172
1.60E−10

Saccharomyces

e253285
probable membrane protein YDL246cS.cerevisae chromosome IV











cerevisiae


reading frame ORF YDL246c.alcohol dehydrogenaseORF YDL246c


Contig363D
4964677_c2_263
2555
5392
444
148
126
2.30E−15

Bacillus subtilis

P37455
ssbsingle strand DNA binding proteinB. subtilis DNA, 180 kilobase region of












replication origin.single-stranded DNA-binding protein homology.


Contig363D
5080092_c3_303
2556
5393
744
248
529
5.40E−51

Bacillus subtilis

e1182188
ybfTglucosamine-6-phosphate isomerase homolog yblTBacillus subtilis complete












genome (section 2 of 21) similar to glucosamine-6-phosphate isomerase


Contig363D
5125076_f2_107
2557
5394
810
270
873
1.90E−87

Bacillus subtilis

P39645
ipa-87rconserved hypothetical protein ywflB.subtilis genomic region (325 to












333).alternative gene name


Contig363D
5251588_c1_234
2558
5395
582
194


Contig363D
5258515_c3_325
2559
5396
1314
438
1298
1.80E−132
Bacteriophage
P54308
SPP1 gene 2terminaseBacteriophage SPP1 complete nucleotide sequence.gene 2










SPP1


Contig363D
5370450_f3_127
2560
5397
1284
428
305
2.90E−27

Archaeoglobus

g2650605
AF0049A. fulgidus predicted coding region AF0049Archaeoglobus fulgidus











fulgidus


section 4 of 172 of the complete genome.hypothetical protein; identified












by GeneMark;


Contig363D
56626_c2_280
2561
5398
336
112


Contig363D
587811_f3_168
2562
5399
345
115


Contig363D
6056625_c1_238
2563
5400
258
86


Contig363D
6406337_f3_133
2564
5401
210
70


Contig363D
6407136_c2_270
2565
5402
1455
485
667
1.30E−65
Bacteriophage
P54309
SPP1 gene 6portal proteinBacteriophage SPP1 complete nucletide sequence.gene 6










SPP1


Contig363D
6757338_c2_246
2566
5403
1089
363
1129
1.40E−114

Bacillus subtilis

e1182191
ybgEbranched-chain amino acid aminotransferase homolog ybgEBacillus













subtilis complete genome (section 2 of 21) similar to branched-chain amino acid



Contig363D
6932750_f1_40
2567
5404
378
126
266
4.00E−23

Bacillus subtilis

g3169322
yojFYojFBacillus subtilis YojA (yojA), YojB (yojB), YojC (yojC), YojD (yojD),












YojE (yojE), YojF (yojF), YojG (yojG), YojH (yojH), YojI (yojI), YojJ (yojJ),












YojK (yojK), YojL (yojL), YojM (yojM), YojN (yojN), and YojO (yojO)












genes, complete cds; and OdhA (odh


Contig363D
7068751_c3_336
2568
5405
945
315
974
3.80E−98

Bacillus subtilis

P46336
iolSmyo-inositol catabolism iolSBacillus subtilis genomic DNA, 36 kb region












between gnt and ioloperons.plausubly involved in inositol catabolism


Contig363D
7275263_c1_327
2569
5406
441
147
158
1.10E−11
Bacteriophage
e244713
Bacteriophage SPP1 complete nucleotide sequence.gene 17










sPP1


Contig363D
818942_c3_338
2570
5407
477
159
173
2.80E−17

Bacillus subtilis

P46922
opuACglycine betaine-binding protein precursorBacillus subtilis ATPase












(opuAA), transmembrane protein (opuAB) andglycine betaine-binding












protein precursor (opuAC) genes, completecds.


Contig363D
819575_c2_279
2571
5408
1857
619
158
1.20E−08
Bacteriophage
e247163
Rorf372Lactobacillus bacteriophage phigle complete genomic DNA.










phigle


Contig363D
821012_c3_298
2572
5409
1725
575
469
5.70E−44

Haemophilus

e547513
hypothetical protein 3 (capsulation locus) Haemophilus influenzae serotype a











influenzae


capsulation locus region II DNA.orf3


Contig363D
833125_f3_149
2573
5410
285
95


Contig363D
89284Z_c1_205
2574
5411
387
129
337
1.20E−30

Bacillus subtilis

P39619
ipa-61dconserved hypothetical protein ywdKB.subtilis genomic region (325 to












333).alternate gene name


Contig363D
9765677_c3_312
2575
5412
804
268
226
6.90E−19

Lactococcus lactis

g928839
Bacteriophage BK5-T ORF′410, 3′ end pf cds, 20 ORFs, repressorprotein, and










phage BK5-T

Cro repressor protein genes, complete cds, ORF70′gene, 5′ end of cds.ORF266;












putative


Contig363D
978377_c2_257
2576
5413
264
88


Contig363D
9819392_c2_248
2577
5414
789
263
179
5.60E−13

Caenorhabditis

g1463023
F45E1Caenorhabditis elegans cosmid F45E1.











elegans



Contig363D
9926903_c2_266
2578
5415
309
103


Contig363D
994052_c3_333
2579
5416
1536
512


Contig364D
10006340_f3_215
2580
5417
501
167


Contig364D
10267016_c1_259
2581
5418
789
263
210
3.40E−17

Streptomyces

P32184
tipATipAL-AStipAL-AS complexthiostrepton-specific recognition











lividans


protein; Method


Contig364D
10268818_f1_41
2582
5419
234
78


Contig364D
10581693_f1_214
2583
5420
684
228
842
3.70E−84

Bacillus subtilis

e1184962
ykvJconserved hypothetical protein ykvJBacillus subtilis complete genome












(section 8 of 21) similar to hypothetical proteins


Contig364D
10589818_f3_160
2584
5423
201
67


Contig364D
10667002_c2_365
2585
5422
201
67


Contig364D
10737818_f2_133
2586
5423
471
157
223
1.40E−18

Bacillus subtilis

P17868
yqxDYqfMBacillus subtilis DNA, 283 Kb region containing skin element.P23












(aa 1-196); unidentified reading frame


Contig364D
10941007_f3_176
2587
5424
291
97
103
7.50E−06

Leishmania

S51910
cryptogene protein G4











tarentolae



Contig364D
30976387_c2_397
2588
5425
210
70


Contig364D
11023402_f1_34
2589
5426
273
91
127
2.10E−08

Pyrococcus

d1028459
PHAU021101aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA, 1195819-1238496 nt position, clone


Contig364D
110275_f3_245
2590
5427
276
92
292
7.00E−26

Staphylococcus

e255528
membrane proteinS.epidermidis gene encoding ABC transport system.











epidermidis



Contig364D
11152176_c3_418
2591
5428
1029
343
1111
1.10E−112

Bacillus subtilis

e1181485
ykaBYkaBBacillus subtilis 168 56 kb DNA fragment between xlyA and












ykoR.homologous to low affinity phosphate transporter


Contig364D
11883557_f2_150
2592
5429
195
65


Contig364D
11910927_f3_249
2593
5430
327
109


Contig364D
1199063_f2_102
2594
5431
510
170
165
4.40E−12

Haemophilus

P44520
H10108hypotheticalHaemophilus influenzae from bases 111654 to 122227











influenzae


(section 11 of 163) of the complete genome.similar to GB


Contig364D
1214688_f2_104
2595
5432
939
313
526
1.10E−50

Bacillus subtilis

P18579
murBUDP-N-acetylenolpyruvoylglucosamine












reductaseBacillus subtilis (clone lambda-BSI) cell division and sporulationprotein












(dds) gene, complete cds.ORF2


Contig364D
12595301_f2_108
2596
5433
258
86
95
7.00E−05

Pyrococcus

d1027485
PHAY036173aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA, 299830-340636 nt position, clone contains prokaryotic












membrane lipoprotein lipid


Contig364D
12616018_f3_159
2597
5434
270
90


Contig364D
12617827_c3_469
2598
5435
762
254
856
1.20E−85

Bacillus subtilis

e1186080
tpitriose phosphate isomeraseBacillus subtilis compelte genome (section 18 of












21) alternate gene name


Contig364D
12789077_c2_380
2599
5436
1107
369
1311
7.30E−134

Bacillus subtilis

g2618842
uvrAexcinuclease ABC subunit ABacillus subtilis 300-304 degree












genomic sequence.


Contig364D
12948336_c2_384
2600
5437
273
91
316
2.00E−28

Bacillus subtilis

g2668494
clpPClpPBacillus subtilis Clp protease proteolytic component (clpP)












gene, complete cds.proteolytic component of Clp protease


Contig364D
1351533_c1_309
2601
5438
2571
857
3966
0

Staphylococcus

O06446
secASecAStaphylococcus aureus NCTC 8325 SecA (secA) gene, complete cds.











aureus



Contig364D
13710887_c1_322
2602
5439
753
251
315
2.60E−28

Acinetobacter sp.

g3172120
quiBcatabolic dehydroquinate dehydrataseAcinebacter sp. ADP1 pca-










ADP1

qui-pob supraoperonic cluster, completesequence.


Contig364D
13714193_c2_375
2603
5440
582
194
583
1.00E−56

STAPHYLO-

P47995
HYPOTHETICAL PROTEIN IN SECA 5′REGION (ORF1) (FRAGMENT)











COCCUS












CARNOSUS



Contig364D
13727318_f2_138
2604
5441
813
271
348
8.20E−32

Staphylococcus

g2735506
SceBSceB precursorStaphylococcus carnosus N5, N10-











carnosus


methylenetetrahydromethanopterinreductase homolog, SceB precursor (sceB) and












putative transmembraneprotein genes, complete cds, and putative Na+/H+












antiporter NhaC (nhaC) gene, partial cds.major secret pro


Contig364D
1376577_f3_170
2605
5442
675
225


Contig364D
13803167_f3_169
2606
5443
552
184
157
6.60E−11

Bacillus subtilis

d1020071
ydcLintegrase homolog ydcLBacillus subtilis genome sequence, 148 kb












sequence of the regionbetween 35 and 47 degree.PROBABLE INTEGRASE.


Contig364D
13921942_c2_387
2607
5444
1554
518
1690
5.10E−174

Bacillus subtilis

e1186079
pgmphosphoglycerate mutaseBacillus subtilis complete genome (section 18 of












21)


Contig364D
13931527_c2_327
2608
5445
723
241


Contig364D
1408438_f2_147
2609
5446
948
316
110
6.80E−06

Escherichia coli

g1787718
hypothetical protein b1447Escherichia coli K-12 MG1655 section 131 of 400 of












the completegenome.f149; This 149 aa ORF is 31 pct identical (11 gaps)


Contig364D
14120465_f2_78
2610
5447
513
171


Contig364D
14460882_f1_33
2611
5448
183
61
128
5.00E−08

Staphylococcus

g1022726
unknownStaphylococcus haemolyticus IS1272 ORF1 and ORF2 genes,











haemolyticus


completecds.ORF1


Contig364D
14478377_c2_349
2612
5449
1149
383
637
1.90E−62

Bacillus subtilis

P49852
ykiAYkiABacillus subtilis hmp DNA for 7 ORFs, complete cds.high homology to












flavohemoprotein (Haemoglobin-like


Contig364D
14500052_f2_83
2613
5450
204
68


Contig364D
14564005_f3_198
2614
5451
249
83


Contig364D
14642203_c2_339
2615
5452
834
278
772
9.60E−77

Bacillus subtilis

e1186383
yxkDconserved hypothetical protein yxkDBacillus subtilis complete genome












(section 20 of 21) similar to hypothetical proteins


Contig364D
14648452_c2_378
2616
5453
801
267
346
1.30E−31

Staphylococcus

e244971

S.aureus orfs 1,2,3 & 4.ORF1












aureus



Contig364D
14875590_c2_361
2617
5454
846
282
713
1.70E−70

Bacillus subtilis

e1249784
yvgNputative reductase protein, YvgNBacillus subtilis 42.7 kB DNA












fragment from yvsA to yvqA.alternate gene name


Contig364D
14878807_13_255
2618
5455
960
320
162
2.40E−09

Enterococcus

e321943
hypothetical proteinE.faecalis plasmid DNA containing gene cluster involved











faecalis


inproduction and immunity to peptide antibiotic AS-48.ORF7


Contig364D
14886052_c2_352
2619
5456
495
165
307
1.80E−27

Bacillus subtilis

P54486
yqgCYqgCBacillus subtilis DNA, 283 Kb region containing skin element.


Contig364D
15057762_c1_284
2620
5457
1575
525
1194
1.80E−421

Alcaligenes

Q07252
putative membrane-bound protein with four timesA.eutrophus genes for lactate











eutrophus


dehydrogenase, putativemembrane-bound protein with four times repitition












of Pro-Ser-Ala atthe N-terminus (function unknown) and transglycosidase












(partial).


Contig364D
1561_c3_443
2621
5458
1944
648
1406
6.30E−144

Bacillus subtilis

e1182716
yfmRYfmRBacillus subtilis complete genome (section 4 of 21) similar to ABC












transporter (ATP-binding protein)


Contig364D
15661088_c1_268
2622
5459
513
171


Contig364D
15751312_f2_111
2623
5460
2136
712
1980
9.40E−205

Entamoeba

Q24803
ADH2alcohol dehydrogenase 2Entamoaba histolytica HM1The derived











histolytica


amino acid sequence of EhADH2 is


Contig364D
157767_c2_340
2624
5461
1077
359
227
1.20E−17

Rhodococcus sp.

g2088525
herheroin esteraseRhodococcus sp. heroin esterase (her) gene, complete












cds.acetylmorphine carboxyesterase; Ser-160 is the


Contig364D
15781336_c1_257
2625
5462
471
157
150
7.80E−11

Bacillus subtilis

e1186235
ywiBhypothetical protein ywiBBacillus subtilis complete genome (section 20 of












21)


Contig364D
16595927_f3_251
2626
5463
213
71


Contig364D
16603207_f1_13
2627
5464
378
126
217
6.20E−18

Mycobacterium

g466873
B1496_F1_41Mycobacterium leprae cosmid B1496.











leprae



Contig364D
166713_c1_311
2628
5465
2001
667
2697
9.90E−281

Bacillus subtilis

g2618841
uvrBexcinuclease ABC subunit BBacillus subtilis 300-304 degree












genomic sequence.alternate gene name


Contig364D
16834512_c2_355
2629
5466
1380
460
1661
5.60E−65

Bacillus firmus

Q04449
phrDNAphotolyaseBacillus firmus DNA photolyase (phr) gene, 3′ end, and












cytochromeooxidase (cta) operon.putative


Contig364D
16850303_c3_473
2630
5467
477
159
510
5.60E−49

Bacillus subtilis

e1186048
yvalconserved hypothetical protein yvalBacillus subtilis complete genome












(section 18 of 21) similar to hypothetical proteins


Contig364D
181500_c2_335
2631
5468
798
266
415
6.50E−39

Bacillus subtilis

P27620
tagAinvolved in polyglycerol phosphate teichoic acid biosynthesis tagAB.subtilis












tagA, tagB, tagC and tagD genes, complete cds.putative


Contig364D
187568_c1_264
2632
5469
327
109
178
8.50E−14

Bacillus subtilis

e1184242
yufCunknownBacillus subtilis complete genome (section 17 of 21)


Contig364D
187916_c1_277
2633
5470
612
204
134
3.90E−09

Bacillus subtilis

g1750115
ynaDYnaDBacillus subtilis SpoVK (spoVK), YnbA (ynbA), YnbB (ynbB),












GlnR (glnR), glutamine synthetase (glnA), YnaA (ynaA, YnaB (ynaB),












YnaC (ynaC, YnaD (ynaD), YnaE (ynaE), YnaF (ynaF), YnaG (ynaG),












YnaH (ynaH), YnaI (ynaI), YnaJ (ynaJ) xylan beta-1,4-xylo


Contig364D
19547783_f3_216
2634
5471
771
257
438
2.40E−41

Thermotoga

g1575577
drrADNA-binding response regulatorThermotoga maritima DNA-











maritima


binding response regulator (drrA) and histidine protein kinase (hpkA)












genes, complete cds; thymidne/pyrimidine phosphorylase












homolog gene, partial cds.complete cds.DrrA; OmpR/PhoB subfamily












response


Contig364D
19589187_f1_4
2635
5472
207
69


Contig364D
19696951_c2_390
2636
5473
183
61
193
2.20E−15

Bacillus subtilis

e1186051
yvaLhypothetical protein yvaLBacillus subtilis complete genome (section 18 of












21)


Contig364D
19704062_f3_231
2637
5474
183
61


Contig364D
197152_c2_330
2638
5475
348
116
247
4.10E−21

Bacillus sp.

d1007183
ORF3Bacillus sp. Na+/H+ antiporter system responsible genes.Na+/H+












antiporter system responsible gene


Contig364D
19765965_c3_478
2639
5476
249
83
323
3.60E−29

Staphylococcus

g2226349
cspCCspCStaphylococcus aureus CspC (cspC) gene, complete cds.similar to











aureus


major cold-shock protein


Contig364D
19766886_f2_81
2640
5477
435
145
167
1.60E−12

Bacillus

e1294701

Bacillus thuringiensis plasmid pG12 with transposon Tn4430.ORF 2












thuringiensis



Contig364D
20322153_c1_289
2641
5478
219
73


Contig364D
20485663_f3_240
2642
5479
210
70


Contig364D
20604832_f1_5
2643
5480
558
186


Contig364D
20893828_c3_421
2644
5481
219
73


Contig364D
20900017_c1_297
2645
5482
2169
723
2007
1.30E−207

Bacillus subtilis

P50620
nrdENrdEB.subtilis cwlC, nrdE, nrdF, ymaA and ymaB genes.similarity to












NrdE of Enterobacteriaceae


Contig364D
209452_f2_145
2646
5483
648
216
754
7.80E−75

Staphylococcus

e255528
membrane proteinS.epidermidis gene encoding ABC transport system.











epidermidis



Contig364D
209627_c2_369
2647
5484
1032
344
830
6.90E−83

Bacillus subtilis

P50621
nrdFNrdFB.subtilis cwlC, nrdE, nrdF, ymaA and ymaB genes.similarity to












NrdF of Enterobacteriaceae


Contig364D
2151937_c3_400
2648
5485
186
62


Contig364D
21525061_c3_439
2649
5486
681
227
175
1.80E−13

Schizosaccharo-

e1251110
SPBC19G7.02hypothetical proteinS.pombe chromosome II cosmid











myces pombe


c19G7.SPBC19G7.02, unknown len


Contig364D
21537811_c3_435
2650
5487
1137
379
925
5.90E−93

Bacillus subtilis

Q45539
csbBstress response proteinBacillus subtilis csbB gene, complete cds.similar












to hypothetical protein from Synechocystis


Contig364D
21897308_f3_233
2651
5488
261
87


Contig364D
22265936_c2_372
2652
5489
1128
376
1557
6.30E−160

Staphylococcus

d1005198
IImlipophilic protein which affects bacterial lysisStaphylococcus aureus











aureus


gene for a participant in homogeneousexpressioin of high-level












methicillin resistance, complete cds.


Contig364D
22381590_f3_179
2653
5490
207
69


Contig364D
22381693_c2_381
2654
5491
852
284
1187
1.00E−120

Staphylococcus

P52282
lgtprolipoprotein diacylglyceryl transferaseStaphylococcus aureus











aureus


prolipoprotein diacylglyceryl transferase (lgt) gene, complete cds.


Contig364D
22391068_c3_454
2655
5492
1056
352
627
2.20E−61

Bacillus subtilis

e1182350
yclQferric anguibactin-binding protein precursor FatBBacillus subtilis complete












genome (section 3 of 21) similar to ferrichrome ABC transporter (binding


Contig364D
22446053_c1_258
2656
5493
726
242
335
2.00E−30

Methanococcus

g1592082
MJ1434endonuclease III, putative (nth2) Methanococcus jannaschii section











jannaschii


126 of 150 of the complete genome.similar to GB


Contig364D
22687900_c2_342
2657
5494
681
227
685
1.60E−67

Bacillus subtilis

g2293175
ytsAsignal transduction regulatorBacillus subtilis rrnB-dnaB genomic












region.similar to two-component response regulator [YtsB


Contig364D
23438461_c3_401
2658
5495
687
229


Contig364D
23439061_c3_427
2659
5496
531
177
258
2.80E−22

Bacillus subtilis

g2522410
yojVunknownBacillus subtilis yojP gene, partial cds; yojQ/S, yojR, yojT, yojU,












yojV, yojW, yojX, yojY, yojZm and yokA genes, complete cds.


Contig364D
23444838_c1_313
2660
5497
264
88
373
1.80E−34

Staphylococcus

e1256407
trxBthioredoxin reductaseStaphylococcus aureus trxB gene.











aureus



Contig364D
23445890_c1_274
2661
5498
492
164
333
3.20E−30

Synechocystis sp.

d1017593
hypothetical proteinSynechocystis sp. PCC6803 complete genome, 3/27,












271600-402289.ORF_ID


Contig364D
23450_c2_393
2662
5499
189
63


Contig364D
23476517_c1_308
2663
5500
1296
432
638
1.S0E−62

Bacillus subtilis

P39145
comForfIFIB.subtilis comF gene.involved in transformation


Contig364D
23492127_f3_166
2664
5501
453
151


Contig364D
23494051_f3_193
2665
5502
1101
367
336
1.50E−30

Bacillus subtilis

P54595
yhcKhypothetical proteinB.subtilis chromosomal DNA (region 75












degreessimlarity to hypothetical proteins from


Contig364D
23523326_c2_351
2666
5503
1242
414
416
5.10E−39

Escherichia coli

P31436
yicKhypothetical 43.5 kD protein in selC nlpAEscherichia coli K-12 MG1655












section 333 of 400 of the completegenome.o394; 100 pct identical












to YICK_ECOLI SW


Contig364D
23572177_c2_386
2667
5504
1194
398
1322
5.00E−135

Lactobacillus

e1175767
pgkphosphoglycerate kinaseLactobacillus delbrueckii ygaP,











delbrueckii


gap, pgk, tpi, and ycsE genes.


Contig364D
23617338_f2_84
2668
5505
528
176
215
9.70E−25

Escherichia coli

P77262
yagUyagU proteinEscherichia coli K-12 MG1655 section 26 of 400 of the












completegenome.o204; 26 pct identical to 46 residues of approx.


Contig364D
23621010_c3_419
2669
5506
843
281
167
1.30E−10

Bacillus subtilis

d1020103
ydeCtranscriptional regulator (AraC/XylS famil) homolog












ydeCBacillus subtilis genome sequence, 148 kb sequence of the regionbetween 35












and 47 degree.PROBABLE HTH_ARAC_FAMILY OF












TRANSCRIPTIONAL


Contig364D
23631928_f3_225
2670
5507
228
76


Contig364D
23634651_c3_417
2671
5508
1044
348
549
4.10E−53

Bacillus subtilis

g2293176
ytsBsignal transduction protein kinaseBacillus subtilis rrnB-dnaB












genomic region.similar to two-component sensor histidine kinase


Contig364D
23672137_c1_282
2672
5509
957
319
260
5.40E−32

Synechocystis sp.

d1019609
47 kD proteinSynechocystis sp. PCC6803 complete genome, 27/27,












3418852-3573470 ORF_ID


Contig364D
23703750_c3_476
2673
5510
639
213


Contig364D
23844575_c1_316
2674
5511
1062
354
771
1.20E−76

Bacillus

P35168
hypothetical 37.7 K proteinBacillus megaterium glyceraldehyde-3-phosphate











megaterium


dehydrogenase (gap), phosphoglycerate kinase (pgk), and triose phosphate












isomerase (tpi) genes, complete cds.


Contig364D
2401430_c2_382
2675
5512
762
254
1076
5.90E−109

Staphylococcus

c1256407
trxBthioredoxin reductaseStaphylococcus aureus trxB gene.











aureus



Contig364D
24218785_c1_317
2676
5513
1047
349
1258
3.00E−128

Clostridium

g2829138
gapglyceraldehyde-3-phosphate dehydrogenaseClostridium











acetobutylicum



acetobutylicum glyceraldehyde-3-phosphate dehydrogenase (gap),













phosphoglycerate kinase (pgk), and triosephosphate isomerase (lpi) genes,












complete cds; and 2,3-bpg-independent phosphoglyceratemutase (pgm


Contig364D
24230001_f3_162
2677
5514
258
86


Contig364D
24258388_c2_358
2678
5515
507
169


Contig364D
24272125_c1_321
2679
5516
261
87


Contig364D
24297000_f3_236
2680
5517
225
75


Contig364D
24329053_c3_424
2681
5518
444
148
134
1.50E−08

Caenorhabditis

g1825636
ZK354.3Caernorhabditis elegans cosmid ZK354.











elegans



Contig364D
24391937_c3_464
2682
5519
759
253


Contig364D
24397952_c3_463
2683
5520
681
227
119
9.50E−05

Bacillus subtilis

e1186169
yvcDhypothetical proteinBacillus subtilis complete genome (section 18 of 21)


Contig364D
24406577_c2_362
2684
5521
390
130


Contig364D
24407637_f2_39
2685
5522
243
81


Contig364D
24429650_c2_360
2686
5523
1197
399
848
8.50E−85

Bacillus subtilis

g2618856
nagAN-acetylglucosamine 6-P deacetylaseBacillus subtilis 300-304












degree genomic sequence.


Contig364D
24479842_c3_481
2687
5524
558
186
256
4.60E−22

Bacillus subtilis

e1182838
yfhCYfhCBacillus subtilis complete genome (section 5 of 21) similar to












hypothetical proteins


Contig364D
24506712_c1_298
2688
5525
975
325
692
2.90E−68

Bacillus subtilis

e1182348
yclOhomologue of ferric anguibactin transport systemBacillus subtilis












complete genome (section 3 of 21) similar to ferrichrome ABC












transporter (permease)


Contig364D
24507932_c3_445
2689
5526
600
200
322
4.70E−29

Bacillus subtilis

e1185499
yorSunknownBacillus subtilis complete genome (section 11 of 21)


Contig364D
24640828_c1_262
2690
5527
516
172


Contig364D
24642632_f1_31
2691
5528
1245
415
1245
7.20E−127

Bacillus subtilis

P55179
pepTpeptidase T (tripeptidase) B.subtilis orfs 1,2,3,4, pepT and galE genes.highly












homologous to tripeptidases (peptidase T)


Contig364D
24650427_f3_155
2692
5529
330
110
331
5.20E−30

Bacillus subtilis

d1020045
ydbPthioredoxin homolog ydbPBacillus subtilis genome sequence, 148 kb












sequence of the region between 35 and 47 degree.PROBABLE THIOREDOXIN.


Contig364D
24650462_c3_407
2693
5530
1515
505
848
8.50E−85

Bacillus subtilis

e1184241
yufDNADH dehydrogenase (ubiquinone) homolog yufDBBacillus subtilis complete












genome (section 17 of 21) similar to NADH dehydrogenase (ubiquinone)


Contig364D
24664840_c1_287
2694
5531
1968
656
1694
1.90E−174

Bacillus subtilis

e1185030
fruAphosphotransferase system (PTS) Bacillus subtilis complete genome












(section 8 of 21)


Contig364D
24796927_f2_82
2695
5532
789
263
325
2.20E−29

Bacillus subtilis

e1183386
ymaCphage-related protein homolog ymaCBacillus subtilis complete genome












(section 10 of 21) similar to phage-related protein


Contig364D
24803125_c3_431
2696
5533
978
326
982
5.40E−99

Bacillus israeli

Q59202
MDHmalate dehydrogenaseB.israeli DNA for malate dehydrogenase gene.


Contig364D
25401377_c3_453
2697
5534
852
284
698
6.70E−69

Bacillus subtilis

e1182349
yclPhomologue of iron dicitrate transportBacillus subtilis complete












genome (section 3 of 21) similar to ferrichrome ABC transporter (ATP-












binding


Contig364D
25473782_c2_396
2698
5535
186
62


Contig364D
25572180_c3_413
2699
5536
1272
424
895
8.90E−90

Bacillus subtilis

P42312
yxjApyrimidine nucleoside transport homolog yxjABacillus subtilis complete












genome (section 20 of 21) similar to pyrimidine nucleoside transport


Contig364D
25585891_c1_291
2700
5537
1980
660
1949
1.80E−201

Baciliussubtilis

e1182705
yfnlYfnlBacillus subtilis complete genome (section 4 of 21) alternate gene












name


Contig364D
25806300_f2_144
2701
5538
750
250
1270
1.60E−129

Staphylococcus

e255626
ATP binding proteinS.epidermidis gene encoding ABC transport system.











epidermidis



Contig364D
26171927_c1_302
2702
5539
342
114
221
2.30E−18

Bacillus subtilis

P39914
ytxJYtxJBacillus subtilis rrnB-dnaB genomic region.alternate gene name


Contig364D
26176693_f3_210
2703
5540
828
276
685
1.60E−67

Methanobacterium

g2621542
MTH473conserved proteinMethanobacterium











thermoautotro-



thermoautptrophicum from bases 404817 to 415582 (section 37 of 148) of the












phicum


complete genome.Function Code


Contig364D
2618827_c3_451
2704
5541
288
96


Contig364D
26211552_c1_314
2705
5542
984
328
1034
1.70E−104

Bacillus subtilis

e1186163
yvcLhypothetical proteinBacillus subtilis complete genome (section 18 of












21) simialr to hypothetical proteins


Contig364D
26259638_f2_101
2706
5543
765
255
376
1.90E−11

Mycobacterium

e1264597
MTV025.085putative membrane proteinMycobacterium tuberculosis











tuberculosis


sequence v025.MTV025.085, len


Contig364D
26578577_c3_461
2707
5544
1791
597
2276
1.50E−238

Bacillus subtilis

g2618842
uvrAexcinuclease ABC subunit ABacillus subtilis 300-304 degree












genomic sequence.


Contig364D
26735877_c2_399
2708
5545
402
134
446
3.40E−42

Bacillus subtilis

e1184358
yusHglycine cleavage system protein H homolog yusHBacillus subtilis complete












genome (section 17 of 21) similar to glycine cleavage system protein H


Contig364D
26753150_f2_105
2709
5546
336
112
295
3.40E−26

Saccharomyces

P36078
YKL084Whypotheyical protein YKL084wS.cerevisiae chromosome X1











cerevisiae


reading frame ORF YKL084w.ORF YKL084w


Contig364D
26757807_f3_246
2710
5547
951
317
1619
1.70E−166

Staphylococcus

e255529
lipoproteinS.epidermidis gene encoding ABC transport system.











epidermidis



Contig364D
26834387_f2_135
2711
5548
711
237
115
9.70E−07

Lacrococcus lactis

g3043880
transmembrane protein Tmp6Lactococcus lactis transmembrane












protein Tmp6 gene, partial cds.identified as a fusion to a signal peptide-less


Contig364D
26839462_c2_383
2712
5549
1011
337
817
1.60E−81

Bacillus subtilis

e1186164
yvcKconserved hypothetical protein yvcKBacillus subtilis complete genome












(section 18 of 21) similar to hypothetical proteins


Contig364D
2752262_c2_366
2713
5550
1014
338
652
5.00E−64

Bacillus subtilis

g2293447
opuBAATPaseBacillus subtilis choline transport system including












ATPase(opuBA), transmembrane protein (opuBB), choline binding












protein precursor (opuBC) and transmembrane protein (opuBD) genes,












completecds; and unknown gene.OpuBA; part of choline uptake sys


Contig364D
275268_c1_294
2714
5551
1125
375
773
7.50E−77

BACILLUS

P17731
HISHPHOSPHATE TRANSAMINASE)











SUBTILIS



Contig364D
2917200_f2_146
2715
5552
192
64


Contig364D
2926425_f3_204
2716
5553
960
320
456
2.90E−43

Bacillus subtilis

P39074
bmrUBmrUBacillus subtilis bmrU, multidrug efflux transporter (bmr) and












itsregulator (bmrR) genes, complete cds, and branched-chain 2-oxo












aciddehydrogenase (bfmB) gene, 3′ end.


Contig364D
29376503_f3_217
2717
5554
246
82


Contig364D
29501510_c3_410
2718
5555
1125
375
432
1.00E−40

Bacillus subtilis

P27621
tagBinvolved in polyglycerol phosphate teichoic acid biosynthesis tagBB.subtilis












tagA, tagB, tagC and tagD genes, complete cds.putative


Contig364D
3001313_c1_310
2719
5556
681
227
154
3.00E−11

Escherichia coli

g1788628
hypothetical protein b2291Escherichia coli K-12 MG1655 section 208 of 400 of












the completegenome.o199


Contig364D
30491275_c3_415
2720
5557
1104
368
391
2.30E−36

Bacillus subtilis

e1184961
ykvlconserved hypothatical protein ykvlBacillus subtilis complete genome












(section 8 of 21) similar to hypothetical proteins from B. subtilis


Contig364D
30601588_c2_337
2721
5558
834
278
561
2.20E−54

Bacillus subtilis

P42953
tagGhighly hydrophobic integral membrane proteinBacillus subtilis 168












highly hydrophobic integral membrane protein (tagG) gene and ATP-binding












protein (tagH) gene, complete cds.


Contig364D
30745328_c3_480
2722
5559
606
202
200
3.90E−16

Escherichia coli

g1790856
gpmBgpmB proteinEscherichia coli K-12 MG1655 section 399 of 400 of the












complete genome.Kenn Rudd identifies as gpmB


Contig364D
31257943_c1_267
2723
5560
414
138
669
7.90E−66

Staphylococcus

g1913907
tagDTagDStaphylococcus aureus teichoic acid biosynthesis TagB gene,











aureus


partialcds and TagX and TagD genes, complete cds.similar to Bacillus subtilis












TagD


Contig364D
31267503_c1_270
2724
5561
813
271
784
5.10E−78

Bacillus subtilis

g2293177
ytsCtransporterBacillus subtilis rrnB-dnaB genomic region.similar to ABC












transporter (ATP-binding protein)


Contig364D
31289687_c3_456
2725
5562
681
227
134
4.70E−06

Schizosaccharo-

e334260
SPAC14C4.02hypothetical proteinS.pombe chromosome I cosmid











myces pombe


c14C4.SPAC14C4.02c, unknown; SMC family; coiled coil,


Contig364D
31428188_f3_178
2726
5563
222
74


Contig364D
31578_c1_212
2727
5564
537
179
463
5.30E−44

Bacillus subtilis

g2618861
yvoFputative acetyltransferaseBacillus subtilis 300-304 degree genomic












sequence.similar to O-acetyltransferase


Contig364D
31803377_f1_66
2728
5565
612
204


Contig364D
32062553_c3_406
2729
5566
468
156
354
1.90E−32

Bacillus sp.

d1007182
ORF2Bacillus sp. Na+/H+ antiporter system responsible genes.Na+/H+












antiporter system responsible gene


Contig364D
32212902_c1_261
2730
5567
1035
345
468
1.60E−44

Bacillus subtilis

e1249808
yvrBputative hemin permease, YvrBBacillus subtilis 42.7 kB DNA












fragment from yvsA to yvqA.similar to iron permease


Contig364D
32225012_f1_77
2731
5568
498
166
276
3.50E−24

Bacillus subtilis

e1181516
yknAYknABacillus subtilis 168 56 kb DNA fragment between xlyA and












ykoR.homologous to OsmC from Escherichia coli


Contig364D
32611068_c3_402
2732
5569
1674
558
1694
1.90E−174

Bacillus subtilis

e1186234
argSarginyl-tRNA synthetaseBacillus subtilis complete genome (section 20 of












21)


Contig364D
33210952_f3_168
2733
5570
234
78


Contig364D
33239001_f3_158
2734
5571
276
92


Contig364D
33414143_c2_354
2735
5572
1710
570
619
1.60E−60

Shigella flexneri

g2773332
cydCABC transporter CydCShigella flexneri ABC transporter CydC (cydC)












gene, complete cds.similar to E. coli CydC


Contig364D
34160625_c2_341
2736
5573
438
146


Contig364D
34173385_c3_422
2737
5574
621
207
151
6.10E−11

Pyrococcus

d1028675
PHBQ005166aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA. 1393354-1434541 nt position (complementary strand). clone


Contig364D
34173750_c2_389
2738
5575
480
160


Contig364D
34189817_c3_408
2739
5576
2052
684
888
4.90E−89

Bacillus subtilis

e1186030
yvgPconserved hypothetical protein tvgPBacillus subtilis complete genome












(section 18 of 21) similar to hypothetical proteins


Contig364D
34261088_c2_353
2740
5577
312
104


Contig364D
34562762_c2_326
2741
5578
750
250
230
2.60E−19

Pyrococcus

d1027599
PHBH026232aa long hypothetical proteinPyrococcus horikoshii OT3











horikoshii


genomic DNA, 415465-442351 nt position (complementary strand), clone


Contig364D
34571000_f2_110
2742
5579
537
179
393
1.40E−35

Entamoeba

Q24803
ADH2alcohol dehydrogenase 2Entamoaba histolytica HM1The derived











histolytica


amino acid sequence of EhADH2 is


Contig364D
34589027_c1_283
2743
5580
315
105


Contig364D
34612887_f3_221
2744
5581
465
155
260
1.70E−22

Bacillus subtilis

e1181515
ykmAYkmABacillus subtilis 168 56 kb DNA fragment between xlyA and












ykoR.simimlar to hypothetical proteins


Contig364D
34627136_f1_3
2745
5582
306
102


Contig364D
34641875_c2_359
2746
5583
939
313
704
1.50E−69

Bacillus subtilis

e1185029
fruBfructose-1-phosphate kinaseBacillus subtilis complete genome (section 8 of












21)


Contig364D
34642567_c3_472
2747
5584
2406
802
2175
1.70E−228

Bacillus subtilis

e1186049
yvaJconserved hypothetical protein yvaHBacillus subtilis complete genome












(section 18 of 21) similar to hypothetical proteins


Contig364D
34645311_f1_62
2748
5585
525
175
135
3.00E−09

Escherichia coli

P46854
YHHYhypothetical protein b3441Escherichia coli K-12 MG1655












section 310 of 400 of the completegenome.o162


Contig364D
35166012_c3_432
2749
5586
210
70


Contig364D
35444127_f3_192
2750
5587
663
221
514
2.10E−49

Bacillus subtilis

g1762328
yvhKYcr59c/YigZ homologBacillus subtilis putative transcriptional regulator












(yvhJ), Ycr59c/YigZ homolog (yvhK), histidine kinase












(degS), transcriptionalregulator of degradation enzyme (degU), (degV),












(comFA), (comFB), (comFC), flagellar protein (yviB), negat


Contig364D
35945277_c2_377
2751
5588
1065
355
1275
4.80E−130

Bacillus subtilis

g2331287
prfBrelease factor 2Bacillus subtilis release factor 2 (prfB) gene, complete












cds.orf3


Contig364D
36131311_c2_374
2752
5589
696
232
194
1.70E−15

Bacillus subtilis

g451867

Bacillus subtilis (clones pDM116 and pDM113) flagellin synthesisregulatory













protein (flgM) and flagellar hook-filament junctionprotein (flgK) genes












and orf139, orf160, orfX, complete cds's.in Z18629, ORFX is called












comForf3; ORFX; putative


Contig364D
36133385_c2_345
2753
5590
681
227
203
1.90E−16

Bacillus subtilis

e1182699
yetJhypothetical protein yetJBacillus subtilis complete genome (section 4 of












21)


Contig364D
36212541_c1_299
2754
5591
204
68


Contig364D
36229676_c3_404
2755
5592
795
265
238
3.70E−20

Acinetobacter sp.

g3172115
pcaDbeta-ketoadipate enol-lactone hydrolaseAcinebacter sp. ADP1 pca-










ADP1

qui-pob supraoperonic cluster, completesequence.ELH


Contig364D
36230252_c3_434
2756
5593
777
259
480
8.40E−46

Bacillus subtilis

e1185028
fruRtranscriptional regulator (DeoR family) Bacillus subtilis complete












genome (section 8 of 21)


Contig364D
36601562_c2_357
2757
5594
1182
394
1669
8.50E−172

Staphylococcus

P21191
norAORF for norAS. aureus norA gene.











aureus



Contig364D
390942_c1_318
2758
5595
456
152
112
7.30E−06
Kinetoplast
g896286
MURF1Leishmania tarentolae kinetoplast pre-editied











Leishmania


mitochondrialmaxcircle DNA complete transcribed region and flanks.NH2











tarentolae


terminus uncertain


Contig364D
391527_f1_65
2759
5596
930
310
700
4.10E−69

Bacillus subtilis

P42954
tagHATP-binding protienBacillus subtilis 168 highly hydrophobic integral












membrane protein (tagG) gene and ATP-binding protein (tagH) gene, complete












cds.


Contig364D
3928762_f3_167
2760
5597
1368
456
839
7.60E−84

Bacillus subtilis

e1185983
yubBNa+-transporting ATP synthase homolog yubGBacillus subtilis complete












genome (section 16 of 21) similar to Na+-transporting ATP synthase


Contig364D
3942263_c2_348
2761
5598
726
242
913
1.10E−91

Bacillus subtilis

e1182664
yeelconserved hypothetical protein yeelBacillus subtilis complete genome












(section 4 of 21) similar to hypothetical proteins


Contig364D
3953452_c1_285
2762
5599
507
169
1328
1.10E−29

Bacillus subtilis

e1183226
yjdltranscription regulation homolog yjdlBacillus subtilis complete genome












(section 7 of 21) similar to transcription regulation


Contig364D
3962915_f3_218
2763
5600
627
209
137
4.00E−08

Synechocystis sp.

d1011025
hypothetical proteinSynechocystis sp. PCC6803 complete genome, 21/27,












2644795-2755702.ORF_ID


Contig364D
39818_f3_229
2764
5601
240
80
234
9.80E−20

Staphylococcus

g1575061
scdAScdAStaphylococcus aureus scdA gene, complete cds.S. aureus cells











aureus


containing a scdA disruption have


Contig364D
4023518_f3_177
2765
5602
909
303
579
2.70E−56

Bacillus subtilis

e1182841
yfhFYfhFBacillus subtilis complete genome (section 5 of 21) similar to cell-












division inhibitor


Contig364D
4036093_c2_350
2766
5603
864
288
461
8.70E−44

Bacillus subtilis

e1181918
ykuMYkuM proteinBacillus subtilis 29 kB DNA fragment from ykwC gene to












cse15 gene.homologous to LysR type transcriptional regulators


Contig364D
4072006_f1_53
2767
5604
203
67


Contig364D
4095055_f3_202
2768
5605
894
298
258
2.80E−22

Sphingomonas

g1314584
unknownSphingomonas S88 shingan polysaccharide synthesis (spsG),










S88

(spsS), (spsR), glycosyl transferase (spsQ), (spsI), glycosyl












transferase (spsK), glycosyl transferase (spsL), (spsJ), (spsF), (spsD), (spsC),












(spsE), Urf32, Urf32, Urf26, ATP-binding cassette tran


Contig364D
4096093_c2_395
2769
5606
354
318
155
2.30E−11

Paracoccus

B42573
urf120











denitrificans



Contig364D
4100093_c2_363
2770
5607
1161
387
489
9.40E−47

Helicobacter

g2313385
HP0293para-aminobenzoate synthetase (pabB) Helicobacter pylori section 25 of











pylori


134 of the complete genome.similar to EGAD


Contig364D
4103393_c1_290
2771
5608
597
199
436
3.90E−41

Salmonella

P06193
PABApabA proteinSalmonella typhimurium pabA gene for para-











typhimurium


aminobenzoate synthaseglutamine amidotransferase.glutamine












amidotransferasepabA gene product (aa 1-187)


Contig364D
4110888_c2_347
2772
5609
405
135


Contig364D
4111691_c3_441
2773
5610
744
248
351
1.20E−31

Bacillus subtilis

P42967
ycsJurea amidolysaseBacillus subtilis genome around 39 degree region












encoding 17 ORFs, complete cds.similar to allophanate hydrolase


Contig364D
4195817_c3_412
2774
5611
1743
581
2597
3.90E−270

Staphylococcus

e264711
abcAATP-binding cassette transporter AS.aureus abcA, pbp4, and tagD genes.











aureus



Contig364D
42167_c3_414
2775
5612
834
278
834
2.60E−83

Bacillus subtilis

P49938
fhuCferrichrome transport protein, FhuCBacillus subtilis 42.7 kB DNA












fragment from yvsA to yvqA.protein-dependent


Contig364D
422162_f1_36
2776
5613
456
152
439
1.90E−41

Bacillus subtilis

e1184963
ykvK6-pyruvoyl tetrahydrobiopterin synthase homolog ykvKBacillus subtilis












complete genome (section 8 of 21) similar to 6-pyruvoyl












tetrahydrobiopterin synthase


Contig364D
422800_f1_71
2777
5614
447
149
542
2.30E−52

Staphylococcus

g684950
sarAstaphylococcal accessory regulator AStapgylococcus aureus staphylococcal











aureus


accessory regulator A (sarA) gene, complete cds.


Contig364D
429675_f3_238
2778
5615
216
72


Contig364D
4461693_f3_254
2779
5616
240
80


Contig364D
4487588_f1_38
2780
5617
609
203


Contig364D
4501250_c3_477
2781
5618
1080
360
871
3.10E−87

Bacillus

d1020364
membrane proteinBacillus stearothermophilu DNA for glycogen











stearothermophilus


operon, complete cds. The ORF is similar to the Alkaligenes eutrophus


Contig364D
4511550_c1_303
2782
5619
1278
426
318
1.20E−28

Escherichia coli

P23524
yhaDhypothetical 42.1 kD protein in mpB-sohAEscherichia coli K-12












MG1655 section 284 of 400 of the completegenome.f408; 100 pct identical












amino acid sequence and


Contig364D
4535652_f2_142
2783
5620
225
75


Contig364D
4539143_c3_462
2784
5621
942
314
970
1.00E−97

Bacillus subtilis

g2618857
ptsKHPr (Ser) kinaseBacillus subtilis 300-304 degree genomic sequence.similar to












the Mycoplasma genitalium hypothetical


Contig364D
4578956_f2_91
2785
5622
297
99


Contig364D
4689077_c1_315
2786
5623
333
111
466
2.60E−44

Bacillus subtilis

g2668494
clpPClpPBacillus subtilis Clp protease proteolytic component (clpP)












gene, complete cds.proteolytic component of Clp protease


Contig364D
4689130_f3_256
2787
5624
306
102


Contig364D
4703180_c3_450
2788
5625
453
151
251
1.60E−21

Bacillus subtilis

P50618
ymaA YmaAB.subtilis cwlC, nrdE, nrdF, ymaA and ymaB genes.similar to












ribonucleoprotein


Contig364D
4726527_f1_32
2789
5626
528
176
749
2.60E−74

Bacillus subtilis

e1184965
ykvMconserved hypothetical protein ykvMBacillus subtilis complete genome












(section 8 of 21) similar to hypothetical proteins


Contig364D
4773392_f3_161
2790
5627
288 96


Contig364D
4775287_c2_364
2791
5628
1008
336
238
1.10E−34

Escherichia coli

P75745
YBGKhypothetical protein b0712Eschericha coli K-12 MG1655












section 64 of 400 of the completegenome.o310; This 310 aa ORF












is 48 pct identical (1 gap)


Contig364D
4804643_f2_89
2792
5629
246
82


Contig364D
4806575_c1_272
2793
5630
651
217
503
3.10E−48

Bacillus subtilis

e1181486
ykaA YkaABacillus subtilis 168 56 kb DNA fragment between xlyA and ykoR.


Contig364D
4876077_f1_37
2794
5631
714
238
778
2.20E−77

Bacillus subtilis

e1184964
ykvLcoenzyme PQQ synthesis homolog ykvLBacillus subtilis complete genome












(section 8 of 21) similar to coenzyme PQQ synthesis


Contig364D
4885876_c3_466
2795
5632
918
306
829
8.80E−83

Bacillus subtilis

O06973
yvcJhypothetical proteinBacillus subtilis complete genome (section 18 of












21) similar to hypothetical proteins


Contig364D
4892878_c2_338
2796
5633
1077
359
455
3.80E−43

Staphylococcus

g1913906
tagXTagXStaphylococcus aureus teichoic acid biosynthesis TagB gene,











aureus


partialcds and TagX and TagD genes, complete cds.


Contig364D
4898376_f3_244
2797
5634
207
69


Contig364D
5084652_f1_56
2798
5635
507
169
536
9.80E−52

Staphylococcus

g1575061
scdAScdAStaphylococcus aureus scdA gene, complete cds.S. aureus cells











aureus


containing a scdA disruption have


Contig364D
5131265_c1_300
2799
5636
276
92


Contig364D
5182962_f2_119
2800
5637
1068
356
295
1.10E−30

Bacillus subtilis

P35164
resEtwo-component sensor histidine kinaseBacillus subtilis spoVA to serA












region.ORFX18


Contig364D
5195393_c2_334
2801
5638
654
218
1088
3.10E−110

Staphylococcus

e255543
sirRputative iron dependant repressorS.epidermidis sirR gene.











epidermidis



Contig364D
5276677_c3_444
2802
5639
1566
522
703
2.00E−69

Helicobacter

g2313949
HP0818osmoprotection protein (proWX)Helicobacter pylori section 71











pylori


of 134 of the complete genome.similar to EGAD


Contig364D
5283592_f2_126
2803
5640
288
96


Contig364D
5292175_c2_388
2804
5641
1323
441
2112
9.70E−219

Staphylococcus

g3152725
enoenolaseStaphylococcus aureus enolase (eno) gene, complete cds.ENO;











aureus


laminin binding protein


Contig364D
53552_f3_194
2805
5642
660
220
179
6.60E−14

Bacillus firmus

Q45133
grpBglutamate-rich proteinBacillus firmus OrfA, OrfB, glutamate-rich












protein (grpA), OrfC, and glutamate-rich protein (grpB) genes, complete cds.


Contig364D
5355325_c2_373
2806
5643
888
296
526
1.10E−50

Bacillus subtilis

P32436
degUorf3U3B.subtilis comF gene.alternate gene name


Contig364D
5367843_c2_391
2807
5644
759
253
791
9.30E−79

Bacillus

Q06174
ESTesteraseBacillus stearothermophilus esterase gene.











stearothermophilus



Contig364D
5869702_f3_253
2808
5645
309
103


Contig364D
5938762_c3_428
2809
5646
1704
568
566
6.50E−55

Haemophilus

P45082
H11157transport ATP-binding protein (cydD) Haemophilus influenzae from











influenzae


bases 1218795 to 1228832 (section 110 of 163) of the complete












genome.unassigned ATP-binding cassette proteinssimilar to GB


Contig364D
6051500_c3_420
2810
5647
189
63


Contig364D
6051537_c3_460
2811
5648
276
92
112
8.30E−07

Bacillus subtilis

P37953
csbACsbABacillus subtilis 300-304 degree genomic sequence putative












membrane protein; putative


Contig364D
6053176_f2_118
2812
5649
519
173


Contig364D
6053540_c3_458
2813
5650
198
66


Contig364D
6257763_c2_385
2814
5651
660
220
187
2.40E−13
Kapasi's sarcoma-
g2246532
Kaposi's sarcoma-associated herpesvirus glycoprotein M, DNAreplication protein,










associated

glycoprotein, DNA replication protein, FLICEinhibitory protein and v-cyclin










herpesvirus

genes, complete cds, and legumentprotein gene, partial cds.ORF












73, contains large complex repeat CR


Contig364D
626592_c3_403
2815
5652
852
284
233
1.30E−19

Archaeoglobus

g2648849
AF17062-hydroxy-6-oxo-6-phynylhexa-2,4-dienoic acidArchaeoglobus fulgidus











Fulgidus


section 121 of 172 of the complete genome.similar to GP


Contig364D
6437525_c1_60
2816
5653
294
98


Contig364D
6440640_c2_346
2817
5654
1278
426


Contig364D
6642827_c2_329
2818
5655
2403
801
1527
9.50E−157

Bacillus subtilis

e1184238
yufTunknownBacillus subtilis complete genome (section 17 of 21) similar to












NADH dehydrogenase


Contig364D
6680312_f3_223
2819
5656
714
238
208
5.60E−17

Caenorhabditis

g1825636
ZK354.3Caernorhabditis elegans cosmid ZK354.











elegans



Contig364D
6681577_c3_483
2820
5657
432
144
277
2.70E−24

Bacillus subtilis

e1184356
yusFhypothetical protein yusFBacillus subtilis complete genome (section 17 of












21)


Contig364D
6822175_c1_293
2821
5658
1914
638
1229
3.60E−125

Bacillus subtilis

g2619051
yoclRecQ homologBacillus subtilis chromosome region between lerC and












odhAB.similar to E.coli RecQ protein (607 aa)


Contig364D
6823453_c2_331
2822
5659
483
161
123
5.70E−08

Pyrococcus

d1028563
PHCC005174aa long hypothetical proteinPyrococcus horokoshii OT3











horikoshii


genomic DNA, 1300517-1338254 nt position, clone


Contig364D
6829638_c2_356
2823
5660
186
62


Contig364D
6833313_c2_343
2824
5661
1920
640
550
3.20E−53

Bacillus subtilis

g2293178
ytsDYtsDBacillus subtilis rrnB-dnaB genomic regioin.similarity to NADH












dehydrogenase


Contig364D
7239188_f3_224
2825
5662
675
225
491
5.70E−47

Bacillus subtilis

e1186152
yvdDhypothetical proteinBacillus subtilis complete genome (section 18 of












21) similar to hypothetical proteins


Contig364D
7800_c3_474
2826
5663
198
66


Contig364D
788950_c2_332
2827
5664
531
177
219
3.80E−18

Bacillus subtilis

e1184243
yufBunknownBacillus subtilis complete genome (section 17 of 21) similar to












hypothetical proteins


Contig364D
821963_c1_269
2828
5665
546
182


Contig364D
867260_f1_48
2829
5666
225
75


Contig364D
899177_c2_325
2830
5667
930
310
596
4.30E−58

Bacillus subtilis

e1249807
yvrCputative metal binding protein, YvrCBacillus subtilis 42.7 kB DNA












fragment from yvsA to yvqA.similar to iron-binding protein


Contig364D
900256_c3_440
2831
5668
210
70


Contig364D
9642_f2_131
2832
5669
876
292
769
2.00E−76

Bacillus subtilis

e1185988
yubBbacitracin resistance protein (undecapreno) homolog yubBBacillus













subtilis complete genome (Section 16 of 21) similar to bacitracin resistance protein



Contig364D
969075_c3_482
2833
5670
354
118
359
5.60E−33

Bacillus subtilis

e1184359
yuslarsenate reductase homolog yuslBacillus subtilis complete genome












(section 17 of 21) similar to arsenate reductase


Contig364D
970327_c1_323
2834
5671
297
99
167
1.20E−12

Bacillus subtilis

e1184355
yusEthioredoxin homolog yusEBacillus subtilis complete genome (section 17 of












21) similar to thioredoxin


Contig364D
978426_c3_452
2835
5672
978
326
960
1.10E−96

Bacillus subtilis

e1182347
yclNhomologue of ferric anguibactin transport systemBacillus subtilis












complete genome (section 3 of 21) similar to ferrichrome ABC












transporter (permease)


Contig364D
9882950_c1_288
2836
5673
1350
450
1090
1.90E−110

Bacillus subtilis

e1182956
yhdPhypothetical proteinBacillus subtilis complete genome (section 6 of












21) similar to hemolysin


Contig364D
9884625_f3_203
2837
5674
1509
503
1226
7.50E−125

Bacillus subtilis

P94408
yclFhomologue of Di-tripeptide transporter Dtp of L.Bacillus subtilis












complete genome (section 3 of 21) similar to di-tripeptide ABC












transporter (membrane








Claims
  • 1. An isolated nucleic acid molecule comprising a nucleotide sequence encoding Staphylococcus epidermidis polypeptide SEQ ID NO: 3746.
  • 2. A recombinant expression vector comprising the nucleic acid of claim 1 operably linked to a transcription regulatory element.
  • 3. An isolated cell comprising a recombinant expression vector of claim 2.
  • 4. The isolated nucleic acid of claim 1, wherein the nucleic acid comprises SEQ ID NO: 909.
  • 5. The isolated nucleic acid of claim 1, wherein said nucleic acid consists of SEQ ID NO: 909.
  • 6. The nucleic acid molecule of claim 1, wherein the nucleic acid molecule is DNA or RNA.
  • 7. An isolated nucleic acid molecule, wherein the nucleic acid molecule is DNA, RNA, single-stranded antisense, or an RNA/DNA duplex comprising SEQ ID NO: 909, a transcription product of SEQ ID NO: 909, or an antisense strand of SEQ ID NO: 909.
Parent Case Info

This application is a divisional of application Ser. No. 10/902,411, filed Jul. 30, 2004, now U.S. Pat. No. 7,416,862, which is a continuation of application Ser. No. 10/092,411, filed Mar. 7, 2002, abandoned, which is a divisional of application Ser. No. 09/134,001, filed on Aug. 13, 1998, now U.S. Pat. No. 6,380,370, issued Apr. 30, 2002, which claims priority of U.S. Provisional Application 60/055,779, filed Aug. 14, 1997 and U.S. Provisional Application 60/064,964, filed Nov. 8, 1997, all of which are hereby incorporated herein by reference in their entirety.

US Referenced Citations (2)
Number Name Date Kind
6528289 Fleischmann et al. Mar 2003 B1
6593114 Kunsch et al. Jul 2003 B1
Foreign Referenced Citations (1)
Number Date Country
WO 9608582 Mar 1996 WO
Related Publications (1)
Number Date Country
20070042391 A1 Feb 2007 US
Provisional Applications (2)
Number Date Country
60055779 Aug 1997 US
60064964 Nov 1997 US
Divisions (2)
Number Date Country
Parent 10902441 Jul 2004 US
Child 11207802 US
Parent 09134001 Aug 1998 US
Child 10092411 US
Continuations (1)
Number Date Country
Parent 10092411 Mar 2002 US
Child 10902441 US