-- dump date 20140619_114737 -- class Genbank::CDS -- table cds_note -- id note YP_001678651.1 molecular chaperone YP_001678693.1 contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway YP_001678719.1 tryptophan RNA-binding attenuator protein; binds leader Trp transcript causing transcription termination YP_001678725.1 Shows two nucleoside-recognition domains YP_001678733.1 Member of the metallo-beta-lactamase superfamily YP_001678741.1 Catalyzes the conversion of citrate to isocitrate YP_001678747.1 catalyzes the formation of N-acetyl-L-glutamate from acetyl-CoA and L-glutamate YP_001678754.1 The structure is a tetramer of two-domain subunits. In each monomer, the N-terminus forms a 4-alpha-helix bundle containing the diiron-oxo site (centre I). The C-terminus forms a rubredoxin-like FeS4 domain YP_001679240.1 contains helix-turn-helix motif YP_001679235.1 similar to Sel1-like repeat YP_001679194.1 Member of the S-layer homology domain, PF00395, and the PKD domain, PF00801 YP_001679180.1 catalyzes the hydrolysis of pyrophosphate to phosphate YP_001679173.1 This enzyme is a homodimer consisting of two monomers, each having a flavodoxin-like domain and a Zn-beta-lactamase-like domain containing a di-iron center for the reduction of dioxygen to water. This enzyme has been characterized in Desulfovibrio gigas YP_001679155.1 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_001679153.1 anaerobic cobalt chelatase YP_001679122.1 Missing cache domain, PF02743 YP_001679102.1 Member of spore germination B3/ GerAC like, C-terminal, PF05504 YP_001679101.1 Also known by the gene symbol of gerKA YP_001679097.1 binds and unfolds substrates as part of the ClpXP protease YP_001679090.1 Synonym: 2-hydroxyglutaryl-CoA dehydratase component A YP_001679068.1 Stage II sporulation protein AA YP_001679063.1 The structure is a tetramer of two-domain subunits. In each monomer, the N-terminus forms a 4-alpha-helix bundle containing the diiron-oxo site (centre I). The C-terminus forms a rubredoxin-like FeS4 domain YP_001679041.1 Does not match cache domain, PF02743, or HAMP domain, PF00672 YP_001679010.1 also has gene sym pycB YP_001679003.1 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_001679002.1 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_001678964.1 tungstate transporter YP_001678954.1 Also member of Bacillus/Clostridium GerA spore germination protein PFAM, PF03323 YP_001678951.1 Also known as spoIIAC YP_001678950.1 binds to sigma F preventing its association with RNA polymerase during sporulation YP_001678945.1 catalyzes the transfer of phosphate between the C1 and C5 carbons of pentose YP_001678936.1 Missing cache domain, PF02743 YP_001678929.1 Also member of COG0500, SAM-dependent methyltransferases YP_001678912.1 catalyzes the formation of oxaloacetate from pyruvate YP_001678901.1 Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA YP_001678900.1 Member of 3-dehydroquinate dehydratase, type II equivalog, TIGR01088 YP_001678895.1 Member of prepilin-type N-terminal cleavage/methylation domain, TIGR02532 YP_001678890.1 Member of the prepilin-type N-terminal cleavage/methylation domain, TIGR02532 YP_001678882.1 Matches prepilin-type N-terminal cleavage/methylation domain, TIGR02532, and prokaryotic N-terminal methylation motif PFAM, PF07963 YP_001678881.1 Member of bacterial type II secretion system protein F domain PFAM, PF00482 YP_001678876.1 catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis YP_001678864.1 sigma-28; sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; this sigma factor is responsible for the expression of sporulation specific genes and is expressed in the mother cell after engulfment YP_001678854.1 Has a 4Fe-4S binding domain. which is similar to a ferredoxin COG. Other protiens with this domain include bacterial ferredoxins, various dehydrogenases, and various reductases YP_001678845.1 Decarboxylation of S-adenosylmethionine provides the aminopropyl moiety required for spermidine biosynthesis from putrescine YP_001678843.1 also named cobalt transport protein CbiM YP_001678828.1 catalyzes the reduction of hydroxylamine to ammonia and water YP_001678805.1 Member of COG0489, ATPases involved in chromosome partitioning YP_001678792.1 Synonym: 2-hydroxyglutaryl-CoA dehydratase component A YP_001679259.1 similar to Chaperone protein htpG (Heat shock protein htpG) YP_001679261.1 catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate YP_001679265.1 Similar to protein cotJC; Sometimes known as ''pseudocatalase'' YP_001679270.1 pyrophosphate-energized proton pump; pyrophosphate-energized inorganic pyrophosphatase; H+-PPase; can cleave pyrophosphate to two phosphates; can generate a proton motive force and drive pyrophosphate synthesis when PMF is sufficient YP_001679272.1 enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis YP_001679273.1 catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate YP_001679276.1 Also known as gerG YP_001679279.1 may contain bacterial transferase hexapeptide (three repeats) YP_001679287.1 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_001679295.1 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_001679300.1 C-terminal frameshift induces homology to gram-negative strains YP_001679310.1 Member of S-layer homology domain, PF00395 YP_001679312.1 Matches methyl-accepting chemotaxis protein (MCP) signaling domain, PF00015 YP_001679313.1 modulates transcription in response to the NADH/NAD(+) redox state YP_001679317.1 Also a member of the permease domain, PF02687 YP_001679318.1 Member of ABC transporter PFAM, PF00005, and predicted ATPase involved in cell division COG, COG2884 YP_001679329.1 Member of the DegT/DnrJ/EryC1/StrS aminotransferase PFAM, PF01041, and also Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis COG, COG0399 YP_001679330.1 Member of cytidylyltransferase domain, PF02348 YP_001679404.1 Member of NADH-ubiquinone/plastoquinone oxidoreductase chain 6, PF00499 YP_001679408.1 Member of glycosyl transferase, group 2 family protein, PF00535 YP_001679418.1 with CysN catalyzes the formation of adenylylsulfate from sulfate and ATP YP_001679433.1 Member of histidinol-phosphate phosphatase family domain, TIGR01656, and hydrolase, HAD-superfamily, subfamily IIIA domain, TIGR01662 YP_001679440.1 similar to transposase YP_001679441.1 polysaccharide transporter YP_001679451.1 Member of tetratricopeptide repeat PFAM, PF07721 YP_001679481.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit YP_001679482.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit YP_001679484.1 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_001679493.1 Matches cytidine and deoxycytidylate deaminase zinc-binding region PFAM, PF00383 YP_001679502.1 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_001679507.1 type II fructose 1,6-bisphosphatae; in Escherichia coli this protein forms a dimer and binds manganese YP_001679509.1 class II aldolase; catalyzes the formation of fructose 1,6-bisphosphate from dihydroxyacetone phosphate and glyceraldehyde 3-phosphate YP_001679517.1 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_001679519.1 Seems to be missing the C-termial region of rpoE with the N-terminal region present YP_001679520.1 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_001679523.1 S-adenosylmethionine provides the aminopropyl moiety required for spermidine biosynthesis from putrescine YP_001679524.1 Does not match cache domain, PF02743 or HAMP domain, PF00672 YP_001679562.1 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_001679567.1 Member of permeases of the drug/metabolite transporter (DMT) superfamily, COG0697 YP_001679585.1 phytoene dehydrogenase and related proteins YP_001679586.1 catalyzes the interconversion of tetrahydrodipicolinate and L,L-diaminopimelate in lysine biosynthesis YP_001679594.1 contains TPR domain YP_001679597.1 Member of Arylsulfatase regulator (Fe-S oxidoreductase), COG0641 YP_001679604.1 in Escherichia coli this protein is wrapped around the base of the L1 stalk YP_001679606.1 Member of NADH-ubiquinone/plastoquinone oxidoreductase chain 6 PFAM, PF00499 YP_001679615.1 catalyzes the removal of amino acids from the N termini of peptides YP_001679617.1 acts to load the DnaB helicase onto the initiation site during DNA replication YP_001679626.1 Acs; catalyzes the conversion of acetate and CoA to acetyl-CoA YP_001679636.1 Also similar to gerKC YP_001679659.1 Also known as selenocysteine lyase, gene symbol csdB YP_001679663.1 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_001679666.1 Also known by the gene symbol of oxaA YP_001679669.1 in Escherichia coli transcription of this gene is enhanced by polyamines YP_001679710.1 functions with NifE to assemble FeMo cofactor; functions in assembly of nitrogenase MoFe YP_001679717.1 with PdxT forms pyridoxal 5'-phosphate from glutamine, either ribose 5-phosphate or ribulose 5-phosphate, and either glyceraldehyde 3-phosphate or dihydroxyacetone phosphate YP_001679721.1 catalyzes the formation of 3-phosphonooxypyruvate from 3-phospho-D-glycerate in serine biosynthesis; can also reduce alpha ketoglutarate to form 2-hydroxyglutarate YP_001679722.1 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_001679724.1 similar to GGDEF domain YP_001679728.1 Does not match cache domain, PF02743 YP_001679731.1 with DhaL and DhaM forms dihydroxyacetone kinase, which is responsible for phosphorylating dihydroxyacetone; DhaK is the dihydroxyacetone binding subunit of the dihydroxyacetone kinase YP_001679733.1 Also called glycerone kinase YP_001679737.1 similar to proteins with 4Fe-4S binding domains YP_001679738.1 similar to iron-sulfur cluster binding protein YP_001679757.1 similar to UPF0133 protein YP_001679758.1 involved in a recombinational process of DNA repair, independent of the recBC complex YP_001679760.1 Contains alpha, beta and gamma subunits of 2-oxoacid:ferredoxin oxidoreductase, a gene related to pyruvate:ferredoxin (flavodoxin) oxidoreductase. These genes have the gene symbols porA, porB, porG and napF YP_001679771.1 May be involved in chromosome condensation YP_001679784.1 This protein, in combination with CcmC, is involved in C-type cytochrome biogenesis YP_001679842.1 Also known as spoVC YP_001679848.1 Member of polysaccharide biosynthesis protein domain, PF01943, and COG2244, membrane protein involved in the export of O-antigen and teichoic acid YP_001679856.1 CobB/CobQ-like glutamine amidotransferase YP_001679859.1 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_001679876.1 light-independent; with chlN(bchN) and chlB(bchB) reduces ring D of protochlorophyllide to form chlorophyllide a in chlorophyll/bacteriochlorophyll production YP_001679877.1 light-independent reduction of protochlorophyllide to form chlorophyllide a YP_001679878.1 light-independent reduction of protochlorophyllide to form chlorophyllide a YP_001679881.1 catalyzes the formation of Mg-protoporphyrin IX from protoporphyrin IX and Mg(2+); first committed step of chlorophyll biosynthesis YP_001679882.1 Phytoene dehydrogenase and related proteins YP_001679884.1 (tRNA(ile)-lysidinesynthetase) (tRNA(ile)-2-lysyl-cytidine synthase) YP_001679891.1 catalyzes the formation of 10-formyltetrahydrofolate from formate and tetrahydrofolate YP_001679894.1 N-terminus corresponds to folB gene with C-terminus corresponding to folK gene YP_001679896.1 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_001679897.1 3 different subfamilies; catalyzes the formation of quinolinate from iminoaspartate and dihydroxyacetone phosphate YP_001679904.1 BchX is homologous to NifH YP_001679918.1 Member of shikimate / quinate 5-dehydrogenase PFAM, PF01488 YP_001679920.1 may contain an OB-fold nucleic acid binding domain YP_001679926.1 Member of COG4872, predicted membrane proteins YP_001679932.1 Member of ATPase family associated with various cellular activities (AAA) PFAM, PF07724 YP_001679934.1 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_001679935.1 non-specific DNA-binding; scans chromosomes during sporulation for DNA-damage; delays initiation of sporulation; participates in a checkpoint signaling cascade for cell-cycle progression and DNA repair YP_001679949.1 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates YP_001679951.1 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_001679953.1 binds directly to 23S ribosomal RNA YP_001679954.1 in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA YP_001679955.1 binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit YP_001679958.1 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_001679959.1 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_001679961.1 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_001679962.1 binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit YP_001679963.1 EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene YP_001679964.1 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_001679965.1 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_001679969.1 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_001679970.1 protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA YP_001679973.1 located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e YP_001679976.1 binds to the 23S rRNA between the centers for peptidyl transferase and GTPase YP_001679977.1 assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel YP_001679981.1 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_001679982.1 binds 5S rRNA along with protein L5 and L25 YP_001679983.1 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_001679986.1 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_001679987.1 essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP YP_001679991.1 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_001679993.1 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_001680001.1 in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit YP_001680006.1 Missing cache domain, PF02743 YP_001680010.1 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_001680018.1 catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate YP_001680024.1 catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming YP_001680042.1 contains Hes B-like domain YP_001680046.1 Protein biochemically characterized by Heinnickel et al. Biochemistry, 46, 2530-2536, 2007 YP_001680055.1 Also known as citC YP_001680056.1 Catalyzes the reversible oxidation of malate to oxaloacetate YP_001680085.1 multidrug resistance transporter YP_001680093.1 catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids YP_001680095.1 Member of ACT domain, PF01842 YP_001680098.1 catalyzes the formation of 2-isopropylmalate from acetyl-CoA and 2-oxoisovalerate in leucine biosynthesis YP_001680099.1 catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis YP_001680101.1 catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis YP_001680108.1 catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate YP_001680112.1 Does not match cache domain, PF02743, methyl-accepting chemotaxis protein (MCP) signaling domain, PF00015, or HAMP domain, PF00672 YP_001680137.1 Member of YibE/F-like protein PFAM, PF07907, and COG5438, predicted multitransmembrane proteins YP_001680144.1 similar to transposase YP_001680157.1 Acriflavin resistance protein YP_001680167.1 Similar to stage II sporulation protein E, PF07228, and matches COG2208, serine phosphatase RsbU, regulator of sigma subunit YP_001680179.1 sn-glycerol-3-phosphate dehydrogenase (anaerobic); catalyzes the formation of dihydroxyacetone from glycerol 3-phosphate; part of GlpABC complex; presumably this subunit is responsible for membrane interactions and contains iron-sulfur clusters YP_001680180.1 anaerobic; with GlpAB catalyzes the conversion of glycerol-3-phosphate to dihydroxyacetone phosphate YP_001680184.1 Also known as gerG YP_001680195.1 peptidase M24 YP_001680217.1 Similar to YccB YP_001680220.1 Member of NCAIR mutase (PurE)-related proteins, COG1691 YP_001680223.1 catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate YP_001680229.1 Homology to full length transposase interrupted by insertion of a transposase gene YP_001680232.1 Homology to full length transposase interrupted by insertion of a transposase gene YP_001680242.1 Member of the methyl-accepting chemotaxis protein (MCP) signaling domain PFAM, PF00015 YP_001680261.1 Member of the undecaprenol kinase PFAM, PF02673 YP_001680268.1 similar to ATP-utilizing enzymes of the PP-loop superfamily YP_001680272.1 May be involved in multi-copper enzyme maturation YP_001680278.1 binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21 YP_001680291.1 Peptidase C26 YP_001680302.1 catalyzes the transfer of the N5-methyl group from (6S)-methyl tetrahydrofolate to the cobalt center of a corrinoid iron-sulfur protein YP_001680317.1 similar to Cytochrome b subunit of formate dehydrogenase YP_001680321.1 modulates transcription in response to the NADH/NAD(+) redox state YP_001680338.1 PvlArgDC; converts arginine to agmatine and carbon dioxide; has a role in polyamine metabolism; in Methanococcus jannaschii this enzyme self-cleaves at serine-serine bond to form alpha (N-terminal) and beta (C-terminal) subunits; the alpha subunit contains a catalytically active pyruvoyl group; the beta subunit contains the substrate-binding residues; forms homotrimers of the alpha/beta complex YP_001680339.1 catalyzes the formation of spermidine from putrescine and S-adenosylmethioninamine YP_001680342.1 may contain a LysM domain YP_001680356.1 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_001680388.1 catalyzes the formation of tyrosyl-tRNA(Tyr) from tyrosine and tRNA(Tyr) YP_001680396.1 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_001680398.1 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_001680401.1 Heat shock-induced YP_001680409.1 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_001680410.1 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_001680413.1 hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr); possible defense mechanism against a harmful effect of D-tyrosine YP_001680415.1 catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III YP_001680417.1 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_001680418.1 may be involved in molybdopterin biosynthesis YP_001680422.1 contains an EAL domain, PAS domain, and a GGDEF domain YP_001680425.1 Member of S-layer homology domain, PF00395 YP_001680428.1 containing two conserved CbiO domain1 regions YP_001680436.1 May contain a PRC barrel domain YP_001680452.1 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_001680463.1 Member of nucleoside recognition domain, PF07670 YP_001680467.1 cob(I)alamin adenosyltransferase YP_001680470.1 similar to flavoproteins YP_001680490.1 catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate YP_001680492.1 catalyzes the formation of 3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate YP_001680493.1 Also matches prephenate dehydratase PFAM/equivalog domain, PF00800 YP_001680505.1 catalyzes the formation of L-aspartate 4-semialdehyde from L-homoserine YP_001680506.1 catalyzes the formation of L-threonine from O-phospho-L-homoserine YP_001680507.1 catalyzes the formation of O-phospho-L-homoserine from L-homoserine in threonine biosynthesis from asparate YP_001680508.1 catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP, in Bacillus, lysine sensitive; regulated by response to starvation. YP_001680516.1 similar to SAM domain protein YP_001680518.1 similar to SAM domain protein YP_001680530.1 Gene also known as resB YP_001680533.1 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_001680535.1 C-terminal region containing conserved CysG domain and N-ternimal region containing HemD domain protein YP_001680537.1 catalyzes the formation of porphobilinogen from 5-aminolevulinate YP_001680538.1 Member of COG0535, predicted Fe-S oxidoreductases YP_001680541.1 Converts (S)-4-amino-5-oxopentanoate to 5-aminolevulinate during the porphyrin biosynthesis pathway YP_001680549.1 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_001680550.1 catalyzes the isomerization of isopentenyl pyrophosphate to dimethylallyl diphosphate YP_001680554.1 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_001680555.1 Similar to membrane protein YP_001680562.1 dGTPase family type 2 subfamily; presumably hydrolyzes dGTP to deoxyguanosine and triphosphate YP_001680564.1 sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; primary sigma factor of bacterium YP_001680566.1 similar to NIF-3 related protein YP_001680569.1 similar to small, acid soluble spore protein YP_001680588.1 Member of COG0784, FOG: CheY-like receiver YP_001680593.1 Does not match cache domain, PF02743 or HAMP domain, PF00672 YP_001680604.1 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_001680620.1 Also bears the gene symbol mraR YP_001680621.1 Also matches penicillin binding protein transpeptidase domain, PF00905, and penicillin-binding protein dimerisation domain PFAM, PF03717 YP_001680626.1 Member of the cell cycle protein, FtsW/RodA/SpoVE PFAM, PF01098 YP_001680629.1 catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis YP_001680634.1 sigma-29; sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; this sigma factor is responsible for the expression of sporulation specific genes and is expressed in the mother cell at the onset of sporulation YP_001680635.1 sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; this sigma factor is responsible for the expression of sporulation specific genes and is expressed after engulfment; this factor is involved in the transcription of small acid-soluble proteins involved in protecting the forespore chromatin YP_001680638.1 Catalyzes the reduction of nucleoside 5'-triphosphates to 2'-deoxynucleoside 5'-triphosphates YP_001680649.1 contains an EAL domain and a GGDEF domain YP_001680653.1 ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation YP_001680657.1 similar to enzyme with TIM-barrel fold YP_001680664.1 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_001680673.1 regulates pyrimidine biosynthesis by binding to the mRNA of the pyr genes, also has been shown to have uracil phosphoribosyltransferase activity YP_001680680.1 catalyzes the conversion of dihydroorotate to orotate in the pyrimidine biosynthesis pathway, using a flavin nucleotide as an essential cofactor; subclass 1B is a heterotetramer consisting of two PyrDB subunits, similar to the PyrDA subunits and two PyrK subunits YP_001680682.1 may contain NlpC/P60 domain YP_001680684.1 Missing methyl-accepting chemotaxis protein (MCP) signaling domain, PF00015: , and cache domain, PF02743 YP_001680692.1 similar to stress-induced protein YP_001680709.1 catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine YP_001680714.1 required for 70S ribosome assembly YP_001680719.1 Initiates the rapid degradation of small, acid-soluble proteins during spore germination YP_001680727.1 negative regulator of genes involved in fatty acid and phospholipid biosynthesis for gram positive bacteria YP_001680728.1 involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY YP_001680733.1 carries the fatty acid chain in fatty acid biosynthesis YP_001680750.1 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_001680751.1 similar to rna binding protein YP_001680755.1 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_001680764.1 The point of entry for the majority of electrons that traverse the respiratory chain eventually resulting in the reduction of oxygen YP_001680775.1 Mg chelatase-related protein, ChlI subunit YP_001680781.1 heat shock protein involved in degradation of misfolded proteins YP_001680782.1 heat shock protein involved in degradation of misfolded proteins YP_001680783.1 CodY; DNA-binding protein that represses the expression of many genes that are induced as cells make the transition from rapid exponential growth to stationary phase (By similarity). It is a GTP-binding protein that senses the intracellular GTP concentration as an indicator of nutritional limitations. At low GTP concentration it no longer binds GTP and stop to act as a transcriptional repressor YP_001680803.1 Member of cheC-like PFAM, PF04509 YP_001680810.1 membrane protein involved in the flagellar export apparatus YP_001680824.1 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_001680826.1 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_001680831.1 catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate YP_001680835.1 Member of glycosyl transferase, group 2 family protein, PF00535 YP_001680850.1 may contain a cupin domain YP_001680858.1 contains GTP binding domain protein YP_001680870.1 may contain a PRC barrel domain YP_001680871.1 catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis YP_001680872.1 catalyzes the synthesis of dipicolinic acid from dihydroxydipicolinic acid; plays a role in spore heat resistance YP_001680873.1 involved in production of dipicolinic acid (pyridine-2,6-dicarboxylic acid, DPA) which is synthesized late in sporulation in the mother cell and accumulates in the spore; mutations in this gene result in a lack of DPA synthesis; presumably functions with SpoVFA to form the synthase enzyme YP_001680875.1 catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP; diaminopimelate sensitive YP_001680883.1 catalyzes the selenophosphate-dependent transfer of selenium from selenophosphate for conversion of 2-thiouridine to 2-selenouridine at the wobble position in tRNA YP_001680885.1 nucleotide binding property based on structural studies of Haemophilus influenzae crystallized protein in PDB Accession Number 1IN0 and NMR studies of Escherichia coli YajQ; the YajQ protein from Pseudomonas synringae appears to play a role in activation of bateriophage phi6 segment L transcription YP_001680901.1 ATP-dependent DNA ligase YP_001680904.1 Ku-like subfamily; composed of prokaryotic homologs of the eukaryotic DNA binding protein Ku. YP_001680913.1 PcrB family protein; GGGP synthase; possible member of prenyltransferases that transfer isoprenoid groups to nonisoprenoid acceptors; functions in form GGGP from glycerol-1-phosphate (G-1-P) and geranylgeranyl pyrophosphate (GGPP); important in lipid meta; PcrB-like protein; GGGP synthase; member of prenyltransferases that transfer isoprenoid groups to nonisoprenoid acceptors; functions in form GGGP from glycerol-1-phosphate (G-1-P) and geranylgeranyl pyrophosphate (GGPP); important in lipid metabolism and especially important as the ether linkages in archaea are different than those in bacteria; GGGP synthase lies at the branch point for membrane lipid biosynthesis; cytosolic; T acidophilum protein acts as a homodimer while M thermoautotrophicum protein has been reported to function as a pentamer YP_001680929.1 Member of COG1032, Fe-S oxidoreductase YP_001680940.1 protein from Staphylococcus aureus has phosphodiesterase activity against 2'-3'-cAMP and 2'-3'-cGMP YP_001680942.1 similar to Ser/Thr protein phosphatase family YP_001680951.1 precorrin-3B C17-methyltransferase, CbiG YP_001680954.1 Sirohydrochlorin cobalt chelatase (CbiX) and sirohydrochlorin iron chelatase (SirB), N-terminal domain protein YP_001680958.1 catalyzes amidations at positions B, D, E, and G on adenosylcobyrinic A,C-diamide. NH(2) groups are provided by glutamine, and one molecule of ATP is hydrogenolyzed for each amidation YP_001680961.1 cob(I)alamin adenosyltransferase YP_001680971.1 Cof subfamily of IIB subfamily of haloacid dehalogenase superfamily YP_001680988.1 binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase YP_001680989.1 similar to membrane protein YP_001680993.1 binds to the ribosome on the universally-conserved alpha-sarcin loop YP_001681018.1 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_001681021.1 Has high identity with proteins from other organisms upstream from start site, suggesting a possible incorrect start site, but no other start codon between one called and upstream stop codon. Sequence has been checked and appears to be OK YP_001681022.1 catalyzes the formation of phosphoenolpyruvate from pyruvate YP_001681027.1 cell wall binding protein YP_001681051.1 domain similar to spore protein ykuD YP_001681057.1 Matches vitamin B12 dependent methionine synthase, activation domain, PF02965 YP_001681058.1 contains B12 binding domains YP_001681071.1 Member of cell wall hydrolase PFAM, PF07486 YP_001681080.1 Does not match cache domain, PF02743, or HAMP domain, PF00672 YP_001681089.1 catalyzes the formation of L-homocysteine from S-adenosyl-L-homocysteine YP_001681090.1 Member of HAD-superfamily hydrolase, subfamily IB (PSPase-like) superfamily, TIGR01488, and haloacid dehalogenase-like hydrolase domain, PF00702 YP_001681106.1 catalyzes the conversion of a phosphate monoester to an alcohol and a phosphate YP_001681108.1 Member of polysaccharide biosynthesis protein, PF01943 YP_001681114.1 contains 4Fe-4S binding domain YP_001681115.1 peptidase YP_001681118.1 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_001681120.1 Member of the cys/met metabolism PLP-dependent enzyme PFAM, PF01053 YP_001681125.1 Also matces ATPase, AAA family domain, PF00004 YP_001681144.1 Does not match cache domain, PF02743, or HAMP domain, PF00672 YP_001681150.1 Member of competence protein ComEA helix-hairpin-helix repeat region domain, TIGR00426, and helix-hairpin-helix motif PFAM, PF00633 YP_001681163.1 Homologous to peptidyl-prolyl cis-trans isomerase, cyclophilin-type YP_001681165.1 Matches methyl-accepting chemotaxis protein (MCP) signaling domain, PF00015, but not HAMP domain, PF00672, or cache domain, PF02743 YP_001681178.1 similar to synthase YP_001681183.1 catalyzes the reversible synthesis of carbamate and ATP from carbamoyl phosphate and ADP YP_001681185.1 Zn-dependent extracellular dipeptidase; similar to succinyl-diaminopimelate desuccinylases YP_001681187.1 FAD-binding subunit; with XdhA and XdhC participates in purine salvage YP_001681188.1 molybdenum cofactor-binding protein; participates in purine salvage YP_001681191.1 with YgfM and YgfN forms a selenate reductase, which seems to catalyze the reduction of selenate to selenite; YgfK mutants are unable to reduce selenate; involved in purine salvage process; seems to act as an oxidoreductase, but sequence similarity suggests it is a dihydrothymine dehydrogenase YP_001681192.1 in Escherichia coli expression is induced in response to phase-specific signals and controlled by RpoS YP_001681212.1 catalyzes oxidation of 4-(phosphohydroxy)-L-threonine into 2-amino-3-oxo-4-(phosphohydroxy)butyric acid which decarboxylates to form 1-amino-3-(phosphohydroxy)propan-2-one (3-amino-2-oxopropyl phosphate) YP_001681213.1 contains YgbK domain YP_001681229.1 Catalyzes the hydrolytic cleavage of a carbon-halogen bond in N-ethylammeline YP_001681242.1 Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway YP_001681243.1 catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis YP_001681249.1 involved in the peptidyltransferase reaction during translation YP_001681253.1 Member of COG5011, uncharacterized protein conserved in bacteria YP_001681254.1 Member of COG1032 Fe-S oxidoreductase YP_001681271.1 functions in MreBCD complex in some organisms YP_001681272.1 Involved in DNA double-strand break repair and recombination. Promotes the annealing of complementary single-stranded DNA and by simulation of RAD51 recombinase YP_001681280.1 Shows homology with membrane transporter proteins YP_001681285.1 modulates transcription in response to the NADH/NAD(+) redox state YP_001681289.1 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_001681309.1 Member of the Hpt domain, PF01627 YP_001681311.1 Member of cell wall hydrolase PFAM, PF07486 YP_001681313.1 PEP carboxykinase; PEP carboxylase; PEPCK; catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using ATP YP_001681326.1 Does not match cache domain, PF02743 YP_001681363.1 Possibly related to a daunorubicin resistance ABC transporter YP_001681373.1 Member of the extracytoplasmic function sigma factors which are active under specific conditions; binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription YP_001681387.1 Member of LysM domain, PF01476 YP_001681389.1 similar to glycosyl hydrolase YP_001681399.1 possible DNA packaging YP_001681489.1 similar to phage tail tape measure protein YP_001681513.1 in Methanococcus jannaschii this protein catalyzes the condensation of alpha-ketoglutarate and acetyl-CoA to form trans-homoaconitate; functions in alphaketosuberate synthesis which is a precursor in coenzyme B and biotin synthesis YP_001681539.1 Does not match cache domain, PF02743, or HAMP domain, PF00672 YP_001681543.1 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_001681544.1 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; some Mycoplasma proteins contain an N-terminal fusion to an unknown domain YP_001681562.1 Also matches phosphoribosyl-ATP pyrophosphohydrolase equivalog domain, PF01503 YP_001681563.1 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_001681565.1 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_001681569.1 catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer YP_001681570.1 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_001681577.1 catalyzes the formation of L-tryptophan from indole and L-serine YP_001681615.1 Does not match cache domain, PF02743, or HAMP domain, PF00672 YP_001681620.1 catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis YP_001681621.1 Catalyzes first step of the de novo purine nucleotide biosynthetic pathway YP_001681623.1 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_001681630.1 Also known as gerAC YP_001681636.1 similar to septation protein spoVG