U.S. patent application number 10/329624 was filed with the patent office on 2004-03-04 for staphylococcus aureus polynucleotides and sequences.
This patent application is currently assigned to Human Genome Sciences, Inc.. Invention is credited to Barash, Steven, Choi, Gil H., Dillon, Patrick J., Fannon, Michael R., Kunsch, Charles A., Rosen, Craig A..
Application Number | 20040043037 10/329624 |
Document ID | / |
Family ID | 46149777 |
Filed Date | 2004-03-04 |
United States Patent
Application |
20040043037 |
Kind Code |
A1 |
Kunsch, Charles A. ; et
al. |
March 4, 2004 |
Staphylococcus aureus polynucleotides and sequences
Abstract
The present invention provides polynucleotide sequences of the
genome of Staphylococcus aureus, polypeptide sequences encoded by
the polynucleotide sequences, corresponding polynucleotides and
polypeptides, vectors and hosts comprising the polynucleotides, and
assays and other uses thereof. The present invention further
provides polynucleotide and polypeptide sequence information stored
on computer readable media, and computer-based systems and methods
which facilitate its use.
Inventors: |
Kunsch, Charles A.;
(Norcross, GA) ; Choi, Gil H.; (Rockville, MD)
; Barash, Steven; (Rockville, MD) ; Dillon,
Patrick J.; (Carlsbad, CA) ; Fannon, Michael R.;
(Silver Spring, MD) ; Rosen, Craig A.;
(Laytonsville, MD) |
Correspondence
Address: |
HUMAN GENOME SCIENCES INC
9410 KEY WEST AVENUE
ROCKVILLE
MD
20850
|
Assignee: |
Human Genome Sciences, Inc.
9410 Key West Avenue
Rockville
MD
20850
|
Family ID: |
46149777 |
Appl. No.: |
10/329624 |
Filed: |
December 27, 2002 |
Related U.S. Patent Documents
|
|
|
|
|
|
Application
Number |
Filing Date |
Patent Number |
|
|
10329624 |
Dec 27, 2002 |
|
|
|
08956171 |
Oct 20, 1997 |
|
|
|
6593114 |
|
|
|
|
08956171 |
Oct 20, 1997 |
|
|
|
08781986 |
Jan 3, 1997 |
|
|
|
60009861 |
Jan 5, 1996 |
|
|
|
Current U.S.
Class: |
424/190.1 ;
435/252.3; 435/320.1; 435/69.3; 530/350; 536/23.7 |
Current CPC
Class: |
C07K 14/31 20130101;
C12N 15/1093 20130101; A61K 39/00 20130101; C12N 15/52
20130101 |
Class at
Publication: |
424/190.1 ;
435/069.3; 435/252.3; 435/320.1; 530/350; 536/023.7 |
International
Class: |
A61K 039/02; C07H
021/04; C12P 021/02; C12N 001/21; C07K 014/31 |
Claims
What is claimed is:
1. An isolated polynucleotide comprising a nucleic acid fragment of
the Staphylococcus aureus genome, wherein said fragment consists of
the nucleotide sequence of any one of SEQ ID NOS: 1-5,191 as
depicted in Tables 2 and 3.
2. A vector comprising the polynucleotide of claim 1.
3. An organism which has been altered to contain the polynucleotide
of claim 1.
4. An isolated polypeptide encoded by any one of the fragments of
the Staphylococcus aureus genome of SEQ ID NOS: 1-5,191 and
depicted in Tables 2 and 3.
5. An antibody which specifically binds the polypeptide of claim
4.
6. An isolated polynucleotide encoding the polypeptide of claim
4.
7. A vector comprising the polynucleotide of claim 6.
8. An organism which has been altered to contain the polynucleotide
of claim 6.
9. A method for producing a polypeptide in a host cell comprising
the steps of: (a) incubating a host containing a heterologous
nucleic acid molecule whose nucleotide sequence consists of the
polynucleotide of claim 6 under conditions where said heterologous
nucleic acid molecule is expressed to produce said polypeptide, and
(b) isolating said polypeptide.
10. An isolated polypeptide comprising an amino acid sequence
identical to a Staphylococcus aureus polypeptide amino acid
sequence selected from the group consisting of SEQ ID NOS: 5,192 to
5,255.
Description
CROSS REFERENCE TO RELATED APPLICATIONS
[0001] This application is a divisional of and claims priority
under 35 U.S.C. .sctn. 120 to U.S. application Ser. No. 08/956,171,
filed Oct. 20, 1997, which is a continuation-in-part of and claims
priority under 35 U.S.C. .sctn. 120 to U.S. application Ser. No.
08/781,986, filed Jan. 3, 1997, which is a non-provisional of and
claims benefit under 35 U.S.C. .sctn. 119(e) of U.S. Provisional
Application No. 60/009,861, filed Jan. 5, 1996.
REFERENCE TO A SEQUENCE LISTING PROVIDED ON COMPACT DISC
[0002] This application refers to a "Sequence Listing", which is
provided as an electronic document on two identical compact discs
(CD-R), labeled "Copy 1" and "Copy 2." These compact discs each
contain the electronic document, filename "PB248P1D1 sequence
listing.txt" (6,143,385 bytes in size, created on Dec. 23, 2002),
which is hereby incorporated in its entirety herein.
FIELD OF THE INVENTION
[0003] The present invention relates to the field of molecular
biology. In particular, it relates to, among other things,
nucleotide sequences of Staphylococcus aureus, contigs, ORFs,
fragments, probes, primers and related polynucleotides thereof,
peptides and polypeptides encoded by the sequences, and uses of the
polynucleotides and sequences thereof, such as in fermentation,
polypeptide production, assays and pharmaceutical development,
among others.
BACKGROUND OF THE INVENTION
[0004] The genus Staphylococcus includes at least 20 distinct
species. (For a review see Novick, R. P., The Staphylococcus as a
Molecular Genetic System, Chapter 1, pgs. 1-37 in MOLECULAR BIOLOGY
OF THE STAPHYLOCOCCI, R. Novick, Ed., VCH Publishers, New York
(1990)). Species differ from one another by 80% or more, by
hybridization kinetics, whereas strains within a species are at
least 90% identical by the same measure.
[0005] The species Staphylococcus aureus, a gram-positive,
facultatively aerobic, clump-forming cocci, is among the most
important etiological agents of bacterial infection in humans, as
discussed briefly below.
[0006] Human Health and S. Aureus
[0007] Staphylococcus aureus is a ubiquitous pathogen. (See, for
instance, Mims et al., MEDICAL MICROBIOLOGY, Mosby-Year Book Europe
Limited, London, UK (1993)). It is an etiological agent of a
variety of conditions, ranging in severity from mild to fatal. A
few of the more common conditions caused by S. aureus infection are
bums, cellulitis, eyelid infections, food poisoning, joint
infections, neonatal conjunctivitis, osteomyelitis, skin
infections, surgical wound infection, scalded skin syndrome and
toxic shock syndrome, some of which are described further
below.
[0008] Burns
[0009] Burn wounds generally are sterile initially. However, they
generally compromise physical and immune barriers to infection,
cause loss of fluid and electrolytes and result in local or general
physiological dysfunction. After cooling, contact with viable
bacteria results in mixed colonization at the injury site.
Infection may be restricted to the non-viable debris on the bum
surface ("eschar"), it may progress into full skin infection and
invade viable tissue below the eschar and it may reach below the
skin, enter the lymphatic and blood circulation and develop into
septicemia. S. aureus is among the most important pathogens
typically found in burn wound infections. It can destroy
granulation tissue and produce severe septicemia.
[0010] Cellulitis
[0011] Cellulitis, an acute infection of the skin that expands from
a typically superficial origin to spread below the cutaneous layer,
most commonly is caused by S. aureus in conjunction with S.
pyrogenes. Cellulitis can lead to systemic infection. In fact,
cellulitis can be one aspect of synergistic bacterial gangrene.
This condition typically is caused by a mixture of S. aureus and
microaerophilic streptococci. It causes necrosis and treatment is
limited to excision of the necrotic tissue. The condition often is
fatal.
[0012] Eyelid Infections
[0013] S. aureus is the cause of styes and of sticky eye" in
neonates, among other eye infections. Typically such infections are
limited to the surface of the eye, and may occasionally penetrate
the surface with more severe consequences.
[0014] Food Poisoning
[0015] Some strains of S. aureus produce one or more of five
serologically distinct, heat and acid stable enterotoxins that are
not destroyed by digestive process of the stomach and small
intestine (enterotoxins A-E). Ingestion of the toxin, in sufficient
quantities, typically results in severe vomiting, but not diarrhea.
The effect does not require viable bacteria. Although the toxins
are known, their mechanism of action is not understood.
[0016] Joint Infections
[0017] S. aureus infects bone joints causing diseases such
osteomyelitis.
[0018] Osteomyelitis
[0019] S. aureus is the most common causative agent of
haematogenous osteomyelitis. The disease tends to occur in children
and adolescents more than adults and it is associated with
non-penetrating injuries to bones. Infection typically occurs in
the long end of growing bone, hence its occurrence in physically
immature populations. Most often, infection is localized in the
vicinity of sprouting capillary loops adjacent to epiphysial growth
plates in the end of long, growing bones.
[0020] Skin Infections
[0021] S. aureus is the most common pathogen of such minor skin
infections as abscesses and boils. Such infections often are
resolved by normal host response mechanisms, but they also can
develop into severe internal infections. Recurrent infections of
the nasal passages plague nasal carriers of S. aureus.
[0022] Surgical Wound Infections
[0023] Surgical wounds often penetrate far into the body. Infection
of such wound thus poses a grave risk to the patient. S. aureus is
the most important causative agent of infections in surgical
wounds. S. aureus is unusually adept at invading surgical wounds;
sutured wounds can be infected by far fewer S. aureus cells then
are necessary to cause infection in normal skin. Invasion of
surgical wound can lead to severe S. aureus septicemia. Invasion of
the blood stream by S. aureus can lead to seeding and infection of
internal organs, particularly heart valves and bone, causing
systemic diseases, such as endocarditis and osteomyelitis.
[0024] Scalded Skin Syndrome
[0025] S. aureus is responsible for "scalded skin syndrome" (also
called toxic epidermal necrosis, Ritter's disease and Lyell's
disease). This diseases occurs in older children, typically in
outbreaks caused by flowering of S. aureus strains produce
exfoliation (also called scalded skin syndrome toxin). Although the
bacteria initially may infect only a minor lesion, the toxin
destroys intercellular connections, spreads epidermal layers and
allows the infection to penetrate the outer layer of the skin,
producing the desquamiation that typifies the diseases. Shedding of
the outer layer of skin generally reveals normal skin below, but
fluid lost in the process can produce severe injury in young
children if it is not treated properly.
[0026] Toxic Shock Syndrome
[0027] Toxic shock syndrome is caused by strains of S. aureus that
produce the so-called toxic shock syndrome toxin. The disease can
be caused by S. aureus infection at any site, but it is too often
erroneously viewed exclusively as a disease solely of women who use
tampons. The disease involves toxaemia and septicemia, and can be
fatal.
[0028] Nocosomial Infections
[0029] In the 1984 National Nocosomial Infection Surveillance Study
("NNIS") S. aureus was the most prevalent agent of surgical wound
infections in many hospital services, including medicine, surgery,
obstetrics, pediatrics and newborns.
[0030] Resistance to Drugs of S. aureus Strains
[0031] Prior to the introduction of penicillin the prognosis for
patients seriously infected with S. aureus was unfavorable.
Following the introduction of penicillin in the early 1940s even
the worst S. aureus infections generally could be treated
successfully. The emergence of penicillin-resistant strains of S.
aureus did not take long, however. Most strains of S. aureus
encountered in hospital infections today do not respond to
penicillin; although, fortunately, this is not the case for S.
aureus encountered in community infections.
[0032] It is well known now that penicillin-resistant strains of S.
aureus produce a lactamase which converts penicillin to
pencillinoic acid, and thereby destroys antibiotic activity.
Furthermore, the lactamase gene often is propagated episomally,
typically on a plasmid, and often is only one of several genes on
an episomal element that, together, confer multidrug
resistance.
[0033] Methicillins, introduced in the 1960s, largely overcame the
problem of penicillin resistance in S. aureus. These compounds
conserve the portions of penicillin responsible for antibiotic
activity and modify or alter other portions that make penicillin a
good substrate for inactivating lactamases. However, methicillin
resistance has emerged in S. aureus, along with resistance to many
other antibiotics effective against this organism, including
aminoglycosides, tetracycline, chloramphenicol, macrolides and
lincosamides. In fact, methicillin-resistant strains of S. aureus
generally are multiply drug resistant.
[0034] The molecular genetics of most types of drug resistance in
S. aureus has been elucidated (See Lyon et al., Microbiology
Reviews 51: 88-134 (1987)). Generally, resistance is mediated by
plasmids, as noted above regarding penicillin resistance; however,
several stable forms of drug resistance have been observed that
apparently involve integration of a resistance element into the S.
aureus genome itself.
[0035] Thus far each new antibiotic gives rise to resistance
strains, stains emerge that are resistance to multiple drugs and
increasingly persistent forms of resistance begin to emerge. Drug
resistance of S. aureus infections already poses significant
treatment difficulties, which are likely to get much worse unless
new therapeutic agents are developed.
[0036] Molecular Genetics of Staphylococcus Aureus
[0037] Despite its importance in, among other things, human
disease, relatively little is known about the genome of this
organism.
[0038] Most genetic studies of S. aureus have been carried out
using the strain NCTC8325, which contains prophages psi11, psi12
and psi13, and the UV-cured derivative of this strain, 8325-4 (also
referred to as RN450), which is free of the prophages.
[0039] These studies revealed that the S. aureus genome, like that
of other staphylococci, consists of one circular, covalently
closed, double-stranded DNA and a collection of so-called variable
accessory genetic elements, such as prophages, plasmids,
transposons and the like.
[0040] Physical characterization of the genome has not been carried
out in any detail. Pattee et al. published a low resolution and
incomplete genetic and physical map of the chromosome of S. aureus
strain NCTC 8325. (Pattee et al. Genetic and Physical Mapping of
Chromosome of Staphylococcus aureus NCTC 8325, Chapter 11, pgs.
163-169 in MOLECULAR BIOLOGY OF THE STAPHYLOCOCCI, R. P. Novick,
Ed., VCH Publishers, New York, (1990) The genetic map largely was
produced by mapping insertions of Tn551 and Tn4001, which,
respectively, confer erythromycin and gentamicin resistance, and by
analysis of SmaI-digested DNA by Pulsed Field Gel Electrophoresis
("PFGE").
[0041] The map was of low resolution; even estimating the physical
size of the genome was difficult, according to the investigators.
The size of the largest SmaI chromosome fragment, for instance, was
too large for accurate sizing by PFGE. To estimate its size,
additional restriction sites had to be introduced into the
chromosome using a transposon containing a SmaI recognition
sequence.
[0042] In sum, most physical characteristics and almost all of the
genes of Staphylococcus aureus are unknown. Among the few genes
that have been identified, most have not been physically mapped or
characterized in detail. Only a very few genes of this organism
have been sequenced. (See, for instance Thomsberry, J.,
Antimicrobial Chemotherapy 21 Suppl C: 9-16 (1988), current
versions of GENBANK and other nucleic acid databases, and
references that relate to the genome of S. aureus such as those set
out elsewhere herein.)
[0043] It is clear that the etiology of diseases mediated or
exacerbated by S. aureus infection involves the programmed
expression of S. aureus genes, and that characterizing the genes
and their patterns of expression would add dramatically to our
understanding of the organism and its host interactions. Knowledge
of S. aureus genes and genomic organization would dramatically
improve understanding of disease etiology and lead to improved and
new ways of-preventing, ameliorating, arresting and reversing
diseases. Moreover, characterized genes and genomic fragments of S.
aureus would provide reagents for, among other things, detecting,
characterizing and controlling S. aureus infections. There is a
need therefore to characterize the genome of S. aureus and for
polynucleotides and sequences of this organism.
SUMMARY OF THE INVENTION
[0044] The present invention is based on the sequencing of
fragments of the Staphylococcus aureus genome. The primary
nucleotide sequences which were generated are provided in SEQ ID
NOS: 1-5,191.
[0045] The present invention provides the nucleotide sequence of
several thousand contigs of the Staphylococcus aureus genome, which
are listed in tables below and set out in the Sequence Listing
submitted herewith, and representative fragments thereof, in a form
which can be readily used, analyzed, and interpreted by a skilled
artisan. In one embodiment, the present invention is provided as
contiguous strings of primary sequence information corresponding to
the nucleotide sequences depicted in SEQ ID NOS: 1-5,191.
[0046] The present invention further provides nucleotide sequences
which are at least 95% identical to the nucleotide sequences of SEQ
ID NOS: 1-5,191.
[0047] The nucleotide sequence of SEQ ID NOS: 1-5,191, a
representative fragment thereof, or a nucleotide sequence which is
at least 95% identical to the nucleotide sequence of SEQ ID NOS:
1-5,191 may be provided in a variety of mediums to facilitate its
use. In one application of this embodiment, the sequences of the
present invention are recorded on computer readable media. Such
media includes, but is not limited to: magnetic storage media, such
as floppy discs, hard disc storage medium, and magnetic tape;
optical storage media such as CD-ROM; electrical storage media such
as RAM and ROM; and hybrids of these categories such as
magnetic/optical storage media.
[0048] The present invention further provides systems, particularly
computer-based systems which contain the sequence information
herein described stored in a data storage means. Such systems are
designed to identify commercially important fragments of the
Staphylococcus aureus genome.
[0049] Another embodiment of the present invention is directed to
fragments of the Staphylococcus aureus genome having particular
structural or functional attributes. Such fragments of the
Staphylococcus aureus genome of the present invention include, but
are not limited to, fragments which encode peptides, hereinafter
referred to as open reading frames or ORFs," fragments which
modulate the expression of an operably linked ORF, hereinafter
referred to as expression modulating fragments or EMFs," and
fragments which can be used to diagnose the presence of
Staphylococcus aureus in a sample, hereinafter referred to as
diagnostic fragments or "DFs."
[0050] Each of the ORFs in fragments of the Staphylococcus aureus
genome disclosed in Tables 1-3, and the EMFs found 5' to the ORFs,
can be used in numerous ways as polynucleotide reagents. For
instance, the sequences can be used as diagnostic probes or
amplification primers for detecting or determining the presence of
a specific microbe in a sample, to selectively control gene
expression in a host and in the production of polypeptides, such as
polypeptides encoded by ORFs of the present invention, particular
those polypeptides that have a pharmacological activity.
[0051] The present invention further includes recombinant
constructs comprising one or more fragments of the Staphylococcus
aureus genome of the present invention. The recombinant constructs
of the present invention comprise vectors, such as a plasmid or
viral vector, into which a fragment of the Staphylococcus aureus
has been inserted.
[0052] The present invention further provides host cells containing
any of the isolated fragments of the Staphylococcus aureus genome
of the present invention. The host cells can be a higher eukaryotic
host cell, such as a mammalian cell, a lower eukaryotic cell, such
as a yeast cell, or a procaryotic cell such as a bacterial
cell.
[0053] The present invention is further directed to isolated
polypeptides and proteins encoded by ORFs of the present invention.
A variety of methods, well known to those of skill in the art,
routinely may be utilized to obtain any of the polypeptides and
proteins of the present invention. For instance, polypeptides and
proteins of the present invention having relatively short, simple
amino acid sequences readily can be synthesized using commercially
available automated peptide synthesizers. Polypeptides and proteins
of the present invention also may be purified from bacterial cells
which naturally produce the protein. Yet another alternative is to
purify polypeptide and proteins of the present invention from cells
which have been altered to express them.
[0054] The invention further provides polypeptides comprising
Staphylococcus aureus epitopes and vaccine compositions comprising
such polypeptides. Also provided are methods for vaccinating an
individual against Staphylococcus aureus infection.
[0055] The invention further provides methods of obtaining homologs
of the fragments of the Staphylococcus aureus genome of the present
invention and homologs of the proteins encoded by the ORFs of the
present invention. Specifically, by using the nucleotide and amino
acid sequences disclosed herein as a probe or as primers, and
techniques such as PCR cloning and colony/plaque hybridization, one
skilled in the art can obtain homologs.
[0056] The invention further provides antibodies which selectively
bind polypeptides and proteins of the present invention. Such
antibodies include both monoclonal and polyclonal antibodies.
[0057] The invention further provides hybridomas which produce the
above-described antibodies. A hybridoma is an immortalized cell
line which is capable of secreting a specific monoclonal
antibody.
[0058] The present invention further provides methods of
identifying test samples derived from cells which express one of
the ORFs of the present invention, or a homolog thereof. Such
methods comprise incubating a test sample with one or more of the
antibodies of the present invention, or one or more of the Dfs or
antigens of the present invention, under conditions which allow a
skilled artisan to determine if the sample contains the ORF or
product produced therefrom.
[0059] In another embodiment of the present invention, kits are
provided which contain the necessary reagents to carry out the
above-described assays.
[0060] Specifically, the invention provides a compartmentalized kit
to receive, in close confinement, one or more containers which
comprises: (a) a first container comprising one of the antibodies,
antigens, or one of the DFs of the present invention; and (b) one
or more other containers comprising one or more of the following:
wash reagents, reagents capable of detecting presence of bound
antibodies, antigens or hybridized DFs.
[0061] Using the isolated proteins of the present invention, the
present invention further provides methods of obtaining and
identifying agents capable of binding to a polypeptide or protein
encoded by one of the ORFs of the present invention. Specifically,
such agents include, as further described below, antibodies,
peptides, carbohydrates, pharmaceutical agents and the like. Such
methods comprise steps of: (a)contacting an agent with an isolated
protein encoded by one of the ORFs of the present invention; and
(b)determining whether the agent binds to said protein.
[0062] The present genomic sequences of Staphylococcus aureus will
be of great value to all laboratories working with this organism
and for a variety of commercial purposes. Many fragments of the
Staphylococcus aureus genome will be immediately identified by
similarity searches against GenBank or protein databases and will
be of immediate value to Staphylococcus aureus researchers and for
immediate commercial value for the production of proteins or to
control gene expression.
[0063] The methodology and technology for elucidating extensive
genomic sequences of bacterial and other genomes has and will
greatly enhance the ability to analyze and understand chromosomal
organization. In particular, sequenced contigs and genomes will
provide the models for developing tools for the analysis of
chromosome structure and function, including the ability to
identify genes within large segments of genomic DNA, the structure,
position, and spacing of regulatory elements, the identification of
genes with potential industrial applications, and the ability to do
comparative genomic and molecular phylogeny.
BRIEF DESCRIPTION OF THE DRAWINGS
[0064] FIG. 1 is a block diagram of a computer system (102) that
can be used to implement computer-based systems of present
invention.
[0065] FIG. 2 is a schematic diagram depicting the data flow and
computer programs used to collect, assemble, edit and annotate the
contigs of the Staphylococcus aureus genome of the present
invention. Both Macintosh and Unix platforms are used to handle the
AB 373 and 377 sequence data files, largely as described in
Kerlavage et al., Proceedings of the Twenty-Sixth Annual Hawaii
International Conference on System Sciences, 585, IEEE Computer
Society Press, Wash. D.C. (1993). Factura (AB) is a Macintosh
program designed for automatic vector sequence removal and
end-trimming of sequence files. The program Loadis runs on a
Macintosh platform and parses the feature data extracted from the
sequence files by Factura to the Unix based Staphylococcus aureus
relational database. Assembly of contigs (and whole genome
sequences) is accomplished by retrieving a specific set of sequence
files and their associated features using extrseq, a Unix utility
for retrieving sequences from an SQL database. The resulting
sequence file is processed by seq_filter to trim portions of the
sequences with more than 2% ambiguous nucleotides. The sequence
files were assembled using TIGR Assembler, an assembly engine
designed at The Institute for Genomic Research (TIGR") for rapid
and accurate assembly of thousands of sequence fragments. The
collection of contigs generated by the assembly step is loaded into
the database with the lassie program. Identification of open
reading frames (ORFs) is accomplished by processing contigs with
zorf. The ORFs are searched against S. aureus sequences from
Genbank and against all protein sequences using the BLASTN and
BLASTP programs, described in Altschul et al., J. Mol. Biol. 215:
403-410 (1990)). Results of the ORF determination and similarity
searching steps were loaded into the database. As described below,
some results of the determination and the searches are set out in
Tables 1-3.
DETAILED DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS
[0066] The present invention is based on the sequencing of
fragments of the Staphylococcus aureus genome and analysis of the
sequences. The primary nucleotide sequences generated by sequencing
the fragments are provided in SEQ ID NOS: 1-5,191. (As used herein,
the "primary sequence" refers to the nucleotide sequence
represented by the IUPAC nomenclature system.)
[0067] In addition to the aforementioned Staphylococcus aureus
polynucleotide and polynucleotide sequences, the present invention
provides the nucleotide sequences of SEQ ID NOS: 1-5,191, or
representative fragments thereof, in a form which can be readily
used, analyzed, and interpreted by a skilled artisan.
[0068] As used herein, a "representative fragment of the nucleotide
sequence depicted in SEQ ID NOS: 1-5,191" refers to any portion of
the SEQ ID NOS: 1-5,191 which is not presently represented within a
publicly available database. Preferred representative fragments of
the present invention are Staphylococcus aureus open reading frames
(ORFS"), expression modulating fragment (EMFs") and fragments which
can be used to diagnose the presence of Staphylococcus aureus in
sample ("DFs"). A non-limiting identification of preferred
representative fragments is provided in Tables 1-3.
[0069] As discussed in detail below, the information provided in
SEQ ID NOS: 1-5,191 and in Tables 1-3 together with routine
cloning, synthesis, sequencing and assay methods will enable those
skilled in the art to clone and sequence all "representative
fragments" of interest, including open reading frames encoding a
large variety of Staphylococcus aureus proteins.
[0070] While the presently disclosed sequences of SEQ ID NOS:
1-5,191 are highly accurate, sequencing techniques are not perfect
and, in relatively rare instances, further investigation of a
fragment or sequence of the invention may reveal a nucleotide
sequence error present in a nucleotide sequence disclosed in SEQ ID
NOS: 1-5,191. However, once the present invention is made available
(i.e., once the information in SEQ ID NOS: 1-5,191 and Tables 1-3
has been made available), resolving a rare sequencing error in SEQ
ID NOS: 1-5,191 will be well within the skill of the art. The
present disclosure makes available sufficient sequence information
to allow any of the described contigs or portions thereof to be
obtained readily by straightforward application of routine
techniques. Further sequencing of such polynucleotide may proceed
in like manner using manual and automated sequencing methods which
are employed ubiquitous in the art. Nucleotide sequence editing
software is publicly available. For example, Applied Biosystem's
(AB) AutoAssembler can be used as an aid during visual inspection
of nucleotide sequences. By employing such routine techniques
potential errors readily may be identified and the correct sequence
then may be ascertained by targeting further sequencing effort,
also of a routine nature, to the region containing the potential
error.
[0071] Even if all of the very rare sequencing errors in SEQ ID
NOS: 1-5,191 were corrected, the resulting nucleotide sequences
would still be at least 95% identical, nearly all would be at least
99% identical, and the great majority would be at least 99.9%
identical to the nucleotide sequences of SEQ ID NOS: 1-5,191.
[0072] As discussed elsewhere herein, polynucleotides of the
present invention readily may be obtained by routine application of
well known and standard procedures for cloning and sequencing DNA.
Detailed methods for obtaining libraries and for sequencing are
provided below, for instance. A wide variety of Staphylococcus
aureus strains that can be used to prepare S aureus genomic DNA for
cloning and for obtaining polynucleotides of the present invention
are available to the public from recognized depository
institutions, such as the American Type Culture Collection
(ATCC").
[0073] The nucleotide sequences of the genomes from different
strains of Staphylococcus aureus differ somewhat. However, the
nucleotide sequences of the genomes of all Staphylococcus aureus
strains will be at least 95% identical, in corresponding part, to
the nucleotide sequences provided in SEQ ID NOS: 1-5,191. Nearly
all will be at least 99% identical and the great majority will be
99.9% identical.
[0074] Thus, the present invention further provides nucleotide
sequences which are at least 95%, preferably 99% and most
preferably 99.9% identical to the nucleotide sequences of SEQ ID
NOS: 1-5,191, in a form which can be readily used, analyzed and
interpreted by the skilled artisan.
[0075] Methods for determining whether a nucleotide sequence is at
least 95%, at least 99% or at least 99.9% identical to the
nucleotide sequences of SEQ ID NOS: 1-5,191 are routine and readily
available to the skilled artisan. For example, the well known fasta
algorithm described in Pearson and Lipman, Proc. Natl. Acad. Sci.
USA 85: 2444 (1988) can be used to generate the percent identity of
nucleotide sequences. The
[0076] BLASTN program also can be used to generate an identity
score of polynucleotides compared to one another.
COMPUTER RELATED EMBODIMENTS
[0077] The nucleotide sequences provided in SEQ ID NOS: 1-5,191, a
representative fragment thereof, or a nucleotide sequence at least
95%, preferably at least 96%, 97%, 98% or 99% and most preferably
at least 99.9% identical to a polynucleotide sequence of SEQ ID
NOS: 1-5,191 may be "provided" in a variety of mediums to
facilitate use thereof. As used herein, "provided" refers to a
manufacture, other than an isolated nucleic acid molecule, which
contains a nucleotide sequence of the present invention; i.e., a
nucleotide sequence provided in SEQ ID NOS: 1-5,191, a
representative fragment thereof, or a nucleotide sequence at least
95%, preferably at least 96%, 97%, 98% or 99% and most preferably
at least 99.9% identical to a polynucleotide of SEQ ID NOS:
1-5,191. Such a manufacture provides a large portion of the
Staphylococcus aureus genome and parts thereof (e.g., a
Staphylococcus aureus open reading frame (ORF)) in a form which
allows a skilled artisan to examine the manufacture using means not
directly applicable to examining the Staphylococcus aureus genome
or a subset thereof as it exists in nature or in purified form.
[0078] In one application of this embodiment, a nucleotide sequence
of the present invention can be recorded on computer readable
media. As used herein, "computer readable media" refers to any
medium which can be read and accessed directly by a computer. Such
media include, but are not limited to: magnetic storage media, such
as floppy discs, hard disc storage medium, and magnetic tape;
optical storage media such as CD-ROM; electrical storage media such
as RAM and ROM; and hybrids of these categories, such as
magnetic/optical storage media. A skilled artisan can readily
appreciate how any of the presently known computer readable mediums
can be used to create a manufacture comprising computer readable
medium having recorded thereon a nucleotide sequence of the present
invention. Likewise, it will be clear to those of skill how
additional computer readable media that may be developed also can
be used to create analogous manufactures having recorded thereon a
nucleotide sequence of the present invention.
[0079] As used herein, "recorded" refers to a process for storing
information on computer readable medium. A skilled artisan can
readily adopt any of the presently know methods for recording
information on computer readable medium to generate manufactures
comprising the nucleotide sequence information of the present
invention.
[0080] A variety of data storage structures are available to a
skilled artisan for creating a computer readable medium having
recorded thereon a nucleotide sequence of the present invention.
The choice of the data storage structure will generally be based on
the means chosen to access the stored information. In addition, a
variety of data processor programs and formats can be used to store
the nucleotide sequence information of the present invention on
computer readable medium. The sequence information can be
represented in a word processing text file, formatted in
commercially-available software such as WordPerfect and MicroSoft
Word, or represented in the form of an ASCII file, stored in a
database application, such as DB2, Sybase, Oracle, or the like. A
skilled artisan can readily adapt any number of data-processor
structuring formats (e.g., text file or database) in order to
obtain computer readable medium having recorded thereon the
nucleotide sequence information of the present invention.
[0081] Computer software is publicly available which allows a
skilled artisan to access sequence information provided in a
computer readable medium. Thus, by providing in computer readable
form the nucleotide sequences of SEQ ID NOS: 1-5,191, a
representative fragment thereof, or a nucleotide sequence at least
95%, preferably at least 96%, 97%, 98% or 99% and most preferably
at least 99.9% identical to a sequence of SEQ ID NOS: 1-5,191 the
present invention enables the skilled artisan routinely to access
the provided sequence information for a wide variety of
purposes.
[0082] The examples which follow demonstrate how software which
implements the BLAST (Altschul et al., J. Mol. Biol. 215:403-410
(1990)) and BLAZE (Brutlag et al., Comp. Chem. 17:203-207 (1993))
search algorithms on a Sybase system was used to identify open
reading frames (ORFs) within the Staphylococcus aureus genome which
contain homology to ORFs or proteins from both Staphylococcus
aureus and from other organisms. Among the ORFs discussed herein
are protein encoding fragments of the Staphylococcus aureus genome
useful in producing commercially important proteins, such as
enzymes used in fermentation reactions and in the production of
commercially useful metabolites.
[0083] The present invention further provides systems, particularly
computer-based systems, which contain the sequence information
described herein. Such systems are designed to identify, among
other things, commercially important fragments of the
Staphylococcus aureus genome.
[0084] As used herein, "a computer-based system" refers to the
hardware means, software means, and data storage means used to
analyze the nucleotide sequence information of the present
invention. The minimum hardware means of the computer-based systems
of the present invention comprises a central processing unit (CPU),
input means, output means, and data storage means. A skilled
artisan can readily appreciate that any one of the currently
available computer-based system are suitable for use in the present
invention.
[0085] As stated above, the computer-based systems of the present
invention comprise a data storage means having stored therein a
nucleotide sequence of the present invention and the necessary
hardware means and software means for supporting and implementing a
search means.
[0086] As used herein, "data storage means" refers to memory which
can store nucleotide sequence information of the present invention,
or a memory access means which can access manufactures having
recorded thereon the nucleotide sequence information of the present
invention.
[0087] As used herein, "search means" refers to one or more
programs which are implemented on the computer- based system to
compare a target sequence or target structural motif with the
sequence information stored within the data storage means. Search
means are used to identify fragments or regions of the present
genomic sequences which match a particular target sequence or
target motif. A variety of known algorithms are disclosed publicly
and a variety of commercially available software for conducting
search means are and can be used in the computer-based systems of
the present invention. Examples of such software includes, but is
not limited to, MacPattern (EMBL), BLASTN and BLASTX (NCBIA). A
skilled artisan can readily recognize that any one of the available
algorithms or implementing software packages for conducting
homology searches can be adapted for use in the present
computer-based systems.
[0088] As used herein, a "target sequence" can be any DNA or amino
acid sequence of six or more nucleotides or two or more amino
acids. A skilled artisan can readily recognize that the longer a
target sequence is, the less likely a target sequence will be
present as a random occurrence in the database. The most preferred
sequence length of a target sequence is from about 10 to 100 amino
acids or from about 30 to 300 nucleotide residues. However, it is
well recognized that searches for commercially important fragments,
such as sequence fragments involved in gene expression and protein
processing, may be of shorter length.
[0089] As used herein, "a target structural motif," or "target
motif," refers to any rationally selected sequence or combination
of sequences in which the sequence(s) are chosen based on a
three-dimensional configuration which is formed upon the folding of
the target motif. There are a variety of target motifs known in the
art. Protein target motifs include, but are not limited to,
enzymatic active sites and signal sequences. Nucleic acid target
motifs include, but are not limited to, promoter sequences, hairpin
structures and inducible expression elements (protein binding
sequences).
[0090] A variety of structural formats for the input and output
means can be used to input and output the information in the
computer-based systems of the present invention. A preferred format
for an output means ranks fragments of the Staphylococcus aureus
genomic sequences possessing varying degrees of homology to the
target sequence or target motif. Such presentation provides a
skilled artisan with a ranking of sequences which contain various
amounts of the target sequence or target motif and identifies the
degree of homology contained in the identified fragment.
[0091] A variety of comparing means can be used to compare a target
sequence or target motif with the data storage means to identify
sequence fragments of the Staphylococcus aureus genome. In the
present examples, implementing software which implement the BLAST
and BLAZE algorithms, described in Altschul et al., J. Mol. Biol.
215: 403-410 (1990), was used to identify open reading frames
within the Staphylococcus aureus genome. A skilled artisan can
readily recognize that any one of the publicly available homology
search programs can be used as the search means for the
computer-based systems of the present invention. Of course,
suitable proprietary systems that may be known to those of skill
also may be employed in this regard.
[0092] FIG. 1 provides a block diagram of a computer system
illustrative of embodiments of this aspect of present invention.
The computer system 102 includes a processor 106 connected to a bus
104. Also connected to the bus 104 are a main memory 108
(preferably implemented as random access memory, RAM) and a variety
of secondary storage devices 110, such as a hard drive 112 and a
removable medium storage device 114. The removable medium storage
device 114 may represent, for example, a floppy disk drive, a
CD-ROM drive, a magnetic tape drive, etc. A removable storage
medium 116 (such as a floppy disk, a compact disk, a magnetic tape,
etc.) containing control logic and/or data recorded therein may be
inserted into the removable medium storage device 114. The computer
system 102 includes appropriate software for reading the control
logic and/or the data from the removable medium storage device 114,
once it is inserted into the removable medium storage device
114.
[0093] A nucleotide sequence of the present invention may be stored
in a well known manner in the main memory 108, any of the secondary
storage devices 110, and/or a removable storage medium 116. During
execution, software for accessing and processing the genomic
sequence (such as search tools, comparing tools, etc.) reside in
main memory 108, in accordance with the requirements and operating
parameters of the operating system, the hardware system and the
software program or programs.
BIOCHEMICAL EMBODIMENTS
[0094] Other embodiments of the present invention are directed to
isolated fragments of the Staphylococcus aureus genome. The
fragments of the Staphylococcus aureus genome of the present
invention include, but are not limited to fragments which encode
peptides, hereinafter open reading frames (ORFs), fragments which
modulate the expression of an operably linked ORF, hereinafter
expression modulating fragments (EMFs) and fragments which can be
used to diagnose the presence of Staphylococcus aureus in a sample,
hereinafter diagnostic fragments (DFs).
[0095] As used herein, an "isolated nucleic acid molecule" or an
"isolated fragment of the Staphylococcus aureus genome" refers to a
nucleic acid molecule possessing a specific nucleotide sequence
which has been subjected to purification means to reduce, from the
composition, the number of compounds which are normally associated
with the composition. Particularly, the term refers to the nucleic
acid molecules having the sequences set out in SEQ ID NOS: 1-5,191,
to representative fragments thereof as described above, to
polynucleotides at least 95%, preferably at least 96%, 97%, 98% or
99% and especially preferably at least 99.9% identical in sequence
thereto, also as set out above.
[0096] A variety of purification means can be used to generated the
isolated fragments of the present invention. These include, but are
not limited to methods which separate constituents of a solution
based on charge, solubility, or size.
[0097] In one embodiment, Staphylococcus aureus DNA can be
mechanically sheared to produce fragments of 15-20 kb in length.
These fragments can then be used to generate an Staphylococcus
aureus library by inserting them into lambda clones as described in
the Examples below. Primers flanking, for example, an ORF, such as
those enumerated in Tables 1-3 can then be generated using
nucleotide sequence information provided in SEQ ID NOS: 1-5,191.
Well known and routine techniques of PCR cloning then can be used
to isolate the ORF from the lambda DNA library of Staphylococcus
aureus genomic DNA. Thus, given the availability of SEQ ID NOS:
1-5,191, the information in Tables 1, 2 and 3, and the information
that may be obtained readily by analysis of the sequences of SEQ ID
NOS: 1-5,191 using methods set out above, those of skill will be
enabled by the present disclosure to isolate any ORF-containing or
other nucleic acid fragment of the present invention.
[0098] The isolated nucleic acid molecules of the present invention
include, but are not limited to single stranded and double stranded
DNA, and single stranded RNA.
[0099] As used herein, an "open reading frame," ORF, means a series
of triplets coding for amino acids without any termination codons
and is a sequence translatable into protein.
[0100] Tables 1, 2 and 3 list ORFs in the Staphylococcus aureus
genomic contigs of the present invention that were identified as
putative coding regions by the GeneMark software using
organism-specific second-order Markov probability transition
matrices. It will be appreciated that other criteria can be used,
in accordance with well known analytical methods, such as those
discussed herein, to generate more inclusive, more restrictive or
more selective lists.
[0101] Table 1 sets out ORFs in the Staphylococcus aureus contigs
of the present invention that are at least 80 amino acids long and
over a continuous region of at least 50 bases which are 95% or more
identical (by BLAST analysis) to an S. aureus nucleotide sequence
available through Genbank in November 1996.
[0102] Table 2 sets out ORFs in the Staphylococcus aureus contigs
of the present invention that are not in Table 1 and match, with a
BLASTP probability score of 0.01 or less, a polypeptide sequence
available through Genbank by September 1996.
[0103] Table 3 sets out ORFs in the Staphylococcus aureus contigs
of the present invention that do not match significantly, by BLASTP
analysis, a polypeptide sequence available through Genbank by
September 1996.
[0104] In each table, the first and second columns identify the ORF
by, respectively, contig number (SEQ ID NO) and ORF number within
the contig; the third column indicates the first nucleotide of the
ORF, counting from the 5' end of the contig strand shown in the
sequence listing; and the fifth column indicates the length of each
ORF in nucleotides. It will be appreciated that some ORFs are
located on the reverse strand. The numbering identifying such ORFs
also represents nucleotide positions counting from the 5' end of
the strand shown in the sequence listing.
[0105] In Tables 1 and 2, column five, lists the "match accession"
for the closest matching sequence available through Genbank. These
reference numbers are the databases entry numbers commonly used by
those of skill in the art, who will be familiar with their
denominators. Descriptions of the nomenclature are available from
the National Center for Biotechnology Information. Column six in
Tables 1 and 2 provides the "gene name" of the matching sequence;
column seven provides the BLAST "similarity"; column eight provides
the BLAST "identity" score from the comparison of the ORF and the
homologous gene; and column nine indicates the length in
nucleotides of the highest scoring "segment pair" identified by the
BLAST identity analysis.
[0106] The concepts of percent identity and percent similarity of
two polypeptide sequences is well understood in the art. For
example, two polypeptides 10 amino acids in length which differ at
three amino acid positions (e.g., at positions 1, 3 and 5) are said
to have a percent identity of 70%. However, the same two
polypeptides would be deemed to have a percent similarity of 80%
if, for example at position 5, the amino acids moieties, although
not identical, were "similar" (i.e., possessed similar biochemical
characteristics). Many programs for analysis of nucleotide or amino
acid sequence similarity, such as fasta and BLAST specifically list
percent identity of a matching region as an output parameter. Thus,
for instance, Tables 1 and 2 herein enumerate the percent identity
"of the highest scoring segment pair" in each ORF and its listed
relative. Further details concerning the algorithms and criteria
used for homology searches are provided below and are described in
the pertinent literature highlighted by the citations provided
below.
[0107] It will be appreciated that other criteria can be used to
generate more inclusive and more exclusive listings of the types
set out in the tables. As those of skill will appreciate, narrow
and broad searches both are useful. Thus, a skilled artisan can
readily identify ORFs in contigs of the Staphylococcus aureus
genome other than those listed in Tables 1-3, such as ORFs which
are overlapping or encoded by the opposite strand of an identified
ORF in addition to those ascertainable using the computer-based
systems of the present invention.
[0108] As used herein, an "expression modulating fragment," EMF,
means a series of nucleotide molecules which modulates the
expression of an operably linked ORF or EMF.
[0109] As used herein, a sequence is said to "modulate the
expression of an operably linked sequence" when the expression of
the sequence is altered by the presence of the EMF. EMFs include,
but are not limited to, promoters, and promoter modulating
sequences (inducible elements). One class of EMFs are fragments
which induce the expression or an operably linked ORF in response
to a specific regulatory factor or physiological event.
[0110] EMF sequences can be identified within the contigs of the
Staphylococcus aureus genome by their proximity to the ORFs
provided in Tables 1-3. An intergenic segment, or a fragment of the
intergenic segment, from about 10 to 200 nucleotides in length,
taken from any one of the ORFs of Tables 1-3 will modulate the
expression of an operably linked ORF in a fashion similar to that
found with the naturally linked ORF sequence. As used herein, an
"intergenic segment" refers to fragments of the Staphylococcus
aureus genome which are between two ORF(s) herein described. EMFs
also can be identified using known EMFs as a target sequence or
target motif in the computer-based systems of the present
invention. Further, the two methods can be combined and used
together.
[0111] The presence and activity of an EMF can be confirmed using
an EMF trap vector. An EMF trap vector contains a cloning site
linked to a marker sequence. A marker sequence encodes an
identifiable phenotype, such as antibiotic resistance or a
complementing nutrition auxotrophic factor, which can be identified
or assayed when the EMF trap vector is placed within an appropriate
host under appropriate conditions. As described above, a EMF will
modulate the expression of an operably linked marker sequence. A
more detailed discussion of various marker sequences is provided
below.
[0112] A sequence which is suspected as being an EMF is cloned in
all three reading frames in one or more restriction sites upstream
from the marker sequence in the EMF trap vector. The vector is then
transformed into an appropriate host using known procedures and the
phenotype of the transformed host in examined under appropriate
conditions. As described above, an EMF will modulate the expression
of an operably linked marker sequence.
[0113] As used herein, a "diagnostic fragment," DF, means a series
of nucleotide molecules which selectively hybridize to
Staphylococcus aureus sequences. DFs can be readily identified by
identifying unique sequences within contigs of the Staphylococcus
aureus genome, such as by using well-known computer analysis
software, and by generating and testing probes or amplification
primers consisting of the DF sequence in an appropriate diagnostic
format which determines amplification or hybridization
selectivity.
[0114] The sequences falling within the scope of the present
invention are not limited to the specific sequences herein
described, but also include allelic and species variations thereof.
Allelic and species variations can be routinely determined by
comparing the sequences provided in SEQ ID NOS: 1-5,191, a
representative fragment thereof, or a nucleotide sequence at least
99% and preferably 99.9% identical to SEQ ID NOS: 1-5,191, with a
sequence from another isolate of the same species.
[0115] Furthermore, to accommodate codon variability, the invention
includes nucleic acid molecules coding for the same amino acid
sequences as do the specific ORFs disclosed herein. In other words,
in the coding region of an ORF, substitution of one codon for
another which encodes the same amino acid is expressly
contemplated.
[0116] Any specific sequence disclosed herein can be readily
screened for errors by resequencing a particular fragment, such as
an ORF, in both directions (i.e., sequence both strands).
Alternatively, error screening can be performed by sequencing
corresponding polynucleotides of Staphylococcus aureus origin
isolated by using part or all of the fragments in question as a
probe or primer.
[0117] Each of the ORFs of the Staphylococcus aureus genome
disclosed in Tables 1, 2 and 3, and the EMFs found 5' to the ORFs,
can be used as polynucleotide reagents in numerous ways. For
example, the sequences can be used as diagnostic probes or
diagnostic amplification primers to detect the presence of a
specific microbe in a sample, particular Staphylococcus aureus.
Especially preferred in this regard are ORF such as those of Table
3, which do not match previously characterized sequences from other
organisms and thus are most likely to be highly selective for
Staphylococcus aureus. Also particularly preferred are ORFs that
can be used to distinguish between strains of Staphylococcus
aureus, particularly those that distinguish medically important
strain, such as drug-resistant strains.
[0118] In addition, the fragments of the present invention, as
broadly described, can be used to control gene expression through
triple helix formation or antisense DNA or RNA, both of which
methods are based on the binding of a polynucleotide sequence to
DNA or RNA. Triple helix-formation optimally results in a shut-off
of RNA transcription from DNA, while antisense RNA hybridization
blocks translation of an mRNA molecule into polypeptide.
Information from the sequences of the present invention can be used
to design antisense and triple helix-forming oligonucleotides.
Polynucleotides suitable for use in these methods are usually 20 to
40 bases in length and are designed to be complementary to a region
of the gene involved in transcription, for triple-helix formation,
or to the mRNA itself, for antisense inhibition. Both techniques
have been demonstrated to be effective in model systems, and the
requisite techniques are well known and involve routine procedures.
Triple helix techniques are discussed in, for example, Lee et al.,
Nucl. Acids Res. 6: 3073 (1979); Cooney et al, Science 241: 456
(1988); and Dervan et al., Science 251: 1360 (1991). Antisense
techniques in general are discussed in, for instance, Okano, J.
Neurochem. 56: 560 (1991) and OLIGODEOXYNUCLEOTIDES AS ANTISENSE
INHIBITORS OF GENE EXPRESSION, CRC Press, Boca Raton, Fla.
(1988)).
[0119] The present invention further provides recombinant
constructs comprising one or more fragments of the Staphylococcus
aureus genomic fragments and contigs of the present invention.
Certain preferred recombinant constructs of the present invention
comprise a vector, such as a plasmid or viral vector, into which a
fragment of the Staphylococcus aureus genome has been inserted, in
a forward or reverse orientation. In the case of a vector
comprising one of the ORFs of the present invention, the vector may
further comprise regulatory sequences, including for example, a
promoter, operably linked to the ORF. For vectors comprising the
EMFs of the present invention, the vector may further comprise a
marker sequence or heterologous ORF operably linked to the EMF.
[0120] Large numbers of suitable vectors and promoters are known to
those of skill in the art and are commercially available for
generating the recombinant constructs of the present invention. The
following vectors are provided by way of example. Useful bacterial
vectors include phagescript, PsiX174, pBluescript SK and KS (+and
-), pNH8a, pNH16a, pNH18a, pNH46a (available from Stratagene);
pTrc99A, pKK223-3, pKK233-3, pDR540, pRIT5 (available from
Pharmacia). Useful eukaryotic vectors include pWLneo, pSV2cat,
pOG44, pXT1, pSG (available from Stratagene) pSVK3, pBPV, pMSG,
pSVL (available from Pharmacia).
[0121] Promoter regions can be selected from any desired gene using
CAT (chloramphenicol transferase) vectors or other vectors with
selectable markers. Two appropriate vectors are pKK232-8 and pCM7.
Particular named bacterial promoters include lacI, lacZ, T3, T7,
gpt, lambda PR, and trc. Eukaryotic promoters include CMV immediate
early, HSV thymidine kinase, early and late SV40, LTRs from
retrovirus, and mouse metallothionein-I. Selection of the
appropriate vector and promoter is well within the level of
ordinary skill in the art.
[0122] The present invention further provides host cells containing
any one of the isolated fragments of the Staphylococcus aureus
genomic fragments and contigs of the present invention, wherein the
fragment has been introduced into the host cell using known
methods. The host cell can be a higher eukaryotic host cell, such
as a mammalian cell, a lower eukaryotic host cell, such as a yeast
cell, or a procaryotic cell, such as a bacterial cell.
[0123] A polynucleotide of the present invention, such as a
recombinant construct comprising an ORF of the present invention,
may be introduced into the host by a variety of well established
techniques that are standard in the art, such as calcium phosphate
transfection, DEAE, dextran mediated transfection and
electroporation, which are described in, for instance, Davis, L. et
al., BASIC METHODS IN MOLECULAR BIOLOGY (1986).
[0124] A host cell containing one of the fragments of the
Staphylococcus aureus genomic fragments and contigs of the present
invention, can be used in conventional manners to produce the gene
product encoded by the isolated fragment (in the case of an ORF) or
can be used to produce a heterologous protein under the control of
the EMF.
[0125] The present invention further provides isolated polypeptides
encoded by the nucleic acid fragments of the present invention or
by degenerate variants of the nucleic acid fragments of the present
invention. By "degenerate variant" is intended nucleotide fragments
which differ from a nucleic acid fragment of the present invention
(e.g., an ORF) by nucleotide sequence but, due to the degeneracy of
the Genetic Code, encode an identical polypeptide sequence.
[0126] Preferred nucleic acid fragments of the present invention
are the ORFs depicted in Tables 2 and 3 which encode proteins.
[0127] A variety of methodologies known in the art can be utilized
to obtain any one of the isolated polypeptides or proteins of the
present invention. At the simplest level, the amino acid sequence
can be synthesized using commercially available peptide
synthesizers. This is particularly useful in producing small
peptides and fragments of larger polypeptides. Such short fragments
as may be obtained most readily by synthesis are useful, for
example, in generating antibodies against the native polypeptide,
as discussed further below.
[0128] In an alternative method, the polypeptide or protein is
purified from bacterial cells which naturally produce the
polypeptide or protein. One skilled in the art can readily employ
well-known methods for isolating polypeptides and proteins to
isolate and purify polypeptides or proteins of the present
invention produced naturally by a bacterial strain, or by other
methods. Methods for isolation and purification that can be
employed in this regard include, but are not limited to,
immunochromatography, HPLC, size-exclusion chromatography,
ion-exchange chromatography, and immuno-affinity
chromatography.
[0129] The polypeptides and proteins of the present invention also
can be purified from cells which have been altered to express the
desired polypeptide or protein. As used herein, a cell is said to
be altered to express a desired polypeptide or protein when the
cell, through genetic manipulation, is made to produce a
polypeptide or protein which it normally does not produce or which
the cell normally produces at a lower level. Those skilled in the
art can readily adapt procedures for introducing and expressing
either recombinant or synthetic sequences into eukaryotic or
prokaryotic cells in order to generate a cell which produces one of
the polypeptides or proteins of the present invention.
[0130] Any host/vector system can be used to express one or more of
the ORFs of the present invention. These include, but are not
limited to, eukaryotic hosts such as HeLa cells, CV-1 cell, COS
cells, and Sf9 cells, as well as prokaryotic host such as E. coli
and B. subtilis. The most preferred cells are those which do not
normally express the particular polypeptide or protein or which
expresses the polypeptide or protein at low natural level.
[0131] "Recombinant," as used herein, means that a polypeptide or
protein is derived from recombinant (e.g., microbial or mammalian)
expression systems. "Microbial" refers to recombinant polypeptides
or proteins made in bacterial or fungal (e.g., yeast) expression
systems. As a product, "recombinant microbial" defines a
polypeptide or protein essentially free of native endogenous
substances and unaccompanied by associated native glycosylation.
Polypeptides or proteins expressed in most bacterial cultures,
e.g., E. coli, will be free of glycosylation modifications;
polypeptides or proteins expressed in yeast will have a
glycosylation pattern different from that expressed in mammalian
cells.
[0132] "Nucleotide sequence" refers to a heteropolymer of
deoxyribonucleotides. Generally, DNA segments encoding the
polypeptides and proteins provided by this invention are assembled
from fragments of the Staphylococcus aureus genome and short
oligonucleotide linkers, or from a series of oligonucleotides, to
provide a synthetic gene which is capable of being expressed in a
recombinant transcriptional unit comprising regulatory elements
derived from a microbial or viral operon.
[0133] "Recombinant expression vehicle or vector" refers to a
plasmid or phage or virus or vector, for expressing a polypeptide
from a DNA (RNA) sequence. The expression vehicle can comprise a
transcriptional unit comprising an assembly of (1) a genetic
regulatory elements necessary for gene expression in the host,
including elements required to initiate and maintain transcription
at a level sufficient for suitable expression of the desired
polypeptide, including, for example, promoters and, where
necessary, an enhancers and a polyadenylation signal; (2) a
structural or coding sequence which is transcribed into mRNA and
translated into protein, and (3) appropriate signals to initiate
translation at the beginning of the desired coding region and
terminate translation at its end. Structural units intended for use
in yeast or eukaryotic expression systems preferably include a
leader sequence enabling extracellular secretion of translated
protein by a host cell. Alternatively, where recombinant protein is
expressed without a leader or transport sequence, it may include an
N-terminal methionine residue. This residue may or may not be
subsequently cleaved from the expressed recombinant protein to
provide a final product.
[0134] "Recombinant expression system" means host cells which have
stably integrated a recombinant transcriptional unit into
chromosomal DNA or carry the recombinant transcriptional unit extra
chromosomally. The cells can be prokaryotic or eukaryotic.
Recombinant expression systems as defined herein will express
heterologous polypeptides or proteins upon induction of the
regulatory elements linked to the DNA segment or synthetic gene to
be expressed.
[0135] Mature proteins can be expressed in mammalian cells, yeast,
bacteria, or other cells under the control of appropriate
promoters. Cell-free translation systems can also be employed to
produce such proteins using RNAs derived from the DNA constructs of
the present invention. Appropriate cloning and expression vectors
for use with prokaryotic and eukaryotic hosts are described in
Sambrook et al., MOLECULAR CLONING:A LABORATORY MANUAL, 2.sup.nd
Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor,
N.Y. (1989), the disclosure of which is hereby incorporated by
reference in its entirety.
[0136] Generally, recombinant expression vectors will include
origins of replication and selectable markers permitting
transformation of the host cell, e.g., the ampicillin resistance
gene of E. coli and S. cerevisiae TRPI gene, and a promoter derived
from a highly expressed gene to direct transcription of a
downstream structural sequence. Such promoters can be derived from
operons encoding glycolytic enzymes such as 3-phosphoglycerate
kinase (PGK), alpha-factor, acid phosphatase, or heat shock
proteins, among others. The heterologous structural sequence is
assembled in appropriate phase with translation initiation and
termination sequences, and preferably, a leader sequence capable of
directing secretion of translated protein into the periplasmic
space or extracellular medium. Optionally, the heterologous
sequence can encode a fusion protein including an N-terminal
identification peptide imparting desired characteristics, e.g.,
stabilization or simplified purification of expressed recombinant
product.
[0137] Useful expression vectors for bacterial use are constructed
by inserting a structural DNA sequence encoding a desired protein
together with suitable translation initiation and termination
signals in operable reading phase with a functional promoter. The
vector will comprise one or more phenotypic selectable markers and
an origin of replication to ensure maintenance of the vector and,
when desirable, provide amplification within the host.
[0138] Suitable prokaryotic hosts for transformation include
strains of Staphylococcus aureus, E. coli, B. subtilis, Salmonella
typhimurium and various species within the genera Pseudomonas,
Streptomyces, and Staphylococcus. Others may, also be employed as a
matter of choice.
[0139] As a representative but non-limiting example, useful
expression vectors for bacterial use can comprise a selectable
marker and bacterial origin of replication derived from
commercially available plasmids comprising genetic elements of the
well known cloning vector pBR322 (ATCC 37017). Such commercial
vectors include, for example, pKK223-3 (available form Pharmacia
Fine Chemicals, Uppsala, Sweden) and GEM 1 (available from Promega
Biotec, Madison, Wis., USA). These pBR322 "backbone" sections are
combined with an appropriate promoter and the structural sequence
to be expressed.
[0140] Following transformation of a suitable host strain and
growth of the host strain to an appropriate cell density, the
selected promoter, where it is inducible, is derepressed or induced
by appropriate means (e.g., temperature shift or chemical
induction) and cells are cultured for an additional period to
provide for expression of the induced gene product. Thereafter
cells are typically harvested, generally by centrifugation,
disrupted to release expressed protein, generally by physical or
chemical means, and the resulting crude extract is retained for
further purification.
[0141] Various mammalian cell culture systems can also be employed
to express recombinant protein. Examples of mammalian expression
systems include the COS-7 lines of monkey kidney fibroblasts,
described in Gluzman, Cell 23: 175 (1981), and other cell lines
capable of expressing a compatible vector, for example, the C127,
3T3, CHO, HeLa and BHK cell lines.
[0142] Mammalian expression vectors will comprise an origin of
replication, a suitable promoter and enhancer, and also any
necessary ribosome binding sites, polyadenylation site, splice
donor and acceptor sites, transcriptional termination sequences,
and 5' flanking nontranscribed sequences. DNA sequences derived
from the SV40 viral genome, for example, SV40 origin, early
promoter, enhancer, splice, and polyadenylation sites may be used
to provide the required nontranscribed genetic elements.
[0143] Recombinant polypeptides and proteins produced in bacterial
culture is usually isolated by initial extraction from cell
pellets, followed by one or more salting-out, aqueous ion exchange
or size exclusion chromatography steps. Microbial cells employed in
expression of proteins can be disrupted by any convenient method,
including freeze-thaw cycling, sonication, mechanical disruption,
or use of cell lysing agents. Protein refolding steps can be used,
as necessary, in completing configuration of the mature protein.
Finally, high performance liquid chromatography (HPLC) can be
employed for final purification steps.
[0144] An additional aspect of the invention includes
Staphylococcus aureus polypeptides which are useful as
immunodiagnostic antigens and/or immunoprotective vaccines,
collectively "immunologically useful polypeptides". Such
immunologically useful polypeptides may be selected from the ORFs
disclosed herein based on techniques well known in the art and
described elsewhere herein. The inventors have used the following
criteria to select several immunologically useful polypeptides:
[0145] As is known in the art, an amino terminal type I signal
sequence directs a nascent protein across the plasma and outer
membranes to the exterior of the bacterial cell. Such outer
membrane polypeptides are expected to be immunologically useful.
According to Izard, J. W. et al., Mol. Microbiol. 13, 765-773;
(1994), polypeptides containing type I signal sequences contain the
following physical attributes: The length of the type I signal
sequence is approximately 15 to 25 primarily hydrophobic amino acid
residues with a net positive charge in the extreme amino terminus;
the central region of the signal sequence must adopt an
alpha-helical conformation in a hydrophobic environment; and the
region surrounding the actual site of cleavage is ideally six
residues long, with small side-chain amino acids in the -1 and -3
positions.
[0146] Also known in the art is the type IV signal sequence which
is an example of the several types of functional signal sequences
which exist in addition to the type I signal sequence detailed
above. Although functionally related, the type IV signal sequence
possesses a unique set of biochemical and physical attributes
(Strom, M. S. and Lory, S., J. Bacteriol. 174, 7345-7351; 1992)).
These are typically six to eight amino acids with a net basic
charge followed by an additional sixteen to thirty primarily
hydrophobic residues. The cleavage site of a type IV signal
sequence is typically after the initial six to eight amino acids at
the extreme amino terminus. In addition, all type IV signal
sequences contain a phenylalanine residue at the +1 site relative
to the cleavage site.
[0147] Studies of the cleavage sites of twenty-six bacterial
lipoprotein precursors has allowed the definition of a consensus
amino acid sequence for lipoprotein cleavage. Nearly three-fourths
of the bacterial lipoprotein precursors examined contained the
sequence L-(A,S)-(G,A)-C at positions -3 to +1, relative to the
point of cleavage (Hayashi, S. and Wu, H. C. Lipoproteins in
bacteria. J Bioenerg. Biomembr. 22, 451-471; 1990).
[0148] It is well known that most anchored proteins found on the
surface of gram-positive bacteria possess a highly conserved
carboxy terminal sequence. More than fifty such proteins from
organisms such as S. pyogenes, S. mutans, E. faecalis, S.
pneumoniae, and others, have been identified based on their
extracellular location and carboxy terminal amino acid sequence
(Fischetti, V. A. Gram-positive commensal bacteria deliver antigens
to elicit mucosal and systemic immunity. ASM News 62, 405-410;
1996). The conserved region is comprised of six charged amino acids
at the extreme carboxy terminus coupled to 15-20 hydrophobic amino
acids presumed to function as a transmembrane domain. Immediately
adjacent to the transmembrane domain is a six amino acid sequence
conserved in nearly all proteins examined. The amino acid sequence
of this region is L-P-X-G-X (SEQ ID NO:5256), where X is any amino
acid.
[0149] Amino acid sequence similarities to proteins of known
function by BLAST enables the assignment of putative functions to
novel amino acid sequences and allows for the selection of proteins
thought to function outside the cell wall. Such proteins are well
known in the art and include "lipoprotein", "periplasmic", or
"antigen".
[0150] An algorithm for selecting antigenic and immunogenic
Staphylococcus aureus polypeptides including the foregoing criteria
was developed by the present inventors. Use of the algorithm by the
inventors to select immunologically useful Staphylococcus aureus
polypeptides resulted in the selection of several ORFs which are
predicted to be outer membrane-associated proteins. These proteins
are identified below, and shown in the Sequence Listing as SEQ ID
NOS: 5,192 to 5,255. Thus the amino acid sequence of each of
several antigenic Staphylococcus aureus polypeptides can be
determined, for example, by locating the amino acid sequence of the
ORF in the Sequence Listing. Likewise the polynucleotide sequence
encoding each ORF can be found by locating the corresponding
polynucleotide SEQ ID in Tables 1, 2, or 3, and finding the
corresponding nucleotide sequence in the sequence listing.
[0151] As will be appreciated by those of ordinary skill in the
art, although a polypeptide representing an entire ORF may be the
closest approximation to a protein found in vivo, it is not always
technically practical to express a complete ORF in vitro. It may be
very challenging to express and purify a highly hydrophobic protein
by common laboratory methods. As a result, the immunologically
useful polypeptides described herein as SEQ ID NOS: 5,192-5,255 may
have been modified slightly to simplify the production of
recombinant protein, and are the preferred embodiments. In general,
nucleotide sequences which encode highly hydrophobic domains, such
as those found at the amino terminal signal sequence, are excluded
for enhanced in vitro expression of the polypeptides. Furthermore,
any highly hydrophobic amino acid sequences occurring at the
carboxy terminus are also excluded. Such truncated polypeptides
include for example the mature forms of the polypeptides expected
to exist in nature.
[0152] Those of ordinary skill in the art can identify soluble
portions the polypeptide, and in the case of truncated polypeptides
sequences shown as SEQ ID NOS: 5,192-5,255, may obtain the complete
predicted amino acid sequence of each polypeptide by translating
the corresponding polynucleotides sequences of the corresponding
ORF listed in Tables 1,2 and 3 and found in the sequence
listing.
[0153] Accordingly, polypeptides comprising the complete amino acid
sequence of an immunologically useful polypeptide selected from the
group of polypeptides encoded by the ORFs shown as SEQ ID NOS:
5,192-5,255, or an amino acid sequence at least 95% identical
thereto, preferably at least 97% identical thereto, and most
preferably at least 99% identical thereto form an embodiment of the
invention; in addition, polypeptides comprising an amino acid
sequence selected from the group of amino acid sequences shown in
the sequence listing as SEQ ID NOS: 5,191-5,255, or an amino acid
sequence at least 95% identical thereto, preferably at least 97%
identical thereto and most preferably 99% identical thereto, form
an embodiment of the invention. Polynucleotides encoding the
foregoing polypeptides also form part of the invention.
[0154] In another aspect, the invention provides a peptide or
polypeptide comprising an epitope-bearing portion of a polypeptide
of the invention, particularly those epitope-bearing portions
(antigenic regions) identified in the sequence listing as SEQ ID
NOS: 5,191-5,255. The epitope-bearing portion is an immunogenic or
antigenic epitope of a polypeptide of the invention. An
"immunogenic epitope" is defined as a part of a protein that
elicits an antibody response when the whole protein is the
immunogen. On the other hand, a region of a protein molecule to
which an antibody can bind is defined as an "antigenic epitope."
The number of immunogenic epitopes of a protein generally is less
than the number of antigenic epitopes. See, for instance, Geysen et
al., Proc. Natl. Acad. Sci. USA 81:3998-4002 (1983).
[0155] As to the selection of peptides or polypeptides bearing an
antigenic epitope (i.e., that contain a region of a protein
molecule to which an antibody can bind), it is well known in that
art that relatively short synthetic peptides that mimic part of a
protein sequence are routinely capable of eliciting an antiserum
that reacts with the partially mimicked protein. See, for instance,
Sutcliffe, J. G., Shinnick, T. M., Green, N. and Learner, R. A.
(1983) "Antibodies that react with predetermined sites on
proteins", Science, 219:660-666. Peptides capable of eliciting
protein-reactive sera are frequently represented in the primary
sequence of a protein, can be characterized by a set of simple
chemical rules, and are confined neither to immunodominant regions
of intact proteins (i.e., immunogenic epitopes) nor to the amino or
carboxyl terminals.
[0156] Antigenic epitope-bearing peptides and polypeptides of the
invention are therefore useful to raise antibodies, including
monoclonal antibodies, that bind specifically to a polypeptide of
the invention. See, for instance, Wilson et al., Cell 37:767-778
(1984) at 777.
[0157] Antigenic epitope-bearing peptides and polypeptides of the
invention preferably contain a sequence of at least seven, more
preferably at least nine and most preferably between about 15 to
about 30 amino acids contained within the amino acid sequence of a
polypeptide of the invention. Non-limiting examples of antigenic
polypeptides or peptides that can be used to generate S. aureus
specific antibodies include: a polypeptide comprising peptides
shown below. These polypeptide fragments have been determined to
bear antigenic epitopes of indicated S. aureus proteins by the
analysis of the Jameson-Wolf antigenic index, a representative
sample of which is shown in FIG. 3.
[0158] The epitope-bearing peptides and polypeptides of the
invention may be produced by any conventional means. See, e.g.,
Houghten, R. A. (1985) General method for the rapid solid-phase
synthesis of large numbers of peptides: specificity of
antigen-antibody interaction at the level of individual amino
acids. Proc. Natl. Acad. Sci. USA 82:5131-5135; this "Simultaneous
Multiple Peptide Synthesis (SMPS)" process is further described in
U.S. Pat. No. 4,631,211 to Houghten et al. (1986).
[0159] Epitope-bearing peptides and polypeptides of the invention
are used to induce antibodies according to methods well known in
the art. See, for instance, Sutcliffe et al., supra; Wilson et al.,
supra; Chow, M. et al., Proc. Natl. Acad. Sci. USA 82:910-914; and
Bittle, F. J. et al., J. Gen. Virol. 66:2347-2354 (1985).
Immunogenic epitope-bearing peptides of the invention, i.e., those
parts of a protein that elicit an antibody response when the whole
protein is the immunogen, are identified according to methods known
in the art. See, for instance, Geysen et al., supra. Further still,
U.S. Pat. No. 5,194,392 to Geysen (1990) describes a general method
of detecting or determining the sequence of monomers (amino acids
or other compounds) which is a topological equivalent of the
epitope (i.e., a "mimotope") which is complementary to a particular
paratope (antigen binding site) of an antibody of interest. More
generally, U.S. Pat. No. 4,433,092 to Geysen (1989) describes a
method of detecting or determining a sequence of monomers which is
a topographical equivalent of a ligand which is complementary to
the ligand binding site of a particular receptor of interest.
Similarly, U.S. Pat. No. 5,480,971 to Houghten, R. A. et al. (1996)
on Peralkylated Oligopeptide Mixtures discloses linear C1-C7-alkyl
peralkylated oligopeptides and sets and libraries of such peptides,
as well as methods for using such oligopeptide sets and libraries
for determining the sequence of a peralkylated oligopeptide that
preferentially binds to an acceptor molecule of interest. Thus,
non-peptide analogs of the epitope-bearing peptides of the
invention also can be made routinely by these methods.
[0160] Immunologically useful polypeptides may be identified by an
algorithm which locates novel Staphylococcus aureus outer membrane
proteins, as is described above. Also listed are epitopes or
"antigenic regions" of each of the identified polypeptides. The
antigenic regions, or epitopes, are delineated by two numbers x-y,
where x is the number of the first amino acid in the open reading
frame included within the epitope and y is the number of the last
amino acid in the open reading frame included within the epitope.
For example, the first epitope in ORF 168-6 is comprised of amino
acids 36 to 45 of SEQ ID NO: 5,192. The inventors have identified
several epitopes for each of the antigenic polypeptides identified.
Accordingly, forming part of the present invention are polypeptides
comprising an amino acid sequence of one or more antigenic regions
identified. The invention further provides polynucleotides encoding
such polypeptides.
[0161] The present invention further includes isolated
polypeptides, proteins and nucleic acid molecules which are
substantially equivalent to those herein described. As used herein,
substantially equivalent can refer both to nucleic acid and amino
acid sequences, for example a mutant sequence, that varies from a
reference sequence by one or more substitutions, deletions, or
additions, the net effect of which does not result in an adverse
functional dissimilarity between reference and subject sequences.
For purposes of the present invention, sequences having equivalent
biological activity, and equivalent expression characteristics are
considered substantially equivalent. For purposes of determining
equivalence, truncation of the mature sequence should be
disregarded.
[0162] The invention further provides methods of obtaining homologs
from other strains of Staphylococcus aureus, of the fragments of
the Staphylococcus aureus genome of the present invention and
homologs of the proteins encoded by the ORFs of the present
invention. As used herein, a sequence or protein of Staphylococcus
aureus is defined as a homolog of a fragment of the Staphylococcus
aureus fragments or contigs or a protein encoded by one of the ORFs
of the present invention, if it shares significant homology to one
of the fragments of the Staphylococcus aureus genome of the present
invention or a protein encoded by one of the ORFs of the present
invention. Specifically, by using the sequence disclosed herein as
a probe or as primers, and techniques such as PCR cloning and
colony/plaque hybridization, one skilled in the art can obtain
homologs.
[0163] As used herein, two nucleic acid molecules or proteins are
said to "share significant homology" if the two contain regions
which possess greater than 85% sequence (amino acid or nucleic
acid) homology. Preferred homologs in this regard are those with
more than 90% homology. Especially preferred are those with 93% or
more homology. Among especially preferred homologs those with 95%
or more homology are particularly preferred. Very particularly
preferred among these are those with 97% and even more particularly
preferred among those are homologs with 99% or more homology. The
most preferred homologs among these are those with 99.9% homology
or more. It will be understood that, among measures of homology,
identity is particularly preferred in this regard.
[0164] Region specific primers or probes derived from the
nucleotide sequence provided in SEQ ID NOS: 1-5,191 or from a
nucleotide sequence at least 95%, particularly at least 99%,
especially at least 99.5% identical to a sequence of SEQ ID NOS:
1-5,191 can be used to prime DNA synthesis and PCR amplification,
as well as to identify colonies containing cloned DNA encoding a
homolog. Methods suitable to this aspect of the present invention
are well known and have been described in great detail in many
publications such as, for example, Innis et al., PCR PROTOCOLS,
Academic Press, San Diego, Calif. (1990)).
[0165] When using primers derived from SEQ ID NOS: 1-5,191 or from
a nucleotide sequence having an aforementioned identity to a
sequence of SEQ ID NOS: 1-5,191, one skilled in the art will
recognize that by employing high stringency conditions (e.g.,
annealing at 50-60.degree. C. in 6.times. SSPC and 50% formamide,
and washing at 50-65.degree. C. in 0.5.times. SSPC) only sequences
which are greater than 75% homologous to the primer will be
amplified. By employing lower stringency conditions (e.g.,
hybridizing at 35-37.degree. C. in 5.times. SSPC and 40-45%
formamide, and washing at 42.degree. C. in 0.5.times. SSPC),
sequences which are greater than 40-50% homologous to the primer
will also be amplified.
[0166] When using DNA probes derived from SEQ ID NOS: 1-5,191, or
from a nucleotide sequence having an aforementioned identity to a
sequence of SEQ ID NOS: 1-5,191, for colony/plaque hybridization,
one skilled in the art will recognize that by employing high
stringency conditions (e.g., hybridizing at 50-65.degree. C. in
5.times. SSPC and 50% formamide, and washing at 50-65.degree. C. in
0.5.times. SSPC), sequences having regions which are greater than
90% homologous to the probe can be obtained, and that by employing
lower stringency conditions (e.g., hybridizing at 35-37.degree. C.
in 5.times. SSPC and 40-45% formamide, and washing at 42.degree. C.
in 0.5.times. SSPC), sequences having regions which are greater
than 35-45% homologous to the probe will be obtained.
[0167] Any organism can be used as the source for homologs of the
present invention so long as the organism naturally expresses such
a protein or contains genes encoding the same. The most preferred
organism for isolating homologs are bacterias which are closely
related to Staphylococcus aureus.
ILLUSTRATIVE USES OF COMPOSITIONS OF THE INVENTION
[0168] Each ORF provided in Tables 1 and 2 is identified with a
function by homology to a known gene or polypeptide. As a result,
one skilled in the art can use the polypeptides of the present
invention for commercial, therapeutic and industrial purposes
consistent with the type of putative identification of the
polypeptide. Such identifications permit one skilled in the art to
use the Staphylococcus aureus ORFs in a manner similar to the known
type of sequences for which the identification is made; for
example, to ferment a particular sugar source or to produce a
particular metabolite. A variety of reviews illustrative of this
aspect of the invention are available, including the following
reviews on the industrial use of enzymes, for example, BIOCHEMICAL
ENGINEERING AND BIOTECHNOLOGY HANDBOOK, 2.sup.nd Ed., Macmillan
Publications, Ltd. NY (1991) and BIOCATALYSTS IN ORGANIC SYNTHESES,
Tramper et al., Eds., Elsevier Science Publishers, Amsterdam, The
Netherlands (1985). A variety of exemplary uses that illustrate
this and similar aspects of the present invention are discussed
below.
[0169] 1. Biosynthetic Enzymes
[0170] Open reading frames encoding proteins involved in mediating
the catalytic reactions involved in intermediary and macromolecular
metabolism, the biosynthesis of small molecules, cellular processes
and other functions includes enzymes involved in the degradation of
the intermediary products of metabolism, enzymes involved in
central intermediary metabolism, enzymes involved in respiration,
both aerobic and anaerobic, enzymes involved in fermentation,
enzymes involved in ATP proton motor force conversion, enzymes
involved in broad regulatory function, enzymes involved in amino
acid synthesis, enzymes involved in nucleotide synthesis, enzymes
involved in cofactor and vitamin synthesis, can be used for
industrial biosynthesis.
[0171] The various metabolic pathways present in Staphylococcus
aureus can be identified based on absolute nutritional requirements
as well as by examining the various enzymes identified in Table 1-3
and SEQ ID NOS: 1-5,191.
[0172] Of particular interest are polypeptides involved in the
degradation of intermediary metabolites as well as
non-macromolecular metabolism. Such enzymes include amylases,
glucose oxidases, and catalase.
[0173] Proteolytic enzymes are another class of commercially
important enzymes. Proteolytic enzymes find use in a number of
industrial processes including the processing of flax and other
vegetable fibers, in the extraction, clarification and
depectinization of fruit juices, in the extraction of vegetables'
oil and in the maceration of fruits and vegetables to give
unicellular fruits. A detailed review of the proteolytic enzymes
used in the food industry is provided in Rombouts et al., Symbiosis
21: 79 (1986) and Voragen et al. in BIOCATALYSTS IN AGRICULTURAL
BIOTECHNOLOGY, Whitaker et al., Eds., American Chemical Society
Symposium Series 389: 93 (1989).
[0174] The metabolism of sugars is an important aspect of the
primary metabolism of Staphylococcus aureus. Enzymes involved in
the degradation of sugars, such as, particularly, glucose,
galactose, fructose and xylose, can be used in industrial
fermentation. Some of the important sugar transforming enzymes,
from a commercial viewpoint, include sugar isomerases such as
glucose isomerase. Other metabolic enzymes have found commercial
use such as glucose oxidases which produces ketogulonic acid (KGA).
KGA is an intermediate in the commercial production of ascorbic
acid using the Reichstein's procedure, as described in Krueger et
al., Biotechnology 6(A), Rhine et al., Eds., Verlag Press,
Weinheim, Germany (1984).
[0175] Glucose oxidase (GOD) is commercially available and has been
used in purified form as well as in an immobilized form for the
deoxygenation of beer. See, for instance, Hartmeir et al.,
Biotechnology Letters 1: 21 (1979). The most important application
of GOD is the industrial scale fermentation of gluconic acid.
Market for gluconic acids which are used in the detergent, textile,
leather, photographic, pharmaceutical, food, feed and concrete
industry, as described, for example, in Bigelis et al., beginning
on page 357 in GENE MANIPULATIONS AND FUNGI; Benett et al., Eds.,
Academic Press, New York (1985). In addition to industrial
applications, GOD has found applications in medicine for
quantitative determination of glucose in body fluids recently in
biotechnology for analyzing syrups from starch and cellulose
hydrosylates. This application is described in Owusu et al.,
Biochem. et Biophysica. Acta. 872: 83 (1986), for instance.
[0176] The main sweetener used in the world today is sugar which
comes from sugar beets and sugar cane. In the field of industrial
enzymes, the glucose isomerase process shows the largest expansion
in the market today. Initially, soluble enzymes were used and later
immobilized enzymes were developed (Krueger et al., Biotechnology,
The Textbook of Industrial Microbiology, Sinauer Associated
Incorporated, Sunderland, Mass. (1990)). Today, the use of glucose-
produced high fructose syrups is by far the largest industrial
business using immobilized enzymes. A review of the industrial use
of these enzymes is provided by Jorgensen, Starch 40:307
(1988).
[0177] Proteinases, such as alkaline serine proteinases, are used
as detergent additives and thus represent one of the largest
volumes of microbial enzymes used in the industrial sector. Because
of their industrial importance, there is a large body of published
and unpublished information regarding the use of these enzymes in
industrial processes. (See Faultman et al., Acid Proteases
Structure Function and Biology, Tang, J., ed., Plenum Press, New
York (1977) and Godfrey et al., Industrial Enzymes, MacMillan
Publishers, Surrey, UK (1983) and Hepner et al, Report Industrial
Enzymes by 1990, Hel Hepner & Associates, London (1986)).
[0178] Another class of commercially usable proteins of the present
invention are the microbial lipases, described by, for instance,
Macrae et al., Philosophical Transactions of the Chiral Society of
London 310:227 (1985) and Poserke, Journal of the American Oil
Chemist Society 61:1758 (1984). A major use of lipases is in the
fat and oil industry for the production of neutral glycerides using
lipase catalyzed inter-esterification of readily available
triglycerides. Application of lipases include the use as a
detergent additive to facilitate the removal of fats from fabrics
in the course of the washing procedures.
[0179] The use of enzymes, and in particular microbial enzymes, as
catalyst for key steps in the synthesis of complex organic
molecules is gaining popularity at a great rate. One area of great
interest is the preparation of chiral intermediates. Preparation of
chiral intermediates is of interest to a wide range of synthetic
chemists particularly those scientists involved with the
preparation of new pharmaceuticals, agrochemicals, fragrances and
flavors. (See Davies et al., Recent Advances in the Generation of
Chiral Intermediates Using Enzymes, CRC Press, Boca Raton, Fla.
(1990)). The following reactions catalyzed by enzymes are of
interest to organic chemists: hydrolysis of carboxylic acid esters,
phosphate esters, amides and nitriles, esterification reactions,
trans-esterification reactions, synthesis of amides, reduction of
alkanones and oxoalkanates, oxidation of alcohols to carbonyl
compounds, oxidation of sulfides to sulfoxides, and carbon bond
forming reactions such as the aldol reaction.
[0180] When considering the use of an enzyme encoded by one of the
ORFs of the present invention for biotransformation and organic
synthesis it is sometimes necessary to consider the respective
advantages and disadvantages of using a microorganism as opposed to
an isolated enzyme. Pros and cons of using a whole cell system on
the one hand or an isolated partially purified enzyme on the other
hand, has been described in detail by Bud et al., Chemistry in
Britain (1987), p. 127.
[0181] Amino transferases, enzymes involved in the biosynthesis and
metabolism of amino acids, are useful in the catalytic production
of amino acids. The advantages of using microbial based enzyme
systems is that the amino transferase enzymes catalyze the stereo-
selective synthesis of only L-amino acids and generally possess
uniformly high catalytic rates. A description of the use of amino
transferases for amino acid production is provided by
Roselle-David, Methods of Enzymology 136:479 (1987).
[0182] Another category of useful proteins encoded by the ORFs of
the present invention include enzymes involved in nucleic acid
synthesis, repair, and recombination. A variety of commercially
important enzymes have previously been isolated from members of
Staphylococcus aureus. These include Sau3A and Sau96I.
[0183] 2. Generation of Antibodies
[0184] As described here, the proteins of the present invention, as
well as homologs thereof, can be used in a variety procedures and
methods known in the art which are currently applied to other
proteins. The proteins of the present invention can further be used
to generate an antibody which selectively binds the protein. Such
antibodies can be either monoclonal or polyclonal antibodies, as
well fragments of these antibodies, and humanized forms.
[0185] The invention further provides antibodies which selectively
bind to one of the proteins of the present invention and hybridomas
which produce these antibodies. A hybridoma is an immortalized cell
line which is capable of secreting a specific monoclonal
antibody.
[0186] In general, techniques for preparing polyclonal and
monoclonal antibodies as well as hybridomas capable of producing
the desired antibody are well known in the art (Campbell, A. M.,
MONOCLONAL ANTIBODY TECHNOLOGY: LABORATORY TECHNIQUES IN
BIOCHEMISTRY AND MOLECULAR BIOLOGY, Elsevier Science Publishers,
Amsterdam, The Netherlands (1984); St. Groth et al., J. Immunol.
Methods 35: 1-21 (1980), Kohler and Milstein, Nature 256: 495-497
(1975)), the trioma technique, the human B-cell hybridoma technique
(Kozbor et al., Immunology Today-4: 72 (1983), pgs. 77-96 of Cole
et al., in MONOCLONAL ANTIBODIES AND CANCER THERAPY, Alan R. Liss,
Inc. (1985)).
[0187] Any animal (mouse, rabbit, etc.) which is known to produce
antibodies can be immunized with the pseudogene polypeptide.
Methods for immunization are well known in the art. Such methods
include subcutaneous or interperitoneal injection of the
polypeptide. One skilled in the art will recognize that the amount
of the protein encoded by the ORF of the present invention used for
immunization will vary based on the animal which is immunized, the
antigenicity of the peptide and the site of injection.
[0188] The protein which is used as an immunogen may be modified or
administered in an adjuvant in order to increase the protein's
antigenicity. Methods of increasing the antigenicity of a protein
are well known in the art and include, but are not limited to
coupling the antigen with a heterologous protein (such as globulin
or galactosidase) or through the inclusion of an adjuvant during
immunization.
[0189] For monoclonal antibodies, spleen cells from the immunized
animals are removed, fused with myeloma cells, such as SP2/0-Ag14
myeloma cells, and allowed to become monoclonal antibody producing
hybridoma cells.
[0190] Any one of a number of methods well known in the art can be
used to identify the hybridoma cell which produces an antibody with
the desired characteristics. These include screening the hybridomas
with an ELISA assay, western blot analysis, or radioimmunoassay
(Lutz et al., Exp. Cell Res. 175: 109-124 (1988)).
[0191] Hybridomas secreting the desired antibodies are cloned and
the class and subclass is determined using procedures known in the
art (Campbell, A. M., Monoclonal Antibody Technology: Laboratory
Techniques in Biochemistry and Molecular Biology, Elsevier Science
Publishers, Amsterdam, The Netherlands (1984)).
[0192] Techniques described for the production of single chain
antibodies (U.S. Pat. No. 946,778) can be adapted to produce single
chain antibodies to proteins of the present invention.
[0193] For polyclonal antibodies, antibody containing antisera is
isolated from the immunized animal and is screened for the presence
of antibodies with the desired specificity using one of the
above-described procedures.
[0194] The present invention further provides the above- described
antibodies in detectably labeled form. Antibodies can be detectably
labeled through the use of radioisotopes, affinity labels (such as
biotin, avidin, etc.), enzymatic labels (such as horseradish
peroxidase, alkaline phosphatase, etc.) fluorescent labels (such as
FITC or rhodamine, etc.), paramagnetic atoms, etc. Procedures for
accomplishing such labeling are well-known in the art, for example
see Stemberger et al., J. Histochem. Cytochem. 18:315 (1970);
Bayer, E. A. et al., Meth. Enzym. 62:308 (1979); Engval, E. et al.,
Immunol. 109-129 (1972); Goding, J. W. J. Immunol. Meth. 13:215
(1976)).
[0195] The labeled antibodies of the present invention can be used
for in vitro, in vivo, and in situ assays to identify cells or
tissues in which a fragment of the Staphyococcus aureus genome is
expressed.
[0196] The present invention further provides the above-described
antibodies immoblized on a solid support. Examples of such solid
supports include plastics such as polycarbonate, complex
carbohydrates such as agarose and sepharose, acrylic resins and
such as polyacrylamide and latex beads. Techniques for coupling
antibodies to such solid supports are well known in the art (Weir,
D. M. et al., "Handbook of Experimental Immunology" 4th Ed.,
Blackwell Scientific Publications, Oxford, England, Chapter 10
(1986); Jacoby, W. D. et al., Meth. Enzym. 34 Academic Press, N.Y.
(1974)). The immobilized antibodies of the present invention can be
used for in vitro, in vivo, and in situ assays as well as for
immunoaffinity purification of the proteins of the present
invention.
[0197] 3. Diagnostic Assays and Kits
[0198] The present invention further provides methods to identify
the expression of one of the ORFs of the present invention, or
homolog thereof, in a test sample, using one of the DFs, antigens
or antibodies of the present invention.
[0199] In detail, such methods comprise incubating a test sample
with one or more of the antibodies, or one or more of the DFs, or
one or more antigens of the present invention and assaying for
binding of the DFs, antigens or antibodies to components within the
test sample.
[0200] Conditions for incubating a DF, antigen or antibody with a
test sample vary. Incubation conditions depend on the format
employed in the assay, the detection methods employed, and the type
and nature of the DF or antibody used in the assay. One skilled in
the art will recognize that any one of the commonly available
hybridization, amplification or immunological assay formats can
readily be adapted to employ the Dfs, antigens or antibodies of the
present invention. Examples of such assays can be found in Chard,
T., An Introduction to Radioimmunoassay and Related Techniques,
Elsevier Science Publishers, Amsterdam, The Netherlands (1986);
Bullock, G. R. et al., Techniques in inmunocytochemistry, Academic
Press, Orlando, Fla. Vol. 1 (1982), Vol. 2 (1983), Vol. 3 (1985);
Tijssen, P., Practice and Theory of Enzyme Immunoassays: Laboratory
Techniques in Biochemistry; PCT publication W095/32291, and
Molecular Biology, Elsevier Science Publishers, Amsterdam, The
Netherlands (1985), all of which are hereby incorporated herein by
reference.
[0201] The test samples of the present invention include cells,
protein or membrane extracts of cells, or biological fluids such as
sputum, blood, serum,, plasma, or urine. The test sample used in
the above-described method will vary based on the assay format,
nature of the detection method and the tissues, cells or extracts
used as the sample to be assayed. Methods for preparing protein
extracts or membrane extracts of cells are well known in the art
and can be readily be adapted in order to obtain a sample which is
compatible with the system utilized.
[0202] In another embodiment of the present invention, kits are
provided which contain the necessary reagents to carry out the
assays of the present invention.
[0203] Specifically, the invention provides a compartmentalized kit
to receive, in close confinement, one or more containers which
comprises:(a) a first container comprising one of the Dfs, antigens
or antibodies of the present invention; and (b) one or more other
containers comprising one or more of the following: wash reagents,
reagents capable of detecting presence of a bound DF, antigen or
antibody.
[0204] In detail, a compartmentalized kit includes any kit in which
reagents are contained in separate containers. Such containers
include small glass containers, plastic containers or strips of
plastic or paper. Such containers allows one to efficiently
transfer reagents from one compartment to another compartment such
that the samples and reagents are not cross-contaminated, and the
agents or solutions of each container can be added in a
quantitative fashion from one compartment to another. Such
containers will include a container which will accept the test
sample, a container which contains the antibodies used in the
assay, containers which contain wash reagents (such as phosphate
buffered saline, Tris-buffers, etc.), and containers which contain
the reagents used to detect the bound antibody, antigen or DF.
[0205] Types of detection reagents include labeled nucleic acid
probes, labeled secondary antibodies, or in the alternative, if the
primary antibody is labeled, the enzymatic, or antibody binding
reagents which are capable of reacting with the labeled antibody.
One skilled in the art will readily recognize that the disclosed
Dfs, antigens and antibodies of the present invention can be
readily incorporated into one of the established kit formats which
are well known in the art.
[0206] 4. Screening Assay for Binding Agents
[0207] Using the isolated proteins of the present invention, the
present invention further provides methods of obtaining and
identifying agents which bind to a protein encoded by one of the
ORFs of the present invention or to one of the fragments and the
Staphylococcus aureus fragment and contigs herein described.
[0208] In general, such methods comprise steps of:
[0209] contacting an agent with an isolated protein encoded by one
of the ORFs of the present invention, or an isolated fragment of
the Staphylococcus aureus genome; and
[0210] determining whether the agent binds to said protein or said
fragment.
[0211] The agents screened in the above assay can be, but are not
limited to, peptides, carbohydrates, vitamin derivatives, or other
pharmaceutical agents. The agents can be selected and screened at
random or rationally selected or designed using protein modeling
techniques.
[0212] For random screening, agents such as peptides,
carbohydrates, pharmaceutical agents and the like are selected at
random and are assayed for their ability to bind to the protein
encoded by the ORF of the present invention.
[0213] Alternatively, agents may be rationally selected or
designed. As used herein, an agent is said to be "rationally
selected or designed" when the agent is chosen based on the
configuration of the particular protein. For example, one skilled
in the art can readily adapt currently available procedures to
generate peptides, pharmaceutical agents and the like capable of
binding to a specific peptide sequence in order to generate
rationally designed antipeptide peptides, for example see Hurby et
al., Application of Synthetic Peptides: Antisense Peptides," In
Synthetic Peptides, A User's Guide, W. H. Freeman, NY (1992), pp.
289-307, and Kaspczak et al., Biochemistry 28:9230-8 (1989), or
pharmaceutical agents, or the like.
[0214] In addition to the foregoing, one class of agents of the
present invention, as broadly described, can be used to control
gene expression through binding to one of the ORFs or EMFs of the
present invention. As described above, such agents can be randomly
screened or rationally designed/selected. Targeting the ORF or EMF
allows a skilled artisan to design sequence specific or element
specific agents, modulating the expression of either a single ORF
or multiple ORFs which rely on the same EMF for expression
control.
[0215] One class of DNA binding agents are agents which contain
base residues which hybridize or form a triple helix by binding to
DNA or RNA. Such agents can be based on the classic phosphodiester,
ribonucleic acid backbone, or can be a variety of sulfhydryl or
polymeric derivatives which have base attachment capacity.
[0216] Agents suitable for use in these methods usually contain 20
to 40 bases and are designed to be complementary to a region of the
gene involved in transcription (triple helix--see Lee et al., Nucl.
Acids Res. 6:3073 (1979); Cooney et al., Science 241:456 (1988);
and Dervan et al., Science 251: 1360 (1991)) or to the mRNA itself
(antisense--Okano, J. Neurochem. 56:560 (1991);
Oligodeoxynucleotides as Antisense Inhibitors of Gene Expression,
CRC Press, Boca Raton, Fla. (1988)). Triple helix- formation
optimally results in a shut-off of RNA transcription from DNA,
while antisense RNA hybridization blocks translation of an mRNA
molecule into polypeptide. Both techniques have been demonstrated
to be effective in model systems. Information contained in the
sequences of the present invention can be used to design antisense
and triple helix-forming oligonucleotides, and other DNA binding
agents.
[0217] 5. Pharmaceutical Compositions and Vaccines
[0218] The present invention further provides pharmaceutical agents
which can be used to modulate the growth or pathogenicity of
Staphylococcus aureus, or another related organism, in vivo or in
vitro. As used herein, a "pharmaceutical agent" is defined as a
composition of matter which can be formulated using known
techniques to provide a pharmaceutical compositions. As used
herein, the "pharmaceutical agents of the present invention" refers
the pharmaceutical agents which are derived from the proteins
encoded by the ORFs of the present invention or are agents which
are identified using the herein described assays.
[0219] As used herein, a pharmaceutical agent is said to "modulate
the growth or pathogenicity of Staphylococcus aureus or a related
organism, in vivo or in vitro," when the agent reduces the rate of
growth, rate of division, or viability of the organism in question.
The pharmaceutical agents of the present invention can modulate the
growth or pathogenicity of an organism in many fashions, although
an understanding of the underlying mechanism of action is not
needed to practice the use of the pharmaceutical agents of the
present invention. Some agents will modulate the growth or
pathogenicity by binding to an important protein thus blocking the
biological activity of the protein, while other agents may bind to
a component of the outer surface of the organism blocking
attachment or rendering the organism more prone to act the bodies
nature immune system. Alternatively, the agent may comprise a
protein encoded by one of the ORFs of the present invention and
serve as a vaccine. The development and use of vaccines derived
from membrane associated polypeptides are well known in the art.
The inventors have identified particularly preferred immunogenic
Staphylococcus aureus polypeptides for use as vaccines. Such
immunogenic polypeptides are described above and summarized
below.
[0220] As used herein, a "related organism" is a broad term which
refers to any organism whose growth or pathogenicity can be
modulated by one of the pharmaceutical agents of the present
invention. In general, such an organism will contain a homolog of
the protein which is the target of the pharmaceutical agent or the
protein used as a vaccine. As such, related organisms do not need
to be bacterial but may be fungal or viral pathogens.
[0221] The pharmaceutical agents and compositions of the present
invention may be administered in a convenient manner, such as by
the oral, topical, intravenous, intraperitoneal, intramuscular,
subcutaneous, intranasal or intradermal routes. The pharmaceutical
compositions are administered in an amount which is effective for
treating and/or prophylaxis of the specific indication. In general,
they are administered in an amount of at least about 1 mg/kg body
weight and in most cases they will be administered in an amount not
in excess of about 1 g/kg body weight per day. In most cases, the
dosage is from about 0.1 mg/kg to about 10 g/kg body weight daily,
taking into account the routes of administration, symptoms,
etc.
[0222] The agents of the present invention can be used in native
form or can be modified to form a chemical derivative. As used
herein, a molecule is said to be a "chemical derivative" of another
molecule when it contains additional chemical moieties not normally
a part of the molecule. Such moieties may improve the molecule's
solubility, absorption, biological half life, etc. The moieties may
alternatively decrease the toxicity of the molecule, eliminate or
attenuate any undesirable side effect of the molecule, etc.
Moieties capable of mediating such effects are disclosed in, among
other sources, REMINGTON'S PHARMACEUTICAL SCIENCES (1980) cited
elsewhere herein.
[0223] For example, such moieties may change an immunological
character of the functional derivative, such as affinity for a
given antibody. Such changes in immunomodulation activity are
measured by the appropriate assay, such as a competitive type
immunoassay. Modifications of such protein properties as redox or
thermal stability, biological half-life, hydrophobicity,
susceptibility to proteolytic degradation or the tendency to
aggregate with carriers or into multimers also may be effected in
this way and can be assayed by methods well known to the skilled
artisan.
[0224] The therapeutic effects of the agents of the present
invention may be obtained by providing the agent to a patient by
any suitable means (e.g., inhalation, intravenously,
intramuscularly, subcutaneously, enterally, or parenterally). It is
preferred to administer the agent of the present invention so as to
achieve an effective concentration within the blood or tissue in
which the growth of the organism is to be controlled. To achieve an
effective blood concentration, the preferred method is to
administer the agent by injection. The administration may be by
continuous infusion, or by single or multiple injections.
[0225] In providing a patient with one of the agents of the present
invention, the dosage of the administered agent will vary depending
upon such factors as the patient's age, weight, height, sex,
general medical condition, previous medical history, etc. In
general, it is desirable to provide the recipient with a dosage of
agent which is in the range of from about 1 pg/kg to 10 mg/kg (body
weight of patient), although a lower or higher dosage may be
administered. The therapeutically effective dose can be lowered by
using combinations of the agents of the present invention or
another agent.
[0226] As used herein, two or more compounds or agents are said to
be administered "in combination" with each other when either (1)
the physiological effects of each compound, or (2) the serum
concentrations of each compound can be measured at the same time.
The composition of the present invention can be administered
concurrently with, prior to, or following the administration of the
other agent.
[0227] The agents of the present invention are intended to be
provided to recipient subjects in an amount sufficient to decrease
the rate of growth (as defined above) of the target organism.
[0228] The administration of the agent(s) of the invention may be
for either a "prophylactic" or "therapeutic" purpose. When provided
prophylactically, the agent(s) are provided in advance of any
symptoms indicative of the organisms growth. The prophylactic
administration of the agent(s) serves to prevent, attenuate, or
decrease the rate of onset of any subsequent infection. When
provided therapeutically, the agent(s) are provided at (or shortly
after) the onset of an indication of infection. The therapeutic
administration of the compound(s) serves to attenuate the
pathological symptoms of the infection and to increase the rate of
recovery.
[0229] The agents of the present invention are administered to a
subject, such as a mammal, or a patient, in a pharmaceutically
acceptable form and in a therapeutically effective concentration. A
composition is said to be "pharmacologically acceptable" if its
administration can be tolerated by a recipient patient. Such an
agent is said to be administered in a "therapeutically effective
amount" if the amount administered is physiologically significant.
An agent is physiologically significant if its presence results in
a detectable change in the physiology of a recipient patient.
[0230] The agents of the present invention can be formulated
according to known methods to prepare pharmaceutically useful
compositions, whereby these materials, or their functional
derivatives, are combined in admixture with a pharmaceutically
acceptable carrier vehicle. Suitable vehicles and their
formulation, inclusive of other human proteins, e.g., human serum
albumin, are described, for example, in REMINGTON'S PHARMACEUTICAL
SCIENCES, 16.sup.th Ed., Osol, A., Ed., Mack Publishing, Easton Pa.
(1980). In order to form a pharmaceutically acceptable composition
suitable for effective administration, such compositions will
contain an effective amount of one or more of the agents of the
present invention, together with a suitable amount of carrier
vehicle.
[0231] Additional pharmaceutical methods may be employed to control
the duration of action. Control release preparations may be
achieved through the use of polymers to complex or absorb one or
more of the agents of the present invention. The controlled
delivery may be effectuated by a variety of well known techniques,
including formulation with macromolecules such as, for example,
polyesters, polyamino acids, polyvinyl, pyrrolidone,
ethylenevinylacetate, methylcellulose, carboxymethylcellulose, or
protamine, sulfate, adjusting the concentration of the
macromolecules and the agent in the formulation, and by appropriate
use of methods of incorporation, which can be manipulated to
effectuate a desired time course of release. Another possible
method to control the duration of action by controlled release
preparations is to incorporate agents of the present invention into
particles of a polymeric material such as polyesters, polyamino
acids, hydrogels, poly(lactic acid) or ethylene vinylacetate
copolymers. Alternatively, instead of incorporating these agents
into polymeric particles, it is possible to entrap these materials
in microcapsules prepared, for example, by coacervation techniques
or by interfacial polymerization with, for example,
hydroxymethylcellulose or gelatine-microcapsules and
poly(methylmethacylate) microcapsules, respectively, or in
colloidal drug delivery systems, for example, liposomes, albumin
microspheres, microemulsions, nanoparticles, and nanocapsules or in
macroemulsions. Such techniques are disclosed in REMINGTON'S
PHARMACEUTICAL SCIENCES (1980).
[0232] The invention further provides a pharmaceutical pack or kit
comprising one or more containers filled with one or more of the
ingredients of the pharmaceutical compositions of the invention.
Associated with such container(s) can be a notice in the form
prescribed by a governmental agency regulating the manufacture, use
or sale of pharmaceuticals or biological products, which notice
reflects approval by the agency of manufacture, use or sale for
human administration.
[0233] In addition, the agents of the present invention may be
employed in conjunction with other therapeutic compounds.
[0234] 6. Shot-Gun Approach to Megabase DNA Sequencing
[0235] The present invention further demonstrates that a large
sequence can be sequenced using a random shotgun approach. This
procedure, described in detail in the examples that follow, has
eliminated the up front cost of isolating and ordering overlapping
or contiguous subclones prior to the start of the sequencing
protocols.
[0236] Certain aspects of the present invention are described in
greater detail in the examples that follow. The examples are
provided by way of illustration. Other aspects and embodiments of
the present invention are contemplated by the inventors, as will be
clear to those of skill in the art from reading the present
disclosure.
ILLUSTRATIVE EXAMPLES
[0237] Libraries and Sequencing
[0238] 1. Shotgun Sequencing Probability Analysis
[0239] The overall strategy for a shotgun approach to whole genome
sequencing follows from the Lander and Waterman (Landerman and
Waterman, Genomics 2: 231 (1988)) application of the equation for
the Poisson distribution. According to this treatment, the
probability, P.sub.0, that any given base in a sequence of size L,
in nucleotides, is not sequenced after a certain amount, n, in
nucleotides, of random sequence has been determined can be
calculated by the equation P.sub.0=e.sup.-m, where m is L/n, the
fold coverage." For instance, for a genome of 2.8 Mb, m=1 when 2.8
Mb of sequence has been randomly generated (1.times. coverage). At
that point, P.sub.0=e.sup.-1=0.37. The probability that any given
base has not been sequenced is the same as the probability that any
region of the whole sequence L has not been determined and,
therefore, is equivalent to the fraction of the whole sequence that
has yet to be determined. Thus, at one-fold coverage, approximately
37% of a polynucleotide of size L, in nucleotides has not been
sequenced. When 14 Mb of sequence has been generated, coverage is
5.times. for a 0.2.8 Mb and the unsequenced fraction drops to
0.0067 or 0.67%. 5.times. coverage of a 2.8 Mb sequence can be
attained by sequencing approximately 17,000 random clones from both
insert ends with an average sequence read length of 410 bp.
[0240] Similarly, the total gap length, G, is determined by the
equation G=Le.sup.-m, and the average gap size, g, follows the
equation, g=L/n. Thus, 5.times. coverage leaves about 240 gaps
averaging about 82 bp in size in a sequence of a polynucleotide 2.8
Mb long.
[0241] The treatment above is essentially that of Lander and
Waterman, Genomics 2: 231 (1988).
[0242] 2. Random Library Construction
[0243] In order to approximate the random model described above
during actual sequencing, a nearly ideal library of cloned genomic
fragments is required. The following library construction procedure
was developed to achieve this end.
[0244] Staphylococcus aureus DNA was prepared by phenol extraction.
A mixture containing 600 ug DNA in 3.3 ml of 300 mM sodium acetate,
10 mM Tris-HCl, 1 mM Na-EDTA, 30% glycerol was sonicated for 1 min.
at 0.degree. C. in a Branson Model 450 Sonicator at the lowest
energy setting using a 3 mm probe. The sonicated DNA was ethanol
precipitated and redissolved in 500 ul TE buffer.
[0245] To create blunt-ends, a 100 ul aliquot of the resuspended
DNA was digested with 5 units of BAL31 nuclease (New England
BioLabs) for 10 min at 30.degree. C. in 200 ul BAL31 buffer. The
digested DNA was phenol-extracted, ethanol-precipitated,
redissolved in 100 ul TE buffer, and then size-fractionated by
electrophoresis through a 1.0% low melting temperature agarose gel.
The section containing DNA fragments 1.6-2.0 kb in size was excised
from the gel, and the LGT agarose was melted and the resulting
solution was extracted with phenol to separate the agarose from the
DNA. DNA was ethanol precipitated and redissolved in 20 ul of TE
buffer for ligation to vector.
[0246] A two-step ligation procedure was used to produce a plasmid
library with 97% inserts, of which >99% were single inserts. The
first ligation mixture (50 ul) contained 2 ug of DNA fragments, 2
ug pUC18 DNA (Pharmacia) cut with SmaI and dephosphorylated with
bacterial alkaline phosphatase, and 10 units of T4 ligase
(GIBCO/BRL) and was incubated at 14.degree. C. for 4 hr. The
ligation mixture then was phenol extracted and ethanol
precipitated, and the precipitated DNA was dissolved in 20 ul TE
buffer and electrophoresed on a 1.0% low melting agarose gel.
Discrete bands in a ladder were visualized by ethidium
bromide-staining and UV illumination and identified by size as
insert (i), vector (v), v+i, v+2i, v+3i, etc. The portion of the
gel containing v+i DNA was excised and the v+i DNA was recovered
and resuspended into 20 ul TE. The v+i DNA then was blunt-ended by
T4 polymerase treatment for 5 min. at 37.degree. C. in a reaction
mixture (50 ul) containing the v+i linears, 500 uM each of the 4
dNTPs, and 9 units of T4 polymerase (New England BioLabs), under
recommended buffer conditions. After phenol extraction and ethanol
precipitation the repaired v+i linears were dissolved in 20 ul TE.
The final ligation to produce circles was carried out in a 50 ul
reaction containing 5 ul of v+i linears and 5 units of T4 ligase at
14.degree. C overnight. After 10 min. at 70.degree. C. the
following day, the reaction mixture was stored at -20.degree.
C.
[0247] This two-stage procedure resulted in a molecularly random
collection of single-insert plasmid recombinants with minimal
contamination from double-insert chimeras (<1%) or free vector
(<3%).
[0248] Since deviation from randomness can arise from propagation
the DNA in the host, E. coli host cells deficient in all
recombination and restriction functions (A. Greener, Strategies 3
(1):5 (1990)) were used to prevent rearrangements, deletions, and
loss of clones by restriction. Furthermore, transformed cells were
plated directly on antibiotic diffusion plates to avoid the usual
broth recovery phase which allows multiplication and selection of
the most rapidly growing cells.
[0249] Plating was carried out as follows. A 100 ul aliquot of
Epicurian Coli SURE II Supercompetent Cells (Stratagene 200152) was
thawed on ice and transferred to a chilled Falcon 2059 tube on ice.
A 1.7 ul aliquot of 1.42 M beta-mercaptoethanol was added to the
aliquot of cells to a final concentration of 25 mM. Cells were
incubated on ice for 10 min. A 1 ul aliquot of the final ligation
was added to the cells and incubated on ice for 30 min. The cells
were heat pulsed for 30 sec. at 42.degree. C. and placed back on
ice for 2 min. The outgrowth period in liquid culture was
eliminated from this protocol in order to minimize the preferential
growth of any given transformed cell. Instead the transformation
mixture was plated directly on a nutrient rich SOB plate containing
a 5 ml bottom layer of SOB agar (5% SOB agar: 20 g tryptone, 5 g
yeast extract, 0.5 g NaCl, 1.5% Difco Agar per liter of media). The
5 ml bottom layer is supplemented with 0.4 ml of 50 mg/ml
ampicillin per 100 ml SOB agar. The 15 ml top layer of SOB agar is
supplemented with 1 ml X-Gal (2%), 1 ml MgCl.sub.2 (1 M), and 1 ml
MgSO.sub.4/100 ml SOB agar. The 15 ml top layer was poured just
prior to plating. Our titer was approximately 100 colonies/10 ul
aliquot of transformation.
[0250] All colonies were picked for template preparation regardless
of size. Thus, only clones lost due to "poison" DNA or deleterious
gene products would be deleted from the library, resulting in a
slight increase in gap number over that expected.
[0251] 3. Random DNA Sequencing
[0252] High quality double stranded DNA plasmid templates were
prepared using an alkaline lysis method developed in collaboration
with 5Prime- - - >3Prime Inc. (Boulder, Co.). Plasmid
preparation was performed in a 96-well format for all stages of DNA
preparation from bacterial growth through final DNA purification.
Average template concentration was determined by running 25% of the
samples on an agarose gel. DNA concentrations were not
adjusted.
[0253] Templates were also prepared from a Staphylococcus aureus
lambda genomic library. An unamplified library was constructed in
Lambda DASH II vector (Stratagene). Staphylococcus aureus DNA
(>100 kb) was partially digested in a reaction mixture (200 ul)
containing 50 ug DNA, 1.times. Sau3AI buffer, 20 units Sau3AI for 6
min. at 23 C. The digested DNA was phenol-extracted and centrifuges
over a 10-40% sucrose gradient. Fractions containing genomic DNA of
15-25 kb were recovered by precipitation. One ul of fragments was
used with 1 ul of DASHII vector (Stratagene) in the recommended
ligation reaction. One ul of the ligation mixture was used per
packaging reaction following the recommended protocol with the
Gigapack II XL Packaging Extract Phage were plated directly without
amplification from the packaging mixture (after dilution with 500
ul of recommended SM buffer and chloroform treatment). Yield was
about 2.5.times.10.sup.9 pfu/ul.
[0254] An amplified library was prepared from the primary packaging
mixture according to the manufacturer's protocol. The amplified
library is stored frozen in 7% dimethylsulfoxide. The phage titer
is approximately 1.times.10.sup.9 pfu/ml.
[0255] Mini-liquid lysates (0.1 ul) are prepared from randomly
selected plaques and template is prepared by long range PCR.
Samples are PCR amplified using modified T3 and T7 primers, and
Elongase Supermix (LTI).
[0256] Sequencing reactions are carried out on plasmid templates
using a combination of two workstations (BIOMEK 1000 and Hamilton
Microlab 2200) and the Perkin-Elmer 9600 thermocycler with Applied
Biosystems PRISM Ready Reaction Dye Primer Cycle Sequencing Kits
for the M13 forward (M13-21) and the M13 reverse (M13RP1) primers.
Dye terminator sequencing reactions are carried out on the lambda
templates on a Perkin-Elmer 9600 Thermocycler using the Applied
Biosystems Ready Reaction Dye Terminator Cycle Sequencing kits.
Modified T7 and T3 primers are used to sequence the ends of the
inserts from the Lambda DASH II library. Sequencing reactions are
on a combination of AB 373 DNA Sequencers and ABI 377 DNA
sequencers. All of the dye terminator sequencing reactions are
analyzed using the 2.times.9 hour module on the AB 377. Dye primer
reactions are analyzed on a combination of ABI 373 and ABI 377 DNA
sequencers. The overall sequencing success rate very approximately
is about 85% for M13-21 and M13RP1 sequences and 65% for
dye-terminator reactions. The average usable read length is 485 bp
for M13-21 sequences, 445bp for M13RP1 sequences, and 375 bp for
dye-terminator reactions.
[0257] 4. Protocol for Automated Cycle Sequencing
[0258] The sequencing was carried out using Hamilton Microstation
2200, Perkin Elmer 9600 thermocyclers, ABI 373 and ABI 377
Automated DNA Sequencers. The Hamilton combines pre-aliquoted
templates and reaction mixes consisting of deoxy- and
dideoxynucleotides, the thermostable Taq DNA polymerase,
fluorescently-labeled sequencing primers, and reaction buffer.
Reaction mixes and templates were combined in the wells of a
96-well thermocycling plate and transferred to the Perkin Elmer
9600 thermocycler. Thirty consecutive cycles of linear
amplification (i.e.., one primer synthesis) steps were performed
including denaturation, annealing of primer and template, and
extension; i.e., DNA synthesis. A heated lid with rubber gaskets on
the thermocycling plate prevents evaporation without the need for
an oil overlay.
[0259] Two sequencing protocols were used: one for dye-labeled
primers and a second for dye-labeled dideoxy chain terminators. The
shotgun sequencing involves use of four dye-labeled sequencing
primers, one for each of the four terminator nucleotide. Each
dye-primer was labeled with a different fluorescent dye, permitting
the four individual reactions to be combined into one lane of the
373 or 377 DNA Sequencer for electrophoresis, detection, and
base-calling. ABI currently supplies pre-mixed reaction mixes in
bulk packages containing all the necessary non-template reagents
for sequencing. Sequencing can be done with both plasmid and PCR-
generated templates with both dye-primers and dye-terminators with
approximately equal fidelity, although plasmid templates generally
give longer usable sequences.
[0260] Thirty-two reactions were loaded per ABI 373 Sequencer each
day and 96 samples can be loaded on an ABI 377 per day.
Electrophoresis was run overnight (ABI 373) or for 21/2 hours (ABI
377) following the manufacturer's protocols. Following
electrophoresis and fluorescence detection, the ABI 373 or ABI 377
performs automatic lane tracking and base-calling. The
lane-tracking was confirmed visually. Each sequence
electropherogram (or fluorescence lane trace) was inspected
visually and assessed for quality. Trailing sequences of low
quality were removed and the sequence itself was loaded via
software to a Sybase database (archived daily to 8 mm tape).
Leading vector polylinker sequence was removed automatically by a
software program. Average edited lengths of sequences from the
standard ABI 373 or ABI 377 were around 400 bp and depend mostly on
the quality of the template used for the sequencing reaction.
[0261] Imformatics
[0262] 1. Data Management
[0263] A number of information management systems for a large-scale
sequencing lab have been developed. (For review see, for instance,
Kerlavage et al., Proceedings of the Twenty-Sixth Annual Hawaii
International Conference on System Sciences, IEEE Computer Society
Press, Wash. D.C., 585 (1993)) The system used to collect and
assemble the sequence data was developed using the Sybase
relational database management system and was designed to automate
data flow wherever possible and to reduce user error. The database
stores and correlates all information collected during the entire
operation from template preparation to final analysis of the
genome. Because the raw output of the ABI 373 Sequencers was based
on a Macintosh platform and the data management system chosen was
based on a Unix platform, it was necessary to design and implement
a variety of multi- user, client-server applications which allow
the raw data as well as analysis results to flow seamlessly into
the database with a minimum of user effort.
[0264] 2. Assembly
[0265] An assembly engine (TIGR Assembler) developed for the rapid
and accurate assembly of thousands of sequence fragments was
employed to generate contigs. The TIGR assembler simultaneously
clusters and assembles fragments of the genome. In order to obtain
the speed necessary to assemble more than 10.sup.4 fragments, the
algorithm builds a hash table of 12 bp oligonucleotide subsequences
to generate a list of potential sequence fragment overlaps. The
number of potential overlaps for each fragment determines which
fragments are likely to fall into repetitive elements. Beginning
with a single seed sequence fragment, TIGR Assembler extends the
current contig by attempting to add the best matching fragment
based on oligonucleotide content. The contig and candidate fragment
are aligned using a modified version of the Smith-Waterman
algorithm which provides for optimal gapped alignments (Waterman,
M. S., Methods in Enzymology 164: 765 (1988)). The contig is
extended by the fragment only if strict criteria for the quality of
the match are met. The match criteria include the minimum length of
overlap, the maximum length of an unmatched end, and the minimum
percentage match. These criteria are automatically lowered by the
algorithm in regions of minimal coverage and raised in regions with
a possible repetitive element. The number of potential overlaps for
each fragment determines which fragments are likely to fall into
repetitive elements. Fragments representing the boundaries of
repetitive elements and potentially chimeric fragments are often
rejected based on partial mismatches at the ends of alignments and
excluded from the current contig. TIGR Assembler is designed to
take advantage of clone size information coupled with sequencing
from both ends of each template. It enforces the constraint that
sequence fragments from two ends of the same template point toward
one another in the contig and are located within a certain ranged
of base pairs (definable for each clone based on the known clone
size range for a given library).
[0266] 3. Identifying Genes
[0267] Tables 1, 2, and 3 list ORFs in the Staphylococcus aureus
genomic contigs of the present invention that were identified as
putative coding regions by the GeneMark software using
organism-specific second-order Markov probability transition
matrices. It will be appreciated that other criteria can be used,
in accordance with well known analytical methods, such as those
discussed herein, to generate more inclusive, more restrictive, or
more selective lists.
[0268] Table 1 sets out ORFs in the Staphylococcus aureus contigs
of the present invention that over a continuous region of at least
50 bases are 95% or more identical (by BLASTN analysis) to a
nucleotide sequence available through Genbank in November 1996.
[0269] Table 2 sets out ORFs in the Staphylococcus aureus contigs
of the present invention that are not in Table 1 and match, with a
BLASTP probability score of 0.01 or less, polypeptide sequence
available through a non-redundant database of known protein
generated by combining the Swiss-Prot, PIR, and GenPept
databases.
[0270] Table 3 sets out the remaining ORFs in the Staphylococcus
aureus contigs of the present invention, which did not have
significant matches to the public databases by the criteria
described above.
[0271] Illustrative Applications
[0272] 1. Production of an Antibody to a Staphylococcus aureus
Protein
[0273] Substantially pure protein or polypeptide is isolated from
the transfected or transformed cells using any one of the methods
known in the art. The protein can also be produced in a recombinant
prokaryotic expression system, such as E. coli, or can by
chemically synthesized. Concentration of protein in the final
preparation is adjusted, for example, by concentration on an Amicon
filter device, to the level of a few micrograms/ml. Monoclonal or
polyclonal antibody to the protein can then be prepared as
follows.
[0274] 2. Monoclonal Antibody Production by Hybridoma Fusion
[0275] Monoclonal antibody to epitopes of any of the peptides
identified and isolated as described can be prepared from murine
hybridomas according to the classical method of Kohler, G. and
Milstein, C., Nature 256:495 (1975) or modifications of the methods
thereof. Briefly, a mouse is repetitively inoculated with a few
micrograms of the selected protein over a period of a few weeks.
The mouse is then sacrificed, and the antibody producing cells of
the spleen isolated. The spleen cells are fused by means of
polyethylene glycol with mouse myeloma cells, and the excess
unfused cells destroyed by growth of the system on selective media
comprising aminopterin (HAT media). The successfully fused cells
are diluted and aliquots of the dilution placed in wells of a
microtiter plate where growth of the culture is continued.
Antibody-producing clones are identified by detection of antibody
in the supernatant fluid of the wells by immunoassay procedures,
such as ELISA, as originally described by Engvall, E., Meth.
Enzymol. 70:419 (1980), and modified methods thereof. Selected
positive clones can be expanded and their monoclonal antibody
product harvested for use. Detailed procedures for monoclonal
antibody production are described in Davis, L. et al. Basic Methods
in Molecular Biology Elsevier, New York. Section 21-2 (1989).
[0276] 3. Polyclonal Antibody Production by Immunization
[0277] Polyclonal antiserum containing antibodies to heterogenous
epitopes of a single protein can be prepared by immunizing suitable
animals with the expressed protein described above, which can be
unmodified or modified to enhance immunogenicity. Effective
polyclonal antibody production is affected by many factors related
both to the antigen and the host species. For example, small
molecules tend to be less immunogenic than other and may require
the use of carriers and adjuvant. Also, host animals vary in
response to site of inoculations and dose, with both inadequate or
excessive doses of antigen resulting in low titer antisera. SmaII
doses (ng level) of antigen administered at multiple intradermal
sites appears to be most reliable. An effective immunization
protocol for rabbits can be found in Vaitukaitis, J. et al., J.
Clin. Endocrinol. Metab. 33:988-991 (1971).
[0278] Booster injections can be given at regular intervals, and
antiserum harvested when antibody titer thereof, as determined
semi-quantitatively, for example, by double immunodiffusion in agar
against known concentrations of the antigen, begins to fall. See,
for example, Ouchterlony, O. et al, Chap. 19 in: Handbook of
Experimental Immunology, Wier, D., ed, Blackwell (1973). Plateau
concentration of antibody is usually in the range of 0.1 to 0. 2
mg/ml of serum (about 12M). Affinity of the antisera for the
antigen is determined by preparing competitive binding curves, as
described, for example, by Fisher, D., Chap. 42 in: Manual of
Clinical Immunology, second edition, Rose and Friedman, eds., Amer.
Soc. For Microbiology, Wash., D.C. (1980)
[0279] Antibody preparations prepared according to either protocol
are useful in quantitative immunoassays which determine
concentrations of antigen-bearing substances in biological samples;
they are also used semi-quantitatively or qualitatively to identify
the presence of antigen in a biological sample. In addition, they
are useful in various animal models of Staphylococcal disease known
to those of skill in the art as a means of evaluating the protein
used to make the antibody as a potential vaccine target or as a
means of evaluating the antibody as a potential immunothereapeutic
reagent.
[0280] 4. Preparation of PCR Primers and Amplification of DNA
[0281] Various fragments of the Staphylococcus aureus genome, such
as those of Tables 1-3 and SEQ ID NOS: 1-5,191 can be used, in
accordance with the present invention, to prepare PCR primers for a
variety of uses. The PCR primers are preferably at least 15 bases,
and more preferably at least 18 bases in length. When selecting a
primer sequence, it is preferred that the primer pairs have
approximately the same G/C ratio, so that melting temperatures are
approximately the same. The PCR primers and amplified DNA of this
Example find use in the Examples that follow.
[0282] 5. Gene Expression from DNA Sequences Corresponding to
ORFs
[0283] A fragment of the Staphylococcus aureus genome provided in
Tables 1-3 is introduced into an expression vector using
conventional technology. Techniques to transfer cloned sequences
into expression vectors that direct protein translation in
mammalian, yeast, insect or bacterial expression systems are well
known in the art. Commercially available vectors and expression
systems are available from a variety of suppliers including
Stratagene (La Jolla, Calif.), Promega (Madison, Wis.), and
Invitrogen (San Diego, Calif.). If desired, to enhance expression
and facilitate proper protein folding, the codon context and codon
pairing of the sequence may be optimized for the particular
expression organism, as explained by Hatfield et al., U.S. Pat. No.
5,082,767, incorporated herein by this reference.
[0284] The following is provided as one exemplary method to
generate polypeptide(s) from cloned ORFs of the Staphylococcus
aureus genome fragment. Bacterial ORFs generally lack a poly A
addition signal. The addition signal sequence can be added to the
construct by, for example, splicing out the poly A addition
sequence from pSG5 (Stratagene) using BglI and SalI restriction
endonuclease enzymes and incorporating it into the mammalian
expression vector pXT1 (Stratagene) for use in eukaryotic
expression systems. pXT1 contains the LTRs and a portion of the gag
gene of Moloney Murine Leukemia Virus. The positions of the LTRs in
the construct allow efficient stable transfection. The vector
includes the Herpes Simplex thymidine kinase promoter and the
selectable neomycin gene. The Staphylococcus aureus DNA is obtained
by PCR from the bacterial vector using oligonucleotide primers
complementary to the Staphylococcus aureus DNA and containing
restriction endonuclease sequences for PstI incorporated into the
5' primer and BglII at the 5' end of the corresponding
Staphylococcus aureus DNA 3' primer, taking care to ensure that the
Staphylococcus aureus DNA is positioned such that its followed with
the poly A addition sequence. The purified fragment obtained from
the resulting PCR reaction is digested with PstI, blunt ended with
an exonuclease, digested with BglII, purified and ligated to pXT1,
now containing a poly A addition sequence and digested BglII.
[0285] The ligated product is transfected into mouse NIH 3T3 cells
using Lipofectin (Life Technologies, Inc., Grand Island, N.Y.)
under conditions outlined in the product specification. Positive
transfectants are selected after growing the transfected cells in
600 ug/ml G418 (Sigma, St. Louis, Mo.). The protein is preferably
released into the supernatant. However if the protein has membrane
binding domains, the protein may additionally be retained within
the cell or expression may be restricted to the cell surface. Since
it may be necessary to purify and locate the transfected product,
synthetic 15-mer peptides synthesized from the predicted
Staphylococcus aureus DNA sequence are injected into mice to
generate antibody to the polypeptide encoded by the Staphylococcus
aureus DNA.
[0286] Alternatively and if antibody production is not possible,
the Staphylococcus aureus DNA sequence is additionally incorporated
into eukaryotic expression vectors and expressed as, for example, a
globin fusion. Antibody to the globin moiety then is used to purify
the chimeric protein. Corresponding protease cleavage sites are
engineered between the globin moiety and the polypeptide encoded by
the Staphylococcus aureus DNA so that the latter may be freed from
the formed by simple protease digestion. One useful expression
vector for generating globin chimerics is pSG5 (Stratagene). This
vector encodes a rabbit globin. Intron II of the rabbit globin gene
facilitates splicing of the expressed transcript, and the
polyadenylation signal incorporated into the construct increases
the level of expression. These techniques are well known to those
skilled in the art of molecular biology. Standard methods are
published in methods texts such as Davis et al., cited elsewhere
herein, and many of the methods are available from the technical
assistance representatives from Stratagene, Life Technologies,
Inc., or Promega. Polypeptides of the invention also may be
produced using in vitro translation systems such as in vitro
Express.TM. Translation Kit (Stratagene).
[0287] While the present invention has been described in some
detail for purposes of clarity and understanding, one skilled in
the art will appreciate that various changes in form and detail can
be made without departing from the true scope of the invention.
[0288] All patents, patent applications and publications referred
to above are hereby incorporated by reference.
1TABLE 1 S. aureus - Coding regions containing known sequences HSP
ORF Contig ID ORF ID Start (nt) Stop (nt) match acession match gene
name percent ident nt length nt length 1 1 757 95
emb.vertline.X17301.vertline.SAHD S. aureus DNA for hld gene and
for part of agr gene 100 663 663 1 2 2452 1631
emb.vertline.X52543.vertline.SAAG S. aureus agrA, agrB and hld
genes 99 809 822 1 5 5651 4884 dbj.vertline.D14711.vertline.STAH
Staphylococcus aureus HSP10 and HSP60 genes 98 223 768 5 1 439 71
emb.vertline.X72700.vertline.SAPV S. aureus genes for S and F
components of Panton-Valentine leucocidins 81 216 369 5 4 3571 2111
emb.vertline.X72700.vertline.SAPV S. aureus genes for S and F
components of Panton-Valentine leucocidins 95 424 1461 10 1 86 904
gb.vertline.L25288.vertline. Staphylococcus aureus gyrase-like
protein alpha and beta subunit (grlA and 98 715 819 grlB) genes,
complete cds 16 5 5302 6246 gb.vertline.U35773.vertline.
Staphylococcus aureus prolipoprotein diacylglyceryl transferase
(lgt) gene, complete cds 94 251 945 16 6 6249 7091
gb.vertline.U35773.vertline. Staphylococcus aureus prolipoprotein
diacylglyceryl transferase (lgt) gene, 99 843 843 complete cds 16 7
7084 7584 gb.vertline.U35773.vertline. Staphylococcus aureus
prolipoprotein diacylglyceryl transferase (lgt) gene, 99 342 501
complete cds 20 1 549 103 gb.vertline.L19300.vertline.
Staphylococcus aureus DNA sequence encoding three ORFs, complete
cds; prophage phi-11 100 443 447 sequence homology, 5' flank 20 2
841 671 gb.vertline.L19300.vertline. Staphylococcus aureus DNA
sequence encoding three ORFs, complete cds; prophage phi-11 91 137
171 sequence homology, 5' flank 20 3 1798 1586
gb.vertline.L19300.vertline. Staphylococcus aureus DNA sequence
encoding three ORFs, complete cds; prophage phi-11 100 110 213
sequence homology, 5' flank 20 4 3825 2350 gb.vertline.M76714.vert-
line. Staphylococcus aureus peptidoglycan hydrolase gene, complete
cds 100 948 1476 20 5 4282 3776 gb.vertline.M76714.vertline.
Staphylococcus aureus peptidoglycan hydrolase gene, complete cds
100 309 507 26 1 2 145 gb.vertline.U41072.vertline. Staphylococcus
aureus isoleucyl-tRNA synthetase (ileS) gene, partial cds 100 126
144 26 2 84 557 gb.vertline.U41072.vertline. Staphylococcus aureus
isoleucyl-tRNA synthetase (ileS) gene, partial cds 99 430 474 26 3
763 3531 emb.vertline.X74219.vertline.SAIL S. aureus gene for
isoleucyl-tRNA synthetase 99 2769 2769 29 3 1261 4392
gb.vertline.U66665.vertline. Staphylococcus aureus DNA fragment
with class II promoter activity 100 117 3132 31 14 13463 11949
emb.vertline.X73889.vertline.SAP1 S. aureus genes P1 and P2 99 1351
1515 31 15 13855 13469 emb.vertline.X73889.vertline.SAP1 S. aureus
genes P1 and P2 98 258 387 38 17 13112 11940
gb.vertline.M12715.vertline. S. aureus geh gene encoding lipase
(glycerol ester hydrolase) 100 372 1173 38 19 13434 15518
gb.vertline.M12715.vertline. S. aureus geh gene encoding lipase
(glycerol ester hydrolase) 100 2085 2085 46 2 519 1727
gb.vertline.U73374.vertline. Staphylococcus aureus type 8 capsule
genes, cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G, 98 1209
1209 cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N, cap8O, cap8P,
complete cds 46 3 1720 2295 gb.vertline.U73374.vertline.
Staphylococcus aureus type 8 capsule genes, cap8A, cap8B, cap8C,
cap8D, cap8E, cap8F, cap8G, 98 576 576 cap8H, cap8I, cap8J, cap8K,
cap8L, cap8M, cap8N, cap8O, cap8P, complete cds 46 4 2259 3182
gb.vertline.U73374.vertline. Staphylococcus aureus type 8 capsule
genes, cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G, 97 924 924
cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N, cap8O, cap8P,
complete cds 46 5 3173 4498 gb.vertline.U73374.vertline.
Staphylococcus aureus type 8 capsule genes, cap8A, cap8B, cap8C,
cap8D, cap8E, cap8F, cap8G, 98 1283 1326 cap8H, cap8I, cap8J,
cap8K, cap8L, cap8M, cap8N, cap8O, cap8P, complete cds 46 6 4536
5720 gb.vertline.U73374.vertline. Staphylococcus aureus type 8
capsule genes, cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G, 98
1185 1185 cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N, cap8O,
cap8P, complete cds 46 7 6120 5785 gb.vertline.U73374.vertline.
Staphylococcus aureus type 8 capsule genes, cap8A, cap8B, cap8C,
cap8D, cap8E, cap8F, cap8G, 99 278 336 cap8H, cap8I, cap8J, cap8K,
cap8L, cap8M, cap8N, cap8O, cap8P, complete cds 48 1 2 955
gb.vertline.L25893.vertli- ne. Staphylococcus aureus recA gene,
complete cds 99 954 954 50 3 2924 1383
emb.vertline.X85029.vertline.SAAH S. aureus AhpC gene 100 88 1542
50 4 3515 2922 emb.vertline.X85029.vertline.SAAH S. aureus AhpC
gene 98 540 594 54 3 3392 1710 emb.vertline.X62992.vertline.S- AFN
S. aureus fnbB gene for fibronectin binding protein B 100 1668 1683
54 4 4122 3379 emb.vertline.X62992.vertline.SAFN S. aureus fnbB
gene for fibronectin binding protein B 99 720 744 54 5 4562 4068
emb.vertline.X62992.vertline.SAFN S. aureus fnbB gene for
fibronectin binding protein B 100 463 495 54 6 8300 5214
gb.vertline.J04151.vertline. S. aureus fibronectin-binding protein
(fnbA) mRNA, complete cds 100 3087 3087 58 3 1743 2819
emb.vertline.X87104.vertline.SADN S. aureus mdr, pbp4 and taqD
genes (SG511-55 isolate) 89 68 1077 58 4 2858 3280
emb.vertline.X91786.vertline.SAPB S. aureus abcA, pbp4, and tagD
genes 99 423 423 58 5 4701 3397 emb.vertline.X91786.vertline.SAPB
S. aureus abcA, pbp4, and tagD genes 99 1305 1305 58 6 5378 5079
gb.vertline.U29478.vertline. Staphylococcus aureus ABC
transporter-like protein AbcA (abcA) gene, 100 300 300 partial cds
58 7 5086 6840 emb.vertline.X91786.vertline.SAPB S. aureus abcA,
pbp4, and tagD genes 99 1755 1755 72 1 445 2
gb.vertline.M21854.vertline. S. aureus agr gene encoding an
accessory gene regulator protein, complete 100 444 444 cds 72 2
1453 449 emb.vertline.X52543.vert- line.SAAG S. aureus agrA, agrB
and hld genes 99 673 1005 82 1 357 3917
emb.vertline.X64172.vertline.SARP S. aureus rp1L, orf202, rpoB(rif)
and rpoC genes for ribosomal protein 99 2396 3561 L7/L12,
hypothetical protein ORF202, DNA-directed RNA polymerase beta &
beta` chains 82 2 4027 7677 emb.vertline.X89233.vertline.SARP S.
aureus DNA for rpoC gene 99 3171 3651 82 3 7745 8068
gb.vertline.U20869.vertline. Staphylococcus aureus ribosomal
protein S12 (rpsL) gene, complete cds, 100 320 324 ribosomal
protein S7 (rpsG) and ORF 1 genes, partial cds 82 4 8103 8579
gb.vertline.U20869.vertline. Staphylococcus aureus ribosomal
protein S12 (rpsL) gene, complete cds, 100 477 477 ribosomal
protein S7 (rpsG) and ORF 1 genes, partial cds 82 5 8618 8821
gb.vertline.U20869.vertline. Staphylococcus aureus ribosomal
protein S12 (rpsL) gene, complete cds, 100 154 204 ribosomal
protein S7 (rpsG) and ORF 1 genes, partial cds 84 1 18 191
gb.vertline.U73374.vertline. Staphylococcus aureus type 8 capsule
genes, cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G, 98 164 174
cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N, cap8O, cap8P,
complete cds 84 2 189 893 gb.vertline.U73374.vertline.
Staphylococcus aureus type 8 capsule genes, cap8A, cap8B, cap8C,
cap8D, cap8E, cap8F, cap8G, 94 705 705 cap8H, cap8I, cap8J, cap8K,
cap8L, cap8M, cap8N, cap8O, cap8P, complete cds 84 3 887 1660
gb.vertline.U73374.vertline. Staphylococcus aureus type 8 capsule
genes, cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G, 99 774 774
cap8I, cap8J, cap8K, cap8L, cap8M, cap8N, cap8O, cap8P, complete
cds 84 4 1584 3503 gb.vertline.U73374.vertl- ine. Staphylococcus
aureus type 8 capsule genes, cap8A, cap8B, cap8C, cap8D, cap8E,
cap8F, cap8G, 98 1920 1920 cap8H, cap8I, cap8J, cap8K, cap8L,
cap8M, cap8N, cap8O, cap8P, complete cds 84 5 3394 4521
gb.vertline.U73374.vertline. Staphylococcus aureus type 8 capsule
genes, cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G, 97 1128
1128 cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N, cap8O, cap8P,
complete cds 84 6 4519 5643 gb.vertline.U73374.vertline.
Staphylococcus aureus type 8 capsule genes, cap8A, cap8B, cap8C,
cap8D, cap8E, cap8F, cap8G, 97 1125 1125 cap8H, cap8I, cap8J,
cap8K, cap8L, cap8M, cap8N, cap8O, cap8P, complete cds 96 2 1245
3896 emb.vertline.Z18852.vertline.SA- CF S. aureus gene for
clumping factor 83 660 2652 97 2 625 882
gb.vertline.U41072.vertline. Staphylococcus aureus isoleucyl-tRNA
synthetase (ileS) gene, partial cds 97 68 258 111 1 3 452
gb.vertline.L41499.vertline. Staphylococcus aureus ORF1, partial
cds, ORF2, ORF3, autolysin (atl) genes, 100 450 450 complete cds
111 2 526 1041 gb.vertline.L41499.vertline. Staphylococcus aureus
ORF1, partial cds, ORF2, ORF3, autolysin (atl) genes, 99 516 516
complete cds 117 2 1278 1958 gb.vertline.M83994.vertline.
Staphylococcus aureus prolipoprotein signal peptidase (lsp) gene,
complete 100 61 681 cds 118 4 3787 4254
dbj.vertline.D30690.vertline.STAN Staphylococcus aureus genes for
ORF37; HSP20; HSP70; HSP40; ORF35, complete 99 467 468 cds 130 4
2597 3640 emb.vertline.X13290.vertline.SATN Staphylococcus aureus
multi-resistance plasmid pSK1 DNA containing 78 956 1044 transposon
Tn4003 130 5 3813 4265 emb.vertline.z16422.vertline.SAD- I S.
aureus dfrB gene for dihydrofolate reductase 98 416 453 130 6 4309
5172 emb.vertline.z16422.vertline.SADI S. aureus dfrB gene for
dihydrofolate reductase 98 607 864 136 4 5296 6207
emb.vertline.X71437.vertline.SAGY S. aureus genes gyrB, gyrA and
recF (partial) 97 838 912 136 5 8987 6294
dbj.vertline.D10489.vertline.- STAG Staphylococcus aureus genes for
DNA gyrase A and B, complete cds 100 2694 2694 136 6 10940 8994
dbj.vertline.D10489.vertline.STAG Staphylococcus aureus genes for
DNA gyrase A and B, complete cds 99 1947 1947 136 7 11765 10938
gb.vertline.S77055.vertline. recF cluster: dnaA = replisome
assembly protein...gyrB = DNA gyrase beta 99 822 828 subunit
[Staphylococcus aureus, YB886, Genomic, 5 genes, 3573 nt] 143 3
2867 1563 gb.vertline.U36379.vertline. Staphylococcus aureus
S-adenosylmethionine synthetase gene, complete cds 99 1305 1305 143
4 3100 4281 gb.vertline.L42943.vertline. Staphylococcus aureus
(clone KIN50) phosphoenolpyruvate carboxykinase 100 1170 1182
(pckA) gene, complete cds 143 5 4254 4718
gb.vertline.U51133.vertline. Staphylococcus aureus
phosphoenolpyruvate carboxykinase (pcka) gene, 100 449 465 complete
cds 143 9 6977 7261 gb.vertline.U51132.vertline. Staphylococcus
aureus o-succinylbenzoic acid CoA ligase (mene), and o- 100 75 285
succinylbenzoic acid synthetase (menc) genes, complete cds 143 10
8361 7258 gb.vertline.U51132.vertline. Staphylococcus aureus
o-succinylbenzoic acid CoA ligase (mene), and o- 100 1104 1104
succinylbenzoic acid synthetase (menc) genes, complete cds 143 11
9748 8264 gb.vertline.U51132.vertline. Staphylococcus aureus
o-succinylbenzoic acid CoA ligase (mene), and o- 100 1485 1485
succinylbenzoic acid synthetase (menc) genes, complete cds 143 12
10320 9901 gb.vertline.U51132.vertline. Staphylococcus aureus
o-succinylbenzoic acid CoA ligase (mene), and o- 100 332 420
succinylbenzoic acid synthetase (mene) genes, complete cds 152 5
2454 3437 emb.vertline.X58434.vertline.SAPD S. aureus pdhB, pdhC
and pdhD genes for pyruvate decarboxylase, 99 305 984
dihydrolipoamide acetyltransferase and dihydrolipoamide
dehydrogenase 152 6 3513 4820 emb.vertline.X58434.vertline.SAPD S.
aureus pdhB, pdhC and pdhD genes for pyruvate decarboxylase, 98
1308 1308 dihydrolipoamide acetyltransferase and dihydrolipoamide
dehydrogenase 152 7 4818 6230 emb.vertline.X58434.vertline.SAPD S.
aureus pdhB, pdhC and pdhD genes for pyruvate decarboxylase, 99
1413 1413 dihydrolipoamide acetyltransferase and dihydrolipoamide
dehydrogenase 153 1 387 1526 gb.vertline.S77055.vertline. recF
cluster: dnaA = replisome assembly protein.. .gyrB = DNA gyrase
beta 99 1140 1140 subunit [Staphylococcus aureus, YB886, Genomic, 5
genes, 3573 nt] 153 2 1877 2152 gb.vertline.S77055.vertline. recF
cluster: dnaA = replisome assembly protein...gyrB = DNA gyrase beta
100 276 276 subunit [Staphylococcus aureus, YB886, Genomic, 5
genes, 3573 nt] 153 3 2143 2289 gb.vertline.S77055.vertline. recF
cluster; dnaA = replisome assembly protein...gyrB = DNA gyrase beta
99 113 147 subunit [Staphylococcus aureus, YB886, Genomic, 5 genes,
3573 nt] 154 10 9314 7836 gb.vertline.U06451.vertline.
Staphylococcus aureus proline permease homolog (putP) gene,
complete cds 91 154 1479 154 11 9615 9295
gb.vertline.U06451.vertline. Staphylococcus aureus proline permease
homolog (putP) gene, complete cds 99 229 321 154 12 9943 10167
gb.vertline.U06451.vertline. Staphylococcus aureus proline permease
homolog (putP) gene, complete cds 94 123 225 154 13 10089 11501
gb.vertline.U06451.vertline. Staphylococcus aureus proline permease
homolog (putP) gene, complete cds 99 1326 1413 159 2 1212 229
dbj.vertline.D28879.vertline.STAP Staphylococcus aureus gene for
penicillin-binding protein 1, complete cds 100 71 984 161 3 2270
1944 gb.vertline.M83994.vertline. Staphylococcus aureus
prolipoprotein signal peptidase (lsp) gene, complete 92 203 327 cds
162 1 705 4 gb.vertline.U21221.vertline. Staphylococcus aureus
hyaluronate lyase (hysA) gene, complete cds 100 702 702 163 4 1263
1772 gb.vertline.U19770.vertline. Staphylococcus aureus pyrrolidone
carboxyl peptidase (pcp) gene, complete 96 127 510 cds 164 7 4774
9117 dbj.vertline.D86727.vertline.D867 Staphylococcus aureus DNA
for DNA polymerase III, complete cds 99 3470 4344 168 7 6447 5446
gb.vertline.U21636.vertline. Staphylococcus aureus
cmp-binding-factor 1 (cbf1) and ORF X genes, complete 100 1002 1002
cds 168 8 7961 6384 gb.vertline.U21636.vertline. Staphylococcus
aureus cmp-binding-factor 1 (cbf1) and ORF X genes, complete 99
1158 1578 cds 173 6 7801 6362 gb.vertline.J03479.vertline. S.
aureus enzyme III-lac (lacF), enzyme II-lac (lacE), and
phospho-beta- 100 1440 1440 galactosidase (lacG) genes, complete
cds 173 7 9522 7792 gb.vertline.J03479.vert- line. S. aureus enzyme
III-lac (lacF), enzyme II-lac (lacE), and phospho-beta- 99 1731
1731 galactosidase (lacG) genes, complete cds 173 8 8285 8704
gb.vertline.J03479.vertline. S. aureus enzyme III-lac (lacF),
enzyme II-lac (lacE), and phospho-beta- 100 420 420 galactosidase
(lacG) genes, complete cds 173 9 9839 9510
gb.vertline.J03479.vertline. S. aureus enzyme III-lac (lacF),
enzyme II-lac (lacE), and phospho-beta- 100 330 330 galactosidase
(lacG) genes, complete cds 173 10 10829 9843
emb.vertline.X14827.vertline.SALA Staphylococcus aureus lacC and
lacD genes 100 987 987 173 11 11774 10827
emb.vertline.X14827.vertline.- SALA Staphylococcus aureus lacC and
lacD genes 100 948 948 173 12 12305 11772
gb.vertline.M64724.vertline. S. aureus tagatose 6-phosphate
isomerase gene, complete cds 100 534 534 173 13 12773 12303
gb.vertline.M32103.vertline. Staphylococcus aureus lac repressor
(lacR) gene, complete cds and lacA 100 471 471 repressor (lacA),
partial cds 173 14 13866 13099 gb.vertline.M32103.vertline.
Staphylococcus aureus lac repressor (lacR) gene, complete cds and
lacA 100 768 768 repressor (lacA), partial cds 178 1 2 655
gb.vertline.U52961.vertline. Staphylococcus aureus holin-like
protein LrgA (lrgA) and LrgB (lrgB) genes, 100 115 654 complete cds
178 2 1482 763 gh.vertline.U52961.vertline. Staphylococcus aureus
holin-like protein LrgA (lrgA) and LrgB (lrgB) genes, 100 720 720
complete cds 178 3 1909 1457 gb.vertline.U52961.vertline.
Staphylococcus aureus holin-like protein LrgA (lrgA) and LrgB
(lrgB) genes, 100 453 453 complete cds 178 4 1551 1853
gb.vertline.U52961.vertline. Staphylococcus aureus holin-like
protein LrgA (lrgA) and LrgB (lrgB) genes, 100 303 303 complete cds
178 5 2777 2013 gb.vertline.L42945.vertline. Staphylococcus aureus
lytS and lytR genes, complete cds 99 765 765 178 6 3025 2756
gb.vertline.L42945.vertline. Staphylococcus aureus lytS and lytR
genes, complete cds 99 270 270 181 1 590 66
gb.vertline.M63177.vertline. S. aureus sigma factor (plaC) gene,
complete cds 99 499 525 182 1 3 341
emb.vertline.X61307.vertline.SASP Staphylococcus aureus spa
gene
for protein A 98 277 339 182 2 690 2312 gb.vertline.J01786.vertlin-
e. S. aureus spa gene coding for protein A, complete csd 97 1332
1623 182 3 4251 2641 emb.vertline.X61307.vertline.SASP
Staphylococcus aureus spa gene for protein A 99 119 1611 185 1 3
824 gb.vertline.U31979.vertline. Staphylococcus aureus chorismate
synthase (aroC) and nucleoside diphosphate 90 132 822 kinase (ndk)
genes, complete cds, dehydroauinate synthase (aroB) and
geranylgeranyl pyrophosphate synthetase homolog (gerCC) genes,
partial cds 191 3 841 2760 emb.vertline.X17679.vertline.SACO
Staphylococcus aureus coa gene for coagulase 99 1920 1920 191 4
2967 3143 emb.vertline.X16457.vertline.SAST Staphylococcus aureus
gene for staphylocoagulase 99 177 177 191 5 4566 3364
emb.vertline.X16457.vertline.SAST Staphylococcus aureus gene for
staphylocoagulase 99 250 1203 196 1 872 3 gb.vertline.L36472.vertl-
ine. Staphylococcus aureus lysyl-tRNA sythetase gene, complete cds,
transfer RNA 99 870 870 (tRNA) genes, 5S ribosomal RNA (5S rRNA)
gene, 16S ribosomal RNA (16S rRNA) gene, 23S ribosomal RNA (23S
rRNA) gene 198 3 1688 2011 emb.vertline.X93205.vertline.S- APT S.
aureus ptsH and ptsI genes 99 324 324 198 4 2005 2310
emb.vertline.X93205.vertline.SAPT S. aureus ptsH and ptsI genes 97
304 306 202 1 163 1305 emb.vertline.X97985.vertline.SA12 S. aureus
orfs 1,2,3 & 4 99 1143 1143 202 2 1303 2175
emb.vertline.X73889.vertline.SAP1 S. aureus genes P1 and P2 94 444
873 210 1 1558 2 dbj.vertline.D17366.vertline.STAA Staphylococcus
aureus atl gene for autolysin, complete cds and other ORFs 99 1552
1557 210 2 2232 1525 gb.vertline.L41499.vertline. Staphylococcus
aureus ORF1, partial cds, ORF2, ORF3, autolysin (atl) genes, 99 684
708 complete cds 214 11 7429 7770 dbj.vertline.D86240.vertline.D862
Staphylococcus aureus gene for unkown function and dlt operon dltA,
dltB, 96 157 342 dltC and dltD genes, complete cds 216 3 398 1318
emb.vertline.X72700.vertline.SAPV S. aureus genes for S and F
components of Panton-Valentine leucocidins 88 265 921 219 2 1073
336 dbj.vertline.D30690.vertline.STAN Staphylococcus aureus genes
for ORF37; HSP20; HSP70; HSP40; ORF35, complete 100 60 738 cds 219
3 2035 1091 dbj.vertline.D30690.vertline.STAN Staphylococcus aureus
genes for ORF37; HSP20; HSP70; HSP40; ORF35, complete 99 945 945
cds 219 4 3196 2033 dbj.vertline.D30690.vertline.STAN
Staphylococcus aureus genes for ORF37; HSP20; HSP70; HSP40; ORF35,
complete 99 1164 1164 cds 219 5 5176 3308
dbj.vertline.D30690.vertline.STAN Staphylococcus aureus genes for
ORF37; HSP20; HSP70; HSP40; ORF35, complete 98 1869 1869 cds 219 6
5883 5209 dbj.vertline.D30690.vertline.STAN Staphylococcus aureus
genes for ORF37; HSP20; HSP70; HSP40, ORF35, complete 99 675 675
cds 219 7 6334 5867 dbj.vertline.D30690.vertline.STAN
Staphylococcus aureus genes for ORF37; HSP20; HSP70; HSP40; ORF35,
complete 98 468 468 cds 221 8 10034 9252
gb.vertline.L19298.vertline. Staphylococcus aureus
phosphatidylinositol-specific phospholipase C (plc) 91 67 783 gene,
complete cds 223 1 1506 157 gb.vertline.U73374.vertline.
Staphylococcus aureus type 8 capsule genes, cap8A, cap8B, cap8C,
cap8D, 99 102 1350 cap8E, cap8F, cap8G, cap8H, cap8I, cap8J, cap8K,
cap8L, cap8M, cap8N, cap8O, cap8P, complete cds 234 1 2 1357
emb.vertline.X97985.vertline.SA12 S. aureus orfs 1,2,3 & 4 100
176 1356 234 2 1694 2485 emb.vertline.X97985.vertline.SA12 S.
aureus orfs 1,2,3 & 4 100 792 792 234 3 2648 3148
emb.vertline.X97985.ver- tline.SA12 S. aureus orfs 1,2,3 & 4 99
501 501 234 4 3120 4604 emb.vertline.X97985.vertline.SA12 S. aureus
orfs 1,2,3 & 4 99 1305 1485 236 6 3826 5322
gb.vertline.U48826.vertline. Staphylococcus aureus elastin binding
protein (ebpS) gene, complete cds 96 648 1497 248 1 2 403
emb.vertline.X62288.vertline.SAPE S. aureus DNA for
penicillin-binding protein 2 100 103 402 248 2 388 852
gb.vertline.L25426.vertline. Staphylococcus aureus
penicillin-binding protein 2 (pbp2) gene, complete 99 465 465 cds
253 2 1093 647 gb.vertline.U46541.vertline. Staphylococcus aureus
sarA gene, complete cds 96 447 447 254 2 150 1835
gb.vertline.U57060.vertline- . Staphylococcus aureus scdA gene,
complete cds 94 142 1686 254 3 1973 2728
gb.vertline.U57060.vertline. Staphylococcus aureus scdA gene,
complete cds 99 756 756 260 1 2 1900 gb.vertline.M90693.vertline.
Staphylococcus aureus glycerol ester hydrolase (lip) gene, complete
cds 99 1213 1899 265 1 1 942 dbj.vertline.D21131.vertline.STAS
Staphylococcus aureus gene for a participant in homogeneous
expression of 99 941 942 high-level methicillin resistance,
complete cds 265 2 476 264 dbj.vertline.D21131.vertline.STAS
Staphylococcus aureus gene for a participant in homogeneous
expression of 99 213 213 high-level methicillin resistance,
complete cds 265 3 1765 1112 dbj.vertline.D21131.vertline.STAS
Staphylococcus aureus gene for a participant in homogeneous
expression of 98 69 654 high-level methicillin resistance, complete
cds 266 1 2 1018 dbj.vertline.D14711.vertline.STAH Staphylococcus
aureus HSP10 and HSP60 genes 98 743 1017 282 1 1 525
gb.vertline.S72488.vertline. hemB = porphobilinogen synthase
[Staphylococcus aureus, SA1959, Genomic, 1087 100 110 525 nt] 282 2
516 1502 gb.vertline.S72488.vert- line. hemB = porphobilinogen
synthase [Staphylococcus aureus, SA1959, Genomic, 1087 100 952 987
nt] 284 1 3 170 gb.vertline.M63176.vertline. Staphylococcus aureus
helicase required for T181 replication (pcrA) gene, 98 84 168
complete cds 284 2 282 1034 gb.vertline.M63176.vertline.
Staphylococcus aureus helicase required for T181 replication (pcrA)
gene, 100 712 753 complete cds 284 3 1028 2026
gb.vertline.M63176.vertline. Staphylococcus aureus helicase
required for T181 replication (pcrA) gene, 99 979 999 complete cds
284 4 1990 2202 gb.vertline.M63176.vertline. Staphylococcus aureus
helicase required for T181 replication (pcrA) gene, 98 187 213
complete cds 289 3 1536 1991 gb.vertline.M32470.vertline. S. aureus
Sau3AI-restriction-enzyme and Sau3AI-modification-enzyme genes, 99
338 456 complete cds 303 1 2 868 gb.vertline.L01055.vertli- ne.
Staphylococcus aureus gamma-hemolysin components A, B and C (hlgA,
hlgB, 99 867 867 hglC) genes, complete cds 303 2 1409 2383
gb.vertline.L01055.vertline. Staphylococcus aureus gamma-hemolysin
components A, B and C (hlgA, hlgB, 100 975 975 hglC) genes,
complete cds 303 3 2367 3161 gb.vertline.L01055.vertline.
Staphylococcus aureus gamma-hemolysin components A, B and C (hlgA,
hlgB, 99 793 795 hglC) genes, complete cds 305 1 1355 3
dbj.vertline.D17366.vertline.STAA Staphylococcus aureus atl gene
for autolysin, complete cds and other ORFs 99 1343 1353 311 1 1315
2 gb.vertline.L42945.vertline. Staphylococcus aureus lytS and lytR
genes, complete cds 98 1314 1314 312 6 7019 7870
gb.vertline.L14017.vertl- ine. Staphylococcus aureus
methicillin-resistance protein (mecR) gene and 74 351 852 unknown
ORF, complete cds 323 1 1003 8 gb.vertline.U31175.vertline.
Staphylococcus aureus D-specific D-2-hydroxyacid dehydrogenase
(ddh) gene, 98 996 996 complete cds 326 1 1 237
emb.vertline.Y00356.vertline.SASP Staphylococcus aureus V8 serine
protease gene 100 108 237 338 1 388 89
emb.vertline.X64389.vertline.SALE S. aureus leuF-P83 gene for F
component of leucocidin R 98 259 300 338 2 1088 348
emb.vertline.X64389.vert- line.SALE S. aureus leuF-P83 gene for F
component of leucocidin R 97 137 741 342 2 579 1754
gb.vertline.U06462.vertline. Staphylococcus aureus SA4 FtsZ (ftsZ)
gene, complete cds 100 1176 1176 344 2 517 1248
emb.vertline.V01281.vertline.SANU S. aureus mRNA for nuclease 98
732 732 349 1 230 3 gb.vertline.M20393.vertline. S. aureus
bacteriophage phi-11 attachment site (attB) 96 172 228 353 1 516 16
gb.vertline.M83994.vertline. Staphylococcus aureus prolipoprotein
signal peptidase (lsp) gene, complete 100 187 501 cds 353 2 1046
510 gb.vertline.M83994.vertline. Staphylococcus aureus
prolipoprotein signal peptidase (lsp) gene, complete 99 537 537 cds
356 1 3 674 gb.vertline.U20503.vertline. Staphylococcus aureus MHC
class II analog gene, complete cds 75 671 672 361 1 1 903
gb.vertline.L19298.vertline. Staphylococcus aureus
phosphatidylinositol-specific phospholipase C (plc) 98 747 903
gene, complete cds 361 2 1103 1507 gb.vertline.L19298.vertline.
Staphylococcus aureus phosphatidylinositol-specific phospholipase C
(plc) 97 68 405 gene, complete cds 373 1 3 1148
emb.vertline.X62288.vertline.SAPE S. aureus DNA for
penicillin-binding protein 2 99 1146 1146 389 3 1248 592
emb.vertline.X62282.vertline- .SATS S. aureus target site DNA for
IS431 insertion 97 349 657 400 1 1 540
emb.vertline.X61716.vertline.SAHL S. aureus hlb gene encoding
sphingomyelinase 99 389 540 400 2 1187 681 emb.vertline.X13404.ver-
tline.SAHL Staphylococcus aureus hlb gene for beta-hemolysin 99 178
507 408 1 1049 288 gb.vertline.S76213.vertline. asp23 = alkaline
shock protein 23 (methicillin resistant) [Staphylococcus 99 163 762
aureus, 912, Genomic, 1360 nt] 418 1 2 217 gb.vertline.L41499.vert-
line. Staphylococcus aureus ORF1, partial cds, ORF2, ORF3,
autolysin (at1) genes, 100 216 216 complete cds 418 2 639 424
dbj.vertline.D17366.vertline.STAA Staphylococcus aureus at1 gene
for autolysin, complete cds and other ORFs 100 188 216 421 2 1262
2509 gb.vertline.L43098.vertline. Transposon Tn5404 and insertion
sequences IS1181 and IS1182 (from 99 1248 1248 Staphylococcus
aureus) DNA 422 1 2 325 gb.vertline.K02985.vertline. S. aureus
(strain RN450) transposon Tn554 insertion site 96 200 324 427 1 434
3 dbj.vertline.D28879.vertline.STAP Staphylococcus aureus gene for
penicillin-binding protein 1, complete cds 100 432 432 427 2 1122
415 dbj.vertline.D28879.vertline.STAP Staphylococcus aureus gene
for penicillin-binding protein 1, complete cds 100 151 708 435 1 2
808 dbj.vertline.D86240.vertline.D862 Staphylococcus aureus gene
for unkown function and dlt operon dltA, dltB, 100 556 807 dltC and
dltD genes,complete cds 435 2 832 999
dbj.vertline.D86240.vertline.D862 Staphylococcus aureus gene for
unkown function and dlt operon dltA, dltB, 100 134 168 dltC and
dltD genes, complete cds 436 1 685 29
emb.vertline.X17688.vertline.SAFE S. aureus factor essential for
expression of methicillin resistance (femA) 97 657 657 gene,
complete cds, and trpA gene, 3' end 436 2 1657 911
emb.vertline.X17688.vertline.SAFE S. aureus factor essential for
expression of methicillin resistance (femA) 100 294 747 gene,
complete cds, and trpA gene, 3' end 442 1 347 1300
emb.vertline.X72700.vertline.SAPV S. aureus genes for S and F
components of Panton-Valentine leucocidins 84 204 954 445 2 1906
2178 gb.vertline.L01055.vertline. Staphylococcus aureus
gamma-hemolysin components A, B and C (hlgA, hlgB, 98 187 273 hglC)
genes, complete cds 447 1 167 1078 gb.vertline.U19770.vertline.
Staphylococcus aureus pyrrolidone carboxyl peptidase (pcp) gene,
complete 100 51 912 cds 447 2 1176 1784 gb.vertline.U19770.vert-
line. Staphylococcus aureus pyrrolidone carboxyl peptidase (pcp)
gene, complete 96 597 609 cds 454 3 4319 1329
emb.vertline.Z18852.vertline.SACF S. aureus gene for clumping
factor 75 653 2991 472 4 5479 3062 gb.vertline.L25288.vertline.
Staphylococcus aureus gyrase-like protein alpha and beta subunit
(grlA and 99 2418 2418 grlB) genes, complete cds 472 5 6792 5464
gb.vertline.L25288.vertline. Staphylococcus aureus gyrase-like
protein alpha and beta subunit (grlA and 99 1328 1329 grlB) genes,
complete cds 475 2 566 889 emb.vertline.X52543.vertline.SAA- G S.
aureus agrA, agrB and hld genes 100 76 324 481 4 1560 1198
emb.vertline.X64172.vertline.SARP S. aureus rplL, orf202, rpoB(rif)
and rpoC genes for ribosomal protein 100 250 363 L7/L12,
hypothetical protein ORF202, DNA-directed RNA polymerase beta &
beta' chains 481 5 1244 1534 emb.vertline.X64172.vertline.SARP S.
aureus rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein
100 224 291 L7/L12, hypothetical protein ORF202, DNA-directed RNA
polymerase beta & beta' chains 487 2 1188 988
gb.vertline.M83994.vertline. Staphylococcus aureus prolipoprotein
signal peptidase (lsp) gene, complete 98 72 201 cds 489 1 1370 3
gb.vertline.U21221.vertline. Staphylococcus aureus hyaluronate
lyase (hysA) gene, complete cds 99 1368 1368 503 2 653 171
gb.vertline.M83994.vertline. Staphylococcus aureus prolipoprotein
signal peptidase (lsp) gene, complete 100 108 483 cds 511 3 1613
2242 gb.vertline.L14017.vertline. Staphylococcus aureus
methicillin-resistance protein (mecR) gene and 84 323 630 unknown
ORF, complete cds 511 4 2700 2278 gb.vertline.S76213.vertl- ine.
asp23 = alkaline shock protein 23 (methicillin resistant)
[Staphylococcus 96 423 423 aureus, 912, Genomic, 1360 nt] 520 2 758
1297 emb.vertline.X72014.vertline.SAFI S. aureus fib gene for
fibrinogen-binding protein 99 540 540 520 3 1436 1801
emb.vertline.X72013.vertline.SAFI S. aureus fib gene for
fibrinogen-binding protein 99 221 366 526 1 1092 34
dbj.vertline.D17366.vertline.STAA Staphylococcus aureus atl gene
for autolysin, complete cds and other ORFs 99 641 1059 528 2 58 963
gb.vertline.L19300.vertline. Staphylococcus aureus DNA sequence
encoding three ORFs, complete cds; 99 260 906 prophage phi-11
sequence homology, 5' flank 528 3 1098 2870
gb.vertline.L19300.vertline. Staphylococcus aureus DNA sequence
encoding three ORFs, complete cds; 99 866 1773 prophage phi-11
sequence homology, 5' flank 530 1 3 434
gb.vertline.U31979.vertline. Staphylococcus aureus chorismate
synthase (aroC) and nucleoside diphosphate 99 432 432 kinase (ndk)
genes, complete cds, dehydroauinate synthase (aroB) and
geranylgeranyl pyrophosphate synthetase homolog (gerCC) genes,
partial cds 530 2 1211 2395 gb.vertline.U31979.vertline.
Staphylococcus aureus chorismate synthase (aroC) and nucleoside
diphosphate 91 1185 1185 kinase (ndk) genes; complete cds,
dehydroauinate synthase (aroB) and geranylgeranyl pyrophosphate
synthetase homolog (gerCC) genes, partial cds 530 3 2409 2801
gb.vertline.U31979.vert- line. Staphylococcus aureus chorismate
synthase (aroC) and nucleoside diphosphate 88 181 393 kinase (ndk)
genes, complete cds, dehydroauinate synthase (aroB) and
geranylgeranyl pyrophosphate synthetase homolog (gerCC) genes,
partial cds 530 4 2690 3484 gb.vertline.L05004.vertline.
Staphylococcus aureus dehydroquinate synthase (aroB) gene, 3' end
cds; 3- 100 75 795 phosphoshikimate-1-carboxyvinyltransferase
(aroA) gene, complete cds; ORF3, complete cds 530 5 3482 4792
gb.vertline.L05004.vertline. Staphylococcus aureus dehydroquinate
synthase (aroB) gene, 3' end cds; 3- 99 905 1311
phosphoshikimate-1-carboxyvinyltransferase (aroA) gene, complete
cds; ORF3, complete cds 530 6 4790 5380 gb.vertline.L05004.vert-
line. Staphylococcus aureus dehydroquinate synthase (aroB) gene, 3'
end cds; 3- 100 196 591 phosphoshikimate-1-carboxyvinyltransferas-
e (aroA) gene, complete cds; ORF3, complete cds 539 1 3 338
emb.vertline.X76490.vertline.SAGL S. aureus (bb270) glnA and glnR
genes 99 336 336 539 2 336 527 emb.vertline.X76490.vertline.SAGL S.
aureus (bb270) glnA and glnR genes 100 189 192 554 1 365 3
gb.vertline.U73374.vertline. Staphylococcus aureus type 8 capsule
genes, cap8A, cap8B, cap8C, cap8D, 100 54 363 cap8E, cap8F, cap8G,
cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N, cap8O, cap8P,
complete cds 554 2 1252 329 gb.vertline.U73374.vertline.
Staphylococcus aureus type 8 capsule genes, cap8A, cap8B, cap8C,
cap8D, 99 918 924 cap8E, cap8F, cap8G, cap8H, cap8I, cap8J, cap8K,
cap8L, cap8M, cap8N, cap8O, cap8P, complete cds 554 3 1374 1174
gb.vertline.U73374.vertline. Staphylococcus aureus type 8 capsule
genes, cap8A, cap8B, cap8C, cap8D, 96 122 201 cap8E, cap8F, cap8G,
cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N, cap8O, cap8P,
complete cds 584 2 705 391 gb.vertline.U21221.vertl- ine.
Staphylococcus aureus hyaluronate lyase (hysA) gene, complete cds
99 306 315 587 3 1475 4288 emb.vertline.Z18852.vertline.SACF S.
aureus gene for clumping factor 98 2588 2814 598 1 1953 25
dbj.vertline.D28879.vertline.STAP Staphylococcus aureus gene for
penicillin-binding protein 1, complete cds 99 1873 1929 605 1 2 745
dbj.vertline.D86240.vertline.D862 Staphylococcus aureus gene for
unkown function and dlt operon dltA, dltB, 98 338 744 dltC and dltD
genes, complete cds 609 1 816 4 emb.vertline.X76490.vertl- ine.SAGL
S. aureus (bb270) glnA and glnR genes 100 495 813 614 1 642 4
gb.vertline.M32103.vertline. Staphylococcus aureus lac repressor
(lacR) gene, complete cds and lacA 99 639 639 repressor (lacA),
partial cds 626 1 1255 2 gb.vertline.M63176.vertline.
Staphylococcus aureus helicase required for T181 replication (pcrA)
gene, 100 225 1254 complete cds 626 2 2284 1253
gb.vertline.M63176.vertline. Staphylococcus aureus helicase
required for T181 replication (pcrA) gene, 99 838 1032 complete cds
629 1 1001 3 emb.vertline.X17688.vertline.SAFE S. aureus factor
essential for expression of methicillin resistance (femA) 99 990
999 gene, complete cds, and trpA gene, 3' end 629 2 1195 983
emb.vertline.X17688.vertline.SAFE S. aureus factor essential for
expression of methicillin resistance (femA) 98 194 213 gene,
complete cds, and trpA gene, 3' end 631 2 3228 1330
emb.vertline.Z18852.vertline.SACF S. aureus gene for clumping
factor 82 489 1899 632 1 3 551 emb.vertline.Z30588.vertline.SAST S.
aureus (RN4220) genes for potential ABC transporter and potential
99 549 549 membrane spanning protein 632 2 529 1323
emb.vertline.Z30588.vertline.SAST S. aureus (RN4220) genes for
potential ABC transporter and potential 99 795 795 membrane
spanning protein 651 1 1070 231 gb.vertline.L19300.vertline.
Staphylococcus aureus DNA sequence encoding three ORFs, complete
cds; 99 478 840 prophage phi-11 sequence homology, 5' flank 657 2
1105 410 gb.vertline.L14017.vertline. Staphylococcus aureus
methicillin-resistance protein (mecR) gene and 84 456 696 unknown
ORF, complete cds 662 1 456 4 emb.vertline.X13404.vertline.SAHL
Staphylococcus aureus hlb gene for beta-hemolysin 100 369 453 662 2
230 475 emb.vertline.X13404.vertline.SAHL Staphylococcus aureus hlb
gene for beta-hemolysin 100 246 246 662 3 746 1399
emb.vertline.X13404.vert- line.SAHL Staphylococcus aureus hlb gene
for beta-hemolysin 99 653 654 682 1 480 4
gb.vertline.M63177.vertline. S. aureus sigma factor (plaC) gene,
complete cds 100 136 477 685 1 592 2 gb.vertline.U65000.vert- line.
Staphylococcus aureus type-I signal peptidase SpsA (spsA) gene, and
type-I 98 534 591 signal peptidase SpsB (spaB) gene, complete cds
685 2 1153 590 gb.vertline.U65000.vertline. Staphylococcus aureus
type-I signal peptidase SpsA (spsA) gene, and type-I 96 564 564
signal peptidase SpsB (spsB) gene, complete cds 697 1 3 527
gb.vertline.M63177.vertline. S. aureus sigma factor (plaC) gene,
complete cds 100 195 525 697 2 485 784 gb.vertline.M63177.vertline-
. S. aureus sigma factor (plaC) gene, complete cds 97 280 300 710 1
15 503 dbj.vertline.D86240.vertline.D862 Staphylococcus aureus gene
for unkown function and dlt operon dltA, dltB, 99 217 489 dltC and
dltD genes, complete cds 733 1 26 205 gb.vertline.M80252.vertl-
ine. Staphylococcus aureus norA1199 gene (which mediates active
efflux of 97 140 180 fluoroguinolones), complete cds 741 1 1197 658
dbj.vertline.D83951.vertline.STAL Staphylococcus aureus DNA for
LukM component, LukF-PV like component, 81 522 540 complete cds 752
1 1 636 emb.vertline.Y00356.vertline.SASP Staphylococcus aureus V8
serine protease gene 99 618 636 752 2 588 956
emb.vertline.Y00356.vertline.SASP Staphylococcus aureus V8 serine
protease gene 99 340 369 756 1 709 110 emb.vertline.X01645.vertlin-
e.SATO Staphylococcus aureus (Wood 46) gene for alpha-toxin 98 567
600 777 1 950 318 emb.vertline.Z49245.vertline.SA42 S. aureus
partial sod gene for superoxide dismutase 99 429 633 780 1 557 3
gb.vertline.U20503.vertline. Staphylococcus aureus MHC class II
analog gene, complete cds 86 550 555 784 1 73 687
gb.vertline.U63529.vert- line. Staphylococcus aureus novel antigen
gene, complete cds 99 568 615 797 1 182 544
dbj.vertline.D14711.vertline.STAH Staphylococcus aureus HSP10 and
HSP60 genes 98 363 363 798 1 302 72
emb.vertline.X58434.vertline.SAPD S. aureus pdhB, pdhC and pdhD
genes for pyruvate decarboxylase, 95 196 231 dihydrolipoamide
acetyltransferase and dihydrolipoamide dehydrogenase 823 1 3 467
gb.vertline.S77055.vertline. recF cluster: dnaA = replisome
assembly protein...gyrB = DNA gyrase beta 99 156 465 subunit
[Staphylococcus aureus, YB886, Genomic, 5 genes, 3573 nt] 848 1 175
2 gb.vertline.L25288.vertline. Staphylococcus aureus gyrase-like
protein alpha and beta subunit (grlA and 99 174 174 grlB) genes,
complete cds 848 2 318 160 gb.vertline.L25288.vertline.
Staphylococcus aureus gyrase-like protein alpha and beta subunit
(grlA and 100 131 159 grlB) genes, complete cds 866 1 397 2
emb.vertline.X64172.vertline.SARP S. aureus rplL, orf202, rpoB(rif)
and rpoC genes for ribosomal protein 99 395 396 L7/L12,
hypothetical protein ORF202, DNA-directed RNA polymerase beta &
beta' chains 883 1 1 285 dbj.vertline.D90119.vertline.STAN S.
aureus norA gene 99 131 285 884 1 334 62 emb.vertline.X52543.vertl-
ine.SAAG S. aureus agrA, agrB and hld genes 98 265 273 884 2 522
328 emb.vertline.X52543.vertline.SAAG S. aureus agrA, agrB and hld
genes 100 195 195 912 2 517 681 emb.vertline.Z30588.vertline.SAST
S. aureus (RN4220) genes for potential ABC transporter and
potential 99 163 165 membrane spanning protein 917 1 2 265
gb.vertline.M64724.vertline. S. aureus tagatose 6-phosphate
isomerase gene, complete cds 99 247 264 917 2 238 396
gb.vertline.M64724.vertline. S. aureus tagatose 6-phosphate
isomerase gene, complete cds 95 147 159 918 1 1215 4
emb.vertline.X93205.ver- tline.SAPT S. aureus ptsH and ptsI genes
99 1212 1212 967 1 1 411 dbj.vertline.D90119.vertline.STAN S.
aureus norA gene 97 395 411 991 1 337 2
emb.vertline.X52543.vertline.SAAG S. aureus agrA, agrB and hld
genes 99 336 336 1000 1 845 573 gb.vertline.L14017.vertline.
Staphylococcus aureus methicillin-resistance protein (mecR) gene
and 78 190 273 unknown ORF, complete cds 1001 1 265 32
dbj.vertline.D86240.vertline.D862 Staphylococcus aureus gene for
unkown function and dlt operon dltA, dltB, 99 234 234 dltC and dltD
genes, complete cds 1010 1 1 285 gb.vertline.U21221.vertline.
Staphylococcus aureus hyaluronate lyase (hysA) gene, complete cds
99 224 285 1046 1 330 4 emb.vertline.X72700.vertline.SAPV S. aureus
genes for S and F components of Panton-Valentine leucocidins 85 205
327 1060 1 286 92 emb.vertline.X58434.vertline.SAPD S. aureus pdhB,
pdhC and pdhD genes for pyruvate decarboxylase, 99 180 195
dihydrolipoamide acetyltransferase and dihydrolipoamide
dehydrogenase 1073 1 589 2 gb.vertline.K02985.vertline. S. aureus
(strain RN450) transposon Tn554 insertion site 100 131 588 1079 1 3
230 dbj.vertline.D86240.vertline.D862 Staphylococcus aureus gene
for unkown function and dlt operon dltA, dltB, 99 228 228 dltC and
dltD genes, complete cds 1079 2 218 484
dbj.vertline.D86240.vertline.D8- 62 Staphylococcus aureus gene for
unkown function and dlt operon dltA, dltB, 100 267 267 dltC and
dltD genes, complete cds 1079 3 460 645
dbj.vertline.D86240.vertline.D862 Staphylococcus aureus gene for
unkown function and dlt operon dltA, dltB, 100 186 186 dltC and
dltD genes, complete cds 1092 1 146 3
emb.vertline.X58434.vertline.SAPD S. aureus pdhB, pdhC and pdhD
genes for pyruvate decarboxylase, 98 124 144 dihydrolipoamide
acetyltransferase and dihydrolipoamide dehydrogenase 1143 1 1 243
gb.vertline.M63177.vertline. S. aureus sigma factor (plaC) gene,
complete cds 99 243 243 1157 1 2 136
emb.vertline.Z48003.vertline.SADN S. aureus gene for DNA polymerase
III 97 127 135 1189 1 361 2 gb.vertline.S74031.vertline. norA =
NorA (ISP794) [Staphylococcus aureus, NCTC 8325, Insertion, 1820
nt] 99 360 360 1190 1 2 283 gb.vertline.M21854.vertline. S. aureus
agr gene encoding an accessory gene regulator protein, complete 100
282 282 cds 1190 2 888 649 emb.vertline.X52543.vertline.SAAG S.
aureus agrA, agrB and hld genes 100 240 240 1225 1 2 163
emb.vertline.X17679.vertline.SACO Staphylococcus aureus coa gene
for coagulase 97 124 162 1243 1 2 529
dbj.vertline.D86240.vertline.D862 Staphylococcus aureus gene for
unkown function and dlt operon dltA, dltB, 99 495 528 dltC and dltD
genes, complete cds 1244 1 1 210 gb.vertline.S74031.vertl- ine.
norA = NorA (ISP794) [Staphylococcus aureus, NCTC 8325, Insertion,
1820 nt] 100 210 210 1301 1 41 472 emb.vertline.X76490.vertline.SA-
GL S. aureus (bb270) glnA and glnR genes 99 299 432 1315 1 18 326
emb.vertline.X64172.vertline.SARP S. aureus rplL, orf202, rpoB(rif)
and rpoC genes for ribosomal protein 98 277 309 L7/L12,
hypothetical protein ORF202, DNA-directed RNA polymerase beta &
beta' chains 1519 1 2 175 dbj.vertline.D28879.vertline.STAP
Staphylococcus aureus gene for penicillin-binding protein 1,
complete cds 98 139 174 1663 1 675 4
dbj.vertline.D86240.vertline.D862 Staphylococcus aureus gene for
unkown function and dlt operon dltA, dltB, 98 672 672 dltC and dltD
genes, complete cds 1797 1 324 4 gb.vertline.U73374.vertline.
Staphylococcus aureus type 8 capsule genes, cap8A, cap8B, cap8C,
csp8D, 99 321 321 cap8E, cap8F, cap8G, cap8H, cap8I, cap8J, cap8K,
cap8L, cap8M, cap8N, cap8O, cap8P, complete cds 1857 1 1 192
gb.vertline.M90536.vertlin- e. Staphylococcus aureus
alpha-hemolysin gene, 3' end 98 192 192 1923 1 2 181
emb.vertline.X17688.vertline.SAFE S. aureus factor essential for
expression of methicillin resistance (femA) 100 180 180 gene,
complete cds, and trpA gene, 3' end 1957 1 2 346
gb.vertline.U60589.vertline. Staphylococcus aureus novel antigen
gene, complete cds 99 345 345 1988 1 1 402
dbj.vertline.D86240.vertline.- D862 Staphylococcus aureus gene for
unkown function and dlt operon dltA, dltB, 100 402 402 dltC and
dltD genes, complete cds 2100 1 208 2 gb.vertline.M63177.vertline.
S. aureus sigma factor (plaC) gene, complete cds 99 207 207 2199 1
1 402 gb.vertline.U66664.vert- line. Staphylococcus aureus DNA
fragment with class II promoter activity 99 131 402 2537 1 156 4
emb.vertline.X17688.vertline.SAFE S. aureus factor essential for
expression of methicillin resistance (femA) 99 153 153 gene,
complete cds, and trpA gene, 3' end 2891 1 2 400
gb.vertline.L25426.vertline. Staphylococcus aureus
penicillin-binding protein 2 (pbp2) gene, complete 99 399 399 cds
2950 1 398 18 dbj.vertline.D30690.vertline.STAN Staphylococcus
aureus genes for ORF37; HSP20; HSP70; HSP40; ORF35, complete 100
358 381 cds 2971 1 3 398 gb.vertline.U51132.vertline.
Staphylococcus aureus o-succinylbenzoic acid CoA ligase (mene), and
o- 97 272 396 succinylbenzoic acid synthetase (menc) genes,
complete cds 2978 1 328 38 gb.vertline.U31979.vertline.
Staphylococcus aureus chorismate synthase (aroC) and nucleoside
diphosphate 98 250 291 kinase (ndk) genes, complete cds,
dehydroauinate synthase (aroB) and geranylgeranyl pyrophosphate
synthetase homolog (gerCC) genes, partial cds 2985 1 464 96
emb.vertline.X17679.vertline.SACO Staphylococcus aureus coa gene
for coagulase 98 347 369 3006 1 1784 1398 gb.vertline.U11779.vertl-
ine. Staphylococcus aureus methicillin-resistant ATCC 33952 clone
RRNV30 16S-23S 87 82 387 rRNA spacer region 3008 1 238 2
dbj.vertline.D30690.vertline.STAN Staphylococcus aureus genes for
ORF37; HSP20; HSP70; HSP40; ORF35, complete 88 178 237 cds 3008 2
281 111 dbj.vertline.D30690.vertline.STAN Staphylococcus aureus
genes for ORF37; HSP20; HSP70; HSP40; ORF35, complete 97 120 171
cds 3011 1 398 3 emb.vertline.X62992.vertline.SAFN S. aureus fnbB
gene for fibronectin binding protein B 93 72 396 3019 1 2 235
gb.vertline.J03479.vertline. S. aureus enzyme III-lac (lacF),
enzyme II-lac (lacE), and phospho-beta- 97 234 234 galactosidase
(lacG) genes, complete cds 3023 1 81 233 gb.vertline.U06451.vertli-
ne. Staphylococcus aureus proline permease homolog (putP) gene,
complete cds 87 100 153 3029 1 90 287 gb.vertline.U51133.vertline.
Staphylococcus aureus phosphoenolpyruvate carboxykinase (pcka)
gene, 100 135 198 complete cds 3039 1 18 164
gb.vertline.U51133.vertline. Staphylococcus aureus
phosphoenolpyruvate carboxykinase (pcka) gene, 97 135 147 complete
cds 3039 2 70 327 gb.vertline.U51133.vertline. Staphylococcus
aureus phosphoenolpyruvate carboxykinase (pcka) gene, 77 183 258
complete cds 3056 1 3 215 emb.vertline.X64172.vertline.SARP S.
aureus rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein
99 213 213 L7/L12, hypothetical protein ORF202, DNA-directed RNA
polymerase beta & beta` chains 3059 1 1 261
dbj.vertline.D30690.vertline.STAN Staphylococcus aureus genes for
ORF37; HSP20; HSP70; HSP40; ORF35, complete 98 234 261 cds 3073 1
27 284 gb.vertline.U06451.vertline. Staphylococcus aureus proline
permease homolog (putP) gene, complete cds 99 229 258 3074 1 2 397
emb.vertline.X64172.vertline.SARP S. aureus rplL, orf202, rpoB(rif)
and rpoC genes for ribosomal protein 96 250 396 L7/L12,
hypothetical protein ORF202, DNA-directed RNA polymerase beta &
beta` chains 3088 1 3 239 dbj.vertline.D86727.vertline.D867
Staphylococcus aureus DNA for DNA polymerase III, complete cds 95
215 237 3097 1 244 44 emb.vertline.Z48003.vertline.SADN S. aureus
gene for DNA polymerase III 97 160 201 3102 1 155 3
gb.vertline.J03479.vert- line. S. aureus enzyme III-lac (lacF),
enzyme II-lac (lacE), and phospho-beta- 97 142 153 galactosidase
(lacG) genes, complete cds 3121 1 398 228
emb.vertline.X58434.vertline.SAPD S. aureus pdhB, pdhC and pdhD
genes for pyruvate decarboxylase, 100 88 171 dihydrolipoamide
acetyltransferase and dihydrolipoamide dehydrogenase 3125 1 233 3
emb.vertline.X89233.vertline.SARP S. aureus DNA for rpoC gene 98
192 231 3133 1 2 175 emb.vertline.Z18852.vertline.SAC- F S. aureus
gene for clumping factor 96 154 174 3160 1 211 2
dbj.vertline.D10489.vertline.STAG Staphylococcus aureus genes for
DNA gyrase A and B, complete cds 89 197 210 3176 1 1 378
emb.vertline.X58434.vertline.SAPD S. aureus pdhB, pdhC and pdhD
genes for pyruvate decarboxylase, 96 91 378 dihydrolipoamide
acetyltransferase and dihydrolipoamide dehydrogenase 3192 1 211 2
gb.vertline.J03479.vertline. S. aureus enzyme III-lac (lacF),
enzyme II-lac (lacE), and phospho-beta- 98 72 210 galactosidase
(lacG) genes, complete cds 3210 1 3 143 gb.vertline.M76714.vertlin-
e. Staphylococcus aureus peptidoglycan hydrolase gene, complete cds
96 141 141 3232 3 1282 458 gb.vertline.L14017.vertline.
Staphylococcus aureus methicillin-resistance protein (mecR) gene
and 71 257 825 unknown ORF, complete cds 3538 1 2 394
emb.vertline.X89233.vert- line.SARP S. aureus DNA for rpoC gene 99
350 393 3543 1 392 634 gb.vertline.L11530.vertline. Staphylococcus
aureus transfer RNA sequence with two rRNAs 99 102 243 3555 1 320 3
emb.vertline.Z18852.vertlin- e.SACF S. aureus gene for clumping
factor 99 307 318 3559 1 3 182 emb.vertline.X17679.vertline.SACO
Staphylococcus aureus coa gene for coagulase 100 141 180 3559 2 95
313 emb.vertline.X17679.vertline.S- ACO Staphylococcus aureus coa
gene for coagulase 98 174 219 3563 1 141 4
gb.vertline.U35773.vertline. Staphylococcus aureus prolipoprotein
diacylglyceryl transferase (lgt) gene, 100 79 138 complete cds 3563
2 363 199 gb.vertline.U35773.vertline. Staphylococcus aureus
prolipoprotein diacylglyceryl transferase (lgt) gene, 98 162 165
complete cds 3566 1 3 422 emb.vertline.X16457.vertline.S- AST
Staphylococcus aureus gene for staphylocoagulase 98 175 420 3588 1
2 262 gb.vertline.L43098.vertline. Transposon Tn5404 and insertion
sequences IS1181 and IS1182 (from 99 253 261 Staphylococcus aureus)
DNA 3593 1 3 350 gb.vertline.J03479.vertline. S. aureus enzyme
III-lac (lacF), enzyme II-lac (lacE), and phospho-beta- 99 345 348
galactosidase (lacG) genes, complete cds 3600 1 381 4
emb.vertline.Z18852.vertline.SACF S. aureus gene for clumping
factor 72 346 378 3602 1 396 4 emb.vertline.Z18852.vertline.SACF S.
aureus gene for clumping factor 98 319 393 3656 1 528 43
emb.vertline.Z18852.vertline.SACF S. aureus gene for clumping
factor 84 403 486 3682 1 3 236 emb.vertline.X64172.vertline.SARP S.
aureus rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein
100 231 234
L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase
beta & beta` chains 3682 2 224 415
emb.vertline.X64172.vertline.SARP S. aureus rplL, orf202, rpoB(rif)
and rpoC genes for ribosomal protein 100 112 192 L7/L12,
hypothetical protein ORF202, DNA-directed RNA polymerase beta &
beta` chains 3693 1 423 88 emb.vertline.X62992.vertline.SAFN S.
aureus fnbB gene for fibronectin binding protein B 100 229 336 3702
1 354 115 gb.vertline.L11530.vertline. Staphylococcus aureus
transfer RNA sequence with two rRNAs 96 81 240 3725 1 463 2
emb.vertline.Z18852.vertline.SACF S. aureus gene for clumping
factor 71 367 462 3761 1 450 91 gb.vertline.L14017.vertline.
Staphylococcus aureus methicillin-resistance protein (mecR) gene
and 85 333 360 unknown ORF, complete cds 3767 1 1 402
emb.vertline.X64172.vert- line.SARP S. aureus rplL, orf202,
rpoB(rif) and rpoC genes for ribosomal protein 98 387 402 L7/L12,
hypothetical protein ORF202, DNA-directed RNA polymerase beta &
beta` chains 3775 1 2 286 emb.vertline.X64172.vertline.SARP S.
aureus rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein
100 227 285 L7/L12, hypothetical protein ORF202, DNA-directed RNA
polymerase beta & beta' chains 3786 1 229 2
dbj.vertline.D10489.vertline.STAG Staphylococcus aureus genes for
DNA gyrase A and B, complete cds 100 204 228 3786 2 366 190
dbj.vertline.D10489.vertline.STAG Staphylococcus aureus genes for
DNA gyrase A and B, complete cds 95 123 177 3798 1 3 251
emb.vertline.X17679.vertline.SACO Staphylococcus aureus coa gene
for coagulase 99 249 249 3813 1 398 3 gb.vertline.J04151.vertline.
S. aureus fibronectin-binding protein (fnbA) mRNA, complete cds 98
396 396 3819 1 184 402 emb.vertline.X68425.vertline.SA23 S. aureus
gene for 23S rRNA 99 161 219 3844 1 468 4
gb.vertline.U48826.vertline. Staphylococcus aureus elastin binding
protein (ebpS) gene, complete cds 87 204 465 3845 1 1 381
emb.vertline.X58434.vertline.SAPD S. aureus pdhB, pdhC and pdhD
genes for pyruvate decarboxylase, 94 356 381 dihydrolipoamide
acetyltransferase and dihydrolipoamide dehydrogenase 3856 1 400 2
gb.vertline.L14017.vertline. Staphylococcus aureus
methicillin-resistance protein (mecR) gene and 76 192 399 unknown
ORF, complete cds 3859 1 573 97 emb.vertline.Z18852.vertline.SACF
S. aureus gene for clumping factor 85 347 477 3871 1 327 4
gb.vertline.M76714.vertlin- e. Staphylococcus aureus peptidoglycan
hydrolase gene, complete cds 100 299 324 3876 1 2 253
dbj.vertline.D10489.vertline.STAG Staphylococcus aureus genes for
DNA gyrase A and B, complete cds 100 217 252 3877 1 288 4
gb.vertline.J03479.vertline. S. aureus enzyme III-lac (lacF),
enzyme II-lac (lacE), and phospho-beta- 97 209 285 galactosidase
(lacG) genes, complete cds 3878 1 1 237
emb.vertline.X58434.vertline.SAPD S. aureus pdhB, pdhC and pdhD
genes for pyruvate decarboxylase, 96 155 237 dihydrolipoamide
acetyltransferase and dihydrolipoamide dehydrogenase 3888 1 3 173
emb.vertline.X16457.vertline.SAST Staphylococcus aureus gene for
staphylocoagulase 98 171 171 3893 1 1 183 emb.vertline.X89233.vert-
line.SARP S. aureus DNA for rpoC gene 100 170 183 3893 2 181 357
emb.vertline.X89233.vertline.SARP S. aureus DNA for rpoC gene 98 79
177 3894 1 3 485 emb.vertline.X64172.vertline.SARP S. aureus rplL,
orf202, rpoB(rif) and rpoC genes for ribosomal protein 99 450 483
L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase
beta & beta` chains 3895 1 420 4 gb.vertline.J04151.vertlin- e.
S. aureus fibronectin-binding protein (fnbA) mRNA, complete cds 99
411 417 3905 1 48 239 gb.vertline.L05004.vertline. Staphylococcus
aureus dehydroquinate synthase (aroB) gene, 3' end cds; 3- 100 159
192 phosphoshikimate-1-carboxyvinyltransferase (aroA) gene,
complete cds; ORF3, complete cds 3905 2 188 400
gb.vertline.L05004.vertline. Staphylococcus aureus dehydroquinate
synthase (aroB) gene, 3' end cds; 3- 97 88 213
phosphoshikimate-1-carboxyvinyltransferase (aroA) gene, complete
cds; ORF3, complete cds 3910 1 3 359 emb.vertline.X58434.vertli-
ne.SAPD S. aureus pdhB, pdhC and pdhD genes for pyruvate
decarboxylase, 99 278 357 dihydrolipoamide acetyltransferase and
dihydrolipoamide dehydrogenase 3915 1 1 330
gb.vertline.L14017.vertline. Staphylococcus aureus
methicillin-resistance protein (mecR) gene and 75 175 330 unknown
ORF, complete cds 3964 1 347 3 emb.vertline.Z48003.vertline.SADN S.
aureus gene for DNA polymerase III 100 295 345 4007 1 199 390
emb.vertline.X16457.vertline.SAST Staphylococcus aureus gene for
staphylocoagulase 98 163 192 4036 1 3 371 dbj.vertline.D10489.vert-
line.STAG Staphylococcus aureus genes for DNA gyrase A and B,
complete cds 99 339 369 4046 1 348 4
emb.vertline.Z18852.vertline.SACF S. aureus gene for clumping
factor 87 221 345 4060 1 1 375 emb.vertline.Z18852.vertline.SACF S.
aureus gene for clumping factor 96 271 375 4061 1 432 4
emb.vertline.Z48003.vertline.SADN S. aureus gene for DNA polymerase
III 99 429 429 4062 1 304 2 gb.vertline.L14017.vertline.
Staphylococcus aureus methicillin-resistance protein (mecR) gene
and 75 198 303 unknown ORF, complete cds 4085 1 58 402
gb.vertline.U11786.vertline. Staphylococcus aureus
methicillin-resistant ATCC 33952 clone RRNV42 16S-23S 98 127 345
rRNA spacer region 4088 1 2 301 gb.vertline.L43098.vertline.
Transposon Tn5404 and insertion sequences IS1181 and IS1182 (from
99 227 300 Staphylococcus aureus) DNA 4093 1 2 277
emb.vertline.X58434.vertline.SAPD S. aureus pdhB, pdhC and pdhD
genes for pyruvate decarboxylase, 99 276 276 dihydrolipoamide
acetyltransferase and dihydrolipoamide dehydrogenase 4097 1 1 402
emb.vertline.Z18852.vertline.SACF S. aureus gene for clumping
factor 74 307 402 4116 1 22 402 gb.vertline.L05004.vertline.
Staphylococcus aureus dehydroquinate synthase (aroB) gene, 3' end
cds; 3- 98 157 381 phosphoshikimate-1-carboxyvinyltransferase
(aroA) gene, complete cds; ORF3, complete cds 4125 1 240 401
gb.vertline.U73374.vertline. Staphylococcus aureus type 8 capsule
genes, cap8A, cap8B, cap8C, cap8D, 100 86 162 cap8E, cap8F, cap8G,
cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N, cap8O, cap8P,
complete cds 4149 1 35 247 gb.vertline.J04151.vertline. S. aureus
fibronectin-binding protein (fnbA) mRNA, complete cds 99 200 213
4151 1 366 103 gb.vertline.L14017.vertline. Staphylococcus aureus
methicillin-resistance protein (mecR) gene and 87 150 264 unknown
ORF, complete cds 4154 1 398 42 emb.vertline.X64172.vertli- ne.SARP
S. aureus rplL, orf202, rpoB(rif) and rpoC genes for ribosomal
protein 99 297 357 L7/L12, hypothetical protein ORF202,
DNA-directed RNA polymerase beta & beta` chains 4179 1 1 294
emb.vertline.X64172.vertline.SARP S. aureus rplL, orf202, rpoB(rif)
and rpoC genes for ribosomal protein 98 240 294 L7/L12,
hypothetical protein ORF202, DNA-directed RNA polymerase beta &
beta` chains 4203 1 1 255 emb.vertline.X89233.vertline.SARP S.
aureus DNA for rpoC gene 99 239 255 4206 1 1 303
emb.vertline.Z18852.vertline.SACF S. aureus gene for clumping
factor 100 236 303 4206 2 195 344 emb.vertline.Z18852.vertline.SACF
S. aureus gene for clumping factor 95 65 150 4208 1 108 314
emb.vertline.X58434.vertline.SAPD S. aureus pdhB, pdhC and pdhD
genes for pyruvate decarboxylase, 89 76 207 dihydrolipoamide
acetyltransferase and dihydrolipoamide dehydrogenase 4216 1 330 4
emb.vertline.X58434.vertline.SAPD S. aureus pdhB, pdhC and pdhD
genes for pyruvate decarboxylase, 98 326 327 dihydrolipoamide
acetyltransferase and dihydrolipoamide dehydrogenase 4226 1 298 2
gb.vertline.L11530.vertline. Staphylococcus aureus transfer RNA
sequence with two rRNAs 97 132 297 4260 1 216 383
gb.vertline.U11784.vertli- ne. Staphylococcus aureus
methicillin-resistant ATCC 33952 clone RRNV40 16S-23S 83 141 168
rRNA spacer region 4272 1 179 3 emb.vertline.Z48003.vertline.SADN
S. aureus gene for DNA polymerase III 100 164 177 4276 1 4 177
emb.vertline.X16457.vertline.SAST Staphylococcus aureus gene for
staphylocoagulase 99 150 174 4277 1 1 270
emb.vertline.X64172.vertline.SARP S. aureus rplL, orf202, rpoB(rif)
and rpoC genes for ribosomal protein 99 265 270 L7/L12,
hypothetical protein ORF202, DNA-directed RNA polymerase beta &
beta` chains 4282 1 377 63 emb.vertline.X64172.vertline.SARP S.
aureus rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein
98 282 315 L7/L12, hypothetical protein ORF202, DNA-directed RNA
polymerase beta & beta` chains 4291 1 191 3
emb.vertline.X64172.vertline.SARP S. aureus rplL, orf202, rpoB(rif)
and rpoC genes for ribosomal protein 99 183 189 L7/L12,
hypothetical protein ORF202, DNA-directed RNA polymerase beta &
beta` chains 4295 1 3 329 emb.vertline.X16457.vertline.SAST
Staphylococcus aureus gene for staphylocoagulase 94 144 327 4313 1
280 125 gb.vertline.L11530.vertline. Staphylococcus aureus transfer
RNA sequence with two rRNAs 100 94 156 4315 1 3 185
gb.vertline.J03479.vertline. S. aureus enzyme III-lac (lacF),
enzyme II-lac (lacE), and phospho-beta- 100 158 183 galactosidase
(lacG) genes, complete cds 4315 2 101 310 gb.vertline.J03479.vertl-
ine. S. aureus enzyme III-lac (lacF), enzyme II-lac (lacE), and
phospho-beta- 98 75 210 galactosidase (lacG) genes, complete cds
4327 1 1 294 gb.vertline.L43098.vertline. Transposon Tn5404 and
insertion sequences IS1181 and IS1182 (from 98 294 294
Staphylococcus aureus) DNA 4360 1 319 35 gb.vertline.U02910.vertli-
ne. Staphylococcus aureus ATCC 25923 16S rRNA gene, partial
sequence 100 116 285 4364 1 3 146 emb.vertline.X64172.vertline.SARP
S. aureus rplL, orf202, rpoB(rif) and rpoC genes for ribosomal
protein 95 140 144 L7/L12, hypothetical protein ORF202,
DNA-directed RNA polymerase beta & beta` chains 4388 1 167 310
emb.vertline.X62992.vertline.SAFN S. aureus fnbB gene for
fibronectin binding protein B 73 119 144 4401 1 2 313
emb.vertline.X62992.vert- line.SAFN S. aureus fnbB gene for
fibronectin binding protein B 97 243 312 4421 1 36 281
dbj.vertline.D12572.vertline.STA2 Staphylococcus aureus rrnA gene
for 23S ribosomal RNA 100 112 246 4426 1 3 293
emb.vertline.Z18852.vertline.SACF S. aureus gene for clumping
factor 85 185 291 4428 1 248 3 emb.vertline.X64172.vertline.SARP S.
aureus rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein
100 139 246 L7/L12, hypothetical protein ORF202, DNA-directed RNA
polymerase beta & beta' chains 4462 1 2 271
emb.vertline.X64172.vertline.SARP S. aureus rplL, orf202, rpoB(rif)
and rpoC genes for ribosomal protein 99 270 270 L7/L12,
hypothetical protein ORF202, DNA-directed RNA polymerase beta &
beta' chains 4466 1 1 240 emb.vertline.Z18852.vertline.SACF S.
aureus gene for clumping factor 99 231 240 4469 1 1 312
gb.vertline.J03479.vertline. S. aureus enzyme III-lac (lacF),
enzyme II-lac (lacE), and phospho-beta- 99 265 312 galactosidase
(lacG) genes, complete cds 4485 1 3 263 gb.vertline.L43098.vertlin-
e. Transposon Tn5404 and insertion sequences IS1181 and IS1182
(from 98 259 261 Staphylococcus aureus) DNA 4492 1 74 400
gb.vertline.M86227.vertline. Staphylococcus aureus DNA gyrase B
subunit (gyrB) RecF homologue (recF) and 85 104 327 DNA gyrase A
subunit (gyrA) gene, complete cds 4497 1 269 3
emb.vertline.Z18852.vertline.SACF S. aureus gene for clumping
factor 99 213 267 4529 1 2 172 emb.vertline.X64172.vertline.SARP S.
aureus rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein
100 151 171 L7/L12, hypothetical protein ORF202, DNA-directed RNA
polymerase beta & beta' chains 4547 1 1 300
emb.vertline.X62992.vertline.SAFN S. aureus fnbB gene for
fibronectin binding protein B 100 157 300 4554 1 160 2
emb.vertline.Z18852.ver- tline.SACF S. aureus gene for clumping
factor 84 126 159 4565 1 9 227 emb.vertline.Z18852.vertline.SACF S.
aureus gene for clumping factor 84 213 219 4569 1 79 222
emb.vertline.Z18852.vertline.SACF S. aureus gene for clumping
factor 98 127 144 4608 1 22 216 emb.vertline.X58434.vertline.SAPD
S. aureus pdhB, pdhC and pdhD genes for pyruvate decarboxylase, 92
168 195 dihydrolipoamide acetyltransferase and dihydrolipoamide
dehydrogenase 4614 1 234 4 emb.vertline.Z18852.vertline.SACF S.
aureus gene for clumping factor 86 169 231 4623 1 105 302
gb.vertline.J04151.vertline. S. aureus fibronectin-binding protein
(fnbA) mRNA, complete cds 99 152 198 4632 1 18 206
gb.vertline.J03479.vertline. S. aureus enzyme III-lac (lacF),
enzyme II-lac (lacE), and phospho-beta- 98 183 189 galactosidase
(lacG) genes, complete cds 4646 1 1 222
emb.vertline.Z18852.vertline.SACF S. aureus gene for clumping
factor 84 100 222 4687 1 2 166 gb.vertline.J04151.vertline. S.
aureus fibronectin-binding protein (fnbA) mRNA, complete cds 98 156
165 4695 1 158 3 gb.vertline.L14017.vertline. Staphylococcus aureus
methicillin-resistance protein (mecR) gene and 75 155 156 unknown
ORF, complete cds 4703 1 1 153 emb.vertline.X58434.vertlin- e.SAPD
S. aureus pdhB, pdhC and pdhD genes for pyruvate decarboxylase, 98
103 153 dihydrolipoamide acetyltransferase and dihydrolipoamide
dehydrogenase
[0289]
2TABLE 2 S. aureus - Putative coding regions of novel proteins
similar to known proteins Start Stop match Contig ID ORF ID (nt)
(nt) acession match gene name % sim % ident length (nt) 20 6 4679
4269 gi.vertline.511839 ORF1 [Staphylococcus bacteriophage phi 11]
100 100 411 149 3 1577 1122 pir.vertline.B49703.vertline.B497 int
gene activator RinA - bacteriophage phi 11 100 100 456 149 5 1912
1715 gi.vertline.166161 Bacteriophage phi-11 int gene activator
[Staphylococcus acteriophage phi 100 100 198 11] 349 2 409 260
gi.vertline.166159 integrase (int) [Staphylococcus bacteriophage
phi 11] 100 100 150 398 1 707 42 gi.vertline.166159 integrase (int)
[Staphylococcus bacteriophage phi 11] 100 99 666 398 2 783 1001
gi.vertline.455128 excisionase (xis) [Staphylococcus bacteriophage
phi 11] 100 100 219 502 4 1744 1574 gi.vertline.1204912 H.
influenzae predicted coding region HI0660 [Haemophilus influenzae]
100 71 171 849 1 2 262 gi.vertline.1373002 polyprotein [Bean common
mosaic virus] 100 46 261 1349 1 140 3 gi.vertline.143359 protein
synthesis initiation factor 2 (infB) [Bacillus subtilis]
gi.vertline.49319 100 82 138 IF2 gene product [Bacillus subtilis]
2880 1 21 308 gi.vertline.862933 protein kinase C inhibitor-I [Homo
sapiens] 100 98 288 3085 1 216 4 gi.vertline.1354211 PET112-like
protein [Bacillus subtilis] 100 100 213 4168 2 398 225
gi.vertline.1354211 PET112-like protein [Bacillus subtilis] 100 100
174 331 1 2 247 gi.vertline.426473 nusG gene product
[Staphylococcus carnosus] 98 95 246 207 2 1272 1463
gi.vertline.460259 enolase [Bacillus subtilis] 97 90 192 331 2 395
850 gi.vertline.581638 L11 protein [Staphylococcus carnosus] 97 93
456 366 1 39 215 gi.vertline.166161 Bacteriophage phi-11 int gene
activator [Staphylococcus acteriophage phi 97 95 177 11] 680 3 718
936 gi.vertline.426473 nusG gene product [Staphylococcus carnosus]
97 97 219 3578 1 144 4 gi.vertline.1339950 large subunit of
NADH-dependent glutamate synthase [Plectonema boryanum] 97 79 141
157 1 321 518 gi.vertline.1022726 unknown [Staphylococcus
haemolyticus] 96 88 198 205 33 16147 15824 gi.vertline.1165302 S10
[Bacillus subtilis] 96 91 324 3919 1 48 401 gi.vertline.871784
Clp-like ATP-dependent protease binding subunit [Bos taurus] 96 81
354 4133 1 417 4 gi.vertline.1022726 unknown [Staphylococcus
haemolyticus] 96 84 414 4168 1 355 2 gi.vertline.1354211
PET112-like protein [Bacillus subtilis] 96 95 354 4207 1 157 2
gi.vertline.602031 similar to trimethylamine DH [Mycoplasma
capricolum]pir.vertline.S49950.vertline.S49- 950 96 86 156 probable
trimethylamine dehydrogenase (EC .5.99.7) - Mycoplasma capricolum
(SGC3) (fragment) 4227 2 152 331 gi.vertline.871784 Clp-like
ATP-dependent protease binding subunit [Bos taurus] 96 81 180 4416
1 286 2 gi.vertline.1022726 unknown [Staphylococcus haemolyticus]
96 84 285 22 1 430 2 gi.vertline.511070 UreG [Staphylococcus
xylosus] 95 88 429 22 7 4036 3710 gi.vertline.581787 urease gamma
subunit [Staphylococcus xylosus] 95 79 327 82 6 8794 9114
pir.vertline.JG0008.vertline.JG0- 0 ribosomal protein S7 - Bacillus
stearothermophilus 95 83 321 154 9 7838 6396 gi.vertline.1354211
PET112-like protein [Bacillus subtilis] 95 92 1443 186 3 2055 1312
gi.vertline.1514656 serine 0-acetyltransferase [Staphylococcus
xylosus] 95 87 744 205 5 4014 3622 gi.vertline.142462 ribosomal
protein S11 [Bacillus subtilis] 95 85 393 205 7 4793 4569
gi.vertline.142459 initiation factor 1 [Bacillus subtilis] 95 84
225 205 21 10991 10617 gi.vertline.1044974 ribosomal protein L14
[Bacillus subtilis] 95 93 375 259 5 6644 6000
sp.vertline.P47995.vertline.YSEA.sub.-- HYPOTHETICAL PROTEIN IN
SECA 5'REGION (ORF1) (FRAGMENT). 95 85 645 302 3 795 1097
gi.vertline.40186 homologous to E. coli ribosomal protein L27
[Bacillus subtilis] i.vertline.143592 L27 95 89 303 ribosomal
protein [Bacillus subtilis] ir.vertline.C21895.vertline.C21895
ribosomal protein L27 - Bacillus subtilis
p.vertline.P05657.vertline.RL- 27_BACSU 50S RIBOSOMAL PROTEIN L27
(BL30) (BL24). i.vertline.40175 L24 gene prod 310 1 579 1523
gi.vertline.1177684 chorismate mutase [Staphylococcus xylosus] 95
92 945 414 1 2 163 pir.vertline.C48396.vertline.C483 ribosomal
protein L34 - Bacillus stearothermophilus 95 90 162 4185 2 125 277
gi.vertline.1276841 glutamate synthase (GOGAT) [Porphyra purpurea]
95 86 153 22 2 723 418 gi.vertline.511069 UreF [Staphylococcus
xylosus] 94 91 306 22 5 3310 1574 gi.vertline.410516 urease alpha
subunit [Staphylococcus xylosus] 94 85 1737 60 4 815 1372
gi.vertline.666116 glucose kinase [Staphylococcus xylosus] 94 87
558 205 18 9536 9060 gi.vertline.1044978 ribosomal protein S8
[Bacillus subtilis] 94 78 477 326 4 2542 1706 gi.vertline.557492
dihydroxynapthoic acid (DHNA) synthetase [Bacillus subtilis]
gi.vertline.143186 94 85 837 dihydroxynapthoic acid (DHNA)
synthetase [Bacillus subtilis] 414 3 737 955 gi.vertline.467386
thiophen and furan oxidation [Bacillus subtilis] 94 77 219 426 3
1823 1386 gi.vertline.1263908 putative [Staphylococcus epidermidis]
94 87 438 534 1 2 355 gi.vertline.633650 enzyme II(mannitol)
[Staphylococcus carnosus] 94 84 354 1017 1 2 229 gi.vertline.149435
putative [Lactococcus lactis] 94 73 228 3098 1 184 38
gi.vertline.413952 ipa-28d gene product [Bacillus subtilis] 94 50
147 3232 1 316 2 gi.vertline.1022725 unknown [Staphylococcus
haemolyticus] 94 84 315 42 5 2089 2259
pir.vertline.B48396.vertline.B483 ribosomal protein L33 - Bacillus
stearothermophilus 93 81 171 101 2 1383 1021 gi.vertline.155345
arsenic efflux pump protein [Plasmid pSX267] 93 82 363 205 24 11865
11503 sp.vertline.P14577.vertline.RL16.sub.-- 50S RIBOSOMAL PROTEIN
L16. 93 83 363 259 4 5673 3055 gi.vertline.499335 secA protein
[Staphylococcus carnosus] 93 85 2619 275 1 1114 2
gi.vertline.633650 enzyme II(mannitol) [Staphylococcus carnosus] 93
86 1113 444 6 5773 5339 gi.vertline.1022726 unknown [Staphylococcus
haemolyticus] 93 81 435 491 1 152 622 gi.vertline.46912 ribosomal
protein L13 [Staphylococcus carnosus] 93 88 471 607 6 1674 2033
gi.vertline.1022726 unknown [Staphylococcus haemolyticus] 93 83 360
653 1 488 3 gi.vertline.580890 translation initiation factor IF3
(AA 1-172) [Bacillus tearothermophilus] 93 77 486 1864 1 3 194
gi.vertline.306553 ribosmal protein small subunit [Homo sapiens] 93
93 192 2997 1 28 300 gi.vertline.143390 carbamyl phosphate
synthetase [Bacillus subtilis] 93 82 273 3232 2 596 285
gi.vertline.1022725 unknown [Staphylococcus haemolyticus] 93 84 312
3761 2 621 448 gi.vertline.1022725 unknown [Staphylococcus
haemolyticus] 93 88 174 16 1 3 374 gi.vertline.142781 putative
cytoplasmic protein; putative [Bacillus subtilis] 92 83 372
sp.vertline.P37954.vertline.UVR- B_BACSU EXCINUCLEASE ABC SUBUNIT B
(DINA PROTEIN) FRAGMENT). 31 7 5915 6124 gi.vertline.1136430
KIAA0185 protein [Homo sapiens] 92 46 210 56 19 26483 27391
gi.vertline.467401 unknown [Bacillus subtilis] 92 80 909 69 6 5882
6130 gi.vertline.530200 trophoblastin [Ovis aries] 92 53 249 145 3
2038 1508 gi.vertline.1022725 unknown [Staphylococcus haemolyticus]
92 80 531 171 3 2362 1964 gi.vertline.517475 D-amino acid
transaminase [Staphylococcus haemolyticus] 92 86 399 205 12 6962
6429 gi.vertline.49189 secY gene product [Staphylococcus carnosus]
92 85 534 205 19 10255 9698 gi.vertline.1044976 ribosomal protein
L5 [Bacillus subtilis] 92 82 558 219 1 357 4 gi.vertline.1303812
YqeV [Bacillus subtilis] 92 88 354 344 3 1575 1805
gi.vertline.1405474 CspC protein [Bacillus cereus] 92 85 231 699 1
20 361 gi.vertline.413999 ipa-75d gene product [Bacillus subtilis]
92 81 342 1343 1 2 160 pir.vertline.A45434.ver- tline.A454
ribosomal protein L19 - Bacillus stearothermophilus 92 84 159 1958
1 264 4 gi.vertline.407908 EIIscr [Staphylococcus xylosus] 92 80
261 3578 2 386 54 gi.vertline.1339950 large subunit of
NADH-dependent glutamate synthase [Plectonema boryanum] 92 78 333
3585 1 324 4 gi.vertline.1339950 large subunit of NADH-dependent
glutamate synthase [Plectonema boryanum] 92 81 321 3640 1 4 402
gi.vertline.1022726 unknown [Staphylococcus haemolyticus] 92 81 399
4362 1 14 178 gi.vertline.450688 hsdM gene of EcoprrI gene product
[Escherichia coli] pir.vertline.S38437.vertline.S38437 hsdM 92 78
165 protein - Escherichia coli pir.vertline.S09629.vertline.S09629
hypothetical protein A - Escherichia coli (SUB 40-520) 4446 1 182 6
gi.vertline.1022725 unknown [Staphylococcus haemolyticus] 92 82 177
4549 1 232 2 gi.vertline.1022726 unknown [Staphylococcus
haemolyticus] 92 80 231 4626 1 3 224 gi.vertline.1022725 unknown
[Staphylococcus haemolyticus] 92 84 222 2 4 3980 4531
gi.vertline.535349 Codw [Bacillus subtilis] 91 74 552 28 1 2 1126
gi.vertline.1001376 hypothetical protein [Synechocystis sp.] 91 78
1125 60 5 1354 1701 gi.vertline.1226043 orf2 downstream of glucose
kinase [Staphylococcus xylosus] 91 80 348 101 1 1036 83
gi.vertline.150728 arsenic efflux pump protein [Plasmid pI258] 91
80 954 187 2 412 1194 gi.vertline.142559 ATP synthase alpha subunit
[Bacillus megaterium] 91 79 783 205 22 11298 11017
gi.vertline.40149 S17 protein (AA 1-87) [Bacillus subtilis] 91 83
282 206 7 8184 10262 gi.vertline.1072418 glcA gene product
[Staphylococcus carnosus] 91 83 2079 306 2 2326 767
gi.vertline.143012 GMP synthetase [Bacillus subtilis] 91 78 1560
306 3 3826 2333 gi.vertline.467399 IMP dehydrogenase [Bacillus
subtilis] 91 79 1494 310 3 2194 3207 gi.vertline.1177685 ccpA gene
product [Staphylococcus xylosus] 91 81 1014 343 4 2974 3150
gi.vertline.949974 sucrose repressor [Staphylococcus xylosus] 91 82
177 480 3 1606 3042 gi.vertline.433991 ATP synthase subunit beta
[Bacillus subtilis] 91 85 1437 536 3 1280 534 gi.vertline.143366
adenylosuccinate lyase (PUR-B) [Bacillus subtilis]
pir.vertline.C29326.vertline.WZBSDS 91 79 747 adenylosuccinate
lyase (EC 4.3.2.2) - Bacillus subtilis 552 1 615 166
gi.vertline.297874 fructose-bisphosphate aldolase [Staphylococcus
carnosus] pir.vertline.A49943.vertline.A49943 91 79 450
fructose-bisphosphate aldolase (EC 4.1.2.13) - Staphylococcus
carnosus (strain TM300) 637 1 1 1536 gi.vertline.143597 CTP
synthetase [Bacillus subtilis] 91 79 1536 859 1 21 359
gi.vertline.385178 unknown [Bacillus subtilis] 91 66 339 1327 1 339
530 gi.vertline.496558 orfX [Bacillus subtilis] 91 71 192 2515 1
275 84 gi.vertline.511070 UreG [Staphylococcus xylosus] 91 85 192
2594 1 2 202 gi.vertline.146824 beta-cystathionase [Escherichia
coli] 91 75 201 3764 1 425 3 gi.vertline.1022725 unknown
[Staphylococcus haemolyticus] 91 78 423 4011 1 127 495
gi.vertline.1022726 unknown [Staphylococcus haemolyticus] 91 79 369
4227 1 1 177 gi.vertline.296464 ATPase [Lactococcus lactis] 91 66
177 42 3 815 1033 gi.vertline.520401 catalase [Haemophilus
influenzae] 90 86 219 51 8 3717 4607 gi.vertline.580899 OppF gene
product [Bacillus subtilis] 90 74 891 129 3 4001 2685
gi.vertline.1146206 glutamate dehydrogenase [Bacillus subtilis] 90
76 1317 164 17 16628 16933 sp.vertline.P05766.vertline.RS15.sub.--
30S RIBOSOMAL PROTEIN S15 (BS18) 90 74 306 171 5 2819 2655
gi.vertline.517475 D-amino acid transaminase [Staphylococcus
haemolyticus] 90 78 165 205 4 3550 2603 gi.vertline.142463 RNA
polymerase alpha-core-subunit [Bacillus subtilis] 90 76 948 205 6
4410 4072 gi.vertline.1044989 ribosomal protein S13 [Bacillus
subtilis] 90 73 339 205 10 6404 5643 gi.vertline.49189 secY gene
product [Staphylococcus carnosus] 90 81 762 205 11 6472 6299
gi.vertline.49189 secY gene product [Staphylococcus carnosus] 90 78
174 205 27 13345 12998 gi.vertline.786157 Ribosomal Protein S19
[Bacillus subtilis] 90 79 348 205 31 15496 15134
gi.vertline.1165303 L3 [Bacillus subtilis] 90 79 363 260 5 5773
4523 gi.vertline.1161380 IcaA [Staphylococcus epidermidis] 90 78
1251 299 6 3378 3947 gi.vertline.467440 `phosphoribosylpyrophospha-
te synthetase [Bacillus subtilis] gi.vertline.40218 PRPP 90 78 570
synthetase (AA 1-317) [Bacillus subtilis] 320 2 1025 1717
gi.vertline.312443 carbamoyl-phosphate synthase
(glutamine-hydrolysing) [Bacillus aldolyticus] 90 75 693 330 4 1581
1769 gi.vertline.986963 beta-tubulin [Sporidiobolus pararoseus] 90
80 189 369 1 523 92 pir.vertline.S34762.vertline.S347 L-serine
dehydratase beta chain - Clostridium sp. 90 77 432 557 1 3 188
gi.vertline.1511589 M. jannaschii predicted coding region MJ1624
[Methanococcus jannaschii] 90 54 186 663 2 667 1200
gi.vertline.143786 tryptophanyl-tRNA synthetase (EC 6.1.1.2)
[Bacillus subtilis] 90 73 534 pir.vertline.JT0481.vertline.YWBS
tryptophan-tRNA ligase (EC 6.1.1.2) - Bacillus subtilis 717 1 1 261
gi.vertline.143065 hubst [Bacillus stearothermophilus] 90 79 261
745 4 865 671 gi.vertline.1205433 H. influenzae predicted coding
region HI1190 [Haemophilus influenzae] 90 81 195 1007 1 386 565
gi.vertline.143366 adenylosuccinate lyase (PUR-B) [Bacillus
subtilis] pir.vertline.C29326.vertline.WZBSDS 90 77 180
adenylosuccinate lyase EC 4.3.2.2) - Bacillus subtilis 1054 1 331
83 gi.vertline.1033122 ORF_f729 [Escherichia coli] 90 50 249 1156 1
117 707 gi.vertline.1477776 ClpP [Bacillus subtilis] 90 80 591 1180
1 205 2 gi.vertline.1377831 unknown [Bacillus subtilis] 90 74 204
1253 1 1 462 gi.vertline.40046 phosphoglucose isomerase A (AA
1-449) [Bacillus stearothermophilus] 90 75 462
ir.vertline.S15936.vertline.NUBSSA glucose-6-phosphate isomerase
(EC 5.3.1.9) A - Bacillus stearothermophilus 2951 1 3 269
gi.vertline.144816 formyltetrahydrofolate synthetase (FTHFS) (ttg
start codon) (EC .3.4.3) 90 76 267 [Moorella thermoacetica] 3140 1
166 5 gi.vertline.1070014 protein-dependent [Bacillus subtilis] 90
52 162 4594 1 3 233 gi.vertline.871784 Clp-like ATP-dependent
protease binding subunit [Bos taurus] 90 76 231 87 1 1028 1750
gi.vertline.467327 unknown [Bacillus subtilis] 89 75 723 112 1 2
505 gi.vertline.153741 ATP-binding protein [Streptococcus mutans]
89 77 504 118 1 120 398 gi.vertline.1303804 YqeQ [Bacillus
subtilis] 89 75 279 128 4 3545 3757 gi.vertline.460257 triose
phosphate isomerase [Bacillus subtilis] 89 84 213 164 12 11667
12755 gi.vertline.39954 IF2 (aa 1-741) [Bacillus
stearothermophilus] 89 80 1089 205 13 7405 6935 gi.vertline.216338
ORF for L15 ribosomal protein [Bacillus subtilis] 89 76 471 205 32
15823 15494 gi.vertline.1165303 L3 [Bacillus subtilis] 89 80 330
270 3 2207 2007 pir.vertline.C41902.vertline.C419 arsenate
reductase (EC 1,--,--,--) - Staphylococcus xylosus plasmid pSX267
89 81 201 395 2 157 672 gi.vertline.520574 glutamate racemase
[Staphylococcus haemolyticus] 89 80 516 494 1 3 839
gi.vertline.396259 protease [Staphylococcus epidermidis] 89 77 837
510 1 1 444 gi.vertline.40046 phosphoglucose isomerase A (AA 1-449)
[Bacillus stearothermophilus] 89 74 444
ir.vertline.S15936.vertline.NUBSSA glucose-6-phosphate isomerase
(EC 5.3.1.9) A - Bacillus stearothermophilus 615 1 1210 296
gi.vertline.1303812 YqeV [Bacillus subtilis] 89 74 915 841 1 18 341
gi.vertline.1165303 L3 [Bacillus subtilis] 89 80 324 1111 1 352 813
gi.vertline.47146 thermonuclease [Staphylococcus intermedius] 89 70
462 1875 1 2 256 gi.vertline.1205108 ATP-dependent protease binding
subunit [Haemophilus influenzae] 89 82 255 2963 1 11 367
gi.vertline.467458 cell division protein [Bacillus subtilis] 89 83
357 3020 1 90 362 gi.vertline.1239988 hypothetical protein
[Bacillus subtilis] 89 66 273 3565 1 2 400 gi.vertline.1256635
dihydroxy-acid dehydratase [Bacillus subtilis] 89 75 399 3586 1 105
314 gi.vertline.580832 ATP synthase subunit gamma [Bacillus
subtilis] 89 82 210 3629 1 399 4 gi.vertline.1009366 Respiratory
nitrate reductase [Bacillus subtilis] 89 78 396 3688 1 2 400
gi.vertline.1146206 glutamate dehydrogenase [Bacillus subtilis] 89
75 399 3699 1 399 4 gi.vertline.1339950 large subunit of
NADH-dependent glutamate synthase [Plectonema boryanum] 89 75 396
4016 1 216 4 gi.vertline.1009366 Respiratory nitrate reductase
[Bacillus subtilis] 89 71 213 4177 1 301 131 gi.vertline.149426
putative [Lactococcus lactis] 89 76 171 4436 1 302 3
gi.vertline.1022725 unknown [Staphylococcus haemolyticus] 89 80 300
4635 1 162 4 gi.vertline.1022725 unknown [Staphylococcus
haemolyticus] 89 73 159 2 2 1330 2676 gi.vertline.520754 putative
[Bacillus subtilis] 88 76 1347 42 2 468 848
sp.vertline.P42321.vertline.CATA.sub.-- CATALASE (EC 1.11.1.6). 88
76 381 53 5 4722 3055 gi.vertline.474177
alpha-D-1,4-glucosidase [Staphylococcus xylosus] 88 80 1668 56 16
18018 18617 gi.vertline.467411 recombination protein [Bacillus
subtilis] 88 77 600 60 3 376 843 gi.vertline.666116 glucose kinase
[Staphylococcus xylosus] 88 77 468 70 2 1245 907 gi.vertline.44095
replication initiator protein [Listeria monocytogenes] 88 74 339 82
8 11514 12719 pir.vertline.A60663.vertline.A606 translation
elongation factor Tu - Bacillus subtilis 88 79 1206 103 7 4179 4391
gi.vertline.167181 serine/threonine kinase receptor [Brassica
napus] 88 77 213 114 8 7732 8232 gi.vertline.1022726 unknown
[Staphylococcus haemolyticus] 88 72 501 118 2 308 2011
gi.vertline.1303804 YqeQ [Bacillus subtilis] 88 77 1704 141 3 657
1136 gi.vertline.1405446 transketolase [Bacillus subtilis] 88 72
480 148 7 5871 6116 gi.vertline.1118002 dihydropteroate synthase
[Staphylococcus haemolyticus] 88 78 246 165 3 1428 2231
gi.vertline.40053 phenylalanyl-tRNA synthetase alpha subunit
[Bacillus subtilis] 88 80 804 ir.vertline.S11730.vertline.YFBSA
phenylalanine-tRNA ligase (EC 6.1.1.20) alpha ain - Bacillus
subtilis 205 28 14185 13343 gi.vertline.1165306 L2 [Bacillus
subtilis] 88 82 843 225 1 898 227 gi.vertline.1303840 YqfS
[Bacillus subtilis] 88 78 672 235 1 2 1975 gi.vertline.452309
valyl-tRNA synthetase [Bacillus subtilis] 88 76 1974 339 3 1566
1072 gi.vertline.1118002 dihydropteroate synthase [Staphylococcus
haemolyticus] 88 73 495 443 4 2928 1531 gi.vertline.558559
pyrimidine nucleoside phosphorylase [Bacillus subtilis] 88 73 1398
532 1 3 419 gi.vertline.143797 valyl-tRNA synthetase [Bacillus
stearothermophilus]sp.vertline.P11931.ver- tline.SYV_BACST 88 78
417 VALYL-TRNA SYNTHETASE (EC 6.1.1.9) VALINE-TRNA LIGASE) (VALRS).
534 3 2504 2968 gi.vertline.153049 mannitol-specific enzyme-III
[Staphylococcus carnosus]pir.vertline.JQ0088- .vertline.JQ0088 88
82 465 phosphotransferase system enzyme II (EC .7.1.69),
mannitol-specific, factor III - Staphylococcus carnosus
sp.vertline.P17876.vertline.PTMA_STACA PTS SYSTEM,
MANNITOL-SPECIFIC IIA COMPONENT EIIA-MTL) ( 705 2 399 214
gi.vertline.710018 nitrite reductase (nirB) [Bacillus subtilis] 88
70 186 1000 2 1309 794 gi.vertline.1022726 unknown [Staphylococcus
haemolyticus] 88 78 516 1299 1 324 61 gi.vertline.401786
phosphomannomutase [Mycoplasma pirum] 88 55 264 1341 2 170 400
gi.vertline.39963 ribosomal protein L20 (AA 1-119) [Bacillus
stearothermophilus] 88 82 231 ir.vertline.S05348.vertline.R5B- S20
ribosomal protein L20 - Bacillus stearothermophilus 1386 1 41 214
pir.vertline.B47154.vertline.B471 signal recognition particle 54 K
chain homolog Ffh - Bacillus subtilis 88 71 174 1386 2 183 533
pir.vertline.B47154.vertline.B471 signal recognition particle 54 K
chain homolog Ffh - Bacillus subtilis 88 73 351 2949 1 399 94
gi.vertline.535350 CodX [Bacillus subtilis] 88 73 306 2984 1 5 169
gi.vertline.218277 O-acetylserine(thiol) lyase [Spinacia oleracea]
88 70 165 3035 1 1 138 gi.vertline.493083 dihydroxyacetone kinase
[Citrobacter freundii] 88 67 138 3089 1 3 152 gi.vertline.606055
ORF_f746 [Escherichia coli] 88 88 150 3917 1 410 3
gi.vertline.143378 pyruvate decarboxylase (E-1) beta subunit
[Bacillus subtilis]gi.vertline.1377836 88 77 408 pyruvate
decarboxylase E-1 beta subunit [Bacillus subtilis] 4199 1 342 4
gi.vertline.1405454 aconitase [Bacillus subtilis] 88 82 339 4201 1
369 4 gi.vertline.515938 glutamate synthase (ferredoxin)
[Synechocystis sp.]pir.vertline.S46957.vertline.S46957 88 84 366
glutamate synthase (ferredoxin) (EC 1.4.7.1) - ynechocystis sp.
4274 1 1 336 gi.vertline.515938 glutamate synthase (ferredoxin)
[Synechocystis sp.]pir.vertline.S46957.vertline.S46957 88 84 336
glutamate synthase (ferredoxin) (EC 1.4.7.1) - ynechocystis sp.
4308 1 399 4 gi.vertline.1146206 glutamate dehydrogenase [Bacillus
subtilis] 88 71 396 2 5 4570 6000 gi.vertline.535350 CodX [Bacillus
subtilis] 87 70 1431 52 8 6482 6183 gi.vertline.1064791 function
umknown [Bacillus subtilis] 87 66 300 73 3 1584 2480
gi.vertline.142992 glycerol kinase (glpK) (EC 2.7.1.30) [Bacillus
subtilis] pir.vertline.B45868.vertl- ine.B45868 87 72 897 glycerol
kinase (EC 2.7.1.30) - Bacillus subtilis
sp.vertline.P18157.vertline.GLPK_BACSU GLYCEROL KINASE (EC
2.7.1.30) (ATP: GLYCEROL-PHOSPHOTRANSFERASE) (GLYCEROKINASE) (GK).
98 12 8813 9100 gi.vertline.467433 unknown [Bacillus subtilis] 87
62 288 124 4 2988 1711 gi.vertline.556886 serine
hydroxymethyltransferase [Bacillus subtilis]
pir.vertline.S49363.vertline.S49363 87 77 1278 serine
hydroxymethyltransferase - Bacillus subtilis 124 6 4032 3607
gi.vertline.556883 Unknown [Bacillus subtilis] 87 66 426 148 5 3741
4559 gi.vertline.467460 unknown [Bacillus subtilis] 87 70 819 164
13 12710 13810 gi.vertline.39954 IF2 (aa 1-741) [Bacillus
stearothermophilus] 87 72 1101 177 2 1104 2126 gi.vertline.467385
unknown [Bacillus subtilis] 87 78 1023 199 1 1158 334
gi.vertline.143527 iron-sulfur protein [Bacillus subtilis] 87 77
825 199 2 2933 1149 pir.vertline.A27763.vertline.A277 succinate
dehydrogenase (EC 1.3.99.1) flavoprotein - Bacillus subtilis 87 80
1785 205 23 11543 11304 gi.vertline.1044972 ribosomal protein L29
[Bacillus subtilis] 87 78 240 205 25 12607 11939
gi.vertline.1165309 S3 [Bacillus subtilis] 87 75 669 222 1 1107 181
gi.vertline.1177249 rec233 gene product [Bacillus subtilis] 87 70
927 236 3 1333 1031 gi.vertline.1146198 ferredoxin [Bacillus
subtilis] 87 80 303 246 5 2292 1999 gi.vertline.467373 ribosomal
protein S18 [Bacillus subtilis] 87 77 294 260 2 3422 2655
gi.vertline.1161382 IcaC [Staphylococcus epidermidis] 87 72 768 320
3 1696 2391 gi.vertline.312443 carbamoyl-phosphate synthase
(glutamine-hydrolysing) [Bacillus aldolyticus] 87 80 696 380 4 1165
1383 gi.vertline.142570 ATP synthase c subunit [Bacillus firmus] 87
80 219 414 4 900 1073 gi.vertline.467386 thiophen and furan
oxidation [Bacillus subtilis] 87 77 174 425 2 794 585
gi.vertline.1046166 pilin repressor [Mycoplasma genitalium] 87 69
210 448 1 722 189 gi.vertline.405134 acetate kinase [Bacillus
subtilis] 87 75 534 480 1 1 711 gi.vertline.142559 ATP synthase
alpha subunit [Bacillus megaterium] 87 79 711 481 1 2 352
sp.vertline.Q06797.vertline.RL1_- B 50S RIBOSOMAL PROTEIN L1 (BL1).
87 72 351 677 2 359 955 gi.vertline.460911 fructose-bisphosphate
aldolase [Bacillus subtilis] 87 78 597 677 3 934 1284
gi.vertline.460911 fructose-bisphosphate aldolase [Bacillus
subtilis] 87 78 351 876 1 3 452 gi.vertline.1146247
asparaginyl-tRNA synthetase [Bacillus subtilis] 87 79 450 1376 1
214 2 gi.vertline.1065555 F46H6.4 gene product [Caenorhabditis
elegans] 87 75 213 2206 1 3 374 gi.vertline.215098 excisionase
[Bacteriophage 154a] 87 72 372 2938 1 3 290 gi.vertline.508979
GTP-binding protein [Bacillus subtilis] 87 69 288 3081 2 126 308
gi.vertline.467399 IMP dehydrogenase [Bacillus subtilis] 87 72 183
3535 1 3 401 gi.vertline.1405454 aconitase [Bacillus subtilis] 87
80 399 4238 1 275 3 gi.vertline.603769 HutU protein, urocanase
[Bacillus subtilis] 87 73 273 4 8 8736 7045 gi.vertline.603769 HutU
protein, urocanase [Bacillus subtilis] 86 72 1692 22 6 3738 3286
gi.vertline.410515 urease beta subunit [Staphylococcus xylosus] 86
73 453 54 2 1572 664 gi.vertline.289287 UDP-glucose
pyrophosphorylase [Bacillus subtilis] 86 70 909 124 3 1713 1090
gi.vertline.556887 uracil phosphoribosyltransferase [Bacillus
subtilis] pir.vertline.S49364.vertlin- e.S49364 86 74 624 uracil
phosphoribosyltransferase - Bacillus subtilis 148 3 1349 3448
gi.vertline.467458 cell division protein [Bacillus subtilis] 86 75
2100 148 4 3638 3859 gi.vertline.467460 unknown [Bacillus subtilis]
86 73 222 152 3 1340 2086 gi.vertline.1377835 pyruvate
decarboxylase E-1 alpha subunit [Bacillus subtilis] 86 75 747 164
18 17347 19467 gi.vertline.1184680 polynucleotide phosphorylase
[Bacillus subtilis] 86 72 2121 180 2 554 1159 gi.vertline.143467
ribosomal protein S4 [Bacillus subtilis] 86 80 606 205 3 2592 2218
gi.vertline.142464 ribosomal protein L17 [Bacillus subtilis] 86 77
375 205 26 12990 12616 gi.vertline.40107 ribosomal protein L22
[Bacillus stearothermophilus] ir.vertline.S10612.vertline.S10612 86
75 375 ribosomal protein L22 - Bacillus stearothermophilus 246 7
3140 2817 gi.vertline.467375 ribosomal protein S6 [Bacillus
subtilis] 86 70 324 299 3 1196 1540 gi.vertline.39656 spoVG gene
product [Bacillus megaterium] 86 70 345 299 7 3884 4345
gi.vertline.467440 `phosphoribosylpyrophosphate synthetase
[Bacillus subtilis] gi.vertline.40218 PRPP 86 78 462 synthetase (AA
1-317) [Bacillus subtilis] 304 5 2170 2523 gi.vertline.666983
putative ATP binding subunit [Bacillus subtilis] 86 65 354 310 2
1487 1678 gi.vertline.1177684 chorismate mutase [Staphylococcus
xylosus] 86 71 192 337 5 2086 3405 gi.vertline.487434 isocitrate
dehydrogenase [Bacillus subtilis] 86 78 1320 339 2 1109 729
gi.vertline.1118003 dihydroneopterin aldolase [Staphylococcus
haemolyticus] 86 77 381 358 2 2124 3440 gi.vertline.1146219 28.2%
of identity to the Escherichia coli GTP-binding protein Era;
putative 86 73 1317 [Bacillus subtilis] 404 2 1015 2058
gi.vertline.1303817 YqfA [Bacillus subtilis] 86 78 1044 581 2 452
243 gi.vertline.40056 phoP gene product [Bacillus subtilis] 86 71
210 642 2 338 1075 gi.vertline.1176399 EpiF [Staphylococcus
epidermidis] 86 72 738 770 1 347 72 gi.vertline.143328 phoP protein
(put.); putative [Bacillus subtilis] 86 69 276 865 1 890 3
gi.vertline.1146247 asparaginyl-tRNA synthetase [Bacillus subtilis]
86 74 888 868 2 963 1133 gi.vertline.1002911 transmembrane protein
[Saccharomyces cerevisiae] 86 69 171 904 1 1 162
gi.vertline.1303912 YqhW [Bacillus subtilis] 86 72 162 989 1 35 433
gi.vertline.1303993 YqkL [Bacillus subtilis] 86 76 399 1212 1 150 4
gi.vertline.414014 ipa-90d gene product [Bacillus subtilis] 86 70
147 1323 1 2 148 gi.vertline.40041 pyruvate dehydrogenase
(lipoamide) [Bacillus stearothermophilus] 86 75 147
ir.vertline.S10798.vertline.DEB- SPF pyruvate dehydrogenase
(lipoamide) (EC 1.2.4.1) pha chain - Bacillus stearothermophilus
3085 2 310 80 gi.vertline.1354211 PET112-like protein [Bacillus
subtilis] 86 86 231 3847 1 1 228 gi.vertline.296464 ATPase
[Lactococcus lactis] 86 63 228 4487 1 240 4 gi.vertline.1022726
unknown [Staphylococcus haemolyticus] 86 73 237 4583 1 187 2
gi.vertline.1022725 unknown [Staphylococcus haemolyticus] 86 79 186
25 5 4287 5039 gi.vertline.1502421 3-ketoacyl-acyl carrier protein
reductase [Bacillus subtilis] 85 64 753 56 21 29395 28163
gi.vertline.1408507 pyrimidine nucleoside transport protein
[Bacillus subtilis] 85 69 1233 68 2 332 1192 gi.vertline.467376
unknown [Bacillus subtilis] 85 74 861 73 2 880 1707
gi.vertline.142992 glycerol kinase (glpK) (EC 2.7.1.30) [Bacillus
subtilis] pir.vertline.B45868.vertline.B45868 85 72 828 glycerol
kinase (EC 2.7.1.30) - Bacillus subtilis sp.vertline.P18157.vert-
line.GLPK_BACSU GLYCEROL KINASE (EC 2.7.1.30) (ATP:
GLYCEROL-PHOSPHOTRANSFERASE) (GLYCEROKINASE) (GK). 106 4 1505 3490
gi.vertline.143766 (thrSv) (EC 6.1.1.3) [Bacillus subtilis] 85 74
1986 128 2 1153 2202 gi.vertline.311924 glycerladehyde-3-phosphate
dehydrogenase [Clostridium pasteurianum] 85 75 1050
pir.vertline.S34254.vertline.S34254 glyceraldehyde-3-phosphate
dehydrogenase (EC .2.1.12) - Clostridium pasteurianum 129 4 5252
4038 gi.vertline.1064807 ORTHININE AMINOTRANSFERASE [Bacillus
subtilis] 85 73 1215 138 6 3475 5673 gi.vertline.1072419 glcB gene
product [Staphylococcus carnosus] 85 74 2199 189 1 2 169
gi.vertline.467385 unknown [Bacillus subtilis] 85 65 168 205 15
8106 7588 gi.vertline.1044981 ribosomal protein S5 [Bacillus
subtilis] 85 75 519 205 20 10596 10264
pir.vertline.A02819.vertline.R5BS ribosomal protein L24 - Bacillus
stearothermophilus 85 72 333 220 6 6101 5712 gi.vertline.48980 secA
gene product [Bacillus subtilis] 85 66 390 231 4 3159 1441
gi.vertline.1002520 MutS [Bacillus subtilis] 85 70 1719 243 9 8013
8783 gi.vertline.414011 ipa-87r gene product [Bacillus subtilis] 85
72 771 249 2 3186 478 gi.vertline.1405454 aconitase [Bacillus
subtilis] 85 73 2709 302 1 140 475 gi.vertline.40173 homolog of E.
coli ribosomal protein L21 [Bacillus subtilis] 85 72 336
ir.vertline.S18439.vertline.S18439 Ribosomal protein L21 - Bacillus
subtilis p.vertline.P26908.vertline.RL21_BACSU 50S RIBOSOMAL
PROTEIN L21 [BL20]. 333 1 2968 491 gi.vertline.442360 ClpC
adenosine triphosphatase [Bacillus subtilis] 85 69 2478 364 6 6082
8196 gi.vertline.871784 Clp-like ATP-dependent protease binding
subunit [Bos taurus] 85 68 2115 448 2 1339 686 gi.vertline.405134
acetate kinase [Bacillus subtilis] 85 68 654 747 1 853 455
gi.vertline.1373157 orf-X; hypothetical protein; Method: conceptual
translation supplied by 85 73 399 author [Bacillus subtilis] 886 2
159 467 gi.vertline.541768 hemin permease [Yersinia enterocolitica]
85 55 309 1089 1 606 4 pir.vertline.B47154.vertlin- e.B471 signal
recognition particle 54K chain homolog Ffh - Bacillus subtilis 85
71 603 1163 1 409 2 gi.vertline.304155 diaminopimelate
decarboxylase [Bacillus methanolicus]
sp.vertline.P41023.vertline.DCDA_BA- CMT 85 62 408 DIAMINOPIMELATE
DECARBOXYLASE (EC 4.1.1.20) DAP DECARBOXYLASE]. 1924 1 251 15
gi.vertline.215098 excisionase [Bacteriophage 154a] 85 73 237 2932
1 390 4 gi.vertline.1041099 Pyruvate Kinase [Bacillus
licheniformis] 85 71 387 3030 1 3 275 gi.vertline.42370 pyruvate
formate-lyase [AA 1-760] [Escherichia coli]
ir.vertline.S01788.vertline.S01788 85 74 273 formate
C-acetyltransferase (EC 2.3.1.54) - Escherichia coli 3111 1 299 3
gi.vertline.63568 limb deformity protein [Gallus gallus] 85 85 297
3778 1 316 2 gi.vertline.391840 beta-subunit of HDT [Pseudomonas
fragi] 85 67 315 3835 1 1 387 gi.vertline.1204472 type I
restriction enzyme ECOR124/3 I M protein [Haemophilus influenzae]
85 56 387 4042 1 3 386 gi.vertline.18178 formare acetyltransferase
[Chlamydomonas reinhardtii] ir.vertline.S24997.vertline.S24997 85
70 384 formate C-acetyltransferase (EC 2.3.1.54) - Chlamydomonas
reinhardtii 4053 1 35 340 gi.vertline.1204472 type I restriction
enzyme ECOR124/3 I M protein [Haemophilus influenzae] 85 56 306
4108 1 2 181 gi.vertline.1072418 glcA gene product [Staphylococcus
carnosus] 85 61 180 4300 1 330 85 gi.vertline.151932 fructose
enzyme II [Rhodobacter capsulatus] 85 59 246 4392 1 355 83
gi.vertline.1022725 unknown [Staphylococcus haemolyticus] 85 74 273
4408 1 2 235 gi.vertline.871784 Clp-like ATP-dependent protease
binding subunit [Bos taurus] 85 62 234 4430 1 291 4
gi.vertline.1009366 Respiratory nitrate reductase [Bacillus
subtilis] 85 68 288 4555 1 2 253 gi.vertline.450688 hsdM gene of
EcoprrI gene product [Escherichia coli]
pir.vertline.S38437.vertline.S38437 hsdM 85 52 252 protein -
Escherichia coli pir.vertline.S09629.vertline.S09629 hypothetical
protein A - Escherichia coli (SUB 40-520) 4611 1 242 3
gi.vertline.1256635 dihydroxy-acid dehydratase [Bacillus subtilis]
85 65 240 4 10 10061 10591 gi.vertline.46982 fosB gene product
[Staphylococcus epidermidis] 84 68 531 13 2 1172 996
gi.vertline.142450 ahrC protein [Bacillus subtilis] 84 56 177 16 4
1803 4652 gi.vertline.1277198 DNA repair protein [Deinococcus
radiodurans] 84 67 2850 22 3 1128 721 gi.vertline.511069 UreF
[Staphylococcus xylosus] 84 73 408 23 7 5055 5306
gi.vertline.603320 Yer082p [Saccharomyces cerevisiae] 84 61 252 53
11 11145 10693 gi.vertline.1303948 YqiW [Bacillus subtilis] 84 68
453 53 12 12770 11481 gi.vertline.142613 branched chain alpha-keto
acid dehydrogenase E2 [Bacillus subtilis] 84 71 1290
gi.vertline.1303944 BfmBB [Bacillus subtilis] 70 1 982 632
gi.vertline.46647 ORF (repE) [Staphylococcus aureus] 84 68 351 73 4
2512 4311 gi.vertline.142993 glycerol-3-phosphate dehydrogenase
(glpD) (EC 1.1.99.5) [Bacillus subtilis] 84 74 1800 98 7 4324 6096
gi.vertline.467427 methionyl-tRNA synthetase [Bacillus subtilis] 84
66 1773 100 9 8680 7859 gi.vertline.1340128 ORF1 [Staphylococcus
aureus] 84 78 822 117 3 1934 3208 gi.vertline.1237019 Srb [Bacillus
subtilis] 84 68 1275 148 6 4720 5670 gi.vertline.467462 cysteine
synthetase A [Bacillus subtilis] 84 69 951 152 4 2064
2456 gi.vertline.143377 pyruvate decarboxylase (E-1) alpha subunit
[Bacillus subtilis] 84 70 393 pir.vertline.B36718.vertline.DE- BSPA
pyruvate dehydrogenase (lipoamide) (EC 1.2.4.1) lpha chain -
Bacillus subtilis 169 7 3634 3861 gi.vertline.1001342 hypothetical
protein [Synechocystis sp.] 84 66 228 171 4 2657 2322
gi.vertline.517475 D-amino acid transaminase [Staphylococcus
haemolyticus] 84 71 336 186 6 6216 5491 gi.vertline.467475 unknown
[Bacillus subtilis] 84 70 726 205 9 5692 5123 gi.vertline.216340
ORF for adenylate kinase [Bacillus subtilis] 84 71 570 224 2 915
1391 gi.vertline.288269 beta-fructofuranosidase [Staphylococcus
xylosus] 84 70 477 251 1 92 388 gi.vertline.1303790 YqeI [Bacillus
subtilis] 84 65 297 282 3 1526 2836 gi.vertline.143040
glutamate-1-semialdehyde 2,1-aminotransferase [Bacillus subtilis]
84 75 1311 pir.vertline.D42728.vertline.D42728
glutamate-1-semialdehyde 2,1-aminomutase (EC.4.3.8) - Bacillus
subtilis 307 5 2959 2780 gi.vertline.1070014 protein-dependent
[Bacillus subtilis] 84 62 180 320 4 2343 4229 gi.vertline.143390
carbamyl phosphate synthetase [Bacillus subtilis] 84 70 1887 372 1
3 296 gi.vertline.1022725 unknown [Staphylococcus haemolyticus] 84
70 294 413 2 1341 481 gi.vertline.1256146 YbbQ [Bacillus subtilis]
84 65 861 439 1 3 392 gi.vertline.1046173 osmotically inducible
protein [Mycoplasma genitalium] 84 53 390 461 3 1362 2270
gi.vertline.40211 threonine synthase (thrC) (AA 1-352) [Bacillus
subtilis] ir.vertline.A25364.vertline.A25364 84 69 909 threonine
synthase (EC 4.2.99.2) - Bacillus subtilis 487 1 3 299
gi.vertline.1144531 integrin-like protein alpha Intlp [Candida
albicans] 84 46 297 491 2 624 905 pir.vertline.S08564.vertline.R3B-
S ribosomal protein S9 - Bacillus stearothermophilus 84 69 282 491
3 836 1033 pir.vertline.S08564.vertline.R3BS ribosomal protein S9 -
Bacillus stearothermophilus 84 77 198 548 1 3 341
gi.vertline.431231 uracil permease [Bacillus caldolyticus] 84 74
339 728 2 1748 795 gi.vertline.912445 DNA polymerase [Bacillus
caldotenax] 84 68 954 769 1 3 257 gi.vertline.1510953 cobalamin
biosynthesis protein N [Methanococcus jannaschii] 84 38 255 954 1
156 4 gi.vertline.1405454 aconitase [Bacillus subtilis] 84 57 153
957 1 3 395 gi.vertline.143402 recombination protein (ttg start
codon) [Bacillus subtilis] gi.vertline.1303923 RecN 84 68 393
[Bacillus subtilis] 975 1 3 452 gi.vertline.885934 ClpB
[Synechococcus sp.] 84 70 450 1585 1 3 257 gi.vertline.510140
ligoendopeptidase F [Lactococcus lactis] 84 56 255 2954 1 3 323
gi.vertline.603769 HutU protein, urocanase [Bacillus subtilis] 84
73 321 2996 1 348 46 gi.vertline.18178 formate acetyltransferase
[Chlamydomonas reinhardtii] ir.vertline.S24997.vertline.S24997 84
65 303 formate C-acetyltransferase (EC 2.3.1.54) - Chlamydomonas
reinhardtii 3766 1 375 13 gi.vertline.517205 67 kDa
Myosin-crossreactive streptococcal antigen [Streptococcus yogenes]
84 72 363 4022 1 2 169 gi.vertline.1146206 glutamate dehydrogenase
[Bacillus subtilis] 84 54 168 4058 1 312 4 gi.vertline.151932
fructose enzyme II [Rhodobacter capsulatus] 84 71 309 4108 2 106
351 gi.vertline.1072418 glcA gene product [Staphylococcus carnosus]
84 77 246 4183 1 3 308 gi.vertline.603769 HutU protein, urocanase
[Bacillus subtilis] 84 72 306 4726 1 55 234 gi.vertline.146208
glutamate synthase large subunit (EC 2.6.1.53) [Escherichia coli]
84 73 180 pir.vertline.A29617.vertline.A29617 glutamate synthase
(NADPH) (EC 1.4.1.13) large hain - Escherichia coli 22 4 1576 1109
gi.vertline.393297 urease accessory protein [Bacillus sp.] 83 64
468 53 13 13745 12768 gi.vertline.142612 branched chain alpha-keto
acid dehydrogenase E1-beta [Bacillus subtilis] 83 68 978 57 16
12872 12387 gi.vertline.143132 lactate dehydrogenase (AC 1.1.1.27)
[Bacillus caldolyticus] 83 66 486 pir.vertline.B29704.vertlin-
e.B29704 L-lactate dehydrogenase (EC 1.1.1.27) - Bacillus
aldolyticus 66 3 2274 1429 gi.vertline.1303894 YqhM [Bacillus
subtilis] 83 63 846 66 5 4643 3168 gi.vertline.1212730 YqhK
[Bacillus subtilis] 83 68 1476 70 3 1523 1182 gi.vertline.44095
replication initiator protein [Listeria monocytogenes] 83 73 342 90
1 377 1429 gi.vertline.155571 alcohol dehydrogenase I (adhA) (EC
1.1.1.1) [Zymomonas mobilis] 83 70 1053
pir.vertline.A35260.vertline.A35260 alcohol dehydrogenase (EC
1.1.1.1) I - Zymomonas obilis 95 2 708 2162 gi.vertline.506381
phospho-beta-glucosidase [Bacillus subtilis] 83 70 1455 137 1 68
694 gi.vertline.467391 initiation protein of replicaton [Bacillus
subtilis] 83 77 627 140 4 2742 2275 gi.vertline.634107 kdpB
[Escherichia coli] 83 65 468 142 3 2989 2510 gi.vertline.1212776
lumazine synthase (b-subunit) [Bacillus amyloliquefaciens] 83 69
480 161 12 5749 6696 gi.vertline.903307 ORF75 [Bacillus subtilis]
83 64 948 164 9 9880 11070 gi.vertline.49316 ORF2 gene product
[Bacillus subtilis] 83 66 1191 164 14 14148 14546
gi.vertline.580902 ORF6 gene product [Bacillus subtilis] 83 60 399
170 2 2467 1790 gi.vertline.520844 orf4 [Bacillus subtilis] 83 64
678 186 2 1370 711 gi.vertline.289284 cysteinyl-tRNA synthetase
[Bacillus subtilis] 83 72 660 205 14 7607 7392 gi.vertline.216337
ORF for L30 ribosomal protein [Bacillus subtilis] 83 74 216 237 6
3683 4540 gi.vertline.1510488 imidazoleglycerol-phosphate synthase
(cyclase) [Methanococcus jannaschii] 83 60 858 301 1 638 291
gi.vertline.467419 unknown [Bacillus subtilis] 83 65 348 302 4 1421
2743 gi.vertline.508979 GTP-binding protein [Bacillus subtilis] 83
68 1323 321 4 3571 3209 gi.vertline.39844 fumarase (citG) (aa
1-462) [Bacillus subtilis] 83 68 363 367 1 2 352
gi.vertline.1039479 ORFU [Lactococcus lactis] 83 54 351 387 1 3 662
gi.vertline.806281 DNA polymerase I [Bacillus stearothermophilus]
83 70 660 527 2 916 1566 gi.vertline.396259 protease
[Staphylococcus epidermidis] 83 67 651 533 1 179 3
gi.vertline.142455 alanine dehydrogenase (EC 1.4.1.1) [Bacillus
stearothermophilus] 83 66 177 pir.vertline.B34261.vertline.B34261
alanine dehydrogenase (EC 1.4.1.1) - Bacillus stearothermophilus
536 4 1438 1259 gi.vertline.143366 adenylosuccinate lyase (PUR-B)
[Bacillus subtilis] pir.vertline.C29326.vertline.WZBSDS 83 67 180
adenylosuccinate lyase (EC 4.3.2.2) - Bacillus subtilis 652 1 2 859
gi.vertline.520753 DNA topoisomerase I [Bacillus subtilis] 83 72
858 774 2 200 361 gi.vertline.1522665 M. jannaschii predicted
coding region MJECL28 [Methanococcus jannaschii] 83 58 162 897 1
120 296 gi.vertline.1064807 ORTHININE AMINOTRANSFERASE [Bacillus
subtilis] 83 76 177 1213 1 3 491 gi.vertline.289288 lexA [Bacillus
subtilis] 83 67 489 2529 1 150 4 gi.vertline.143786
tryptophanyl-tRNA synthetase (EC 6.1.1.2) [Bacillus subtilis] 83 69
147 pir.vertline.JT0481.vertline.YWBS tryptophan - tRNA ligase (EC
6.1.1.2) - Bacillus subtilis 2973 1 326 3 gi.vertline.1109687 ProZ
[Bacillus subtilis] 83 58 324 3009 1 366 4 gi.vertline.882532
ORF_o294 [Escherichia coli] 83 65 363 3035 2 45 305
gi.vertline.950062 hypothetical yeast protein 1 [Mycoplasma
capricolum] pir.vertline.S48578.vertline.S48578 83 59 261
hypothetical protein - Mycoplasma capricolum SGC3) (fragment) 3906
1 67 309 gi.vertline.1353197 thioredoxin reductase [Eubacterium
acidaminophilum] 83 61 243 4458 1 271 2 gi.vertline.397526 clumping
factor [Staphylococcus aureus] 83 78 270 4570 1 223 2
gi.vertline.1022726 unknown [Staphylococcus haemolyticus] 83 74 222
4654 1 97 261 gi.vertline.1072419 glcB gene product [Staphylococcus
carnosus] 83 79 165 16 2 295 1191 gi.vertline.153854 uvs402 protein
[Streptococcus pneumoniae] 82 67 897 16 3 1193 1798
gi.vertline.153854 uvs402 protein [Streptococcus pneumoniae] 82 70
606 38 12 8724 7804 gi.vertline.1204400 N-acetylneuraminate lyase
[Haemophilus influenzae] 82 58 921 42 4 988 2019 gi.vertline.841192
catalase [Bacteroides fragilis] 82 70 1032 51 6 2590 3489
gi.vertline.143607 sporulation protein [Bacillus subtilis] 82 69
900 56 11 12270 13925 gi.vertline.39431 oligo-1,6-glucosidase
[Bacillus cereus] 82 60 1656 56 15 17673 18014 gi.vertline.467410
unknown [Bacillus subtilis] 82 66 342 61 2 881 3313
gi.vertline.143148 transfer RNA-Leu synthetase [Bacillus subtilis]
82 70 2433 82 7 9162 11318 gi.vertline.48240 elongation factor G
(AA 1-691) [Thermus aquaticus thermophilus] 82 64 2157
ir.vertline.S15928.vertline.EFTWG translation elongation factor G -
Thermus aquaticus p.vertline.P13551.vertline.EFG_T- HETH ELONGATION
FACTOR G (EF-G). 85 2 3260 1050 gi.vertline.143369
phosphoribosylformyl glycinamidine synthetase II (PUR-Q) [Bacillus
subtilis] 82 66 2211 102 6 3662 5380 gi.vertline.1256635
dihydroxy-acid dehydratase [Bacillus subtilis.vertline. 82 65 1719
117 4 3242 3493 pir.vertline.A47154.vertline.A471 orf1 5' of Ffh -
Bacillus subtilis 82 53 252 128 6 4377 5933 gi.vertline.460258
phosphoglycerate mutase [Bacillus subtilis] 82 66 1557 129 2 1229
2182 gi.vertline.403373 glycerophosphoryl diester phosphodiesterase
[Bacillus subtilis] 82 62 954 pir.vertline.S37251.vertline.S3- 7251
glycerophosphoryl diester phosphodiesterase -Bacillus subtilis 170
1 2 1441 gi.vertline.1377831 unknown [Bacillus subtilis] 82 67 1440
177 1 3 1094 gi.vertline.467386 thiophen and furan oxidation
[Bacillus subtilis] 82 65 1092 184 4 3572 4039 gi.vertline.153566
ORF (19 K protein) [Enterococcus faecalis] 82 59 468 189 8 4225
3995 gi.vertline.1001878 CspL protein [Listeria monocytogenes] 82
73 231 206 19 20707 20048 gi.vertline.473916 lipopeptide
antibiotics iturin A [Bacillus subtilis]sp.vertline.P39144.ve-
rtline.LP14_BACSU 82 50 660 LIPOPEPTIDE ANTIBIOTICS ITURIN A AND
SURFACTIN IOSYNTHESIS PROTEIN. 221 2 805 1722 gi.vertline.517205 67
kDa Myosin-crossreactive streptococcal antigen [Streptococcus
yogenes] 82 63 918 223 4 3651 3436 gi.vertline.439619 [Salmonella
typhimurium IS200 insertion sequence from SARA17, artial.], 82 69
216 gene product [Salmonella typhimurium] 260 3 4296 3385
gi.vertline.1161381 IcaB [Staphylococcus epidermidis] 82 61 912 315
3 2855 846 gi.vertline.143397 quinol oxidase [Bacillus subtilis] 82
67 2010 321 10 7945 7370 gi.vertline.142981 ORF5; This ORF includes
a region (aa23-103) containing a potential ron- 82 62 576 sulphur
centre homologous to a region of Rhodospirillum rubrum nd
Chromatium vinosum; putative [Bacillus stearothermophilus]
pir.vertline.PQ0299.vertline.PQ0299 hypothetical protein 5 (gldA 3'
region) - 331 3 1055 1342 gi.vertline.436574 ribosomal protein L1
[Bacillus subtilis] 82 71 288 370 2 262 618 gi.vertline.1303793
YqeL [Bacillus subtilis] 82 59 357 404 4 3053 4024
gi.vertline.1303821 YqfE [Bacillus subtilis] 82 68 972 405 4 3073
1706 gi.vertline.1303913 YqhX [Bacillus subtilis] 82 67 1368 436 3
2864 1632 gi.vertline.149521 tryptophan synthase beta subunit
[Lactococcus lactis]pir.vertline.S35129.vertline.S35129 82 67 1233
tryptophan synthase (EC 4.2.1.20) beta chain - Lactococcus lactis
subsp. lactis 441 4 2573 1752 gi.vertline.142952
glyceraldehyde-3-phosphate dehydrogenase [Bacillus
tearothermophilus] 82 67 822 444 12 10415 11227 gi.vertline.1204354
spore germination and vegetative growth protein [Haemophilus
influenzae] 82 67 813 446 1 3 191 gi.vertline.143387 aspartate
transcarbamylase [Bacillus subtilis] 82 66 189 462 3 1007 1210
gi.vertline.142521 deoxyribodipyrimidine photolyase [Bacillus
subtilis] pir.vertline.A37192.vertline.A37192 uvrB 82 64 204
protein - Bacillus subtilis sp.vertline.P14951.vertline.UVRC_BACSU
EXCINUCLEASE ABC SUBUNIT C. 537 1 784 8 gi.vertline.853767
UDP-N-acetylglucosamine 1-carboxyvinyltransferase [Bacillus
subtilis] 82 61 777 680 2 407 700 gi.vertline.426472 secE gene
product [Staphylococcus carnosus] 82 69 294 724 2 386 207
gi.vertline.143373 phosphoribosyl aminoimidazole carboxy formyl
ormyltransferase/inosine 82 68 180 monophosphate cyclohydrolase
(PUR-H(J)) Bacillus subtilis) 763 1 213 4 gi.vertline.467458 cell
division protein [Bacillus subtilis] 82 35 210 818 1 283 2
gi.vertline.1064787 function unknown [Bacillus subtilis] 82 69 282
858 1 175 1176 gi.vertline.143043 uroporphyrinogen decarboxylase
[Bacillus subtilis] pir.vertline.B47045.vertline.B47045 82 71 1002
uroporphyrinogen decarboxylase (EC 4.1.1.37) - Bacillus subtilis
895 1 3 599 gi.vertline.1027507 ATP binding protein [Borrelia
burgdorferi] 82 72 597 939 1 10 399 gi.vertline.143795 transfer
RNA-Tyr synthetase [Bacillus subtilis] 82 60 390 961 1 1 306
gi.vertline.577647 gamma-hemolysin [Staphylococcus aureus] 82 69
306 1192 1 155 3 gi.vertline.146974 NH3-dependent NAD synthetase
[Escherichia coli] 82 71 153 1317 1 49 375 gi.vertline.407908
EIIscr [Staphylococcus xylosus] 82 72 327 1341 1 1 150
gi.vertline.39962 ribosomal protein L35 (AA 1-66) [Bacillus
stearothermophilus] 82 68 150 ir.vertline.S05347.vertline.R5B- S35
ribosomal protein L35 - Bacillus earothermophilus 2990 2 349 131
gi.vertline.534855 ATPase subunit epsilon [Bacillus
stearothermophilus]sp.vertline.P42009.vertline.ATPE_BACST 82 47 219
ATP SYNTHASE EPSILON CHAIN (EC 3.6.1.34). 3024 1 45 224
gi.vertline.467402 unknown [Bacillus subtilis] 82 64 180 3045 1 139
2 gi.vertline.467335 ribosomal protein L9 [Bacillus subtilis] 82 60
138 3045 2 400 242 gi.vertline.467335 ribosomal protein L9
[Bacillus subtilis] 82 82 159 3091 1 238 2 gi.vertline.499335 secA
protein [Staphylococcus carnosus] 82 78 237 3107 1 210 4
gi.vertline.546918 orfY 3' of comK [Bacillus subtilis, E26, Peptide
Partial, 140 aa] 82 64 207 pir.vertline.S43612.vertline.S4361- 2
hypothetical protein Y - Bacillus subtilis
sp.vertline.P40398.vertline.YHXD_BACSU HYPOTHETICAL PROTEIN IN COMK
3' REGION (ORFY) FRAGMENT). 4332 1 2 319 gi.vertline.42086 nitrate
reductase alpha subunit [Escherichia coli]
p.vertline.P09152.vertline.NARG_ECOLI 82 75 318 RESPIRATORY NITRATE
REDUCTASE 1 ALPHA CHAIN (EC 7.99.4). (SUB 2-1247) 23 3 2574 1873
gi.vertline.1199573 spsB [Sphingomonas sp.] 81 64 702 42 1 321 4
gi.vertline.466778 lysine specific permease [Escherichia coli] 81
59 318 48 5 4051 4350 gi.vertline.1045937 M. genitalium predicted
coding region MG246 [Mycoplasma genitalium] 81 62 300 51 4 1578
2579 pir.vertline.S16649.vertline.S166 dciAC protein - Bacillus
subtilis 81 55 1002 53 2 364 1494 gi.vertline.1303961 YqjJ
[Bacillus subtilis] 81 67 1131 53 8 7971 6523 gi.vertline.146930
6-phosphogluconate dehydrogenase [Escherichia coli] 81 66 1449 54 9
10119 9481 gi.vertline.143016 permease [Bacillus subtilis] 81 65
639 54 10 11786 10212 gi.vertline.143015 gluconate kinase [Bacillus
subtilis] 81 64 1575 57 17 13366 12749 pir.vertline.A25805.vertlin-
e.A258 L-lactate dehydrogenase (EC 1.1.1.27) - Bacillus subtilis 81
74 618 81 2 2217 1726 gi.vertline.1222302 NifU-related protein
[Haemophilus influenzae] 81 54 492 86 1 374 3 gi.vertline.414017
ipa-93d gene product [Bacillus subtilis] 81 70 372 103 6 4861 3284
gi.vertline.971342 nitrate reductase beta subunit [Bacillus
subtilis] sp.vertline.P42176.vertline.NARH_BACSU 81 64 1578 NITRATE
REDUCTASE BETA CHAIN (EC 1.7.99.4). 120 15 10845 12338
gi.vertline.1524392 GbsA [Bacillus subtilis] 81 67 1494 128 5 3676
4413 gi.vertline.143319 triose phosphate isomerase [Bacillus
megaterium] 81 64 738 131 9 9280 8252 gi.vertline.299163 alanine
dehydrogenase [Bacillus subtilis] 81 68 1029 143 6 5471 4854
gi.vertline.439619 [Salmonella typhimurium IS200 insertion sequence
from SARA17, artial.], 81 61 618 gene product [Salmonella
typhimurium] 169 1 43 825 gi.vertline.897795 30S ribosomal protein
[Pediococcus acidilactici] sp.vertline.P49668.vertline.RS2_PEDAC
30S 81 65 783 RIBOSOMAL PROTEN S2. 230 1 226 2 gi.vertline.1125826
short region of weak similarity to tyrosine-protein kinase
receptors in a 81 54 225 fibronectin type III-like domain
[Caenorhabditis elegans] 233 5 2000 2677 gi.vertline.467404 unknown
[Bacillus subtilis] 81 63 678 241 2 2149 1217 gi.vertline.16510
succinate - CoA ligase (GDP-forming) [Arabidopsis thaliana]
ir.vertline.S30579.vertline.S30579 81 69 933 succinate--CoA ligase
(GDP-forming) (EC 6.2.1.4) pha chain - Arabidopsis thaliana
(fragment) 256 1 1
981 pir.vertline.S09411.vertline.S094 spoIIIE protein - [Bacillus
subtilis] 81 65 981 259 3 2691 1630 sp.vertline.P28367.vertline.RF-
2_B PROBABLE PEPTIDE CHAIN RELEASE FACTOR 2 (RF-2) (FRAGMENT). 81
65 1062 275 2 1728 3581 gi.vertline.726480
L-glutamine-n-fructose-6-phosph- ate amidotransferase [Bacillus
subtilis] 81 68 1854 285 1 735 4 gi.vertline.1204844 H. influenzae
predicted coding region HI0594 [Haemophilus influenzae] 81 63 732
296 1 99 1406 gi.vertline.467328 adenylosuccinate synthetase
[Bacillus subtilis] 81 67 1308 302 9 5590 5889 gi.vertline.147485
queA [Escherichia coli] 81 64 300 317 2 1137 1376
gi.vertline.154961 resolvase [Transposon Tn917] 81 51 240 343 2
1034 1342 gi.vertline.405955 yeeD [Escherichia coli] 81 60 309 360
2 1404 2471 gi.vertline.1204570 aspartyl-tRNA synthetase
[Haemophilus influenzae] 81 67 1068 364 5 5706 5161
gi.vertline.1204652 methylated-DNA-protein-cysteine
methyltransferase [Haemophilus influenzae] 81 63 546 372 2 1135 563
gi.vertline.467416 unknown [Bacillus subtilis] 81 65 573 392 1 43
603 pir.vertline.S09411.vertline.S094 spoIIIE protein - Bacillus
subtilis 81 65 561 404 9 5252 6154 gi.vertline.606745 Bex [Bacillus
subtilis] 81 65 903 426 2 1119 511 gi.vertline.39453 Manganese
superoxide dismutase [Bacillus caldotenax]
ir.vertline.S22053.vertline.S22053 81 66 609 superoxide dismutase
(EC 1.15.1.1) (Mn) - Bacillus ldotenax 480 7 5653 5889
pir.vertline.C37083.vertline.C370 hypothetical protein II (ompH 3'
region) - Salmonella typhimurium 81 57 237 [fragment] 625 3 1105
2070 gi.vertline.1262360 protein kinase PknB [Mycobacterium leprae]
81 56 966 754 2 504 1064 gi.vertline.1303902 YqhU [Bacillus
subtilis] 81 71 561 842 1 86 430 gi.vertline.1405446 transketolase
[Bacillus subtilis] 81 68 345 953 1 400 2 gi.vertline.1205429
dipeptide transport ATP-binding protein [Haemophilus influenzae] 81
57 399 961 2 252 401 gi.vertline.487686 synergohymenotropic toxin
[Staphylococcus intermedius] pir.vertline.S44944.vertline.S44944 81
72 150 synergohymenotropic toxin - Staphylococcus intermedius 1035
1 1 189 gi.vertline.1046138 M. genitalium predicted coding region
MG423 [Mycoplasma genitalium] 81 43 189 1280 1 449 228
gi.vertline.559164 helicase [Autographa californica nuclear
polyhedrosis virus] 81 43 222
sp.vertline.P24307.vertline.V143_NPVAC HELICASE. 3371 1 68 241
gi.vertline.1322245 mevalonate pyrophosphate decarboxylase [Rattus
norvegicus] 81 62 174 3715 1 239 3 gi.vertline.537137 ORF_f388
[Escherichia coli] 81 58 237 3908 1 2 325 gi.vertline.439619
[Salmonella typhimurium IS200 insertion sequence from SARA17,
artial.], 81 68 324 gene product [Salmonella typhimurium] 3940 1 3
401 gi.vertline.296464 ATPase [Lactococcus lactis] 81 69 399 3954 1
1 318 gi.vertline.1224069 amidase [Moraxella catarrhalis] 81 68 318
4049 1 170 3 gi.vertline.603768 HutI protein,
imidazolone-5-propionate hydrolase [Bacillus subtilis] 81 68 168
gi.vertline.603768 HutI protein, imidazolone-5-propionate hydrolase
Bacillus subtilis] 4209 1 1 324 gi.vertline.403373
glycerophosphoryl diester phosphodiesterase [Bacillus subtilis] 81
58 324 pir.vertline.S37251.vertline.S37251 glycerophosphoryl
diester phosphodiesterase - Bacillus subtilis 4371 1 322 17
gi.vertline.216677 indolepyruvate decarboxylase [Enterobacter
cloacae] pir.vertline.S16013.vertline.S16013 81 72 306
indolepyruvate decarboxylase (EC 4.1.1.--) - Enterobacter cloacae
4387 1 19 228 gi.vertline.460689 TVG [Thermoactinomyces vulgaris]
81 59 210 4391 1 306 31 gi.vertline.1524193 unknown [Mycobacterium
tuberculosis] 81 67 276 4425 1 3 341 gi.vertline.143015 gluconate
kinase [Bacillus subtilis] 81 66 339 9 1 847 101
gi.vertline.1064786 function unknown [Bacillus subtilis] 80 62 747
17 1 311 78 gi.vertline.559164 helicase [Autographa californica
nuclear polyhedrosis virus] 80 40 234
sp.vertline.P24307.vertline.V143_NPVAC HELICASE. 45 2 1159 2448
gi.vertline.1109684 ProV [Bacillus subtilis] 80 63 1290 45 5 4032
4733 gi.vertline.1109687 ProZ [Bacillus subtilis] 80 55 702 54 8
9502 8738 gi.vertline.563952 gluconate permease [Bacillus
licheniformis] 80 62 765 62 12 7545 6238 gi.vertline.854655 Na/H
antiporter system [Bacillus alcalophilus] 80 62 1308 62 14 8087
8683 gi.vertline.559713 ORF [Homo sapiens] 80 68 597 67 16 13781
14122 gi.vertline.305002 ORF_f356 [Escherichia coli] 80 65 342 70
13 10296 9097 gi.vertline.1303995 YqkN [Bacillus subtilis] 80 64
1200 98 9 6336 7130 gi.vertline.467428 unknown [Bacillus subtilis]
80 68 795 98 10 7294 7833 gi.vertline.467430 unknown [Bacillus
subtilis] 80 64 540 98 11 7820 8737 gi.vertline.467431 high level
kasgamycin resistance [Bacillus subtilis] 80 61 918 109 16 14154
14813 gi.vertline.580875 ipa-57d gene product [Bacillus subtilis]
80 63 660 112 15 14294 16636 gi.vertline.1072361
pyruvate-formate-lyase [Clostridium pasteurianum] 80 65 2343 139 1
726 4 gi.vertline.506699 CapC [Staphylococcus aureus] 80 58 723 139
2 1448 717 gi.vertline.506698 CapB [Staphylococcus aureus] 80 59
732 174 4 2870 2469 gi.vertline.1146242 aspartate 1-decarboxylase
[Bacillus subtilis] 80 61 402 177 3 2102 2842 gi.vertline.467385
unknown [Bacillus subtilis] 80 70 741 184 6 5912 5700
gi.vertline.161953 85-kDa surface antigen [Trypanosoma cruzi] 80 46
213 186 4 3875 2382 gi.vertline.289282 glutamyl-tRNA synthetase
[Bacillus subtilis] 80 65 1494 205 30 15140 14484 gi.vertline.40103
ribosomal protein L4 [Bacillus stearothermophilus] 80 66 657 207 1
140 1315 gi.vertline.460259 enolase [Bacillus subtilis] 80 67 1176
211 3 1078 1590 gi.vertline.410131 ORFX7 [Bacillus subtilis] 80 61
513 235 2 1962 2255 gi.vertline.143797 valyl-tRNA synthetase
[Bacillus stearothermophilus] sp.vertline.P11931.vertline.SYV_BACST
80 55 294 VALYL-TRNA SYNTHETASE (EC 6.1.1.9) VALINE-TRNA LIGASE)
(VALRS). 239 1 1 1263 gi.vertline.143000 proton glutamate symport
protein [Bacillus stearothermophilus] 80 59 1263
pir.vertline.S26247.vertline.S26247 glutamate/aspartate transport
protein - Bacillus stearothermophilus 272 5 2461 2198
gi.vertline.709993 hypothetical protein [Bacillus subtilis] 80 54
264 301 3 1111 776 gi.vertline.467418 unknown [Bacillus subtilis]
80 58 336 310 4 4501 3305 gi.vertline.1177686 acuC gene product
[Staphylococcus xylosus] 80 67 1197 310 6 5258 7006
gi.vertline.348053 acetyl-CoA synthetase [Bacillus subtilis] 80 67
1749 310 7 7410 9113 gi.vertline.1103865 formyl-tetrahydrofolate
synthetase [Streptococcus mutans] 80 67 1704 325 3 1114 1389
gi.vertline.310325 outer capsid protein [Rotavirus sp.] 80 40 276
337 1 636 4 gi.vertline.537049 ORF_o470 [Escherichia coli] 80 55
633 374 2 929 1228 gi.vertline.1405448 YneF [Bacillus subtilis] 80
70 300 375 5 3062 3331 gi.vertline.467448 unknown [Bacillus
subtilis] 80 68 270 388 1 267 587 gi.vertline.1064791 function
unknown [Bacillus subtilis] 80 65 321 394 1 9 659
gi.vertline.304976 matches PS00017: ATP_GTP_A and PS00301:
EFACTOR_GTP; similar to longation 80 65 651 factor G, TetM/Tet0
tetracycline-resistance proteins Escherichia coli] 456 1 625 1263
gi.vertline.1146183 putative [Bacillus subtilis] 80 65 639 475 1 1
654 gi.vertline.288269 beta-fructofuranosidase [Staphylococcus
xylosus] 80 66 654 544 2 1449 2240 gi.vertline.529754 speC
[Streptococcus pyogenes] 80 50 792 622 4 1623 1871
gi.vertline.1483545 unknown [Mycobacterium tuberculosis] 80 65 249
719 1 1 1257 gi.vertline.1064791 function unknown [Bacillus
subtilis] 80 68 1257 739 1 107 838 gi.vertline.666983 putative ATP
binding subunit [Bacillus subtilis] 80 61 732 745 2 414 247
gi.vertline.1511600 coenzyme PQQ synthesis protein III
[Methanococcus jannaschii] 80 61 168 822 1 17 679
gi.vertline.410141 ORFX17 [Bacillus subtilis] 80 68 663 827 2 836
681 gi.vertline.1205301 leukotoxin secretion ATP-binding protein
[Haemophilus influenzae] 80 54 156 1044 1 3 149 gi.vertline.60632
vp2 [Marburg virus] 80 55 147 1220 2 413 255
pir.vertline.A61072.vertline.EPSG gallidermin precursor -
Staphylococcus gallinarum 80 74 159 2519 1 75 275
gi.vertline.147556 dpj [Escherichia coli] 80 45 201 2947 1 279 55
gi.vertline.1184680 polynucleotide phosphorylase [Bacillus
subtilis] 80 62 225 3120 1 2 226 gi.vertline.517205 67 kDa
Myosin-crossreactive streptococcal antigen [Streptococcus yogenes]
80 65 225 3191 1 148 2 gi.vertline.151259 HMG-CoA reductase (EC
1.1.1.88) [Pseudomonas mevalonii]
pir.vertline.A44756.vertline.A44756 80 59 147
hydroxymethylglutaryl-CoA reductase (EC 1.1.1.88) Pseudomonas sp.
3560 2 285 434 gi.vertline.217130 photosystem I core protein B
[Synechococcus vulcanus] 80 70 150 3655 1 47 346 gi.vertline.415855
deoxyribose aldolase [Mycoplasma hominis] 80 56 300 3658 2 324 584
gi.vertline.551531 2-nitropropane dioxygenase [Williopsis saturnus]
80 54 261 3769 1 400 2 gi.vertline.1339950 large subunit of
NADH-dependent glutamate synthase [Plectonema boryanum] 80 68 399
3781 1 348 4 gi.vertline.166412 NADH-glutamate synthase [Medicago
sativa] 80 62 345 3988 1 48 287 gi.vertline.1204696
fructose-permease IIBC component [Haemophilus influenzae] 80 69 240
4030 1 287 3 gi.vertline.1009366 Respiratory nitrate reductase
[Bacillus subtilis] 80 60 285 4092 1 275 3 gi.vertline.1370207 orf6
[Lactobacillus sake] 80 69 273 4103 1 342 4 gi.vertline.39956 IIGlc
[Bacillus subtilis] 80 65 339 4231 1 348 4 gi.vertline.289287
UDP-glucose pyrophosphorylase [Bacillus subtilis] 80 65 345 4265 1
299 3 gi.vertline.603768 HutI protein, imidazolone-5-propionate
hydrolase [Bacillus subtilis] 80 63 297 gi.vertline.603768 HutI
protein, imidazolone-5-propionate hydrolase Bacillus subtilis] 4504
1 250 2 gi.vertline.1339950 large subunit of NADH-dependent
glutamate synthase [Plectonema boryanum] 80 68 249 2 6 5998 6798
gi.vertline.535351 codY [Bacillus subtilis] 79 63 801 4 7 7051 5807
gi.vertline.603768 HutI protein, imidazolone-5-propionate hydrolase
[Bacillus subtilis] 79 64 1245 gi.vertline.603768 HutI protein,
imidazolone-5-propionate hydrolase Bacillus subtilis] 25 6 5273
5515 pir.vertline.A36728.vertline.A367 acyl carrier protein -
Rhizobium meliloti 79 65 243 59 2 1173 1424 gi.vertline.147923
threonine dehydratase 2 (EC 4.2.1.16) [Escherichia coli] 79 75 252
60 1 1 204 gi.vertline.666115 orf1 upstream of glucose kinase
[Staphylococcus xylosus]pir.vertline.S52351.vertline.S52351 79 60
204 hypothetical protein 1 - Staphylococcus xylosus 81 1 1590 178
gi.vertline.466882 pps1; B1496_C2_189 [Mycobacterium leprae] 79 64
1413 85 7 6505 5987 gi.vertline.143364 phosphoribosyl
aminoimidazole carboxylase I (PUR-E) [Bacillus subtilis] 79 60 519
89 6 4554 3448 gi.vertline.144906 product homologous to E. coli
thioredoxin reductase: J. Biol. Chem. 1988) 79 35 1107 263:
9015-9019, and to F52a protein of alkyl hydroperoxide eductase from
S. typhimurium: J.Biol.Chem. (1990) 265: 10535-10540; pen reading
frame A [Clostridium pasteurianum] 102 11 7489 8571
gi.vertline.143093 ketol-acid reductoisomerase [Bacillus subtilis]
sp.vertline.P37253.vertli- ne.ILVC_BACSU KETOL- 79 64 1083 ACID
REDUCTOISOMERASE (EC 1.1.1.86) ACETOHYDROXY-ACID ISOMEROREDUCTASE)
(ALPHA-KETO-BETA-HYDROXYLACIL EDUCTOISOMERASE). 102 14 11190 12563
gi.vertline.149428 putative [Lactococcus lactis] 79 65 1374 127 9
7792 9372 gi.vertline.458688 PrfC/RF3 [Dichelobacter nodosus] 79 68
1581 139 3 1983 1426 gi.vertline.506697 CapA [Staphylococcus
aureus] 79 55 558 144 2 1156 668 gi.vertline.1498296 peptide
methionine sulfoxide reductase [Streptococcus pneumoniae] 79 47 489
148 2 529 1098 gi.vertline.467457 hypoxanthine-guanine
phosphoribosyltransferase [Bacillus subtilis] 79 59 570
gi.vertline.467457 hypoxanthine-guanine phosphoribosyltransferase
[Bacillus subtilis] 150 1 591 217 gi.vertline.755602 unknown
[Bacillus subtilis] 79 61 375 176 1 587 135 gi.vertline.297874
fructose-bisphosphate aldolase [Staphylococcus carnosus]
pir.vertline.A49943.vertline.A49943 79 65 453 fructose-bisphosphate
aldolase (EC 4.1.2.13) - Staphylococcus carnosus (strain TM300) 186
7 6874 6164 gi.vertline.1314298 ORF5; putative Sms protein; similar
to Sms proteins from Haemophilus 79 64 711 influenzae and
Escherichia coli [Listeria monocytogenes] 205 16 8498 8109
gi.vertline.1044980 ribosomal protein L18 [Bacillus subtilis] 79 70
390 211 1 1 519 gi.vertline.1303994 YqkM [Bacillus subtilis] 79 62
519 223 2 2801 1419 gi.vertline.488430 alcohol dehydrogenase 2
[Entamoeba histolytica] 79 60 1383 243 8 7896 6877
gi.vertline.580883 ipa-88d gene product [Bacillus subtilis] 79 60
1020 279 4 3721 4329 gi.vertline.413930 ipa-6d gene product
[Bacillus subtilis] 79 59 609 300 1 11 1393 gi.vertline.403372
glycerol 3-phosphate permease [Bacillus subtilis] 79 62 1383 307 3
1935 940 gi.vertline.950062 hypothetical yeast protein 1
[Mycoplasma capricolum] pir.vertline.S48578.vertline.S48578 79 60
996 hypothetical protein - Mycoplasma capricolum SGC3) (fragment)
352 6 8886 7666 gi.vertline.216854 P47K [Pseudomonas chlororaphis]
79 59 1221 412 1 578 3 gi.vertline.143177 putative [Bacillus
subtilis] 79 51 576 481 3 621 1124 gi.vertline.786163 Ribosomal
Protein L10 [Bacillus subtilis] 79 66 504 516 1 352 2
gi.vertline.805090 NisF [Lactococcus lactis] 79 48 351 525 2 1426
395 gi.vertline.143371 phosphoribosyl aminoimidazole synthetase
(PUR-M) [Bacillus subtilis] 79 61 1032
pir.vertline.H29326.vertline.AJBSCL
phosphoribosylformylglycinamidine cyclo-ligase EC 6.3.3.1) -
Bacillus subtilis 538 4 2825 2202 gi.vertline.1370207 orf6
[Lactobacillus sake] 79 67 624 570 1 2 421 gi.vertline.476160
arginine permease substrate-binding subunit [Listeria
monocytogenes] 79 61 420 645 8 2663 3241 gi.vertline.153898
transport protein [Salmonella typhimurium] 79 62 579 683 1 75 374
gi.vertline.1064795 function unknown [Bacillus subtilis] 79 62 300
816 3 3987 3274 gi.vertline.1407784 orf-1; novel antigen
[Staphylococcus aureus] 79 62 714 2929 1 3 401 gi.vertline.1524397
glycine betaine transporter OpuD [Bacillus subtilis] 79 61 399 2937
1 202 47 pir.vertline.S52915.vertline.S529 nitrate reductase alpha
chain - Bacillus subtilis (fragment) 79 58 156 2940 1 385 2
gi.vertline.149429 putative [Lactococcus lactis] 79 72 384 2946 1
286 2 gi.vertline.143267 2-oxoglutarate dehydrogenase (odhA; EC
1.2.4.2) [Bacillus subtilis] 79 61 285 2999 1 3 212
gi.vertline.710020 nitrite reductase (nirB) [Bacillus subtilis] 79
59 210 3022 1 332 150 gi.vertline.450686 3-phosphoglycerate kinase
[Thermotoga maritima] 79 61 183 3064 1 3 314 gi.vertline.1204436
pyruvate formate-lyase [Haemophilus influenzae] 79 60 312 3083 1 2
220 gi.vertline.1149662 hypD gene product [Clostridium perfringens]
79 56 219 3126 1 411 121 gi.vertline.1339950 large subunit of
NADH-dependent glutamate synthase [Plectonema boryanum] 79 55 291
3181 1 326 45 gi.vertline.1339950 large subunit of NADH-dependent
glutamate synthase [Plectonema boryanum] 79 59 282 3345 1 3 476
gi.vertline.871784 Clp-like ATP-dependent protease binding subunit
[Bos taurus] 79 63 474 3718 1 270 4
pir.vertline.C36889.vertline.C368 leuB protein, inactive -
Lactococcus lactis subsp. lactis (strain IL1403) 79 71 267 3724 2
159 401 gi.vertline.1009366 Respiratory nitrate reductase [Bacillus
subtilis] 79 64 243 3836 1 312 16 gi.vertline.1524193 unknown
[Mycobacterium tuberculosis] 79 65 297 3941 1 2 334
gi.vertline.415855 deoxyribose aldolase [Mycoplasma hominis] 79 54
333 4113 1 3 341 gi.vertline.143015 gluconate kinase [Bacillus
subtilis] 79 63 339 4501 1 209 12 gi.vertline.1022726 unknown
[Staphylococcus haemolyticus] 79 66 198 4612 1 2 238
gi.vertline.460689 TVG [Thermoactinomyces vulgaris] 79 58 237 2 1 2
1213 gi.vertline.520753 DNA topoisomerase I [Bacillus subtilis] 78
64 1212 8 2 1220 174 gi.vertline.216151 DNA polymerase (gene L; ttg
start codon) [Bacteriophage SP02] gi.vertline.579197 78 72 1047
SP02 DNA polymerase (aa 1-648) [Bacteriophage SP02]
pir.vertline.A21498.vertline.DJBPS2 DNA- directed DNA polymerase
(EC 2.7.7.7) - phage P02 9 2 1089 838
gi.vertline.1064787 function unknown [Bacillus subtilis] 78 57 252
32 8 6803 7702 gi.vertline.146974 NH3-dependent NAD synthetase
[Escherichia coli] 78 63 900 36 4 2941 3138 gi.vertline.290503
glutamate permease [Escherichia coli] 78 53 198 53 15 16221 14758
gi.vertline.1303941 YqiV [Bacillus subtilis] 78 58 1464 57 14 10520
12067 gi.vertline.1072418 glcA gene product [Staphylococcus
carnosus] 78 65 1548 66 7 5812 4826 gi.vertline.1212729 YqhJ
[Bacillus subtilis] 78 67 987 67 4 4029 4376 gi.vertline.466612
nikA [Escherichia coli] 78 71 348 91 9 10058 10942
gi.vertline.467380 stage 0 sporultion [Bacillus subtilis] 78 50 885
102 12 8574 10130 gi.vertline.149426 putative [Lactococcus lactis]
78 61 1557 112 6 3540 4463 gi.vertline.854234 cymG gene product
[Klebsiella oxytoca] 78 56 924 124 2 1061 234 gi.vertline.405622
unknown [Bacillus subtilis] 78 60 828 130 3 1805 2260
gi.vertline.1256636 putative [Bacillus subtilis] 78 71 456 133 1
377 3 gi.vertline.168060 lamB [Emericella nidulans] 78 59 375 166 4
6163 5201 gi.vertline.451216 Mannosephosphate Isomerase
[Streptococcus mutans] 78 63 963 186 1 795 4 gi.vertline.289284
cysteinyl-tRNA synthetase [Bacillus subtilis] 78 63 792 195 4 2315
1881 gi.vertline.1353874 unknown [Rhodobacter capsulatus] 78 58 435
199 3 3623 2967 gi.vertline.143525 succinate dehydrogenase
cytochrome b-558 subunit [Bacillus subtilis] 78 57 657
pir.vertline.A29843.ver- tline.DEBSSC succinate dehydrogenase (EC
1.3.99.1) cytochrome 558 - Bacillus subtilis 199 4 5557 3905
gi.vertline.142521 deoxyribodipyrimidine photolyase [Bacillus
subtilis] pir.vertline.A37192.vertline.A37192 uvrB 78 62 1653
protein - Bacillus subtilis sp.vertline.P14951.vertline.UVRC_BACSU
EXCINUCLEASE ABC SUBUNIT C. 223 3 3523 3215 gi.vertline.439596
[Escherichia coli IS200 insertion sequence from ECOR63, partial.),
ene 78 47 309 product [Escherichia coli] 299 4 1865 2149
gi.vertline.467439 temperature sensitive cell division [Bacillus
subtilis] 78 62 285 321 9 7315 6896 gi.vertline.142979 ORF3 is
homologous to an ORF downstream of the spoT gene of E. coli; RF3 78
55 420 [Bacillus stearothermophilus] 352 4 3714 3944
gi.vertline.349050 actin 1 [Pneumocystis carinii] 78 42 231 352 5
6093 4594 gi.vertline.903587 NADH dehydrogenase subunit 5 [Bacillus
subtilis] sp.vertline.P39755.vertline.NDHF_BACSU NADH 78 58 1500
DEHYDROGENASE SUBUNIT 5 (EC 1.6.5.3) NADH-UBIQUINONE OXIDOREDUCTASE
CHAIN 5). 376 1 2 583 gi.vertline.551693 dethiobiotin synthase
[Bacillus sphaericus] 78 34 582 424 2 1595 1768 gi.vertline.1524117
alpha-acetolactate decarboxylase [Lactococcus lactis] 78 68 174 450
1 988 62 gi.vertline.1030068 NAD(P)H oxidoreductase, isoflavone
reductase homologue [Solanum tuberosum] 78 63 927 558 1 562 362
gi.vertline.1511588 bifunctional protein [Methanococcus jannaschii]
78 60 201 670 3 1152 1589 gi.vertline.1122759 unknown [Bacillus
subtilis] 78 64 438 714 1 64 732 gi.vertline.143460 37 kd minor
sigma factor (rpoF, sigB; ttg start codon) [Bacillus subtilis] 78
57 669 814 1 3 368 gi.vertline.1377833 unknown [Bacillus subtilis]
78 59 366 981 1 692 3 gi.vertline.143802 GerC2 [Bacillus subtilis]
78 64 690 995 2 727 476 gi.vertline.296947 uridine kinase
[Escherichia coli] 78 64 252 1045 1 3 401 gi.vertline.1407784
orf-1; novel antigen [Staphylococcus aureus] 78 61 399 1163 2 186 4
gi.vertline.410117 diaminopimelate decarboxylase [Bacillus
subtilis] 78 54 183 2191 1 399 4 gi.vertline.215098 excisionase
[Bacteriophage 154a] 78 65 396 2933 1 2 181 gi.vertline.1204436
pyruvate formate-lyase [Haemophilus influenzae] 78 73 180 3041 2
129 317 gi.vertline.624632 GltL [Escherichia coli] 78 53 189 3581 1
105 401 gi.vertline.763186 3-ketoacyl-coA thiolase [Saccharomyces
cerevisiae] 78 55 297 3709 1 3 230 gi.vertline.460689 TVG
[Thermoactinomyces vulgaris] 78 58 228 3974 1 265 2
gi.vertline.558839 unknown [Bacillus subtilis] 78 65 264 3980 1 3
401 gi.vertline.39956 IIGlc [Bacillus subtilis] 78 62 399 4056 1
354 61 gi.vertline.1256635 dihydroxy-acid dehydratase [Bacillus
subtilis] 78 55 294 4114 1 316 2 pir.vertline.S09372.vertline.S093
hypothetical protein - Trypanosoma brucei 78 62 315 4185 1 3 179
gi.vertline.1339950 large subunit of NADH-dependent glutamate
synthase [Plectonema boryanum] 78 58 177 4235 1 329 3
gi.vertline.558839 unknown [Bacillus subtilis] 78 60 327 4352 1 302
63 gi.vertline.603768 HutI protein, imidazolone-5-propionate
hydrolase [Bacillus subtilis] 78 63 240 gi.vertline.603768 HutI
protein, imidazolone-5-propionate hydrolase Bacillus subtilis] 4368
1 307 2 gi.vertline.1353678 heavy-metal transporting P-type ATPase
[Proteus mirabilis] 78 59 306 4461 1 216 4 gi.vertline.1276841
glutamate synthase (GOGAT) [Porphyra purpurea] 78 36 213 4530 1 238
2 gi.vertline.39956 IIGlc [Bacillus subtilis] 78 65 237 3 2 2073
1177 gi.vertline.1109684 ProV [Bacillus subtilis] 77 56 897 12 2
1965 1504 gi.vertline.467335 ribosomal protein L9 [Bacillus
subtilis] 77 59 462 27 1 2 388 gi.vertline.1212728 YqhI [Bacillus
subtilis] 77 63 387 39 2 590 1252 gi.vertline.40054
phenylalanyl-tRNA synthetase beta subunit (AA 1-804) [Bacillus
subtilis] 77 60 663 42 6 2704 2931 gi.vertline.606241 30S ribosomal
subunit protein S14 [Escherichia coli]
sp.vertline.P02370.vertline.RS14_ECOLI 77 65 228 30S RIBOSOMAL
PROTEIN S14. (SUB 2-101) 46 18 15459 16622 gi.vertline.297798
mitochondrial formate dehydrogenase precursor [Solanum tuberosum]
77 55 1164 pir.vertline.JQ2272.vertline.JQ2272 formate
dehydrogenase (EC 1.2.1.2) precursor, itochondrial - potato 100 4
4002 3442 gi.vertline.1340128 ORF1 [Staphylococcus aureus] 77 54
561 102 8 5378 5713 gi.vertline.1311482 acetolactate synthase
[Thermus aquaticus] 77 57 336 109 7 4742 5383 gi.vertline.710637
Unknown [Bacillus subtilis] 77 56 642 117 1 2 1228
gi.vertline.1237015 ORF4 [Bacillus subtilis] 77 53 1227 124 10 7688
7053 gi.vertline.405819 thymidine kinase [Bacillus subtilis] 77 63
636 147 3 985 824 gi.vertline.849027 hypothetical 15.9-kDa protein
[Bacillus subtilis] 77 37 162 152 10 7354 7953 gi.vertline.1205583
spermidine/putrescine transport ATP-binding protein [Haemophilus 77
55 600 influenzae] 169 2 1004 1282 gi.vertline.473825 `elongation
factor EF-Ts` [Escherichia coli] 77 58 279 184 2 380 1147
gi.vertline.216314 esterase [Bacillus stearothermophilus] 77 60 768
189 7 3296 3868 gi.vertline.853809 ORF3 [Clostridium perfringens]
77 48 573 193 1 132 290 gi.vertline.1303788 YqeH [Bacillus
subtilis] 77 54 159 195 8 8414 8088 gi.vertline.1499620 M.
jannaschii predicted coding region MJ0798 [Methanococcus
jannaschii] 77 44 327 205 8 5204 4980 gi.vertline.216340 ORF for
adenylate kinase [Bacillus subtilis] 77 61 225 205 29 14502 14209
gi.vertline.786155 Ribosomal Protein L23 [Bacillus subtilis] 77 62
294 211 5 1908 2084 gi.vertline.410132 ORFX8 [Bacillus subtilis] 77
47 177 217 5 3478 4416 gi.vertline.496254
fibronectin/fibrinogen-binding protein [Streptococcus pyogenes] 77
54 939 232 1 267 998 gi.vertline.1407784 orf-1; novel antigen
[Staphylococcus aureus] 77 57 732 233 2 1346 873 gi.vertline.467408
unknown [Bacillus subtilis] 77 61 474 243 3 2299 1937
gi.vertline.516155 unconventional myosin [Sus scrofa] 77 32 363 299
1 68 769 gi.vertline.467436 unknown [Bacillus subtilis] 77 54 702
301 4 1283 1098 gi.vertline.950071 ATP-bind. pyrimidine kinase
[Mycoplasma capricolum] pir.vertline.S48605.vertline.S48605 77 48
186 hypothetical protein - Mycoplasma capricolum SGC3) (fragment)
302 5 2741 3211 gi.vertline.508980 pheB [Bacillus subtilis] 77 57
471 302 7 3835 4863 gi.vertline.147783 ruvB protein [Escherichia
coli] 77 60 1029 307 9 4797 4192 gi.vertline.1070015
protein-dependent [Bacillus subtilis] 77 60 606 312 1 99 1391
gi.vertline.143165 malic enzyme (EC 1.1.1.38) [Bacillus
stearothermophilus] pir.vertline.A33307.vertline.DEBSXS 77 62 1293
malate dehydrogenase oxaloacetate-decarboxylating) (EC 1.1.1.38) -
Bacillus tearothermophilus 312 2 1541 2443 gi.vertline.1399855
carboxyltransferase beta subunit [Synechococcus PCC7942] 77 58 903
321 5 4596 3526 gi.vertline.39844 fumarase (citG) (aa 1-462)
[Bacillus subtilis] 77 65 1071 354 1 47 568 gi.vertline.1154634
YmaB [Bacillus subtilis] 77 57 522 365 1 2 1021 gi.vertline.143374
phosphoribosyl glycinamide synthetase (PUR-D; gtg start codon)
Bacillus 77 62 1020 subtilis] 374 1 1 708 gi.vertline.1405446
transketolase [Bacillus subtilis] 77 61 708 385 1 565 2
gi.vertline.533099 endonuclease III [Bacillus subtilis] 77 63 564
392 2 594 1940 gi.vertline.556014 UDP-N-acetyl muramate-alanine
ligase [Bacillus subtilis] 77 65 1347
sp.vertline.P40778.vertline.MU- RC_BACSU
UDP-N-ACETYLMURAMATE-ALANINE LIGASE (EC .3.2.8)
(UDP-N-ACETYLMURANOYL-L-ALANINE SYNTHETASE) (FRAGMENT). 405 5 3570
3061 gi.vertline.1303912 YqhW [Bacillus subtilis] 77 64 510 487 4
1302 1472 gi.vertline.432427 ORF1 gene product (Acinetobacter
calcoaceticus) 77 48 171 522 1 2 562 pir.vertline.A01179.vertline.-
SYBS tyrosine-tRNA ligase (EC 6.1.1.1) - Bacillus
stearothermophilus 77 63 561 523 2 1351 1115 gi.vertline.1387979
44% identity over 302 residues with hypothetical protein from
Synechocystis 77 48 237 sp, accession D64006_CD; expression induced
by environmental stress; some similarity to glycosyl transferases;
two potential membrane-spanning helices [Bacillus subtil 536 2 612
241 gi.vertline.143366 adenylosuccinate lyase (PUR-B) [Bacillus
subtilis] pir.vertline.C29326.vertline.WZBSDS 77 61 372
adenylosuccinate lyase (EC 4.3.2.2) - Bacillus subtilis 548 2 339
872 gi.vertline.143387 aspartate transcarbamylase [Bacillus
subtilis] 77 56 534 597 1 2 481 gi.vertline.904198 hypothetical
protein [Bacillus subtilis] 77 33 480 633 2 1313 879
gi.vertline.387577 ORF1A [Bacillus subtilis] 77 64 435 642 1 85 360
gi.vertline.46971 epiP gene product [Staphylococcus epidermidis] 77
61 276 659 1 125 1219 gi.vertline.1072381 glutamyl-aminopeptidase
[Lactococcus lactis] 77 62 1095 670 4 1587 1820 gi.vertline.1122760
unknown [Bacillus subtilis] 77 58 234 789 1 2 391
gi.vertline.1377823 aminopeptidase [Bacillus subtilis] 77 65 390
815 1 10 573 gi.vertline.1303861 YqgN [Bacillus subtilis] 77 49 564
899 1 1 225 gi.vertline.1204844 H. influenzae predicted coding
region HI0594 [Haemophilus influenzae] 77 55 225 1083 1 3 188
gi.vertline.460828 B969 [Saccharomyces cerevisiae] 77 66 186 1942 1
209 3 gi.vertline.160047 p101/acidic basic repeat antigen
[Plasmodium falciparum] pir.vertline.A29232.vertline- .A29232 77 38
207 101 K malaria antigen precursor - Plasmodium alciparum (strain
Camp) 2559 1 1 171 gi.vertline.1499034 M. jannaschii predicted
coding region MJ0255 [Methanococcus jannaschii] 77 61 171 2933 2
243 401 gi.vertline.42370 pyruvate formate-lyase (AA 1-760)
[Escherichia coli] ir.vertline.S01788.vertline.S01788 77 72 159
formate C-acetyltransferase (EC 2.3.1.54) - Echerichia coli 2966 1
56 292 gi.vertline.1524397 glycine betaine transporter OpuD
[Bacillus subtilis] 77 45 237 2976 1 309 4 gi.vertline.40003
oxoglutarate dehydrogenase (NADP+) [Bacillus subtilis]
p.vertline.P23129.vertline.ODO1_BACSU 77 60 306 2-OXOGLUTARATE
DEHYDROGENASE E1 COMPONENT (EC 2.4.2) (ALPHA-KETOGLUTARATE
DEHYDROGENASE). 2979 2 400 122 gi.vertline.1204354 spore
germination and vegetative growth protein [Haemophilus influenzae]
77 61 279 2988 1 377 153 gi.vertline.438465 Probable operon with
orfF. Possible alternative initiation codon, ases 77 55 225
2151-2153. Homology with acetyltransferases.; putative Bacillus
subtilis] 2990 1 167 3 gi.vertline.142562 ATP synthase epsilon
subunit [Bacillus megaterium] pir.vertline.B28599.vertline.PWBSEM
H+- 77 63 165 transporting ATP synthase (EC 3.6.1.34) psilon chain
- Bacillus megaterium 3032 1 3 389 gi.vertline.488430 alcohol
dehydrogenase 2 [Entamoeba histolytica] 77 56 387 3057 1 1 195
gi.vertline.468764 mocR gene product (Rhizobium meliloti) 77 50 195
4008 1 400 74 gi.vertline.603768 HutI protein,
imidazolone-5-propionate hydrolase [Bacillus subtilis] 77 52 327
gi.vertline.603768 HutI protein, imidazolone-5-propionate hydrolase
Bacillus subtilis] 4048 1 386 69 gi.vertline.216278 gramicidin S
synthetase 1 [Bacillus brevis] 77 55 318 4110 1 3 368
pir.vertline.S52915.ver- tline.S529 nitrate reductase alpha chain -
Bacillus subtilis (fragment) 77 61 366 4115 1 1 348
gi.vertline.517205 67 kDa Myosin-crossreactive streptococcal
antigen [Streptococcus yogenes] 77 65 348 4225 1 297 4
gi.vertline.1322245 mevalonate pyrophosphate decarboxylase [Rattus
norvegicus] 77 60 294 4611 2 327 160 gi.vertline.508979 GTP-binding
protein [Bacillus subtilis] 77 57 168 4668 1 182 3
pir.vertline.S52915.vertline.S529 nitrate reductase alpha chain -
Bacillus subtilis (fragment) 77 61 180 25 1 2 1627
gi.vertline.1150620 MmsA [Streptococcus pneumoniae] 76 58 1626 38 5
1488 2537 pir.vertline.A43577.vertline.A435 regulatory protein pfoR
- Clostridium perfringens 76 57 1050 52 5 2962 4041
gi.vertline.1161061 dioxygenase [Methylobacterium extorquens] 76 62
1080 56 20 27389 27955 gi.vertline.467402 unknown [Bacillus
subtilis] 76 56 567 57 15 12046 12219 gi.vertline.1206040 weak
similarity to keratin [Caenorhabditis elegans] 76 40 174 91 2 1062
2261 gi.vertline.475715 acetyl coenzyme A acetyltransferase
(thiolase) [Clostridium cetobutylicum] 76 57 1200 98 2 818 1624
gi.vertline.467422 unknown [Bacillus subtilis] 76 62 807 98 5 2965
3228 gi.vertline.897793 y98 gene product [Pediococcus acidilactici]
76 52 264 98 8 5922 6326 gi.vertline.467427 methionyl-tRNA
synthetase [Bacillus subtilis] 76 53 405 104 3 1322 1885
gi.vertline.216151 DNA polymerase (gene L; ttg start codon)
[Bacteriophage SPO2] gi.vertline.579197 76 63 564 SPO2 DNA
polymerase (aa 1-648) [Bacteriophage SPO2)
pir.vertline.A21498.vertline.DJBPS2 DNA- directed DNA polymerase
(EC 2.7.7.7) - phage PO2 124 9 7055 5976 gi.vertline.853776 peptide
chain release factor 1 [Bacillus subtilis]
pir.vertline.S55437.vertline.S55437 76 58 1080 peptide chain
release factor 1 - Bacillus subtilis 164 5 2832 3311
gi.vertline.1204976 prolyl-tRNA synthetase [Haemophilus influenzae]
76 53 480 168 2 1841 1065 gi.vertline.1177253 putative ATP-binding
protein of ABC-type [Bacillus subtilis] 76 58 777 189 2 163 888
gi.vertline.467384 unknown [Bacillus subtilis] 76 63 726 235 3 2253
3518 gi.vertline.142936 folyl-polyglutamate synthetase [Bacillus
subtilis] pir.vertline.B40646.vertline.B40646 folC - 76 53 1266
Bacillus subtilis 236 1 335 925 gi.vertline.1146197 putative
[Bacillus subtilis] 76 54 591 237 8 5323 5541 gi.vertline.1279261
F13G3.6 [Caenorhabditis elegans] 76 47 219 263 5 4585 3680
gi.vertline.1510348 dihydrodipicolinate synthase [Methanococcus
jannaschii] 76 49 906 304 3 1051 1794 gi.vertline.666982 putative
membrane spanning subunit [Bacillus
subtilis]pir.vertline.S52382.vertline- .S52382 76 60 744 probable
membrane spanning protein - Bacillus subtilis 312 4 3611 4624
gi.vertline.143312 6-phospho-1-fructokinase (gtg start codon; EC
2.7.1.11) [Bacillus 76 56 1014 tearothermophilus) 343 1 2 1036
gi.vertline.405956 yeeE [Escherichia coli] 76 59 1035 347 1 409
1701 gi.vertline.396304 acetylornithine deacetylase [Escherichia
coli] 76 72 1293 358 1 672 1907 gi.vertline.1146215 39.0% identity
to the Escherichia coli S1 ribosomal protein; putative 76 58 1236
[Bacillus subtilis] 371 1 1 222 gi.vertline.537084 alternate gene
name mgt; CG Site No. 497 [Escherichia coli] 76 61 222
pir.vertline.S56468.vertline.S56468 mgtA protein - Escherichia coli
379 4 4331 4858 gi.vertline.143268 dihydrolipoamide
transsuccinylase (odhB; EC 2.3.1.61) [Bacillus subtilis] 76 61 528
404 5 4022 4492 gi.vertline.1303823 YqfG [Bacillus subtilis] 76 60
471 411 1 2 307 gi.vertline.486025 ORF YKL027w [Saccharomyces
cerevisiae] 76 55 306 472 3 2854 1352 gi.vertline.1405464 AlsT
[Bacillus subtilis] 76 57 1503 546 1 273 995 gi.vertline.153821
streptococcal pyrogenic exotoxin type C (speC) precursor
Streptococcus 76 36 723 pyogenes] 588 1 557 60 gi.vertline.1002520
MutS [Bacillus subtilis] 76 61 498 591 1 16 735 gi.vertline.885934
ClpB [Synechococcus sp.] 76 44 720 602 2 175 798
gi.vertline.1486422 OppD homologue [Rhizobium sp.] 76
52 624 619 2 290 33 gi.vertline.330613 major capsid protein [Human
cytomegalovirus] 76 47 258 660 4 2568 3302 gi.vertline.904199
hypothetical protein [Bacillus subtilis] 76 55 735 677 1 228 4
gi.vertline.40177 spoOF gene product [Bacillus subtilis] 76 58 225
962 1 24 206 gi.vertline.142443 adenylosuccinate synthetase
[Bacillus subtilis]sp.vertline.P29726.vertline.PURA_BACSU 76 67 183
ADENYLOSUCCINATE SYNTHETASE (EC 6.3.4.4) IMP --ASPARTATE LIGASE).
978 1 580 2 gi.vertline.1511333 M. jannaschii predicted coding
region MJ1322 [Methanococcus jannaschii] 76 56 579 997 1 244 2
gi.vertline.467154 No definition line found [Mycobacterium leprae]
76 38 243 1563 1 266 3 gi.vertline.1303984 YqkG [Bacillus subtilis]
76 52 264 2184 1 182 3 gi.vertline.506706 CapJ [Staphylococcus
aureus] 76 38 180 2572 1 1 387 gi.vertline.153898 transport protein
[Salmonella typhimurium] 76 65 387 2942 1 29 400 gi.vertline.710020
nitrite reductase (nirB) [Bacillus subtilis] 76 59 372 2957 1 216
55 gi.vertline.1511251 hypothetical protein (SP: P42404)
[Methanococcus janneschii] 76 47 162 2980 1 279 4
gi.vertline.1405464 AlsT [Bacillus subtilis] 76 53 276 3015 1 326 3
gi.vertline.408115 ornithine acetyltransferase [Bacillus subtilis]
76 61 324 3124 1 13 174 gi.vertline.882705 ORF_o401 (Escherichia
coli) 76 65 162 3179 1 3 161 gi.vertline.168477
ferredoxin-dependent glutamate synthase [Zea
mays]pir.vertline.A38596.ver- tline.A38596 76 53 159 glutamate
synthase (ferredoxin) (EC 1.4.7.1)- maize 3789 1 2 379
gi.vertline.39956 IIGlc [Bacillus subtilis) 76 55 378 3892 1 3 314
gi.vertline.1510398 ferripyochelin binding protein [Methanococcus
jannaschii] 76 52 312 3928 1 400 2 gi.vertline.143016 permease
[Bacillus subtilis] 76 59 399 4159 1 386 15
sp.vertline.P80544.vertline.MRSP.sub.-- METHICILLIN-RESISTANT
SURFACE PROTEIN (FRAGMENTS) 76 66 372 4204 1 17 331
gi.vertline.29646 ATPase [Lactococcus lactis] 76 56 315 4398 1 249
4 gi.vertline.987255 Menkes disease gene [Homo sapiens] 76 48 246
4506 1 2 313 gi.vertline.216746 (D-lactate dehydrogenase
[Lactobacillus plantarum] 76 47 312 4546 1 247 17
gi.vertline.1339950 large subunit of NADH-dependent glutamate
synthase [Plectonema boryanum] 76 61 231 4596 1 191 3
gi.vertline.560027 cellulose synthase [Acetobacter xylinum] 76 70
189 4 5 4337 3417 gi.vertline.882532 ORF_o294 [Escherichia coli] 75
59 921 6 1 164 952 gi.vertline.40960 OTCase [Escherichia coli] 75
56 789 12 3 3944 1953 gi.vertline.467336 unknown [Bacillus
subtilis] 75 57 1992 23 18 17310 16348 gi.vertline.1296433
0-acetylserine sulfhydrylase B [Alcaligenes eutrophus] 75 55 963 25
3 2356 3393 gi.vertline.1502419 PlsX [Bacillus subtilis] 75 56 1038
36 8 5765 6037 gi.vertline.1256517 unknown [Schizosaccharomyces
pombe] 75 45 273 46 13 11186 12058 gi.vertline.48972 nitrate
transporter [Synechococcus sp.] 75 46 873 51 7 3474 3677
gi.vertline.143607 sporulation protein [Bacillus subtilis] 75 61
204 53 16 16590 16330 gi.vertline.143402 (recombination protein
(ttg start codon) [Bacillus subtilis] gi.vertline.1303923 RecN 75
51 261 [Bacillus subtilis] 74 3 2568 1564 gi.vertline.1204847
ornithine carbamoyltransferase [Haemophilus influenzae] 75 61 1005
85 3 3930 3232 gi.vertline.143368 phosphoribosylformyl
glycinamidine synthetase I (PUR-L; gtg start odon) 75 63 699
[Bacillus subtilis] 85 5 4878 4168 gi.vertline.143367
phosphoribosyl aminoidazole succinocarboxamide synthetase (PUR-C;
tg start 75 55 711 codon) [Bacillus subtilis] 85 8 6625 7530
gi.vertline.1303916 YqiA [Bacillus subtilis] 75 53 906 87 3 2340
3590 gi.vertline.1064813 homologous to sp: PHOR_BACSU [Bacillus
subtilis] 75 56 1251 87 6 6084 6896 gi.vertline.1064810 function
unknown [Bacillus subtilis] 75 61 813 108 2 1503 1162
gi.vertline.1001824 hypothetical protein [Synechocystis sp.] 75 51
342 110 3 1748 3727 gi.vertline.1147593 putative ppGpp synthetase
[Streptomyces coelicolor] 75 55 1980 110 7 4353 5252
gi.vertline.1177251 clwD gene product [Bacillus subtilis] 75 75 900
120 14 10649 10032 gi.vertline.1524394 ORF-2 upstream of gbsAB
operon [Bacillus subtilis] 75 55 618 121 5 2050 4221
gi.vertline.1154632 NrdE [Bacillus subtilis] 75 54 2172 124 1 143 3
gi.vertline.405622 unknown [Bacillus subtilis] 75 56 141 128 1 81
1139 gi.vertline.143316 (gap) gene products [Bacillus megaterium]
75 48 1059 130 8 5760 5903 gi.vertline.1256654 54.8% identity with
Neisseria gonorrhoeae regulatory protein PilB; putative 75 62 144
[Bacillus subtilis] 136 2 3185 1890 gi.vertline.467403 seryl-tRNA
synthetase [Bacillus subtilis] 75 54 1296 161 10 5439 5798
gi.vertline.1001195 hypothetical protein [Synechocystis sp.] 75 55
360 172 4 2995 2171 gi.vertline.755153 ATP-binding protein
[Bacillus subtilis] 75 52 825 179 1 1107 190 gi.vertline.143037
porphobilinogen deaminase [Bacillus subtilis] 75 58 918 195 10 9374
9219 sp.vertline.P25745.vertline.YCFB.sub.-- HYPOTHETICAL PROTEIN
IN PURB 5' REGION (ORF-15) (FRAGMENT) 75 60 156 200 4 2605 4596
gi.vertline.142440 ATP-dependent nuclease [Bacillus subtilis] 75 56
1992 206 3 5620 4340 gi.vertline.1256135 YbbF [Bacillus subtilis]
75 53 1281 216 2 159 389 gi.vertline.1052800 unknown
[Schizosaccharomyces pombe] 75 58 231 229 1 29 847
gi.vertline.1205958 branched chain aa transport system II carrier
protein [Haemophilus 75 49 819 influenzae] 230 2 518 1714
gi.vertline.971337 nitrite extrusion protein [Bacillus subtilis] 75
53 1197 231 1 1122 4 gi.vertline.1002521 MutL [Bacillus subtilis]
75 54 1119 233 3 1314 1859 gi.vertline.467405 unknown [Bacillus
subtilis] 75 59 546 269 1 164 3 gi.vertline.1511246 methyl coenzyme
M reductase system, component A2 [Methanococcus jannaschii] 75 50
162 292 1 772 155 gi.vertline.1511604 M. jannaschii predicted
coding region MJ1651 [Methanococcus jannaschii] 75 46 618 304 4
1773 2261 gi.vertline.1205328 surfactin [Haemophilus influenzae] 75
55 489 312 3 2437 3387 gi.vertline.285621 undefined open reading
frame [Bacillus stearothermophilus] 75 62 951 312 5 4622 6403
gi.vertline.1041097 Pyruvate Kinase [Bacillus psychrophilus] 75 57
1782 319 1 353 877 gi.vertline.1212728 YqhI [Bacillus subtilis] 75
54 525 320 5 4321 5031 gi.vertline.1070361 OMP decarboxylase
[Lactococcus lactis] 75 56 711 320 6 5010 5642 gi.vertline.143394
OMP-PRPP transferase [Bacillus subtilis] 75 60 633 337 4 1519 2088
gi.vertline.487433 citrate synthase II [Bacillus subtilis] 75 58
570 394 2 669 1271 gi.vertline.304976 matches PS00017: ATP_GTP_A
and PS00301: EFACTOR_GTP; similar to longation 75 51 603 factor G,
TetM/TetO tetracycline-resistance proteins Escherichia coli] 423 1
127 570 gi.vertline.1183839 unknown [Pseudomonas aeruginosa] 75 59
444 433 2 1603 1929 gi.vertline.149211 acetolactate synthase
[Klebsiella pneumoniae] 75 63 327 446 2 176 1540 gi.vertline.312441
dihydroorotase [Bacillus caldolyticus] 75 62 1365 486 1 249 4
gi.vertline.1149682 potF gene product [Clostridium perfringens] 75
55 246 496 1 3 794 gi.vertline.143582 spoIIIEA protein [Bacillus
subtilis] 75 59 792 498 2 824 1504 gi.vertline.143328 phoP protein
(put.); putative [Bacillus subtilis] 75 47 681 499 2 1061 1624
gi.vertline.1387979 44% identity over 302 residues with
hypothetical protein from Synechocystis 75 51 564 sp, accession
D64006_CD; expression induced by environmental stress; some
similarity to glycosyl transferases; two potential
membrane-spanning helices [Bacillus subtil 568 1 453 265
pir.vertline.JC4110.vertline.JC41 triacylglycerol lipase (EC
3.1.1.3) 2 - Mycoplasma mycoides subsp. mycoides 75 50 189 (SGC3)
613 2 233 36 gi.vertline.330993 tegument protein [Saimiriine
herpesvirus 2] 75 75 198 621 1 1 525 gi.vertline.529754 speC
[Streptococcus pyogenes] 75 43 525 642 5 1809 2474
gi.vertline.1176401 EpiG [Staphylococcus epidermidis] 75 51 666 646
2 454 657 gi.vertline.172442 ribonuclease P [Saccharomyces
cerevisiae] 75 37 204 657 1 3 347 gi.vertline.882541 ORF_o236
[Escherichia coli] 75 47 345 750 1 832 2 gi.vertline.46971 epiP
gene product [Staphylococcus epidermidis] 75 57 831 754 1 2 481
gi.vertline.1303901 YqhT [Bacillus subtilis] 75 57 480 763 2 393
223 gi.vertline.1205145 multidrug resistance protein [Haemophilus
influenzae] 75 51 171 775 1 482 3 pir.vertline.B36889.vertline.B36-
8 leuA protein, inactive - Lactococcus lactis subsp. lactis (strain
IL1403) 75 63 480 793 1 1 180 gi.vertline.143316 [gap] gene
products [Bacillus megaterium] 75 57 180 800 1 160 2
gi.vertline.509411 NFRA protein [Azorhizobium caulinodans] 75 34
159 811 1 560 3 gi.vertline.143434 Rho Factor [Bacillus subtilis]
75 60 558 940 1 329 165 gi.vertline.1276985 arginase [Bacillus
caldovelox] 75 50 165 971 2 37 252 gi.vertline.1001373 hypothetical
protein [Synechocystis sp.] 75 58 216 1059 1 232 80
gi.vertline.726480 L-glutamine-D-fructose-6-phosphate
amidotransferase [Bacillus subtilis] 75 67 153 1109 2 219 374
gi.vertline.143331 alkaline phosphatase regulatory protein
[Bacillus subtilis] 75 53 156 pir.vertline.A27650.vertline.A27650
regulatory protein phoR - Bacillus subtilis
sp.vertline.P23545.vertline.PHOR_BACSU ALKALINE PHOSPHATASE
SYNTHESIS SENSOR PROTEIN HOR (EC 2.7.3.--). 1268 1 137 3
gi.vertline.304135 ornithine acetyltransferase [Bacillus
stearothermophilus] 75 63 135 sp.vertline.Q07908.vertline.ARG-
J_BACST GLUTAMATE N-ACETYLTRANSFERASE (EC 2.3.1.35) ORNITHINE
ACETYLTRANSFERASE) (ORNITHINE TRANSACETYLASE) (OATASE)/MINO-ACID
ACETYLTRANSFERASE (EC 2.3.1.1) (N-ACETYLGLUTAMATE YNTHA 1500 1 163
2 gi.vertline.1205488 excinuclease ABC subunit B [Haemophilus
influenzae] 75 57 162 1529 1 400 2 gi.vertline.1002521 MutL
[Bacillus subtilis] 75 54 399 3010 1 387 4 gi.vertline.1204435
pyruvate formate-lyase activating enzyme [Haemophilus influenzae]
75 54 384 3105 1 1 180 gi.vertline.1041097 Pyruvate Kinase
[Bacillus psychrophilus] 75 57 180 3117 1 45 212 gi.vertline.899317
peptide synthetase module [Microcystis
aeruginosa]pir.vertline.S49111.vertline.S4- 9111 75 42 168 probable
amino acid activating domain - Microcystis aeruginosa (fragment)
(SUB 144-528) 3139 2 139 345 gi.vertline.145294 adenine
phosphoribosyl-transferase [Escherichia coli] 75 66 207 3880 1 310
2 gi.vertline.1009366 Respiratory nitrate reductase [Bacillus
subtilis] 75 58 309 3911 1 48 401 gi.vertline.433991 ATP synthase
subunit beta [Bacillus subtilis] 75 68 354 3957 1 2 379
pir.vertline.D36889.vertline.D368 3-isopropylmalate dehydratase (EC
4.2.1.33) chain leuC - Lactococcus lactis 75 65 378 subsp. lactis
(strain IL1403) 4005 1 5 259 gi.vertline.216746 D-lactate
dehydrogenase [Lactobacillus plantarum] 75 48 255 4080 1 73 333
gi.vertline.415855 deoxyribose aldolase [Mycoplasma hominis] 75 59
261 4111 1 1 339 gi.vertline.149435 putative [Lactococcus lactis]
75 57 339 4136 1 303 4 gi.vertline.450688 hsdM gene of EcoprrI gene
product [Escherichia coli] pir.vertline.S38437.vertline.S38437 hsdM
75 56 300 protein - Escherichia coli
pir.vertline.S09629.vertline.S09629 hypothetical protein A -
Escherichia coli (SUB 40-520) 4144 1 336 4 gi.vertline.48972
nitrate transporter [Synechococcus sp.] 75 49 333 4237 1 374 84
gi.vertline.1339950 large subunit of NADH-dependent glutamate
synthase [Plectonema boryanum] 75 55 291 4306 2 73 318
gi.vertline.294260 major surface glycoprotein [Pneumocystis
carinii] 75 68 246 4343 1 359 3 gi.vertline.1204652
methylated-DNA-protein-cysteine methyltransferase [Haemophilus
influenzae] 75 52 357 4552 1 312 4 gi.vertline.296464 ATPase
[Lactococcus lactis] 75 55 309 38 9 5776 6126 gi.vertline.443793
NupC [Escherichia coli] 74 50 351 50 8 6221 5532
gi.vertline.1239988 hypothetical protein [Bacillus subtilis] 74 55
690 56 9 10770 12221 gi.vertline.1000451 TreP [Bacillus subtilis]
74 57 1452 64 2 1622 978 gi.vertline.41015 aspartate-tRNA ligase
[Escherichia coli] 74 57 645 66 6 4848 4633 gi.vertline.1212729
YqhJ [Bacillus subtilis] 74 47 216 67 18 14334 14897
gi.vertline.1510631 endoglucanase [Methanococcus jannaschii] 74 52
564 102 15 12561 13136 gi.vertline.149429 putative [Lactococcus
lactis] 74 67 576 102 16 13121 14419 gi.vertline.149435 putative
[Lactococcus lactis] 74 57 1299 108 4 3902 2931 gi.vertline.39478
ATP binding protein of transport ATPases [Bacillus firmus]
ir.vertline.S15486.vertline.S15486 74 59 972 ATP-binding protein -
Bacillus firmus p.vertline.P26946.vertline.YATR_BACFI HYPOTHETICAL
ATP-BINDING TRANSPORT PROTEIN. 116 5 7093 5612 gi.vertline.1205430
dipeptide transport system permease protein [Haemophilus influenzae
74 49 1482 120 7 4342 4803 gi.vertline.146970 ribonucleoside
triphosphate reductase [Escherichia coli]
pir.vertline.A47331.vertline.A47331 74 58 462 anaerobic
ribonucleotide reductase - Escherichia coli 121 7 5961 6581
gi.vertline.1107528 ttg start [Campylobacter coli] 74 51 621 128 3
2320 3531 gi.vertline.143318 phosphoglycerate kinase [Bacillus
megaterium] 74 57 1212 130 7 5237 5791 gi.vertline.1256653
DNA-binding protein [Bacillus subtilis] 74 60 555 136 3 5150 3555
gi.vertline.143076 histidase [Bacillus subtilis] 74 58 1596 145 2
664 1368 gi.vertline.407773 devA gene product [Anabaena sp.] 74 45
705 152 1 277 2 gi.vertline.1377833 unknown [Bacillus subtilis] 74
54 276 164 10 11064 11375 gi.vertline.580900 ORF3 gene product
[Bacillus subtilis] 74 52 312 175 2 2624 2139 gi.vertline.642656
unknown [Rhizobium meliloti] 74 34 486 175 9 5612 5160
gi.vertline.854656 Na/H antiporter system ORF2 [Bacillus
alcalophilus] 74 46 453 195 11 10339 9332 gi.vertline.1204430
hypothetical protein (SP: P25745) [Haemophilus influenzae] 74 55
1008 205 17 9059 8499 gi.vertline.1044979 ribosomal protein L6
[Bacillus subtilis] 74 64 561 236 7 5574 6710 gi.vertline.1146207
putative [Bacillus subtilis] 74 63 1137 241 3 3334 2147
gi.vertline.694121 malate thiokinase [Methylobacterium extorquens]
74 52 1188 246 6 2799 2293 gi.vertline.467374 single strand DNA
binding protein [Bacillus subtilis] 74 64 507 249 4 5313 4075
gi.vertline.1524397 glycine betaine transporter OpuD [Bacillus
subtilis] 74 55 1239 261 7 4081 3773 gi.vertline.809542 CbrB
protein [Erwinia chrysanthemi] 74 42 309 278 6 4665 3616
gi.vertline.1204872 ATP-binding protein [Haemophilus influenzae] 74
54 1050 309 1 666 112 gi.vertline.1205579 hypothetical protein (GB:
U14003_302) [Haemophilus influenzae] 74 53 555 315 2 862 251
gi.vertline.143398 quinol oxidase [Bacillus subtilis] 74 57 612 320
1 1 1065 gi.vertline.143389 glutaminase of carbamyl phosphate
synthetase [Bacillus subtilis] 74 60 1065
pir.vertline.E39845.vertline.E39845 carbamoyl-phosphate synthase
glutamine-hydrolyzing) (EC 6.3.5.5), pyrimidine-repressible, small
hain - Bacillus subtilis 380 2 382 1128 gi.vertline.534857 ATPase
subunit a [Bacillus stearothermophilus] 74 56 747 405 2 1311 880
gi.vertline.1303915 YqhZ [Bacillus subtilis] 74 65 432 433 5 2503
3270 gi.vertline.473902 alpha-acetolactate synthase [Lactococcus
lactis] 74 56 768 452 1 1 942 gi.vertline.413982 ipa-58r gene
product [Bacillus subtilis] 74 52 942 461 1 3 1193
gi.vertline.558494 homoserine dehydrogenase [Bacillus subtilis] 74
51 1191 461 2 1174 1407 gi.vertline.40211 threonine synthase (thrC)
(AA 1-352) [Bacillus subtilis] ir.vertline.A25364.vertline.A25364
74 56 234 threonine synthase (EC 4.2.99.2) - Bacillus subtilis 462
2 402 734 gi.vertline.142520 thioredoxin [Bacillus subtilis] 74 62
333 478 1 320 66 gi.vertline.1499005 glycyl-tRNA synthetase
[Methanococcus jannaschii] 74 52 255 501 2 739 1740
gi.vertline.217040 acid glycoprotein [Streptococcus pyogenes] 74 58
1002 551 2 2791 1499 gi.vertline.143040 glutamate-1-semialdehyde
2,1-aminotransferase [Bacillus subtilis] 74 51 1293
pir.vertline.D42728.vertline.D42728 glutamate-1-semialdehyde
2,1-aminomutase (EC .4.3.8) - Bacillus subtilis 573 1 1 477
gi.vertline.1006605 hypothetical protein [Synechocystis sp.] 74 45
477 596 2 1298 816 gi.vertline.1303853 YqgF [Bacillus subtilis] 74
55 483 618 2 1758 592 gi.vertline.1146237 21.4% of identity to
trans-acting transcription factor of Sacharomyces 74 55 1167
cerevisiae; 25% of identity to sucrose synthase of Zee mays;
putative [Bacillus subtilis] 659 2 1269 1595
gi.vertline.1072380
ORF3 [Lactococcus lactis] 74 62 327 724 1 188 3 gi.vertline.143374
phosphoribosyl glycinamide synthetase (PUR-D; gtg start codon)
Bacillus 74 58 186 subtilis] 743 2 604 1209 gi.vertline.153833
ORF1; putative [Streptococcus parasanguis] 74 50 606 836 1 2 259
gi.vertline.143458 ORF V [Bacillus subtilis] 74 47 258 989 2 443
724 gi.vertline.1303994 YqkM [Bacillus subtilis] 74 46 282 1106 1 1
492 gi.vertline.46970 epiD gene product [Staphylococcus
epidermidis] 74 54 492 1135 2 373 528 gi.vertline.413948 ipa-24d
gene product [Bacillus subtilis] 74 48 156 1234 1 452 87
gi.vertline.495245 recJ gene product [Erwinia chrysanthemi] 74 36
366 2586 1 2 238 gi.vertline.1149701 sbcC gene product [Clostridium
perfringens] 74 62 237 2959 1 400 2 gi.vertline.1405454 aconitase
[Bacillus subtilis] 74 60 399 2962 1 363 76 gi.vertline.450686
3-phosphoglycerate kinase [Thermotoga maritima] 74 58 288 2983 1 3
191 gi.vertline.1303893 YqhL [Bacillus subtilis] 74 56 189 3018 1 2
223 gi.vertline.143040 glutamate-1-semialdehyde
2,1-aminotransferase [Bacillus subtilis] 74 56 222
pir.vertline.D42728.vertline.D42728 glutamate-1-semialdehyde
2,1-aminomutase (EC .4.3.8) - Bacillus' subtilis 3038 1 256 2
pir.vertline.S52915.vertline.S529 nitrate reductase alpha chain -
Bacillus subtilis (fragment) 74 57 255 3062 1 189 4
gi.vertline.1107528 ttg start [Campylobacter coli] 74 51 186 4035 1
184 360 gi.vertline.1022725 unknown [Staphylococcus haemolyticus]
74 64 177 4045 1 305 3 gi.vertline.1510977 M. jannaachii predicted
coding region MJ0938 [Methanococcus jannaschii] 74 41 303 4283 1
304 137 gi.vertline.520844 orf4 [Bacillus subtilis] 74 58 168 4449
1 3 221 gi.vertline.580910 peptide-synthetase ORF1 [Bacillus
subtilis] 74 54 219 4587 1 231 4 gi.vertline.1370207 orf6
[Lactobacillus sake] 74 59 228 4603 1 29 214 gi.vertline.146208
glutamate synthase large subunit (EC 2.6.1.53) [Escherichia coli]
74 60 186 pir.vertline.A29617.vertline.A29- 617 glutamate synthase
(NADPH) (EC 1.4.1.13) large hain- Escherichia coli 4670 1 184 2
gi.vertline.1256135 YbbF [Bacillus subtilis] 74 61 183 5 10 7162
6371 gi.vertline.143727 putative [Bacillus subtilis] 73 42 792 11 2
1372 290 gi.vertline.166338 dihydroorotate dehydrogenase [Agrocybe
aegerita] 73 55 1083 14 1 1020 16 gi.vertline.143373 phosphoribosyl
aminoimidazole carboxy formyl ormyltransferase/inosine 73 54 1005
monophosphate cyclohydrolase (PUR-H(J)) Bacillus subtilis] 23 5
4635 3844 gi.vertline.1468939 meso-2,3-butanediol dehydrogenase
(D-acetoin forming) [Klebsiella 73 58 792 pneumoniae] 23 17 16360
15341 gi.vertline.297060 ornithine cyclodeaminase [Rhizobium
meliloti] 73 37 1020 29 2 692 1273 gi.vertline.467442 stage V
sporulation [Bacillus subtilis] 73 54 582 31 5 4914 3361
gi.vertline.414000 ipa-76d gene product [Bacillus subtilis] 73 55
1554 37 8 7402 6146 gi.vertline.1429259 pepT gene product [Bacillus
subtilis] 73 59 1257 37 9 7562 7386 gi.vertline.168367
alpha-isopropylmalate isomerase (put.); putative [Rhizomucor
ircinelloides] 73 52 177 38 7 3931 4896 gi.vertline.405885 yeiN
[Escherichia coli] 73 58 966 44 6 4238 3435 gi.vertline.580895
unknown [Bacillus subtilis] 73 53 804 44 11 7767 8306
gi.vertline.42009 moaB gene product [Eacherichia coli] 73 50 540 45
3 2439 3080 gi.vertline.1109685 ProW [Bacillus subtilis] 73 47 642
54 13 13794 13552 gi.vertline.413931 ipa-7d gene product [Bacillus
subtilis] 73 61 243 59 4 1430 2248 gi.vertline.147923 threonine
dehydratase 2 (EC 4.2.1.16) [Escherichia coli] 73 53 819 65 1 730 2
gi.vertline.677944 AppF [Bacillus subtilis] 73 56 729 80 2 860 345
gi.vertline.580932 murD gene product [Bacillus subtilis] 73 53 516
102 13 10124 11179 gi.vertline.580891 3-isopropylmalate
dehydrogenase (AA 1-365) [Bacillus subtilis] 73 55 1056
pir.vertline.A26522.vertline.A26522 3-isopropylmalate dehydrogenase
(EC 1.1.1.85) - Bacillus subtilis 109 2 2600 1707
gi.vertline.1510849 M. jannaschii predicted coding region MJ0775
[Methanococcus jannaschii] 73 40 894 120 8 4782 5756
gi.vertline.146970 ribonucleoside triphosphate reductase
[Escherichia coli] pir.vertline.A47331.vertline.A47331 73 56 975
anaerobic ribonucleotide reductase - Escherichia coli 120 9 5726
6223 gi.vertline.1204333 anaerobic ribonucleoside-triphosphate
reductase [Haemophilus influenzae] 73 62 498 132 5 4151 4363
gi.vertline.871048 HPSR2 - heavy chain potential motor protein
[Giardia inrestinalis] 73 43 213 140 6 4324 2696 gi.vertline.634107
kdpB [Eacherichia coli] 73 59 1629 142 6 5939 4918
gi.vertline.410125 ribG gene product [Bacillus subtilis] 73 57 1122
149 4 1717 1568 gi.vertline.460892 heparin binding protein-44,
HBP-44 [mice, Peptide, 360 aa] 73 53 150
pir.vertline.JX0281.vertline.JX0281 heparin-binding protein-44
precursor - mouse gi.vertline.220434 ORF [Mus musculus] (SUB 2-360)
158 1 1 1431 gi.vertline.882504 ORF_f560 [Eacherichia coli] 73 57
1431 174 6 4525 3698 gi.vertline.1146240 ketopantoate
hydroxymethyltransferase [Bacillus subtilis] 73 55 828 175 8 5178
4819 gi.vertline.854657 Na/H antiporter system ORF3 [Bacillus
alcalophilus) 73 56 360 186 5 5493 4393 gi.vertline.467477 unknown
[Bacillus subtilis] 73 48 1101 249 6 5729 5175 gi.vertline.1524397
glycine betaine transporter OpuD [Bacillus subtilis] 73 56 555 265
4 1873 2280 gi.vertline.39848 U3 [Bacillus subtilis] 73 41 408 270
1 328 582 gi.vertline.780461 220 kDa polyprotein [African swine
fever virus] 73 53 255 278 4 3618 2953 gi.vertline.1208965
hypothetical 23.3 kd protein [Eacherichia coli] 73 49 666 279 3
3593 2202 gi.vertline.1185288 isochorismate synthase [Bacillus
subtilis] 73 58 1392 291 4 1207 1575 gi.vertline.1511440 glutamine
- fructose-6-phosphate transaminase (Methanococcus jannaschii) 73
63 369 299 2 735 1166 gi.vertline.467437 unknown [Bacillus
subtilis] 73 58 432 299 5 2050 3234 gi.vertline.467439 temperature
sensitive cell division [Bacillus subtilis] 73 53 1185 334 1 728
219 gi.vertline.536655 ORF YBR244w [Saccharomyces cerevisise] 73 43
510 336 2 1036 245 gi.vertline.790943 urea amidolyase [Bacillus
subtilis] 73 51 792 374 3 1389 1874 gi.vertline.1405451 YneJ
[Bacillus subtilis] 73 55 486 433 4 1916 2554 gi.vertline.473902
alpha-aceholactate synthase [Lactococcus lactis] 73 54 639 509 2
1028 261 gi.vertline.467483 unknown [Bacillus subtilis] 73 56 768
513 1 918 127 gi.vertline.1146220 NAD+ dependent
glycerol-3-phosphate dehydrogenase [Bacillus subtilis] 73 56 792
533 2 239 733 gi.vertline.1510605 hypothetical protein (SP: P42297)
[Methanococcus jannaschii] 73 44 495 546 2 1148 2815
gi.vertline.41748 hsdM protein (AA 1-520) [Eacherichia coli] 73 52
1668 549 1 382 2 gi.vertline.1314847 CinA [Bacillus subtilis] 73 57
381 567 1 675 4 gi.vertline.410137 ORFX13 [Bacillus subtilis] 73 58
672 716 2 654 1112 gi.vertline.1256623 exodeoxyribonuclease
[Bacillus subtilis] 73 56 459 772 1 3 677 gi.vertline.142010 Shows
70.2% similarity and 48.6% identity to the EnvM protein of
almonella 73 57 675 typhimurium [Anabaena sp.] 774 1 3 209
gi.vertline.409286 bmrU [Bacillus subtilis] 73 52 207 782 1 1 402
gi.vertline.143320 [gap] gene products [Bacillus megaterium] 73 56
402 789 2 451 762 gi.vertline.1063246 low homology to P14 protein
of Heamophilus influenzar and 14.2 kDa protein 73 56 312 of
Escherichia coli [Bacillus subtilis] 796 1 3 911 gi.vertline.853754
ABC transporter [Bacillus subtilis] 73 58 909 806 3 949 689
gi.vertline.143786 tryptophanyl-tRNA synthetase (EC 6.1.1.2)
[Bacillus subtilis] 73 51 261 pir.vertline.JT0481.vertline.YWBS
tryptophan-tRNA ligase (EC 6.1.1.2) - Bacillus subtilis 816 2 3097
1355 gi.vertline.41748 hsdM protein (AA 1-520) [Escherichia coli]
73 52 1743 839 1 400 2 gi.vertline.886906 argininosuccinate
synthetase [Streptomyces clavuligerus]
pir.vertline.S57659.vertline.S57659 73 59 399 argininosuccinate
synthase (EC 6.3.4.5) - treptomyces clavuligerus 857 1 3 290
gi.vertline.348052 acetoin utilization protein [Bacillus subtilis]
73 50 288 1008 1 398 6 gi.vertline.40100 rodC (tag3) polypeptide
(AA 1-746) [Bacillus subtilis] ir.vertline.S06049.vertline.S0- 6049
73 41 393 rodC protein - Bacillus subtilis
p.vertline.P13485.vertline.TAGF_BACSU TECHOIC ACID BIOSYNTHESIS
PROTEIN F. 1018 1 1 213 gi.vertline.529357 No definition line found
[Caenorhabditis elegans] sp.vertline.P46975.vertlin- e.STT3_CAEEL
73 53 213 OLIGOSACCHARYL TRANSFERASE STT3 SUBUNIT OMOLOG. 1033 1 3
491 gi.vertline.142706 comG1 gene product [Bacillus subtilis] 73 51
489 1174 1 204 13 gi.vertline.1149513 alpha3a subunit of laminin 5
[Homo sapiens] 73 60 192 1175 1 329 3 gi.vertline.473817 `ORF`
[Escherichia coli] 73 57 327 1187 1 3 209 gi.vertline.580870
ipa-37d qoxA gene product [Bacillus subtilis] 73 52 207 1206 1 72
245 gi.vertline.144816 formyltetrahydrofolate synthetase (FTHFS)
(ttg start codon) (EC .3.4.3) 73 43 174 [Moorella thermoacetica]
1454 1 241 59 gi.vertline.1213253 unknown [Schizosaccharomyces
pombe] 73 53 183 1469 1 260 3 gi.vertline.1303787 YqeG [Bacillus
subtilis] 73 55 258 1761 1 189 4 gi.vertline.9135 Mst26Aa gene
product [Drosophila simulans] 73 34 186 1849 1 243 19
gi.vertline.162307 DNA topoisomerase II [Trypanosoma cruzi] 73 60
225 2055 1 2 400 gi.vertline.559381 P47K protein [Rhodococcus
erythropolis] 73 34 399 2556 1 2 244 gi.vertline.145925 fecB
[Escherichia coli] 73 62 243 2947 2 400 251 gi.vertline.1184680
polynucleotide phosphorylase [Bacillus subtilis] 73 51 150 2956 1
375 4 gi.vertline.143397 quinol oxidase [Bacillus subtilis] 73 58
372 3037 1 329 3 gi.vertline.143091 acetolactate synthase [Bacillus
subtilis] 73 55 327 3115 1 194 3 gi.vertline.323866 overlapping
out-of-phase protein [Eggplant mosaic virus] 73 53 192
sp.vertline.P20129.vertline.V70K_EPMV 70 KD PROTEIN. 3603 2 527 354
gi.vertline.1439521 glutaryl-CoA dehydrogenase precursor [Mus
musculus] 73 48 174 3743 1 400 2 gi.vertline.450688 hsdM gene of
EcoprrI gene product [Escherichia
coli]pir.vertline.S38437.vertline.S38437 hsdM 73 54 399 protein -
Escherichia coli pir.vertline.S09629.vertline.S09629 hypothetical
protein A - Escherichia coli (SUB 40-520) 3752 1 359 78
gi.vertline.1524193 unknown (Mycobacterium tuberculosis] 73 59 282
3852 1 2 181 gi.vertline.216746 D-lactate dehydrogenase
[Lactobacillus plantarum] 73 68 180 3914 1 239 3
pir.vertline.S13490.vertline.S134 Hydroxymethylglutaryl-CoA
synthase (EC 4.1.3.5) - Chicken (fragment) 73 53 237 3914 2 343 116
gi.vertline.528991 unknown [Bacillus subtilis] 73 38 228 4069 1 2
316 gi.vertline.40003 oxoglutarate dehydrogenase (NADP+) [Bacillus
subtilis] p.vertline.P23129.vertline.OD01_BACSU 73 55 315
2-OXOGLUTARATE DEHYDROGENASE E1 COMPONENT (EC 2.4.2)
(ALPHA-KETOGLUTARATE DEHYDROGENASE). 4165 1 365 15
gi.vertline.1439521 glutaryl-CoA dehydrogenase precursor [Mus
musculus] 73 48 351 4196 1 1 177 gi.vertline.809660
deoxyribose-phosphate aldolase [Bacillus subtilis]
pir.vertline.S49455.vertline.S49455 73 60 177 deoxyribose-phosphate
aldolase (EC 4.1.2.4) - Bacillus subtilis 4202 1 378 184
gi.vertline.528991 unknown [Bacillus subtilis) 73 38 195 4314 1 2
193 gi.vertline.436797 N-acyl-L-amino acid amidohydrolase [Bacillus
stearothermophilus] 73 47 192 sp.vertline.P37112.vertline.AMA_BACST
N-ACYL-L-AMINO ACID AMIDOHYDROLASE (EC .5.1.14) (AMINOACYLASE).
4393 1 3 263 gi.vertline.216267 ORF2 [Bacillus megaterium) 73 47
261 35 2 903 1973 gi.vertline.1146196 phosphoglycerate
dehydrogenase [Bacillus subtilis] 72 53 1071 38 22 17877 16660
gi.vertline.602031 similar to trimethylamine DH [Mycoplasma
capricolum] pir.vertline.S49950.vertline- .S49950 72 54 1218
probable trimethylamine dehydrogenase (EC .5.99.7) - Mycoplasma
capricolum (SGC3) (fragment) 38 23 18134 19162 gi.vertline.413968
ipa-44d gene product [Bacillus subtilis] 72 54 1029 44 19 11895
12953 gi.vertline.516272 unknown [Bacillus subtilis] 72 49 1059 48
7 6248 7117 gi.vertline.43499 pyruvate synthase [Halobacterium
halobium) 72 49 870 50 7 5691 4819 gi.vertline.1205399 proton
glutamate symport protein [Haemophilus influenzae] 72 53 873 53 9
9259 7997 gi.vertline.1303956 YqjE [Bacillus subtilis] 72 52 1263
56 23 29549 29995 gi.vertline.467471 unknown [Bacillus subtilis] 72
47 447 69 4 4123 2948 gi.vertline.1354775 pfoS/R [Treponema
pallidum] 72 46 1176 69 5 4377 4982 gi.vertline.904198 hypothetical
protein [Bacillus subtilis] 72 43 606 73 1 2 856 gi.vertline.142997
glycerol uptake facilitator [Bacillus subtilis] 72 59 855 98 13
9371 10258 gi.vertline.467435 unknown [Bacillus subtilis] 72 50 888
127 1 1 1593 gi.vertline.217144 alanine carrier protein
[thermophilic bacterium PS3] pir.vertline.A45111.vertline.A45111 72
56 1593 alanine transport protein - thermophilic acterium PS-3 131
1 2600 3 gi.vertline.153952 polymerase III polymerase subunit
(dnaE) [Salmonella typhimurium] 72 53 2598
pir.vertline.A45915.vertline.A45915 DNA-directed DNA polymerase (EC
2.7.7.7) III lpha chain - Salmonella typhimurium 141 4 1040 1978
gi.vertline.1405446 transketolase [Bacillus subtilis] 72 54 939 149
8 2535 2251 gi.vertline.606234 secY [Escherichia coli] 72 44 285
149 17 5245 5018 gi.vertline.1304472 DNA polymerase [Unidentified
phycodnavirus clone OTU4] 72 55 228 154 1 1 210 gi.vertline.1205620
ferritin like protein [Haemophilus influenzae] 72 40 210 155 1 1320
433 gi.vertline.391610 farnesyl diphosphate synthase [Bacillus
stearothermophilus] 72 57 888 pir.vertline.JX0257.vertline.JX- 0257
geranyltranstransferase (EC 2.5.1.10) - Bacillus stearothermophilus
180 1 2 328 gi.vertline.433630 A180 [Saccharomyces cerevisiae] 72
62 327 184 3 1145 3553 gi.vertline.1205110 virulence associated
protein homolog [Haemophilus influenzae] 72 49 2409 195 2 1279 635
gi.vertline.1001730 hypothetical protein [Synechocystis sp.] 72 45
645 206 13 14646 15869 gi.vertline.1064807 ORTHININE
AMINOTRANSFERASE [Bacillus subtilis] 72 50 1224 209 2 462 932
gi.vertline.1204666 hypothetical protein (GB: X73124_53)
[Haemophilus influenzae] 72 60 471 215 2 522 280 gi.vertline.881513
insulin receptor homolog [Drosophila melanogaster]
pir.vertline.S57245.vertline.S57245 72 63 243 insulin receptor
homolog - fruit fly (Drosophila elanogaster) (SUB 46- 2146) 224 1 2
790 gi.vertline.949974 sucrose repressor [Staphylococcus xylosus]
72 54 789 233 1 765 4 gi.vertline.1408493 homologous to SwissProt:
YIDA_ECOLI hypothetical protein [Bacillus subtilis] 72 52 762 240 1
220 1485 gi.vertline.537049 ORF_o470 [Escherichia coli] 72 52 1266
245 1 3 1340 gi.vertline.1204578 hypothetical protein (GB:
U06949_1) [Haemophilus influenzae] 72 46 1338 259 2 1245 382
gi.vertline.1340128 ORF1 [Staphylococcus aureus] 72 59 864 304 2
285 1094 gi.vertline.1205330 glutamine-binding periplasmic protein
[Haemophilus influenzae] 72 52 810 307 10 5039 4752
gi.vertline.1070015 protein-dependent [Bacillus subtilis] 72 53 288
315 1 260 3 gi.vertline.143399 quinol oxidase [Bacillus subtilis]
72 55 258 316 11 9308 8994 gi.vertline.1204445 hypothetical protein
(SP: P27857) [Haemophilus influenzae] 72 52 315 337 3 926 1609
gi.vertline.487433 citrate synthase II [Bacillus subtilis] 72 55
684 364 7 10493 8448 gi.vertline.1510643 ferrous iron transport
protein B [Methanococcus jannaschii] 72 53 2046 409 2 340 1263
gi.vertline.1402944 orfRM1 gene product [Bacillus subtilis] 72 49
924 441 3 1590 1003 gi.vertline.312379 highly conserved among
eubacteria [Clostridium acetobutylicum] 72 48 588
pir.vertline.S34312.vertline.S34312 hypothetical protein V -
Clostridium cetobutylicum 453 6 2505 2356
pir.vertline.S00601.vertline.BXSA antibacterial protein 3 -
Staphylococcus haemolyticus 72 70 150 460 1 2 625
gi.vertline.1016162 ABC transporter subunit [Cyanophora paradoxa]
72 51 624 463 1 1628 3 gi.vertline.666014 The polymorphysm (RFLP)
of this gene is associated with usceptibility to 72 60 1626
essential hypertension. The SA gene product has light homology to
acetyl- CoA synthetase [Homo sapiens] 480 4 3047 3466
gi.vertline.433992 ATP synthase subunit epsilon [Bacillus subtilis]
72 53 420 502 1 586 86 gi.vertline.310859 ORF2 [synechococcus sp.]
72 50 501 519 1 81 1184 gi.vertline.1303704
YrkE [Bacillus subtilis] 72 54 1104 559 1 3 746 gi.vertline.1107530
ceuD gene product [Campylobacter coli] 72 56 744 575 1 573 4
gi.vertline.1303866 Yqgs [Bacillus subtilis] 72 56 570 671 1 2 592
gi.vertline.1204497 protein-export membrane protein [Haemophilus
influenzae] 72 44 591 679 2 295 1251 gi.vertline.563258
virulence-associated protein E [Dichelobacter nodosus] 72 52 957
687 2 295 957 gi.vertline.1146214 44% identical amino acids with
the Escherichia coli smba supress; putative 72 49 663 [Bacillus
subtilis] 837 1 1 435 gi.vertline.1146183 putative [Bacillus
subtilis] 72 54 435 868 1 150 788 gi.vertline.1377842 unknown
[Bacillus subtilis] 72 55 639 922 1 130 432 gi.vertline.1088269
unknown protein [Azotobacter vinelandii] 72 58 303 941 1 2 238
gi.vertline.153929 NADPH-sulfite reducatase flavoprotein component
[Salmonella yphimurium] 72 49 237 980 1 421 2 gi.vertline.853767
UDP-N-acetylglucosamine 1-carboxyvinyltransferase [Bacillus
subtilis] 72 59 420 1209 1 213 43 gi.vertline.144735 neurotoxin
type B [Clostridium botulinum] 72 44 171 1469 2 474 277
gi.vertline.1205458 hypothetical protein (GB: D26562_47)
[Haemophilus influenzae] 72 63 198 1956 1 365 3 gi.vertline.154409
hexosephosphate transport protein [Salmonella typhimurium] 72 44
363 pir.vertline.B41853.vertline.B41853 hexose phosphate transport
system regulatory rotein uhpB - salmonella typhimurium 2101 1 3 401
gi.vertline.1303950 YqiY [Bacillus subtilis] 72 50 399 2503 1 399
229 gi.vertline.149713 formate dehydrogenase [Methanobacterium
formicicum] pir.vertline.A42712.vertline.A42712 72 56 171 formate
dehydrogenase (EC 1.2.1.2) - Methanobacterium formicicum 2967 1 3
155 gi.vertline.1212729 YqhJ [Bacillus subtilis] 72 46 153 3004 1
185 3 gi.vertline.665999 hypothetical protein [Bacillus subtilis]
72 55 183 3109 1 141 4 gi.vertline.413968 ipa-44d gene product
[Bacillus subtilis] 72 45 138 3171 1 3 287 gi.vertline.515938
glutamate synthase (ferredoxin) [Synechocystis sp.]
pir.vertline.S46957.vertline.S46957 72 52 285 glutamate synthase
(ferredoxin) (EC 1.4.7.1) - Synechocystis sp. 3771 1 26 367
gi.vertline.1408501 homologous to N-acyl-L-amino acid
amidohydrolase of Bacillus 72 63 342 stearothermophilus [Bacillus
subtilis] 3951 1 1 222 gi.vertline.1500409 M. jannaschii predicted
coding region MJ1519 [Methanococcus jannaschii] 72 38 222 4190 1
362 3 gi.vertline.39956 IIGlc [Bacillus subtilis] 72 57 360 4444 1
3 347 gi.vertline.1009366 Respiratory nitrate reductase [Bacillus
subtilis] 72 55 345 6 2 931 1200 gi.vertline.537095 ornithine
carbamoyltransferase [Escherichia coli] 71 55 270 11 15 10859 10368
gi.vertline.532309 25 kDa protein [Escherichia coli] 71 47 492 19 2
1248 2435 gi.vertline.1244574 D-alanine; D-alanine ligase
[Enterococcus hirae] 71 52 1188 21 2 898 1488 gi.vertline.149629
anthranilate synthase component 2 [Leptospira biflexa]
pir.vertline.C32840.vertline.C32840 71 45 591 anthranilate synthase
(EC 4.1.3.27) component II Leptospira biflexa 34 1 1 567
gi.vertline.1303983 YqkF [Bacillus subtilis] 71 59 567 37 3 2806
2420 gi.vertline.1209681 glutamate-rich protein [Bacillus firmus]
71 50 387 38 18 12250 12462 gi.vertline.927645 arginyl
endopeptidase [Porphyromonas gingivalis] 71 50 213 39 3 1246 4431
pir.vertline.S09411.vertline.S094 spoIIIE protein - Bacillus
subtilis 71 49 3186 53 14 14760 13750 gi.vertline.142611 branched
chain alpha-keto acid dehydrogenase E1-alpha [Bacillus subtilis] 71
58 1011 54 11 12625 11789 gi.vertline.143014 gnt repressor
[Bacillus subtilis] 71 46 837 57 7 5860 4568 gi.vertline.508175
EIIC domain of PTS-dependent Gat transport and phosphorylation
Escherichia 71 48 1293 coli] 57 18 13897 14334 gi.vertline.1063247
high homology to flavohemoprotein (Haemoglobin-like protein) of
Alcaligenes 71 56 438 eutrophus and Saccharomyces cerevisiae
[Bacillus subtilis] 62 16 9831 10955 gi.vertline.1303926 YgiG
[Bacillus subtilis] 71 54 1125 70 12 8505 8966 gi.vertline.147198
phnE protein [Escherichia coli] 71 38 462 86 5 2089 1784
gi.vertline.904205 hypothetical protein [Bacillus subtilis] 71 51
306 96 7 7601 8269 gi.vertline.709991 hypothetical protein
[Bacillus subtilis] 71 49 669 100 6 4822 5931 gi.vertline.1060848
Opine dehydrogenase [Arthrobacter sp.] 71 45 1110 103 1 532 2
gi.vertline.143089 iep protein [Bacillus subtilis] 71 41 531 109 18
15312 15695 gi.vertline.413985 ipa-61d gene product [Bacillus
subtilis] 71 57 384 113 1 316 2 gi.vertline.663254 probable protein
kinase [Saccharomyces cerevisiae] 71 57 315 114 5 5603 4608
gi.vertline.143156 membrane bound protein [Bacillus subtilis] 71 40
996 133 2 1723 359 gi.vertline.1303913 YqhX [Bacillus subtilis] 71
53 1365 149 19 5895 5455 gi.vertline.529650 G40P [Bacteriophage
SPP1] 71 51 441 154 5 3087 2539 gi.vertline.425488 repressor
protein [Streptococcus sobrinus] 71 47 549 164 11 11354 11689
gi.vertline.49318 ORF4 gene product [Bacillus subtilis] 71 52 336
169 5 1936 2745 gi.vertline.1403403 unknown [Mycobacterium
tuberculosis] 71 56 810 193 2 272 1234 gi.vertline.1303788 YqeH
[Bacillus subtilis] 71 49 963 205 1 895 47 gi.vertline.1215694 GlnQ
[Mycoplasma pneumoniae] 71 46 849 233 4 1849 2022
gi.vertline.633732 ORF1 [Campylobacter jejuni] 71 50 174 237 7 4501
5169 gi.vertline.149384 HisIE [Lactococcus lactis] 71 54 669 272 4
2273 1698 gi.vertline.709993 hypothetical protein [Bacillus
subtilis] 71 48 576 274 2 618 1496 gi.vertline.143035 NAD(P)H:
glutamyl-transfer RNA reductase [Bacillus subtilis] 71 53 879
pir.vertline.A35252.vertline.A35252 5-aminolevulinate synthase (EC
2.3.1.37) - Bacillus subtilis 276 5 2720 2091 gi.vertline.303562
ORF210 [Escherichia coli] 71 50 630 287 1 136 660
gi.vertline.310634 20 kDa protein [Streptococcus gordonii] 71 53
525 288 6 2771 2220 gi.vertline.1256625 putative [Bacillus
subtilis] 71 47 552 301 6 2461 1430 gi.vertline.467417 similar to
lysine decarboxylase [Bacillus subtilis] 71 57 1032 306 4 5222 3837
gi.vertline.1256618 transport protein [Bacillus subtilis] 71 56
1386 307 2 925 314 gi.vertline.602683 orfC [Mycoplasma capricolum]
71 45 612 310 5 5146 4499 gi.vertline.348052 acetoin utilization
protein [Bacillus subtilis] 71 51 648 322 1 2 1303
gi.vertline.1001819 hypothetical protein [Synechocystis sp.] 71 46
1302 333 4 3995 3819 gi.vertline.467473 unknown [Bacillus subtilis]
71 57 177 350 2 548 922 gi.vertline.551879 ORF 1 [Lactococcus
lactis] 71 55 375 375 4 1860 3071 gi.vertline.467447 unknown
[Bacillus subtilis] 71 57 1212 380 5 1560 2102 gi.vertline.142557
ATP synthase b subunit [Bacillus megaterium] 71 43 543 414 2 251
637 gi.vertline.580904 homologous to E. coli rnpA [Bacillus
subtilis] 71 49 387 424 1 335 1354 gi.vertline.581305 L-lactate
dehydrogenase [Lactobacillus plantarum] 71 57 1020 436 4 3270 2839
pir.vertline.PN0501.vertline.PN05 phosphoribosylanthranilate
isomerase (EC 5.3.1.24) - Bacillus subtilis 71 66 432 [fragment]
482 1 3 1280 gi.vertline.410142 ORFX18 [Bacillus subtilis] 71 49
1278 525 3 1844 1416 gi.vertline.143370 Phosphoribosylpyrophosphate
amidotransferase [PUR-F; EC 2.4.2.14] Bacillus 71 56 429 subtilis]
529 4 2047 1355 gi.vertline.606150 ORF_f309 [Escherichia coli] 71
43 693 563 1 22 969 gi.vertline.1237015 ORF4 [Bacillus subtilis] 71
53 948 581 1 255 4 gi.vertline.1301730 T25G3.2 [Caenorhabditis
elegans] 71 47 252 612 2 913 758 gi.vertline.153968 fimbriae Z
[Salmonella typhimurium] 71 55 156 613 1 1 654 gi.vertline.466778
lysine specific permease [Escherichia coli] 71 50 654 618 1 623 3
gi.vertline.1146238 poly(A) polymerase [Bacillus subtilis] 71 52
621 630 1 586 2 gi.vertline.1486243 unknown [Bacillus subtilis] 71
53 585 691 1 641 156 gi.vertline.289260 comE ORF1 [Bacillus
subtilis] 71 51 486 694 2 149 427 gi.vertline.12971 NADH
dehydrogenase subunit V (AA 1-605) [Gallus gallus]
ir.vertline.s10197.vertline.S10197 71 47 279 NADH dehydrogenase
(ubiquinone) (EC 1.6.5.3) chain - chicken mitochondrion (SGC1) 715
2 169 777 gi.vertline.1303830 YqfL [Bacillus subtilis] 71 53 609
746 2 970 467 gi.vertline.1377843 unknown [Bacillus subtilis] 71 52
504 748 1 802 167 gi.vertline.1405459 YneS [Bacillus subtilis] 71
49 636 753 1 524 30 gi.vertline.1510389 M. jannaschii predicted
coding region MJ0296 [Methanococcus jannaschii] 71 53 495 761 1 3
215 gi.vertline.475972 pentafunctional enzyme [Pneumocystis
carinii] 71 47 213 783 1 703 203 gi.vertline.536655 ORF YBR244w
[Saccharomyces cerevisiae] 71 52 501 800 3 987 682
gi.vertline.1204326 tRNA delta (2)-isopentenylpyrophosphate
transferase [Haemophilus influenzae] 71 48 306 806 1 116 286
gi.vertline.1419075 cbiM gene product [Methanobacterium
thermoautotrophicum] 71 50 171 931 1 488 3 gi.vertline.893358 PgsA
[Bacillus subtilis] 71 56 486 1041 1 2 262 gi.vertline.1408507
pyrimidine nucleoside transport protein [Bacillus subtilis] 71 45
261 1070 1 2 172 gi.vertline.709993 hypothetical protein [Bacillus
subtilis] 71 46 171 1176 1 57 365 gi.vertline.151259 HMG-CoA
reductase (EC 1.1.1.88) [Pseudomonas mevalonii]
pir.vertline.A44756.vertline.A44756 71 49 309
hydroxymethylglutaryl-CoA reductase (EC 1.1.1.88) Pseudomonas sp.
1181 1 184 2 gi.vertline.46971 epiP gene product [Staphylococcus
epidermidis] 71 50 183 1281 1 3 290 gi.vertline.153016 ORF 419
protein [Staphylococcus aureus] 71 50 288 1348 1 229 2
gi.vertline.602683 orfc [Mycoplasma capricolum] 71 48 228 2002 1
379 2 gi.vertline.1008177 ORF YJL046w [Saccharomyces cerevisiae] 71
48 378 2119 1 2 217 gi.vertline.1046088 arginyl-tRNA synthetase
[Mycoplasma genitalium] 71 50 216 2418 1 3 320 gi.vertline.1499771
M. jannaschii predicted coding region MJ0936 [Methanococcus
jannaschii] 71 57 318 2961 1 2 187 gi.vertline.312443
carbamoyl-phosphate synthase (glutamine-hydrolysing) [Bacillus
aldolyticus] 71 57 186 2999 2 67 306 gi.vertline.710020 nitrite
reductase (nirB) [Bacillus subtilis] 71 43 240 3033 1 2 184
gi.vertline.1262335 YmaA [Bacillus subtilis] 71 57 183 3584 1 3 338
gi.vertline.401716 beta-isopropylmalate dehydrogenase [Neurospora
crassa] 71 55 336 3715 2 399 55 gi.vertline.563952 gluconate
permease [Bacillus licheniformis] 71 59 345 3785 1 387 4
gi.vertline.47382 acyl-CoA-dehydrogenase [Streptomyces
purpurascens] 71 57 384 3875 1 272 3 gi.vertline.1001541
hypothetical protein [Synechocystis sp.] 71 38 270 4135 1 320 3
gi.vertline.142695 S-adenosyl-L-methionine: uroporphyrinogen III
methyltransferase Bacillus 71 52 318 megaterium] 4249 1 63 239
gi.vertline.1205363 deoxyribose aldolase [Haemophilus influenzae]
71 63 177 4508 1 267 4 gi.vertline.1197667 vitellogenin [Anolis
pulchellus] 71 46 264 1976 1 237 22 gi.vertline.9806 lysine-rich
aspartic acid-rich protein [Plasmodium chabaudi] 56 33 216
r.vertline.S22183.vertline.S2- 2183 lysine/aspartic acid-rich
protein - Plasmodiom baudi 2161 1 2 400 gi.vertline.1237015 ORF4
[Bacillus subtilis] 56 27 399 2958 1 183 4 gi.vertline.466685 No
definition line found [Escherichia coli] 56 26 180 2979 1 212 3
gi.vertline.1204354 spore germination and vegetative growth protein
[Haemophilus infiuenzae] 56 40 210 2994 2 326 126
gi.vertline.836646 phosphoribosylformimino-praic ketoisomerase
[Rhodobacter phaeroides] 56 29 201 3026 1 179 328
gi.vertline.143306 penicllin V amidase [Bacillus sphaericus] 56 30
150 3189 1 146 3 gi.vertline.1166604 Similar to aldehyde
dehydrogenase [Caenorhabditis elegans] 56 37 144 3770 1 63 401
gi.vertline.1129145 acetyl-CoA C-acyltransferase [Mangifera indica]
56 43 339 4054 2 361 2 gi.vertline.1205355 Na+/H+ antiporter
[Haemophilus influenzae] 56 31 360 4145 1 1 324 gi.vertline.726095
long-chain acyl-CoA dehydrogenase [Mus musculus] 56 36 324 4200 1
254 3 gi.vertline.155588 glucose-fructose oxidoreductase [Zymomonas
mobilis.vertline.pir.vertline.A42289.vertline.A42289 56 40 252
glucose-fructose oxidoreductase (EC 1.1.--.--) recursor - Zymomonas
mobilis 4273 1 355 35 gi.vertline.308861 GTG start codon
[Lactococcus lactis] 56 33 321 1 3 3436 2777 gi.vertline.5341
Putative orF YCLX8c, len: 192 [Saccharomyces cerevisiae]
r.vertline.S53591.vertline.S53591 55 25 660 hypothetical protein -
yeast (Saccharomyces evisiae) 11 12 8505 7633 gi.vertline.216773
haloacetate dehalogenase H-1 [Moraxella sp.] 55 32 873 12 4 4534
3935 gi.vertline.467337 unknown [Bacillus subtilis] 55 26 600 19 5
5404 5844 gi.vertline.1001719 hypothetical protein [Synechocystis
sp.] 55 25 441 23 13 12339 10591 gi.vertline.474190 iucA gene
product [Escherichia coli] 55 30 1749 32 7 5368 6888
gi.vertline.1340096 unknown [Mycobacterium tuberculosis] 55 37 1521
34 3 1808 1047 gi.vertline.1303968 YqjQ [Bacillus subtilis] 55 39
762 34 5 3412 2864 gi.vertline.1303962 Yqjk [Bacillus subtilis] 55
33 549 36 1 647 3 gi.vertline.606045 ORF_o118 [Escherichia coli] 55
27 645 36 6 5243 4266 gi.vertline.1001341 hypothetical protein
[Synechocystis sp.] 55 31 978 47 3 3054 3821 gi.vertline.1001819
hypothetical protein [Synechocystis sp.] 55 21 768 49 1 1127 189
gi.vertline.403373 glycerophosphoryl diester phosphodiesterase
[Bacillus subtilis] 55 36 939 pir.vertline.S37251.vertline.S37251
glycerophosphoryl diester phosphodiesterase - Bacillus subtilis 67
11 8966 9565 gi.vertline.153053 norA1199 protein [Staphylococcus
aureus] 55 23 600 75 3 881 1273 gi.vertline.41698 L-histidinol:
NAD+ oxidoreductase (EC 1.1.1.23) (aa 1-434) Escherichia coli) 55
33 393 82 9 14194 13001 gi.vertline.1136221 carboxypeptidase
[Sulfolobus solfataricus] 55 35 1194 87 4 3517 4917
gi.vertline.1064812 function unknown [Bacillus subtilis] 55 26 1401
88 2 1172 1636 gi.vertline.882463 protein-N(pi)-phosphohistldine-s-
ugar phosphotransferase [Escherichia coli] 55 35 465 92 1 127 516
gi.vertline.1377832 unknown [Bacillus subtilis] 55 36 390 100 2 836
2035 gi.vertline.1370274 zeaxanthin epoxidase [Nicotiana
plumbaginifolia] 55 36 1200 100 5 4658 4179 gi.vertline.396660
unknown open reading frame [Buchnera aphidicola] 55 29 480 108 3
2986 1706 gi.vertline.1499866 M. jannaschii predicted coding region
MJ1024 [Methanococcus jannaschli] 55 31 1281 114 3 1834 1052
gi.vertline.1511367 formate dehydrogenase, alpha subunit
[Methanococcus jannaschii] 55 29 783 144 3 1476 1147
gi.vertline.1100787 unkown [Saccharomyces cerevisiae] 55 35 330 165
5 5508 4804 gi.vertline.1045884 M. genitalium predicted coding
region MG199 [Hycoplasma genitalium] 55 27 705 189 5 2205 2576
gi.vertline.142569 ATP synthase a subunit [Bacillus firmus] 55 35
372 191 6 6857 4578 gi.vertline.559411 B0272.3 [Caenorhabditis
elegans] 55 39 2280 194 2 364 636 gi.vertline.1145768 K7
kinesin-like protein [Dictyostelium discoideum] 55 34 273 209 4
1335 1676 gi.vertline.473357 thi4 gene product [Schizosaccharomyces
pombe] 55 35 342 211 2 1145 597 gi.vertline.410130 ORFX6 [Bacillus
subtilis] 55 37 549 213 2 644 1372 gi.vertline.633692 TrsA
[Yersinia enterocolitica] 55 28 729 214 7 4144 5481
gi.vertline.1001793 hypothetical protein [Synechocystis sp.] 55 30
1338 221 7 9197 6921 gi.vertline.466520 pocR [Salmonella
typhimurium] 55 32 2277 233 8 4817 3726 gi.vertline.1237063 unknown
[Mycobacterium tuberculosis] 55 38 1092 236 4 1375 2340
gi.vertline.1146199 putative [Bacillus subtilis] 55 32 966 243 2
380 1885 gi.vertline.459907 mercuric reductase (Plasmid pI258] 55
29 1506 258 1 394 2 gi.vertline.455006 orf6 [Rhodococcus fascians]
55 36 393 281 1 126 938 gi.vertline.1408493 homologous to
SwissProt: YIDA_ECOLI hypothetical protein [Bacillus subtilis] 55
35 813 316 3 1323 2102 gi.vertline.1486447 LuxA homologue
[Rhizobium sp.] 55 30 780 326 5 2744 2520 gi.vertline.1296824
proline iminopeptidase [Lactobacillus helveticus] 55 36 225 351 2
1429 536 gi.vertline.1204820 hydrogen peroxide-inducible activator
[Haemophilus influenzae] 55 28 894 353 4 2197 2412
gi.vertline.1272475 chitin synthase [Emericella nidulans] 55 50 216
380 1 14 379 gi.vertline.142554 ATP synthase i subunit [Bacillus
megaterium] 55 37 366 383 1 232 2 gi.vertline.289272
ferrichrome-binding protein [Bacillus subtilis] 55 36 231 386 1 3
938 gi.vertline.1510251 DNA helicase, putative [Methanococcus
jannaschii] 55 30 936 410 2 1208 1891 gi.vertline.1205144 multidrug
resistance protein [Haemophilus influenzae] 55 27 684 483 2 411
833
gi.vertline.413934 ipa-10r gene product [Bacillus subtilis] 55 26
423 529 3 1433 1089 gi.vertline.606150 ORF_f309 [Escherichia coli]
55 33 345 555 1 585 82 gi.vertline.143407 para-aminobenzoic acid
synthase, component I (pab) [Bacillus subtilis] 55 28 504 565 1 202
2 gi.vertline.1223961 CDP-tyvelose epimerase [Yersinia
pseudotuberculosis] 55 41 201 582 1 452 153 gi.vertline.1256643
20.2% identity with NADH dehydrogenase of the Leishmania major 55
36 300 mitochondrion; putative [Bacillus subtilis] 645 5 2057 1854
gi.vertline.210824 fusion protein F [Bovine respiratory syncytial
virus] pir.vertline.JQ1481.vertline.VGNZBA 55 25 204 fusion
glycoprotein precursor - bovine espiratory syncytial virus (strain
A51908) 672 2 957 2216 gi.vertline.1511333 M. jannaschii predicted
coding region MJ1322 [Methanococcus jannaschii] 55 36 1260 730 1
479 3 gi.vertline.537007 ORF_f379 [Escherichia coli] 55 30 477 737
1 945 31 gi.vertline.536963 CG Site No. 18166 [Escherichia coli] 55
30 915 742 2 228 572 gi.vertline.304160 product unknown [Bacillus
subtilis] 55 38 345 817 2 903 595 gi.vertline.1136289 histidine
kinase A [Dictyostelium discoideum] 55 29 309 819 1 355 128
gi.vertline.558073 polymorphic antigen [Plasmodium falciparum] 55
22 228 832 2 724 296 gi.vertline.40367 ORFC [Clostridium
acetobutylicum] 55 32 429 840 1 386 3 gi.vertline.1205875
pseudouridylate synthase I [Haemophilus influenzae] 55 39 384 1021
1 23 529 gi.vertline.48563 beta-lactamase [Yersinia enterocolitica]
55 38 507 1026 1 60 335 gi.vertline.47804 Opp C (AA1-301)
[Salmonella typhimurium] 55 26 276 1525 1 1 282 gi.vertline.1477533
sarA [Staphylococcus aureus] 55 29 282 1814 2 224 985
gi.vertline.1046078 M. genitalium predicted coding region MG369
[Mycoplasma genitalium] 55 38 762 3254 1 254 81 gi.vertline.413968
ipa-44d gene product [Bacillus subtilis] 55 30 174 3695 1 345 4
gi.vertline.216773 haloacetate dehalogenase H-1 [Moraxella sp.] 55
32 342 3721 1 1 312 gi.vertline.42029 ORF1 gene product
[Escherichia coli] 55 31 312 3799 1 3 272 gi.vertline.42029 ORF1
gene product [Escherichia coli] 55 38 270 3889 1 22 423
gi.vertline.1129145 acetyl-CoA C-acyltransferase [Mangifera indica]
55 45 402 3916 1 2 385 gi.vertline.529754 speC [Streptococcus
pyogenes] 55 38 384 3945 1 4 198 gi.vertline.476252 phase 1
flagellin [Salmonella enterica] 55 36 195 4074 1 246 4
gi.vertline.42029 ORF1 gene product [Escherichia coli] 55 38 243
4184 1 2 343 gi.vertline.1524267 unknown [Hycobacterium
tuberculosis] 55 28 342 4284 1 14 208 gi.vertline.1100774
ferredoxin-dependent glutamate synthase [Synechocystis sp.] 55 36
195 4457 2 378 112 gi.vertline.180189
cerebellar-degeneration-related antigen (CDR34) [Homo sapiens]
gi.vertline.182737 55 38 267 cerebellar degeneration-associated
protein [Homo sapiens] pir.vertline.A29770.vertline.A29770
cerebellar degeneration-related protein - human 4514 1 2 244
gi.vertline.216773 haloacetate dehalogenase H-1 [Moraxella sp.] 55
32 243 4599 1 217 2 gi.vertline.1129145 acetyl-CoA
C-acyltransferase [Mangifera indica] 55 42 216 4606 1 210 4
gi.vertline.386120 myosin alpha heavy chain (S2 subfragment)
[rabbits, masseter, eptide 55 27 207 Partial, 234 aa] 5 8 4932 4516
gi.vertline.536069 ORF YBL047c [Saccharomyces cerevisiae] 54 27 417
12 7 6165 5164 gi.vertline.1205504 homoserine acetyltransferase
[Haemophilus influenzae] 54 30 1002 23 16 15326 13566
gi.vertline.474192 iucC gene product [Escherichia coli] 54 31 1761
35 1 2 979 gi.vertline.48054 small subunit of soluble hydrogenase
(AA 1-384) [Synechococcus sp.] 54 36 978
ir.vertline.S06919.vertline.HQYCSS soluble hydrogenase (EC
1.12.--.--) small chain - nechococcus sp. (PCC 6716) 37 11 8667
7897 gi.vertline.537207 ORF_f277 [Escherichia coli] 54 38 771 37 12
8165 8332 gi.vertline.1160967 palmitoyl-protein thioesterase [Homo
sapiens] 54 37 168 46 15 13025 13804 gi.vertline.438473 protein is
hydrophobic, with homology to E. coli ProW; putative Bacillus 54 28
780 subtilis] 56 2 203 736 gi.vertline.1256139 YbbJ [Bacillus
subtilis] 54 34 534 57 13 10179 9241 gi.vertline.1151248
inosine-uridine preferring nucleoside hydrolase [Crithidia
fasciculata] 54 32 939 66 2 516 1133 gi.vertline.1335781 Cap
[Drosophila melanogaster] 54 29 618 70 10 8116 8646
gi.vertline.1399823 PhoE [Rhizobium meliloti] 54 31 531 70 15 11801
11046 sp.vertline.P02983.vertline.TCR_S TETRACYCLINE RESISTANCE
PROTEIN. 54 29 756 87 5 4915 5706 gi.vertline.1064811 function
unknown [Bacillus subtilis] 54 33 792 92 4 2289 1573
gi.vertline.1205366 oligopeptide transport ATP-binding protein
[Haemophilus influenzae] 54 33 717 103 2 1556 516
gi.vertline.710495 protein kinase [Bacillus brevis] 54 33 1041 105
2 2095 605 gi.vertline.143727 putative [Bacillus subtilis] 54 30
1491 112 4 2337 2732 gi.vertline.153724 MalC [Streptococcus
pneumoniae] 54 41 396 127 2 1720 2493 gi.vertline.144297 acetyl
esterase (XynC) [Caldocellum saccharolyticum]
pir.vertline.B37202.vertline.B37202 54 34 774 acetylesterase (EC
3.1.1.6) (XynC) - Caldocellum accharolyticum 138 5 1600 3306
gi.vertline.42473 pyruvate oxidase [Escherichia coli] 54 36 1707
152 2 525 1172 gi.vertline.1377834 unknown [Bacillus subtilis] 54
23 648 161 9 4831 5469 gi.vertline.903305 ORF73 [Bacillus subtilis]
54 28 639 161 13 6694 7251 gi.vertline.1511039 phosphate transport
system regulatory protein [Methanococcus jannaschii] 54 32 558 164
6 3263 4543 gi.vertline.1204976 prolyl-tRNA synthetase [Haemophilus
influenzae] 54 34 1281 164 20 21602 22243 gi.vertline.143582
spoIIIEA protein [Bacillus subtilis] 54 32 642 171 6 4250 2817
gi.vertline.436965 [malA] gene products [Bacillus
stearothermophilus] pir.vertline.S43914.vertline.S43914 54 37 1434
hypothetical protein 1 - Bacillus stearothermophilus 206 18 19208
19720 gi.vertline.1240016 R09E10.3 [Caenorhabditis elegans] 54 38
513 218 2 1090 1905 gi.vertline.467378 unknown [Bacillus subtilis]
54 26 816 220 1 663 4 gi.vertline.1353761 myosin II heavy chain
[Naegleria fowleri] 54 22 660 220 13 12655 13059
pir.vertline.S00485.vertline- .S004 gene 11-1 protein precursor -
Plasmodium falciparum (fragments) 54 35 405 221 3 2030 3709
gi.vertline.1303813 YqeW [Bacillus subtilis] 54 34 1680 272 7 4219
3383 gi.vertline.62964 arylamine N-acetyltransferase (AA 1-290)
[Gallus gallus] ir.vertline.S06652.vertlin- e.XYCHY3 54 33 837
arylamine N-acetyltransferase (EC 2.3.1.5) (clone NAT-3) - chicken
316 7 4141 4701 gi.vertline.682769 mccE gene product [Escherichia
coli] 54 31 561 316 10 6994 8742 gi.vertline.413951 ipa-27d gene
product [Bacillus subtilis] 54 28 1749 338 3 2214 1051
gi.vertline.490328 LORF F [unidentified] 54 28 1164 341 4 3201 3614
gi.vertline.171959 myosin-like protein [Saccharomyces cerevisiae]
54 25 414 346 1 912 4 gi.vertline.396400 similar to eukaryotic
Na+/H+ exchangers [Escherichia coli] 54 34 909
sp.vertline.P32703.vertline.YJCE_ECOLI HYPOTHETICAL 60.5 KD PROTEIN
IN SOXR-ACS NTERGENIC REGION (0549). 348 2 623 1351
gi.vertline.537109 ORF_f343a [Escherichia coli] 54 34 729 378 2
1007 1942 sp.vertline.P02983.vertline.TCR_S TETRACYCLINE RESISTANCE
PROTEIN 54 31 936 408 6 4351 5301 gi.vertline.474190 iucA gene
product [Escherichia coli] 54 29 951 444 9 7934 8854
gi.vertline.216267 ORF2 [Bacillus megaterium] 54 32 921 463 2 2229
1741 gi.vertline.304160 product unknown [Bacillus subtilis] 54 50
489 502 2 1133 570 gi.vertline.1205015 hypothetical protein (SP:
P10120) [Haemophilus influenzae] 54 38 564 505 6 5357 4452
gi.vertline.1500558 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase
[Methanococcus jannaschii] 54 41 906 550 1 1522 308
gi.vertline.40100 rodC (tag3) polypeptide (AA 1-746) [Bacillus
subtilis] ir.vertline.S06049.vertline.S06049 54 35 1215 rodC
protein - Bacillus subtilis p.vertline.P13485.vertline.TAGF_BACSU
TECHOIC ACID BIOSYNTHESIS PROTEIN F. 551 5 3305 4279
gi.vertline.950197 unknown [Corynebacterium glutamicum] 54 34 975
558 2 958 560 gi.vertline.485090 No definition line found
[Caenorhabditis elegans] 54 32 399 580 1 91 936 gi.vertline.331906
fused envelope glycoprotein precursor [Friend spleen focus-forming
irus] 54 45 846 603 3 554 757 gi.vertline.1323423 ORF YGR234w
[Saccharomyces cerevisiae] 54 36 204 617 1 25 249
gi.vertline.219959 ornithine transcarbamylase [Homo sapiens] 54 40
225 622 3 1097 1480 gi.vertline.1303873 YqgZ [Bacillus subtilis] 54
25 384 623 1 3 404 gi.vertline.1063250 low homology to P20 protein
of Bacillus lichiniformis and bleomycin 54 45 402 acetyltransferase
of Streptomyces verticillus [Bacillus subtilis] 689 1 1011 475
gi.vertline.552446 NADH dehydrogenase subunit 4 [Apis mellifera
ligustica]pir.vertline.S52968.vertline.S52968 54 30 537 NADH
dehydrogenase chain 4 - honeybee itochondrion (SGC4) 725 2 686 1441
gi.vertline.987096 sensory protein kinase [Streptomyces
hygroscopicus] 54 26 756 956 1 1 249
pir.vertline.S30782.vertline.S307 integrin homolog - yeast
[Saccharomyces cerevisiae] 54 24 249 978 2 859 581
gi.vertline.1301994 ORF YNL091w [Saccharomyces cerevisiae] 54 33
279 1314 1 3 281 gi.vertline.1001108 hypothetical protein
[Synechocystis sp.] 54 33 279 2450 1 1 228 gi.vertline.1045057
ch-TOG [Homo sapiens] 54 32 228 2934 1 1 387 gi.vertline.580870
ipa-37d qoxA gene product [Bacillus subtilis] 54 36 387 2970 1 251
3 sp.vertline.P37348.vertline.YECE.- sub.-- HYPOTHETICAL PROTEIN IN
ASPS 5'REGION (FRAGMENT). 54 42 249 3002 1 1 309 gi.vertline.44027
Tma protein [Lactococcus lactis] 54 33 309 3561 1 9 464
gi.vertline.151259 HMG-CoA reductase (EC 1.1.1.88) [Pseudomonas
mevalonii] pir.vertline.A44756.vertline.A44756 54 35 456
hydroxymethylglutaryl-CoA reductase (EC 1.1.1.88) Pseudomonas sp.
3572 1 72 401 gi.vertline.450688 hsdM gene of EcoprrI gene product
[Escherichia coli] pir.vertline.S38437.vertline.S38437 hsdM 54 36
330 protein - Escherichia coli pir.vertline.S09629.vertline.S09629
hypothetical protein A - Escherichia coli (SUB 40-520) 3829 1 400 2
gi.vertline.1322245 mevalonate pyrophosphate decarboxylase [Rattus
norvegicus] 54 29 399 3909 1 1 273 gi.vertline.29865 CENP-E [Homo
sapiens] 54 30 273 3921 1 3 209 pir.vertline.S24325.vertline.S243
glucan 1,4-beta-glucosidase (EC 3.2.1.74) - Pseudomonas fluorescens
subsp. 54 34 207 cellulosa 4438 1 285 4 gi.vertline.1196657 unknown
protein [Mycoplasma pneumoniae] 54 30 282 4459 1 3 272
gi.vertline.1046081 hypothetical protein (GB: D26185_10)
[Mycoplasma genitalium] 54 38 270 4564 1 3 221 gi.vertline.216267
ORF2 [Bacillus megaterium] 54 38 219 23 12 10685 8832
gi.vertline.474192 iucC gene product [Escherichia coli] 53 35 1854
23 14 13579 12317 gi.vertline.42029 ORF1 gene product [Escherichia
coli] 53 32 1263 24 3 3940 3440 gi.vertline.1369947 c2 gene product
[Bacteriophage B1] 53 36 501 26 4 3818 4618 gi.vertline.1486247
unknown [Bacillus subtilis] 53 37 801 38 6 2856 3998
gi.vertline.405880 yeil [Escherichia coli] 53 40 1143 38 10 7806
6232 gi.vertline.1399954 thyroid sodium/iodide symporter NIS
[Rattus norvegicus] 53 29 1575 56 10 12100 11876
pir.vertline.A54592.vertline.A545 110k actin filament-associated
protein - chicken 53 32 225 57 6 4583 4119
pir.vertline.A00341.vertline.DE- ZP alcohol dehydrogenase (EC
1.1.1.1) - fission yeast [Schizosaccharomyces 53 39 465 pombe] 57
12 8932 7349 gi.vertline.1480429 putative transcriptional regulator
[Bacillus stearothermophilus] 53 30 1584 67 12 9496 10218
gi.vertline.1511555 quinolone resistance norA protein protein
[Methanococcus jannaschii] 53 31 723 69 3 2382 1639
gi.vertline.1087017 arabinogalactan-protein, AGP [Nicotiana alata,
cell-suspension culture 53 30 744 filtrate, Peptide, 461 aa] 79 1 3
1031 gi.vertline.1523802 glucanase [Anabaena variabilis] 53 32 1029
80 1 338 3 gi.vertline.452428 ATPase 3 [Plasmodium falciparum] 53
36 336 88 4 1910 2524 gi.vertline.537034 ORF_o488 [Escherichia
coli] 53 25 615 88 5 2467 3282 gi.vertline.537034 ORF_o488
[Escherichia coli] 53 29 816 92 8 5505 5140 gi.vertline.399598
amphotropic murine retrovirus receptor [Rattus norvegicus] 53 33
366 94 5 3239 2061 gi.vertline.173038 tropomyosin (TPM1)
[Saccharomyces cerevisiae] 53 25 1179 99 5 4207 5433
sp.vertline.P28246.vertline.BCR_E BICYCLOMYCIN RESISTANCE PROTEIN
(SULFONAMIDE RESISTANCE PROTEIN) 53 30 1227 120 3 1639 2262
gi.vertline.576655 ORF1 [Vibrio anguillarum] 53 35 624 120 11 7257
8897 gi.vertline.1524397 glycine betaine transporter OpuD [Bacillus
subtilis] 53 33 1641 127 6 5685 4477 gi.vertline.1256630 putative
[Bacillus subtilis] 53 32 1209 147 2 255 557 gi.vertline.581648
epiB gene product [Staphylococcus epidermidis] 53 34 303 158 4 4256
3807 gi.vertline.151004 mucoidy regulatory protein AlgR
[Pseudomonas aeruginosa] pir.vertline.A32802.vertline.A32802 53 32
450 regulatory protein algR --Pseudomonas aeruginosa
sp.vertline.P26275.vertl- ine.ALGR_PSEAE POSITIVE ALGINATE
BIOSYNTHESIS REGULATORY ROTEIN. 171 7 5421 5125 gi.vertline.1510669
hypothetical protein (GP: D64044_18) [Methanococcus jannaschii] 53
34 297 191 9 11483 9879 gi.vertline.298085 acetoacetate
decarboxylase [Clostridium acetobutylicum]
pir.vertline.B49346.vertline.B49346 53 31 1605
butyrate--acetoacetate CoA-transferase (EC .8.3.9) small chain -
Clostridium acetobutylicum sp.vertline.P33752.vertline.CTFA_CLOAB
BUTYRATE-ACETOACETATE COA- TRANSFERASE SUBUNIT (EC 2.8.3.9) (COAT
A) 203 5 3763 4326 gi.vertline.143456 rpoE protein (ttg start
codon) [Bacillus subtilis] 53 29 564 206 17 18204 18971
gi.vertline.304136 acetylglutamate kinase [Bacillus
stearothermophilus] sp.vertline.Q07905.vertline.ARGB_BACST 53 36
768 ACETYLGLUTAMATE KINASE (EC 2.7.2.8) (NAG INASE) (AGK)
(N-ACETYL-L- GLUTAMATE 5-PHOSPHOTRANSFERASE). 212 10 4021 4221
gi.vertline.9878 protein kinase [Plasmodium falciparum] 53 28 201
231 2 1350 1120 gi.vertline.537506 paramyosin [Dirofilaria immitis]
53 34 231 272 6 2719 3249 pir.vertline.A33141.vertline.A331
hypothetical protein (gtfD 3' region) - Streptococcus mutans 53 34
531 308 3 927 2576 gi.vertline.606292 ORF_o696 [Escherichia coli]
53 33 1650 320 7 5645 5884 gi.vertline.160596 RNA polymerase III
largest subunit [Plasmodium falciparum] 53 33 240
sp.vertline.P27625.vertline- .RPC1_PLAFA DNA-DIRECTED RNA
POLYMERASE III LARGEST UBUNIT (EC 2.7.7.6). 327 1 218 901
gi.vertline.854601 unknown [Schizosaccharomyces pombe] 53 31 684
341 2 212 2500 gi.vertline.633732 ORF1 [Campylobacter jejuni] 53 31
2289 351 1 383 3 sp.vertline.P31675.vertline.YABM.sub.--
HYPOTHETICAL 42.7 KD PROTEIN IN TBPA-LEUD INTERGENIC REGION
(ORF104). 53 32 381 433 7 4731 4375 gi.vertline.1001961 MHC class
II analog [Staphylococcus aureus] 53 30 357 454 2 980 720
pir.vertline.A60328.vertline.A603 40K cell wall protein precursor
(sr 5' region) - Streptococcus mutans 53 27 261 (strain OMZ175,
serotype f) 470 4 1123 1761 gi.vertline.516826 rat GCP360 [Rattus
rattus] 53 30 639 483 1 217 2 gi.vertline.1480429 putative
transcriptional regulator [Bacillus stearothermophilus] 53 33 216
544 1 516 1259 gi.vertline.46587 ORF 1 (AA 1-121) (1 is 2nd base in
codon) [Staphylococcus aureus] 53 38 744
ir.vertline.S15765.vertline.S15765 hypothetical protein 1 (hlb 5'
region) - Staphylococcus aureus (fragment) 558 10 3754 3551
gi.vertline.15140 res gene [Bacteriophage P1] 53 32 204 603 2 339
620 gi.vertline.507738 Hmp [Vibrio parahaemolyticus] 53 26 282 693
1 941 213 gi.vertline.153123 toxic shock syndrome toxin-1 precursor
[Staphylococcus aureus] 53 38 729
pir.vertline.A24606.vertline.XCSAS1 toxic shock syndrome toxin-1
precursor - Staphylococcus aureus 766 1 2 673 gi.vertline.687600
orfA2; orfA2 forms an operon with orfA1 [Listeria monocytogenes] 53
43 672 781 1 335 3 gi.vertline.1204551 pilin biogenesis protein
[Haemophilus influenzae] 53 26 333 801 1 3 545 gi.vertline.1279400
SapA protein [Escherichia coli] 53 25 543 803 1 2 910
gi.vertline.695278 lipase-like enzyme [Alcaligenes eutrophus] 53 30
909 872 1 590 3 gi.vertline.298032 EF [Streptococcus suis] 53 30
588 910 1 2 184 gi.vertline.1044936 unknown [Schizosaccharomyces
pombe] 53 29 183 943 1 399 4 gi.vertline.290508 similar to
unidentified ORF near 47 minutes [Escherichia coli] 53 30 396
sp.vertline.P31436.vertline.YICK-
_ECOLI HYPOTHETICAL 43.5 KD PROTEIN IN SELC-NLPA NTERGENIC REGION.
988 1 504 4 gi.vertline.142441 ORF 3; putative [Bacillus subtilis]
53 28 501 1064 1 3 434 gi.vertline.305080 myosin heavy chain
[Entamoeba histolytica] 53 26 432 1366 1 3 452 gi.vertline.308852
transmembrane protein [Lactococcus lactis] 53 33 450 1758 1 397 2
gi.vertline.1001774 hypothetical protein [Synechocystis sp.] 53 30
396 1897 1 1 447 gi.vertline.1303949 YqiX [Bacillus subtilis] 53 27
447 2381 1 400 2 gi.vertline.1146243 22.4% identity with
Escherichia coli DNA-damage inducible protein ...; 53 37 399
putative [Bacillus subtilis] 3537 1 1 327 gi.vertline.450688 hsdM
gene of EcoprrI gene product [Escherichia coli]
pir.vertline.S38437.vertline.S38437 hsdM 53 35 327 protein -
Escherichia coli pir.vertline.S09629.vertline.S09629 hypothetical
protein A - Escherichia coli [SUB 40-520] 3747 2 137 397
gi.vertline.1477486 transposase [Burkholderia cepacia] 53 53 261 11
5 3049 3441 gi.vertline.868224 No definition line found
[Caenorhabditis elegans] 52 33 393 15 5 2205 2369
gi.vertline.215966 G41 protein (gtg start codon) [Bacteriophage T4]
52 34 165 19 3 2429 3808 gi.vertline.1205379
UDP-murnac-pentapeptide synthetase [Haemophilus influenzae] 52 31
1380 24 1 3462 4 gi.vertline.579124 predicted 86.4 kd protein; 52
Kd observed [Mycobacteriophage 15] 52 32 3459
pir.vertline.S30971.vertlin- e.S30971 gene 26 protein -
Mycobacterium phage L5 sp.vertline.Q05233.vertline.VG26_BPML5 MINOR
TAIL PROTEIN GP26. (SUB 2-837) 37 5 3015 3935 gi.vertline.1500543
P115 protein [Methanococcus jannaschii] 52 25 921 38 13 8795 9703
gi.vertline.46851 glucose kinase [Streptomyces coelicolor] 52 29
909 44 16 10617 11066 gi.vertline.42012 moaE gene product
[Escherichia coli] 52 36 450 46 1 3 521 gi.vertline.1040957 NADH
dehydrogenase subunit 6 [Anopheles trinkae] 52 25 519 51 10 5531
6280 gi.vertline.388269 traC [Plasmid pAD1] 52 32 750 56 5 2826
1684 gi.vertline.181949 endothelial differentiation protein (edg-1)
[Homo sapiens] 52 23 1143 pir.vertline.A35300.vertline.A35300 G
protein-coupled receptor edg-1 - human
sp.vertline.P21453.vertline.EDG1_HUMAN PROBABLE G PROTEIN-COUPLED
RECEPTOR EDG-1. 57 5 4173 3496 gi.vertline.304153 sorbitol
dehydrogenase [Bacillus subtilis] 52 27 678 62 5 2870 2376
gi.vertline.1072399 phaE gene product [Rhizobium meliloti] 52 25
495 62 6 3651 2857 gi.vertline.46485 NADH dehydrogenase
[Synechococcus PCC7942] 52 27 795 67 14 11355 12962
gi.vertline.1511365 glutamate synthase (NADPH), subunit alpha
[Methanococcus jannaschii] 52 30 1608 67 21 16935 18158
gi.vertline.1204393 hypothetical protein (SP: P31122) [Haemophilus
influenzae] 52 25 1224 70 4 1997 1809 gi.vertline.7227 cytoplasmic
dynein heavy chain [Dictyostelium
discoldeum]r.vertline.A44357.vertline.A44357 52 36 189 dynein heavy
chain, cytosolic - slime mold Dictyostelium discoideum) 96 10 10005
10664 gi.vertline.1408485 B65G gene product [Bacillus subtilis] 52
26 660 103 5 3351 2716 gi.vertline.1009368 Respiratory nitrate
reductase [Bacillus subtilis] 52 42 636 109 3 3350 2598
gi.vertline.699274 lmbE gene product [Mycobacterium leprae] 52 39
753 109 19 15732 17300 gi.vertline.1526981 amino acid permease YeeF
like protein [Salmonella typhimurium] 52 30 1569 121 3 981 550
gi.vertline.732931 unknown [Saccharomyces cerevisiae] 52 32 432 125
3 865 1680 gi.vertline.1296975 puT gene product [Porphyromonas
gingivalis] 52 38 816 130 2 659 1807 gi.vertline.1256634 25.8%
identity over 120 aa with the Synenococcus sp. MpeV protein;
putative 52 36 1149 [Bacillus subtilis] 149 1 583 2
gi.vertline.1225943 PBSX terminase [Bacillus subtilis] 52 33 582
149 14 4415 4143 gi.vertline.1510368 M. jannaschii predicted coding
region MJ0272 [Methanococcus jannaschii] 52 35 273 167 1 216 1001
gi.vertline.146025 cell division protein [Escherichia coli] 52 43
786 188 1 120 1256 gi.vertline.474915 orf 337; translated orf
similarity to SW: BCR_ECOLI bicyclomycin esistance 52 26 1137
protein of Escherichia coli [Coxiella burnetii]
pir.vertline.S44207.vertline.S44207 hypothetical protein 337 -
Coxiella burnetii (SUB -338) 195 9 8760 8359 gi.vertline.3028
mitochondrial outer membrane 72K protein [Neurospora crassa] 52 25
402 r.vertline.A36682.vertl- ine.A36682 72K mitochondrial outer
membrane protein - Neurospora crassa 200 3 2065 2607
gi.vertline.142439 ATP-dependent nuclease [Bacillus subtilis] 52 35
543 203 4 2776 3684 gi.vertline.303698 BltD [Bacillus subtilis] 52
25 909 227 8 5250 5651 gi.vertline.305080 myosin heavy chain
[Entamoeba histolytica] 52 24 402 242 1 21 1424 gi.vertline.1060877
EmrY [Escherichia coli] 52 32 1404 249 5 4526 4753
pir.vertline.C37222.vertline.C372 cytochrome P450 1A1, hepatic -
dog (fragment) 52 23 228 255 1 1055 3 gi.vertline.143290
penicillin-binding protein [Bacillus subtills] 52 28 1053 276 7
3664 3365 gi.vertline.1001610 hypothetical protein [Synechocystis
sp.] 52 30 300 276 8 4055 3654 gi.vertline.416235 orf L3
[Mycoplasma capricolum] 52 26 402 289 2 1449 1042
gi.vertline.150900 GTP phosphohydrolase [Proteus vulgaris] 52 34
408 325 1 1 279 gi.vertline.1204874 polypeptide deformylase
(formylmethionine deformylase) [Haemophilus 52 33 279 influenzae]
340 1 1010 3 gi.vertline.1215695 peptide transport system protein
SapF homolog; SapF homolog [Mycoplasma 52 33 1008 pneumoniae] 375 3
340 1878 gi.vertline.467446 similar to SpoVB [Bacillus subtilis] 52
28 1539 424 4 3262 2420 gi.vertline.1478239 unknown [Mycobacterium
tuberculosis] 52 34 843 430 1 3 575 pir.vertline.A42606.vertline.A-
426 orfA 5' to orf405 - Saccharopolyspora erythraea (fragment) 52
28 573 444 4 3712 2696 gi.vertline.1408494 homologous to penicillin
acylase [Bacillus subtilis] 52 31 1017 465 1 903 4
gi.vertline.143331 alkaline phosphatase regulatory protein
[Bacillus subtilis] 52 36 900 pir.vertline.A27650.vertline.A27650
regulatory protein phoR - Bacillus subtilis
sp.vertline.P23545.vertline.PHOR_BACSU ALKALINE PHOSPHATASE
SYNTHESIS SENSOR PROTEIN HOR (EC 2.7.3.--) 469 5 4169 3633
gi.vertline.755152 highly hydrophobic integral membrane protein
[Bacillus subtilis] 52 32 537
sp.vertline.P42953.vertline.TAGG_BACSU TEICHOIC ACID TRANSLOCATION
PERMEASE PROTEIN AGG. 495 1 633 4 gi.vertline.1204607 transcription
activator [Haemophilus influenzae] 52 25 630 505 7 5762 5520
gi.vertline.142440 ATP-dependent nuclease [Bacillus subtilis] 52 28
243 517 2 1162 1614 gi.vertline.166162 Bacteriophage phi-11 int
gene activator [Staphylococcus acteriophage phi 52 35 453 11] 543 2
444 1295 gi.vertline.1215693 putative orf; GT9_orf434 [Mycoplasma
pneumoniae] 52 25 852 586 1 1 336 gi.vertline.581648 epiB gene
product [Staphylococcus epidermidis] 52 36 336 773 1 426 4
gi.vertline.1279769 FdhC [Methanobacterium thermofomicicum] 52 30
423 1120 2 100 330 gi.vertline.142439 ATP-dependent nuclease
[Bacillus subtilis] 52 35 231 1614 1 347 3 gi.vertline.289262 comE
ORF3 [Bacillus subtilis] 52 28 345 2495 1 1 324 gi.vertline.216151
DNA polymerase (gene L; ttg start codon) [Bacteriophage SP02]
gi.vertline.579197 52 34 324 SP02 DNA polymerase (aa 1-648)
[Bacteriophage SPO2] pir.vertline.A21498.vertline.DJBPS2 DNA-
directed DNA polymerase (EC 2.7.7.7) - phage PO2 2931 1 285 4
gi.vertline.1256136 YbbG [Bacillus subtilis] 52 30 282 2943 1 320
63 gi.vertline.41713 hisA ORF (AA 1-245) [Escherichia coli] 52 35
258 2993 1 295 2 gi.vertline.298032 EF [Streptococcus suis] 52 34
294 3667 1 307 2 gi.vertline.849025 hypothetical 64.7-kDa protein
[Bacillus subtilis] 52 36 306 3944 1 260 42 gi.vertline.1218040 BAA
[Bacillus licheniformis] 52 36 219 3954 2 347 81 gi.vertline.854064
U87 [Human herpesvirus 6] 52 50 267 3986 1 90 401
gi.vertline.1205919 Na+ and Cl- dependent gamma-aminobutryic acid
transporter [Haemophilus 52 33 312 influenzae] 4002 1 3 389
gi.vertline.40003 oxoglutarate dehydrogenase (NADP+) [Bacillus
subtilis] p.vertline.P23129.vertline.ODO1_BACSU 52 42 387
2-OXOGLUTARATE DEHYDROGENASE E1 COMPONENT (EC 2.4.2)
(ALPHA-KETOGLUTARATE DEHYDROGENASE). 4020 1 1 249
gi.vertline.159388 ornithine decarboxylase [Leishmania donovani] 52
47 249 4098 1 220 2 gi.vertline.409795 No definition line found
[Escherichia coli] 52 32 219 4248 1 3 212 gi.vertline.965077 Adr6p
[Seccharomyces cerevisiae] 52 40 210 7 1 3 575 gi.vertline.895747
putative cel operon regulator [Bacillus subtilis] 51 28 573 21 4
2479 3276 gi.vertline.1510962 indole-3-glycerol phosphate synthase
[Methanococcus jannaschii] 51 32 798 22 9 5301 5966
gi.vertline.1303933 YqiN [Bacillus subtilis] 51 25 666 43 3 1283
1050 gi.vertline.1519460 Srp1 [Schizosaccharomyces pombe] 51 31 234
44 17 11042 11305 gi.vertline.42011 moaD gene product [Escherichia
coli] 51 35 264 51 11 6453 6731 gi.vertline.495471 vacuolating
toxin [Helicobacter pylori] 51 37 279 52 4 2537 2995
gi.vertline.1256652 25% identity to the E. coli regulatory protein
MprA; putative [Bacillus 51 32 459 subtilis] 57 10 6843 6355
gi.vertline.508173 EIIA domain of PTS-dependent Gat transport and
phosphorylation Escherichia 51 32 489 coli] 59 1 29 1111
gi.vertline.299163 alanine dehydrogenase [Bacillus subtilis] 51 33
1083 67 20 15791 16576 gi.vertline.1510977 M. jannaschii predicted
coding region MJ0938 [Methanococcus jannaschii] 51 24 786 69 2 1218
877 gi.vertline.467359 unknown [Bacillus subtilis] 51 34 342 71 1 3
1196 gi.vertline.298032 EF [Streptococcus suis] 51 32 1194 78 2 176
3 gi.vertline.1161242 proliferating cell nuclear antigen [Styela
clava] 51 28 174 99 4 3357 4040 gi.vertline.642795 TFIID subunit
TAFII55 [Homo sapiens] 51 25 684 109 1 1428 4 gi.vertline.580920
rodD (gtaA) polypeptide (AA 1-673) [Bacillus subtilis]
pir.vertline.S06048.vertline.S06048 51 27 1425 probable rodD
protein - Bacillus subtilis sp.vertline.P13484.vertline.TAGE_BACSU
PROBABLE POLY (GLYCEROL-PHOSPHATE) LPHA-GLUCOSYLTRANSFERASE (EC
2.4.1.52) (TECHOIC ACID BIOSYNTHESIS ROTEIN E) 109 9 6007 6693
gi.vertline.1204815 hypothetical protein (SP: P32662) [Haemophilus
influenzae] 51 23 687 112 3 1066 2352
pir.vertline.S05330.vertline.S053 maltose-binding protein precursor
- Enterobacter aerogenes 51 42 1287 112 13 12855 11278
gi.vertline.405857 yehU [Escherichia coli] 51 29 1578 114 9 8967
8209 gi.vertline.435098 orf1 [Mycoplasma capricolum] 51 30 759 115
1 1 912 gi.vertline.1431110 ORF YDL085w [Saccharomyces cerevisiae]
51 25 912 127 10 9647 10477 gi.vertline.1204314 H. influenzae
predicted coding region HI0056 [Haemophilus influenzae] 51 37 831
152 9 6814 7356 gi.vertline.431929 MunI regulatory protein
[Mycoplasma sp.] 51 38 543 154 2 575 1153 gi.vertline.1237044
unknown [Mycobacterium tuberculosis] 51 36 579 154 7 5634 4681
gi.vertline.409286 bmrU [Bacillus subtilis] 51 27 954 171 8 6236
5529 gi.vertline.1205484 hypothetical protein (SP: P33918)
[Haemophilus influenzae] 51 32 708 184 1 1 291 gi.vertline.466886
B1496_C3_206 [Mycobacterium leprae] 51 33 291 212 5 1501 2139
pir.vertline.A45605.vertline.A456 mature-parasite-infected
erythrocyte surface antigen MESA - Plasmodium 51 23 639 falciparum
228 2 707 1378 gi.vertline.8204 nuclear protein [Drosophila
melanogaster] 51 27 672 236 8 7481 6825 gi.vertline.49272
Asparaginase [Bacillus licheniformis] 51 31 657 243 4 3546 2455
gi.vertline.1511102 melvalonate kinase [Methanococcus jannaschii]
51 29 1092 257 4 3373 3206 gi.vertline.1204579 H. influenzae
predicted coding region HI0326 [Haemophilus influenzae] 51 22 168
258 3 1609 821 gi.vertline.160299 glutamic acid-rich protein
[Plasmodium falciparum] pir.vertline.A54514.vertline.A54514 51 34
789 glutamic acid-rich protein precursor - Plasmodium falciparum
265 5 2419 3591 gi.vertline.580841 F1 [Bacillus subtilis] 51 32
1173 298 2 518 748 gi.vertline.1336162 SCPB [Streptococcus
agalactiae.vertline. 51 34 231 316 9 5817 7049 gi.vertline.413953
ipa-29d gene product [Bacillus subtilis] 51 39 1233 332 2 2057 339
gi.vertline.1209012 mutS [Thermus aquaticus thermophilus] 51 26
1719 364 4 3816 4991 gi.vertline.528991 unknown [Bacillus subtilis]
51 32 1176 440 2 448 684 gi.vertline.2819 transferase (GAL10) (AA
1-687) [Kluyveromyces lactis] r.vertline.S01407.vertline.XUVKG 51
32 237 UDPglucose 4-epimerase (EC 5.1.3.2) - yeast uyveromyces
marxianus var. lactis) 495 2 1177 1001 gi.vertline.297861 protease
G [Erwinia chrysanthemi] 51 41 177 495 3 1718 1149
gi.vertline.1513317 serine rich protein [Entamoeba histolytica] 51
25 570 506 1 421 2 gi.vertline.455320 cII protein [Bacteriophage
P4] 51 33 420 600 1 983 492 gi.vertline.587532 orf, len: 201, CAI:
0.16 [Saccharomyces cerevisiae] pir.vertline.S48818.vertline.S48818
51 30 492 hypothetical protein - yeast (Saccharomyces erevisiae)
607 3 479 934 gi.vertline.1511524 hypothetical protein (SP: P37002)
[Methanococcus jannaschii] 51 40 456 686 2 127 600
gi.vertline.493017 endocarditis specific antigen [Enterococcus
faecalis] 51 30 474 726 1 33 230 gi.vertline.1353851 unknown
[Prochlorococcus marinus] 51 45 198 861 1 176 652
gi.vertline.410145 dehydroquinate dehydratase [Bacillus subtilis]
51 34 477 869 1 393 4 gi.vertline.40100 rodC (tag3) polypeptide (AA
1-746) [Bacillus subtilis] ir.vertline.S06049.vertline.S06049 51 23
390 rodC protein - Bacillus subtilis
p.vertline.P13485.vertline.TAG- F_BACSU TECHOIC ACID BIOSYNTHESIS
PROTEIN F. 1003 1 322 2 gi.vertline.1279707 hypothetical
phosphoglycerate mutase [Saccharomyces cerevisiae] 51 39 321 1046 2
624 382 gi.vertline.510257 glycosyltransferase [Escherichia coli]
51 29 243 1467 1 352 2 gi.vertline.1511175 M. jannaschii predicted
coding region MJ1177 [Methanococcus jannaschii] 51 32 351 2558 1
230 3 sp.vertline.P10582.vertline.DPOM.sub.-- DNA POLYMERASE (EC
2.7.7.7) (S-1 DNA ORF 3). 51 26 228 3003 1 399 19
gi.vertline.809543 CbrC protein [Erwinia chrysanthemi] 51 27 381
3604 1 1 399 pir.vertline.JC4210.vertline.JC42 3-hydroxyacyl-CoA
dehydrogenase (EC 1.1.1.35) - mouse 51 37 399 3732 1 2 316
gi.vertline.145906 acyl-CoA synthetase [Escherichia coli] 51 33 315
3791 1 2 274 gi.vertline.1061351 semaphorin III family homolog
[Homo sapiens] 51 37 273 3995 1 46 336 gi.vertline.216346 surfactin
synthetase [Bacillus subtilis] 51 38 291 4193 1 307 2
gi.vertline.42749 ribosomal protein L12 (AA 1-179) [Escherichia
coli] ir.vertline.S04776.vertline.XXECPL 51 25 306 peptide
N-acetyltransferase rimL (EC 2.3.1.--) - Echerichia coli 4539 1 185
3 gi.vertline.1408494 homologous to penicillin acylase [Bacillus
subtilis] 51 40 183 4562 1 239 36 gi.vertline.1458280 coded for by
C. elegans cDNA cm01e7; Similar to hydroxymethylglutaryl-CoA 51 35
204 synthase [Caenorhabditis elegans] 1 4 3576 4859
gi.vertline.559160 GRAIL score: null; cap site and late promoter
motifs present pstream; 50 44 1284 putative [Autographa californica
nuclear polyhedrosis irus] 11 7 4044 5165 gi.vertline.1146207
putative [Bacillus subtilis] 50 35 1122 11 13 9496 8483
gi.vertline.1208451 hypothetical protein [Synechocystis sp.] 50 39
1014 19 1 1018 2 gi.vertline.413966 ipa-42d gene product [Bacillus
subtilis] 50 29 1017 20 11 8407 8228 gi.vertline.1323159 ORF
YGR103w [Saccharomyces cerevisiae] 50 28 180 24 5 4824 4240
gi.vertline.496280 structural protein [Bacteriophage Tuc2009] 50 29
585 34 4 1926 2759 gi.vertline.1303966 Yqj0 [Bacillus subtilis] 50
36 834 38 30 22865 23440 gi.vertline.1072179 Similar to
dihydroflavonol-4-reductase (maize, petunia, tomato) 50 32 576
[Caenorhabditis elegans] 47 2 1705 2976 gi.vertline.153015 FemA
protein [Staphylococcus aureus] 50 29 1272 56 13 15290 15841
gi.vertline.606096 ORF_f167; end overlaps end of o100 by 14 bases;
start overlaps f174, ther 50 30 552 starts possible [Escherichia
coli] 57 1 1077 19 gi.vertline.640922 xylitol dehydrogenase
(unidentified hemiascomycete) 50 29 1059 58 2 628 1761
gi.vertline.143725 putative [Bacillus subtilis] 50 29 1134 88 6
3884 3375 gi.vertline.1072179 Similar to
dihydroflavonol-4-reductase (maize, petunia, tomato) 50 32 510
[Caenorhabditis elegans] 89 5 3356 3012 gi.vertline.1276658 ORF174
gene product [Porphyra purpurea] 50 25 345 141 1 3 239
gi.vertline.476024 carbamoyl
phosphate synthetase II [Plasmodium falciparum] 50 33 237 151 1 186
626 gi.vertline.1403441 unknown [Mycobacterium tuberculosis] 50 35
441 166 7 9623 8181 gi.vertline.895747 putative cel operon
regulator [Bacillus subtilis] 50 32 1443 201 6 5096 4908
gi.vertline.160229 circumsporozoite protein [Plasmodium reichenowi]
50 42 189 206 22 29555 28326 gi.vertline.1052754 LmrP integral
membrane protein [Lactococcus lactis] 50 24 1230 211 4 1523 1927
gi.vertline.410131 ORFX7 [Bacillus subtilis] 50 29 405 214 4 2411
3295 sp.vertline.P37348.vertline.YECE.sub.-- HYPOTHETICAL PROTEIN
IN ASPS 5' REGION (FRAGMENT) 50 37 885 228 7 4406 3744
gi.vertline.313580 envelope protein [Human immunodeficiency virus
type 1] pir.vertline.S35835.vertline.S35835 50 35 663 envelope
protein - human immunodeficiency virus type 1 (fragment) (SUB 1-
77) 272 2 1723 398 gi.vertline.1408485 B65G gene product [Bacillus
subtilis] 50 22 1326 273 2 984 352 gi.vertline.984186
phosphoglycerate mutase [Saccharomyces cerevisiae] 50 28 633 328 2
1605 703 gi.vertline.148896 lipoprotein [Haemophilus influenzae] 50
26 903 332 4 3802 2135 gi.vertline.1526547 DNA polymerase family X
[Thermus aquaticus] 50 27 1668 342 5 3473 3931 gi.vertline.456562
G-box binding factor [Dictyostelium discoideum] 50 35 459 352 1 741
4 gi.vertline.288301 ORF2 gene product [Bacillus megaterium] 50 29
738 408 7 5299 5523 gi.vertline.11665 ORF2136 [Marchantia
polymorpha] 50 27 225 420 3 650 1825 gi.vertline.757842 UDP-sugar
hydrolase [Escherichia coli] 50 30 1176 464 1 1 591
gi.vertline.487282 Na+ -ATPase subunit J [Enterococcus hirae] 50 29
591 472 2 864 310 gi.vertline.551875 Bg1R [Lactococcus lactis] 50
23 555 520 1 23 541 gi.vertline.567036 CapE [Staphylococcus aureus]
50 27 519 529 1 6 410 gi.vertline.1256652 25% identity to the E.
coli regulatory protein MprA; putative [Bacillus 50 34 405
subtilis] 534 5 6059 4392 gi.vertline.295671 selected as a weak
suppressor of a mutant of the subunit AC40 of DNA 50 18 1668
ependant RNA polymerase I and III [Saccharomyces cerevisiae] 647 1
1497 4 gi.vertline.405568 TraI protein shares sequence similarity
with a family of opoisomerases 50 31 1494 [Plasmid pSK41] 664 3 711
289 gi.vertline.410007 leukocidin F component [Staphylococcus
aureus, MRSA No. 4, Peptide, 23 aa] 50 32 423 678 1 1 627
gi.vertline.298032 EF [Streptococcus suis] 50 29 627 755 3 947 1171
gi.vertline.150572 cytochrome c1 precursor (EC 1.10.2.2)
[Paracoccus denitrificans] gi.vertline.45465 50 37 225 cytochrome
c1 (AA 1-450) [Paracoccus denitrificans]
pir.vertline.C29413.vertline.C29413 ubiquinol - cytochrome-c
reductase (EC 1.10.2.2) ytochrome c1 precursor - Paracoccus
denitrificans sp.vertline.P13627.vertl- ine.CY1 827 1 683 3
gi.vertline.142020 heterocyst differentiation protein [Anabaena
sp.] 50 21 681 892 1 3 752 gi.vertline.1408485 B65G gene product
[Bacillus subtilis] 50 27 750 910 2 438 887 gi.vertline.1204727
tyrosine-specific transport protein [Haemophilus influenzae] 50 25
450 933 1 524 760 gi.vertline.1205451 cell division inhibitor
[Haemophilus influenzae] 50 32 237 973 1 236 48 gi.vertline.886947
orf3 gene product [Saccharomyces cerevisiae] 50 40 189 1009 1 429
205 gi.vertline.153727 M protein [group G streptococcus] 50 28 225
1027 1 257 3 gi.vertline.413934 ipa-10r gene product [Bacillus
subtilis] 50 25 255 1153 2 326 96 gi.vertline.773676 nccA
[Alcaligenes xylosoxydans] 50 36 231 1222 1 400 2
gi.vertline.1408485 B65G gene product [Bacillus subtilis] 50 21 399
1350 1 399 106 gi.vertline.289272 ferrichrome-binding protein
[Bacillus subtilis] 50 32 294 2945 1 184 2 gi.vertline.171704
hexaprenyl pyrophosphate synthetase (COQ1) [Saccharomyces
erevisiae] 50 34 183 2968 2 804 4 gi.vertline.397526 clumping
factor [Staphylococcus aureus] 50 33 801 2998 2 394 131
gi.vertline.495696 F54E7.3 gene product [Caenorhabditis elegans] 50
40 264 3046 2 306 106 pir.vertline.S13819.vertline.S138 acyl
carrier protein - Anabaena variabilis (fragment) 50 32 201 3063 1
275 3 gi.vertline.474190 iucA gene product [Escherichia coli] 50 29
273 3174 1 3 146 gi.vertline.151900 alcohol dehydrogenase
[Rhodobacter sphaeroides] 50 31 144 3792 1 314 3
gi.vertline.1001423 hypothetical protein [Synechocystis sp.] 50 35
312 3800 1 2 262 gi.vertline.144733 NAD-dependent
beta-hydroxybutyryl coenzyme A dehydrogenase Clostridium 50 28 261
acetobutylicum] 3946 1 188 3 gi.vertline.576765 cytochrome b
[Myrmecia pilosula] 50 38 186 3984 1 291 4
sp.vertline.P37348.vertline.YECE.sub.-- HYPOTHETICAL PROTEIN IN
ASPS 5' REGION (FRAGMENT). 50 37 288 37 10 7885 7520
gi.vertline.1204367 hypothetical protein (GB: U14003_278)
[Haemophilus influenzae] 49 30 366 46 16 13802 14848
gi.vertline.466860 acd: B1308_F1_34 [Mycobacterium leprae] 49 24
1047 59 5 2267 3601 gi.vertline.606304 ORF_o462 [Escherichia coli]
49 27 1335 112 18 17884 18615 gi.vertline.559502 ND4 protein (AA
1-409) [Caenorhabditis elegans] 49 25 732 138 9 6973 7902
gi.vertline.303953 esterase [Acinetobacter calcoaceticus] 49 29 930
217 6 4401 5138 gi.vertline.496254 fibronectin/fibrinogen-blnding
protein [Streptococcus pyogenes] 49 31 738 220 12 11803 12657
gi.vertline.397526 clumping factor [Staphylococcus aureus] 49 31
855 228 4 1842 2492 pir.vertline.S23692.vertline.S236 hypothetical
protein 9 - Plasmodium falciparum 49 24 651 268 1 2614 212
gi.vertline.143047 ORFB [Bacillus subtilis] 49 26 2403 271 2 1164
1373 gi.vertline.1001257 hypothetical protein [Synechocystis sp.]
49 38 210 300 3 3180 2020 gi.vertline.1510796 hypothetical protein
(GP: X91006_2) [Methanococcus jannaschii] 49 26 1161 381 1 1142 3
gi.vertline.396301 matches PS00041: Bacterial regulatory proteins,
araC family ignature 49 29 1140 [Escherichia coli] 466 1 3 947
gi.vertline.1303863 YqgP [Bacillus subtilis] 49 26 945 666 1 191 3
gi.vertline.633112 ORF1 [Streptococcus sobrinus] 49 29 189 670 2
403 1014 gi.vertline.1122758 unknown [Bacillus subtilis] 49 32 612
709 1 795 157 gi.vertline.143830 xpaC [Bacillus subtilis] 49 29 639
831 1 473 3 gi.vertline.401786 phosphomannomutase [Mycoplasma
pirum] 49 29 471 1052 1 213 4 gi.vertline.1303799 YqeN [Bacillus
subtilis] 49 21 210 1800 1 172 2 gi.vertline.216300 peptidoglycan
synthesis enzyme [Bacillus subtilis]
sp.vertline.P37585.vertline.MURG_BAC- SU 49 28 171 MURG PROTEIN
UPD-N-ACETYLGLUCOSAMINE--N-ACETYLMUR- AMYL- PENTAPEPTIDE)
PYROPHOSPHORYL-UNDECAPRENOL N-ACETYLGLUCOSAMINE RANSFERASE). 2430 1
2 376 sp.vertline.P27434.vertline.YFGA.sub.-- HYPOTHETICAL 36.2 KD
PROTEIN IN NDK-GCPE INTERGENIC REGION. 49 26 375 3096 1 273 4
gi.vertline.516360 surfactin synthetase [Bacillus subtilis] 49 25
270 32 4 3100 2429 gi.vertline.1217963 hepatocyte nuclear factor 4
gamma (HNF4gamma) [Homo sapiens] 48 36 672 38 1 1 609
gi.vertline.1205790 H. influenzae predicted coding region HI1555
[Haemophilus influenzae] 48 28 609 45 6 5021 6427
gi.vertline.1524267 unknown [Mycobacterium tuberculosis] 48 20 1407
59 14 16346 31096 gi.vertline.1197336 Lmp3 protein [Mycoplasma
hominis] 48 28 14751 61 1 3 608 gi.vertline.1511555 quinolone
resistance norA protein protein [Methanococcus jannaschii] 48 30
606 61 3 3311 3646 gi.vertline.1303893 YqhL [Bacillus subtilis] 48
29 336 114 1 98 415 gi.vertline.671708 su(s) homolog; similar to
Drosophila melanogaster suppressor of able 48 25 318 (su(s))
protein, Swiss-Prot Accession Number P22293 Drosophila virilis) 121
1 610 89 gi.vertline.1314584 unknown [Sphingomonas S88] 48 29 522
136 1 1280 546 gi.vertline.1205968 H. influenzae predicted coding
region HI1738 [Haemophilus influenzae] 48 23 735 171 10 8220 9557
gi.vertline.1208454 hypothetical protein [Synechocystis sp.] 48 34
1338 175 1 1814 3 gi.vertline.396400 similar to eukaryotic Na+/H+
exchangers [Escherichia coli] 48 29 1812
sp.vertline.P32703.vertline.YJCE_ECOLI HYPOTHETICAL 60.5 KD PROTEIN
IN SOXR-ACS NTERGENIC REGION (O549). 194 1 2 385
gi.vertline.1510493 M. jannaschii predicted coding region MJ0419
[Methanococcus jannaschii] 48 25 384 197 1 452 3
gi.vertline.1045714 spermidine/putrescine transport ATP-binding
protein [Mycoplasma genitalium] 48 25 450 203 1 1 396
gi.vertline.940288 protein localized in the nucleoli of pea nuclei;
ORF; putative Pisum 48 29 396 sativum] 204 1 698 33
gi.vertline.529202 No definition line found [Caenorhabditis
elegans] 48 25 666 206 20 27760 20705 gi.vertline.511490 gramicidin
S synthetase 2 [Bacillus brevis] 48 27 7056 212 1 2 166
gi.vertline.295899 nucleolin [Xenopus laevis] 48 34 165 220 10
11426 10200 gi.vertline.44073 SecY protein [Lactococcus lactis] 48
23 1227 243 6 5491 4532 gi.vertline.1184118 mevalonate kinase
[Methanobacterium thermoautotrophicum] 48 30 960 264 4 3308 1182
gi.vertline.1015903 ORF YJR151c [Saccharomyces cerevisiae] 48 26
2127 441 1 768 4 gi.vertline.142863 replication initiation protein
[Bacillus subtilis] pir.vertline.B26580.vertline.B26580 48 23 765
replication initiation protein - Bacillus subtilis 444 5 3898 5298
gi.vertline.145836 putative [Escherichia coli] 48 24 1401 484 2 388
1110 gi.vertline.146551 transmembrane protein (kdpD) [Escherichia
coli] 48 18 723 542 3 1425 2000 pir.vertline.S28969.vertline.S289
N-carbamoylsarcosine amidohydrolase (EC 3.5.1.59) - Arthrobacter
sp. 48 27 576 566 1 3 1019 gi.vertline.153490 tetracenomycin C
resistance and export protein [Streptomyces laucescens] 48 24 1017
611 1 2 730 gi.vertline.1103507 unknown [Schizosaccharomyces pombe]
48 38 729 624 1 665 75 gi.vertline.144859 ORF B [Clostridium
perfringens] 48 26 591 846 1 508 2 gi.vertline.537506 paramyosin
[Dirofilaria immitis] 48 27 507 1020 1 66 950 gi.vertline.1499876
magnesium and cobalt transport protein [Methanococcus jannaschii]
48 30 885 1227 1 1 174 gi.vertline.493730 lipoxygenase [Pisum
sativum] 48 35 174 1266 1 1 405 gi.vertline.882452 ORF_f211;
alternate name yggA; orf5 of X14436 [Escherichia coli]
gi.vertline.41425 48 24 405 ORF5 (AA 1-197) [Escherichia coli] (SUB
15-211) 2071 1 381 55 gi.vertline.1408486 HS74A gene product
[Bacillus subtilis] 48 25 327 2398 1 233 3 gi.vertline.1500401
reverse gyrase [Methanococcus jannaschii] 48 40 231 2425 1 246 16
pir.vertline.H48563.vertline.H- 485 G1 protein - fowlpox virus
(strain HP444) (fragment) 48 40 231 2432 1 225 4
gi.vertline.1353703 Trio [Homo sapiens] 48 33 222 2453 1 399 4
gi.vertline.142850 division initiation protein [Bacillus subtilis]
48 29 396 2998 1 236 3 gi.vertline.577569 PepV [Lactobacillus
delbrueckii] 48 31 234 3042 1 14 280 gi.vertline.945219 mucin [Homo
sapiens] 48 35 267 3686 1 1 405 gi.vertline.145836 putative
[Escherichia coli] 48 25 405 4027 2 301 110
pir.vertline.S51177.vertline.S511 trans-activator protein - Equine
infectious anemia virus 48 32 192 4 2 2232 823 gi.vertline.1303989
YqkI [Bacillus subtilis] 47 24 1410 24 2 599 1084
gi.vertline.540083 PC4-1 gene product [Bradysia hygida] 47 28 486
36 10 6925 6326 gi.vertline.1209223 esterase [Acinetobacter
lwoffii] 47 26 600 43 2 196 1884 gi.vertline.1403455 unknown
[Mycobacterium tuberculosis] 47 27 1689 44 22 15108 14098
gi.vertline.1511555 quinolone resistance norA protein protein
[Methanococcus jannaschii] 47 31 1011 69 7 6710 6279
gi.vertline.438466 Possible operon with orfG. Hydrophilic, no
homologue in the atabase; 47 29 432 putative [Bacillus subtilis] 81
4 4279 3536 gi.vertline.466882 ppsl; B1496_C2_189 [Mycobacterium
leprae] 47 24 744 120 12 8863 8591 gi.vertline.927340 D9509.27p;
CAI: 0.12 [Saccharomyces cerevisiae] 47 38 273 142 1 1174 326
gi.vertline.486143 ORF YKL094w [Saccharomyces cerevisiae] 47 32 849
168 1 1093 8 gi.vertline.1177254 hypothetical EcsB protein
[Bacillus subtilis] 47 29 1086 263 1 943 2 gi.vertline.142822
D-alanine racemase cds [Bacillus subtilis] 47 34 942 279 1 561 13
gi.vertline.516608 2 predicted membrane helices, homology with B.
subtilis men Orf3 Rowland 47 31 549 et. al. unpublished Accession
number M74183), approximately 1 minutes on updated Rudd map;
putative [Escherichia coli] sp.vertline.P37355.vertline.YFBB_ECOLI
HYPOTHETICAL 26.7 KD PROTEIN IN MEND-MENB 345 2 1676 732
gi.vertline.1204835 hippuricase [Haemophilus influenzae] 47 28 945
389 2 152 400 gi.vertline.456562 G-box binding factor
[Dictyostelium discoideum] 47 32 249 391 1 1 831
gi.vertline.1420856 myo-inositol transporter [Schizosaccharomyces
pombe] 47 19 831 404 3 2072 2773 gi.vertline.1255425 C33G8.2 gene
product [Caenorhabditis elegans] 47 17 702 529 5 2145 3107
gi.vertline.1303973 YqjV [Bacillus subtilis] 47 29 963 565 2 1257
193 gi.vertline.142824 processing protease [Bacillus subtilis] 47
28 1065 654 1 483 4 gi.vertline.243353 ORF 5' of ECRF3 [herpesvirus
saimiri HVS, host-squirrel monkey, eptide, 407 47 23 480 aa] 692 1
115 633 gi.vertline.150756 40 kDa protein [Plasmid pJM1] 47 25 519
765 1 819 4 gi.vertline.1256621 26.7% of identity in 165 aa to a
Thermophilic bacterium hypothetical 47 28 816 protein 6; putative
[Bacillus subtilis] 825 2 211 1023 gi.vertline.397526 clumping
factor [Staphylococcus aureus] 47 32 813 914 1 1 615
gi.vertline.558073 polymorphic antigen [Plasmodium falciparum] 47
29 615 1076 1 1 753 gi.vertline.1147557 Aspartate aminotransferase
[Bacillus circulans] 47 33 753 1351 1 398 3 gi.vertline.755153
ATP-binding protein [Bacillus subtilis] 47 20 396 4192 1 3 293
gi.vertline.145836 putative [Escherichia coli] 47 24 291 5 6 4361
4014 gi.vertline.305080 myosin heavy chain [Entamoeba histolytica]
46 30 348 11 4 2777 3058 gi.vertline.603639 Ye1040p [Saccharomyces
cerevisiae] 46 28 282 46 11 10300 10082 gi.vertline.1246901
ATP-dependent DNA ligase [Candida albicans] 46 28 219 61 4 3941
7930 gi.vertline.298032 EF [Streptococcus suis] 46 35 3990 132 4
4093 3158 gi.vertline.1511057 hypothetical protein SP: P45869
[Methanococcus jannaschii] 46 25 936 170 4 3652 2585
pir.vertline.S51910.vertline.S519 G4 protein - sauroleishmania
tarentolae 46 26 1068 191 7 8284 7025 gi.vertline.1041334 F54D5.7
[Caenorhabditis elegans] 46 25 1260 253 1 1 396 gi.vertline.1204449
dihydrolipoamide acetyltransferase [Haemophilus influenzae] 46 35
396 264 3 437 973 gi.vertline.180189
cerebellar-degeneration-related antigen (CDR34) [Homo sapiens]
gi.vertline.182737 46 29 537 cerebellar degeneration-associated
protein [Homo sapiens] pir.vertline.A29770.vertline.A29770
cerebellar degeneration-related protein - human 273 1 285 85
gi.vertline.607573 envelope glycoprotein C2V3 region [Human
immunodeficiency virus type] 46 35 201 350 1 3 563
gi.vertline.537052 ORF_E286 [Escherichia coli] 46 35 561 384 1 2
862 gi.vertline.1221884 (urea?) amidolyase [Haemophilus influenzae]
46 31 861 410 4 1876 2490 gi.vertline.1110518 proton antiporter
efflux pump [Mycobacterium smegmatis] 46 24 615 432 1 1455 247
gi.vertline.1197634 orf4; putative transporter; Method: conceptual
translation supplied by 46 27 1209 author [Mycobacterium smegmatis]
458 1 1211 3 gi.vertline.15470 portal protein [Bacteriophage SPP1]
46 30 1209 517 5 2477 4192 gi.vertline.1523812 orf5 [Bacteriophage
A2] 46 23 1716 540 3 1285 1058 gi.vertline.215635 pacA
[Bacteriophage P1] 46 30 228 587 2 649 1242 gi.vertline.537148
ORF_f181 [Escherichia coli] 46 29 594 1218 1 391 35
gi.vertline.1205456 single-stranded-DNA-specific exonuclease
[Haemophilus influenzae] 46 30 357 3685 1 1 402 gi.vertline.450688
hsdM gene of EcoprrI gene product [Escherichia coli]
pir.vertline.S38437.vertline.S38437 hsdM 46 33 402 protein -
Escherichia coli pir.vertline.S09629.vertline.S09629 hypothetical
protein A - Escherichia coli (SUB 40-520) 4176 1 338 3
gi.vertline.951460 FIM-C.1 gene product [Xenopus laevis] 46 31 336
37 7 4813 5922 gi.vertline.606064 ORF_f408 [Escherichia coli] 45 24
1110 38 16 11699 12004 gi.vertline.452192 protein tyrosine
phosphatase (PTP-BAS, type 2) [Homo sapiens] 45 24 306 87 2 1748
2407 gi.vertline.1064813 homologous to sp: PHOR_BACSU [Bacillus
subtilis] 45 23 660 103 12 13385 12588 gi.vertline.1001307
hypothetical protein [Synechocystis sp.] 45 22 798 112 14 13811
12831 gi.vertline.1204389 H. influenzae predicted coding region
HI0131 [Haemophilus influenzae] 45 23 981 145 4 3461 2439
gi.vertline.220578 open reading frame [Mus musculus] 45 20 1023 170
6 4965 3601 gi.vertline.238657 AppC = cytochrome d oxidase, subunit
I homolog [Escherichia coli, K12, 45 27 1365 eptide, 514 aa] 206 2
4346 3462 gi.vertline.1222056 aminotransferase [Haemophilus
influenzae] 45 27 885 228 1 60 716 gi.vertline.160299 glutamic
acid-rich protein [Plasmodium falciparum]
pir.vertline.A54514.vertline.A5- 4514 45 23 657 glutamic acid-rich
protein precursor - Plasmodium alciparum 288 1 2 1015
gi.vertline.1255425 C33G8.2 gene product [Caenorhabditis elegans]
45 23 1014 313 3 3128 1917 gi.vertline.581140 NADH dehydrogenase
[Escherichia coli] 45 30 1212 332 1 459 4 gi.vertline.870966
F47A4.2 [Caenorhabditis elegans] 45 20 456 344 1 3 221
gi.vertline.171225 kinesin-related protein [Saccharomyces
cerevisiae] 45 26 219 441 2 1073 645 gi.vertline.142863 replication
initiation protein [Bacillus subtilis]
pir.vertline.B26580.vertline.B26580 45 27 429 replication
initiation protein - Bacillus subtilis 672 1 2 982
gi.vertline.1511334 M. jannaschii predicted coding region MJ1323
[Methanococcus jannaschii] 45 22 981 763 3 851 357
gi.vertline.606180 ORF_f310 [Escherichia coli] 45 24 495 886 3 379
846 gi.vertline.726426 similar to protein kinases and C. elegans
proteins F37C12.8 and 37C12.5 45 30 468 [Caenorhabditis elegans]
948 1 3 473 gi.vertline.156400 myosin heavy chain (isozyme unc-54)
[Caenorhabditis elegans] 45 25 471 pir.vertline.A93958.vertli-
ne.MWKW myosin heavy chain B - Caenorhabditis elegans
sp.vertline.P02566.vertline.MYSB_CAEEL MYOSIN HEAVY CHAIN B (MHC
B). 1158 1 2 376 gi.vertline.441155 ransmission-blocking target
antigen [Plasmodium falciparum] 45 35 375 2551 1 4 285
gi.vertline.1276705 ORF287 gene product [Porphyra purpurea] 45 28
282 3967 1 42 374 gi.vertline.976025 MrsA [Escherichia coli] 45 28
333 52 7 5846 4761 gi.vertline.467378 unknown [Bacillus subtilis]
44 22 1086 138 8 6475 6849 gi.vertline.173028 thioredoxin II
[Saccharomyces cerevisiae] 44 28 375 221 5 5617 4202
gi.vertline.153490 tetracenomycin C resistance and export protein
[Streptomyces laucescens] 44 21 1416 252 2 1122 913
gi.vertline.1204989 hypothetical protein (GB: U00022_9)
[Haemophilus influenzae] 44 30 210 263 2 2093 921
gi.vertline.1136221 carboxypeptidase [Sulfolobus solfataricus] 44
26 1173 365 4 3524 2085 gi.vertline.1296822 orf1 gene product
[Lactobacillus helveticus] 44 31 1440 543 3 1315 1833
gi.vertline.1063250 low homology to P20 protein of Bacillus
lichiniformis and bleomycin 44 24 519 acetyltransferase of
Streptomyces verticillus [Bacillus subtilis] 544 4 3942 4892
gi.vertline.951460 FIM-C.1 gene product [Xenopus laevis] 44 32 951
792 1 613 2 gi.vertline.205680 high molecular weight neurofilament
[Rattus norveglcus] 44 28 612 44 18 11303 11911 gi.vertline.1511614
molybdopterin-guanine dinucleotide biosynthesis protein A
[Methanococcus 43 27 609 jannaschii] 59 8 3665 5128
gi.vertline.153490 tetracenomycin C resistance and export protein
[Streptomyces laucescens] 43 21 1464 59 10 5536 7527
gi.vertline.153022 lipase Staphylococcus epidermidis] 43 22 1992 99
1 681 16 gi.vertline.1419051 unknown [Mycobacterium tuberculosis]
43 21 666 310 8 9402 12134 gi.vertline.397526 clumping factor
[Staphylococcus aureus] 43 21 2733 432 3 2303 1824
pir.vertline.A60540.vertline.A605 sporozoite surface protein 2 -
Plasmodium yoelii (fragment) 43 29 480 519 3 2547 3122
sp.vertline.Q06530.vertline.DHSU.sub.-- SULFIDE DEHYDROGENASE
(FLAVOCYTOCHROME C) FLAVOPROTEIN CHAIN PRECURSOR (EC 43 23 576
1.8.2.--) (FC) (FCSD). 4 13 12053 13321 gi.vertline.295671 selected
as a weak suppressor of a mutant of the subunit AC40 of DNA 42 18
1269 ependant RNA polymerase I and III [Saccharomyces cerevisiae]
94 2 1091 414 gi.vertline.501027 ORF2 [Trypanosoma brucei] 42 31
678 127 4 4550 3309 gi.vertline.42029 ORF1 gene product
[Escherichia coli] 42 21 1242 297 3 1036 557 gi.vertline.142790
ORF1; putative [Bacillus firmus] 42 25 480 344 6 3525 2953
gi.vertline.40320 ORF 2 (AA 1-203) [Bacillus thuringiensis] 42 30
573 512 1 1115 63 gi.vertline.405957 yeeF [Escherichia coli] 42 23
1053 631 1 1223 12 gi.vertline.580920 rodD (gtaA) polypeptide (AA
1-673) [Bacillus subtilis] pir.vertline.S06048.vertline.S- 06048 42
24 1212 probable rodD protein - Bacillus subtilis
sp.vertline.P13484.vertline.TAGE_BACSU PROBABLE
POLY(GLYCEROL-PHOSPHATE) LPHA-GLUCOSYLTRANSFERASE (EC 2.4.1.52)
(TECHOIC ACID BIOSYNTHESIS ROTEIN E). 685 3 1739 1119
gi.vertline.1303784 YqeD [Bacillus subtilis] 42 19 621 4132 1 395 3
gi.vertline.1022910 protein tyrosine phosphatase [Dictyostelium
discoideum] 42 25 393 86 2 884 393 gi.vertline.309506
spermidine/spermine N1-acetyltransferase [Mus saxicola]
pir.vertline.S43430.vertline.S43430 41 30 492 spermidine/spermine
N1-acetyltransferase - spiny ouse (Mus saxicola) 191 12 14075 13353
gi.vertline.1124957 orf4 gene product [Methanosarcina barkeri] 41
22 723 212 6 2150 3127 gi.vertline.15873 observed 35.2 Kd protein
[Mycobacteriophage 15] 41 26 978 213 3 1263 2000 gi.vertline.633692
TrsA [Yersinia enterocolitica] 41 18 738 408 4 2625 3386
gi.vertline.1197634 orf4; putative transporter; Method: conceptual
translation supplied by 41 24 762 author [Mycobacterium smegmatis]
542 1 3 1103 gi.vertline.457146 rhoptry protein [Plasmodium,
yoelii] 41 21 1101 924 1 2 475 pir.vertline.JH0148.vertline.JH01
nucleolin - rat 41 30 474 1562 1 1 402 gi.vertline.552184
asparagine-rich antigen Pfa35-2 [Plasmodium falciparum]
pir.vertline.S27826.vertline.S27826 40 20 402 asparagine-rich
antigen Pfa35-2 - Plasmodium alciparum (fragment) 2395 1 261 4
pir.vertline.S42251.vertline.S422 hypothetical protein 5 - fowlpox
virus 40 18 258 4077 1 3 305 gi.vertline.1055055 coded for by C.
elegans cDNA yk37g1.5; coded for by C. elegans cDNA 39 21 303
yk5c9.5; coded for by C. elegans cDNA yk1a9.5; alternatively
spliced form of F52C9.8b [Caenorhabditis elegans] 958 1 503 3
gi.vertline.1255425 C33G8.2 gene product [Caenorhabditis elegans]
37 25 501 59 12 8294 10636 gi.vertline.535260 STARP antigen
[Plasmodium reichenowi] 36 24 2343 63 5 3550 8079
gi.vertline.298032 EF [Streptococcus suis] 36 19 4530 544 3 2507
3601 gi.vertline.1015903 ORF YJR151c [Saccharomyces cerevisiae] 35
22 1095 63 4 1949 3574 gi.vertline.552195 circumsporozoite protein
(Plasmodium falciparum) sp.vertline.P05691.vertl- ine.CSP_PLAFL 32
27 1626 CIRCUMSPOROZOITE PROTEIN (CS) (FRAGMENT).
[0290]
3TABLE 3 S. aureus - Putative coding regions of novel proteins not
similar to known proteins Contig ORF Start Stop ID ID (nt) (nt) 4 1
692 150 4 3 1712 2278 4 4 3032 2361 4 14 12585 12097 5 2 1601 663 5
3 1532 1771 5 7 4550 4359 5 9 6422 4905 5 12 8547 8383 6 4 1982
1605 8 1 176 3 11 8 5144 5983 11 9 5968 6498 11 10 6284 6096 11 16
10954 11271 12 5 4942 4532 12 6 4596 4862 15 3 1650 1405 16 10
10835 10407 18 2 917 741 20 9 7764 6403 20 10 8230 7889 20 12 8803
8405 20 13 10470 8782 23 1 339 4 23 6 5485 4832 23 8 5942 5508 23 9
6881 6111 23 15 12618 12830 24 4 4185 3814 24 6 5241 4840 25 2 1824
2402 31 2 505 849 31 3 1177 1524 31 4 2454 3005 32 2 765 1388 32 9
7952 8575 32 10 8591 8728 32 11 9379 9020 32 12 10087 9377 34 2
1049 783 36 7 5226 5801 36 11 7261 6947 36 12 7424 7621 37 4 2964
2770 38 2 980 375 38 11 6425 6868 38 20 16371 15760 38 26 20253
20804 38 27 20722 21264 39 1 1 627 40 1 404 3 43 1 428 60 44 4 2324
1974 44 5 2484 3263 44 14 10129 9671 44 20 13536 13348 44 21 13596
13994 45 7 6297 6019 46 8 6365 6520 46 12 10449 10976 46 17 15032
15424 47 1 288 1079 48 9 7620 7778 50 1 962 312 50 2 1316 1011 51 1
370 2 51 5 2245 1970 53 1 287 132 53 7 6319 5933 54 7 8709 8404 55
1 326 60 55 3 786 520 56 1 1 261 56 3 1228 905 56 4 1560 1150 56 17
18712 18332 57 4 3521 3348 57 8 5436 5822 58 9 8553 8221 59 3 1366
1509 59 6 2802 2578 59 7 3570 3370 59 9 4563 4180 59 11 7518 8378
59 13 10401 16403 62 2 1521 346 62 11 5440 5757 63 1 1 336 67 1 900
1781 67 2 1774 2610 67 3 2591 3904 67 8 6955 6800 68 1 78 326 70 6
5199 3637 70 11 8645 8355 77 3 1192 794 79 2 1228 947 79 3 1411
1791 83 1 2 403 85 9 8300 8653 85 10 8781 8593 86 3 1232 1038 87 8
9187 9366 88 3 1620 1922 89 1 3 161 89 7 4878 4714 91 1 550 2 91 3
3141 2344 92 2 449 928 92 3 1467 976 92 9 5638 6024 94 1 332 3 94 3
1813 1181 94 4 2197 1811 96 11 10601 11050 99 6 4523 4374 99 7 4784
4554 100 8 7287 6916 102 7 4368 4039 103 3 2035 1574 104 1 2 694
104 2 699 1277 105 1 693 151 105 3 2655 2077 106 1 3 221 106 3 1209
1355 107 1 542 3 109 4 3651 3277 109 13 11625 11996 109 14 11981
12268 109 20 17401 17688 110 1 2 760 114 10 8764 9384 116 1 1 309
116 3 4462 2651 116 8 9976 8903 116 9 10158 10003 120 5 3320 2937
120 6 3869 3468 120 13 9290 9844 121 2 417 569 126 3 818 546 127 3
2648 3196 127 5 4084 4395 131 6 6438 6103 132 2 715 1695 134 1 2
667 135 2 258 4 135 3 729 334 138 1 3 152 138 7 6008 6463 140 1
1032 4 140 2 1513 1007 140 5 2387 2743 142 2 1360 2388 142 7 7586
6342 143 7 6502 5714 144 1 640 53 146 1 2 511 146 3 502 1350 146 4
2540 1407 146 5 2874 3071 147 1 1 339 149 11 3615 3274 149 12 3785
3534 149 13 4145 3783 149 15 4610 4413 149 16 5049 4603 149 18 5491
5243 149 21 7054 6692 149 23 8521 7826 149 24 9106 8531 149 25 9897
9115 150 2 1587 871 154 3 1508 1221 154 8 6398 6210 154 14 12147
11590 154 15 12803 12075 156 1 315 593 157 3 1183 2232 158 2 1064
657 159 3 452 808 161 2 876 1808 161 6 4279 3905 161 7 4540 4277
161 8 4717 4538 161 11 5638 5459 163 2 840 76 163 5 2344 1892 163 7
2647 2342 163 9 4905 5132 164 3 1147 956 166 3 4854 4495 168 4 2500
2868 168 5 3595 4158 170 3 2517 2777 171 2 1450 623 171 11 11125
9674 172 1 3 278 172 2 1149 358 173 1 708 127 173 5 6114 5227 174 2
593 1105 175 3 2552 2890 175 5 3335 2850 175 7 4342 4506 182 4 4986
4495 184 5 5702 5361 188 2 1210 1755 188 4 2647 2994 189 6 2614
3039 190 3 1998 2564 191 1 1 153 191 2 669 388 191 10 11786 13039
191 11 12363 11824 192 1 91 426 195 3 1932 1558 195 5 2606 2313 198
2 1016 1591 201 1 170 625 203 2 783 1466 206 6 7815 6700 206 12
13636 13325 206 21 27960 27712 212 2 170 817 212 3 796 1167 212 7
3128 3436 212 9 3749 4075 213 1 1 705 214 2 570 64 214 6 3738 3412
214 9 6600 6995 214 10 7469 7074 217 1 965 3 218 1 178 657 218 3
1776 2156 220 2 1369 887 220 3 2262 1273 220 7 7208 6141 220 8 8661
7078 220 9 10216 8636 221 4 2613 2131 221 9 10757 10086 226 1 3 659
226 2 1459 722 226 3 1476 1961 227 1 2 487 227 2 460 975 227 4 1855
2121 227 5 2052 2345 227 6 3768 2776 227 9 5591 6367 228 5 2503
2877 228 6 2846 3526 233 7 3762 3580 236 2 579 349 238 2 1391 807
239 2 905 393 241 5 4334 4173 242 2 1363 1049 243 1 127 576 244 1
647 3 244 2 1962 889 245 2 1258 902 246 1 69 215 246 4 738 1733 249
3 3712 3518 250 1 249 4 254 1 1 156 256 2 956 1144 257 3 3227 2754
260 4 4580 4254 261 4 2196 2606 261 6 3214 3681 264 2 155 439 264 5
4533 3814 264 6 4739 5107 267 2 931 539 268 4 4700 4260 272 1 446
30 272 3 1200 1439 272 9 4691 4909 272 10 6035 5601 276 4 1746 1901
278 1 224 553 278 5 3299 3448 278 7 4849 5127 285 2 551 736 288 3
1756 1950 288 5 2055 2276 289 1 1055 3 290 2 1932 1630 291 2 332
622 291 5 1545 2051 295 3 1349 1092 295 4 2141 1554 295 5 2220 2762
297 2 465 142 298 1 2 205 300 2 1928 1476 301 7 2624 2454 304 1 3
194 306 1 109 654 306 5 4036 4257 307 1 339 4 307 8 3645 3995 308 1
1 654 308 2 599 78 308 4 2332 2021 313 2 1919 1524 314 1 10 702 316
2 982 1341 316 6 2758 3165 317 1 2 1114 317 3 3458 2346 321 6 5217
4789 321 7 6140 5961 321 8 6794 6138 322 2 543 259 326 2 165 1112
326 3 1117 1467 328 1 469 2 328 5 3276 3100 329 1 3 719 329 2 781
1212 329 3 1471 1833 330 1 289 2 330 3 1447 1623 332 3 2204 2055
332 7 4971 5138 333 2 3128 2961 335 1 433 2 337 2 95 526 340 2 1356
1054 341 1 3 281 341 3 2476 3192 341 5 3618 3944 341 6 3929 4558
344 5 2889 2581 345 1 768 4 346 2 221 592 350 3 1410 1598 352 2
1765 1352 352 3 4596 1876 352 7 7967 8404 352 8 8906 9247 352 9
9854 9537 359 1 1 546 362 1 3 656 364 2 1808 1458 364 8 10714 10454
365 2 1313 1014 365 5 4090 3500 365 7 4980 6239 366 3 520 1719 367
3 906 1085 368 1 494 240 375 1 2 136 380 3 1097 843 389 1 1 276 390
1 2 877 390 2 1373 1549 391 2 560 369 395 1 197 3 396 1 1068 4 398
3 1141 938 399 1 178 669 401 3 566 847 402 2 100 465 404 8 5370
5179 408 2 2269 1031 408 3 2672 2469 408 5 3524 4423 410 3 1890
1669 413 1 488 96 416 1 320 33 416 2 578 847 416 3 1590 985 417 1 3
179 417 2 161 616 420 2 513 238 422 2 357 677 431 2 856 1407 432 2
446 1084 433 1 1 417 433 3 2033 1755 434 1 535 128 434 2 1235 381
440 1 1 450 442 2 1269 3320 443 3 1520 1167 444 1 1 696 444 7 6366
5971 451 1 614 288 453 2 636 376 453 8 3833 4786 453 9 4512 4306
453 10 4731 4525 455 1 219 4 455 2 472 930 459 1 265 687 462 1 2
247 466 2 907 320 467 1 349 44 468 1 2 250 469 1 925 362 469 3 2386
3372 469 4 3464 3706 470 1 77 538 470 6 3694 3290 470 7 5686 5042
470 9 7351 8181 470 10 8175 9773 471 1 500 60 471 2 1017 472 476 1
70 267 477 1 2 760 477 3 1764 2081 477 4 2066 2332 480 5 4016 4261
481 2 480 4 486 3 613 774 487 6 1795 2112 488 1 359 3 492 1 127 675
493 1 2 520 493 2 496 1242 502 3 1149 1571 504 1 346 2 505 5 4150
3734 511 2 1232 723 512 2 583 747 515 1 609 812 517 4 2179 2511 520
4 2097 2360 520 6 3669 3430 527 1 1 498 528 1 335 33 529 2 1104 529
530 7 5298 5534 536 1 156 4 538 1 736 110 538 3 2203 2880 538 5
3121 2711 538 6 3731 3114 540 1 664 332 540 2 1031 567 541 1 89 433
541 2 432 145 542 2 1048 1272 545 2 734 456 551 1 1129 113 555 2
704 516 558 3 1154 951 558 4 1458 1156 558 5 1821 1537 558 6 2020
1874 558 7 2322 2008 558 8 2802 2551 558 9 3453 2920 560 1 475 921
565 3 1485 1264 571 1 156 4 571 3 994 1206 577 1 2 199 577 2 163
453 579 1 1 477 579 2 1200 616 583 1 996 4 585 1 539 132 587 1 22
573 588 2 1372 848 588 3 1554 1366 590 1 47 334 592 2 1141 827 593
1 2 775 593 2 817 1122 595 1 87 890 596 3 1435 1277 602 1 8 169 603
5 1071 1469 606 1 322 768 607 5 1226 1008 610 1 541 53 612 1 3 500
616 1 650 309 617 2 491 246 622 1 36 347 625 4 2046 2549 627 1 67
210 628 1 452 3 631 3 4004 3219 634 1 759 70 636 1 189 368 636 2
1063 197 637 2 1994 1665 638 1 227 1081 639 1 261 4 639 2 811 245
641 1 118 444 642 3 1331 1047 642 4 1847 1434 643 1 3 608 645 4
1534 1758 645 6 2025 2321 645 7 2488 2036 648 1 2 1045 660 1 77 601
660 2 576 872 661 1 961 197 664 2 89 304 667 1 3 413 668 1 1 330
671 2 516 220 673 1 3 338 674 2 584 303 679 1 1 237 679 3 1589 1906
688 1 835 434 688 2 1077 802 694 1 3 143 696 2 432 46 706 1 224 81
709 3 1183 1449 711 1 3 908 715 1 3 167 716 1 2 637 721 1 133 570
722 1 383 3 723 1 829 2 723 2 1112 726 727 1 2 472 729 1 268 441
731 1 130 828 735 1 2 214 736 1 3 782 738 1 2 298 742 1 3 230 745 3
780 412 748 2 282 464 749 1 344 3 751 1 452 3 755 1 97 522 755 2
520 918 758 2 400 137 764 2 746 459 767 1 1 405 768 1 2 373 771 1
534 10 778 1 902 69 785 1 1023 256 787 1 631 2 791 1 3 224 799 1 15
260 804 1 304 711 805 1 3 680 808 1 219 842 810 1 1112 3 810 2 1442
1110 812 1 38 979 817 1 358 2 818 2 487 1104 819 2 1032 535 819 3
1419 1090 820 1 195 1064 828 1 255 4 829 1 48 800 830 1 291 4 832 1
298 2 835 1 320 796 840 3 491 709 845 1 457 2 850 2 303 449 853 1
359 3 860 1 2 256 864 1 18 410 864 2 383 715 864 6 1676 1828 870 1
1 588 873 1 454 2 875 1 294 4 877 1 1020 379 878 1 544 107 879 1
785 3 881 1 1 243 882 1 389 604 890 1 2 508 905 1 398 3 906 1 544
236 912 1 188 3 913 1 3 290 913 2 547 2 915 1 6 161 915 2 169 402
921 1 126 386 927 1 808 38 928 1 2 385 929 1 2 400 932 1 2 400 934
1 1 384 936 1 528 4 937 1 2 616 945 1 220 645 945 2 649 1242 946 1
950 198 949 1 1 270 951 1 3 362 955 1 3 143 960 1 400 77 963 1 1
162 965 1 346 2 966 1 606 133 969 1 3 302 971 1 12 170 974 1 161 3
976 1 348 4 977 1 2 211 982 1 982 38 984 1 296 3 987 1 3 467 993 1
1 525 994 1 549 178 1004 1 318 79 1014 1 313 2 1015 1 2 463 1016 1
145 2 1019 1 660 115 1022 1 474 109 1024 1 299 3 1024 2 276 431
1030 1 338 3 1032 1 179 3 1040 1 399 4 1043 1 3 269 1044 2 115 399
1047 1 1 159 1051 1 354 4 1051 2 733 233 1063 1 2 400 1069 1 2 148
1069 2 533 297 1075 1 399 91 1077 1 97 405 1081 1 58 438 1086 1 1
384 1087 2 246 431 1088 1 3 374 1096 1 238 2 1098 1 509 3 1100 1
511 2 1100 2 1158 796 1101 1 353 3 1102 1 194 3 1107 1 2 580 1114 1
3 422 1115 1 2 268 1119 1 22 267 1129 1 40 342 1132 1 181 2 1133 1
376 143 1144 1 225 4 1147 1 280 2 1153 1 1 153 1154 1 3 818 1159 1
1 330 1161 1 186 31 1164 1 254 81 1171 1 19 240 1171 2 108 299 1183
1 2 379 1195 1 179 3 1196 1 1 189 1200 1 33 197 1203 2 129 464 1222
2 105 401 1232 1 1 387 1240 1 2 175 1247 1 311 102 1271 1 221 30
1286 1 2 595 1295 1 1 165 1306 1 185 3 1314 2 158 631 1316 1 58 570
1359 1 193 2 1370 1 1 402 1371 1 1 345 1374 1 357 4 1378 1 2 400
1392 1 3 413 1411 1 202 432 1433 1 167 3 1450 1 2 256 1453 1 149 3
1471 1 398 75 1477 1 639 409 1502 1 399 4 1518 1 126 449 1534 1 143
3 1546 1 3 401 1547 1 255 4 1583 1 3 350 1587 1 3 563 1602 2 170
679 1629 1 1 402 1665 1 235 2 1760 1 314 3 1762 1 3 200 1876 2 119
286 1895 1 2 379 1931 1 400 2 1976 2 383 51 2055 2 252 401 2056 1
167 3 2150 1 263 3 2157 1 399 4 2164 1 283 2 2175 1 218 400 2212 1
331 170 2338 1 367 2 2342 1 3 167 2352 1 166 2 2352 2 398 174 2355
1 47 352 2356 1 341 3 2359 1 152 3 2421 1 150 4 2422 1 306 43 2443
1 263 99 2454 1 3 158 2463 1 253 2 2485 1 3 374 2557 1 246 4 2575 1
2 355 2582 1 3 284 2607 1 1 294 2930 1 17 400 2939 1 242 18 2944 1
3 359 2945 2 399 97 2952 1 2 190 2953 1 399 61 2964 1 166 2 2969 1
144 4 2977 1 2 373 2981 2 334 167 2986 1 7 279 2991 1 363 118 2995
1 1 321 3007 1 191 39 3017 1 308 48 3018 2 136 351 3025 1 197 3
3040 1 180 4 3046 1 185 3 3049 1 278 3 3050 1 3 314 3052 1 253 2
3065 1 2 157 3070 1 190 23 3075 1 222 4 3080 1 1 285 3092 1 162 4
3093 1 250 89 3100 1 52 237 3103 1 47 298 3118 1 174 4 3123 1 2 145
3127 1 1 147 3138 1 169 2 3142 1 203 18 3144 1 386 108 3151 1 170 3
3155 2 202 384 3168 1 12 176 3205 1 145 2 3282 1 1 150 3303 2 239
400 3371 2 211 399 3558 1 2 148 3558 2 36 401 3568 1 377 3 3595 1
380 3 3618 1 2 238 3618 2 130 402 3622 1 86 358 3622 2 398 132 3642
1 439 2 3649 1 398 15 3651 1 314 3 3664 1 467 637 3674 1 55 402
3677 1 311 3 3704 1 1 402 3726 1 269 3 3765 1 256 2 3779 1 357 160
3794 1 135 4 3794 2 377 87 3796 2 375 112 3801 1 262 50 3806 1 298
143 3807 1 42 389 3815 1 400 2 3827 1 3 320 3842 1 392 3 3853 1 399
127 3855 1 1 324 3857 1 2 235 3861 1 297 4 3865 1 399 103 3897 1 3
173
3897 2 143 400 3898 2 225 401 3921 2 103 342 3927 1 70 375 3930 1
76 234 3946 2 382 113 3951 2 105 377 3965 1 344 42 3973 1 400 5
3981 1 3 311 3998 1 3 356 4001 1 296 111 4003 1 90 335 4018 1 2 259
4018 2 186 401 4021 1 1 345 4043 1 3 344 4054 1 3 344 4066 1 1 150
4070 1 1 324 4072 2 187 390 4073 1 1 285 4077 2 127 372 4083 1 3
359 4090 1 27 368 4101 1 103 297 4105 1 1 306 4107 1 286 2 4119 1
339 49 4121 1 372 4 4123 1 3 230 4127 1 3 341 4128 1 2 331 4130 1
415 62 4146 1 97 381 4157 1 3 206 4186 1 254 3 4224 1 256 2 4239 1
1 348 4242 1 356 3 4252 1 296 3 4253 1 1 174 4256 1 323 78 4258 2
334 170 4267 1 144 4 4271 1 2 304 4287 1 163 23 4289 1 319 167 4302
1 153 305 4304 1 1 186 4304 2 96 314 4306 1 2 151 4318 1 289 2 4322
1 5 148 4331 1 221 3 4331 2 364 200 4338 1 399 70 4346 1 277 83
4367 2 117 311 4373 1 2 268 4381 1 326 78 4384 1 309 4 4397 1 9 311
4402 1 1 249 4403 1 328 50 4406 1 3 317 4411 1 2 280 4411 2 398 99
4412 1 2 364 4418 1 3 230 4424 1 398 195 4443 1 215 3 4471 1 323 3
4478 1 271 2 4482 1 50 289 4489 1 302 3 4491 1 12 206 4495 1 3 179
4496 1 252 4 4500 1 130 306 4511 1 248 3 4518 1 1 246 4526 1 241 2
4527 1 2 163 4532 1 3 239 4542 1 11 175 4567 1 36 200 4573 1 1 231
4578 1 322 2 4619 1 1 180 4620 1 176 3 4662 1 1 246 4669 1 2 157
4680 1 28 183 4690 1 174 4
[0291]
Sequence CWU 0
0
* * * * *