-- dump date 20140619_163251 -- class Genbank::CDS -- table cds_note -- id note YP_003082250.1 catalyzes the formation of D-ribulose 5-phosphate from 6-phospho-D-gluconate YP_003082251.1 catalyzes the transfer of 2-keto-3-deoxy-D-manno-octulosonic acid to lipid A YP_003082254.1 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_003082255.1 Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway YP_003082263.1 Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation YP_003082266.1 This protein performs the mismatch recognition step during the DNA repair process YP_003082276.1 catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis YP_003082280.1 Bacteria have multiple sigma factors which are active under specific conditions; the sigma factor 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_003082286.1 recognizes the termination signals UGA 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 RF2; in some organisms control of PrfB protein levels is maintained through a +1 ribosomal frameshifting mechanism; this protein is similar to release factor 1 YP_003082290.1 involved in the import of serine and threonine coupled with the import of sodium YP_003082294.1 catalyzes the formation of arginosuccinate from citrulline and aspartate in arginine biosynthesis YP_003082309.1 Catalyzes the phosphorylation of UMP to UDP YP_003082310.1 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_003082311.2 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_003082315.1 malate dehydrogenase; catalyzes the oxidation of malate to oxaloacetate YP_003082321.1 catalyzes the isomerization of sedoheptulose 7-phosphate to D-glycero-D-manno-heptose 7-phosphate YP_003082325.1 essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication YP_003082328.1 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_003082332.1 catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde YP_003082334.1 catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate YP_003082336.1 activates biotin to form biotinyl-5'-adenylate and transfers the biotin moiety to biotin-accepting proteins and catalyzes the formation of (R)-4'-phosphopantothenate from (R)-pantothenate in coenzyme A biosynthesis; type III; type III pantothenate kinases are not subject to feedback inhibition from coenzyme A and have a high Km for ATP YP_003082339.1 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_003082350.1 catalyzes the formation of oxaloacetate from phosphoenolpyruvate YP_003082351.1 catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate YP_003082354.1 in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit YP_003082355.1 forms a direct contact with the tRNA during translation YP_003082363.1 catalyzes the formation of a phosphodiester at the site of a single-strand break in duplex DNA YP_003082364.1 Catalyzes the salvage synthesis of inosine-5'-monophosphate (IMP) and guanosine-5'-monophosphate (GMP) from the purine bases hypoxanthine and guanine, respectively YP_003082370.1 required for the synthesis of the hydromethylpyrimidine moiety of thiamine YP_003082374.1 mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability YP_003082377.1 Converts the D-glycero-beta-D-manno-heptose 1,7-bisphosphate intermediate into D-glycero-beta-D-manno-heptose 1-phosphate YP_003082379.1 Involved in ubiquinone biosynthesis YP_003082380.1 catalyzes the formation of O-phospho-L-homoserine from L-homoserine YP_003082387.1 SPOUT methyltransferase family protein; crystal structure shows homodimer; in Escherichia coli this protein methylates pseudouridine at position 1915 of the 23S ribosomal RNA YP_003082390.1 Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA YP_003082402.1 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_003082408.1 becomes active under oxidative stress; four conserved cysteines bind a zinc atom when they are in the reduced state and the enzyme is inactive; oxidative stress results in oxidized cysteines, release of zinc, and binding of Hsp33 to aggregation-prone proteins; forms dimers and higher order oligomers YP_003082412.1 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_003082421.1 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_003082422.1 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_003082426.1 defects in the mitochondrial frataxin protein cause Friedreich ataxis which is an autosomal recessive neurodegenerative disease; based on phylogenomic distribution this protein may have a role in iron-sulfur cluster protein assembly YP_003082428.1 catalyzes the hydrolysis of S-ribosylhomocysteine to homocysteine and autoinducer-2 YP_003082434.1 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_003082438.1 NAD-linked YP_003082450.1 RpmE; 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 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_003082457.1 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_003082466.1 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_003082467.1 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_003082468.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B is part of the membrane proton channel. YP_003082469.1 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_003082470.1 produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit YP_003082471.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit YP_003082472.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit YP_003082473.1 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_003082474.1 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_003082476.1 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_003082480.1 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_003082484.1 catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis YP_003082485.1 contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway YP_003082489.1 FabH; beta-ketoacyl-acyl carrier protein synthase III; 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_003082492.1 involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY YP_003082494.1 some L32 proteins have zinc finger motifs consisting of CXXC while others do not YP_003082497.1 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_003082499.1 protein component of RNaseP which catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'terminus; this enzyme also cleaves other RNA substrates YP_003082500.1 in Escherichia coli transcription of this gene is enhanced by polyamines YP_003082501.1 binds to the dnaA-box as an ATP-bound complex at the origin of replication during the initiation of chromosomal replication; can also affect transcription of multiple genes including itself. YP_003082502.1 binds the polymerase to DNA and acts as a sliding clamp YP_003082503.1 catalyzes the reversible transfer of the terminal phosphate of ATP to form a long chain polyphosphate YP_003082506.1 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_003082512.1 Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate YP_003082521.1 catalyzes the formation of N-acetyl-L-glutamate from L-glutamate and acetyl-CoA in arginine biosynthesis YP_003082523.1 involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate YP_003082528.1 class II aldolase; catalyzes the reversible aldol condensation of dihydroxyacetonephosphate and glyceraldehyde 3-phosphate in the Calvin cycle, glycolysis and gluconeogenesis YP_003082530.1 catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate YP_003082531.1 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_003082533.1 Converts (S)-4-amino-5-oxopentanoate to 5-aminolevulinate during the porphyrin biosynthesis pathway YP_003082534.1 3'-5' exoribonuclease specific for small oligoribonuclotides YP_003082535.1 methylates ribosomal protein L11 at multiple amino acid positions; mutations of these genes in Escherichia coli or Thermus thermophilus has no apparent phenotype YP_003082537.1 composes the biotin carboxyl carrier protein subunit of the acetyl-CoA carboxylase complex, the enzyme that catalyzes the carboxylation of acetyl-CoA to malonyl-CoA, which in turn controls the rate of fatty acid metabolism YP_003082539.1 Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step YP_003082542.1 four CarB-CarA dimers form the carbamoyl phosphate synthetase holoenzyme that catalyzes the production of carbamoyl phosphate; CarB is responsible for the amidotransferase activity YP_003082547.1 catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers YP_003082554.1 catalyzes the formation of 10-formyltetrahydrofolate from formate and tetrahydrofolate YP_003082555.1 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_003082558.1 catalyzes the formation of FMN from riboflavin and the formation of FAD from FMN; in Bacillus the ribC gene has both flavokinase and FAD synthetase activities YP_003082559.1 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_003082560.1 lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis YP_003082561.1 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_003082583.1 transaminase C; catalyzes transamination of alanine, valine, and 2-aminobutyrate with their respective 2-keto acids; also catalyzes terminal step in valine biosynthesis YP_003082592.1 catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis YP_003082593.1 catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis YP_003082600.1 binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential YP_003082604.1 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_003082605.1 Acylates the intermediate (KDO)2-lipid IVA to form (KDO)2-(lauroyl)-lipid IVA YP_003082606.1 catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase YP_003082614.1 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_003082615.1 catalyzes branch migration in Holliday junction intermediates YP_003082616.1 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_003082629.1 RNase BN; required for 3' maturation of certain phage T4-encoded tRNAs; forms a dimer; specific for immature tRNA substrates containing incorrect residues within the universal CCA sequence; 3' to 5' exoribonuclease; this protein contains a C-terminal extension of unknown function YP_003082635.1 hydrolyzes the terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides YP_003082644.1 transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis YP_003082645.1 catalyzes the formation of L-glutamate and an aromatic oxo acid from an aromatic amino acid and 2-oxoglutarate YP_003082649.1 catalyzes the formation of 2,3=diacylglucosamine 1-phosphate from UDP-2,3=diacylglucosamine YP_003082651.1 similar to zinc-dependent eukaryotic ADH enzymes and distinct from fermentative ADHs YP_003082656.1 binding of PriA to forked DNA starts the assembly of the primosome, also possesses 3'-5' helicase activity YP_003082657.1 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_003082660.1 essential respiratory protein A; may be involved in the transfer of iron-sulfur clusters; essential for growth using oxygen or alternate electron acceptors YP_003082663.1 an Escherichia coli mutant results in accumulation of octaprenylphenol and no ubiquinone; functions in the formation of 2-octaprenyl-6-hydroxy-phenol from 2-octaprenylphenol in ubiquinone (coenzyme Q) biosynthesis; similar to eukaryotic proteins that exhibit kinase functions YP_003082665.1 with DnaK and DnaJ acts in response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins; may act as a thermosensor YP_003082668.1 uses the energy from reduction of ubiquinone-1 to ubiquinol to move Na(+) ions from the cytoplasm to the periplasm YP_003082669.1 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_003082670.1 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_003082671.1 uses the energy from reduction of ubiquinone-1 to ubiquinol to move Na(+) ions from the cytoplasm to the periplasm YP_003082672.1 uses the energy from reduction of ubiquinone-1 to ubiquinol to move Na(+) ions from the cytoplasm to the periplasm YP_003082673.1 uses the energy from reduction of ubiquinone-1 to ubiquinol to move Na(+) ions from the cytoplasm to the periplasm YP_003082678.1 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_003082679.1 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_003082680.1 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_003082693.1 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_003082694.1 methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA YP_003082695.1 Essential for efficient processing of 16S rRNA YP_003082696.1 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_003082702.1 Maf; overexpression in Bacillus subtilis inhibits septation in the dividing cell YP_003082705.1 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_003082707.1 catalyzes the formation of 1-(5-phosphoribosyl)-AMP from 1-(5-phosphoribolsyl)-ATP in histidine biosynthesis YP_003082711.1 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_003082712.1 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_003082713.1 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_003082720.1 An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes YP_003082721.1 catalyzes the formation of phosphoenolpyruvate from pyruvate YP_003082730.1 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_003082731.1 PR-AMP cyclohydrolase; functions in histidine biosynthesis from PRPP; converts 1-(5-phosphoribosyl)-AMP to 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino]imidazole-4- carboxyamide during the histidine biosynthesis pathway; binds zinc and magnesium; forms homodimers YP_003082732.1 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_003082733.1 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_003082734.1 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_003082740.1 catalyzes the formation of arginine from (N-L-arginino)succinate YP_003082742.1 HAM1-like protein; Rec-dependent growth; RgdB; yggV; it is suspected that this protein functions to remove misincorporated bases such as xanthine or hypoxanthine YP_003082745.1 converts dATP to dAMP and pyrophosphate YP_003082761.1 hydrolyzes P(1),P(4)-bis(5'-adenosyl) tetraphosphate to form 2 ADP YP_003082764.1 catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III YP_003082769.1 catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP) YP_003082772.1 transfers the gamma-phosphate of ATP to the 4' position of a tetraacyldisaccharide 1-phosphate intermediate to form tetraacyldisaccharide 1,4'-bis-phosphate YP_003082775.1 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_003082778.1 catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis YP_003082779.1 catalyzes the carboxylation of acetyl-CoA to malonyl-CoA; forms a tetramer of AccA2D2 subunits YP_003082783.1 catalyzes the formation of N-carbamoyl-L-aspartate from (S)-dihydroorotate in pyrimidine biosynthesis YP_003082786.1 Regulates rRNA biosynthesis by transcriptional antitermination YP_003082787.1 RibE; 6,7-diimethyl-8-ribityllumazine synthase; DMRL synthase; lumazine synthase; beta subunit of riboflavin synthase; condenses 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione with L-3,4-dihydrohy-2-butanone-4-phosphate to generate 6,6-dimethyl-8-lumazine (DMRL); riboflavin synthase then uses 2 molecules of DMRL to produce riboflavin (vitamin B12); involved in the last steps of riboflavin biosynthesis; forms a 60mer (icosahedral shell) in both Bacillus subtilis and Escherichia coli; in Bacillus subtilis this 60mer is associated with the riboflavin synthase subunit (alpha) while in Escherichia coli it is not YP_003082789.1 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_003082790.1 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_003082793.1 catalyzes the formation of 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate from N-(5-phospho-beta-D-ribosyl)-anthranilate in tryptophan biosynthesis YP_003082794.1 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_003082795.1 Catalyzes first step of the de novo purine nucleotide biosynthetic pathway YP_003082802.1 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_003082804.1 catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate YP_003082812.1 required for the assembly and function of the DNAX complex which is required for the assembly of the beta subunit onto primed DNA YP_003082816.1 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_003082817.1 Transfers the fatty acyl group on membrane lipoproteins YP_003082821.1 Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr) YP_003082822.1 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_003082825.1 binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit YP_003082827.1 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_003082830.1 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_003082831.1 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_003082833.1 F exclusion of bacteriophage T7; overproduction of this protein in Escherichia coli inhibits the F plasmid-mediated exclusion of bacteriophage T7; interacts with the F plasmid-encoded PifA protein; inner membrane protein YP_003082835.1 DTB synthetase; dethiobiotin synthase; involved in production of dethiobiotin from ATP and 7,8-diaminononanoate and carbon dioxide; contains magnesium YP_003082837.1 catalyzes the conversion of 4-Hydroxybenzoate into 3-octaprenyl-4-hydroxybenzoate, as part of the ubiquinone biosynthesis pathway YP_003082839.1 catalyzes the phosphorylation of the phosphocarrier protein HPr of the bacterial phosphotransferase system YP_003082841.1 essential GTPase; functions in ribosome assembly; binds a unique part of the 23S rRNA; interacts with ribosomal protein L25(Ctc) YP_003082846.1 Catalyzes the carbon methylation reaction in the biosynthesis of ubiquinone YP_003082858.1 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_003082862.1 involved in lysine biosynthesis; DAP epimerase; produces DL-diaminopimelate from LL-diaminopimelate YP_003082867.1 binds to the ribosome on the universally-conserved alpha-sarcin loop YP_003082870.1 catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the delta' subunit seems to interact with the gamma subunit to transfer the beta subunit on the DNA YP_003082874.1 Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate YP_003082877.1 catalyzes the formation of uroporphyrinogen-III from hydroxymethylbilane; functions in tetrapyrrole and heme biosynthesis YP_003082880.1 catalyzes the formation of coproporphyrinogen from uroporphyrinogen III YP_003082881.1 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_003082894.1 Enables the recycling of peptidyl-tRNAs produced at termination of translation YP_003082901.1 catalyzes the formation of porphobilinogen from 5-aminolevulinate YP_003082903.1 similar protein in Methanocaldococcus converts GTP to 7,8-dihydro-D-neopterin 2',3'-cyclic phosphate as the first step in methanopterin biosynthesis YP_003082907.1 catalyzes the phosphorylation of NAD to NADP YP_003082911.1 catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis YP_003082912.1 NorM; MdtK; functions as a Na(+)/drug antiporter; inactivation in Vibrio cholerae results in susceptibility to fluoroquinolones YP_003082913.1 May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine YP_003082914.1 catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis YP_003082919.1 putative metalloprotease YP_003082920.1 essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP YP_003082921.1 type 1 subfamily; involved in last step of pyrimidine biosynthesis; converts orotidine 5'-phosphate to UMP and carbon dioxide; OMP decarboxylase; OMPDCase; OMPdecase YP_003082941.1 Catalyzes the formation of dUTP from dCTP in thymidylate biosynthesis YP_003082943.1 Required for efficient pilin antigenic variation YP_003082944.1 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_003082946.1 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_003082955.1 catalyzes the formation of spermidine from putrescine and S-adenosylmethioninamine YP_003082956.1 catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate YP_003082957.1 catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine YP_003082959.1 Incorporates lipoproteins in the outer membrane after they are released by the LolA protein YP_003082960.1 An essential enzyme in the nonmevalonate pathway of isopentenyl diphosphate and dimethylallyl diphosphate biosynthesis YP_003082961.1 catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP YP_003082962.1 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_003082964.1 threonine deaminase; threonine dehydratase; in Escherichia coli, IlvA is part of the isoleucine biosynthetic pathway YP_003082971.1 unwinds double stranded DNA YP_003082978.1 catalyzes the formation of dUMP from dUTP YP_003082979.1 catalyzes the formation of succinyldiaminopimelate from N-succinyl-2-amino-6-ketopimelate YP_003083031.1 catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis YP_003083037.1 IPP transferase; isopentenyltransferase; involved in tRNA modification; in Escherichia coli this enzyme catalyzes the addition of a delta2-isopentenyl group from dimethylallyl diphosphate to the N6-nitrogen of adenosine adjacent to the anticodon of tRNA species that read codons starting with uracil; further tRNA modifications may occur; mutations in miaA result in defects in translation efficiency and fidelity YP_003083040.1 Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA YP_003083043.1 Catalyzes the conversion of acetyl-CoA and L-homoserine to CoA and O-acetyl-L-homoserine YP_003083045.1 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 do not have the motif YP_003083046.1 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_003083047.1 MTHFR; catalyzes NADH-linked reduction of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate using FAD as a cofactor YP_003083048.1 catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine to form methionine YP_003083051.1 Catalyzes the oxidation of dihydrolipoamide to lipoamide YP_003083055.1 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_003083057.1 type II enzyme; in Escherichia coli this enzyme forms a trimer of dimers which is allosterically inhibited by NADH and competitively inhibited by alpha-ketoglutarate; allosteric inhibition is lost when Cys206 is chemically modified which also affects hexamer formation; forms oxaloacetate and acetyl-CoA and water from citrate and coenzyme A; functions in TCA cycle, glyoxylate cycle and respiration; enzyme from Helicobacter pylori is not inhibited by NADH YP_003083058.1 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_003083059.1 component of 2-oxoglutarate dehydrogenase complex; catalyzes the transfer of succinyl coenzyme A to form succinyl CoA as part of the conversion of 2-oxoglutarate to succinyl-CoA YP_003083060.1 E3 component of 2-oxoglutarate dehydrogenase complex; catalyzes the oxidation of dihydrolipoamide to lipoamide YP_003083062.1 catalyzes the interconversion of succinyl-CoA and succinate YP_003083063.1 Catalyzes the only substrate-level phosphorylation in the TCA cycle YP_003083067.1 The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrA is an ATPase and a DNA-binding protein. A damage recognition complex composed of 2 uvrA and 2 uvrB subunits scans DNA for abnormalities. When the presence of a lesion has been verified by uvrB, the uvrA molecules dissociate YP_003083068.1 catalyzes the decarboxylaton of phospatidyl-L-sering to phosphatidylethanolamine YP_003083071.1 TrpG; with TrpE catalyzes the formation of anthranilate and glutamate from chorismate and glutamine; TrpG provides the glutamine amidotransferase activity YP_003083072.1 Catalyzes the conversion of N-(5-phospho-D-ribosyl)-anthranilate and diphosphate to anthranilate and 5-phospho-alpha-D-ribose 1-diphosphate YP_003083081.1 catalyzes reversible transfer of hydride ion equivalent between NAD and NADP; membrane-bound proton pump that translocates protons from cytosolic to periplasmic side of the inner membrane; forms a tetramer composed of two alpha and 2 beta subunits; AB-stereospecific enzyme YP_003083083.1 forms a tetramer composed of 2 alpha subunits and 2 beta subunits in the inner membrane; involved in catalyzing transfer of hydride ion equivalents between NAD and NADP; stereospecific (AB-specific); functions as a proton pump by translocating protons from cytoplasm to periplasm YP_003083086.1 involved in de novo purine biosynthesis YP_003083107.1 component of the membrane-bound D-lactate oxidase, FAD-binding, NADH independent YP_003083147.1 With PurE catalyzes the conversion of aminoimidazole ribonucleotide to carboxyaminoimidazole ribonucleotide in the de novo purine nucleotide biosynthetic pathway YP_003083150.1 with component II, the glutamine amidotransferase, catalyzes the formation of anthranilate from chorismate and glutamine YP_003083154.1 catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate YP_003083158.1 catalyzes the formation of D-fructose 6-phosphate from fructose-1,6-bisphosphate YP_003083163.1 may be involved in chromosome condensation; overexpression in Escherichia coli protects against decondensation by camphor; overexpressing the protein results in an increase in supercoiling YP_003083166.1 Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway YP_003083167.1 catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis YP_003083168.1 catalyzes the formation of 2-isopropylmalate from acetyl-CoA and 2-oxoisovalerate in leucine biosynthesis YP_003083170.1 transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein YP_003083172.1 catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate YP_003083183.1 involved in the maturation of iron-sulfur cluster-containing proteins YP_003083190.1 catalyzes the carboxylation of acetyl-CoA to malonyl-CoA; forms a tetramer composed of two alpha (AccA) and two beta (AccD) subunits; one of the two catalytic subunits that can form the acetyl CoA carboxylase enzyme together with a carrier protein YP_003083198.1 catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis YP_003083199.1 hemoprotein; NADPH dependent; with the alpha subunit (a flavoprotein) catalyzes the reduction of sulfite to sulfide YP_003083202.1 with CysN catalyzes the formation of adenylylsulfate from sulfate and ATP YP_003083203.1 catalyzes the reduction of 3'-phosphoadenylyl sulfate into sulfite YP_003083209.1 catalyzes the synthesis of xanthosine monophosphate by the NAD+ dependent oxidation of inosine monophosphate YP_003083214.1 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_003083215.1 lipoyl/octanoyltransferase; catalyzes the transfer of the lipoyl/octanoyl moiety of lipoyl/octanoyl-ACP onto lipoate-dependent enzymes like pyruvate dehydrogenase and the glycine cleavage system H protein YP_003083220.1 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_003083228.1 catalyzes the formation of L-aspartate 4-semialdehyde from L-homoserine YP_003083238.1 involved in a recombinational process of DNA repair, independent of the recBC complex YP_003083242.1 catalyzes the addition and repair of the essential 3'-terminal CCA sequence in tRNAs without using a nucleic acid template; phosphohydrolase activities include hydrolysis of pyrophosphate, 5'-nucleoside tri- and diphosphates, NADP, and 2'-AMP with the production of Pi, metal-dependent phosphodiesterase activity for 2',3'-cAMP, 2',3'-cGMP, and 2',3'-cCMP, and hydrolysis 2',3'-cyclic substrates with the formation of 2'-nucleotides and 3'-nucleotides; these phosphohydrolase activities are probably involved in the repair of the tRNA 3'-CCA terminus degraded by intracellular RNases YP_003083244.1 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_003083248.1 catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine YP_003083253.1 catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis YP_003083256.1 catalyzes the conversion of GTP to formate and 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine and diphosphate YP_003083258.1 bifunctional enzyme DHBP synthase/GTP cyclohydrolase II-like protein; functions in riboflavin synthesis YP_003083267.1 catalyzes the formation of L-threonine from O-phospho-L-homoserine YP_003083275.1 Involved in DNA double-strand break repair and recombination. Promotes the annealing of complementary single-stranded DNA and by simulation of RAD51 recombinase YP_003083277.1 dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate YP_003083279.1 catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis; forms a heterodimer of LeuC/D YP_003083280.1 catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis YP_003083282.1 catalyzes the formation of fumarate from aspartate YP_003083300.1 activates fatty acids by binding to coenzyme A YP_003083307.1 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_003083308.1 catalyzes the formation of 2-dehydro-3-deoxy-D-octonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate in LPS biosynthesis YP_003083310.1 enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis YP_003083313.1 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_003083315.1 Catalyzes the rate-limiting step in dNTP synthesis YP_003083318.1 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_003083323.1 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_003083324.1 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_003083329.1 catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate YP_003083332.1 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_003083333.1 hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates YP_003083334.1 Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer YP_003083340.1 in Escherichia coli this protein is wrapped around the base of the L1 stalk YP_003083341.1 binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit YP_003083343.1 binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21 YP_003083346.1 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_003083348.1 tRNA (guanine-N(7)-)-methyltransferase; catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA by transferring the methyl residue from S-adenosyl-L-methionine YP_003083349.1 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_003083354.1 similar to RuvC resolvase with substantial differences; NMR structural information suggests this protein is monomeric; unknown cellular function YP_003083356.1 catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro) YP_003083357.1 E1 component; part of pyruvate dehydrogenase; forms a complex with DlaT and LpdC YP_003083369.1 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_003083370.1 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_003083372.1 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_003083374.1 catalyzes the formation of pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate YP_003083377.1 bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides YP_003083387.1 DapATase; bifunctional enzyme that functions in arginine and lysine biosynthetic pathways; catalyzes the formation of N-acetyl-L-glutamate 5-semialdehyde from 2-oxoglutarate and N(2)-acetyl-L-ornithine or N-succinyl-2-L-amino-6-oxoheptanedioate from 2-oxoglutarate and N-succinyl-L-2,6-diaminoheptanedioate YP_003083388.1 binds and unfolds substrates as part of the ClpXP protease YP_003083389.1 associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock YP_003083391.1 catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs YP_003083395.1 catalyzes the removal of elemental sulfur from cysteine to produce alanine; involved in NAD biosynthesis YP_003083403.1 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_003083405.1 catalyzes the conversion of ATP and D-glucose to ADP and D-glucose 6-phosphate YP_003083407.1 catalyzes the formation of D-glucono-1,5-lactone 6-phosphate from D-glucose 6-phosphate YP_003083408.1 catalyzes the formation of 2-dehydro-3-deoxy-6-phospho-D-gluconate from 6-phospho-D-gluconate YP_003083409.1 catalyzes the formation of pyruvate and glyoxylate from 4-hydroxy-2-oxoglutarate; or pyruvate and D-glyceraldehyde 3-phosphate from 2-dehydro-3-deoxy-D-glyconate 6-phosphate YP_003083421.1 Acylates the intermediate (KDO)2-lipid IVA to form (KDO)2-(lauroyl)-lipid IVA YP_003083422.1 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_003083428.1 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_003083432.1 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_003083433.1 catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis YP_003083444.1 This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. Promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of a final effector complex YP_003083445.1 catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the tau chain serves as a scaffold to help in the dimerizaton of the alpha,epsilon and theta core complex; the gamma chain seems to interact with the delta and delta' subunits to transfer the beta subunit on the DNA YP_003083447.1 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_003083448.1 catalyzes the dehydration of 3-dehydroquinate to form 3-dehydroshikimate in aromatic amino acid biosynthesis YP_003083450.1 involved in translesion DNA polymerization with beta clamp of polymerase III; belongs to Y family of polymerases; does not contain proofreading function YP_003083457.1 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_003083458.1 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_003083468.1 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_003083470.1 broad specificity; family IV; in Corynebacterium glutamicum this protein can use glutamate, 2-aminobutyrate, and aspartate as amino donors and pyruvate as the acceptor YP_003083475.1 catalyzes the dephosphorylation of 2-phosphoglycolate to form glycolate and phosphate YP_003083476.1 binds RecA and inhibits RecA-mediated DNA strand exchange and ATP hydrolysis and coprotease activities YP_003083480.1 catalyzes the conversion of a phosphate monoester to an alcohol and a phosphate YP_003083488.1 catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP, in Bacillus, lysine sensitive; regulated by response to starvation. YP_003083489.1 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_003083493.1 catalyzes the formation of nictonate and 5-phospho-alpha-D-ribose 1-diphosphate from nicotinate D-ribonucleotide and diphosphate YP_003083494.1 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_003083498.1 Catalyzes D-ribose 5-phosphate --> D-ribulose 5-phosphate in the nonoxidative branch of the pentose phosphate pathway YP_003083499.1 catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate into 2-C-methyl-D-erythritol 2,4-cyclodiphosphate YP_003083500.1 4-diphosphocytidyl-2C-methyl-D-erythritol synthase; MEP cytidylyltransferase; MCT; catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate; involved in isoprenoid and isopentenyl-PP biosynthesis; forms homodimers YP_003083505.1 AckA utilizes acetate and can acetylate CheY which increases signal strength during flagellar rotation; utilizes magnesium and ATP; also involved in conversion of acetate to aceyl-CoA YP_003083506.1 two electrons are transferred from cytoplasmic NADPH to thioredoxin and then to the inner membrane protein DsbD which keeps the disulfide isomerase DsbC in a reduced state in the oxidizing periplasm; DsbC in turns rearranges incorrectly made disulfide bonds in the periplasm YP_003083513.1 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_003083517.1 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_003083522.1 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_003083523.1 synthesizes RNA primers at the replication forks YP_003083524.1 sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; this is the primary sigma factor of bacteria YP_003083529.1 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_003083531.1 catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs YP_003083534.1 catalyzes the second step in the glutathione biosynthesis pathway, where it synthesizes ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione YP_003083535.1 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_003083548.1 catalyzes the conversion of citrate to isocitrate and the conversion of 2-methylaconitate to 2-methylisocitrate YP_003083549.1 catalyzes the formation of ornithine and carbamylphosphate from citrulline in the arginine catabolic pathway YP_003083550.1 catalyzes the formation of (R)-2,3-dihydroxy-3-methylbutanoate from (S)-2-hydroxy-2-methyl-3-oxobutanoate in valine and isoleucine biosynthesis YP_003083552.1 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_003083569.1 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_003083571.1 catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer YP_003083572.1 catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis YP_003083573.1 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_003083577.1 SohB; periplasmic protein; member of the peptidase S49 family YP_003083585.1 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_003083589.1 2,3-bisphosphoglycerate-dependent; catalyzes the interconversion of 2-phosphoglycerate to 3-phosphoglycerate YP_003083590.1 decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling YP_003083600.1 involved in potassium uptake; found to be peripherally associated with the inner membrane in Escherichia coli; contains an NAD-binding domain YP_003083602.1 catalyzes the formation of 4-amino-2-methyl-5-diphosphomethylpyrimidine YP_003083603.1 with TehA confers resistance to tellurite YP_003083604.1 An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids YP_003083616.1 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_003083617.1 in Streptococcus pneumoniae this gene was found to be essential; structure determination of the Streptococcus protein shows that it is similar to a number of other proteins YP_003083618.1 modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination YP_003083619.1 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_003083630.1 ACT domain-containing protein YP_003083632.1 involved in methylation of ribosomal protein L3 YP_003083639.1 Essential for recycling GMP and indirectly, cGMP YP_003083640.1 catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis YP_003083653.1 acts in conjunction with GvcH to form H-protein-S-aminomethyldihydrolipoyllysine from glycine YP_003083655.1 catalyzes the formation of L-glutamate and an aromatic oxo acid from an aromatic amino acid and 2-oxoglutarate YP_003083656.1 catalyzes the formation of 5-methyl-uridine at position 54 in all tRNAs YP_003083657.1 catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis YP_003083659.1 decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling YP_003083660.1 hydrolyzes diadenosine polyphosphate YP_003083661.1 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_003083663.1 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_003083667.1 catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate YP_003083677.1 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_003083678.1 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_003083693.1 CcoO; FixO YP_003083694.1 CcoN; FixN YP_003083703.1 cofactor involved in the reduction of disulfides YP_003083721.1 catalyzes the formation of 8-amino-7-oxononanoate from 6-carboxyhexanoyl-CoA and L-alanine YP_003083724.1 catalyzes the formation of putrescine from agmatine YP_003083725.1 catalyzes the formation of agmatine from arginine in putrescine and spermidine biosynthesis YP_003083727.1 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_003083730.1 binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase YP_003083734.1 converts L-glutamate to D-glutamate, a component of peptidoglycan YP_003083741.1 Catalyzes the formation of holo-ACP, which mediates the essential transfer of acyl fatty acid intermediates during the biosynthesis of fatty acids and lipids YP_003083744.1 involved in the de novo synthesis of pyridoxine (Vitamin B6) YP_003083754.1 AckA utilizes acetate and can acetylate CheY which increases signal strength during flagellar rotation; utilizes magnesium and ATP; also involved in conversion of acetate to aceyl-CoA YP_003083756.1 Catalyzes the conversion of citrate to isocitrate YP_003083759.1 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_003083760.1 catalyzes the formation of pyruvate and succinate from 2-methylisocitrate YP_003083762.1 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_003083765.1 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_003083766.1 Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis YP_003083767.1 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_003083769.1 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_003083771.1 First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan YP_003083775.1 involved in cell wall formation; peptidoglycan synthesis; cytoplasmic enzyme; catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-aceylmuramoyl-l-alanyl-d-glutamate YP_003083779.1 MraZ; UPF0040; crystal structure shows similarity to AbrB YP_003083781.1 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_003083787.1 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 protein from Pseudomonas does not have this domain YP_003083795.1 3 different subfamilies; catalyzes the formation of quinolinate from iminoaspartate and dihydroxyacetone phosphate YP_003083801.1 ChvD; in Agrobacterium tumefaciens, mutations in both Walker boxes were found to affect virulence YP_003083803.1 catalyzes the formation of thiamine diphosphate from thiamine phosphate ant ATP YP_003083807.1 catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III YP_003083809.1 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_003083828.1 glycosyltransferase; polymerizes glycan strands in the peptidoglycan YP_003083834.1 catalyzes the reversible formation of D-erythrose 4-phosphate and D-fructose 6-phosphate from sedoheptulose 7-phosphate and D-glyceraldehyde 3-phosphate YP_003083836.1 this tRNA synthetase lacks the tRNA anticodon interaction domain; instead this enzyme modifies tRNA(Asp) with glutamate by esterifying glutamate to the 2-amino-5-(4,5-dihydroxy-2-cyclopenten-1-yl) moiety of queosine generating a modified nucleoside at the first anticodon position of tRNAAsp; the modified tRNA does not bind elongation factor Tu YP_003083838.1 hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr); possible defense mechanism against a harmful effect of D-tyrosine YP_003083842.1 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_003083843.1 Involved in cell division; probably involved in intracellular septation YP_003083849.1 catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids YP_003083850.1 Catalyzes a key regulatory step in fatty acid biosynthesis YP_003083851.1 catalyzes the formation of N-succinyl-2-amino-6-ketopimelate from succinyl-CoA and tetrahydrodipicolinate in the lysine biosynthetic pathway YP_003083852.1 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_003083861.1 involved in the peptidyltransferase reaction during translation YP_003083863.1 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_003083864.1 required for 70S ribosome assembly YP_003083868.1 NADPH-dependent; catalyzes the reduction of 7-cyano-7-deazaguanine to 7-aminomethyl-7-deazaguanine in queuosine biosynthesis YP_003083878.1 catalyzes the formation of 3-deoxy-D-arabino-hept-2-ulosonate 7 phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate, phenylalanine sensitive YP_003083892.1 helicase involved in DNA repair and perhaps also replication YP_003083895.1 Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide YP_003083905.1 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_003083913.1 plays an essential role in ATP-dependent branch migration of the Holliday junction YP_003083916.1 EngC; RsgA; CpgA; circularly permuted GTPase; ribosome small subunit-dependent GTPase A; has the pattern G4-G1-G3 as opposed to other GTPases; interacts strongly with 30S ribosome which stimulates GTPase activity YP_003083917.1 catalyzes the bidirectional exonucleolytic cleavage of DNA YP_003083920.1 Catalyzes the transfer of electrons from NADH to quinone YP_003083921.1 Catalyzes the transfer of electrons from NADH to quinone YP_003083923.1 Catalyzes the transfer of electrons from NADH to ubiquinone YP_003083925.1 Catalyzes the transfer of electrons from NADH to quinone YP_003083927.1 Catalyzes the transfer of electrons from NADH to quinone YP_003083929.1 Catalyzes the transfer of electrons from NADH to ubiquinone YP_003083934.1 Catalyzes the transfer of electrons from NADH to quinone YP_003083935.1 Catalyzes the transfer of electrons from NADH to quinone YP_003083936.1 Catalyzes the transfer of electrons from NADH to quinone YP_003083937.1 The point of entry for the majority of electrons that traverse the respiratory chain eventually resulting in the reduction of oxygen YP_003083949.1 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_003083955.1 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_003083956.1 carries the fatty acid chain in fatty acid biosynthesis YP_003083957.1 FabF; beta-ketoacyl-ACP synthase II, KASII; catalyzes a condensation reaction in fatty acid biosynthesis: addition of an acyl acceptor of two carbons from malonyl-ACP; required for the elongation of short-chain unsaturated acyl-ACP YP_003083967.1 negatively supercoils closed circular double-stranded DNA YP_003083973.1 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_003083976.1 catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis YP_003083982.1 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_003083984.1 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_003083985.1 RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids YP_003083987.1 glucose-inhibited division protein B; SAM-dependent methyltransferase; methylates the N7 position of guanosine in position 527 of 16S rRNA YP_003083990.1 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_003083993.1 catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate YP_003083997.1 adds the O-linked and N-linked 3(R)-hydroxy fatty acids to the glucosamine disaccharide during lipid A biosynthesis YP_003083998.1 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_003083999.1 catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis YP_003084001.1 catalyzes the oxidative deamination of D-amino acids YP_003084003.1 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_003084005.1 works in conjunction with MinC and MinD to enable cell division at the midpoint of the long axis of the cell YP_003084007.1 blocks the formation of polar Z-ring septums YP_003084008.1 is a component of the macrolide binding site in the peptidyl transferase center YP_003084009.1 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_003084010.1 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_003084011.1 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_003084012.1 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_003084013.1 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_003084014.1 stimulates the activities of the other two initiation factors, IF-2 and IF-3 YP_003084015.1 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_003084016.1 late assembly protein YP_003084017.1 L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7 YP_003084018.1 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_003084019.1 binds 5S rRNA along with protein L5 and L25 YP_003084020.1 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_003084021.1 binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit YP_003084022.1 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_003084023.1 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_003084024.1 assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel YP_003084025.1 binds to the 23S rRNA between the centers for peptidyl transferase and GTPase YP_003084026.1 primary binding protein; helps mediate assembly; involved in translation fidelity YP_003084027.1 one of the stabilizing components for the large ribosomal subunit YP_003084028.1 located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e YP_003084029.1 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_003084030.1 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_003084031.1 protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA YP_003084032.1 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_003084033.1 binds third domain of 23S rRNA and protein L29; part of exit tunnel YP_003084034.1 L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA YP_003084035.1 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_003084036.1 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_003084037.1 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_003084038.1 EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene YP_003084039.1 binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit YP_003084040.1 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_003084043.1 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_003084044.1 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_003084045.1 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_003084046.1 binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit YP_003084047.1 in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA YP_003084048.1 binds directly to 23S ribosomal RNA YP_003084049.1 Modulates Rho-dependent transcription termination YP_003084050.1 forms a complex with SecY and SecG; SecYEG forms a putative 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_003084051.1 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_003084057.1 catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining; maintains net negative superhelicity YP_003084065.1 cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+) YP_003084068.1 involved in the allosteric regulation of aspartate carbamoyltransferase YP_003084069.1 catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis YP_003084087.1 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_003084111.1 Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source YP_003084112.1 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_003084121.1 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