-- dump date   	20140620_032451
-- class       	Genbank::CDS
-- table       	cds_note
-- id	note
YP_529899.1	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_529900.1	binds the polymerase to DNA and acts as a sliding clamp
YP_529901.1	Required for DNA replication; binds preferentially to single-stranded, linear DNA
YP_529903.1	negatively supercoils closed circular double-stranded DNA
YP_529912.1	CcoO; FixO
YP_529913.1	CcoN; FixN
YP_529921.1	involved in de novo purine biosynthesis
YP_529929.1	catalyzes the formation of arginosuccinate from citrulline and aspartate in arginine biosynthesis
YP_529938.1	catalyzes the hydrolysis of pyrophosphate to phosphate
YP_529940.1	Acs; catalyzes the conversion of acetate and CoA to acetyl-CoA
YP_529943.1	catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate
YP_529944.1	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_529954.1	Catalyzes the transfer of the ammonia group from glutamine to a new carbon-nitrogen group
YP_529957.1	catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate
YP_529961.1	with CysN catalyzes the formation of adenylylsulfate from sulfate and ATP
YP_529966.1	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_529968.1	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_529974.1	An electron-transfer protein; flavodoxin binds one FMN molecule, which serves as a redox-active prosthetic group
YP_529991.1	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_529996.1	consists of N-terminal helix-turn-helix domain and C-terminal shikimate kinase-like domain which may bind benzoyl-CoA; controls inducible expression of the bzd catabolic operon that is involved in the anaerobic catabolism of benzoate
YP_529998.1	catalyzes the reaction of formaldehyde with glutathione to form S-hydroxymethylglutathione
YP_530043.1	MobA/MobL family protein
YP_530048.1	involved in the peptidyltransferase reaction during translation
YP_530051.1	essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication
YP_530052.1	catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis
YP_530055.1	Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway
YP_530056.1	transfers an adenyl group from ATP to NaMN to form nicotinic acid adenine dinucleotide (NaAD) which is then converted to the ubiquitous compound NAD by NAD synthetase; essential enzyme in bacteria
YP_530058.1	SPOUT methyltransferase family protein; crystal structure shows homodimer; in Escherichia coli this protein methylates pseudouridine at position 1915 of the 23S ribosomal RNA
YP_530062.1	hydrolyzes diadenosine polyphosphate
YP_530064.1	hydrolyzes diadenosine polyphosphate
YP_530065.1	catalyzes the formation of porphobilinogen from 5-aminolevulinate
YP_530067.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the epsilon subunit is part of the catalytic core of the ATP synthase complex
YP_530068.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit
YP_530069.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit
YP_530070.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit
YP_530071.2	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_530073.1	binding of PriA to forked DNA starts the assembly of the primosome, also possesses 3'-5' helicase activity
YP_530074.1	site-specific tyrosine recombinase which cuts and rejoins DNA molecules; binds cooperatively to specific DNA consensus sites; forms a heterotetrameric complex with XerC; XerCD exhibit similar sequences; essential to convert chromosome dimers to monomers during cell division and functions during plasmid segregation; cell division protein FtsK may regulate the XerCD complex; enzyme from Streptococcus group has unusual active site motifs
YP_530077.1	Catalyzes the oxidation of dihydrolipoamide to lipoamide
YP_530084.1	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_530085.1	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_530087.1	catalyzes the interconversion of succinyl-CoA and succinate
YP_530088.1	Catalyzes the reversible oxidation of malate to oxaloacetate
YP_530098.1	Catalyzes the conversion of citrate to isocitrate
YP_530099.1	ATP-binding protein; required for proper cytochrome c maturation
YP_530105.1	Involved in cell division; probably involved in intracellular septation
YP_530109.1	involved in lysine biosynthesis; DAP epimerase; produces DL-diaminopimelate from LL-diaminopimelate
YP_530116.1	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_530117.1	Essential for efficient processing of 16S rRNA
YP_530118.1	methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA
YP_530119.1	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_530121.1	dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate
YP_530124.1	catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis; forms a heterodimer of LeuC/D
YP_530131.1	catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde
YP_530134.1	catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis
YP_530139.1	catalyzes the formation of malonyl-CoA from malonate and CoA
YP_530178.1	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_530180.1	required for the assembly and function of the DNAX complex which are required for the assembly of the beta subunit onto primed DNA
YP_530183.1	glucose-inhibited division protein B; SAM-dependent methyltransferase; methylates the N7 position of guanosine in position 527 of 16S rRNA
YP_530184.1	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_530185.1	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_530186.1	An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes
YP_530190.1	catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A; involved in coenzyme A biosynthesis
YP_530192.1	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_530196.1	heat shock protein involved in degradation of misfolded proteins
YP_530197.1	heat shock protein involved in degradation of misfolded proteins
YP_530198.1	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_530200.1	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_530201.1	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_530204.1	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_530205.1	catalyzes the formation of 1-(5-phosphoribosyl)-AMP from 1-(5-phosphoribolsyl)-ATP in histidine biosynthesis
YP_530206.1	catalyzes the formation of (R)-4'-phosphopantothenate in coenzyme A biosynthesis
YP_530213.1	catalyzes the second step in the glutathione biosynthesis pathway, where it synthesizes ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione
YP_530217.1	catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III
YP_530218.1	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_530219.1	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_530220.1	Negative regulator of class I heat shock genes (grpE-dnaK-dnaJ and groELS operons). Prevents heat-shock induction of these operons
YP_530221.1	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_530223.1	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_530224.1	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_530227.1	type 1 subfamily; involved in last step of pyrimidine biosynthesis; converts orotidine 5'-phosphate to UMP and carbon dioxide; OMP decarboxylase; OMPDCase; OMPdecase
YP_530229.1	catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis
YP_530230.1	catalyzes the interconversion of 2-phosphoglycerate to 3-phosphoglycerate
YP_530236.1	catalyzes the uridylylation or deuridylylation of the PII nitrogen regulatory protein
YP_530238.1	Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA
YP_530239.1	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_530241.1	Catalyzes a key regulatory step in fatty acid biosynthesis
YP_530242.1	FabB, beta-Ketoacyl-ACP synthase I, KASI; 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_530243.1	catalyzes the dehydration of (3R)-3-hydroxydecanoyl-ACP to 2,3-decenoyl-ACP or 3,4-decenoyl-ACP
YP_530257.1	This protein performs the mismatch recognition step during the DNA repair process
YP_530271.1	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_530272.1	Catalyzes the carbon methylation reaction in the biosynthesis of ubiquinone
YP_530274.1	catalyzes the conjugation of cysteine to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine, which is then decarboxylated to form 4'-phosphopantotheine; in the alphaproteobacteria, this protein contains an N-terminal SbtC-like domain
YP_530275.1	catalyzes the formation of dUMP from dUTP
YP_530284.1	catalyzes the carboxylation of acetyl-CoA to malonyl-CoA; forms a tetramer of AccA2D2 subunits
YP_530285.1	catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis
YP_530286.1	catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate
YP_530287.1	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_530289.1	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_530291.1	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_530292.1	Catalyzes the formation of (d)CDP from ATP and (d)CMP
YP_530294.1	catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis
YP_530302.1	part of the UgpABCE glycerol-3-phosphate uptake system
YP_530309.1	sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; sigma 54 factor is responsible for the expression of enzymes involved in nitrogen assimilation and metabolism; the rhizobia often have 2 copies of this sigma factor; in Rhizobium etli RpoN1 shown to be involved in the assimilation of several nitrogen and carbon sources during free-living aerobic growth and RpoN2 is involved in symbiotic nitrogen fixation; in Bradyrhizobium both RpoN1 and N2 are functional in free-living and symbiotic conditions, rpoN1 gene was regulated in response to oxygen
YP_530322.1	reduces nitrous oxide to nitrogen
YP_530332.1	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_530335.1	putative role in sulfur assimilation
YP_530338.1	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_530341.1	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_530342.1	binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit
YP_530353.1	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_530362.1	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_530366.1	Transfers the fatty acyl group on membrane lipoproteins
YP_530368.1	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_530371.1	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_530372.1	modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination
YP_530374.1	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_530375.1	associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock
YP_530376.1	catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs
YP_530377.1	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_530385.1	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_530392.1	glycosyltransferase; polymerizes glycan strands in the peptidoglycan
YP_530393.1	some L32 proteins have zinc finger motifs consisting of CXXC while others do not
YP_530398.1	Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation; in Rhizobia and Ralstonia is involved in PHB biosynthesis
YP_530406.1	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_530408.1	catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP, in Bacillus, lysine sensitive; regulated by response to starvation.
YP_530409.1	Involved in ubiquinone biosynthesis
YP_530418.1	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_530420.1	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_530422.1	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_530426.1	catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis
YP_530427.1	catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis
YP_530437.1	required for 70S ribosome assembly
YP_530457.1	part of the metNIQ transport system for methionine
YP_530469.1	Involved in DNA double-strand break repair and recombination. Promotes the annealing of complementary single-stranded DNA and by simulation of RAD51 recombinase
YP_530474.1	the Vibrio parahaemolyticus gene VP2867 was found to be a potassium/proton antiporter; can rapidly extrude potassium against a potassium gradient at alkaline pH when cloned and expressed in Escherichia coli
YP_530475.1	D-alanyl-D-alanine endopeptidase; functions in hydrolyzing cell wall peptidoglycan; similar to LAS metallopeptidases; forms a dimer in periplasm
YP_530485.1	binds to the ribosome on the universally-conserved alpha-sarcin loop
YP_530493.1	PEP carboxykinase; PEP carboxylase; PEPCK; catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using ATP
YP_530498.1	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_530503.1	catalyzes the formation of ADP-glucose and diphosphate from ATP and alpha-D-glucose 1-phosphate
YP_530504.1	catalyzes the formation of alpha-1,4-glucan chains from ADP-glucose
YP_530572.1	Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA
YP_530576.1	catalyzes the ring cleavage reaction in phenylacetate degradation and the formation of 3-hydroxyacyl-CoA from crotonyl-CoA
YP_530581.1	with PaaBCDE catalyzes the hydroxylation of phenylacetyl-CoA; involved in phenylacetate degradation
YP_530582.1	with PaaBCDE catalyzes the hydroxylation of phenylacetyl-CoA
YP_530587.1	catalyzes the coenzyme A dependent formation of succinyl-CoA from 2-oxoglutarate and ferredoxin
YP_530590.1	catalyzes the formation of L-tryptophan from indole and L-serine
YP_530594.1	undetermined function
YP_530620.1	class I; LysRS1; 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 this enzyme charges both tRNA molecules for lysine that exist in this organism (but the tRNALysUUU very poorly) and in the presence of LysRS2 can charge tRNAPyl with lysine
YP_530626.1	Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation
YP_530641.1	catalyzes the ATP-dependent formation of a phosphodiester at the site of a single strand break in duplex DNA
YP_530645.1	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_530650.1	glutamate synthase is composed of subunits alpha and beta; beta subunit is a flavin adenine dinucleotide-NADPH dependent oxidoreductase; provides electrons to the alpha subunit, which binds L-glutamine and 2-oxoglutarate and forms L-glutamate
YP_530674.1	stationary phase protein that binds TrpR repressor
YP_530686.1	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 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_530693.1	cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+)
YP_530696.1	modifies the free amino group of the aminoacyl moiety of methionyl-tRNA(fMet) which is important in translation initiation; inactivation of this gene in Escherichia coli severely impairs growth
YP_530697.1	mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability
YP_530699.1	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_530701.1	catalyzes the formation of N-succinyl-2-amino-6-ketopimelate from succinyl-CoA and tetrahydrodipicolinate in the lysine biosynthetic pathway
YP_530704.1	catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate
YP_530706.1	binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential
YP_530707.1	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_530709.1	in Escherichia coli transcription of this gene is enhanced by polyamines
YP_530716.1	with AtoS is a two-component regulatory system involved in the transcriptional regulation of the ato genes for acetoacetate metabolism
YP_530717.1	with AtoC is a member of a two-component regulatory system involved in the transcriptional regulation of the ato genes for acetoacetate metabolism
YP_530723.1	catalyzes the synthesis of acetylphosphate or propionylphosphate from acetyl-CoA or propionyl-CoA and inorganic phosphate; when using propionyl-CoA the enzyme is functioning in the anaerobic pathway catabolizing threonine to propionate
YP_530754.1	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_530760.1	the hook connects flagellar basal body to the flagellar filament
YP_530764.1	with FlgK acts as a hook filament junction protein to join the flagellar filament to the hook
YP_530769.1	possibly involved in transport of pyrroloquinoline quinone transport
YP_530770.1	Required in the synthesis of PPQ, but its exact function is unknown
YP_530780.1	An oxygenase that acts to open the ring of homogentisate formingmaleylacetoacetate as part of the catabolism of L-tyrosine and L-phenylalanine
YP_530782.1	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_530783.1	catalyzes the formation of pyruvate and beta-alanine from L-alanine and 3-oxopropanoate
YP_530790.1	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_530794.1	involved in methylation of ribosomal protein L3
YP_530830.2	the MS-ring anchors the flagellum to the cytoplasmic membrane; part of the flagellar basal body which consists of four rings L, P, S, and M mounted on a central rod
YP_530831.1	One of three proteins involved in switching the direction of the flagellar rotation
YP_530832.1	binds to and inhibits the function of flagella specific ATPase FliI
YP_530833.1	One of three proteins involved in switching the direction of the flagellar rotation
YP_530841.1	periplasmic; catalytic subunit; with NapBC catalyzes the reduction of nitrate to nitrite; NapAB receives electrons from NapC
YP_530849.1	catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers
YP_530859.1	synthesizes RNA primers at the replication forks
YP_530860.1	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_530870.1	catalyzes the reduction of hydroxylamine to ammonia and water
YP_530876.1	catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs
YP_530883.1	MobA/MobL family protein
YP_530919.1	AliA; in Rhodopseudomonas palustris, this enzyme was found to act on 3-chlorobenzoate and allows the organism to grow on this substrate
YP_530942.1	The beta subunit catalyzes the decarboxylation of the malonyl moiety on coenzyme A
YP_530962.1	catalyzes the synthesis of acetylphosphate or propionylphosphate from acetyl-CoA or propionyl-CoA and inorganic phosphate; when using propionyl-CoA the enzyme is functioning in the anaerobic pathway catabolizing threonine to propionate
YP_530966.1	unknown function; when overproduced it confers drug-resistance
YP_530969.1	involved in type III protein export during flagellum assembly
YP_530970.1	FlgF, with FlgB and C, makes up the proximal portion of the flagellar basal body rod; Bradyrhizobium have one thick flagellum and several thin flagella; the protein in this cluster is associated with the thin flagella
YP_530971.1	With MotB forms the ion channels that couple flagellar rotation to proton/sodium motive force across the membrane and forms the stator elements of the rotary flagellar machine
YP_530976.1	membrane protein responsible for substrate specificity switching from rod/hook-type export to filament-type export; Bradyrhizobium has one thick flagellum and several thin flagella; the Bradyrhizobium protein in this cluster is associated with the thin flagella
YP_530977.1	with FlgF and C makes up the proximal portion of the flagellar basal body rod; Bradyrhizobium have one thick flagellum and several thin flagella; the proteins in this cluster are associated with the thin flagella
YP_530978.1	with FlgF and B makes up the proximal portion of the flagellar basal body rod; Bradyrhizobium have one thick flagellum and several thin flagella; the protein in this cluster is associated with the thin flagella
YP_530979.1	forms a junction between the M-ring and FlgB during flagella biosynthesis; Bradyrhizobium has one thick flagellum and several thin flagella; the protein in this cluster is associated with the thin flagella
YP_530980.1	makes up the distal portion of the flagellar basal body rod; Bradyrhizobium has one thick flagellum and several thin flagella; the protein in this cluster is associated with the thin flagella
YP_530981.1	required for the assembly of the flagellar basal body P-ring; Bradyrhizobium japonicum has two types of flagella, a single thick flagella and a few thin flagella; the protein in this cluster is associated with the thin flagella
YP_530982.1	part of the basal body which consists of four rings L, P, S, and M mounted on a central rod; Bradyrhizobium has one thick flagellum and several thin flagella; the Bradyrhizobium protein in this cluster is associated with the thin flagella
YP_530984.1	part of the basal body which consists of four rings L, P, S, and M mounted on a central rod; Bradyrhizobium has one thick flagellum and several thin flagella; the Bradyrhizobium protein in this cluster is associated with the thin flagella
YP_530986.1	FliP, with proteins FliQ and FliR, forms the core of the central channel in the flagella export apparatus; Bradyrhizobium have one thick flagellum and several thin flagella; the Bradyrhizobium protein in this cluster is associated with the thin flagellum
YP_530987.1	structural flagella protein; Bradyrhizobium has 2 types of flagella, thick and thin; the proteins in this cluster have been identified as making up the thin flagella and may be involved in swarming
YP_530988.1	the MS-ring anchors the flagellum to the cytoplasmic membrane; part of the flagellar basal body which consists of four rings L, P, S, and M mounted on a central rod
YP_530990.1	with MotA forms the ion channels that couple flagellar rotation to proton/sodium motive force across the membrane and forms the stator elements of the rotary flagellar machine
YP_530991.1	a periplasmic protein that interacts with and stabilizes MotB; in Rhizobium, interactions between MotB and MotC at the periplasmic surface of the motor control the energy flux or the energy coupling that drives flagellar rotation
YP_530994.1	the hook connects flagellar basal body to the flagellar filament
YP_530995.1	with FlgL acts as a hook filament junction protein to join the flagellar filament to the hook
YP_530996.1	with FlgK acts as a hook filament junction protein to join the flagellar filament to the hook; Bradyrhizobium has one thick flagellum and several thin flagella; the Bradyrhizobium protein in this cluster is associated with the thin flagella
YP_530997.1	acts as an activator or flagellin translation and may be required for filament secretion or assembly; Bradyrhizobium has one thick flagellum and several thin flagella; the protein in this cluster is associated with the thin flagella
YP_530998.1	post-transcriptional repressor of flagellum biosynthesis; promotes degradation of fljK mRNA: Bradyrhizobium has one thick flagellum and several thin flagella; the protein in this cluster is associated with the thin flagella
YP_530999.1	acts as a scaffold for the assembly of hook proteins onto the flagellar basal body rod; Yersinia, Vibrio parahaemolyticus, Bradyrhizobium and other organisms have 2 copies of some flagellar genes; Bradyrhizobium has one thick flagellum and several thin flagella; the protein in this cluster is associated with the thin flagella
YP_531000.1	FliQ, with proteins FliP and FliR, forms the core of the central channel in the flagella export apparatus; Bradyrhizobium have one thick flagellum and several thin flagella; the proteins in this cluster are associated with the thin flagella
YP_531001.1	membrane protein involved in the flagellar export apparatus
YP_531002.1	FliR, with proteins FliP and FliQ, forms the core of the central channel in the flagella export apparatus; Bradyrhizobium has one thick and several thin flagella; the Bradyrhizobium protein in this cluster are associated with the thin flagella
YP_531017.1	catalyzes the hydrolysis of allophanate
YP_531019.1	catalyzes the formation of pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate
YP_531022.1	Catalyzes a key regulatory step in fatty acid biosynthesis
YP_531024.1	catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis
YP_531025.1	involved in the modulation of the specificity of the ClpAP-mediated ATP-dependent protein degradation; binds to the N-terminal domain of the chaperone ClpA
YP_531031.1	catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate
YP_531032.1	catalyzes the bidirectional exonucleolytic cleavage of DNA
YP_531059.1	catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase
YP_531080.1	catalyzes the release of C-terminal glutamate residues from N-acylating moieties
YP_531115.1	catalyzes the interconversion of alpha-D-glucose 1-phosphate to alpha-D-glucose 6-phosphate
YP_531132.1	involved in chelation of magnesium into protoporphyrin IX; involved in bacteriochlorophyll biosynthesis; part of a complex with BchI, BchD, and BchH
YP_531139.1	catalyzes the formation of coproporphyrinogen from uroporphyrinogen III
YP_531144.1	catalyzes the conversion of the propionic acid groups of rings I and III to vinyl groups during heme synthesis
YP_531194.1	light-independent reduction of protochlorophyllide to form chlorophyllide a
YP_531195.1	light-independent reduction of protochlorophyllide to form chlorophyllide a
YP_531196.1	involved in chelation of magnesium into protoporphyrin IX; involved in bacteriochlorophyll biosynthesis; the enzyme from Rhodobacter capsulatus contains an Fe-S cluster; part of a complex with BchI, BchD, and BchH
YP_531197.1	light-independent; with chlN(bchN) and chlB(bchB) reduces ring D of protochlorophyllide to form chlorophyllide a in chlorophyll/bacteriochlorophyll production
YP_531198.1	catalyzes the formation of Mg-protoporphyrin IX methyl ester and S-adenosyl-L-homocysteine from Mg-protoporphyrin IX and S-adenosyl-L-methionine
YP_531204.1	oxidative; catalyzes the formation of divinylprotochlorophyllide from magnesium-protoporphyrin IX 13-monomethyl ester in isocyclic ring formation in chlorophyll biosynthesis
YP_531206.1	catalyzes the formation of 5-aminolevulinate from succinyl-CoA and glycine
YP_531208.1	type III RuBisCO; involved in carbon fixation
YP_531212.1	catalyzes the formation of L-methionine and acetate from O-acetyl-L-homoserine and methanethiol
YP_531242.1	in Escherichia coli this homodimeric enzyme is expressed under aerobic conditions; anaerobic expression is repressed by the arcAB system; converts sn-glycerol-3-phosphate and ubiquinone-8 to dihydroxy acetone phosphate and ubiquinol-8; associates with the cytoplasmic membrane
YP_531260.1	Catalyzes the first step in the glyoxalate cycle, which converts lipids to carbohydrates
YP_531269.1	catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids
YP_531270.1	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_531275.1	lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis
YP_531276.1	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; some organisms carry two different copies of this enzyme
YP_531287.2	catalyzes the formation of L-proline from pyrroline-5-carboxylate
YP_531289.1	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_531290.1	catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP
YP_531294.1	transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein
YP_531296.1	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_531297.1	Enables the recycling of peptidyl-tRNAs produced at termination of translation
YP_531298.1	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_531361.1	this stereospecific enzymes reduces the R isomer of methionine sulfoxide while MsrA reduces the S form; provides protection against oxidative stress
YP_531369.1	structural flagella protein; Bradyrhizobium has one thick flagellum and several thin flagella; the protein in this cluster is associated with the thick flagellum
YP_531370.1	structural flagella protein; Bradyrhizobium has one thick flagellum and several thin flagella; the protein in this cluster is associated with the thick flagellum
YP_531371.1	structural flagella protein; Bradyrhizobium has one thick flagellum and several thin flagella; the protein in this cluster is associated with the thick flagellum
YP_531372.1	post-transcriptional repressor of flagellum biosynthesis; promotes degradation of fljK mRNA; Bradyrhizobium has one thick and several thin flagella, the Bradyrhizobium protein in this cluster is associated with the thin flagella
YP_531373.1	acts as an activator of flagellin translation and may be required for filament secretion or assembly; Bradyrhizobium has one thick flagellum and several thin flagella; the Bradyrhizobium protein in this cluster is associated with the thick flagellum
YP_531378.1	part of the basal body which consists of four rings L, P, S, and M mounted on a central rod; Vibrio parahaemolyticus, Yersinia, Bradyrhizobium and other bacteria have two copies of this and other flagellar genes; the V. parahaemolyticus protein is associated with the polar flagella and the Bradyrhizobium protein is associated with the thick flagellum
YP_531379.1	regulator of the sigma 54 transcriptional activator FlbD; represses FlbD when the class II flagellar structure is absent and activates FlbD when the structure is present
YP_531385.1	part of the flagellar basal body which consists of four rings L,P, S and M mounted on a central rod
YP_531386.1	required for the assembly of the flagellar basal body P-ring; Bradyrhizobium has one thick flagellum and several thin flagella; the Bradyrhizobium protein in this cluster is associated with the thick flagellum
YP_531387.1	makes up the distal portion of the flagellar basal body rod; Bradyrhizobium has one thick flagellum and several thin flagella; the Bradyrhizobium protein in this cluster is associated with the thick flagella
YP_531388.1	FlgF, with FlgB and C, makes up the proximal portion of the flagellar basal body rod; Bradyrhizobium has one thick flagellum and several thin flagella; the Bradyrhizobium protein in this cluster is associated with the thick flagellum
YP_531389.1	interacts with the cytoplasmic MS ring of the basal body and may act to stabilize the MotAB complexes which surround the MS ring
YP_531390.1	with FliG and FliN makes up the switch complex which is involved in switching the direction of the flagella rotation; Bradyrhizobium has one thick flagellum and several thin flagella; the protein in this cluster is associated with the thick flagellum
YP_531396.1	FliP, with proteins FliQ and FliR, forms the core of the central channel in the flagella export apparatus
YP_531398.1	with FlgF and C makes up the proximal portion of the flagellar basal body rod; Bradyrhizobium has one thick flagellum and several thin flagella; the protein in this cluster is associated with the thick flagellum
YP_531399.1	with FlgF and B makes up the proximal portion of the flagellar basal body rod
YP_531400.1	forms a junction between the M-ring and FlgB during flagella biosynthesis; Bradyrhizobium has one thick flagellum and several thin flagella; the protein in this cluster is associated with the thick flagella
YP_531401.1	FliQ, with proteins FliP and FliR, forms the core of the central channel in the flagella export apparatus; Bradyrhizobium have one thick flagellum and several thin flagella; the protein in this cluster is associated with the thick flagellum
YP_531402.1	FliR, with proteins FliP and FliQ, forms the core of the central channel in the flagella export apparatus
YP_531403.1	membrane protein responsible for substrate specificity switching from rod/hook-type export to filament-type export
YP_531422.1	catalyzes the formation of glutamate from glutamine
YP_531448.1	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_531449.1	acts in conjunction with GvcH to form H-protein-S-aminomethyldihydrolipoyllysine from glycine
YP_531450.1	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_531451.1	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_531452.1	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_531457.1	Converts isocitrate to alpha ketoglutarate
YP_531461.1	activates RNA polymerase to cleave back-tracked RNA during elongational pausing
YP_531465.2	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_531466.1	With PurL and PurQ catalyzes the conversion of formylglycinamide ribonucleotide, ATP, and glutamine to formylglycinamidine ribonucleotide, ADP, and glutamate in the fourth step of the purine biosynthetic pathway
YP_531468.1	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_531472.1	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_531484.1	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_531487.1	converts L-glutamate to D-glutamate, a component of peptidoglycan
YP_531491.1	Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide
YP_531548.1	allantoate amidohydrolase and N-carbamoyl-L-amino acid amidohydrolase are very similar; the allantoate amidohydrolase from Escherichia coli forms a dimer and binds zinc ions for catalytic activity and catalyzes the conversion of allantoate to (S)-ureidoglycolate and ammonia; carbamoyl amidohydrolase from Bacillus sp. converts N-carbamoyl amino acids to amino acids, ammonia, and carbon dioxide
YP_531553.1	Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA
YP_531554.1	Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA
YP_531555.1	activates fatty acids by binding to coenzyme A
YP_531557.1	Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA
YP_531562.1	catalyzes the formation of oxaloacetate from phosphoenolpyruvate
YP_531566.1	catalyzes the hydrolysis of a monocarboxylic acid amid to form a monocarboxylate and ammonia
YP_531591.1	catalyzes the formation of acetaldehyde from ethanolamine
YP_531604.1	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_531611.1	DNA polymerase involved in damage-induced mutagenesis and translesion synthesis. It is not the major replicative DNA polymerase.
YP_531618.1	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_531632.1	functions in transport of arginine/ornithine; inner membrane ATPase that cleaves ATP and phosphorylates two periplasmic proteins that function as two distinct transport systems, the AO (arginine and ornithine) and LAO (lysine, arginine, and ornithine) periplasmic binding proteins
YP_531638.1	MDM; functions in conversion of succinate to propionate
YP_531713.1	CycJ; periplasmic heme chaperone that binds heme transiently via a histidine residue and delivers it to newly synthesized and exported c-type cytochromes; requires the ATP hydrolysis activity of the CcmA protein in order to transfer the heme to the apocytochrome; part of the cytochrome c maturation system; periplasmic protein anchored to the inner membrane
YP_531724.1	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_531728.1	ketopantoate reductase; catalyzes the NADPH reduction of ketopantoate to pantoate; functions in pantothenate (vitamin B5) biosynthesis
YP_531732.1	catalyzes the formation of oxalyl-CoA from oxalate and Formyl-CoA
YP_531756.1	catalyzes 2 sequential methylations, the formation of precorrin-1 and S-adenosyl-L-homocysteine from S-adenosyl-L-methionine and uroporphyrin III, and the formation of precorrin-2 and S-adenosyl-L-homocysteine from S-adenosyl-L-methionine and precorrin-1
YP_531757.1	responsible for the amidation of carboxylic groups at position A and C of cobyrinic acid or hydrogenobrynic acid
YP_531761.1	CobK/CbiJ; there are 2 pathways for cobalamin (vitamin B12) production, one aerobic (ex. P. denitrificans), the other anaerobic (ex. S. typhimurium); the CobK/CbiJ perform similar reactions in both; the anaerobic pathway includes the use of a chelated cobalt ion in order for ring contraction to occur; CobK thus converts precorrin 6 into dihydro-precorrin 6 while CbiJ converts cobalt-precorrin 6 into cobalt-deihydro-precorrin 6
YP_531764.1	catalyzes the interconversion of precorrin-8X and hydrogenobyrinate
YP_531765.1	with CobST catalyzes the formation of cobyrinic acid a,c-diamide from hydrogenobyrinic acid a,c-diamide in an ATP-dependent manner; involved in porphyrin and chlorophyll metabolism; vitamin B12 metabolism
YP_531769.1	catalyzes the oxidation of tricarballylate to cis-aconitate; FAD-dependent; required for the utilization of tricarballylate as a carbon and energy source by S. enterica
YP_531772.1	catalyzes the formation of precorrin 6x from precorrin 5
YP_531827.1	catalyzes the ATP-dependent transport of cobalt
YP_531829.1	Inhibits transcription at high concentrations of nickel
YP_531835.1	catalyzes the ATP-dependent transport of cobalt
YP_531843.1	with HmuTU is involved in the transport of hemin
YP_531847.1	catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III
YP_531874.1	Catalyzes a key regulatory step in fatty acid biosynthesis
YP_531882.1	catalyzes the synthesis of acetylphosphate or propionylphosphate from acetyl-CoA or propionyl-CoA and inorganic phosphate; when using propionyl-CoA the enzyme is functioning in the anaerobic pathway catabolizing threonine to propionate
YP_531946.1	together with moaC, is involved in the conversion of a guanosine derivative (GXP) into molybdopterin precursor Z
YP_531949.1	Catalyzes D-ribose 5-phosphate --> D-ribulose 5-phosphate in the nonoxidative branch of the pentose phosphate pathway
YP_531955.1	NH(3)-dependent; catalyzes the formation of nicotinamide adenine dinucleotide (NAD) from nicotinic acid adenine dinucleotide (NAAD) using either ammonia or glutamine as the amide donor and ATP; ammonia-utilizing enzymes include the ones from Bacillus and Escherichia coli while glutamine-utilizing enzymes include the Mycobacterial one; forms homodimers
YP_531959.1	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_531963.1	thiamine-pyrophosphate requiring enzyme
YP_531968.1	catalyzes the decarboxylaton of phospatidyl-L-sering to phosphatidylethanolamine
YP_531970.1	catalyzes the formation of S-adenosyl-4-methylthionine-2-oxobutanoate and 7,8-diaminononanoate from S-adenosyl-L-methionine and 8-amino-7-oxononanoate
YP_531971.1	DTB synthetase; dethiobiotin synthase; involved in production of dethiobiotin from ATP and 7,8-diaminononanoate and carbon dioxide; contains magnesium
YP_531972.1	catalyzes the formation of 8-amino-7-oxononanoate from 6-carboxyhexanoyl-CoA and L-alanine
YP_531979.1	Acylates the intermediate (KDO)2-lipid IVA to form (KDO)2-(lauroyl)-lipid IVA
YP_531981.1	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_531982.1	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_531984.2	Involved in the biosynthetic pathways of fatty acids, phospholipids, lipopolysaccharides, and oligosaccharides
YP_532004.1	ChvD; in Agrobacterium tumefaciens, mutations in both Walker boxes were found to affect virulence
YP_532009.1	catalyzes the formation of (E)-3-(methoxycarbonyl)pent-2-enedioate and S-adenosyl-L-homocysteine from S-adenosyl-L-methionine and trans-aconitate
YP_532035.1	required for the synthesis of the hydromethylpyrimidine moiety of thiamine
YP_532037.1	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_532062.1	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_532064.1	First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
YP_532065.1	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_532066.1	activates fatty acids by binding to coenzyme A
YP_532067.1	Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation
YP_532108.1	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_532112.1	catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity
YP_532118.1	involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsX
YP_532119.1	Catalyzes the reversible hydrolysis of the amide bond within dihydroorotate. This metabolic intermediate is required for the biosynthesis of pyrimidine nucleotides
YP_532120.1	catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis
YP_532128.1	similar to RuvC resolvase with substantial differences; NMR structural information suggests this protein is monomeric; unknown cellular function
YP_532129.1	in group A Streptococci this protein was found to cross react with anti myosin antibodies and may play a role in rheumatic fever
YP_532133.1	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_532137.1	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_532142.1	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_532149.1	catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate
YP_532152.2	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_532155.1	Catalyzes first step of the de novo purine nucleotide biosynthetic pathway
YP_532157.1	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_532163.1	unwinds double stranded DNA
YP_532166.1	in Escherichia coli this protein is wrapped around the base of the L1 stalk
YP_532168.1	binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit
YP_532169.1	binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21
YP_532174.1	carries the fatty acid chain in fatty acid biosynthesis
YP_532175.1	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_532178.1	Essential for recycling GMP and indirectly, cGMP
YP_532181.1	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_532182.1	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_532187.1	catalyzes the removal of N-terminal amino acids preferably leucine from various peptides
YP_532188.1	binds to single-strand binding (SSB) protein and acts as a bridge between the DnaX clamp loader complex and the SSB
YP_532191.1	catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate
YP_532199.1	catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis
YP_532202.1	catalyzes the reversible transfer of the terminal phosphate of ATP to form a long chain polyphosphate
YP_532208.1	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_532209.1	NADP-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; decarboxylates oxaloacetate
YP_532224.1	catalyzes the formation of L-ornithine from N(2)-acetyl-L-ornithine
YP_532252.1	Catalyzes the rate-limiting step in dNTP synthesis
YP_532260.1	VapD
YP_532262.1	Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer
YP_532264.1	binds and unfolds substrates as part of the ClpXP protease
YP_532267.1	catalyzes the release of the N-terminal amino acid from a tripeptide
YP_532270.1	Catalyzes the transfer of electrons from NADH to quinone
YP_532271.1	The point of entry for the majority of electrons that traverse the respiratory chain eventually resulting in the reduction of oxygen
YP_532273.1	Catalyzes the transfer of electrons from NADH to quinone
YP_532274.1	crystal structure of protein from Xanthomonas shows pentameric toroidal structure; physiological function is unknown
YP_532275.1	Catalyzes the transfer of electrons from NADH to quinone
YP_532277.1	Catalyzes the transfer of electrons from NADH to quinone
YP_532279.1	part of NADH-ubiquinone oxidoreductase complex I; shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain; NuoF is part of the soluble NADH dehydrogenase fragment, which represents the electron input part of NADH dehydrogenase
YP_532281.1	Catalyzes the transfer of electrons from NADH to quinone
YP_532282.1	Catalyzes the transfer of electrons from NADH to quinone
YP_532283.1	Catalyzes the transfer of electrons from NADH to quinone
YP_532284.1	Catalyzes the transfer of electrons from NADH to quinone
YP_532286.1	Catalyzes the transfer of electrons from NADH to ubiquinone
YP_532287.1	Catalyzes the transfer of electrons from NADH to quinone
YP_532288.1	Catalyzes the transfer of electrons from NADH to quinone
YP_532297.1	catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro)
YP_532303.1	catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; main replicative polymerase
YP_532306.1	one of the last subunits in the assembly of the 30S subunit; absence of S2 does not inhibit assembly but results in an inactive subunit
YP_532307.1	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_532308.1	Catalyzes the phosphorylation of UMP to UDP
YP_532309.1	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_532310.1	catalyzes the formation of undecaprenyl pyrophosphate from isopentenyl pyrophosphate
YP_532312.1	catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate
YP_532315.1	adds the O-linked and N-linked 3(R)-hydroxy fatty acids to the glucosamine disaccharide during lipid A biosynthesis
YP_532316.1	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_532317.1	catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis
YP_532319.1	catalyzes the formation of lipid A disaccharide from UDP-2,3-diacylglucosamine and 2,3-diacylglucosamine-1-phosphate, lipid A disaccharide is a precursor of lipid A that anchors LPS to the OM
YP_532320.1	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_532321.1	Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation
YP_532322.1	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_532324.1	Represses a number of genes involved in the response to DNA damage
YP_532334.1	adds the O-linked and N-linked 3(R)-hydroxy fatty acids to the glucosamine disaccharide during lipid A biosynthesis
YP_532335.1	MoaC; along with MoaA is involved in conversion of a guanosine derivative into molybdopterin precursor Z; involved in molybdenum cofactor biosynthesis
YP_532336.1	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_532337.1	Catalyzes the conversion of N-(5-phospho-D-ribosyl)-anthranilate and diphosphate to anthranilate and 5-phospho-alpha-D-ribose 1-diphosphate
YP_532343.1	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_532347.1	catalyzes the formation of 2-dehydro-3-deoxy-D-octonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate in LPS biosynthesis
YP_532352.1	NADPH-dependent; catalyzes the reduction of 7-cyano-7-deazaguanine to 7-aminomethyl-7-deazaguanine in queuosine biosynthesis
YP_532353.1	enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis
YP_532360.1	catalyzes the oxidative decarboxylation of pyruvate with concomitant acetylation of a lipoic acid-containing dihydrolipoamide acetyltransferase within the complex. The E1 component of the pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2). It contains multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase(E2) and lipoamide dehydrogenase
YP_532363.1	E3 component of pyruvate complex; catalyzes the oxidation of dihydrolipoamide to lipoamide
YP_532364.1	catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis
YP_532378.1	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_532383.1	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_532387.1	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_532389.1	catalyzes the conversion of a phosphate monoester to an alcohol and a phosphate
YP_532394.1	4-alpha-hydroxytetrahydrobiopterin dehydratase activity; catalyzes the formation of (6R)-6-(L-erythro-1,2-dihydroxypropyl)-7, 8-dihydro-6H-pterin from (6R)-6-(L-erythro-1,2-dihydroxypropyl)-5,6,7, 8-tetrahydro-4a-hydroxypterin; functions in recycling tetrahydrobiopterin (BH4) in phenylalanine hydroxylase reaction
YP_532422.1	CysK; forms a complex with serine acetyltransferase CysE; functions in cysteine biosynthesis
YP_532439.1	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_532440.1	responsible for recognizing base lesions in the genome and initiating base excision DNA repair
YP_532441.1	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_532450.1	catalyzes the transamination of D-amino acids and their alpha-keto acids
YP_532451.1	Stimulates the elongation of poly(A) tails
YP_532453.1	negatively supercoils closed circular double-stranded DNA
YP_532457.1	Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA
YP_532460.1	Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step
YP_532461.1	Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr)
YP_532474.1	forms a homotrimer; catalyzes the acetylation of glucosamine-1-phosphate and uridylation of N-acetylglucosamine-1-phosphate to produce UDP-GlcNAc; function in cell wall synthesis
YP_532475.1	Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source
YP_532489.1	catalyzes the methylthiolation of an aspartic acid residue of the S12 protein of the 30S ribosomal subunit
YP_532498.1	catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis
YP_532500.1	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_532503.1	Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits
YP_532506.1	involved in the de novo synthesis of pyridoxine (Vitamin B6)
YP_532507.1	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_532510.1	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_532512.1	involved in DNA repair and RecFOR pathway recombination; RecFOR proteins displace ssDNA-binding protein and facilitate the production of RecA-coated ssDNA
YP_532513.1	decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling
YP_532518.1	Conjugates Arg from its aminoacyl-tRNA to the N-termini of proteins containing an N-terminal aspartate or glutamate
YP_532520.1	catalyzes the formation of porphobilinogen from 5-aminolevulinate
YP_532528.1	catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate
YP_532531.1	catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine
YP_532532.1	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_532533.1	Regulates rRNA biosynthesis by transcriptional antitermination
YP_532535.1	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_532543.1	involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY
YP_532544.1	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_532545.1	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_532558.1	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_532559.1	catalyzes the formation of L-methionine and acetate from O-acetyl-L-homoserine and methanethiol
YP_532562.1	Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA
YP_532564.2	in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit
YP_532565.1	forms a direct contact with the tRNA during translation
YP_532571.1	catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP)
YP_532572.1	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_532577.1	activates fatty acids by binding to coenzyme A
YP_532619.1	functions in degradation of stringent response intracellular messenger ppGpp; in Escherichia coli this gene is co-transcribed with the toxin/antitoxin genes mazEF; activity of MazG is inhibited by MazEF in vitro; ppGpp inhibits mazEF expression; MazG thus works in limiting the toxic activity of the MazF toxin induced during starvation; MazG also interacts with the GTPase protein Era
YP_532622.1	binds to single stranded DNA and may facilitate the binding and interaction of other proteins to DNA
YP_532624.1	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_532639.1	TrmFO; Gid; glucose-inhibited division protein; similar to GidA; the gene from Bacillus subtilis encodes a tRNA-methyltransferase that utilizes folate as the carbon donor and bound flavin as reductant; modifies tRNA at position 54 (uridine) of the T-psi loop to form a C5-methyluridine
YP_532642.1	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_532643.1	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_532654.1	tryptophan indole-lyase; catalyzes the formation of indole and pyruvate from tryptophan
YP_532667.1	catalyzes the condensation of acetyl-CoA with malonyl-ACP to initiate cycles of fatty acid elongation; differs from 3-oxoacyl-(acyl carrier protein) synthase I and II in that it utilizes CoA thioesters as primers rather than acyl-ACPs
YP_532676.1	Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA
YP_532682.1	type II fructose 1,6-bisphosphatae; in Escherichia coli this protein forms a dimer and binds manganese
YP_532683.1	catalyzes the formation of L-aspartate 4-semialdehyde from L-homoserine
YP_532694.1	decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling
YP_532708.1	with SufCD activates cysteine desulfurase SufS
YP_532711.1	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_532712.1	catalyzes the formation of tyrosyl-tRNA(Tyr) from tyrosine and tRNA(Tyr)
YP_532734.1	catalyzes the formation of 3-dehydroshikimate from 3-dehydroquinate in chorismate biosynthesis
YP_532736.1	an AccC homodimer forms the biotin carboxylase subunit of the acetyl CoA carboxylase, an enzyme that catalyzes the formation of malonyl-CoA, which in turn controls the rate of fatty acid metabolism
YP_532742.1	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_532749.1	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_532755.1	Provides the input to the respiratory chain from the NAD-linked dehydrogenases of the citric acid cycle. The complex couples the oxidation of NADH and the reduction of ubiquinone, to the generation of a proton gradient which is then used for ATP synthesis
YP_532762.1	catalyzes the carboxylation of D-ribulose 1,5-bisphosphate in carbon dioxide fixation
YP_532763.1	class II aldolase; catalyzes the reversible aldol condensation of dihydroxyacetonephosphate and glyceraldehyde 3-phosphate in the Calvin cycle, glycolysis and gluconeogenesis
YP_532764.1	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_532766.1	catalyzes the formation of D-fructose 6-phosphate from fructose-1,6-bisphosphate
YP_532820.1	catalyzes the formation of phosphoenolpyruvate from pyruvate
YP_532926.1	contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway
YP_532932.1	catalyzes the synthesis of xanthosine monophosphate by the NAD+ dependent oxidation of inosine monophosphate
YP_532953.1	catalyzes the formation of 3-hydroxy-2-methylpropanoate from 3-hydroxy-2-methylpropanoyl-CoA
YP_532961.1	Catalyzes the synthesis of acetoacetyl coenzyme A from two molecules of acetyl coenzyme A. It can also act as a thiolase, catalyzing the reverse reaction and generating two-carbon units from the four-carbon product of fatty acid oxidation
YP_532967.1	catalyzes the phosphorylation of NAD to NADP
YP_532974.1	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_532975.1	involved in the first step of tetrahydrofolate biosynthesis; catalyzes the formation of formate and 2-amino-4-hydroxy-6-(erythro-1,2, 3-trihydroxypropyl)dihydropteridine triphosphate from GTP and water; forms a homopolymer
YP_532982.1	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_533014.1	catalyzes the formation of tetrahydropteroyl-L-glutamate and methionine from L-homocysteine and 5-methyltetrahydropteroyltri-L-glutamate
YP_533016.1	catalyzes the conversion of guanine, xanthine and, to a lesser extent, hypoxanthine to GMP, XMP and IMP, respectively
YP_533032.1	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_533033.1	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 co-regulated with symbiotic nitrogen fixation genes
YP_533052.1	catalyzes the formation of 3-methyl-2-oxobutanoate from 2,3,-dihydroxy-3-methylbutanoate
YP_533060.1	Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA
YP_533096.1	catalyzes the formation of 2-isopropylmalate from acetyl-CoA and 2-oxoisovalerate in leucine biosynthesis
YP_533109.1	catalyzes the formation of (R)-2,3-dihydroxy-3-methylbutanoate from (S)-2-hydroxy-2-methyl-3-oxobutanoate in valine and isoleucine biosynthesis
YP_533114.1	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_533127.1	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_533132.1	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_533158.1	zinc-dependent; catalyzes the deacetylation of UDP-(3-O-acyl)-N-acetylglucosamine to UDP-3-O-(3-hydroxytetradecanoyl)-glucosamine in the second step of lipid A biosynthesis
YP_533159.1	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_533162.1	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_533165.1	catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis
YP_533166.1	Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis
YP_533167.1	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_533169.1	involved in swarmer-to-stalked cell differentiation in Caulobacter crescentus; catalyzes the condensation of two GTP molecules to form the secondary messenger cyclic di-GMP (c-di-GMP); upon phosphorylation of domain D1 the protein dimerizes; presumably this allows the two GTP-bound GGDEF (diguanylate cyclase) domains to catalyze the condensation reaction; allosterically inhibited by c-di-GMP
YP_533172.1	involved in translesion DNA polymerization with beta clamp of polymerase III; belongs to Y family of polymerases; does not contain proofreading function
YP_533193.1	catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine
YP_533209.1	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_533211.1	catalyzes the hydrolysis of acylphosphate
YP_533246.1	Catalyzes the ferredoxin-dependent oxidative decarboxylation of arylpyruvates
YP_533258.1	related to flagellar biosynthesis protein FlhB
YP_533282.1	is a component of the macrolide binding site in the peptidyl transferase center
YP_533283.1	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_533284.1	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_533285.2	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_533286.1	essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP
YP_533287.1	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_533288.1	late assembly protein
YP_533289.1	L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7
YP_533290.1	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_533291.1	binds 5S rRNA along with protein L5 and L25
YP_533292.1	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_533293.1	binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit
YP_533294.1	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_533295.1	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_533296.1	assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel
YP_533297.1	binds to the 23S rRNA between the centers for peptidyl transferase and GTPase
YP_533298.1	primary binding protein; helps mediate assembly; involved in translation fidelity
YP_533299.1	one of the stabilizing components for the large ribosomal subunit
YP_533300.1	located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e
YP_533301.1	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_533302.1	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_533303.1	protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA
YP_533304.1	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_533305.1	binds third domain of 23S rRNA and protein L29; part of exit tunnel
YP_533306.1	L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA
YP_533307.1	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_533308.1	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_533309.1	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_533310.1	EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene
YP_533311.1	binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit
YP_533312.1	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_533316.1	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_533317.1	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_533318.1	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_533319.2	binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit
YP_533330.1	in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA
YP_533331.1	binds directly to 23S ribosomal RNA
YP_533332.1	Modulates Rho-dependent transcription termination
YP_533333.1	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_533350.1	thiamine-pyrophosphate requiring enzyme
YP_533351.1	catalyzes the formation of L-ornithine from N(2)-acetyl-L-ornithine
YP_533367.1	catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine to form methionine
YP_533370.1	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_533376.1	Catalyzes the reduction of nucleoside 5'-triphosphates to 2'-deoxynucleoside 5'-triphosphates
YP_533377.1	Catalyzes the rate-limiting step in dNTP synthesis
YP_533378.1	Catalyzes the rate-limiting step in dNTP synthesis
YP_533393.1	type IV secretion VirB6 family
YP_533396.1	type IV secretion system VirB4 family
YP_533406.1	type IV secretion VirD4 coupling protein family
YP_533457.1	in group A Streptococci this protein was found to cross react with anti myosin antibodies and may play a role in rheumatic fever
YP_533502.1	catalyzes the formation of 3-methyl-2-oxobutanoate from 2,3,-dihydroxy-3-methylbutanoate
YP_533505.1	restriction endonuclease; the EcoKI enzyme recognizes 5'-AACN(6)GTGC-3'; subunit R is required for both nuclease and ATPase activities
YP_533520.1	catalyzes the hydrolysis of a monocarboxylic acid amid to form a monocarboxylate and ammonia
YP_533524.1	catalyzes the reversible formation of D-erythrose 4-phosphate and D-fructose 6-phosphate from sedoheptulose 7-phosphate and D-glyceraldehyde 3-phosphate; catalyzes isomerization of glucose 6-phosphate and fructose 6-phosphate
YP_533525.1	similar to full-length Gnd, these proteins seems to have a truncated C-terminal 6PGD domainin; in Methylobacillus flagellatus this gene is essential for NAD+-dependent oxidation of 6-phosphogluconate
YP_533526.1	catalyzes the formation of D-glucono-1,5-lactone 6-phosphate from D-glucose 6-phosphate
YP_533534.1	catalyzes the transfer of a segment of a 1,4-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain
YP_533539.2	catalyzes the ATP dependent formation of a phosphodiester at the site of a single-strand break in duplex DNA
YP_533543.1	in Escherichia coli MobA links a guanosine 5'-phosphate to molydopterin to form molybdopterin guanine dinucleotide during molybdenum cofactor biosynthesis
YP_533546.1	ureases catalyze the hydrolysis of urea into ammonia and carbon dioxide; in Helicobacter pylori the ammonia released plays a key role in bacterial survival by neutralizing acids when colonizing the gastric mucosa; the holoenzyme is composed of 3 ureC (alpha) and 3 ureAB (gamma/beta) subunits
YP_533549.1	ureases catalyze the hydrolysis of urea into ammonia and carbon dioxide; in Helicobacter pylori and Yersinia enterocolitica the ammonia released plays a key role in bacterial survival by neutralizing acids when colonizing the gastric mucosa; the holoenzyme is composed of 3 UreC (alpha) and 3 UreAB (gamma/beta); in Brucella suis the urease encoded by this operon (one of two urease-encoding operons found in its genome) is involved with urease activity, optimum growth, resistance to low-pH killing in-vitro and persistence in-vivo, while the other operon does not seem to be active
YP_533558.1	stimulates the activities of the other two initiation factors, IF-2 and IF-3
YP_533585.1	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_533586.1	catalyzes the formation of phenylpyruvate from prephenate in phenylalanine biosynthesis
YP_533589.1	one of two methionine synthases in Escherichia coli; MetH catalyzes a methyl transfer reaction from methyltetrahydrofolate to homocysteine to create methionine; requires zinc for activity
YP_533591.1	Glycine cleavage system transcriptional activator; activates the gcvTHP operon in the presence of glycine and represses the operon in its absence
YP_533599.1	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_533600.1	catalyzes the formation of adenosylcob(III)yrinic acid a,c-diamide from cob(I)yrinic acid a,c-diamide
YP_533667.1	catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III
YP_533686.1	this stereospecific enzymes reduces the R isomer of methionine sulfoxide while MsrA reduces the S form; provides protection against oxidative stress
YP_533687.1	this stereospecific enzymes reduces the S isomer of methionine sulfoxide while MsrB reduces the R form; provides protection against oxidative stress
YP_533688.1	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_533689.1	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_533704.1	subunit G of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in S. meliloti it is known to be involved specifically with K+ transport
YP_533705.1	subunit F of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in S. meliloti it is known to be involved specifically with K+ transport
YP_533706.1	subunit E of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in S. meliloti it is known to be involved specifically with K+ transport
YP_533707.1	subunit D of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; contains an oxidoreductase domain; catalyzes the transfer of electrons from NADH to ubiquinone
YP_533708.1	subunit C of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali
YP_533709.1	subunit A of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in S. meliloti it is known to be involved with K+
YP_533740.1	type IV secretion VirB6 family
YP_533743.1	type IV secretion system VirB4 family
YP_533748.1	type IV secretion VirD4 coupling protein family
YP_533806.1	With PurE catalyzes the conversion of aminoimidazole ribonucleotide to carboxyaminoimidazole ribonucleotide in the de novo purine nucleotide biosynthetic pathway
YP_533807.2	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_533827.1	catalyzes the formation of phosphoenolpyruvate from pyruvate
YP_533834.1	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_533856.1	catalyzes the reduction of 3'-phosphoadenylyl sulfate into sulfite
YP_533861.1	with CysN catalyzes the formation of adenylylsulfate from sulfate and ATP
YP_533867.1	catalyzes the formation of malate from glyoxylate and acetyl-CoA
YP_533873.1	in Caulobacter crescentus, CC3477 is differentially expressed in minimal salts media with glucose as compared to complex media
YP_533875.1	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_533898.1	response regulator for histidine kinase FixL; part of global network that controls expression of aerobic respiratory terminal oxidases and carbon and nitrogen metabolic enzymes
YP_533900.1	transcriptional regulator that positively regulated fixLJ operon; upregulated transcription by FixJ; part of global network that controls expression of aerobic respiratory terminal oxidases and carbon and nitrogen metabolic enzymes
YP_533909.1	Catalyzes the transfer of electrons from NADH to quinone
YP_533911.1	Catalyzes the transfer of electrons from NADH to quinone
YP_533913.1	Catalyzes the transfer of electrons from NADH to quinone
YP_533914.1	NuoCD; NDH-1 shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain; subunits NuoCD, E, F, and G constitute the peripheral sector of the complex; in Escherichia coli this gene encodes a fusion protein of NuoC and NuoD that are found separate in other organisms
YP_533915.1	The point of entry for the majority of electrons that traverse the respiratory chain eventually resulting in the reduction of oxygen
YP_533917.1	responsible for transport of beta-1,2-glucans from the cytoplasm to periplasm; inner membrane ABC transporter permease component; Cgt; ChvA; NdvA
YP_533919.1	activates fatty acids by binding to coenzyme A
YP_533922.1	catalyzes the formation of O-phospho-L-homoserine from L-homoserine
YP_533923.1	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_533931.1	catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis
YP_533934.1	catalyzes the formation of thymine and 2-deoxy-alpha-D-ribose 1-phosphate from thymidine
YP_533951.1	catalyzes the formation of 3-phosphonooxypyruvate from 3-phospho-D-glycerate in serine biosynthesis; can also reduce alpha ketoglutarate to form 2-hydroxyglutarate
YP_533952.1	catalyzes the formation of 3-phosphonooxypyruvate and glutamate from O-phospho-L-serine and 2-oxoglutarate
YP_533958.1	catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate
YP_533964.1	EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene
YP_533967.1	catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate
YP_533982.1	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_533997.1	catalyzes the formation of L-homocysteine from S-adenosyl-L-homocysteine
YP_533998.1	catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase
YP_534003.1	catalyzes the formation of tetrahydropteroyl-L-glutamate and methionine from L-homocysteine and 5-methyltetrahydropteroyltri-L-glutamate
YP_534008.1	produces formate from formyl-tetrahydrofolate which is the major source of formate for PurT in de novo purine nucleotide biosynthesis; has a role in one-carbon metabolism; forms a homohexamer; activated by methionine and inhibited by glycine
YP_534068.1	membrane protein involved in the flagellar export apparatus
YP_534073.1	catalyzes the formation of inosine from adenosine
YP_534075.1	involved in type III protein export during flagellum assembly
YP_534087.1	regulates chemotaxis by demethylation of methyl-accepting chemotaxis proteins
YP_534100.1	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_534103.1	thiamine-pyrophosphate requiring enzyme
YP_534117.1	proline utilization protein A; multifunctional protein that functions in proline catabolism in the first two enzymatic steps resulting in the conversion of proline to glutamate; in Escherichia coli this protein self regulates transcription via a DNA-binding domain at the N-terminus but the proteins from this group do not and in addition appear to have a truncated C-terminal domain
YP_534124.1	Catalyzes the conversion of acetyl-CoA and L-homoserine to CoA and O-acetyl-L-homoserine
YP_534126.1	catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis
YP_534127.1	dual function enzyme catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate and the formation of tyrosine from arogenate
YP_534135.1	activates fatty acids by binding to coenzyme A
YP_534172.1	Catalyzes the reversible hydrolysis of the amide bond within dihydroorotate. This metabolic intermediate is required for the biosynthesis of pyrimidine nucleotides
YP_534180.1	3 different subfamilies; catalyzes the formation of quinolinate from iminoaspartate and dihydroxyacetone phosphate
YP_534181.1	catalyzes the formation of oxaloacetate from L-aspartate
YP_534185.1	catalyzes the formation of phosphoenolpyruvate from pyruvate
YP_534190.1	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_534191.1	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_534198.1	An essential enzyme in the nonmevalonate pathway of isopentenyl diphosphate and dimethylallyl diphosphate biosynthesis
YP_534203.1	RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids
YP_534229.1	catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis
YP_534230.1	trpE(G); catalyzes the formation of anthranilate from chorismate and glutamine; contains both component I and II
YP_534256.1	Maf; overexpression in Bacillus subtilis inhibits septation in the dividing cell
YP_534259.1	catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer
YP_534260.1	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_534268.1	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_534270.1	transports degraded pectin products into the bacterial cell
YP_534291.1	associates with NifD and may protect the nitrogenase Fe-Mo protein from oxidative damage
YP_534301.1	functions with NifE to assemble FeMo cofactor; functions in assembly of nitrogenase MoFe
YP_534302.1	functions with NifN to assemble FeMo cofactor; functions in assembly of nitrogenase MoFe
YP_534305.1	nitrogenase iron protein; nitrogenase component 2; with component 1, an molybdenum-iron protein, catalyzes the fixation of nitrogen to ammonia; nitrogen reductase provides electrons to the nitrogenase complex; in R. etli there are three essentially identical copies of nifH which are actively expressed during symbiosis
YP_534361.1	MobA/MobL family protein
YP_534389.1	one of the components of the high-affinity ATP-driven potassium transport (or KDP)system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions; the C subunit may be involved in assembly of the KDP complex
YP_534390.1	One of the components of the high-affinity ATP-driven potassium transport (or KDP) system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions
YP_534391.1	catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions
YP_534395.1	forms a trimer; related to eukaryotic protein gephyrin; functions during molybdenum cofactor biosynthesis
YP_534407.1	involved in the C-terminal processing of the large subunit of hydrogenase 3 HycE
YP_534410.1	electron transfer protein for hydrogenase-3; the formate hydrogenlyase complex comprises of a formate dehydrogenase, unidentified electron carriers and hydrogenase-3; in this non-energy conserving pathway, molecular hydrogen and carbodioxide are released from formate
YP_534413.1	interacts with formate dehydrogenase to produce an active formate hydrogenlyase complex which cleaves formate to dihydrogen and carbon dioxide
YP_534429.1	Catalyzes the transfer of 2-(5''-triphosphoribosyl)-3'-dephosphocoenzyme-A to the apo-acyl carrier protein of malonate dehydrogenase to form holo-acyl carrier protein
YP_534431.1	The beta subunit catalyzes the decarboxylation of the malonyl moiety on coenzyme A
YP_534432.1	acyl carrier protein of malonate decarboxylase
YP_534433.1	catalyzes the reversible formation of 2'-(5''-triphosphoribosyl)-3'dephospho-CoA from 3-dephospho-CoA
YP_534460.1	catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis
YP_534462.1	bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides
YP_534485.1	involved in the production or activity of formate dehydrogenase-H which is active when nitrate is not present during anaerobic growth
YP_534488.1	catalyzes the oxidation of formate to carbon dioxide and hydrogen using NAD or NADP as the acceptor
YP_534525.1	nitrogenase iron protein; nitrogenase component 2; with component 1, an molybdenum-iron protein, catalyzes the fixation of nitrogen to ammonia; nitrogen reductase provides electrons to the nitrogenase complex; alternative NifH, may be molybdenum-independent
YP_534533.1	putative metalloprotease
YP_534545.1	transfers the gamma-phosphate of ATP to the 4' position of a tetraacyldisaccharide 1-phosphate intermediate to form tetraacyldisaccharide 1,4'-bis-phosphate
YP_534552.1	UbiA prenyltransferase family catalyzes the transfer of a prenyl group to various acceptors with hydrophobic ring structures in the biosynthesis of respiratory quinones, hemes, chlorophylls, vitamin E, and shikonin
YP_534557.1	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_534558.1	May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine
YP_534559.1	long form of enzyme; catalyzes the formation of N'-5'-phosphoribosyl-ATP from phosphoribosyl pyrophosphate; crucial role in histidine biosynthesis; forms active dimers and inactive hexamers which is dependent on concentration of substrates and inhibitors
YP_534566.1	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_534567.1	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; the rhizobia have multiple copies of the groEL gene which are active under different environmental conditions; the S. meliloti protein in this cluster is not associated with a groES gene
YP_534592.1	forms dimers; may be involved in cell envelope integrity; interacts with outer membrane proteins and with the C-terminal domain of inner membrane protein TolA
YP_534607.1	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_534611.1	Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway
YP_534630.1	converts protoheme IX and farnesyl diphosphate to heme O
YP_534632.1	involved in the insertion of copper into subunit I of cytochrome C oxidase
YP_534636.2	catalyzes the formation of L-threonine from O-phospho-L-homoserine
YP_534644.1	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_534646.1	plays an essential role in ATP-dependent branch migration of the Holliday junction
YP_534647.1	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_534656.1	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_534657.1	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_534665.1	catalyzes the formation of 5-aminolevulinate from succinyl-CoA and glycine
YP_534683.1	protoheme ferro-lyase; catalyzes the insertion of a ferrous ion into protoporphyrin IX to form protoheme; involved in protoheme biosynthesis; in some organisms this protein is membrane-associated while in others it is cytosolic
YP_534687.1	involved in a recombinational process of DNA repair, independent of the recBC complex
YP_534689.1	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_534698.1	has 3'-5' exonuclease, 5'-3' exonuclease and 5'-3'polymerase activities, primarily functions to fill gaps during DNA replication and repair
YP_534699.1	involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate
YP_534716.1	catalyzes the formation of arginine from (N-L-arginino)succinate
YP_534719.1	converts (S)-3-hydroxybutanoyl-CoA to 3-acetoacetyl-CoA
YP_534726.1	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_534744.1	Catalyzes the deamination of dCTP to form dUTP
YP_534745.1	catalyzes the conversion of O-succinylhomoserine and sulfide to homocysteine; second step in methionine biosynthesis
YP_534754.1	protein associated with Co2+ and Mg2+ efflux
YP_534755.1	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_534756.1	catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation
YP_534757.1	DapATase; functions in arginine biosynthetic pathway; catalyzes the formation of N-acetyl-L-glutamate 5-semialdehyde from 2-oxoglutarate and N(2)-acetyl-L-ornithine
YP_534761.1	ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation
YP_534770.1	molecular chaperone
YP_534777.1	isomerizes methylthioribose-1-phosphate into methylthioribulose-1-phosphate; involved in methionine salvage pathway
YP_534778.1	Catalyzes the reversible phosphorolysis of 5'-deoxy-5'- methylthioadenosine (MTA) to adenine and 5-methylthio-D-ribose-1- phosphate
YP_534782.1	this stereospecific enzymes reduces the S isomer of methionine sulfoxide while MsrB reduces the R form; provides protection against oxidative stress
YP_534784.1	binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase