-- dump date   	20111121_015704
-- class       	Genbank::CDS
-- table       	cds_note
-- id	note
YP_198640.1	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_198641.1	binds the polymerase to DNA and acts as a sliding clamp
YP_198642.1	Required for DNA replication; binds preferentially to single-stranded, linear DNA
YP_198643.1	negatively supercoils closed circular double-stranded DNA
YP_198651.1	involved in the de novo synthesis of pyridoxine (Vitamin B6)
YP_198654.6	catalyzes the formation of D-fructose 6-phosphate from fructose-1,6-bisphosphate
YP_198655.2	catalyzes the formation of L-glutamate and an aromatic oxo acid from an aromatic amino acid and 2-oxoglutarate
YP_198661.1	flavin mononucleotide-dependent dehydrogenase; functions in aerobic respiration and also has a role in anaerobic nitrate respiration
YP_198666.6	enzyme from Treponema denticola exhibits NADH-dependent trans-2-enoyl-CoA reductase activity
YP_001001374.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_001001375.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_001001376.1	putative; ORF located using FrameD
YP_198720.1	part of a set of proteins involved in the infection of eukaryotic cells; in plant pathogens involved in the hypersensitivity response
YP_198751.6	catalyzes the formation of alpha-1,4-glucan chains from ADP-glucose
YP_198752.6	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_001001377.1	putative; ORF located using FrameD
YP_001001378.1	putative; ORF located using FrameD
YP_001001379.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_001001380.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_198816.6	catalyzes the formation of glutamate from glutamine and alpha-ketoglutarate
YP_198817.6	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_001001381.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_198833.6	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_198858.1	catalyzes the formation of spermidine from putrescine and S-adenosylmethioninamine
YP_198859.6	catalyzes the formation of agmatine from arginine in putrescine and spermidine biosynthesis
YP_198866.1	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_198878.1	involved in the control of the structural glucose backbone of osmoregulated periplasmic glucans
YP_198880.1	catalyzes the formation of thymidine 5'-phosphate from thymidine
YP_001001382.1	putative; ORF located using FrameD
YP_198886.1	OMP decarboxylase; OMPDCase; OMPdecase; type 1 subfamily; involved in last step of pyrimidine biosynthesis; converts orotidine 5'-phosphate to UMP and carbon dioxide; OMP decarboxylase; OMPDCase; OMPdecase
YP_198893.1	PlsB; catalyzes the formation of 1-acyl-sn-glycerol 3-phosphate by transfering the acyl moiety from acyl-CoA
YP_001001383.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_198906.1	phenylalanine 4-hydroxylase; phenylalanine 4-hydroxylase; catalyzes the formation of 4a-hydroxytetrahydrobiopterin and tyrosine from phenylalanine and tetrahydrobiopterin
YP_001001384.1	putative; ORF located using FrameD
YP_198938.1	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_001001385.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_198989.1	an Escherichia coli mutant results in accumulation of octaprenylphenol and no ubiquinone; functions in the formation of 2-octaprenyl-6-hydroxy-phenol from 2-octaprenylphenol in ubiquinone (coenzyme Q) biosynthesis; similar to eukaryotic proteins that exhibit kinase functions
YP_001001386.1	putative; ORF located using FrameD
YP_198991.6	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_199016.1	ketopantoate reductase; catalyzes the NADPH reduction of ketopantoate to pantoate; functions in pantothenate (vitamin B5) biosynthesis
YP_001001387.1	putative; ORF located using FrameD
YP_199041.6	catalyzes the formation of porphobilinogen from 5-aminolevulinate
YP_001001388.1	AroE; catalyzes the conversion of shikimate to 3-dehydroshikimate
YP_199051.6	helicase involved in DNA repair and perhaps also replication
YP_199067.2	catalyzes the formation of biotinyl-5'-AMP, also acts as a transcriptional repressor of the biotin operon
YP_199068.1	type III; catalyzes the formation of (R)-4'-phosphopantothenate from (R)-pantothenate in coenzyme A biosynthesis; type III pantothenate kinases are not subject to feedback inhibition from coenzyme A and have a high Km for ATP
YP_199070.1	catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP)
YP_001001389.1	putative; ORF located using FrameD
YP_199076.1	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_199092.1	catalyzes the conversion of 4-Hydroxybenzoate into 3-octaprenyl-4-hydroxybenzoate, as part of the ubiquinone biosynthesis pathway
YP_199095.1	catalyzes the formation of 8-amino-7-oxononanoate from 6-carboxyhexanoyl-CoA and L-alanine
YP_199098.1	catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis
YP_199102.1	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_199106.1	catalyzes the formation of D-glucono-1,5-lactone 6-phosphate from D-glucose 6-phosphate
YP_199113.2	Catalyzes the rate-limiting step in dNTP synthesis
YP_199114.1	B2 or R2 protein; type 1b enzyme; catalyzes the rate-limiting step in dNTP synthesis; converts nucleotides to deoxynucleotides; forms a homodimer and then a multimeric complex with NrdE
YP_199115.1	An electron-transfer protein; flavodoxin binds one FMN molecule, which serves as a redox-active prosthetic group
YP_001001390.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_199120.1	catalyzes the thiolytic cleavage of beta-ketoadipyl-CoA to succinate and acetyl-CoA
YP_199123.1	Catalyzes the cycloisomerization of cis,cis-muconate
YP_199133.1	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_199134.1	Involved in DNA double-strand break repair and recombination. Promotes the annealing of complementary single-stranded DNA and by simulation of RAD51 recombinase
YP_199135.1	catalyzes the conjugation of cysteine to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine, which is then decarboxylated to form 4'-phosphopantotheine
YP_199136.1	catalyzes the formation of dUMP from dUTP
YP_199147.2	involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate
YP_199151.1	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_001001391.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_199164.1	essential respiratory protein A; may be involved in the transfer of iron-sulfur clusters; essential for growth using oxygen or alternate electron acceptors
YP_199176.1	catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis
YP_199178.1	involved in de novo purine biosynthesis
YP_001001392.1	putative; ORF located using FrameD
YP_199187.1	Stimulates excision of phage lambda; affects Mu development; acts as an activator of rRNA and iRNA transcription
YP_199191.2	methylates ribosomal protein L11 at multiple amino acid positions; mutations of these genes in Escherichia coli or Thermus thermophilus has no apparent phenotype
YP_199195.1	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_199196.1	crystal structure of protein from Xanthomonas shows pentameric toroidal structure; physiological function is unknown
YP_199197.1	composes the biotin carboxyl carrier protein subunit of the acetyl-CoA carboxylase complex, the enzyme that catalyzes the carboxylation of acetyl-CoA to malonyl-CoA, which in turn controls the rate of fatty acid metabolism
YP_199206.1	binding of PriA to forked DNA starts the assembly of the primosome, also possesses 3'-5' helicase activity
YP_199211.1	NorM; MdtK; functions as a Na(+)/drug antiporter; inactivation in Vibrio cholerae results in susceptibility to fluoroquinolones
YP_199218.1	decatenates replicating daughter chromosomes
YP_199224.2	cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+)
YP_199225.2	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_199233.1	catalyzes the formation of formate and 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine from GTP
YP_199235.1	Acylates the intermediate (KDO)2-lipid IVA to form (KDO)2-(lauroyl)-lipid IVA
YP_199236.6	hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr); possible defense mechanism against a harmful effect of D-tyrosine
YP_199237.1	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_001001393.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_001001394.1	putative; ORF located using FrameD
YP_001001395.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_001001396.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_001001397.1	putative; ORF located using FrameD
YP_001001398.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_199326.1	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_199327.1	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_199329.1	this stereospecific enzymes reduces the R isomer of methionine sulfoxide while MsrA reduces the S form; provides protection against oxidative stress
YP_199332.2	catalyzes the oxidative deamination of D-amino acids
YP_199333.1	converts L-alanine to D-alanine which is used in cell wall biosynthesis; binds one pyridoxal phosphate per monomer; forms a homodimer
YP_199350.6	putative nucleotide binding property based on structural studies of Haemophilus influenzae crystallized protein in PDB Accession Number 1IN0 and NMR studies of Escherichia coli YajQ; the YajQ protein from Pseudomonas synringae appears to play a role in activation of bateriophage phi6 segment L transcription
YP_199352.1	part of the metNIQ transport system for methionine
YP_199359.2	Catalyzes the transfer of acetyl from acetyldihydrolipoamide to coenzyme A to form acetyl CoA
YP_199365.1	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_199366.1	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_199367.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B is part of the membrane proton channel.
YP_199368.1	Produces ATP from ADP in the presence of a proton gradient across the membrane; the delta subunit is part of the catalytic core of the ATP synthase complex
YP_199369.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit
YP_199370.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit
YP_199371.6	Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit
YP_199372.1	part of catalytic core of ATP synthase; alpha(3)beta(3)gamma(1)delta(1)epsilon(1); involved in producing ATP from ADP in the presence of the proton motive force across the membrane
YP_199373.1	catalyzes the interconversion of chorismate to prephenate
YP_199385.1	Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source
YP_001001399.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_199401.1	catalyzes the dehydration of (3R)-3-hydroxydecanoyl-ACP to 2,3-decenoyl-ACP or 3,4-decenoyl-ACP
YP_199402.1	involved in translesion DNA polymerization with beta clamp of polymerase III; belongs to Y family of polymerases; does not contain proofreading function
YP_199406.1	DTB synthetase; dethiobiotin synthase; involved in production of dethiobiotin from ATP and 7,8-diaminononanoate and carbon dioxide; contains magnesium
YP_199448.6	catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro)
YP_001001400.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_199470.1	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_199471.1	binds to single-strand binding (SSB) protein and acts as a bridge between the DnaX clamp loader complex and the SSB
YP_001001401.1	putative; ORF located using FrameD
YP_199473.1	catalyzes the removal of N-terminal amino acids preferably leucine from various peptides
YP_199478.2	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; XerD specifically exchanges the bottom strands; cell division protein FtsK may regulate the XerCD complex; enzyme from Streptococcus group has unusual active site motifs
YP_199480.1	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_001001402.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_199515.1	Maf; overexpression in Bacillus subtilis inhibits septation in the dividing cell
YP_001001403.1	some L32 proteins have zinc finger motifs consisting of CXXC while others do not
YP_199517.2	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_199520.1	Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis
YP_199521.2	carries the fatty acid chain in fatty acid biosynthesis
YP_199522.1	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_199523.1	catalyzes the formation of anthranilate and glutamate from chorismate and glutamine; identified by sequence similarity; putative; ORF located using Blastx/Glimmer/Genemark
YP_199525.1	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_199531.2	catalyzes the formation of pyruvate and succinate from 2-methylisocitrate
YP_199532.1	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_199533.6	catalyzes the conversion of citrate to isocitrate
YP_199554.1	catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis
YP_001001404.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_199564.1	Acylates the intermediate (KDO)2-lipid IVA to form (KDO)2-(lauroyl)-lipid IVA
YP_199565.1	catalyzes the transfer of 2-keto-3-deoxy-D-manno-octulosonic acid to lipid A
YP_001001405.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_199575.1	dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate
YP_199576.2	catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis; forms a heterodimer of LeuC/D
YP_199579.1	catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis
YP_199580.1	catalyzes the formation of 2-isopropylmalate from acetyl-CoA and 2-oxoisovalerate in leucine biosynthesis
YP_199584.1	catalyzes the formation of 2-acetolactate from pyruvate; also known as acetolactate synthase large subunit
YP_199585.6	catalyzes the formation of (R)-2,3-dihydroxy-3-methylbutanoate from (S)-2-hydroxy-2-methyl-3-oxobutanoate in valine and isoleucine biosynthesis
YP_199586.1	required for the synthesis of the hydromethylpyrimidine moiety of thiamine
YP_199591.1	catalyzes the hydrolysis of pyrophosphate to phosphate
YP_199601.1	catalyzes the formation of D-fructose 1,6-bisphosphate from D-fructose 6-phosphate in glycolysis
YP_199602.1	essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP
YP_199610.1	catalyzes the oxidation of malate to oxaloacetate
YP_199618.1	disulfide oxidoreductase; integral membrane protein; required for perioplasmic disulfide bond formation; oxidizes DsbA protein
YP_001001406.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_001001407.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_001001408.1	putative; ORF located using FrameD
YP_199663.2	catalyzes the formation of 2-oxoglutarate from isocitrate
YP_001001409.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_199671.1	Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer
YP_199672.1	hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates
YP_199673.1	binds and unfolds substrates as part of the ClpXP protease
YP_199680.1	An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids
YP_199681.1	3'-5' exonuclease of DNA polymerase III
YP_001001410.1	putative; ORF located using FrameD
YP_199696.1	catalyzes the phosphorylation of 3-deoxy-D-manno-octulosonic acid at the 4-OH position
YP_199698.1	together with moaC, is involved in the conversion of a guanosine derivative (GXP) into molybdopterin precursor Z
YP_199700.1	MoaC; along with MoaA is involved in conversion of a guanosine derivative into molybdopterin precursor Z; involved in molybdenum cofactor biosynthesis
YP_199703.1	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_199705.1	involved in a recombinational process of DNA repair, independent of the recBC complex
YP_199714.1	cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+)
YP_199733.6	broad specificity; family IV; in Corynebacterium glutamicum this protein can use glutamate, 2-aminobutyrate, and aspartate as amino donors and pyruvate as the acceptor
YP_199734.1	EngC; RsgA; CpgA; circularly permuted GTPase; ribosome small subunit-dependent GTPase A; has the pattern G4-G1-G3 as opposed to other GTPases; interacts strongly with 30S ribosome which stimulates GTPase activity
YP_199741.1	catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis
YP_001001411.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_001001412.1	putative; ORF located using FrameD
YP_199756.1	involved in the transport of C4-dicarboxylates across the membrane
YP_199757.6	NADP-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; decarboxylates oxaloacetate
YP_001001413.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_199762.1	Condenses 4-methyl-5-(beta-hydroxyethyl)-thiazole monophosphate and 4-amino-5-hydroxymethyl pyrimidine pyrophosphate to form thiamine monophosphate
YP_199766.6	Catalyzes D-ribose 5-phosphate --> D-ribulose 5-phosphate in the nonoxidative branch of the pentose phosphate pathway
YP_199771.1	the crystal structure of Haemophilus influenzae HI0817 showed that this protein forms dimers; function unknown
YP_199776.6	catalyzes the hydrolysis of dipeptides with a proline at the C-terminal; also catalyzes the low efficiency hydrolysis of organophosphate di- and tri-esters
YP_199779.1	catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III
YP_199780.1	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_199782.2	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_199784.1	Essential for recycling GMP and indirectly, cGMP
YP_199787.1	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_199790.1	catalyzes branch migration in Holliday junction intermediates
YP_199792.2	RpmE2; there appears to be two types of ribosomal proteins L31 in bacterial genomes; some contain a CxxC motif while others do not; Bacillus subtilis has both types; the proteins in this cluster do not have the CXXC motif; RpmE is found in exponentially growing Bacilli while YtiA was found after exponential growth; expression of ytiA is controlled by a zinc-specific transcriptional repressor; RpmE contains one zinc ion and a CxxC motif is responsible for this binding; forms an RNP particle along with proteins L5, L18, and L25 and 5S rRNA; found crosslinked to L2 and L25 and EF-G; may be near the peptidyltransferase site of the 50S ribosome
YP_199793.1	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_001001414.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_199815.1	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_001001415.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_199833.1	part of ModCBA molybdate transporter; member of ABC superfamily; inner membrane component; regulated by repressor protein ModE
YP_199842.1	catalyzes the formation of 3-phospho-D-glyceroyl phosphate from D-glyceraldehyde 3-phosphate; identified by sequence similarity; putative; ORF located using Blastx/Glimmer/Genemark
YP_001001416.1	putative; ORF located using FrameD
YP_199858.1	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_199871.1	Converts (S)-4-amino-5-oxopentanoate to 5-aminolevulinate during the porphyrin biosynthesis pathway
YP_001001417.1	putative; ORF located using FrameD
YP_001001418.1	putative; ORF located using FrameD
YP_001001419.1	putative; ORF located using FrameD
YP_199881.1	catalyzes the formation of coproporphyrinogen from uroporphyrinogen III
YP_001001420.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_199882.1	catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis
YP_199883.2	catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis
YP_199884.1	catalyzes the formation of pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate
YP_001001421.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_199920.1	catalyzes the phosphorylation of the phosphocarrier protein HPr of the bacterial phosphotransferase system
YP_199923.1	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_001001422.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_199929.1	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_199933.1	glycinamide ribonucleotide transformylase; GAR Tfase; catalyzes the synthesis of 5'-phosphoribosylformylglycinamide from 5'-phosphoribosylglycinamide and 10-formyltetrahydrofolate; PurN requires formyl folate for the reaction unlike PurT which uses formate
YP_199936.6	catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis
YP_001001423.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_001001424.1	putative; ORF located using FrameD
YP_001001425.1	putative; ORF located using FrameD
YP_199964.2	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_199965.1	Essential for efficient processing of 16S rRNA
YP_199966.1	methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA
YP_199967.1	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_199989.6	catalyzes ATP-dependent phosphorylation of adenosylcobinamide to form adenosylcobinamide phosphate and the addition of guanosine monophosphate to adenosylcobinamide phosphate to form adenosylcobinamide-GDP
YP_199990.1	catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide and 5,6-dimethylbenzimidazole
YP_199992.6	catalyzes the formation of adenosylcobalamin from Ado-cobinamide-GDP and alpha-ribazole
YP_001001426.1	putative; ORF located using FrameD
YP_001001427.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_200027.1	catalyzes the formation of O-succinyl-L-homoserine from succinyl-CoA and L-homoserine in methionine biosynthesis
YP_200044.1	with SufCD activates cysteine desulfurase SufS
YP_200055.1	catalyzes the formation of L-proline from pyrroline-5-carboxylate
YP_200065.1	similar to RuvC resolvase with substantial differences; NMR structural information suggests this protein is monomeric; unknown cellular function
YP_200066.1	catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis
YP_200072.1	catalyzes the 4-phospho-L-aspartate from L-aspartate and the formation of lysine from meso-2,6-diaminoheptanedioate
YP_200075.1	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_200078.1	binds to single stranded DNA and may facilitate the binding and interaction of other proteins to DNA
YP_001001429.1	putative; ORF located using FrameD
YP_001001430.1	putative; ORF located using FrameD
YP_200098.6	Selectively cleaves double-stranded DNA at the second phosphodiester bond 3' to a deoxyinosine leaving behind the intact lesion on the nicked DNA; cleaves DNA containing urea residues, AP sites, base mismatches, insertion/deletion mismatches, flaps, and pseudo-Y structures
YP_200099.1	2,3-bisphosphoglycerate-dependent; catalyzes the interconversion of 2-phosphoglycerate to 3-phosphoglycerate
YP_200104.2	regulates chemotaxis by demethylation of methyl-accepting chemotaxis proteins
YP_001001431.1	putative; ORF located using FrameD
YP_001001432.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_200143.1	Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation
YP_001001433.1	putative; ORF located using FrameD
YP_001001434.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_200164.1	unwinds double stranded DNA
YP_001001435.1	putative; ORF located using FrameD
YP_001001436.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_200194.6	regulator of RNase E; increases half-life and abundance of RNAs; interacts with RNase E possibly inhibiting catalytic activity
YP_001001437.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_001001438.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_200222.1	catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A; involved in coenzyme A biosynthesis
YP_200232.1	catalyzes the interconversion of succinyl-CoA and succinate
YP_200233.1	Catalyzes the only substrate-level phosphorylation in the TCA cycle
YP_200234.1	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_001001439.1	putative; ORF located using FrameD
YP_200250.2	Conjugates Arg from its aminoacyl-tRNA to the N-termini of proteins containing an N-terminal aspartate or glutamate
YP_200260.1	involved in the peptidyltransferase reaction during translation
YP_200261.1	essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication
YP_200262.1	binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase
YP_200264.1	catalyzes the formation of FMN from riboflavin and the formation of FAD from FMN; in Bacillus the ribC gene has both flavokinase and FAD synthetase activities
YP_200265.1	IleRS; catalyzes the formation of isoleucyl-tRNA(Ile) from isoleucine and tRNA(Ile); since isoleucine and other amino acids such as valine are similar, there are additional editing function in this enzyme; one is involved in hydrolysis of activated valine-AMP and the other is involved in deacylation of mischarged Val-tRNA(Ile); there are two active sites, one for aminoacylation and one for editing; class-I aminoacyl-tRNA synthetase family type 1 subfamily; some organisms carry two different copies of this enzyme
YP_200266.1	lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis
YP_200267.2	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_001001440.1	putative; ORF located using FrameD
YP_200281.1	This protein performs the mismatch recognition step during the DNA repair process
YP_001001441.1	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_001001442.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_001001443.1	putative; ORF located using FrameD
YP_200295.1	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_200299.1	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_200300.2	plays an essential role in ATP-dependent branch migration of the Holliday junction
YP_200302.1	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_200307.1	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_001001444.1	putative; ORF located using FrameD
YP_001001445.1	putative; ORF located using FrameD
YP_200373.1	Required in the synthesis of PPQ, but its exact function is unknown
YP_200374.1	possibly involved in transport of pyrroloquinoline quinone transport
YP_200384.1	catalyzes the second step in the glutathione biosynthesis pathway, where it synthesizes ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione
YP_001001446.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_200424.1	catalyzes the conversion of ATP and D-glucose to ADP and D-glucose 6-phosphate
YP_200425.2	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_200426.1	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_200429.1	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_001001447.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_200433.1	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_200434.1	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_001001448.1	glycosyltransferase; polymerizes glycan strands in the peptidoglycan
YP_001001449.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_200454.1	stimulates the release of release factors 1 and 2 from the ribosome after hydrolysis of the ester bond in peptidyl-tRNA has occurred; GDP/GTP-binding protein
YP_200456.1	catalyzes the formation of O-acetyl -L-homoserine from L-homoserine and acetyl-CoA
YP_200457.1	catalyzes the formation of cystathionine from L-cysteine and O-succinyl-L-homoserine
YP_001001450.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_200483.1	Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA
YP_200488.1	Member of the extracytoplasmic function sigma factors which are active under specific conditions; binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription; this sigma factor is involved in heat shock and oxidative stress response
YP_200491.1	binds to the ribosome on the universally-conserved alpha-sarcin loop
YP_200494.1	cytoplasmic enzyme involved in processing rRNA and some mRNAs; substrates typically have dsRNA regions; forms a homodimer; have N-terminal nuclease and C-terminal RNA-binding domains; requires magnesium as preferred ion for activity
YP_200495.1	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_200496.1	involved in DNA repair and RecFOR pathway recombination; RecFOR proteins displace ssDNA-binding protein and facilitate the production of RecA-coated ssDNA
YP_200498.1	in Escherichia coli this enzyme catalyzes the SAM-dependent methylation of U1939 in the 23S ribomal RNA; binds an iron-sulfur cluster [4Fe-4S]
YP_200506.1	hydrolyzes the terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides
YP_200507.1	Catalyzes the salvage synthesis of inosine-5'-monophosphate (IMP) and guanosine-5'-monophosphate (GMP) from the purine bases hypoxanthine and guanine, respectively
YP_200508.1	Catalyzes the phosphorolytic cleavage of 6-oxopurine nucleosides
YP_200514.2	catalyzes the ATP-dependent formation of a phosphodiester at the site of a single strand break in duplex DNA
YP_001001451.1	putative; ORF located using FrameD
YP_001001452.1	putative; ORF located using FrameD
YP_200558.6	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_200561.1	Involved in the electron transport chain
YP_200563.1	methionine--tRNA ligase; MetRS; adds methionine to tRNA(Met) with cleavage of ATP to AMP and diphosphate; some MetRS enzymes form dimers depending on a C-terminal domain that is also found in other proteins such as Trbp111 in Aquifex aeolicus and the cold-shock protein CsaA from Bacillus subtilis while others do not; four subfamilies exist based on sequence motifs and zinc content
YP_200569.2	converts homocysteine and S-adenosyl-methionine to methionine and S-adenosyl-homocysteine or S-methyl-methionine and homocysteine to two methionines
YP_200600.1	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_200601.6	catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; main replicative polymerase
YP_200602.1	RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids
YP_200603.1	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_200604.1	catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis
YP_200605.1	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_200606.1	adds the O-linked and N-linked 3(R)-hydroxy fatty acids to the glucosamine disaccharide during lipid A biosynthesis
YP_200609.1	catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate
YP_200611.1	catalyzes the formation of undecaprenyl pyrophosphate from isopentenyl pyrophosphate
YP_200612.1	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_200613.2	Catalyzes the phosphorylation of UMP to UDP
YP_200615.1	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_200616.6	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_200622.6	catalyzes the removal of N-terminal amino acids from peptides and arylamides; generally Co(II) however activity has been shown for some methionine aminopeptidases with Zn, Fe, or Mn
YP_200623.1	catalyzes the uridylylation or deuridylylation of the PII nitrogen regulatory protein
YP_200624.6	catalyzes the formation of N-succinyl-2-amino-6-ketopimelate from succinyl-CoA and tetrahydrodipicolinate in the lysine biosynthetic pathway
YP_200628.1	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_200629.1	functions in asparagine biosynthesis; converts glutamine, aspartate, ATP, and water to glutamate, asparagine, pyrophosphate and AMP
YP_200635.1	decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling
YP_200656.6	catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate
YP_200662.1	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_200668.1	Negative regulator of class I heat shock genes (grpE-dnaK-dnaJ and groELS operons). Prevents heat-shock induction of these operons
YP_200669.1	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_200670.1	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_200671.1	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_200673.1	catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate
YP_200681.2	E3 component of 2-oxoglutarate dehydrogenase complex; catalyzes the oxidation of dihydrolipoamide to lipoamide
YP_200682.1	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_200683.6	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_001001454.1	putative; ORF located using FrameD
YP_200687.6	Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide
YP_001001455.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_200696.1	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_001001456.1	putative; ORF located using FrameD
YP_001001457.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_200732.1	Catalyzes the conversion of acetyl-CoA and L-homoserine to CoA and O-acetyl-L-homoserine
YP_001001458.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_001001459.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_200755.2	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_001001460.1	putative; ORF located using FrameD
YP_200778.1	catalyzes the formation of diketo methylthiopentyl phosphate from methylribulose phosphate in the methionine salvage pathway
YP_200782.6	catalyzes the formation of 3-phosphonooxypyruvate from 3-phospho-D-glycerate in serine biosynthesis; can also reduce alpha ketoglutarate to form 2-hydroxyglutarate
YP_001001461.1	putative; ORF located using FrameD
YP_200790.1	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_200794.1	ATP-binding protein; required for proper cytochrome c maturation
YP_200795.1	catalyzes the transfer of an amino moiety
YP_001001462.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_200818.1	Catalyzes the formation of (d)CDP from ATP and (d)CMP
YP_200819.1	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_200820.1	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_001001463.1	putative; ORF located using FrameD
YP_200832.1	catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate
YP_200833.1	catalyzes the synthesis of xanthosine monophosphate by the NAD+ dependent oxidation of inosine monophosphate
YP_200834.1	contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway
YP_200845.2	Transcriptional regulator that represses the manganese transporter MntH when manganese is present
YP_200848.1	3'-5' exoribonuclease specific for small oligoribonuclotides
YP_200850.6	catalyzes the formation of phosphoenolpyruvate from pyruvate
YP_200868.1	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_200875.1	catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis
YP_200876.1	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_200881.1	multifunctional homotetrameric enzyme that catalyzes the phosphorylation of aspartate to form aspartyl-4-phosphate as well as conversion of aspartate semialdehyde to homoserine; functions in a number of amino acid biosynthetic pathways
YP_200882.1	catalyzes the formation of O-phospho-L-homoserine from L-homoserine in threonine biosynthesis from asparate
YP_200886.1	catalyzes the formation of L-threonine from O-phospho-L-homoserine
YP_200890.1	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_200894.1	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_200895.1	catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer
YP_200896.1	catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis
YP_200897.1	catalyzes the formation of 3-(imidazol-4-yl)-2-oxopropyl phosphate from D-ethythro-1-(imidazol-4-yl)glycerol 3-phosphate and histidinol from histidinol phosphate
YP_200898.1	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_200899.1	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_200900.2	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_200901.1	catalyzes the formation of 1-(5-phosphoribosyl)-AMP from 1-(5-phosphoribosyl)-ATP and the subsequent formation of 1-(5-phosphoribosyl)-5-((5- phosphoribosylamino)methylideneamino)imidazole-4- carboxamide from 1-(5-phosphoribosyl)-AMP in histidine biosynthesis
YP_200931.1	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_200934.1	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_200935.1	transfers the gamma-phosphate of ATP to the 4' position of a tetraacyldisaccharide 1-phosphate intermediate to form tetraacyldisaccharide 1,4'-bis-phosphate
YP_200946.1	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_001001464.1	putative; ORF located using FrameD
YP_200947.1	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_200953.1	catalyzes the formation of D-glucono-1,5-lactone 6-phosphate from D-glucose 6-phosphate
YP_200954.1	catalyzes the conversion of ATP and D-glucose to ADP and D-glucose 6-phosphate
YP_200955.1	catalyzes the formation of 6-phospho-D-gluconate from 6-phospho-D-glucono-1,5-lactone; identified by sequence similarity; putative; ORF located using Blastx/Glimmer/Genemark
YP_200956.1	catalyzes the formation of 2-dehydro-3-deoxy-6-phospho-D-gluconate from 6-phospho-D-gluconate
YP_001001465.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_001001466.1	putative; ORF located using FrameD
YP_001001467.1	putative; ORF located using FrameD
YP_001001468.1	putative; ORF located using FrameD
YP_001001469.1	putative; ORF located using FrameD
YP_200999.1	functions in sugar metabolism in glycolysis and the Embden-Meyerhof pathways (EMP) and in gluconeogenesis; catalyzes reversible isomerization of glucose-6-phosphate to fructose-6-phosphate; member of PGI family
YP_201000.6	Converts L-aspartate to beta-alanine and provides the major route of beta-alanine production in bacteria. Beta-alanine is essential for the biosynthesis of pantothenate (vitamin B5)
YP_201002.1	catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine
YP_201003.1	catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate
YP_201006.1	similar protein in Methanocaldococcus converts GTP to 7,8-dihydro-D-neopterin 2',3'-cyclic phosphate as the first step in methanopterin biosynthesis
YP_001001470.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_201025.1	catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis
YP_201027.1	catalyzes the formation of 3-phosphonooxypyruvate and glutamate from O-phospho-L-serine and 2-oxoglutarate; required both in major phosphorylated pathway of serine biosynthesis and in the biosynthesis of pyridoxine
YP_201028.1	in Escherichia coli this periplasmic enzyme was found to encode the periplasmic catalytic subunit of an oxidoreductase; sulfite oxidase activity not demonstrated; requires inner membrane anchor protein YedZ
YP_201036.6	catalyzes the deimination of N-formimino-L-glutamate to ammonia and N-formyl-L-glutamate
YP_201035.6	catalyzing the hydrolysis of 4-imidazolone-5-propionate to N-formimidoyl-L-glutamate, the third step in the histidine degradation pathway
YP_201037.1	catalyzes the degradation of histidine to urocanate and ammmonia
YP_201039.6	catalyzes the formation of 4-imidazolone-5-propanoate from urocanate during histidine metabolism
YP_201045.1	negatively supercoils closed circular double-stranded DNA
YP_201046.2	isomerizes methylthioribose-1-phosphate into methylthioribulose-1-phosphate; involved in methionine salvage pathway
YP_201049.6	this protein catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction; essential for DNA replication and repair of damaged DNA; similar to ligase LigB
YP_201051.1	interacts with cell division protein FitsZ and may be required to anchor septal ring structure
YP_201053.1	in Escherichia coli this protein is wrapped around the base of the L1 stalk
YP_201054.1	binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit
YP_201055.1	binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21
YP_201057.1	catalyzes a two-step reaction, first charging an asparagine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA
YP_201063.1	catalyzes the oxidative ring opening of 3-hydroxyanthranilate to 2-amino-3-carboxymuconate semialdehyde in the final enzymatic step of quinolinate biosynthesis
YP_201069.2	Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates
YP_201077.1	catalyzes the N2-methyl guanosine modification of the G2445 residue of 23S rRNA
YP_201104.6	ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation
YP_201107.1	Responsible for the end-turnover of tRNA: specifically removes the terminal AMP residue from uncharged tRNA (tRNA-C-C-A)
YP_201120.1	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_201121.1	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_201122.1	member of preprotein translocase; forms a heterotrimer with SecD and SecF; links the SecD/SecF/YajC/YidC complex with the SecY/SecE/SecG complex
YP_201123.1	Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr)
YP_201124.1	Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step
YP_201140.2	Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate
YP_201147.1	Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA
YP_201149.1	molecular chaperone
YP_201153.6	ATP-dependent adenylate transferase, transfers adenyl moiety to the MoeD subunit of molybdopterin synthase
YP_201168.2	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_201174.1	catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate
YP_201177.1	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_201179.1	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_201183.2	participates with LolB in the incorporation of lipoprotein into the outer membrane
YP_201190.1	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_201191.1	stimulates the activities of the other two initiation factors, IF-2 and IF-3
YP_201193.1	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_201195.1	catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs
YP_201196.1	HflD; UPF0274; in Escherichia coli this protein is peripherally associated with the membrane and appears to act with lambda CII protein; in Haemophilus influenzae a knockout of the HI0638 gene affected paracytosis
YP_201206.1	required for the assembly of the flagellar basal body P-ring
YP_201208.1	with FlgF and C makes up the proximal portion of the flagellar basal body rod
YP_201209.1	with FlgF and B makes up the proximal portion of the flagellar basal body rod
YP_201210.1	acts as a scaffold for the assembly of hook proteins onto the flagellar basal body rod
YP_201211.1	the hook connects flagellar basal body to the flagellar filament
YP_201213.2	FlgF, with FlgB and C, makes up the proximal portion of the flagellar basal body rod
YP_201214.2	makes up the distal portion of the flagellar basal body rod
YP_201215.1	part of the flagellar basal body which consists of four rings L,P, S and M mounted on a central rod
YP_201216.1	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_201217.1	Flagellum-specific muramidase which hydrolyzes the peptidoglycan layer to assemble the rod structure in the periplasmic space
YP_201218.1	with FlgL acts as a hook filament junction protein to join the flagellar filament to the hook
YP_201219.1	with FlgK acts as a hook filament junction protein to join the flagellar filament to the hook; Yersinia, Vibrio parahaemolyticus, Bradyrhizobium and other organisms have 2 copies of this and other flagellar genes.
YP_201220.2	structural flagella protein; Vibrio contains multiple flagellin genes usually localized into two region on the chromosome, flaAC and flaCEDB in V. cholerae, flaFBA and flaCDE in V. parahemolyticus; FlaA is sigma 54 dependent and essential for motility in V.cholerae but not in V. parahaemolyticus
YP_201240.1	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_201247.1	with FliG and FliN makes up the switch complex which is involved in switching the direction of the flagella rotation
YP_201250.1	FliP, with proteins FliQ and FliR, forms the core of the central channel in the flagella export apparatus
YP_201256.2	membrane protein responsible for substrate specificity switching from rod/hook-type export to filament-type export
YP_201257.1	membrane protein involved in the flagellar export apparatus
YP_201258.6	Positive regulator of class III flagellar genes
YP_001001471.1	putative; ORF located using FrameD
YP_201304.1	Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway
YP_201305.6	catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis
YP_201308.1	catalyzes the formation of arginine from (N-L-arginino)succinate
YP_201309.2	catalyzes the reduction of N-acetyl-5-glutamyl phosphate to N-acetyl-L-glutamate 5-semialdehyde in arginine biosynthesis and the reduction of N-acetyl-gamma-aminoadipyl-phosphate to N-acetyl-L-aminoadipate-semialdehyde in lysine biosynthesis; involved in both the arginine and lysine biosynthetic pathways; lysine is produced via the AAA pathway, lysine from alpha-aminoadipate
YP_201311.1	catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate
YP_201312.1	catalyzes the formation of L-ornithine from N(2)-acetyl-L-ornithine
YP_201314.1	catalyzes ATP + L-citrulline + L-aspartate = AMP + diphosphate + (N(omega)-L-arginino)succinate
YP_201315.1	catalyzes the conversion of N-acetylornithine to N-acetylcitrulline in an alternative arginine biosynthesis pathway
YP_201317.1	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_201322.1	Catalyzes the reversible hydrolysis of the amide bond within dihydroorotate. This metabolic intermediate is required for the biosynthesis of pyrimidine nucleotides
YP_001001472.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_201335.1	outer membrane lipoprotein that catalyzes the hydrolysis of the thioester bond in palmitoyl-CoA; YbhC localizes to the cellular poles; member of pectinesterase family
YP_201340.1	catalyzes the dephosphorylation of 2-phosphoglycolate to form glycolate and phosphate
YP_201341.1	Involved in ubiquinone biosynthesis
YP_201342.1	Catalyzes the hydrolytic cleavage of a carbon-halogen bond in N-ethylammeline
YP_201344.1	Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA
YP_201355.2	exhibits an RNA-dependent ATPase activity, specifically stimulated by bacterial 23S rRNA
YP_201356.1	catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis
YP_201365.1	putative metalloprotease
YP_201371.1	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_201376.1	bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides
YP_201389.1	responsible for recognizing base lesions in the genome and initiating base excision DNA repair
YP_201405.6	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_201429.1	involved in the production or activity of formate dehydrogenase-H which is active when nitrate is not present during anaerobic growth
YP_201432.1	catalyzes the formation of pyruvate and beta-alanine from L-alanine and 3-oxopropanoate
YP_201469.1	homologous to MotA; this protein with a related protein (a MotB homolog) 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; either MotAB or MotCD is sufficient for swimming, but both are necessary for swarming motility; these organisms have both MotA and MotC
YP_201470.1	Homologous to MotB. These organism have both MotB and MotD. With MotC (a MotA homolog) 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. Either MotAB or MotCD is sufficient for swimming, but both are necessary for swarming motility
YP_201497.6	catalyzes the conversion of glutamine residues to glutamate on methyl-accepting chemotaxis receptors
YP_201498.1	regulates chemotaxis by demethylation of methyl-accepting chemotaxis proteins
YP_201501.1	catalyzes the conversion of citrate to isocitrate and the conversion of 2-methylaconitate to 2-methylisocitrate
YP_201504.1	Catalyzes the conversion of citrate to isocitrate
YP_201507.2	regulator of pathogenicity factor RpfB; probably involved in synthesis of a diffusible signal factor involved in the regulation of extracellular enzymes
YP_201508.1	regulator of pathogenicity factor RpfF; involved in synthesis of a diffusible signal factor involved in the regulation of extracellular enzymes
YP_201511.1	class II; LysRS2; catalyzes a two-step reaction, first charging a lysine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; in Methanosarcina barkeri, LysRS2 charges both tRNA molecules for lysine that exist in this organism and in addition can charge the tRNAPyl with lysine in the presence of LysRS1
YP_201512.1	catalyzes the release of newly synthesized polypeptide chains at the stop codons UAA and UGA
YP_201525.1	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_201526.2	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_201527.2	catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers
YP_201544.1	Stimulates the peptidyltransferase activity of the 70S ribosome and enhances dipeptide synthesis with N-formylmethionyl-tRNA and puromycin in vitro, suggesting its involvement in the formation of the first peptide bond of a protein
YP_201549.1	catalyzes the interconversion of D-xylose to D-xylulose
YP_201556.2	catalyzes the formation of D-glyceraldehyde 3-phosphate and pyruvate from 2-dehydro-3-deoxy-D-galactonate 6-phosphate; functions in galactonate metabolism
YP_201562.6	catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis
YP_201567.1	catalyzes the formation of 4-amino-2-methyl-5-diphosphomethylpyrimidine
YP_201577.1	affects carbohydrate metabolism; has regulatory role in many processes
YP_201578.1	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_201579.1	binds RecA and inhibits RecA-mediated DNA strand exchange and ATP hydrolysis and coprotease activities
YP_201580.1	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_201581.1	Represses a number of genes involved in the response to DNA damage
YP_201585.1	Stimulates the elongation of poly(A) tails
YP_201586.1	IPP transferase; isopentenyltransferase; involved in tRNA modification; in Escherichia coli this enzyme catalyzes the addition of a delta2-isopentenyl group from dimethylallyl diphosphate to the N6-nitrogen of adenosine adjacent to the anticodon of tRNA species that read codons starting with uracil; further tRNA modifications may occur; mutations in miaA result in defects in translation efficiency and fidelity
YP_201595.1	catalyzes the conversion of a phosphate monoester to an alcohol and a phosphate
YP_201598.2	catalyzes the modification of U13 in tRNA(Glu)
YP_201599.1	catalyzes the conversion of 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate into 2-C-methyl-D-erythritol 2,4-cyclodiphosphate
YP_201600.1	4-diphosphocytidyl-2C-methyl-D-erythritol synthase; MEP cytidylyltransferase; MCT; catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate; involved in isoprenoid and isopentenyl-PP biosynthesis; forms homodimers
YP_201601.1	forms a complex with FtsL and FtsQ; colocalizes to the septal region of the dividing cell; membrane protein
YP_201602.1	enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis
YP_201605.6	catalyzes the formation of 2-dehydro-3-deoxy-D-octonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate in LPS biosynthesis
YP_201606.2	CTP synthase; CTP synthase; cytidine triphosphate synthetase; catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen; in Escherichia coli this enzyme forms a homotetramer
YP_201608.1	decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling
YP_201646.2	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_201706.1	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_201820.1	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_201821.1	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_201822.1	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_201823.1	binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit
YP_201825.1	IF-3 has several functions that are required and promote translation initiation including; preventing association of 70S by binding to 30S; monitoring codon-anticodon interactions by promoting disassociation of fMet-tRNA(fMet) from initiation complexes formed on leaderless mRNAs or incorrectly bound noninitiatior tRNAs and complexes with noncanonical start sites; stimulates codon-anticodon interactions at P-site; involved in moving mRNA to the P-site; and in recycling subunits
YP_201826.1	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_201832.6	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_201848.1	With PurE catalyzes the conversion of aminoimidazole ribonucleotide to carboxyaminoimidazole ribonucleotide in the de novo purine nucleotide biosynthetic pathway
YP_201849.1	Catalyzes a step in the de novo purine nucleotide biosynthetic pathway; identified by sequence similarity; putative; ORF located using Blastx/Glimmer/Genemark
YP_201854.2	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_201855.1	catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs
YP_201856.1	associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock
YP_201857.1	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_201858.1	modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination
YP_201860.2	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_201861.1	Catalyzes the transfer of electrons from NADH to quinone
YP_201862.1	Catalyzes the transfer of electrons from NADH to quinone
YP_201863.1	Catalyzes the transfer of electrons from NADH to ubiquinone
YP_201864.1	Catalyzes the transfer of electrons from NADH to quinone
YP_201865.1	Catalyzes the transfer of electrons from NADH to quinone
YP_201866.1	Catalyzes the transfer of electrons from NADH to quinone
YP_201867.2	Catalyzes the transfer of electrons from NADH to quinone
YP_201868.2	Catalyzes the transfer of electrons from NADH to ubiquinone
YP_201871.1	Catalyzes the transfer of electrons from NADH to quinone
YP_201872.1	Catalyzes the transfer of electrons from NADH to quinone
YP_201873.1	Catalyzes the transfer of electrons from NADH to quinone
YP_201874.1	The point of entry for the majority of electrons that traverse the respiratory chain eventually resulting in the reduction of oxygen
YP_201875.1	Catalyzes the transfer of electrons from NADH to quinone
YP_201877.1	Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate
YP_201888.1	catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate
YP_201889.1	catalyzes the carboxylation of acetyl-CoA to malonyl-CoA; forms a tetramer of AccA2D2 subunits
YP_201890.1	catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis
YP_201891.6	catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate
YP_201893.1	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_201894.1	mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability
YP_201898.1	catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde
YP_201899.1	Involved in the metabolism of aromatic amino acids; identified by sequence similarity; putative; ORF located using Blastx/Glimmer/Genemark
YP_201900.1	catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis
YP_201901.1	involved in methylation of ribosomal protein L3
YP_201910.1	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_201911.1	catalyzes the methylthiolation of an aspartic acid residue of the S12 protein of the 30S ribosomal subunit
YP_201917.1	Catalyzes the formation of dUTP from dCTP in thymidylate biosynthesis
YP_201937.2	catalyzes the bidirectional exonucleolytic cleavage of DNA
YP_201955.1	Maf; overexpression in Bacillus subtilis inhibits septation in the dividing cell
YP_201961.1	SPOUT methyltransferase family protein; crystal structure shows homodimer; in Escherichia coli this protein methylates pseudouridine at position 1915 of the 23S ribosomal RNA
YP_201966.1	required for the assembly and function of the DNAX complex which is required for the assembly of the beta subunit onto primed DNA
YP_201968.1	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_001001475.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_202010.1	with ThiF, ThiG, and ThiO catalyzes the formation of the thiazole moiety of thiamine pyrophosphate
YP_202011.1	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_202012.1	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_202020.1	forms homopentamer; channel that opens in response to pressure or hypoosmotic shock
YP_202035.1	in Rhizobium meliloti this protein is involved in the synthesis of nodulation factors that are active on the roots of alfalfa; catalyzes formation of activated sulfate intermediate; converts ATP and sulfate to diphosphate and adenylylsulfate and then ATP and adenylyl sulfate to ADP and 3'-phosphoadenylyl sulfate; the activated intermediate is transferred to the nodulation factors by NodH; may interact with NodP and NodQ; similar to the CysD and CysN proteins from EScherichia coli involved in cysteine biosynthesis
YP_202036.1	with CysN catalyzes the formation of adenylylsulfate from sulfate and ATP
YP_202039.6	hemoprotein; NADPH dependent; with the alpha subunit (a flavoprotein) catalyzes the reduction of sulfite to sulfide
YP_202040.1	catalyzes the reduction of 3'-phosphoadenylyl sulfate into sulfite
YP_202052.1	catalyzes the formation of phosphoenolpyruvate from pyruvate
YP_202054.1	Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway
YP_202081.1	Represses a number of genes involved in the response to DNA damage
YP_001001476.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_202100.1	restriction endonuclease; the EcoKI enzyme recognizes 5'-AACN(6)GTGC-3'; subunit R is required for both nuclease and ATPase activities
YP_001001477.1	putative; ORF located using FrameD
YP_001001478.1	putative; ORF located using FrameD
YP_001001479.1	putative; ORF located using FrameD
YP_001001480.1	putative; ORF located using FrameD
YP_001001481.1	putative; ORF located using FrameD
YP_001001483.1	putative; ORF located using FrameD
YP_001001484.1	putative; ORF located using FrameD
YP_001001485.1	putative; ORF located using FrameD
YP_001001486.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_001001487.1	putative; ORF located using FrameD
YP_001001488.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_202158.1	non-folate utilizing enzyme, catalyzes the production of beta-formyl glycinamide ribonucleotide from formate, ATP, and beta-GAR and a side reaction producing acetyl phosphate and ADP from acetate and ATP; involved in de novo purine biosynthesis
YP_202169.1	blocks the formation of polar Z-ring septums
YP_202171.1	works in conjunction with MinC and MinD to enable cell division at the midpoint of the long axis of the cell
YP_202186.1	acts in conjunction with GvcH to form H-protein-S-aminomethyldihydrolipoyllysine from glycine
YP_202196.1	is a component of the macrolide binding site in the peptidyl transferase center
YP_202197.1	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_202198.1	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_202200.6	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_202201.1	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_202202.2	late assembly protein
YP_202203.1	L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7
YP_202205.1	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_202206.2	binds 5S rRNA along with protein L5 and L25
YP_202207.1	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_202208.1	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_202209.1	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_202210.1	assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel
YP_202212.1	binds to the 23S rRNA between the centers for peptidyl transferase and GTPase
YP_202213.1	primary binding protein; helps mediate assembly; involved in translation fidelity
YP_202214.1	one of the stabilizing components for the large ribosomal subunit
YP_202215.1	located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e
YP_202216.1	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_202217.1	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_202218.1	protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA
YP_202219.1	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_202221.6	L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA
YP_202223.1	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_202226.1	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_202227.2	EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene
YP_001001489.1	binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit
YP_202228.6	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_202229.1	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_202230.1	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_202231.1	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_202232.1	binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit
YP_202233.1	in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA
YP_202235.1	binds directly to 23S ribosomal RNA
YP_202236.1	Modulates Rho-dependent transcription termination
YP_202237.1	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_202238.1	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_202239.1	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_202240.6	Enables the recycling of peptidyl-tRNAs produced at termination of translation
YP_202241.1	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_202242.1	catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP
YP_202243.1	An essential enzyme in the nonmevalonate pathway of isopentenyl diphosphate and dimethylallyl diphosphate biosynthesis
YP_202244.1	Incorporates lipoproteins in the outer membrane after they are released by the LolA protein
YP_202246.1	catalyzes the formation of glutamate-1-semialdehyde from glutamyl-tRNA(Glu) and NADPH; the second step of the pathway is catalyzed by glutamate-1-semialdehyde aminomutase which results in the formation of 5-aminolevulinic acid; functions in porphyrin (tetrapyrroles) biosynthesis; the crystal structure showed a C-terminal dimerization domain that appears to be absent in Chlamydial proteins
YP_202247.1	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_202252.1	catalyzes the hydrolysis of acylphosphate
YP_202254.1	RNase BN; required for 3' maturation of certain phage T4-encoded tRNAs; forms a dimer; specific for immature tRNA substrates containing incorrect residues within the universal CCA sequence; 3' to 5' exoribonuclease; this protein contains a C-terminal extension of unknown function
YP_001001491.1	putative; ORF located using FrameD
YP_202263.1	catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids
YP_202270.1	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates
YP_001001492.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_001001493.1	putative; ORF located using FrameD
YP_202288.1	Maintains the balance of metabolites in the pentose-phosphate pathway
YP_202296.1	this stereospecific enzymes reduces the S isomer of methionine sulfoxide while MsrB reduces the R form; provides protection against oxidative stress
YP_202307.6	catalyzes the reversible transfer of the terminal phosphate of ATP to form a long chain polyphosphate
YP_202311.1	catalyzes the formation of 2,3=diacylglucosamine 1-phosphate from UDP-2,3=diacylglucosamine
YP_202314.1	Catalyzes first step of the de novo purine nucleotide biosynthetic pathway
YP_202323.1	converts threonine and NAD to 1,2-amino-3-oxobutanoate and NADH; functions in threonine catabolism
YP_202330.2	catalyzes the formation of 2-amino-3-oxobutanoate from acetyl-CoA and glycine
YP_202352.1	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_001001494.1	putative; ORF located using FrameD
YP_202367.1	catalyzes the conversion of feruloyl-CoA to vanillin and acetyl-CoA
YP_202369.1	activates fatty acids by binding to coenzyme A
YP_202373.1	extradiol catechol dioxygenase that catalyzes the oxidative cleavage of substituted catechols; part of the bacterial aromatic compound degradation pathway
YP_202379.1	catalyzes the formation of 2-octaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4-benzoquinol from 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinol
YP_202380.1	Oxygenase that introduces the hydroxyl group at carbon four of 2-octaprenyl-6-methoxyphenol resulting in the formation of 2-octaprenyl-6-methoxy-1,4-benzoquinone
YP_202384.1	determines N-hexane tolerance and is involved in outer membrane permeability
YP_202386.1	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_202387.1	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_202388.1	protein associated with Co2+ and Mg2+ efflux
YP_202389.1	hydrolyzes P(1),P(4)-bis(5'-adenosyl) tetraphosphate to form 2 ADP
YP_202391.1	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_202392.1	transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein
YP_202430.1	methionine adenosyltransferase; catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase
YP_202435.1	catalyzes the formation of oxaloacetate from phosphoenolpyruvate
YP_202437.6	catalyzes the formation of L-homocysteine from S-adenosyl-L-homocysteine
YP_202457.2	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_202460.2	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_202461.6	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_202463.1	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_202464.1	Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis
YP_202465.1	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_202467.1	First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
YP_202469.1	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_202473.1	MraZ; UPF0040; crystal structure shows similarity to AbrB
YP_202483.1	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_202484.1	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_202485.1	catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions
YP_202489.1	catalyzes the formation of thiamine diphosphate from thiamine phosphate ant ATP
YP_202490.1	Regulates rRNA biosynthesis by transcriptional antitermination
YP_202491.1	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_202493.6	catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine
YP_202499.1	catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate
YP_202502.1	ChvD; in Agrobacterium tumefaciens, mutations in both Walker boxes were found to affect virulence
YP_202520.1	binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential
YP_001001495.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_202539.6	catalyzes the addition and repair of the essential 3'-terminal CCA sequence in tRNAs without using a nucleic acid template; phosphohydrolase activities include hydrolysis of pyrophosphate, 5'-nucleoside tri- and diphosphates, NADP, and 2'-AMP with the production of Pi, metal-dependent phosphodiesterase activity for 2',3'-cAMP, 2',3'-cGMP, and 2',3'-cCMP, and hydrolysis 2',3'-cyclic substrates with the formation of 2'-nucleotides and 3'-nucleotides; these phosphohydrolase activities are probably involved in the repair of the tRNA 3'-CCA terminus degraded by intracellular RNases
YP_202552.2	predicted polysaccharide polymerase involved in biofilm formation; required for the synthesis of the beta-1,6-N-acetylglucosamine polysaccharide; PgaC; in Yersinia the HmsR protein is an inner membrane protein
YP_202571.1	Involved in pteridine salvage and antifolate resistance
YP_202578.1	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_202587.1	NadM-Nudix subfamily; involved in creation of nicotanimide adenine dinucleotide NAD from either biosynthetic or salvage pathways
YP_003828900.1	recognizing CTGCAG; XorKII
YP_202590.6	similar to methyltransferase M.XphI; recognizing CTGCAG; XorKII
YP_202591.1	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_202592.1	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_202609.1	functions in MreBCD complex in some organisms
YP_202626.1	Catalyzes the carbon methylation reaction in the biosynthesis of ubiquinone
YP_202631.1	heat shock protein involved in degradation of misfolded proteins
YP_202632.6	heat shock protein involved in degradation of misfolded proteins
YP_202633.1	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_202636.2	involved in lysine biosynthesis; DAP epimerase; produces DL-diaminopimelate from LL-diaminopimelate
YP_202646.1	transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis
YP_202650.6	necessary for biosynthesis of osmoregulated periplasmic glucans possibly involved in the transfer to the periplasmic space
YP_202669.6	periplasmic; catalyzes the hydrolysis of trehalose to glucose which can then be imported into the cell
YP_202673.6	involved in the transport across the cytoplasmic membrane of D-alanine, D-serine and glycine
YP_001001497.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_001001498.1	putative; ORF located using FrameD
YP_001001499.1	putative; ORF located using FrameD
YP_001001500.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_202688.1	with component II, the glutamine amidotransferase, catalyzes the formation of anthranilate from chorismate and glutamine
YP_202689.1	cytosolic protein with phosphatidylglycerol kinase activity; undetermined physiological role
YP_202691.6	catalyzes the interconversion of D-ribulose 5-phosphate to xylulose 5-phosphate
YP_202693.1	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_202703.1	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_202704.1	subunit C of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali
YP_202705.1	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_202706.1	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_202707.1	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_202708.1	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_202709.1	An oxygenase that acts to open the ring of homogentisate formingmaleylacetoacetate as part of the catabolism of L-tyrosine and L-phenylalanine
YP_202723.1	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_202727.1	catalyzes the formation of uroporphyrinogen-III from hydroxymethylbilane
YP_202764.1	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_202767.1	synthesizes RNA primers at the replication forks
YP_202771.1	converts protoheme IX and farnesyl diphosphate to heme O
YP_202777.1	involved in the insertion of copper into subunit I of cytochrome C oxidase
YP_202784.1	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_202790.1	hydrolyzes diadenosine polyphosphate
YP_202791.1	forms a direct contact with the tRNA during translation
YP_202792.1	in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit
YP_202796.1	S-adenosylmethionine provides the aminopropyl moiety required for spermidine biosynthesis from putrescine
YP_202797.1	complexes with cyclic AMP and binds to specific DNA sites near the promoter to regulate the transcription of several catabolite-sensitive operons
YP_202799.2	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_202800.1	Catalyzes the conversion of N-(5-phospho-D-ribosyl)-anthranilate and diphosphate to anthranilate and 5-phospho-alpha-D-ribose 1-diphosphate
YP_202802.1	TrpG; with TrpE catalyzes the formation of anthranilate and glutamate from chorismate and glutamine; TrpG provides the glutamine amidotransferase activity
YP_202824.1	catalyzes the NADPH-dependent reduction of 7-cyano-7-deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1) in queuosine biosynthesis
YP_202836.1	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_202837.1	catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate
YP_202839.1	catalyzes the formation of acetate from pyruvate
YP_202848.1	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_202854.6	Catalyzes the specific recognition and activation of amino acids during peptide synthesis
YP_202870.1	catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis
YP_202878.1	catalyzes the conversion of the propionic acid groups of rings I and III to vinyl groups during heme synthesis
YP_202879.1	has 3'-5' exonuclease, 5'-3' exonuclease and 5'-3'polymerase activities, primarily functions to fill gaps during DNA replication and repair
YP_202886.1	forms a homotetramer; requires magnesium for activity; catalyzes the hydrolysis of dGTP to form deoxyguanosine and triphosphate
YP_001001503.1	putative; ORF located using FrameD
YP_202923.6	catalyzes the formation of 3-deoxy-D-arabino-hept-2-ulosonate 7 phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate, phenylalanine sensitive
YP_202927.1	60 kDa chaperone family; promotes refolding of misfolded polypeptides especially under stressful conditions; forms two stacked rings of heptamers to form a barrel-shaped 14mer; ends can be capped by GroES; misfolded proteins enter the barrel where they are refolded when GroES binds; many bacteria have multiple copies of the groEL gene which are active under different environmental conditions; the B.japonicum protein in this cluster is expressed constitutively; in Rhodobacter, Corynebacterium and Rhizobium this protein is essential for growth
YP_202928.2	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_202935.1	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_202936.1	Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine
YP_202940.2	enables ATP-dependent unwinding of double stranded RNA as a component of the RNA degradosome, a multi-enzyme complex important in RNA processing and messenger RNA degradation
YP_202942.6	An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes
YP_202959.6	Involved in the biosynthetic pathways of fatty acids, phospholipids, lipopolysaccharides, and oligosaccharides
YP_202971.2	transports degraded pectin products into the bacterial cell
YP_202972.1	catalyzes the formation of tetrahydropteroyl-L-glutamate and methionine from L-homocysteine and 5-methyltetrahydropteroyltri-L-glutamate
YP_202981.1	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_202986.6	Modulates the activities of several enzymes which are inactive in their acetylated form
YP_203037.1	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_203038.1	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_203043.1	Catalyzes the transfer of the ammonia group from glutamine to a new carbon-nitrogen group
YP_203046.1	mediates the export of protein precursors bearing twin-arginine signal peptides
YP_203047.1	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_203049.1	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_203054.1	Required for efficient pilin antigenic variation
YP_203055.1	TtcA; YdaO; catalyzes the thiolation of cytosine 32 in specific tRNAs
YP_203056.6	catalyzes the interconversion of D-xylose to D-xylulose
YP_203066.2	catalyzes the interconversion of D-glucuronate to D-fructuronate or D-galacturonate to D-tagaturonate; functions in glucuronic and galacturonic metabolism
YP_001001504.1	putative; ORF located using FrameD
YP_001001505.1	putative; ORF located using FrameD
YP_203128.6	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_203144.6	Catalyzes the ferredoxin-dependent oxidative decarboxylation of arylpyruvates
YP_001001506.1	putative; ORF located using FrameD
YP_001001507.1	identified by sequence similarity; putative; ORF located using Blastx/FrameD
YP_203166.2	catalyzes the reduction of 2,5-diketo-D-gluconic acid to 2-keto-L-gulonic acid
YP_001001508.1	putative; ORF located using FrameD
YP_203183.1	Acs; catalyzes the conversion of acetate and CoA to acetyl-CoA
YP_203187.1	member of the sodium:solute symporter family; cotranscribed with the acs gene which encodes acetyl coenzyme A synthase; mutations affect acetate uptake
YP_203195.6	glucose-inhibited division protein B; SAM-dependent methyltransferase; methylates the N7 position of guanosine in position 527 of 16S rRNA
YP_203197.1	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_001001509.1	putative; ORF located using FrameD
YP_203209.1	unwinds DNA duplexes with 3' to 5' polarity with respect to the bound strand and initiates unwinding most effectively when a single-stranded region is present; involved in the post-incision events of nucleotide excision repair and methyl-directed mismatch repair.
YP_203239.1	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_001001510.1	putative; ORF located using FrameD
YP_001001511.1	putative; ORF located using FrameD
YP_001001512.1	putative; ORF located using FrameD
YP_203273.6	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_203275.1	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_203276.1	protein component of RNaseP which catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'terminus; this enzyme also cleaves other RNA substrates