-- dump date 20120504_155801 -- class Genbank::CDS -- table cds_note -- id note YP_263309.1 DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC).; Citation: Skarstad K and Boye E. 1994. The initiator protein DnaA: evolution, properties and function. Biochim Biophys Acta. 1217(2):111-30. YP_263310.1 A dimer of the beta subunit of DNA polymerase forms a ring which encircles duplex DNA.; Citation: Kong XP, Onrust R, O'Donnell M, Kuriyan J. 1992. Three-dimensional structure of the beta subunit of E. coli DNA polymerase III holoenzyme: a sliding DNA clamp. Cell. 69:425-437. YP_263312.1 DNA gyrase is a type II topoisomerase that catalyses an ATP-dependent 2 strand cleavage of DNA. YP_263313.1 Possible transmembrane protein: 6 TM domains YP_263317.1 contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway YP_263323.1 No RBS found. YP_263327.1 similar to Burkholderia pseudomallei hypothetical protein BPSL0749 YP_263328.1 RBS found. YP_263329.1 This protein may be a peroxiredoxin, COG2044. RBS found. YP_263330.1 This protein may contain an alpha/beta-hydrolase fold (COG0429) and an esterase/lipase/thioesterase active site (PS50187). RBS found. YP_263331.1 RBS found. YP_263333.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.996 at residue 24 YP_263335.1 chaperone Hsp40; co-chaperone with DnaK; Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, dnaK-independent fashion YP_263336.1 catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis YP_263338.1 cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+) YP_263339.1 Signal peptide and 3 transmembrane helices predicted. RBS found. YP_263344.1 essential respiratory protein A; may be involved in the transfer of iron-sulfur clusters; essential for growth using oxygen or alternate electron acceptors YP_263346.1 Lipoprotein conserved domain YP_263349.1 involved in the import of serine and threonine coupled with the import of sodium YP_263350.1 Chi forms a 1:1 heterodimer with psi. The chi:psi complex functions by increasing the affinity of tau and gamma for delta.delta allowing a functional clamp-loading complex to form at physiological subunit concentrations. YP_263355.1 Possible 16S RNA G1207 methylase RsmC (COG2813). RBS found. YP_263356.1 Signal peptide and 5 transmembrane helices predicted. YP_263357.1 Signal peptide and 5 transmembrane helices predicted. RBS found. YP_263361.1 This protein contains a SAM (and some other nucleotide) binding motif. RBS found. YP_263362.1 Possible redox protein regulator of disulfide bond formation, Sir A. RBS found. YP_263364.1 This protein contains a ribonuclease RNase H fold (COG0816). RBS found. YP_263365.1 contains DNA binding region also has domain hit to protein DUF 179 YP_263369.1 catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A; involved in coenzyme A biosynthesis YP_263376.1 modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination YP_263377.1 Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits during initiation of protein synthesis. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex YP_263378.1 associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock YP_263379.1 100 aa longer than homologs returned from blastp YP_263381.1 primary rRNA binding protein; helps nucleate assembly of 30S; binds directly to the 16S rRNA and an intersubunit bridge to the 23S rRNA; autoregulates translation through interactions with the mRNA leader sequence YP_263393.1 catalyzes the formation of glycerone phosphate and D-glyceraldehyde 3-phosphate from D-fructose 1,6-bisphosphate in glycolysis YP_263394.1 required for the synthesis of the hydromethylpyrimidine moiety of thiamine YP_263395.1 RBS found. YP_263396.1 catalyzes the formation of arginine from (N-L-arginino)succinate YP_263408.1 part of four member succinate dehydrogenase enzyme complex that forms a trimeric complex (trimer of tetramers); SdhA/B are the catalytic subcomplex and can exhibit succinate dehydrogenase activity in the absence of SdhC/D which are the membrane components and form cytochrome b556; SdhC binds ubiquinone; oxidizes succinate to fumarate while reducing ubiquinone to ubiquinol YP_263409.1 part of four member succinate dehydrogenase enzyme complex that forms a trimeric complex (trimer of tetramers); SdhA/B are the catalytic subcomplex and can exhibit succinate dehydrogenase activity in the absence of SdhC/D which are the membrane components and form cytochrome b556; SdhC binds ubiquinone; oxidizes succinate to fumarate while reducing ubiquinone to ubiquinol; the catalytic subunits are similar to fumarate reductase YP_263410.1 SucA; E1 component of the oxoglutarate dehydrogenase complex which catalyzes the formation of succinyl-CoA from 2-oxoglutarate; SucA catalyzes the reaction of 2-oxoglutarate with dihydrolipoamide succinyltransferase-lipoate to form dihydrolipoamide succinyltransferase-succinyldihydrolipoate and carbon dioxide YP_263412.1 E3 component of pyruvate and 2-oxoglutarate dehydrogenase complex; catalyzes the oxidation of dihydrolipoamide to lipoamide YP_263413.1 catalyzes the interconversion of succinyl-CoA and succinate YP_263417.1 functions in sugar metabolism in glycolysis and the Embden-Meyerhof pathways (EMP) and in gluconeogenesis; catalyzes reversible isomerization of glucose-6-phosphate to fructose-6-phosphate; member of PGI family YP_263420.1 functions in degradation of stringent response intracellular messenger ppGpp; in Escherichia coli this gene is co-transcribed with the toxin/antitoxin genes mazEF; activity of MazG is inhibited by MazEF in vitro; ppGpp inhibits mazEF expression; MazG thus works in limiting the toxic activity of the MazF toxin induced during starvation; MazG also interacts with the GTPase Era YP_263421.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.995) with cleavage site probability 0.936 at residue 24 YP_263424.1 catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate YP_263425.1 catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine YP_263429.1 Involved in ubiquinone biosynthesis YP_263432.1 Citation: Brown L, Gentry D, Elliott T, Cashel M (2002). DksA affects ppGpp induction of RpoS at a translational level. J Bacteriol 184(16);4455-65. PMID: 12142416 YP_263433.1 This protein shows low homology to the cobalamin synthesis protein/P47K family (PFAM cobW). No RBS was found. YP_263434.1 part of two-component system EnvZ/OmpR; regulates transcription of outer membrane porin genes ompC/F; under high osmolarity EnvZ functions as kinase/phosphotransferase and phosphorylates OmpR; the result is increased expression of ompC and repression of ompF; also functions in regulation of other genes; forms dimers upon phosphorylation YP_263437.1 RBS found. YP_263438.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.999) with cleavage site probability 0.198 at residue 28 YP_263440.1 RBS found. YP_263441.1 ChvD; in Agrobacterium tumefaciens, mutations in both Walker boxes were found to affect virulence YP_263442.1 PlsB; catalyzes the formation of 1-acyl-sn-glycerol 3-phosphate by transfering the acyl moiety from acyl-CoA YP_263448.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.990) with cleavage site probability 0.982 at residue 24 YP_263455.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.993) with cleavage site probability 0.989 at residue 47 YP_263456.1 catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis YP_263458.1 catalyzes the formation of (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4- carboxamido)succinate from 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate and L-aspartate in purine biosynthesis; SAICAR synthase YP_263463.1 RBS found. YP_263467.1 Phosphonoacetate hydrolase PhnA is a novel carbon-phosphorus bond cleavage enzyme. The phnA gene is part of a large operon in Escherichia coli associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. YP_263468.1 Converts (S)-4-amino-5-oxopentanoate to 5-aminolevulinate during the porphyrin biosynthesis pathway YP_263476.1 Converts L-aspartate to beta-alanine and provides the major route of beta-alanine production in bacteria. Beta-alanine is essential for the biosynthesis of pantothenate (vitamin B5) YP_263477.1 Enables the recycling of peptidyl-tRNAs produced at termination of translation YP_263478.1 the Ctc family of proteins consists of two types, one that contains the N-terminal ribosomal protein L25 domain only which in Escherichia coli binds the 5S rRNA while a subset of proteins contain a C-terminal extension that is involved in the stress response YP_263479.1 catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP YP_263480.1 An essential enzyme in the nonmevalonate pathway of isopentenyl diphosphate and dimethylallyl diphosphate biosynthesis YP_263483.1 catalyzes the formation of glutamate-1-semialdehyde from glutamyl-tRNA(Glu) and NADPH; the second step of the pathway is catalyzed by glutamate-1-semialdehyde aminomutase which results in the formation of 5-aminolevulinic acid; functions in porphyrin (tetrapyrroles) biosynthesis; the crystal structure showed a C-terminal dimerization domain that appears to be absent in Chlamydial proteins YP_263486.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.953) with cleavage site probability 0.501 at residue 23 YP_263487.1 The family of enzymes includes luciferase, long chain fatty acid Co-A ligase, acetyl-CoA synthetase and various other closely-related synthetases. YP_263489.1 FMN-linked; catalyzes the formation of N-ethylsuccinimide from N-ethylmaleimide YP_263490.1 Member of TIGR00275 family of proteins. RBS found. YP_263491.1 Acs; catalyzes the conversion of acetate and CoA to acetyl-CoA YP_263493.1 This protein has some homology to general stress protein 26 (COG3871). RBS found. YP_263494.1 catalyzes the formation of 2-(formamido)-N1-(5-phospho-D-ribosyl)acetamidine from N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide and L-glutamine in purine biosynthesis YP_263499.1 High homology to COG3328, yet very short sequence. YP_263500.1 contains a TerC, 2 CBS and 1 CorC domains YP_263501.1 Member of bacterial family of proteins related to iojap from plants. The gene iojap is a pattern-striping gene in maize. RBS found. YP_263503.1 catalyzes the synthesis of acetylphosphate or propionylphosphate from acetyl-CoA or propionyl-CoA and inorganic phosphate; when using propionyl-CoA the enzyme is functioning in the anaerobic pathway catabolizing threonine to propionate YP_263505.1 Two transmembrane helices predicted. YP_263507.1 involved in lysine biosynthesis; DAP epimerase; produces DL-diaminopimelate from LL-diaminopimelate YP_263509.1 Hydrolase conserved domain YP_263510.1 contain all necessary domains of rpoN except conserved octapeptide with unkown function; Citation: Merrick M.J. In a class of its own--the RNA polymerase sigma factor sigma 54 (sigma N). Mol. Microbiol. 10: 903- 909 (1993) [PubMed: 7934866 ] YP_263511.1 encoded adjacently (downstream) from to RpoN (Sigma 54); Citation: Heurlier K et al. J Bacteriol. 2003 Apr;185(7):2227-35. PMID: 12644493 [PubMed - indexed for MEDLINE] 2: Oosthuiz et al. Appl. Environ Microbiol. 2002 Jun;68(6):2770-80. PMID: 12039732 [PubMed - indexed for MEDLINE] YP_263513.1 Signal peptide and 4 transmembrane helices predicted. RBS found. YP_263514.1 binds with the catalytic core of RNA polymerase to produce the holoenzyme; this sigma factor is responsible for the expression of heat shock promoters YP_263515.1 RBS found. YP_263517.1 Possible GatB/Yqey domain (tRNA metabolism). RBS found. YP_263518.1 a small basic protein that is one of the last in the subunit assembly; omission does not prevent assembly but the subunit is inactive; binds central domain of 16S rRNA YP_263519.1 Signal peptide predicted; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.603 at residue 31 YP_263520.1 Cytochrome c domain at c-terminus; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.417 at residue 34 YP_263521.1 in most organisms, only the N-terminal domain is present in a single polypeptide; in some archaea this domain is fused to a kinase domain; this gene is essential for growth in Escherichia coli and Bacillus subtilis; the secreted glycoprotease from Pasteurella haemolytica showed specificity for O-sialoglycosylated proteins; the Pyrococcus structure shows DNA-binding properties, iron-binding, ATP-binding, and AP endonuclease activity YP_263523.1 All possess a potential HTH DNA-binding motif towards their N-termini. YP_263526.1 catalyzes the conversion of the propionic acid groups of rings I and III to vinyl groups during heme synthesis YP_263528.1 catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate YP_263531.1 functions in thiamine (vitamin B1) biosynthesis; in Bacillus subtilis this enzyme catalyzes the formation of thiazole from dehydroxyglycine and 1-deoxy-D-xylulose-5-phosphate and ThiS-thiocarboxylate YP_263536.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.980 at residue 48 YP_263538.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.751) with cleavage site probability 0.319 at residue 26 YP_263542.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.999) with cleavage site probability 0.426 at residue 35 YP_263546.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.652) with cleavage site probability 0.517 at residue 33 YP_263548.1 Possible transposase and inactivated derivatives (COG1943). YP_263551.1 This protein performs the mismatch recognition step during the DNA repair process YP_263552.1 functions in protein export; can interact with acidic membrane phospholipids and the SecYEG protein complex; binds to preproteins; binds to ATP and undergoes a conformational change to promote membrane insertion of SecA/bound preprotein; ATP hydrolysis appears to drive release of the preprotein from SecA and deinsertion of SecA from the membrane; additional proteins SecD/F/YajC aid SecA recycling; exists in an equilibrium between monomers and dimers; may possibly form higher order oligomers; proteins in this cluster correspond SecA1; SecA2 is not essential and seems to play a role in secretion of a subset of proteins YP_263553.1 Signal peptide predicted; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.986) with cleavage site probability 0.971 at residue 28 YP_263555.1 PRC barrel domain present YP_263557.1 catalyzes the formation of L-aspartate 4-semialdehyde from L-homoserine YP_263558.1 Citation: Proc Natl Acad Sci U S A. 1992 Jul 1;89(13):6210-4. http://www.cf.ac.uk/biosi/staff/ehrmann/tools/ecce/Peripla smicBySize.html YP_263562.1 could also have efflux ability YP_263563.1 binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential YP_263564.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.911 at residue 35 YP_263565.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.999 at residue 20 YP_263566.1 Possible Na+ dependent transporter of the SNF family. Signal peptide and 11 transmembrane helices predicted. YP_263573.1 Transporter associated domain and two CBS domains present. RBS found. Signal peptide and 4 transmembrane helices predicted. YP_263578.1 RBS found. YP_263581.1 Possible protein serine-threonine phosphatase domain. YP_263582.1 6 transmembrane domains YP_263585.1 hydrolyzes the terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides YP_263586.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.994) with cleavage site probability 0.884 at residue 33 YP_263594.1 catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate YP_263596.1 Citation: Nucleic Acids Res. 1992 Jun 11;20(11):2861-4. YP_263597.1 Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway YP_263599.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.998) with cleavage site probability 0.394 at residue 25 YP_263600.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.968) with cleavage site probability 0.651 at residue 34 YP_263605.1 Esterase/lipase/thioesterase active site present. YP_263607.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.996) with cleavage site probability 0.565 at residue 33 YP_263612.1 activates fatty acids by binding to coenzyme A YP_263614.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA YP_263618.1 type III; catalyzes the formation of (R)-4'-phosphopantothenate from (R)-pantothenate in coenzyme A biosynthesis; type III pantothenate kinases are not subject to feedback inhibition from coenzyme A and have a high Km for ATP YP_263621.1 Citation: Hirano T. 1998. SMC protein complexes and higher-order chromosome dynamics. Curr Opin Cell Biol. 10:317-322. YP_263623.1 This protein also contains a BRCT domain (predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage).; Citation: Lee JY, Chang C, Song HK, Moon J, Yang JK, Kim HK, Kwon ST, Suh SW. 2000. Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications. EMBO J. 19:1119-1129. YP_263628.1 binds to ssrA RNA (tmRNA) and is required for its successful binding to ribosomes; also appears to function in the trans-translation step by promoting accommodation of tmRNA into the ribosomal A site; SmpB protects the tmRNA from RNase R degradation in Caulobacter crescentus; both the tmRNA and SmpB are regulated in cell cycle-dependent manner; functions in release of stalled ribosomes from damaged mRNAs and targeting proteins for degradation YP_263632.1 DTB synthetase; dethiobiotin synthase; involved in production of dethiobiotin from ATP and 7,8-diaminononanoate and carbon dioxide; contains magnesium YP_263633.1 binds to the ribosome on the universally-conserved alpha-sarcin loop YP_263635.1 One transmembrane helix predicted. YP_263636.1 cytoplasmic enzyme involved in processing rRNA and some mRNAs; substrates typically have dsRNA regions; forms a homodimer; have N-terminal nuclease and C-terminal RNA-binding domains; requires magnesium as preferred ion for activity YP_263637.1 Era; Escherichia coli Ras-like protein; Bex; Bacillus Era-complementing segment; essential protein in Escherichia coli that is involved in many cellular processes; GTPase; binds the cell membrane through apparent C-terminal domain; mutants are arrested during the cell cycle; Streptococcus pneumoniae Era binds to RNA and Escherichia coli Era binds 16S rRNA and 30S ribosome YP_263639.1 involved in the de novo synthesis of pyridoxine (Vitamin B6) YP_263641.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.980 at residue 23 YP_263643.1 homopentamer; channel that opens in response to pressure or hypoosmotic shock YP_263645.1 Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases YP_263646.1 The two proteins are strongly similar. In many species, a single homolog to SpoT and RelA appears reponsible for both ppGpp synthesis and ppGpp degradation YP_263647.1 in Escherichia coli this enzyme catalyzes the SAM-dependent methylation of U1939 in the 23S ribomal RNA; binds an iron-sulfur cluster [4Fe-4S] YP_263649.1 catalyzes the formation of cysteine from 3-O-acetyl-L-serine and hydrogen sulfide YP_263651.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA YP_263653.1 one of the last subunits in the assembly of the 30S subunit; absence of S2 does not inhibit assembly but results in an inactive subunit YP_263654.1 EF-Ts; functions during elongation stage of protein translation; forms a dimer; associates with EF-Tu-GDP complex and promotes exchange of GDP to GTP resulting in regeneration of the active form of EF-Tu YP_263662.1 There are 9 addittional ORFs identical to this one. YP_263663.1 Contains TPR repeats, SEL1 subfamily. YP_263666.1 lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis YP_263667.1 IleRS; catalyzes the formation of isoleucyl-tRNA(Ile) from isoleucine and tRNA(Ile); since isoleucine and other amino acids such as valine are similar, there are additional editing function in this enzyme; one is involved in hydrolysis of activated valine-AMP and the other is involved in deacylation of mischarged Val-tRNA(Ile); there are two active sites, one for aminoacylation and one for editing; class-I aminoacyl-tRNA synthetase family type 1 subfamily; some organisms carry two different copies of this enzyme YP_263672.1 catalyzes the formation of 3-phosphonooxypyruvate from 3-phospho-D-glycerate in serine biosynthesis; can also reduce alpha ketoglutarate to form 2-hydroxyglutarate YP_263678.1 Catalyzes the conversion of acetyl-CoA and L-homoserine to CoA and O-acetyl-L-homoserine YP_263679.1 protoheme ferro-lyase; catalyzes the insertion of a ferrous ion into protoporphyrin IX to form protoheme; involved in protoheme biosynthesis; in some organisms this protein is membrane-associated while in others it is cytosolic YP_263683.1 stimulates the release of release factors 1 and 2 from the ribosome after hydrolysis of the ester bond in peptidyl-tRNA has occurred; GDP/GTP-binding protein YP_263684.1 Forkhead-associated (FHA) domain. The domain is present in a diverse range of proteins, such as kinases, phosphatases, kinesins, transcription factors, RNA-binding proteins and metabolic enzymes which partake in many different cellular processes YP_263685.1 EF-Tu; promotes GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis; when the tRNA anticodon matches the mRNA codon, GTP hydrolysis results; the inactive EF-Tu-GDP leaves the ribosome and release of GDP is promoted by elongation factor Ts; many prokaryotes have two copies of the gene encoding EF-Tu YP_263689.1 leucyltransferase; phenylalanyltransferse; functions in the N-end rule pathway; transfers Leu, Phe, Met, from aminoacyl-tRNAs to N-terminal of proteins with Arg or Lys YP_263692.1 SPOUT methyltransferase family protein; crystal structure shows homodimer; in Escherichia coli this protein methylates pseudouridine at position 1915 of the 23S ribosomal RNA YP_263693.1 3'-5' exonuclease of DNA polymerase III YP_263695.1 catalyzes the formation of succinyldiaminopimelate from N-succinyl-2-amino-6-ketopimelate YP_263696.1 Two transmembrane helices predicted. YP_263697.1 Senses intracellular glutamine levels via ACT domain YP_263699.1 Signal peptide predicted.; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.716) with cleavage site probability 0.275 at residue 40 YP_263702.1 Citation: Lauster R, Trautner TA, Noyer-Weidner M. 1989. Cytosine-specific type II DNA methyltransferases. A conserved enzyme core with variable target-recognizing domains. J Mol Biol. 206(2):305-12. YP_263704.1 one of two methionine synthases in Escherichia coli; MetH catalyzes a methyl transfer reaction from methyltetrahydrofolate to homocysteine to create methionine; requires zinc for activity YP_263705.1 fasciclin domain; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.995) with cleavage site probability 0.457 at residue 22 YP_263706.1 fasciclin domain; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.656 at residue 21 YP_263707.1 There are 9 addittional ORFs identical to this one. YP_263708.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.996) with cleavage site probability 0.858 at residue 34 YP_263709.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 1.000 at residue 26 YP_263712.1 There are 9 addittional ORFs identical to this one. YP_263718.1 Part of the pathway of flavonoids, stilbene and lignin biosynthesis. YP_263722.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.748 at residue 24 YP_263725.1 catalyzes the NADPH-dependent reduction of 7-cyano-7-deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1) in queuosine biosynthesis YP_263726.1 catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro) YP_263727.1 Citation: Sancar A, Smith FW, Sancar GB. 1984. Purification of Escherichia coli DNA photolyase. J Biol Chem. 259(9):6028-32. YP_263729.1 catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate YP_263730.1 catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis YP_263733.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.989) with cleavage site probability 0.750 at residue 24 YP_263735.1 Part of a prophage YP_263744.1 Within prophage. YP_263748.1 similar to Shewanella oneidensis hypothetical protein SO2991 YP_263755.1 Part of a prophage YP_263761.1 Often located next to the small subunit. YP_263762.1 Members tend to be adjacent to the phage terminase large subunit gene. YP_263766.1 Within prophage. YP_263768.1 Part of a prophage YP_263769.1 in prophage; helix turn helix motif YP_263770.1 Within prophage. YP_263771.1 Within prophage. YP_263772.1 Within prophage YP_263773.1 Within prophage, signal peptide predicted.; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.726) with cleavage site probability 0.717 at residue 27 YP_263774.1 Within prophage, contains ATP/GTP-binding site motif A. YP_263776.1 Within prophage. YP_263777.1 allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA YP_263778.1 allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA YP_263780.1 functions in MreBCD complex in some organisms YP_263781.1 in some organisms this protein is a transmembrane protein while in others it is periplasmic; involved in some organisms with other components of the MreBCD complex and with penicillin binding proteins in the periplasm or cell wall YP_263785.1 NusE; involved in assembly of the 30S subunit; in the ribosome, this protein is involved in the binding of tRNA; in Escherichia coli this protein was also found to be involved in transcription antitermination; NusB/S10 heterodimers bind boxA sequences in the leader RNA of rrn operons which is required for antitermination; binding of NusB/S10 to boxA nucleates assembly of the antitermination complex YP_263786.1 binds directly near the 3' end of the 23S rRNA, where it nucleates assembly of the 50S subunit; essential for peptidyltransferase activity; mutations in this gene confer resistance to tiamulin YP_263787.1 L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA YP_263788.1 binds third domain of 23S rRNA and protein L29; part of exit tunnel YP_263789.1 one of the primary rRNA-binding proteins; required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation YP_263790.1 protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA YP_263791.1 binds specifically to 23S rRNA during the early stages of 50S assembly; makes contact with all 6 domains of the 23S rRNA in the assembled 50S subunit and ribosome; mutations in this gene result in erythromycin resistance; located near peptidyl-transferase center YP_263792.1 forms a complex with S10 and S14; binds the lower part of the 30S subunit head and the mRNA in the complete ribosome to position it for translation YP_263793.1 located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e YP_263794.1 one of the stabilizing components for the large ribosomal subunit YP_263796.1 binds to the 23S rRNA between the centers for peptidyl transferase and GTPase YP_263797.1 assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel YP_263798.1 part of 50S and 5S/L5/L18/L25 subcomplex; contacts 5S rRNA and P site tRNA; forms a bridge to the 30S subunit in the ribosome by binding to S13 YP_263799.1 located in the peptidyl transferase center and involved in assembly of 30S ribosome subunit; similar to what is observed with proteins L31 and L33, some proteins in this family contain CXXC motifs that are involved in zinc binding; if two copies are present in a genome, then the duplicated copy appears to have lost the zinc-binding motif and is instead regulated by zinc; the proteins in this group do not appear to have the zinc-binding motif YP_263800.1 binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit YP_263801.1 ribosomal protein L6 appears to have arisen as a result of an ancient gene duplication as based on structural comparison of the Bacillus stearothermophilus protein; RNA-binding appears to be in the C-terminal domain; mutations in the L6 gene confer resistance to aminoglycoside antibiotics such as gentamicin and these occur in truncations of the C-terminal domain; it has been localized to a region between the base of the L7/L12 stalk and the central protuberance YP_263802.1 binds 5S rRNA along with protein L5 and L25 YP_263803.1 located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body; contacts S4 and S8; with S4 and S12 plays a role in translational accuracy; mutations in this gene result in spectinomycin resistance YP_263804.1 L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7 YP_263805.1 late assembly protein YP_263806.1 forms heterotrimeric complex in the membrane; in bacteria the complex consists of SecY which forms the channel pore and SecE and SecG; the SecG subunit is not essential; in bacteria translocation is driven via the SecA ATPase YP_263807.1 smallest protein in the large subunit; similar to what is found with protein L31 and L33 several bacterial genomes contain paralogs which may be regulated by zinc; the protein from Thermus thermophilus has a zinc-binding motif and contains a bound zinc ion; the proteins in this group have the motif YP_263808.1 located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA; makes contact with the large subunit via RNA-protein interactions and via protein-protein interactions with L5; contacts P-site tRNA YP_263809.1 located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA; forms part of the Shine-Dalgarno cleft in the 70S ribosome; interacts with S7 and S18 and IF-3 YP_263810.1 primary rRNA binding protein; nucleates 30S assembly; involved in translational accuracy with proteins S5 and S12; interacts with protein S5; involved in autogeneously regulating ribosomal proteins by binding to pseudoknot structures in the polycistronic mRNA; interacts with transcription complex and functions similar to protein NusA in antitermination YP_263811.1 catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Dimerization of the alpha subunit is the first step in the sequential assembly of subunits to form the holoenzyme YP_263812.1 is a component of the macrolide binding site in the peptidyl transferase center YP_263813.1 Possible RNA binding protein YP_263816.1 some L32 proteins have zinc finger motifs consisting of CXXC while others do not YP_263819.1 carries the fatty acid chain in fatty acid biosynthesis YP_263820.1 peptidoglycan-binding LysM motif YP_263821.1 iron-sulfur binding domain YP_263824.1 catalyzes the formation of 2-acetolactate from pyruvate, leucine sensitive; also known as acetolactate synthase large subunit YP_263825.1 with IlvI catalyzes the formation of 2-acetolactate from pyruvate, the small subunit is required for full activity and valine sensitivity; E.coli produces 3 isoenzymes of acetolactate synthase which differ in specificity to substrates, valine sensitivity and affinity for cofactors; also known as acetolactate synthase 3 small subunit YP_263826.1 catalyzes the formation of (R)-2,3-dihydroxy-3-methylbutanoate from (S)-2-hydroxy-2-methyl-3-oxobutanoate in valine and isoleucine biosynthesis YP_263827.1 Four transmembrane helices predicted. YP_263828.1 Citation: Datta PP, Bhadra RK. Cold shock response and major cold shock proteins of Vibrio cholerae. Appl Environ Microbiol. 2003 Nov;69(11):6361-9. PMID: 14602587 [PubMed - in process] YP_263832.1 contains fis type helix turn helix motif suggests binding YP_263833.1 Integrase, catalytic domain YP_263836.1 catalyzes the formation of D-fructose 6-phosphate from fructose-1,6-bisphosphate YP_263837.1 catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis YP_263838.1 This orf is immediately downstream of a strong pyrB homolog.; Citation: J Bacteriol. 1995 April; 177 (7): 1751-1759 YP_263839.1 4 transmembrane domains predicted YP_263840.1 There are 9 addittional ORFs identical to this one. YP_263843.1 extra 100 aa at carboxy terminus. all 6 transmembrane domains present YP_263845.1 Four transmembrane helices predicted. YP_263847.1 10 kDa chaperonin; Cpn10; GroES; forms homoheptameric ring; binds to one or both ends of the GroEL double barrel in the presence of adenine nucleotides capping it; folding of unfolded substrates initiates in a GroEL-substrate bound and capped by GroES; release of the folded substrate is dependent on ATP binding and hydrolysis in the trans ring YP_263848.1 60 kDa chaperone family; promotes refolding of misfolded polypeptides especially under stressful conditions; forms two stacked rings of heptamers to form a barrel-shaped 14mer; ends can be capped by GroES; misfolded proteins enter the barrel where they are refolded when GroES binds; many bacteria have multiple copies of the groEL gene which are active under different environmental conditions; the B.japonicum protein in this cluster is expressed constitutively; in Rhodobacter, Corynebacterium and Rhizobium this protein is essential for growth YP_263851.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.993) with cleavage site probability 0.936 at residue 22 YP_263854.1 protein of unknown function DUF528 YP_263855.1 possible transcriptional activator YP_263856.1 dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE), catalyzes the hydrolysis of N-succinyl-L,Ldiaminopimelate L,L-SDAP to L,L-diaminopimelate and succinate. It is a metalloprotease containing dinuclear active sites. Its structure is similar to the carboxypeptidase G2 from Pseudomonas sp. strain RS-16 and the aminopeptidase from Aeromonas proteolytica. YP_263863.1 strong RBS YP_263869.1 Citation: Song MS, Pham PT, Olson M, Carter JR, Franden MA, Schaaper RM, McHenry CS. 2001. The delta and delta ' subunits of the DNA polymerase III holoenzyme are essential for initiation complex formation and processive elongation. J Biol Chem. 276:35165-35175. YP_263870.1 possible lipoprotein YP_263871.1 leucine--tRNA ligase; LeuRS; class-I aminoacyl-tRNA synthetase; charges leucine by linking carboxyl group to alpha-phosphate of ATP and then transfers aminoacyl-adenylate to its tRNA; due to the large number of codons that tRNA(Leu) recognizes, the leucyl-tRNA synthetase does not recognize the anticodon loop of the tRNA, but instead recognition is dependent on a conserved discriminator base A37 and a long arm; an editing domain hydrolyzes misformed products; in Methanothermobacter thermautotrophicus this enzyme associates with prolyl-tRNA synthetase YP_263872.1 pentapeptide repeat motif present YP_263873.1 aresenate reductase arsC related YP_263874.1 catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate YP_263875.1 catalyzes the formation of dUMP from dUTP YP_263877.1 The Rep proteins function as dimers. YP_263879.1 The point of entry for the majority of electrons that traverse the respiratory chain eventually resulting in the reduction of oxygen YP_263880.1 NuoCD; NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain; subunits NuoCD, E, F, and G constitute the peripheral sector of the complex; in Escherichia coli this gene encodes a fusion protein of NuoC and NuoD that are found separate in other organisms YP_263881.1 Catalyzes the transfer of electrons from NADH to quinone YP_263883.1 Catalyzes the transfer of electrons from NADH to quinone YP_263884.1 Catalyzes the transfer of electrons from NADH to quinone YP_263885.1 Catalyzes the transfer of electrons from NADH to quinone YP_263886.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.676) with cleavage site probability 0.328 at residue 32 YP_263888.1 Catalyzes the transfer of electrons from NADH to ubiquinone YP_263889.1 Catalyzes the transfer of electrons from NADH to quinone YP_263897.1 could also be NarQ unclear but narGHJI present suggesting NarX (Biochem Soc Trans. 2003 Feb;31(Pt 1):1-10.) YP_263905.1 together with moaC, is involved in the conversion of a guanosine derivative (GXP) into molybdopterin precursor Z YP_263907.1 Possible Molybdopterin-guanine dinucleotide biosynthesis protein A, MobA. YP_263911.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.983) with cleavage site probability 0.975 at residue 43 YP_263913.1 -capitalized Hypo YP_263914.1 4 transmembrane helices YP_263915.1 probable bacterial transmembrane pair; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.881) with cleavage site probability 0.867 at residue 32 YP_263920.1 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli YP_263923.1 Membrane protein of unknown function DUF340 YP_263925.1 3 different subfamilies; catalyzes the formation of quinolinate from iminoaspartate and dihydroxyacetone phosphate YP_263928.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.949) with cleavage site probability 0.946 at residue 47 YP_263934.1 similar to sp|022008 YP_263940.1 OMA family; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.928 at residue 29 YP_263953.1 most likely carbohydrate biosynthesis YP_263958.1 There are two asparagine synthase genes present in the Psychrobacter 273-4 genome. YP_263961.1 There are two asparagine synthases in the Psychrobacter 273-4 genome. YP_263965.1 Citation: possible Binding-protein-dependent transport systems inner membrane component domain though these are usually located at c-term; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.941 at residue 32 YP_263966.1 catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate YP_263969.1 Required for the first step of histidine biosynthesis. May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine YP_263970.1 catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis YP_263971.1 catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate YP_263972.1 Other members of this family also contain the Radical SAM domain in central portion of protein generate a radical species by reductive cleavage of S:-adenosylmethionine (SAM) through an unusual Fe-S center YP_263973.1 TPR repeat implicated to be involved in protein-protein interaction YP_263975.1 catalyzes the conversion of 2C-methyl-D-erythritol 2,4-cyclodiphosphate into 4-hydroxy-3-methyl-2-en-1-yl diphosphate; involved in isoprenoid synthesis YP_263976.1 catalyzes a two-step reaction, first charging a histidine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; class II aminoacyl-tRNA synthetase; forms homodimers; some organisms have a paralogous gene, hisZ, that is similar to hisS and produces a protein that performs the first step in histidine biosynthesis along with HisG YP_263978.1 possible bacterial quinoprotein YP_263979.1 EngA; essential Neisserial GTPase; synchronizes cellular events by interacting with multiple targets with tandem G-domains; overexpression in Escherichia coli suppresses rrmJ mutation; structural analysis of the Thermotoga maritima ortholog shows different nucleotide binding affinities in the two binding domains YP_263981.1 Signal peptide predicted. YP_263983.1 Probable membrane bound metallopeptidase; Citation: Members of this family are zinc metallopeptidases with a range of specificities.; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.994) with cleavage site probability 0.511 at residue 23 YP_263984.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.998) with cleavage site probability 0.591 at residue 25 YP_263985.1 catalyzes the formation of 2,3=diacylglucosamine 1-phosphate from UDP-2,3=diacylglucosamine YP_263987.1 catalyzes a two-step reaction, first charging a glutamine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA YP_263991.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.791 at residue 23 YP_263992.1 endonuclease; resolves Holliday structures; forms a complex of RuvABC; the junction binding protein RuvA forms a hexameric ring along with the RuvB helicase and catalyzes branch migration; RuvC then interacts with RuvAB to resolve the Holliday junction by nicking DNA strands of like polarity YP_263994.1 catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate YP_263996.1 Domain arrangement suggests belongs to two-component sensory transduction system activated by phosphorylation by a transmembrane kinase. The proteins that belong to this class include bvgA, comA, dctR; degU, evgA, fimZ, fixJ, gacA, glpR, narL, narP, nodW YP_263997.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.982 at residue 27 YP_263999.1 Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway YP_264000.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.867 at residue 23 YP_264001.1 class II aldolase; catalyzes the reversible aldol condensation of dihydroxyacetonephosphate and glyceraldehyde 3-phosphate in the Calvin cycle, glycolysis and gluconeogenesis YP_264002.1 plays an essential role in ATP-dependent branch migration of the Holliday junction YP_264003.1 promotes strand exchange during homologous recombination; RuvAB complex promotes branch migration; RuvABC complex scans the DNA during branch migration and resolves Holliday junctions at consensus sequences; forms hexameric rings around opposite DNA arms; requires ATP for branch migration and orientation of RuvAB complex determines direction of migration YP_264006.1 Extra 120 amino acids at N-terminus compared to homologs. YP_264008.1 Protein of unknown function DUF344 YP_264010.1 in Corynebacterium glutamicum the aminotransferase can use glutamate, 2-aminobutyrate, and aspartate as amino donors and pyruvate as the acceptor; this protein contains a helix-turn-helix domain at the N-terminus YP_264011.1 Have a SelR domain YP_264013.1 adjacent gene is histidine kinase YP_264016.1 catalyzes the oxidation of choline to betaine aldehyde and betain aldehyde to glycine betaine YP_264017.1 catalyzes the formation of betaine from betaine aldehyde YP_264022.1 strong RBS found; predicted membrane protein YP_264023.1 Signal peptide and 9 transmembrane helices predicted. YP_264025.1 catalyzes the formation of N-succinyl-2-amino-6-ketopimelate from succinyl-CoA and tetrahydrodipicolinate in the lysine biosynthetic pathway YP_264026.1 Esterase/lipase/thioesterase, active site YP_264030.1 Possible membrane protein YP_264032.1 The UvrABC repair system catalyzes the recognition and processing of DNA lesions. The beta-hairpin of the Uvr-B subunit is inserted between the strands, where it probes for the presence of a lesion YP_264033.1 Possible lipoprotein, signal peptide predicted. YP_264034.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.499 at residue 28 YP_264037.1 catalyzes the radical-mediated insertion of two sulfur atoms into an acyl carrier protein (ACP) bound to an octanoyl group to produce a lipoyl group YP_264038.1 involved in protocatechuate catabolism YP_264039.1 catalyzes the conversion of citrate to isocitrate and the conversion of 2-methylaconitate to 2-methylisocitrate YP_264044.1 possible hydrolase of the HAD superfamily YP_264045.1 RBS found YP_264047.1 Response to stress YP_264048.1 Bacterial stress protein YP_264049.1 strong RBS found YP_264050.1 Bacterial stress protein YP_264052.1 Stress protein YP_264053.1 catalyzes the N2-methyl guanosine modification of the G2445 residue of 23S rRNA YP_264055.1 Catalyzes the oxidation of dihydrolipoamide to lipoamide YP_264057.1 Signal peptide predicted YP_264059.1 TtcA; YdaO; catalyzes the thiolation of cytosine 32 in specific tRNAs YP_264061.1 4Fe-4S ferredoxin domain found YP_264064.1 CcoO; FixO YP_264065.1 CcoN; FixN YP_264071.1 4 transmembrane helices YP_264072.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.990) with cleavage site probability 0.913 at residue 21 YP_264075.1 7 transmembrane helices YP_264081.1 involved in a recombinational process of DNA repair, independent of the recBC complex YP_264083.1 acts in conjunction with GvcH to form H-protein-S-aminomethyldihydrolipoyllysine from glycine YP_264085.1 part of multienzyme complex composed of H, L, P, and T proteins which catalyzes oxidation of glycine to yield carbon dioxide, ammonia, 5,10-CH2-H4folate and a reduced pyridine nucleotide; protein H is involved in transfer of methylamine group from the P to T protein; covalently bound to a lipoyl cofactor YP_264086.1 catalyzes the transfer of a methylene carbon from the methylamine-loaded GcvH protein to tetrahydrofolate, causing the release of ammonia and the generation of reduced GcvH protein YP_264088.1 3 transmembrane helices YP_264091.1 This family of bacterial transcriptional regulators includes the acetate operon repressor both of which are members of the iclR family [1, 2]. These proteins have a Helix-Turn-Helix motif at the N-terminus. The C-terminal region may bind to the regulatory YP_264096.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.940) with cleavage site probability 0.907 at residue 28 YP_264099.1 RBS found. similarity to hepatitis A virus cellular receptor YP_264100.1 necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites; arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by cleavage factors such as GreA or GreB allows the resumption of elongation from the new 3'terminus YP_264101.1 There is only one set of carbomoyl-phosphate synthase genes in Psychrobacter 273-4 YP_264102.1 catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers YP_264103.1 PAP2 family YP_264108.1 Probable AMP-dependent synthetase and ligase YP_264114.1 RBS found YP_264115.1 methionine adenosyltransferase; catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase YP_264116.1 Citation: Tainer JA, Thayer MM, Cunningham RP. 1995. DNA repair proteins. Curr Opin Struct Biol. 5(1):20-6. YP_264117.1 4Fe-4S ferredoxin YP_264118.1 MutT anti- mutagenic activity represents only one subgroup within this family. YP_264120.1 Whether this protein is functional is unknown, both functions are coded for separately elsewhere in the genome (or2386 and or0752). YP_264121.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.998) with cleavage site probability 0.529 at residue 31 YP_264122.1 3 transmembrane helices YP_264124.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.950) with cleavage site probability 0.553 at residue 33 YP_264127.1 Citation: Newman JD, Anthony JR, Donohue TJ. The importance of zinc-binding to the function of Rhodobacter sphaeroides ChrR as an anti-sigma factor. J Mol Biol. 2001 Oct 26;313(3):485-99. PMID: 11676534 [PubMed - indexed for MEDLINE] YP_264133.1 catalyzes the formation of tetrahydropteroyl-L-glutamate and methionine from L-homocysteine and 5-methyltetrahydropteroyltri-L-glutamate YP_264135.1 8 transmembrane domains found; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.870) with cleavage site probability 0.699 at residue 22 YP_264139.1 also has a SMP-30 domain but has low identity hit from Blast YP_264141.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.906) with cleavage site probability 0.566 at residue 25 YP_264142.1 catalyzes the synthesis of pseudouridine from U-2604 in the 23S ribosomal RNA YP_264146.1 weak rbs. Predicted by glimmer and critica. YP_264150.1 Integrase, catalytic domain YP_264151.1 Contains a fis type helix turn helix binding motif, which is found in a number of proteins involved in recombination and transcriptional regulation. YP_264153.1 RBS found. predicted phage-related endonuclease YP_264154.1 RBS found. YP_264155.1 found to be upregulated in E.coli during high cell density stress; Citation: Gill RT etal. Genomic analysis of high-cell-density recombinant Escherichia coli fermentation and cell conditioning for improved recombinant protein yield. Biotechnol Bioeng. 2001 Jan 5;72(1):85-95. PMID: 11084598 [PubMed - indexed for MEDLINE] YP_264156.1 ATP/GTP-binding site motif A (P-loop):AAA ATPase:AAA ATPase, central region YP_264157.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.673) with cleavage site probability 0.662 at residue 23 YP_264161.1 similar to Shewanella oneidensis MR-1 hypothetical protein SO2854 YP_264167.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.984 at residue 23 YP_264168.1 DEAD/DEAH box helicase:ATP/GTP-binding site motif A (P-loop)::Protein of unknown function DUF450 YP_264169.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.852 at residue 20 YP_264171.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.986 at residue 22 YP_264172.1 also adjacent to or470, an integrase YP_264174.1 has these domains: Oxidoreductase FAD/NAD(P)-binding:Flavoprotein pyridine nucleotide cytochrome reductase YP_264177.1 This family of proteins are related to a large superfamily of metalloenzymes.; Citation: Wexler M, Sargent F, Jack RL, Stanley NR, Bogsch EG, Robinson C, Berks BC, Palmer T. 2000. TatD is a cytoplasmic protein with DNase activity. No requirement for TatD family proteins in sec-independent protein export. J Biol Chem. 275(22):16717-22. YP_264180.1 dGTPase family type 3 subfamily, presumably hydrolyzes dGTP to deoxyguanosine and triphosphate YP_264181.1 translation-associated GTPase; the crystal structure of the Haemophilus influenzae YchF protein showed similarity to the yeast structure (PDB: 1NI3); fluorescence spectroscopy revealed nucleic acid binding; the yeast protein YBR025c interacts with the translation elongation factor eEF1 YP_264182.1 good rbs. Predicted by generation, glimmer and critica. YP_264183.1 3 base rbs. Predicted by generation, glimmer and critica. YP_264186.1 catalyzes the formation of propionyl-CoA using propionate as a substrate; PrpE from Ralstonia solanacearum can produce acetyl-, propionyl-, butyryl- and acrylyl-coenzyme A, and Salmonella enterica produces propionyl- and butyryl-coenzyme A; not expressed in Escherichia coli when grown on propionate/minimal media; ATP-dependent YP_264189.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA YP_264193.1 Contains an ATP binding domain; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.998 at residue 22 YP_264196.1 Neutral zinc metallopeptidases, zinc-binding region YP_264197.1 catalyzes the formation of 3-deoxy-D-arabino-hept-2-ulosonate 7 phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate, phenylalanine sensitive YP_264201.1 contains following domains: ATP/GTP-binding site motif A (P-loop):Saccharopine dehydrogenase YP_264203.1 predicted integral membrane protein YP_264206.1 The mutL protein binds to mutS, which recognizes and binds to mismatches in DNA duplexes. The mutS-mutL-DNA complex stimulates mutH to cleave the unmethylated DNA strand at the GATC sequence.; Contains following domains: DNA mismatch repair protein:ATP-binding region, ATPase-like. YP_264207.1 contains full domains: ATP/GTP-binding site motif A (P-loop):tRNA isopentenyltransferase YP_264211.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.636) with cleavage site probability 0.578 at residue 26 YP_264212.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.997) with cleavage site probability 0.959 at residue 41 YP_264214.1 Sms; stabilizes the strand-invasion intermediate during the DNA repair; involved in recombination of donor DNA and plays an important role in DNA damage repair after exposure to mutagenic agents YP_264217.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.991) with cleavage site probability 0.990 at residue 31 YP_264220.1 There are 9 addittional ORFs identical to this one. YP_264221.1 GTP-binding signal recognition particle (SRP54) G-domain:ATP/GTP-binding site motif A (P-loop):AAA ATPase YP_264225.1 Protein of unknown function DUF28 Hits to yebC of E.coli but that is called a conserved hypothetical too YP_264227.1 ABC1 binding domain; from interpro: E. coli AarF is required for ubiquinone production. It has been suggested that members of the ABC1 family are novel chaperonins. These proteins are unrelated to the ABC transporter proteins. YP_264228.1 catalyzes the formation of 3-dehydroshikimate from 3-dehydroquinate in chorismate biosynthesis YP_264229.1 contains the cold shock DNA-binding domain 79% homology to capB; Citation: Michel V, Lehoux I, Depret G, Anglade P, Labadie J, Hebraud M. The cold shock response of the psychrotrophic bacterium Pseudomonas fragi involves four low-molecular-mass nucleic acid-binding proteins. J Bacteriol. 1997 Dec;179(23):7331-42. PMID: 93 YP_264230.1 ATP-dependent helicase, DEAD-box:DEAD/DEAH box helicase:Helicase, C-terminal:ATP/GTP-binding site motif A (P-loop) YP_264231.1 There are 10 repeats of this sequence YP_264234.1 Protein of unknown function DUF218 domain YP_264235.1 catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis YP_264237.1 S4 paralog YP_264238.1 threonine deaminase; threonine dehydratase; in Escherichia coli, IlvA is part of the isoleucine biosynthetic pathway YP_264243.1 Catalyzes D-ribose 5-phosphate --> D-ribulose 5-phosphate in the nonoxidative branch of the pentose phosphate pathway YP_264244.1 catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation YP_264245.1 inding-protein-dependent transport systems inner membrane component: YP_264246.1 The N-terminal domain is required both for interaction with other proteins in the primosome and for DnaB helicase activity. The C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. YP_264248.1 catalyzes the transfer of a total of four methyl groups from S-adenosyl-l-methionine (S-AdoMet) to two adjacent adenosine bases A1518 and A1519 in 16S rRNA; mutations in ksgA causes resistance to the translation initiation inhibitor kasugamycin YP_264249.1 hydrolyzes P(1),P(4)-bis(5'-adenosyl) tetraphosphate to form 2 ADP YP_264251.1 one sugar transporter domain likely involved in binding since membrane transporter proteins have 12 of these domains YP_264252.1 contains central domain and c- terminus addtional sequences as seen is Acientobacter YP_264253.1 in Escherichia coli RsmE methylates the N3 position of the U1498 base in 16S rRNA; cells lacking this function can grow, but are outcompeted by wild-type; SAM-dependent m(3)U1498 methyltransferase YP_264254.1 Conversion of 5, 10 methylenetetrahydrofolate to 5-methyltetrahydrofolate is a prerequisite for donation of that methyl group to homocysteine -> methionine. YP_264255.1 catalyzes the formation of L-homocysteine from S-adenosyl-L-homocysteine YP_264256.1 TonB dependent transporter YP_264257.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.989 at residue 50 YP_264258.1 Contains a C-terminal MutS2 domain. Does not contain required N-terminal domain. YP_264259.1 involved in tryptophan biosynthesis; amino acid biosynthesis; converts 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate to C(1)-(3-indolyl)-glycerol 3-phosphate and carbon dioxide and water YP_264260.1 Catalyzes the conversion of N-(5-phospho-D-ribosyl)-anthranilate and diphosphate to anthranilate and 5-phospho-alpha-D-ribose 1-diphosphate YP_264261.1 TrpG; with TrpE catalyzes the formation of anthranilate and glutamate from chorismate and glutamine; TrpG provides the glutamine amidotransferase activity YP_264262.1 Contains adenylation site YP_264263.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.998) with cleavage site probability 0.998 at residue 37 YP_264264.1 RBS found. Contains predicted signal peptidase target sequence. Contains DUF541 domain. YP_264267.1 This gene also had significant hits to phage methylases. YP_264268.1 RBS found. YP_264270.1 good rbs. Predicted by glimmer only. 22base pair cleavage site YP_264271.1 good rbs. Predicted by generation, glimmer and critica. YP_264273.1 Contains a metallopeptidase zinc binding site. YP_264274.1 Predicted by glimmer only. Good rbs YP_264275.1 good rbs. Predicted by glimmer and critica. YP_264276.1 LexA family, clan SF YP_264281.1 strong ribosomal binding site, predicted by glimmer and critica YP_264285.1 Phage related YP_264313.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.995) with cleavage site probability 0.614 at residue 27 YP_264314.1 Predicted by generation, glimmer and critica. 3 base rbs YP_264320.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.838) with cleavage site probability 0.795 at residue 31 YP_264323.1 catalyzes the formation of 3-phosphonooxypyruvate and glutamate from O-phospho-L-serine and 2-oxoglutarate; required both in major phosphorylated pathway of serine biosynthesis and in the biosynthesis of pyridoxine YP_264324.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.996) with cleavage site probability 0.861 at residue 25 YP_264326.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.999) with cleavage site probability 0.977 at residue 30 YP_264327.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.996) with cleavage site probability 0.796 at residue 63 YP_264330.1 this fusion consists of methionine sulfoxide A reductase at the N-terminus and B at the C-terminus; A and B are stereospecific enzymes that recognize the damaged produces of oxidative stress, S and R epimers of methionine sulfoxide, respectively; a fusion YP_264332.1 Glucose/ribitol dehydrogenase contains this domain for substrate YP_264333.1 48 base signalP site at N-terminus, 6 predicted transmembrane spannning helices; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.972) with cleavage site probability 0.560 at residue 26 YP_264334.1 4 base rbs. Predicted by generation, glimmer and critica. YP_264336.1 DEAD/DEAH box helicase:Helicase, C-terminal:ATP/GTP-binding site motif A (P-loop):AAA ATPase:Helicase-associated region YP_264338.1 catalyzes the condensation of acetyl-CoA with malonyl-ACP to initiate cycles of fatty acid elongation; differs from 3-oxoacyl-(acyl carrier protein) synthase I and II in that it utilizes CoA thioesters as primers rather than acyl-ACPs YP_264339.1 recognizes the termination signals UAG and UAA during protein translation a specificity which is dependent on amino acid residues residing in loops of the L-shaped tRNA-like molecule of RF1; this protein is similar to release factor 2 YP_264340.1 class II; LysRS2; catalyzes a two-step reaction, first charging a lysine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; in Methanosarcina barkeri, LysRS2 charges both tRNA molecules for lysine that exist in this organism and in addition can charge the tRNAPyl with lysine in the presence of LysRS1 YP_264341.1 If the gene is translated completely then the tau subunit is synthesized. If translation slips or frameshifts part way through the reading frame then a stop codon is encountered, and the gamma subunit is synthesized. YP_264342.1 contains N' terminal HTH motif and the LysR substrate binding domain but doesn't match closely any of the known family members; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.757) with cleavage site probability 0.523 at residue 25 YP_264343.1 catalyzes the formation of N-acetyl-l-glutamate 5-semialdehyde from 2-oxoglutarate and N(2)-acetyl-L-ornithine YP_264345.1 contains hit to SAM (and some other nucleotide) binding motif over 22% of gene YP_264346.1 Citation: Interpro: This family includes ABC1 from yeast [MEDLINE:91293073] and AarF from E. coli [MEDLINE:98083065]. YP_264347.1 catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis YP_264348.1 Contains a strong alignment Pfam bacterial NAD glutamate dehydrogenase from Streptomyces clavuligerus YP_264349.1 The C subunit contains the ATPase activity of the complex. YP_264353.1 Aligns to COG3749: Uncharacterized bacterial protein. YP_264355.1 ATP sulfurylase; ATPS; converts ATP and sulfate to 5'phosphosulfate and pyrophosphate; in some organisms this enzyme is involved in the incorporation of inorganic sulfate while in others it is involved in the production of ATP in the reverse direction; the enzyme from Thermus thermophilus is dimeric and binds a zinc ion that is coordinated by cysteine and histidine residues that are not found in all related proteins but is found in some thermophilic organisms YP_264357.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.881) with cleavage site probability 0.411 at residue 34 YP_264358.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.882) with cleavage site probability 0.663 at residue 56 YP_264361.1 helix turn helix domain supports regulatory role; Citation: Bairoch A. Nuclic Acids Res. 21: 2515- 2515 (1993) [PubMed: 8506147 ] J Biol Chem. 1996 Feb 2;271(5):2427-32. YP_264366.1 YghU; B2989; one of eight glutathione transferases from E. coli YP_264367.1 65bp signalP site at n-terminus; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.999) with cleavage site probability 0.998 at residue 65 YP_264369.1 12 transmembrane helices, Aligns with DUF819 domain HMM, RBS found YP_264370.1 RBS found. Contains GntR family helix-turn-helix domain. YP_264371.1 10 transmembrane helices, SignalP site; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.950) with cleavage site probability 0.945 at residue 27 YP_264373.1 RBS identified YP_264375.1 weak rbs. 37 bp cleavage site predicted. Predicted by generation, glimmer and critica. YP_264376.1 SignalP detects a signal peptidase target sequence in the N-terminus. Good RBS found.; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.996) with cleavage site probability 0.710 at residue 23 YP_264377.1 contains 11 predicted trans-membrane helices YP_264379.1 has fis type and LysR helix turn helix motifs with LysR substrate domain YP_264388.1 RBS found. YP_264389.1 RBS found. YP_264390.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.869) with cleavage site probability 0.721 at residue 37 YP_264392.1 Predicted by generation, glimmer and critica. good rbs. 1 transmembrane helix YP_264393.1 LysR substrate binding domain and LysR helix- turn- helix motif YP_264395.1 catalyzes the formation of pyruvate and succinate from 2-methylisocitrate YP_264396.1 catalyzes the synthesis of 2-methylcitrate from propionyl-CoA and oxaloacetate; also catalyzes the condensation of oxaloacetate with acetyl-CoA but with a lower specificity YP_264397.1 Catalyzes the conversion of citrate to isocitrate YP_264399.1 RBS found. YP_264400.1 DUF453 family domain YP_264402.1 functions in propionate metabolism; involved in isomerization of (2S,3S)-methylcitrate to (2R,3S)-methylisocitrate; also encodes minor aconitase or dehydratase activity; aconitase C YP_264404.1 Probable integral membrane proteindue to presence of 4 transmembrane domains YP_264405.1 ATP/GTP binding motif YP_264407.1 RBS found. YP_264409.1 RBS found. YP_264410.1 Catalyzes the salvage synthesis of inosine-5'-monophosphate (IMP) and guanosine-5'-monophosphate (GMP) from the purine bases hypoxanthine and guanine, respectively YP_264414.1 Promoter region looks good, but no RBS identified. YP_264415.1 SignalP detects a signal peptidase target site. The site contains a predicted transmembrane helix. No RBS consensus found.; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.761) with cleavage site probability 0.604 at residue 27 YP_264416.1 RBS found. YP_264417.1 All possess a potential HTH DNA-binding motif towards their N-termini YP_264418.1 4 transmembrane domains. DoxD-like. The nearest orf adjacent does not match a terminal quinol oxidase subunit II by hydropathy lot search, so this is probably not DoxD.; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.985) with cleavage site probability 0.873 at residue 34 YP_264421.1 The helix-turn-helix motif found here is found in a large family of proteins with diverse functions. YP_264424.1 8 predicted transmembrane helices. YP_264429.1 The beta subunit catalyzes the decarboxylation of the malonyl moiety on coenzyme A YP_264435.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.998) with cleavage site probability 0.995 at residue 35 YP_264436.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.998 at residue 23 YP_264437.1 No indication of substrate, could be polyamine oxidase or L-amino acid oxidase YP_264438.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.992) with cleavage site probability 0.836 at residue 35 YP_264439.1 RBS found. Aligns weakly to universal stress protein HMM. YP_264440.1 Homology searches provide good matches to archeal and eukaryal 5'-methylthioadenosine phosphorylase, but these enzymes are not noted to occur in bacteria. YP_264441.1 Aligns well to eukaryotic methyltransferases. Contains SAM binding motif. Contains generic methyltransferase motif. YP_264442.1 Contains DUF703 domain. YP_264444.1 RBS found. Contains a predicted signal peptidase target sequence. YP_264445.1 RBS found. Contains a weak alignment to the radical SAM superfamily domain and a cytochrome C heme-binding motif. YP_264446.1 5 probable transmembrane helices near to the N-terminus. YP_264448.1 1 probable transmembrane domain. YP_264450.1 PAP phosphotase domain YP_264451.1 RBS found YP_264452.1 This gene occurs close proximity to six other fatty acid biosynthesis orfs. YP_264454.1 Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation YP_264455.1 converts 3-hydroxyadipyl-CoA to beta-ketoadipyl-CoA in phenylacetate degradation YP_264456.1 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA YP_264458.1 Aromatic Acid:H+ Symporter (AAHS) Family; Citation: Applied and Environmental Microbiology, October 2001, p. 4817-4827, Vol. 67, No. 10 YP_264459.1 Nearly 60% ID to other transcriptional regulators in BLAST and the HTH motif hit is also strong InterPro:buthitstoIclRfamilyoftranscriptional regulators are weak. YP_264460.1 There is no clear indicator of the exact function of this acetyl-CoA hydrolase/transferase family member. YP_264461.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 1.000 at residue 39 YP_264462.1 DNA polymerase III is comprised of three tightly associated subunits, alpha, epsilon and theta. YP_264465.1 Contains four hexapeptide repeat motifs. YP_264468.1 There are 9 transmembrane domains. YP_264469.1 catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate and the formation of tyrosine from arogenate and catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis YP_264470.1 catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis YP_264471.1 Contains 3 domains: chorismate mutase, prephenate dehydratase, and an ACT (amino acid synthesis regulatory domain). This enzyme is bifunctional in the phenylalanine synthesis pathway. YP_264472.1 Maintains the balance of metabolites in the pentose-phosphate pathway YP_264473.1 SignalP detects a signal peptidase target site. RBS found.; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.995 at residue 20 YP_264474.1 catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis YP_264477.1 RBS found. One predicted transmembrane helix. Contains a predicted signal peptidase target sequence. YP_264478.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.754) with cleavage site probability 0.616 at residue 29 YP_264481.1 Beta chain domain at N-terminus followed closely by alpha chain to C-terminus. YP_264482.1 Predicted by generation, glimmer and critica. 4 base rbs. YP_264483.1 bifunctional arginine biosynthesis protein ArgJ; functions at the 1st and 5th steps in arginine biosynthesis; involved in synthesis of acetylglutamate from glutamate and acetyl-CoA and ornithine by transacetylation between acetylornithine and glutmate YP_264484.1 removes the damaged DNA at cytosines and guanines by cleaving on the 3' side of the AP site by a beta-elimination reaction YP_264487.1 SohB; periplasmic protein; member of the peptidase S49 family YP_264488.1 catalyzes a two-step reaction, first charging an aspartate molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; contains discriminating and non-discriminating subtypes YP_264490.1 good rbs YP_264492.1 These glycosyl transferases are involved in LPS biosynthesis. YP_264493.1 RBS found. YP_264494.1 RBS found. YP_264495.1 No rbs. Predicted by glimmer and critica. YP_264500.1 catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids YP_264501.1 catalyzes the ATP-dependent addition of AMP to a subunit of glutamine synthetase; also catalyzes the reverse reaction - deadenylation; adenylation/deadenylation of glutamine synthetase subunits is important for the regulation of this enzyme YP_264503.1 RBS found. This orf occurs between a probable DsrE-like protein and a probable DsrC-like protein. YP_264504.1 RBS found. Overlaps a probable DsrC-like protein by 4 bp. There is a probable DsrE-like protein two orfs upstream. YP_264507.1 similar to E. coli ecnA YP_264508.1 The amino acid sequence also aligns with a radical SAM catalytic HMM. This supports its probable role in an anaerobic oxidation. YP_264509.1 12 probable transmembrane domains.; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.884) with cleavage site probability 0.838 at residue 33 YP_264512.1 4 base rbs. Predicted by generation, glimmer and critica. YP_264515.1 12 transmembrane domains. YP_264517.1 MoeZ_MoeB HMM matched in Pfam. ThiF domain is present. YP_264518.1 SAM binding motif, Methylase motif both found by PROSITE YP_264519.1 14 transmembrane domains. Subcellular location: Integral membrane protein. Category is Drug/analog sensitivity; Citation: Microbiology. 1995 May; 141 ( Pt 5): 1085-92 and http://uqbar.rockefeller.edu/regulons/ClustersWadsworth/u_ prommatches84.html YP_264520.1 possible cbl regulon regulator based on homolgy with BLAST YP_264521.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.663) with cleavage site probability 0.185 at residue 24 YP_264524.1 GidA; glucose-inhibited cell division protein A; involved in the 5-carboxymethylaminomethyl modification (mnm(5)s(2)U) of the wobble uridine base in some tRNAs YP_264525.1 Predicted by generation, glimmer and critica. 3 base rbs. YP_264527.1 catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate into 2-C-methyl-D-erythritol 2,4-cyclodiphosphate YP_264528.1 catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs YP_264529.1 Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide YP_264530.1 Predicted by generation, glimmer. 25 bp cleavage site. 1 transmembrane domain weak rbs YP_264532.1 RBS found. This orf aligns weakly to the C-terminal end of PutA, and occurs immediately downstream of that gene in Psychrobacter 273-4. YP_264533.1 proline utilization protein A; multifunctional protein that functions in proline catabolism in the first two enzymatic steps resulting in the conversion of proline to glutamate; in Escherichia coli this protein self regulates transcription via a DNA-binding domain at the N-terminus but the proteins from this group do not and in addition appear to have a truncated C-terminal domain YP_264535.1 4 bp overlap with a TolQ-like ORF YP_264536.1 RBS found. Weak alignment (above trusted cutoff) to TIGR TonB C-terminal subfamily HMM. Serine rich region identified N-terminal to this. Contains 1 predicted transmembrane domain. YP_264537.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 1.000 at residue 27 YP_264540.1 RBS found. Aligns to TIGR hypothetical equivalog for DUF152 proteins. YP_264541.1 In E. coli, RluD (SfhB) modifies uridine to pseudouridine at 23S RNA U1911, 1915, and 1917, RluC modifies 955, 2504 and 2580, and RluA modifies U746 and tRNA U32. An additional homolog from E. coli, YqcB (EGAD|35358|EC2791), is uncharacterized. YP_264544.1 contains the 4 conserved regions of rpoD also nonessential domains associated with other rpoD YP_264545.1 Protein of unknown function UPF0187 domain YP_264547.1 Catalyzes the rate-limiting step in dNTP synthesis YP_264548.1 1 transmembrane region ,has weak rbs so may be a protein despite only glimmer prediction YP_264549.1 Overlaps a StbE like ORF. YP_264551.1 RBS found. YP_264552.1 B2 or R2 protein; type 1a enzyme; catalyzes the rate-limiting step in dNTP synthesis; converts nucleotides to deoxynucleotides; forms a homodimer and then a multimeric complex with NrdA YP_264555.1 (DUF34) protein domain YP_264557.1 One Transglycosylase domain and 7 LysM lysin domains. YP_264558.1 Predicted by generation, glimmer and critica. 3 base rbs. 1 transmembrane domain, 36 bp cleavage site YP_264559.1 Possible transmembrane protein with CBS domains YP_264561.1 part of the preprotein secretory system; when complexed with proteins SecF and YajC, SecDFyajC stimulates the proton motive force-driven protein translocation, and appears to be required for the release of mature proteins from the extracytoplasmic side of the membrane YP_264562.1 forms a complex with SecD and YajC; SecDFyajC stimulates the proton motive force-driven protein translocation; seems to modulate the cycling of SecA by stabilizing its membrane-inserted state and appears to be required for the release of mature proteins from the extracytoplasmic side of the membrane; in some organisms, such as Bacillus subtilis, SecD is fused to SecF YP_264565.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.958) with cleavage site probability 0.952 at residue 23 YP_264566.1 Catalyzes first step of the de novo purine nucleotide biosynthetic pathway YP_264568.1 catalyzes the conversion of dihydroorotate to orotate in the pyrimidine biosynthesis pathway; uses a flavin nucleotide as an essential cofactor; class 2 enzymes are monomeric and compared to the class 1 class 2 possess an extended N terminus, which plays a role in the membrane association of the enzyme and provides the binding site for the respiratory quinones that serve as physiological electron acceptors YP_264570.2 catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate YP_264574.1 RBS found. SignalP detects a signal peptidase target site.; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.851 at residue 23 YP_264575.1 bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides YP_264576.1 RBS found YP_264577.1 catalyzes the formation of nictonate and 5-phospho-alpha-D-ribose 1-diphosphate from nicotinate D-ribonucleotide and diphosphate YP_264580.1 catalyzes the hydrolysis of pyrophosphate to phosphate YP_264581.1 RBS found. Contains one predicted transmembrane domain. YP_264582.1 RBS found YP_264584.1 nifR3 is thought to be a regulatory protein, rather than a catalytic protein, however, the two families (Dihydrouridylate synthase, and nifR3) may constitute a larger family with conserved cysteine residues. YP_264587.1 RBS found. YP_264588.1 catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis YP_264589.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.726) with cleavage site probability 0.687 at residue 20 YP_264592.1 RBS found YP_264593.1 Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis YP_264594.1 Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation YP_264595.1 domain hit to Protein of unknown function DUF344 YP_264597.1 Citation: Song MS, Pham PT, Olson M, Carter JR, Franden MA, Schaaper RM, McHenry CS. 2001. The delta and delta ' subunits of the DNA polymerase III holoenzyme are essential for initiation complex formation and processive elongation. J Biol Chem. 276:35165-35175. YP_264598.1 CMP-2-keto-3-deoxyoctulosonic acid synthetase; catalyzes the formation of CMP-3-deoxy-D-manno-octulosonate from CTP and 3-deoxy-D-manno-octulosonate which is incorporated into LPS YP_264599.1 transfers the gamma-phosphate of ATP to the 4' position of a tetraacyldisaccharide 1-phosphate intermediate to form tetraacyldisaccharide 1,4'-bis-phosphate YP_264603.1 This group of chromosomal and plasmid partition proteins are related to ParB, including Spo0J, RepB, and SopB. YP_264605.1 glucose-inhibited division protein B; SAM-dependent methyltransferase; methylates the N7 position of guanosine in position 527 of 16S rRNA YP_264607.1 This is a long protein and hits to transcriptinal factors are only in middle also no helix turn helix domains which would signify nucleic acid binding YP_264610.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.995 at residue 22 YP_264612.1 E1 component; part of pyruvate dehydrogenase; forms a complex with DlaT and LpdC YP_264613.1 not enough evidence to determine sub family membership YP_264615.1 RBS found. YP_264617.1 catalyzes the conversion of NADPH to NADH YP_264618.1 RBS found. Aligns to DUF299 domain of unknown function HMM. YP_264619.1 catalyzes the formation of phosphoenolpyruvate from pyruvate YP_264620.1 contains 3 predicted transmembrane domains YP_264621.1 binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21 YP_264622.1 binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit YP_264623.1 in Escherichia coli this protein is wrapped around the base of the L1 stalk YP_264624.1 RBS found. YP_264626.1 RBS found YP_264628.1 Substrate unknown. Aligns to DAO family HMM and DAO COG. YP_264630.1 12 predicted transmembrane helices YP_264631.1 RBS found YP_264636.1 No RBS found. YP_264637.1 Predicted by generation, glimmer and critica. YP_264641.1 catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate YP_264642.1 Two CBS domains are found in this ORF. YP_264643.1 catalyzes a two-step reaction; charges a cysteine by linking its carboxyl group to the alpha-phosphate of ATP then transfers the aminoacyl-adenylate to its tRNA YP_264645.1 not a membrane binding inner protein despite the domain presence because these proteins contain transmembrane helices to either side of domain YP_264649.1 NADP-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; decarboxylates oxaloacetate YP_264651.1 Involved in pteridine salvage and antifolate resistance YP_264652.1 Members of this family cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment. YP_264653.1 RBS found. YP_264654.1 RBS found. Aligns to ThiF family domain. YP_264656.1 Patatin is a phospholipase. YP_264658.1 RBS found. YP_264659.1 DUF262 domain YP_264660.1 Predicted by generation, glimmer and critica. strong rbs YP_264661.1 RBS found. Aligns to COG5579: Uncharacterized conserved protein. YP_264662.1 Predicted by generation, glimmer and critica. strong rbs YP_264663.1 contains p-loop ATP binding domain YP_264665.1 contains ATP/GTP binding Ploop YP_264667.1 RBS found YP_264668.1 RBS found YP_264669.1 malic enzyme; oxaloacetate-decarboxylating; NAD-dependent; catalyzes the formation of pyruvate form malate YP_264672.1 Citation: Appl Microbiol Biotechnol. 2003 Jul;62(1):53-60 YP_264677.1 bind DNA via a helix-turn-helix (HTH) motif. possible acrR subfamily but weak sequence similarity. YP_264680.1 Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation YP_264682.1 Citation: A new family of CoA-transferases. Heider J. FEBS Lett 2001;509:345-349. YP_264685.1 catalyzes the formation of L-glutamate and an aromatic oxo acid from an aromatic amino acid and 2-oxoglutarate YP_264686.1 Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step YP_264687.1 LysM domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation.; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.994) with cleavage site probability 0.849 at residue 36 YP_264688.1 contains TPR repeat know to be involved in protein-protein interaction YP_264690.1 mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability YP_264691.1 stimulates the activities of the other two initiation factors, IF-2 and IF-3 YP_264692.1 catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis YP_264693.1 Predicted by generation, glimmer and critica. 1 transmembrane helice, 23 base cleavage site predicted YP_264694.1 catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis; forms a heterodimer of LeuC/D YP_264695.1 dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate YP_264696.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.701) with cleavage site probability 0.650 at residue 22 YP_264700.1 Predicted by generation, glimmer and critica. 3 site rbs YP_264702.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.906) with cleavage site probability 0.392 at residue 32 YP_264704.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.995 at residue 27 YP_264705.1 -adjacent or2766 is sspB, possible evidence supporting sspA assignment for this protein; Citation: Hansen A.M., Lehnherr H., Wang X., Mobley V., Jin D.J. (2003) Escherichia coli SspA is a transcription activator for bacteriophage P1 late genes. Mol Microbiol 48:1621-1631. YP_264707.1 Catalyzes the formation of dUTP from dCTP in thymidylate biosynthesis YP_264709.1 There are 9 addittional ORFs identical to this one. YP_264710.1 catalyzes the formation of acetoacetate from 3-hydroxybutyrate YP_264713.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.911) with cleavage site probability 0.549 at residue 22 YP_264714.1 methionine--tRNA ligase; MetRS; adds methionine to tRNA(Met) with cleavage of ATP to AMP and diphosphate; some MetRS enzymes form dimers depending on a C-terminal domain that is also found in other proteins such as Trbp111 in Aquifex aeolicus and the cold-shock protein CsaA from Bacillus subtilis while others do not; four subfamilies exist based on sequence motifs and zinc content YP_264715.1 Predicted by generation, glimmer and critica. Predicted signalP cleavage site. strong rbs YP_264716.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.523 at residue 27 YP_264720.1 Response regulatory domain found N-terminal to a DNA binding effector domain of LuxR family; Citation: Pao G.M. , Saier M.H. Response regulators of bacterial signal transduction systems: selective domain shuffling during evolution. J. Mol. Evol. 40: 136- 154 (1995) [PubMed: 7699720 ] YP_264723.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.631) with cleavage site probability 0.394 at residue 34 YP_264728.1 evidence for ATP dependence from binding site, luxR family binding site at C-terminus. Closest match to MalT due to size of protein. YP_264729.1 RBS found. YP_264732.1 Citation: Miriam K. Sluis and Scott A., Proc. Natl. Acad. Sci. USA. 1997 August 5; 94 (16): 8456-8461 YP_264734.1 contains fis type helix turn helix motif suggesting nucleic acid binding YP_264735.1 Integrase, catalytic domain YP_264737.1 catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis YP_264738.1 involved in methylation of ribosomal protein L3 YP_264739.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.997) with cleavage site probability 0.995 at residue 48 YP_264742.1 Catalyzes a two-step reaction, first charging an alanyl molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA YP_264743.1 catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP, in Bacillus, lysine sensitive; regulated by response to starvation. YP_264744.1 affects carbohydrate metabolism; has regulatory role in many processes YP_264746.1 Aligns to COG3139: Uncharacterized protein YP_264747.1 catalyzes the phosphorylation of NAD to NADP YP_264748.1 contains 7 predicted transmembrane regions YP_264751.1 protein interacting Tpr repeat domain; Citation: ieter P. , Tugendreich S. , Lamb J.R. Tetratrico peptide repeat interactions: to TPR or not to TPR? Trends Biochem. Sci. 20: 257- 259 (1995) [PubMed: 7667876 ]; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.989) with cleavage site probability 0.571 at residue 44 YP_264752.1 methylates ribosomal protein L11 at multiple amino acid positions; mutations of these genes in Escherichia coli or Thermus thermophilus has no apparent phenotype YP_264753.1 helix-turn-helix YP_264754.1 involved in de novo purine biosynthesis YP_264757.1 RBS found. Contains two predicted transmembrane domains. YP_264758.1 These are small proteins of 12 to 18 kD which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; Winged helix DNA-binding YP_264760.1 N-terminal only YP_264763.1 involved in the maturation of iron-sulfur cluster-containing proteins YP_264766.1 DExH/D-box domain found in ATPases that have been proposed to mediate RNA structural rearrangements in a variety of cellular processes, including nuclear pre-mRNA splicing, ribosome assembly, protein synthesis, nuclear transport, and RNA degradation .; Citation: Linder P. , Schmid S.R. D-E-A-D protein family of RNA helicases. Mol. Microbiol. 6: 283- 292 (1992) [PubMed: 1552844 ] YP_264767.1 regulator of RNase E; increases half-life and abundance of RNAs; interacts with RNase E possibly inhibiting catalytic activity YP_264769.1 binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase YP_264770.1 Predicted by generation, glimmer and critica. 3 base RBS. YP_264772.1 There are 9 addittional ORFs identical to this one. YP_264773.1 type 1 subfamily; involved in last step of pyrimidine biosynthesis; converts orotidine 5'-phosphate to UMP and carbon dioxide; OMP decarboxylase; OMPDCase; OMPdecase YP_264774.1 Predicted by generation, glimmer and critica. Good rbs. 2 transmembrane helices and predicted signal P cleavage site YP_264776.1 in Escherichia coli this protein is involved in binding to the leader sequence of mRNAs and is itself bound to the 30S subunit; autoregulates expression via a C-terminal domain; in most gram negative organisms this protein is composed of 6 repeats of the S1 domain while in gram positive there are 4 repeats; the S1 nucleic acid-binding domain is found associated with other proteins YP_264778.1 Contains family-specific zinc binding domain YP_264779.1 Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine YP_264781.1 Contains ClpS HMM (formerly DUF174). This orf occurs immediately upstream of clpA. YP_264782.1 1 predicted transmembrane domain. Predicted by glimmer, critica and generation, good rbs YP_264783.1 catalyzes the reduction of N-acetyl-5-glutamyl phosphate to N-acetyl-L-glutamate 5-semialdehyde in arginine biosynthesis and the reduction of N-acetyl-gamma-aminoadipyl-phosphate to N-acetyl-L-aminoadipate-semialdehyde in lysine biosynthesis; involved in both the arginine and lysine biosynthetic pathways; lysine is produced via the AAA pathway, lysine from alpha-aminoadipate YP_264784.1 catalyzes the formation of coproporphyrinogen from uroporphyrinogen III YP_264785.1 catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis YP_264786.1 essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication YP_264787.1 catalyzes the formation of 3-phospho-D-glyceroyl phosphate from D-glyceraldehyde 3-phosphate; involved in growth under gluconeogenic conditions and in glycolytic activity at high ATP concentrations in Corynebacterium; NAD and NADP dependent YP_264790.1 No RBS found. YP_264791.1 RBS found. YP_264794.1 Ubiquinone biosyntheis proteins are central metabolic regulatory proteins and the side chain of ubiquinones play a significant role in respiration YP_264795.1 alanine rich region at N-terminus suggests membrane glycoprotein as do blast hits; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 1.000 at residue 35 YP_264796.1 serine dependent catalytic site present; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.998) with cleavage site probability 0.343 at residue 40 YP_264799.1 eIF-2Bgamma; eIF-2Bepsilon; translation initiation factor 2B gamma and epsilon subunits YP_264800.1 Aligns to COG3178: Predicted phosphotransferase YP_264801.1 PFAM data suggest two domain structure with a MP dehydrogenase/GMP reductase domain in the 5' end; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.982 at residue 28 YP_264802.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.995 at residue 32 YP_264805.1 catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde YP_264806.1 Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr) YP_264808.1 catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis YP_264809.1 in Pseudomonas aeruginosa this enzyme is a trimer of dimers; essential for membrane formation; performs third step of type II fatty acid biosynthesis; catalyzes dehydration of (3R)-hydroxyacyl-ACP to trans-2-acyl-ACP YP_264810.1 adds the O-linked and N-linked 3(R)-hydroxy fatty acids to the glucosamine disaccharide during lipid A biosynthesis YP_264813.1 catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate YP_264816.1 Rrf; Frr; ribosome-recycling factor; release factor 4; RF4; recycles ribosomes upon translation termination along with release factor RF-3 and elongation factor EF-G; A GTPase-dependent process results in release of 50S from 70S; inhibited by release factor RF-1; essential for viability; structurally similar to tRNAs YP_264817.1 Catalyzes the phosphorylation of UMP to UDP YP_264818.1 catalyzes the methylthiolation of an aspartic acid residue of the S12 protein of the 30S ribosomal subunit YP_264820.1 probable nitrogen regulation YP_264822.1 ATP binding P-loop YP_264823.1 predicted by generation, critica and glimmer, 4 base rbs YP_264825.1 DNA gyrase is a type II topoisomerase that cleaves two strands of DNA and is ATP dependent. YP_264830.1 in Escherichia coli RsmE methylates the N3 position of the U1498 base in 16S rRNA; cells lacking this function can grow, but are outcompeted by wild-type; SAM-dependent m(3)U1498 methyltransferase YP_264832.1 RBS found. Contains a Sel1-like repeat. YP_264833.1 catalyzes the transfer of a phosphatidyl group to phosphodidylglycerol to form cardiolipin (diphosphatidylglycerol) YP_264834.1 3'-5' exoribonuclease specific for small oligoribonuclotides YP_264838.1 molecular chaperone that is required for the normal export of envelope proteins out of the cell cytoplasm; in Escherichia coli this proteins forms a homotetramer in the cytoplasm and delivers proteins to be exported to SecA YP_264844.1 strong rbs. Predicted by glimmer, generation and critica. 4 transmembrane helices predicted. YP_264847.1 in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit YP_264848.1 forms a direct contact with the tRNA during translation YP_264850.1 catalyzes a two-step reaction, first charging a tryptophan molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA YP_264851.1 DUF173 domain YP_264854.1 involved in the peptidyltransferase reaction during translation YP_264856.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.677) with cleavage site probability 0.297 at residue 22 YP_264857.1 related to HlyD family; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.916) with cleavage site probability 0.676 at residue 22 YP_264858.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.659) with cleavage site probability 0.413 at residue 30 YP_264859.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.990) with cleavage site probability 0.740 at residue 27 YP_264860.1 catalyzes the formation of porphobilinogen from 5-aminolevulinate YP_264862.1 No RBS found. YP_264863.1 RBS found. SignalP detects one signal peptidase target sequence.; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.760 at residue 23 YP_264866.1 3 transmembrane helices, predicted by glimmer, critica and generation, 3 base rbs YP_264868.1 TatA; similar to TatE that is found in some proteobacteria; part of system that translocates proteins with a conserved twin arginine motif across the inner membrane; capable of translocating folded substrates typically those with bound cofactors; similar to a protein import system in thylakoid membranes YP_264871.1 RBS found. Contains three predicted transmembrane domains. YP_264876.1 Found an AGGA, around 11 nucleotides upstream of the initiation codon. YP_264877.1 predicted only by glimmer, 3 base rbs YP_264878.1 adjacent protein is histidine kinase YP_264879.1 contains 2 transmembrane domains, HAMP, ATP binding Histidine kinase A, N-terminal:Bacterial sensor protein, C-term domains; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.743) with cleavage site probability 0.664 at residue 28 YP_264885.1 RBS found YP_264886.1 catalyzes the formation of pyruvate from D-cysteine YP_264887.1 RBS found. SignalP predicts a signal peptidase target sequence. YP_264888.1 TrK family YP_264889.1 Trk family of K+ tranporters YP_264890.1 RBS found. YP_264891.1 No RBS found. YP_264892.1 gapA domain YP_264894.1 Chloroacetaldehyde is a possible substrate YP_264897.1 This protein contains a DNA binding Zn-finger domain associated with type I topoisomerase (COG0551, PF01396). YP_264898.1 RBS found. YP_264899.1 catalyzes the formation of ribose 5-phosphate and xylulose 5-phosphate from sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate; can transfer ketol groups between several groups; in Escherichia coli there are two tkt genes, tktA expressed during exponential growth and the tktB during stationary phase YP_264900.1 catalyzes a two-step reaction, first charging a serine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA YP_264901.1 RBS found. Contains two predicted transmembrane domains. YP_264902.1 Citation: GRANT, R.A., FILMAN, D.J., FINKEL, S.E., KOLTER, R. AND HOGLE, J.M. The crystal structure of Dps, a ferritin homolog that bind YP_264903.1 1 transmembranne helix, signal P predicted cleavage site, predicted by glitter,generation and critica, good rbs YP_264906.1 catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis YP_264909.1 Catalyzes the first step in the glyoxalate cycle, which converts lipids to carbohydrates YP_264911.1 RBS found. Contains alignment to ErfK/YbiS/YcfS/YnhG domain HMM. YP_264912.1 One predicted transmembrane domain. YP_264913.1 catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming YP_264914.1 catalyzes the formation of N-carbamoyl-L-aspartate from (S)-dihydroorotate in pyrimidine biosynthesis YP_264915.1 Responsible for the end-turnover of tRNA: specifically removes the terminal AMP residue from uncharged tRNA (tRNA-C-C-A) YP_264918.1 enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis YP_264921.1 RBS found YP_264922.1 catalyzes the formation of 2-dehydro-3-deoxy-D-octonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate in LPS biosynthesis YP_264923.1 CTP synthase; CTP synthase; cytidine triphosphate synthetase; catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen; in Escherichia coli this enzyme forms a homotetramer YP_264925.1 catalyzes the formation of malate from glyoxylate and acetyl-CoA YP_264927.1 RBS found YP_264928.1 RBS present, no alignments found YP_264929.1 catalyzes the reversible transfer of the terminal phosphate of ATP to form a long chain polyphosphate YP_264938.1 Citation: J Biol Chem. 1999 Mar 5;274(10):6726-34.; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.980 at residue 34 YP_264939.1 class II family (does not require metal); tetrameric enzyme; fumarase C; reversibly converts (S)-malate to fumarate and water; functions in the TCA cycle YP_264942.1 catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity YP_264943.1 RBS present YP_264947.1 prenylation site indicates possible post- translational modification YP_264952.1 converts 2-oxoglutarate to glutamate; in Escherichia coli this enzyme plays a role in glutamate synthesis when the cell is under energy restriction; uses NADPH; forms a homohexamer YP_264955.1 Protein of unknown function DUF302; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.999) with cleavage site probability 0.445 at residue 21 YP_264956.1 it is proposed that many, if not all, microbial homologs of the transglutaminases are proteases YP_264961.1 Also shares some significant alignments with the DUF160 family of conserved hypothetical proteins. YP_264962.1 Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA YP_264964.1 Citation: Wexler M, Sargent F, Jack RL, Stanley NR, Bogsch EG, Robinson C, Berks BC, Palmer T. 2000. TatD is a cytoplasmic protein with DNase activity. No requirement for TatD family proteins in sec-independent protein export. J Biol Chem. 275:16717-16722 YP_264967.1 UvrA is a member of the ABC transporter superfamily of proteins. Except for UvrA proteins, all members of this family for which functions are known are involved in the transport of material through membranes. YP_264968.1 RBS present, no alignment YP_264972.1 Protein of unknown function DUF503 YP_264973.1 Probably a conserved membrane protein: has 5 TM domains predicted YP_264975.1 catalyzes the reduction of 2 glutathione to glutathione disulfide; maintains high levels of reduced glutathione in the cytosol; involved in redox regulation and oxidative defense YP_264976.1 2 TM domains present YP_264981.1 unknown function; YciI from Haemophilus influenzae presents crystal structure similarity to a muconolactone isomerase, but does not seem to catalyze any of the predicted reactions based on sequence and structure similarity YP_264982.1 2 TM domain and presence of a signal peptide; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.991 at residue 36 YP_264984.1 UbiA prenyltransferase family catalyzes the transfer of a prenyl group to various acceptors with hydrophobic ring structures in the biosynthesis of respiratory quinones, hemes, chlorophylls, vitamin E, and shikonin YP_264985.1 1 TM domain predicted, RBS present, no alignments YP_264987.1 BacA; phosphatase activity in Escherichia coli not kinase; involved in bacitracin resistance as bacitracin supposedly sequesters undecaprenyl disphosphate which reduces the pool of lipid carrier available to the cell YP_264990.1 proposed to be related to ABC transporter permease domains, contains 8 TM domains; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.863) with cleavage site probability 0.282 at residue 17 YP_264992.1 required for 70S ribosome assembly YP_264993.1 in Escherichia coli BM108, a mutation that results in lack of L33 synthesis had no effect on ribosome synthesis or function; there are paralogous genes in several bacterial genomes, and a CXXC motif for zinc binding and an upstream regulation region of the paralog lacking this motif that are regulated by zinc similar to other ribosomal proteins like L31; the proteins in this group lack the CXXC motif YP_264994.1 RBS present YP_264995.1 possible integral membrane protein, 4 TM domains YP_264996.1 possible integral membrane protein, 3 TM domains YP_264999.1 Citation: S-formylglutathione hydrolase of Paracoccus denitrificans is homologous to human esterase D: a universal pathway for formaldehy YP_265001.1 molecular chaperone YP_265004.1 catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate into isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP); functions in the nonmevalonate isoprenoid biosynthesis pathway YP_265005.1 Essential for recycling GMP and indirectly, cGMP YP_265006.1 Promotes RNA polymerase assembly; latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits YP_265007.1 no direct information on the functions of the TGS domain, but its presence in two types of regulatory proteins (the GTPases and guanosine polyphosphate phosphohydrolases/synthetases) suggests a ligand (most likely nucleotide)-binding, regulatory role.; Citation: Koonin E.V. , Grishin N.V. , Aravind L. , Wolf Y.I. Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res. 9: 689- 710 (1999) YP_265008.1 May also play a role in purine biosynthesis regulation.; Citation: J Bacteriol. 1999 Jun 15; 181(12): 3810-3815 YP_265012.1 4 transmembrane helices YP_265014.1 catalyzes the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs YP_265015.1 Citation: Stohl,E.A., Brockman,J.P., Burkle,K.L., Morimatsu,K., Kowalczykowski,S.C. and Seifert,H.S. Escherichia coli RecX inhibits RecA YP_265017.1 2 transmembrane helices and signal peptide present YP_265022.1 Possible RNA-binding protein containing KH domain YP_265026.1 zinc-dependent; catalyzes the deacetylation of UDP-(3-O-acyl)-N-acetylglucosamine to UDP-3-O-(3-hydroxytetradecanoyl)-glucosamine in the second step of lipid A biosynthesis YP_265027.1 GTPase; similar structure to tubulin; forms ring-shaped polymers at the site of cell division; other proteins such as FtsA, ZipA, and ZapA, interact with and regulate FtsZ function YP_265030.1 There are 9 addittional ORFs identical to this one. YP_265031.1 D-alanine--D-alanine ligase; DdlA; DdlB; cytoplasmic; catalyzes the formation of D-alanyl-D-alanine from two D-alanines in peptidoglycan synthesis; there are two forms of this enzyme in Escherichia coli YP_265032.1 Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis YP_265033.1 UDP-N-acetylglucosamine--N-acetylmuramyl- (pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase; involved in cell wall formation; inner membrane-associated; last step of peptidoglycan synthesis YP_265034.1 catalyzes the second step in the glutathione biosynthesis pathway, where it synthesizes ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione YP_265035.1 involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate YP_265040.1 Citation: Rikki N. Hvorup, Brit Winnen, Abraham B. Chang, Yong Jiang, Xiao-Feng Zhou, and Milton H. Saier, Jr The multidrug/oligosaccharidyl-lipid/polysaccharide (MOP) exporter superfamily Eur J Biochem 2003 270: 799-813. YP_265042.1 Citation: Bedford,D.J., Lewis,C.G. and Buttner,M.J. Characterization of a gene conferring bialaphos resistance in Streptomyces coelicolor A3(2) Gene 104 (1), 39-45 (1991) YP_265045.1 catalyzes the oxidation of malate to oxaloacetate YP_265048.1 catalyzes the formation of 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine from N6-(dimethylallyl)adenosine (i(6)A) YP_265049.1 RhtB family is also homologous to the LysE famliy of efflux proteins YP_265050.1 catalyzes the formation of L-ornithine from N(2)-acetyl-L-ornithine YP_265055.1 glycine--tRNA ligase beta chain; glyS; class II aminoacyl tRNA synthetase; tetramer of alpha(2)beta(2); catalyzes a two-step reaction; first charging a glycine molecule by linking the carboxyl group to the alpha-phosphate of ATP; second by transfer of the aminoacyl-adenylate to its tRNA YP_265056.1 glycine--tRNA ligase alpha chain; GlyRS; class II aminoacyl tRNA synthetase; tetramer of alpha(2)beta(2); catalyzes a two-step reaction; first charging a glycine molecule by linking its carboxyl group to the alpha-phosphate of ATP; second by transfer of the aminoacyl-adenylate to its tRNA YP_265057.1 Citation: Brissette JL, Weiner L, Ripmaster TL, Model P. Characterization and sequence of the Escherichia coli stress-induced psp operon. J Mol Biol. 1991 Jul 5;220(1):35-48 YP_265058.1 2 TM domains YP_265065.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.601 at residue 30 YP_265067.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.814) with cleavage site probability 0.283 at residue 29 YP_265068.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.999) with cleavage site probability 0.775 at residue 21 YP_265081.1 thiopurine S-methyltransferase motif: ubiquinone biosynthesis YP_265082.1 DUF45, zinc metalloprotease motif - COG1451 YP_265085.1 cytochrome c heme-binding motif YP_265086.1 possibly iron regulated YP_265089.1 3 transmembrane helices YP_265096.1 adjacent to histidine kinase and response regulator pilH and pilI YP_265097.1 pilI and pilH like genes upstream act os histidine kinases necessary for activity of complex YP_265098.1 adjacent to pilH- like response regulator YP_265099.1 adjacent to sensor component YP_265100.1 response regulator domain only YP_265103.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.992) with cleavage site probability 0.729 at residue 28 YP_265104.1 Citation: J Bacteriol. 2002 Sep;184(17):4930-2 YP_265105.1 Citation: J Bacteriol. 2002 Sep;184(17):4930-2 YP_265106.1 Citation: J Bacteriol. 2002 Sep;184(17):4930-2 YP_265107.1 CycJ; periplasmic heme chaperone that binds heme transiently via a histidine residue and delivers it to newly synthesized and exported c-type cytochromes; requires the ATP hydrolysis activity of the CcmA protein in order to transfer the heme to the apocytochrome; part of the cytochrome c maturation system; periplasmic protein anchored to the inner membrane YP_265108.1 Citation: Proc. Natl. Acad. Sci. USA 96: 6462-6467, 1999 YP_265109.1 Citation: Proc. Natl. Acad. Sci. USA 96: 6462-6467, 1999 YP_265110.1 Citation: Proc. Natl. Acad. Sci. USA 96: 6462-6467, 1999 YP_265111.1 Citation: Proc. Natl. Acad. Sci. USA 96: 6462-6467, 1999 YP_265113.1 -protein is only 100 aa, all best hits are 300+ aa YP_265114.1 DUF81, 7 transmembrane helices YP_265116.1 Involved in DNA double-strand break repair and recombination. Promotes the annealing of complementary single-stranded DNA and by simulation of RAD51 recombinase YP_265117.1 functions in fatty acid oxidation; converts acyl-CoA and FAD to FADH2 and delta2-enoyl-CoA YP_265118.1 8 transmembrane helices identified by tmhmm YP_265119.1 DUF81, 5 transmembrane helices YP_265120.1 exports sodium by using the electrochemical proton gradient to allow protons into the cell; functions in adaptation to high salinity and alkaline pH; activity increases at higher pH; downregulated at acidic pH YP_265121.1 1 transmembrane helix YP_265123.1 Possible protein from MutT/nudix family YP_265125.1 Has an USP domain YP_265126.1 All possess a potential HTH DNA-binding motif towards their N-termini. YP_265127.1 10 TM domains and a signal peptide predicted: Possible membrane protein YP_265128.1 universal stress protein; Citation: Sand O, et al. Microbiology. 2003 Aug;149(Pt 8):2107-17. PMID: 12904550 2: Phadtare S, et al. J Biol Chem. 2002 Mar 1;277(9):7239-45. Epub 2001 Dec 27. PMID: 11756430 Phadadtare S, Inouye M. J. Bacteriol. 2001 Feb;183(4):1205-14. PMID: 1115793 YP_265129.1 DUF454, 3 transmembrane helices YP_265130.1 Found weak RBS, no alignments YP_265131.1 2 transmembrane helices YP_265132.1 valine--tRNA ligase; ValRS; converts valine ATP and tRNA(Val) to AMP PPi and valyl-tRNA(Val); class-I aminoacyl-tRNA synthetase type 1 subfamily; has a posttransfer editing process to hydrolyze mischarged Thr-tRNA(Val) which is done by the editing domain YP_265134.1 DUF74 YP_265135.1 DUF74 YP_265137.1 Found RBS, no alignment obtained YP_265138.1 Found RBS, 2 membrane helices found (POSSIBLE N-term signal sequence from TMHMM). YP_265139.1 This orf contains no alignments to the ACT domain. YP_265140.1 Possible membrane protein: 7 transmembrane helices YP_265144.1 Possible membrane protein: 4 TM domains YP_265145.1 Found RBS, no alignment, found a signal peptide YP_265146.1 2 transmembrane helices YP_265147.1 RNase PH; tRNA nucleotidyltransferase; forms hexamers in Bacillus subtilis; phosphoroltic 3'-5' exoribonuclease; involved in maturation of tRNA precursors and removes terminal nucleotides near CCA acceptor arms of mature tRNAs YP_265148.1 -adjacent gene has same function or1224 YP_265150.1 decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling YP_265152.1 Considering the relationship of this subfamily to the other known members of the HAD-IIB subfamily (TIGR01484), sucrose and trehalose phosphatases and phosphomannomutase, it seems a reasonable hypothesis that these enzymes act on phosphorylated sugars. YP_265154.1 5 transmembrane helices YP_265155.1 glutamate synthase is composed of subunits alpha and beta; beta subunit is a flavin adenine dinucleotide-NADPH dependent oxidoreductase; provides electrons to the alpha subunit, which binds L-glutamine and 2-oxoglutarate and forms L-glutamate YP_265156.1 catalyzes the formation of glutamate from glutamine and alpha-ketoglutarate YP_265158.1 RBS found, no alignment YP_265159.1 catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis YP_265160.1 catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis YP_265161.1 Outer Bacterial Membrane Secretin (Secretin) Family YP_265166.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.951 at residue 32 YP_265168.1 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Subunit beta' binds to sigma factor allowing it to bind to the -10 region of the promoter YP_265169.1 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates; beta subunit is part of the catalytic core which binds with a sigma factor to produce the holoenzyme YP_265170.1 present in two forms; L12 is normal, while L7 is aminoacylated at the N-terminal serine; the only multicopy ribosomal protein; 4:1 ratio of L7/L12 per ribosome; two L12 dimers bind L10; critically important for translation efficiency and fidelity; stimulates GTPase activity of translation factors YP_265171.1 binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit YP_265172.1 in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA YP_265173.1 binds directly to 23S ribosomal RNA YP_265174.1 Citation: Nehrke K.W. , Platt T. , Zalatan F. NusG alters rho-dependent termination of transcription in vitro independent of kinetic coupling. Gene Expr. 3: 119- 133 (1993) [PubMed: 7505669 ] YP_265175.1 forms a complex with SecY and SecG; SecYEG forms a protein-conducting channel to which secA binds and translocates targeted polypeptides across the cytoplasmic membrane, a process driven by ATP and a proton-motive force YP_265176.1 EF-Tu; promotes GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis; when the tRNA anticodon matches the mRNA codon, GTP hydrolysis results; the inactive EF-Tu-GDP leaves the ribosome and release of GDP is promoted by elongation factor Ts; many prokaryotes have two copies of the gene encoding EF-Tu YP_265177.1 EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene YP_265178.1 binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit YP_265179.1 interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone; located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side; mutations in the S12 gene confer streptomycin resistance YP_265180.1 RBS found, no alignment against anything in BLAST YP_265183.1 catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis YP_265184.1 catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer YP_265185.1 short form of enzyme; requires HisZ for function; catalyzes the formation of N'-5'-phosphoribosyl-ATP from phosphoribosyl pyrophosphate; crucial role in histidine biosynthesis; forms heteromultimer of HisG and HisZ YP_265186.1 adds enolpyruvyl to UDP-N-acetylglucosamine as a component of cell wall formation; gram-positive bacteria have 2 copies of MurA which are active YP_265187.1 In E. coli, over-expression of this protein causes round morphology and may be involved in switching the cell between elongation and septation systems during cell division. The expression of BolA is growth rate regulated and is induced during the tran; BolA transcriptional superfamily YP_265188.1 esterase/lipase/thioesterase, active site YP_265189.1 transport-associated domain YP_265190.1 protein of unknown function UPF0102 YP_265191.1 TP methylase domain YP_265193.1 HesB/NifU - like protein YP_265195.1 NadM-Nudix subfamily; involved in creation of nicotanimide adenine dinucleotide NAD from either biosynthetic or salvage pathways YP_265197.1 Lipolytic enzyme, G-D-S-L family, motif YP_265198.2 RpmE2; there appears to be two types of ribosomal proteins L31 in bacterial genomes; some contain a CxxC motif while others do not; Bacillus subtilis has both types; the proteins in this cluster do not have the CXXC motif; RpmE is found in exponentially growing Bacilli while YtiA was found after exponential growth; expression of ytiA is controlled by a zinc-specific transcriptional repressor; RpmE contains one zinc ion and a CxxC motif is responsible for this binding; forms an RNP particle along with proteins L5, L18, and L25 and 5S rRNA; found crosslinked to L2 and L25 and EF-G; may be near the peptidyltransferase site of the 50S ribosome YP_265199.1 Possible base-induced periplasmic protein. Contains a signal peptide; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.984 at residue 28 YP_265200.1 lipoprotein repeat motif YP_265202.1 lysine decarboxylases motif YP_265206.1 hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr); possible defense mechanism against a harmful effect of D-tyrosine YP_265207.1 catalyzes the decarboxylation of phosphatidyl-L-serine to phosphatidylethanoleamine YP_265208.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.993) with cleavage site probability 0.329 at residue 21 YP_265209.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.639) with cleavage site probability 0.626 at residue 45 YP_265211.1 ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation YP_265213.1 contains metal phosphohydrolase domains only but no regulatory domains as seen with signal transduction function proteins YP_265214.1 isochorismatase hydrolase YP_265215.1 FadA; fatty acid oxidation complex component beta; functions in a heterotetramer with FadB; similar to FadI2J2 complex; functions in beta-oxidation of fatty acids YP_265216.1 includes enoyl-CoA hydratase, delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase, 3-hydroxyacyl-CoA dehydrogenase, and 3-hydroxybutyryl-CoA epimerase; catalyzes the formation of an hydroxyacyl-CoA by addition of water on enoyl-CoA; also exhibits 3-hydroxyacyl-CoA epimerase and 3-hydroxyacyl-CoA dehydrogenase activities; forms a heterotetramer with FadA; similar to FadI2J2 complex; functions in beta-oxidation of fatty acids YP_265222.1 Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer YP_265223.1 hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates YP_265224.1 binds and unfolds substrates as part of the ClpXP protease YP_265225.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.887) with cleavage site probability 0.295 at residue 27 YP_265226.1 Perfringolysin O (pfo)is a pore-forming cytolysin that is able to lyse red blood cells. 9 transmembrane helices predicted; Citation: FEMS Microbiology Letters 225 (2003)241-247. YP_265228.1 catalyzes a two-step reaction, first charging an arginine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; class-I aminoacyl-tRNA synthetase YP_265230.1 possible methyltransferase function YP_265234.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 1.000) with cleavage site probability 0.951 at residue 27 YP_265235.1 RBS found, no hit with any other protein YP_265240.1 2 TM domains YP_265248.1 Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate YP_265251.1 catalyzes the formation of tyrosyl-tRNA(Tyr) from tyrosine and tRNA(Tyr) YP_265252.1 catalyzes hydrolysis of 1,6-anhydro bond of anyhydro-N-acetylmuramic acid (anhMurNAc) and phosphorylates anhMurNAc to produce N-acetyl-muramate-6-phosphate; involved in murein recycling YP_265256.1 RBS found, no aligment obtained YP_265259.1 Possible membrane spanning protein: 3 TM domains YP_265263.1 essential GTPase; functions in ribosome assembly; binds a unique part of the 23S rRNA; interacts with ribosomal protein L25(Ctc) YP_265264.1 COG3328 and PFam00872. YP_265265.1 Citation: Michaels ML, Miller JH. 1992. The GO system protects organisms from the mutagenic effect of the spontaneous lesion 8-hydroxyguanine (7,8-dihydro-8-oxoguanine). J Bacteriol. 174(20):6321-5. YP_265267.1 transcription regulator that activates transcription by stimulating RNA polymerase (RNAP) recycling in case of stress conditions such as supercoiled DNA or high salt concentrations. Probably acts by releasing the RNAP, when it is trapped or immobilized on tightly supercoiled DNA YP_265271.1 An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes YP_265272.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.994) with cleavage site probability 0.314 at residue 25 YP_265273.1 Members of this family of bacterial proteins are described as hypothetical proteins or zinc metallopeptidases:there is no evidence to support their function as metallopeptidases. YP_265274.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.999) with cleavage site probability 0.978 at residue 21 YP_265275.1 This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control YP_265276.1 catalyzes a two-step reaction, first charging a phenylalanine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; forms a tetramer of alpha(2)beta(2); binds two magnesium ions per tetramer; type 2 subfamily YP_265277.1 catalyzes a two-step reaction, first charging a phenylalanine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; forms a heterotetramer of alpha(2)beta(2); binds two magnesium ions per tetramer; type 1 subfamily YP_265278.1 binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit YP_265280.1 This orf aligns to domains of both pyrophosphohydrolase and cyclohydrolase functions, suggesting a bifunctional enzyme. YP_265281.1 TatA; similar to TatE that is found in some proteobacteria; part of system that translocates proteins with a conserved twin arginine motif across the inner membrane; capable of translocating folded substrates typically those with bound cofactors; similar to a protein import system in thylakoid membranes YP_265284.1 Low score to superfamily I DNA and RNA helicases, COG0210. YP_265286.1 3 transmembrane helices YP_265288.1 hydrolyzes diadenosine polyphosphate YP_265289.1 Protein with conserved domain:Zn ion binding YP_265290.1 DUF833 YP_265291.1 transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein YP_265292.1 ThyA; catalyzes formation of dTMP and 7,8-dihydrofolate from 5,10-methylenetetrahydrofolate and dUMP; involved in deoxyribonucleotide biosynthesis; there are 2 copies in some Bacilli, one of which appears to be phage-derived YP_265294.1 The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision YP_265295.1 11 transmembrane domains YP_265297.1 this protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site YP_265298.1 methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA YP_265300.1 binds to lower part of 30S body where it stabilizes two domains; required for efficient assembly of 30S; in Escherichia coli this protein has nuclease activity YP_265302.1 adjacent to predicted histidine kinase response regulator YP_265304.1 part of catalytic core of ATP synthase; alpha(3)beta(3)gamma(1)delta(1)epsilon(1); involved in producing ATP from ADP in the presence of the proton motive force across the membrane YP_265305.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit YP_265306.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit YP_265307.1 produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit YP_265308.1 Produces ATP from ADP in the presence of a proton gradient across the membrane; the delta subunit is part of the catalytic core of the ATP synthase complex YP_265309.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B is part of the membrane proton channel. YP_265310.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit C is part of the membrane proton channel F0 YP_265311.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit A is part of the membrane proton channel F0 YP_265314.1 contained winged helix domains so likely DNA binding function YP_265316.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.776) with cleavage site probability 0.559 at residue 23 YP_265318.1 Expression is increased under low pH conditions. Stancik LM, Stancik DM, et al. (2002). pH-dependent expression of periplasmic proteins and amino acid catabolism in Escherichia coli. J Bacteriol 2002;184(15);4246-58. PMID: 12107143; Citation: Brown L, Gentry D, Elliott T, Cashel M (2002). DksA affects ppGpp induction of RpoS at a translational level. J Bacteriol 184(16);4455-65. PMID: 12142416 YP_265321.1 UDP-N-acetylmuramoylalanine--D-glutamate ligase; involved in peptidoglycan biosynthesis; cytoplasmic; catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine during cell wall formation YP_265327.1 Found RBS, no alignment found YP_265329.1 3 transmembrane domains YP_265332.1 First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan YP_265336.1 FtsL motif, although no BLAST hit, contains ftsL motifided from Pfam, contain RBS YP_265338.1 Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation YP_265342.1 catalyzes the conversion of citrate to isocitrate YP_265344.1 6 transmembrane helices predicted; Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.690) with cleavage site probability 0.683 at residue 25 YP_265348.1 catalyzes the formation of O-phospho-L-homoserine from L-homoserine YP_265349.1 catalyzes the conversion of 5-[(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino]- 1-(5-phosphoribosyl)imidazole-4-carboxamideand glutamine to imidazole-glycerol phosphate, 5-aminoimidazol-4-carboxamideribonucleotide and glutamate; the HisF subunit acts as a cyclase YP_265355.1 Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source YP_265358.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.766) with cleavage site probability 0.531 at residue 31 YP_265359.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.992) with cleavage site probability 0.797 at residue 35 YP_265363.1 possible integral membrane proteins: 5 TM domains YP_265365.1 This protein contains homology to the HlyD family secretion proteins (Pfam 00529) and the Membrane-fusion protein AcrA (COG0845). One transmembrane helix predicted. YP_265366.1 catalyzes branch migration in Holliday junction intermediates YP_265367.1 There are 9 addittional ORFs identical to this one. YP_265370.1 catalyzes the formation of N-acetyl-L-glutamate from L-glutamate and acetyl-CoA in arginine biosynthesis YP_265372.1 Probable transmembrane protein: 11 TM domain YP_265374.1 This protein contains an acyltransferase domain (PFam 01553). This family contains acyltransferases involved in phospholipid biosynthesis and other proteins of unknown function. RBS found. YP_265375.1 decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling YP_265376.1 This protein contains an esterase/lipase/thioesterase active site (COG3150). RBS found. YP_265379.1 catalyzes a two-step reaction, first charging a threonine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; catalyzes the formation of threonyl-tRNA(Thr) from threonine and tRNA(Thr) YP_265382.1 Its paralog in E. coli and H.influenzae is designated exoribonuclease II (Rnb). Both are Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff YP_265383.1 COG3415 YP_265384.1 catalyzes the formation of 5-(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino-l- (5-phosphoribosyl)imidazole-4-carboxamide from 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide YP_265385.1 uses the energy from reduction of ubiquinone-1 to ubiquinol to move Na(+) ions from the cytoplasm to the periplasm YP_265386.1 uses the energy from reduction of ubiquinone-1 to ubiquinol to move Na(+) ions from the cytoplasm to the periplasm YP_265387.1 uses the energy from reduction of ubiquinone-1 to ubiquinol to move Na(+) ions from the cytoplasm to the periplasm YP_265388.1 Part of the NQR complex which catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na(+) ions from the cytoplasm to the periplasm YP_265389.1 Part of the NQR complex which consists of NqrA, NqrB, NqrC, NqrD, NqrE and NqrF; NQR complex catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na(+) ions from the cytoplasm to the periplasm; NqrE is probably involved in the second step, the conversion of ubisemiquinone to ubiquinol. YP_265390.1 uses the energy from reduction of ubiquinone-1 to ubiquinol to move Na(+) ions from the cytoplasm to the periplasm YP_265391.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.970) with cleavage site probability 0.607 at residue 41 YP_265393.1 12 TM domains present YP_265394.1 Signal predicted by SignalP 2.0 HMM (Signal peptide probabilty 0.938) with cleavage site probability 0.522 at residue 30 YP_265396.1 Possible transmembrane protein: 10 TM domains; possible lipid exporter YP_265399.1 transaminase C; catalyzes transamination of alanine, valine, and 2-aminobutyrate with their respective 2-keto acids; also catalyzes terminal step in valine biosynthesis YP_265401.1 with HisF IGPS catalyzes the conversion of phosphoribulosyl-formimino-5-aminoimidazole-4-carboxamide ribonucleotide phosphate and glutamine to imidazole-glycerol phosphate, 5-aminoimidazol-4-carboxamide ribonucleotide, and glutamate in histidine biosynthesis; the HisH subunit provides the glutamine amidotransferase activity that produces the ammonia necessary to HisF for the synthesis of imidazole-glycerol phosphate and 5-aminoimidazol-4-carboxamide ribonucleotide YP_265402.1 catalyzes the dehydration of D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate to 3-(imidazol-4-yl)-2-oxopropyl phosphate in histidine biosynthesis YP_265405.1 catalyzes the dephosphorylation of 2-phosphoglycolate to form glycolate and phosphate YP_265406.1 These proteins are a subset of the magnesium chelatase, ChlI subunit family, also called:hypothetical protein yifB and competence protein. YP_265407.1 catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III YP_265409.1 This protein contains a SURF1 domain and may be a membrane protein implicated in the regulation of membrane protease activity(COG1585). Two transmembrane helices predicted. RBS found. YP_265413.1 heat shock protein 70; assists in folding of nascent polypeptide chains; refolding of misfolded proteins; utilizes ATPase activity to help fold; co-chaperones are DnaJ and GrpE; multiple copies in some bacteria YP_265415.1 This protein contains a yrdC domain that has been shown to preferentially bind to dsRNA (PFAM 01300). RBS found.; Citation: Teplova M, Tereshko V, Sanishvili R, Joachimiak A, Bushueva T, Anderson WF, Egli M. 2000. The structure of the yrdC gene product from Escherichia coli reveals a new fold and suggests a role in RNA binding. Protein Sci. 9(12):2557-66. YP_265417.1 This protein contains a LysM (lysin motif) domain. It is found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function. Signal peptide predicted. RBS found. YP_265418.1 catalyzes the formation of L-threonine from O-phospho-L-homoserine YP_265419.1 This protein contains a NusB domain (involved in the regulation of rRNA biosynthesisby transcriptional antitermination, PFAM 01029) and a Sun protein domain (unknown function, PFAM 01189). RBS found. YP_265421.1 catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine YP_265423.1 This protein contains an ATP cone domain (PFAM03477)that is an ATP-binding regulatory domain. RBS found. YP_265424.1 in Escherichia coli this protein is involved in the biosynthesis of the hypermodified nucleoside 5-methylaminomethyl-2-thiouridine, which is found in the wobble position of some tRNAs and affects ribosomal frameshifting; shows potassium-dependent dimerization and GTP hydrolysis; also involved in regulation of glutamate-dependent acid resistance and activation of gadE YP_265425.1 functions to insert inner membrane proteins into the IM in Escherichia coli; interacts with transmembrane segments; functions in both Sec-dependent and -independent membrane insertion; similar to Oxa1p in mitochondria YP_265427.1 In bacteria RNase P is known to be composed of two components: a large (about 400 base pairs) RNA (gene rnpB) and a small protein (119 to 133 amino acids) (gene rnpA). YP_265428.1 in Escherichia coli transcription of this gene is enhanced by polyamines