-- dump date   	20120504_163041
-- class       	Genbank::CDS
-- table       	cds_note
-- id	note
YP_001199561.1	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_001199562.1	PCNA homolog
YP_001199563.1	PCNA homolog
YP_001199569.1	Enables the recycling of peptidyl-tRNAs produced at termination of translation
YP_001199572.1	S4 paralog
YP_001199582.1	in some organisms this protein is a transmembrane protein while in others it is periplasmic; involved in some organisms with other components of the MreBCD complex and with penicillin binding proteins in the periplasm or cell wall
YP_001199584.1	catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP
YP_001199585.1	catalyzes the transamination of the aromatic amino acid forming a ketoacid; first step in aromatic amino acid degradation in lactococci
YP_001199586.1	involved in DNA repair and RecFOR pathway recombination; RecFOR proteins displace ssDNA-binding protein and facilitate the production of RecA-coated ssDNA
YP_001199587.1	involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY
YP_001199589.1	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_001199591.1	Catalyzes first step of the de novo purine nucleotide biosynthetic pathway
YP_001199592.1	catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis
YP_001199593.1	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_001199594.1	involved in de novo purine biosynthesis
YP_001199595.1	catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis
YP_001199597.1	With PurE catalyzes the conversion of aminoimidazole ribonucleotide to carboxyaminoimidazole ribonucleotide in the de novo purine nucleotide biosynthetic pathway
YP_001199600.1	Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide
YP_001199609.1	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_001199615.1	FOG: Transposase and inactivated derivative
YP_001199620.1	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_001199621.1	plays an essential role in ATP-dependent branch migration of the Holliday junction
YP_001199624.1	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_001199625.1	the anti-alpha factor Spx interacts with RNA polymerase alpha subunit C-terminal domain in a region that interacts with the sigma 70 subunit and may interfere with activation of promoters; in Bacillus subtilis this protein is a substrate for ClpXP protease; blocks transcription of the competence regulatory gene encoded by the srf operon; regulates a number of genes involved in thiol homeostasis including trxA and trxB; monomeric member of ArsC family of proteins; does not bind DNA; contains a disulfide bond between C10 and C13 which may sense disulfide stress
YP_001199627.1	similar to RuvC resolvase with substantial differences; NMR structural information suggests this protein is monomeric; unknown cellular function
YP_001199630.1	NusE; involved in assembly of the 30S subunit; in the ribosome, this protein is involved in the binding of tRNA; in Escherichia coli this protein was also found to be involved in transcription antitermination; NusB/S10 heterodimers bind boxA sequences in the leader RNA of rrn operons which is required for antitermination; binding of NusB/S10 to boxA nucleates assembly of the antitermination complex
YP_001199633.1	L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA
YP_001199634.1	binds third domain of 23S rRNA and protein L29; part of exit tunnel
YP_001199635.1	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_001199636.2	protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA
YP_001199637.1	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_001199638.1	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_001199639.1	located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e
YP_001199640.1	one of the stabilizing components for the large ribosomal subunit
YP_001199641.1	primary binding protein; helps mediate assembly; involved in translation fidelity
YP_001199642.1	binds to the 23S rRNA between the centers for peptidyl transferase and GTPase
YP_001199643.1	assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel
YP_001199644.1	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_001199645.1	binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit
YP_001199646.1	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_001199647.1	binds 5S rRNA along with protein L5 and L25
YP_001199648.1	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_001199649.1	L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7
YP_001199653.1	essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP
YP_001199654.1	stimulates the activities of the other two initiation factors, IF-2 and IF-3
YP_001199655.1	located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA; makes contact with the large subunit via RNA-protein interactions and via protein-protein interactions with L5; contacts P-site tRNA
YP_001199656.1	located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA; forms part of the Shine-Dalgarno cleft in the 70S ribosome; interacts with S7 and S18 and IF-3
YP_001199657.1	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_001199658.1	is a component of the macrolide binding site in the peptidyl transferase center
YP_001199680.1	catalyzes the formation of tyrosyl-tRNA(Tyr) from tyrosine and tRNA(Tyr)
YP_001199682.1	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_001199683.1	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_001199685.1	homolog of microcin C7 resistance protein MccF
YP_001199686.1	homolog of microcin C7 resistance protein MccF
YP_001199707.1	binds to single stranded DNA and may facilitate the binding and interaction of other proteins to DNA
YP_001199713.1	interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone; located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side; mutations in the S12 gene confer streptomycin resistance
YP_001199714.1	binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit
YP_001199715.1	EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene
YP_001199720.1	Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway
YP_001199727.1	Inactive homolog of metal-dependent proteases
YP_001199729.1	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_001199756.1	catalyzes the removal of N-terminal dipeptides when proline is the penultimate residue
YP_001199760.1	involved in translesion DNA polymerization with beta clamp of polymerase III; belongs to Y family of polymerases; does not contain proofreading function
YP_001199782.1	An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids
YP_001199784.1	FOG: LysM repeat
YP_001199796.1	FOG: TPR repeat
YP_001199806.1	converts 2-oxoglutarate to glutamate; in Escherichia coli this enzyme plays a role in glutamate synthesis when the cell is under energy restriction; uses NADPH; forms a homohexamer
YP_001199807.1	catalyzes the conversion of dihydroorotate to orotate in the pyrimidine biosynthesis pathway; subclass 1A is a dimer formed by two identical PyrD subunits each containing an FMN group
YP_001199829.1	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_001199830.1	some L32 proteins have zinc finger motifs consisting of CXXC while others do not
YP_001199831.1	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_001199832.1	similar to zinc-dependent eukaryotic ADH enzymes and distinct from fermentative ADHs
YP_001199846.1	catalyzes the isomerization of isopentenyl pyrophosphate to dimethylallyl diphosphate
YP_001199852.1	Negative regulator of class I heat shock genes (grpE-dnaK-dnaJ and groELS operons). Prevents heat-shock induction of these operons
YP_001199853.1	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_001199854.1	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_001199856.1	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_001199858.1	catalyzes the hydrolysis of a monocarboxylic acid amid to form a monocarboxylate and ammonia
YP_001199865.1	mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability
YP_001199866.1	catalyzes the formation of 4-amino-2-methyl-5-diphosphomethylpyrimidine
YP_001199882.1	Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer
YP_001199886.1	participates in both the initiation and recycling phases of transcription; in the presence of the delta subunit, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling
YP_001199887.2	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_001199888.1	catalyzes the formation of glycerone phosphate and glyceraldehyde 3-phosphate from fructose 1,6, bisphosphate
YP_001199889.1	required for 70S ribosome assembly
YP_001199899.1	CodY; DNA-binding protein that represses the expression of many genes that are induced as cells make the transition from rapid exponential growth to stationary phase (By similarity). It is a GTP-binding protein that senses the intracellular GTP concentration as an indicator of nutritional limitations. At low GTP concentration it no longer binds GTP and stop to act as a transcriptional repressor
YP_001199901.1	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_001199903.1	allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA; some Mycoplasma proteins contain an N-terminal fusion to an unknown domain
YP_001199904.1	allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA
YP_001199905.1	PET112 homolog; allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA
YP_001199909.1	catalyzes the formation of alpha-D-galactose 1-phosphate from D-galactose in galactose metabolism
YP_001199910.1	catalyzes the formation of alpha-D-glucose 1-phosphate and UDP-galactose from UDP-glucose and alpha-D-galactose 1-phosphate in galactose metabolism
YP_001199916.1	in Bacillus subtilis this enzyme appears to be involved in 30S ribosomal RNA subunit biogenesis
YP_001199918.1	transfers an adenyl group from ATP to NaMN to form nicotinic acid adenine dinucleotide (NaAD) which is then converted to the ubiquitous compound NAD by NAD synthetase; essential enzyme in bacteria
YP_001199937.1	amylomaltase; acts to release glucose from maltodextrins
YP_001199956.1	glucose-inhibited division protein B; SAM-dependent methyltransferase; methylates the N7 position of guanosine in position 527 of 16S rRNA
YP_001199959.1	functions in homologous recombination, DNA repair, and chromosome segregation; binds preferentially to three- and four-stranded DNA intermediates; introduces specific nick sites in four-stranded DNA substrates; functions similarly to Escherichia coli RuvC
YP_001199961.1	GpsB; guiding PBP1 shuttling; similar to DivIVA
YP_001199965.1	catalyzes the hydrolysis of S-ribosylhomocysteine to homocysteine and autoinducer-2
YP_001199967.1	Essential for recycling GMP and indirectly, cGMP
YP_001199968.1	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_001199969.1	binding of PriA to forked DNA starts the assembly of the primosome, also possesses 3'-5' helicase activity
YP_001199970.1	modifies the free amino group of the aminoacyl moiety of methionyl-tRNA(fMet) which is important in translation initiation; inactivation of this gene in Escherichia coli severely impairs growth
YP_001199989.1	binds RecA and inhibits RecA-mediated DNA strand exchange and ATP hydrolysis and coprotease activities
YP_001200005.1	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_001200014.1	catalyzes the formation of asparagine from aspartate and ammonia
YP_001200027.1	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_001200028.1	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_001200033.1	GTPase; similar structure to tubulin; forms ring-shaped polymers at the site of cell division; other proteins such as FtsA, ZipA, and ZapA, interact with and regulate FtsZ function
YP_001200041.1	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_001200048.1	catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate
YP_001200062.1	catalyzes the reduction of 2 glutathione to glutathione disulfide; maintains high levels of reduced glutathione in the cytosol; involved in redox regulation and oxidative defense
YP_001200069.1	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_001200079.1	catalyzes the formation of oxaloacetate from phosphoenolpyruvate
YP_001200080.1	sigma24 homolog
YP_001200082.1	Streptococcus oralis sp|P33170|EFTU_STROR Elongation factor Tu (EF-Tu); 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_001200083.1	Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate
YP_001200101.1	catalyzes the formation of phosphoenolpyruvate from pyruvate
YP_001200108.1	Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source
YP_001200116.1	catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis
YP_001200117.1	Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway
YP_001200121.1	contains a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs
YP_001200158.1	catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis
YP_001200159.1	catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis
YP_001200160.1	catalyzes the formation of phenylpyruvate from prephenate in phenylalanine biosynthesis
YP_001200171.1	catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate
YP_001200172.1	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_001200181.1	catalyzes the degradation of arginine to citruline and ammonia
YP_001200183.1	catalyzes the formation of ornithine and carbamylphosphate from citrulline in the arginine catabolic pathway
YP_001200184.1	catalyzes the reversible synthesis of carbamate and ATP from carbamoyl phosphate and ADP
YP_001200196.1	transfers D-alanine to the D-alanyl carrier protein during the incorporation of D-alanine into lipoteichoic acid
YP_001200198.1	D-alanyl carrier protein subunit; involved in the incorporation of D-alanine into membrane-associated D-alanyl-lipoteichoic acid; D-alanyl carrier protein is the acceptor of activated D-alanine which it donates to a membrane acceptor(D-alanyl transferase) for incorporation into membrane lipoteichoic acid
YP_001200210.1	involved in cell wall formation; peptidoglycan synthesis; cytoplasmic enzyme; catalyzes the addition of lysine to UDP-N-acetylmuramoyl-L-alanyl-D-glutamate forming UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysine
YP_001200220.1	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_001200221.1	in Bacillus subtilis this protein is involved in the negative regulation of DNA replication initiation; interacts with DnaN and DnaA
YP_001200223.1	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_001200247.1	decarboxylates 4-phosphopantothenoylcysteine to form 4'-phosphopantotheine.
YP_001200249.1	catalyzes the formation of 10-formyltetrahydrofolate from formate and tetrahydrofolate
YP_001200251.1	Involved in disulfide oxidoreductase activity and electron transport
YP_001200272.1	similar to transaldolase from Escherichia coli; many organisms have multiple copies
YP_001200274.1	forms dimers and octamers; involved in conversion of glycerol to dihydroxy-acetone
YP_001200275.1	catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde
YP_001200276.1	catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis
YP_001200279.1	Converts glycerol and ADP to glycerol-3-phosphate and ADP
YP_001200289.1	similar to GA13732-PA
YP_001200290.1	catalyzes the formation of 4-amino-2-methyl-5-diphosphomethylpyrimidine
YP_001200291.1	catalyzes the formation of 4-methyl-5-(2-phosphoethyl)-thiazole and ADP from 4-methyl-5-(2-hydroxyethyl)-thiazole and ATP
YP_001200293.1	Condenses 4-methyl-5-(beta-hydroxyethyl)-thiazole monophosphate and 4-amino-5-hydroxymethyl pyrimidine pyrophosphate to form thiamine monophosphate
YP_001200310.1	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_001200311.1	essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication
YP_001200317.1	involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsX
YP_001200325.1	decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling
YP_001200327.1	catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids
YP_001200329.1	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_001200334.1	Required for the synthesis of the thiazole moiety
YP_001200339.1	involved in the peptidyltransferase reaction during translation
YP_001200348.1	regulates pyrimidine biosynthesis by binding to the mRNA of the pyr genes, also has been shown to have uracil phosphoribosyltransferase activity
YP_001200349.1	catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis
YP_001200350.1	catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers
YP_001200351.1	split gene in MJ; 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_001200353.1	catalyzes the removal of 5-oxoproline from various penultimate amino acid residues except L-proline
YP_001200360.2	catalyzes the formation of L-aspartate 4-semialdehyde from L-homoserine
YP_001200361.1	catalyzes the formation of O-phospho-L-homoserine from L-homoserine in threonine biosynthesis from asparate
YP_001200362.1	catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis
YP_001200378.1	methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA
YP_001200386.1	catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis
YP_001200387.1	catalyzes the addition and repair of the 3'-terminal CCA sequence in tRNA; these proteins belong to the CCA-adding enzyme subfamily 2 which does not have phosphohydrolase activity
YP_001200392.1	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_001200395.1	binds and unfolds substrates as part of the ClpXP protease
YP_001200396.1	binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential
YP_001200397.1	catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate
YP_001200399.1	binds to the ribosome on the universally-conserved alpha-sarcin loop
YP_001200400.1	4-oxalocrotonate tautomerase homolog; 4-OT; member of subfamily 5; forms a dimer; the function in the Escherichia coli cell is unknown
YP_001200404.1	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_001200408.1	catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate
YP_001200420.1	McrC protein together with McrB forms the McrBC restriction system; recognizes N4- and C5-methylcytosine (and 5-hydroxy-methylcytosines); appears to act against 5-methylcytosine preceded by a purine residue; MrcC modulates the specificty of McrB and has DNA cleavage activity
YP_001200434.1	contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway
YP_001200443.1	site-specific tyrosine recombinase which cuts and rejoins DNA molecules; binds cooperatively to specific DNA consensus sites; essential to convert chromosome dimers to monomers during cell division and functions during plasmid segregation; cell division protein FtsK may regulate the XerS
YP_001200453.1	ScnG homolog
YP_001200458.1	split gene in MJ
YP_001200464.1	TrmFO; Gid; glucose-inhibited division protein; similar to GidA; the gene from Bacillus subtilis encodes a tRNA-methyltransferase that utilizes folate as the carbon donor and bound flavin as reductant; modifies tRNA at position 54 (uridine) of the T-psi loop to form a C5-methyluridine
YP_001200555.1	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_001200565.1	hemolysin III homolog
YP_001200567.1	RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids
YP_001200568.1	essential GTPase; functions in ribosome assembly; binds a unique part of the 23S rRNA; interacts with ribosomal protein L25(Ctc)
YP_001200573.1	catalyzes the formation of N-carbamoyl-L-aspartate from (S)-dihydroorotate in pyrimidine biosynthesis
YP_001200574.1	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_001200576.1	involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate
YP_001200578.1	type 1 subfamily; involved in last step of pyrimidine biosynthesis; converts orotidine 5'-phosphate to UMP and carbon dioxide; OMP decarboxylase; OMPDCase; OMPdecase
YP_001200579.1	catalyzes the conversion of dihydroorotate to orotate in the pyrimidine biosynthesis pathway, using a flavin nucleotide as an essential cofactor; subclass 1B is a heterotetramer consisting of two PyrDB subunits, similar to the PyrDA subunits and two PyrK subunits
YP_001200580.1	responsible for channeling the electrons from the oxidation of dihydroorotate from the FMN redox center in the pyrD subunit to the ultimate electron acceptor NAD(+)
YP_001200596.1	The UvrABC repair system catalyzes the recognition and processing of DNA lesions. The beta-hairpin of the Uvr-B subunit is inserted between the strands, where it probes for the presence of a lesion
YP_001200606.2	catalyzes the formation of 6-phospho-galactose from a 6-phospho-beta-galactoside
YP_001200615.1	catalyzes the interconversion of galactose 6-phosphate to tagatose 6-phosphate
YP_001200630.1	in Salmonella this enzyme is required for ethanolamine catabolism; has higher affinity for CoA than Pta
YP_001200632.1	catalyzes the phosphorylation of NAD to NADP
YP_001200640.1	modulates transcription in response to the NADH/NAD(+) redox state
YP_001200642.1	Involved in DNA double-strand break repair and recombination. Promotes the annealing of complementary single-stranded DNA and by simulation of RAD51 recombinase
YP_001200644.1	negatively supercoils closed circular double-stranded DNA
YP_001200645.1	Converts (S)-lactate and NAD(+) to pyruvate and NADH
YP_001200653.1	Reclaims exogenous and endogenous cytidine and 2'-deoxycytidine molecules for UMP synthesis
YP_001200654.1	catalyzes the formation of D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-D-ribose-5-phosphate
YP_001200655.1	Catalyzes the reversible phosphorolysis of pyrimidines in the nucleotide synthesis salvage pathway
YP_001200657.1	catalyzes the formation of (R)-4'-phosphopantothenate in coenzyme A biosynthesis
YP_001200658.1	binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase
YP_001200668.1	ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation
YP_001200669.1	ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation
YP_001200679.1	the anti-alpha factor Spx interacts with RNA polymerase alpha subunit C-terminal domain in a region that interacts with the sigma 70 subunit and may interfere with activation of promoters; in Bacillus subtilis this protein is a substrate for ClpXP protease; blocks transcription of the competence regulatory gene encoded by the srf operon; regulates a number of genes involved in thiol homeostasis including trxA and trxB; monomeric member of ArsC family of proteins; does not bind DNA; contains a disulfide bond between C10 and C13 which may sense disulfide stress
YP_001200681.1	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_001200698.1	catalyzes the release of the N-terminal amino acid from a tripeptide
YP_001200699.1	hemolysin III homolog
YP_001200718.1	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_001200724.1	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_001200726.2	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_001200730.1	Converts D-mannonate to D-mannuronate
YP_001200731.1	catalyzes the formation of 2-dehydro-3-deoxy-D-gluconate from mannonate
YP_001200732.1	catalyzes the interconversion of D-glucuronate to D-fructuronate or D-galacturonate to D-tagaturonate; functions in glucuronic and galacturonic metabolism
YP_001200744.1	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_001200745.1	mitochondrial delta subunit; 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_001200746.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit
YP_001200747.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit
YP_001200748.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit
YP_001200749.1	mitochondrial oligomycin sensitivity protein; 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_001200753.1	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_001200754.1	similar to YegS from E. coli
YP_001200755.1	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_001200759.1	catalyzes the formation of D-glucono-1,5-lactone 6-phosphate from D-glucose 6-phosphate
YP_001200775.1	catalyzes the formation of citrate from acetyl-CoA and oxaloacetate
YP_001200777.1	Catalyzes the conversion of citrate to isocitrate
YP_001200780.1	Catalyzes the rate-limiting step in dNTP synthesis
YP_001200782.1	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_001200795.1	catalyzes the formation of pyruvate and glyoxylate from 4-hydroxy-2-oxoglutarate; or pyruvate and D-glyceraldehyde 3-phosphate from 2-dehydro-3-deoxy-D-glyconate 6-phosphate
YP_001200798.1	Involved in the nonphosphorylative, ketogenic oxidation of glucose and oxidizes gluconate to 5-ketogluconate
YP_001200810.1	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_001200819.1	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_001200822.1	catalyzes the formation of 3-deoxy-D-arabino-hept-2-ulosonate 7 phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate, tyrosine sensitive
YP_001200823.1	catalyzes the formation of 3-deoxy-D-arabino-hept-2-ulosonate 7 phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate, phenylalanine sensitive
YP_001200824.1	AroE; catalyzes the conversion of shikimate to 3-dehydroshikimate
YP_001200825.1	catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis
YP_001200831.1	catalyzes the reversible reaction of dihydroxyacetone phosphate with glyceraldehyde 3-phosphate to produce tagatose 1,6-bisphosphate; in Streptococcus pyogenes there are two paralogs of tagatose-bisphosphate aldolase, encoded by lacD1 and lacD2; expression of lacD1 is highly regulated by environmental conditions while lacD2 specializes in an efficient utilization of carbohydrate sources
YP_001200834.1	catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate
YP_001200835.1	catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis
YP_001200836.1	catalyzes the dehydration of 3-dehydroquinate to form 3-dehydroshikimate in aromatic amino acid biosynthesis
YP_001200840.1	binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit
YP_001200842.1	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_001200843.1	Catalyzes the formation of (d)CDP from ATP and (d)CMP
YP_001200880.1	catalyzes the formation of O-succinyl-L-homoserine from succinyl-CoA and L-homoserine in methionine biosynthesis
YP_001200881.1	catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis
YP_001200888.1	member of metallo-beta-lactamase family; the purified enzyme from Escherichia coli forms dimeric zinc phosphodiesterase; in Bacillus subtilis this protein is a 3'-tRNA processing endoribonuclease and is essential while in Escherichia coli it is not; associates with two zinc ions
YP_001200891.1	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_001200898.1	ketopantoate reductase; catalyzes the NADPH reduction of ketopantoate to pantoate; functions in pantothenate (vitamin B5) biosynthesis
YP_001200900.1	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_001200901.1	Catalyzes the phosphorylation of UMP to UDP
YP_001200905.1	in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA
YP_001200906.1	binds directly to 23S ribosomal RNA
YP_001200920.1	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_001200939.1	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_001200947.1	Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr)
YP_001200951.1	has 3'-5' exonuclease, 5'-3' exonuclease and 5'-3'polymerase activities, primarily functions to fill gaps during DNA replication and repair
YP_001200957.1	antioxidant activity; thioredoxin-dependent thiol peroxidase; forms homodimers in solution; shows substrate specificity to alkyl hydroperoxides; periplasmic protein
YP_001200960.1	with TehA confers resistance to tellurite
YP_001200962.1	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_001200967.1	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_001200968.1	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_001200983.1	recognizes the termination signals UGA and UAA during protein translation a specificity which is dependent on amino acid residues residing in loops of the L-shaped tRNA-like molecule of RF2; in some organisms control of PrfB protein levels is maintained through a +1 ribosomal frameshifting mechanism; this protein is similar to release factor 1
YP_001200999.1	sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; primary sigma factor of bacterium
YP_001201000.1	synthesizes RNA primers at the replication forks
YP_001201008.1	catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III
YP_001201011.1	catalyzes the reversible phosphorolysis of ribonucleosides and 2'- deoxyribonucleosides to the free base and (2'-deoxy)ribose-1- phosphate
YP_001201012.1	catalyzes the formation of a purine and ribose phosphate from a purine nucleoside; in E. coli this enzyme functions in xanthosine degradation
YP_001201016.1	Catalyzes D-ribose 5-phosphate --> D-ribulose 5-phosphate in the nonoxidative branch of the pentose phosphate pathway
YP_001201025.1	in Escherichia coli this protein is involved in the biosynthesis of the hypermodified nucleoside 5-methylaminomethyl-2-thiouridine, which is found in the wobble position of some tRNAs and affects ribosomal frameshifting; shows potassium-dependent dimerization and GTP hydrolysis; also involved in regulation of glutamate-dependent acid resistance and activation of gadE
YP_001201032.1	divalent metal ion-dependent extracellular dipeptidase; able to hydrolyze a broad range of dipeptides but no tri-, tetra-, or larger oligopeptides; differences in the amino acid specificity of the cleavage site varies between species; similar to succinyl-diaminopimelate desuccinylases
YP_001201033.1	involved in the import of serine and threonine coupled with the import of sodium
YP_001201039.1	catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate
YP_001201063.1	FOG: TPR repeat
YP_001201070.1	enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis
YP_001201077.1	acts to negatively regulates ftsZ ring formation by modulating the frequency and position of the ftsZ ring formation
YP_001201100.2	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_001201109.1	required for the assembly and function of the DNAX complex which is required for the assembly of the beta subunit onto primed DNA
YP_001201118.1	hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates
YP_001201119.1	Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate
YP_001201129.1	catalyzes the formation of cystathionine from L-cysteine and O-succinyl-L-homoserine
YP_001201149.1	enables the cleavage of the glycosidic bond in both 5'-methylthioadenosine and S-adenosylhomocysteine
YP_001201152.1	forms a homotrimer; catalyzes the acetylation of glucosamine-1-phosphate and uridylation of N-acetylglucosamine-1-phosphate to produce UDP-GlcNAc; function in cell wall synthesis
YP_001201155.1	Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis
YP_001201166.1	associated with arginine deiminase pathway genes; probably functions in arginine catabolism
YP_001201173.1	transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein
YP_001201174.1	catalyzes the phosphorylation of the phosphocarrier protein HPr of the bacterial phosphotransferase system
YP_001201186.1	catalyzes the removal of N-terminal amino acids from peptides and arylamides
YP_001201188.1	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_001201190.1	catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase
YP_001201194.1	catalyzes the formation of biotinyl-5'-AMP, also acts as a transcriptional repressor of the biotin operon
YP_001201196.1	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_001201208.1	2,3-bisphosphoglycerate-dependent; catalyzes the interconversion of 2-phosphoglycerate to 3-phosphoglycerate
YP_001201223.1	catalyzes the bidirectional exonucleolytic cleavage of DNA
YP_001201224.1	bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides
YP_001201234.1	catalyzes the hydrolysis of pyrophosphate to phosphate
YP_001201241.1	catalyzes the formation of 5-phospho-alpha-D-ribose 1-diphosphate and nicotinate from nicotinate D-ribonucleotide and diphosphate
YP_001201242.1	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_001201244.1	23S rRNA m2A2503 methyltransferase; methylates the C2 position of the A2530 nucleotide in 23S rRNA; may be involved in antibiotic resistance
YP_001201247.1	Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA
YP_001201258.1	similar to MF3 gene in Streptococcus pyogenes MGAS10394
YP_001201270.1	functions during chromosome segregation; may form a condensin-like structure with SMC and ScpA; forms a homodimer
YP_001201271.1	functions during chromosome segregation; may form a condensin-like structure with SMC and ScpB
YP_001201272.1	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_001201273.1	FOG: CBS domain
YP_001201275.1	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_001201276.1	converts L-glutamate to D-glutamate, a component of peptidoglycan
YP_001201284.1	catalyzes the hydrolysis of acylphosphate
YP_001201287.1	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_001201290.1	Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis
YP_001201296.1	EngA; essential Neisserial GTPase; synchronizes cellular events by interacting with multiple targets with tandem G-domains; overexpression in Escherichia coli suppresses rrmJ mutation; structural analysis of the Thermotoga maritima ortholog shows different nucleotide binding affinities in the two binding domains
YP_001201298.1	Primosomal protein that may act to load helicase DnaC during DNA replication
YP_001201303.1	catalyzes the formation of D-ribulose 5-phosphate from 6-phospho-D-gluconate
YP_001201310.1	First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
YP_001201333.1	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_001201334.1	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_001201342.1	catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine to form methionine
YP_001201359.1	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; these proteins present a shorter N-terminus
YP_001201360.1	catalyzes the carboxylation of acetyl-CoA to malonyl-CoA; forms a tetramer of AccA2D2 subunits
YP_001201361.1	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_001201362.1	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_001201363.1	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_001201364.1	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_001201365.1	catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis
YP_001201368.1	carries the fatty acid chain in fatty acid biosynthesis
YP_001201369.1	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_001201371.1	Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA
YP_001201373.1	catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP; lysine and threonine sensitive
YP_001201374.1	converts L-alanine to D-alanine which is used in cell wall biosynthesis; binds one pyridoxal phosphate per monomer; forms a homodimer
YP_001201375.1	Catalyzes the formation of holo-ACP, which mediates the essential transfer of acyl fatty acid intermediates during the biosynthesis of fatty acids and lipids
YP_001201376.1	functions in protein export; can interact with acidic membrane phospholipids and the SecYEG protein complex; binds to preproteins; binds to ATP and undergoes a conformational change to promote membrane insertion of SecA/bound preprotein; ATP hydrolysis appears to drive release of the preprotein from SecA and deinsertion of SecA from the membrane; additional proteins SecD/F/YajC aid SecA recycling; exists in an equilibrium between monomers and dimers; may possibly form higher order oligomers; proteins in this cluster correspond SecA1; SecA2 is not essential and seems to play a role in secretion of a subset of proteins
YP_001201382.1	Regulates rRNA biosynthesis by transcriptional antitermination
YP_001201384.1	translation initiation factor 5A (eIF-5A)
YP_001201386.1	The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrA is an ATPase and a DNA-binding protein. A damage recognition complex composed of 2 uvrA and 2 uvrB subunits scans DNA for abnormalities. When the presence of a lesion has been verified by uvrB, the uvrA molecules dissociate
YP_001201389.1	binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit
YP_001201390.1	binds to single stranded DNA and may facilitate the binding and interaction of other proteins to DNA
YP_001201391.1	binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21
YP_001201405.1	associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock
YP_001201406.1	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_001201409.1	modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination
YP_001201411.1	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_001201440.1	enables recognition and targeting of proteins for proteolysis, involved in negative regulation of competence
YP_001201441.1	BacA; phosphatase activity in Escherichia coli not kinase; involved in bacitracin resistance as bacitracin supposedly sequesters undecaprenyl disphosphate which reduces the pool of lipid carrier available to the cell
YP_001201445.1	stomatin/prohibitin homolog
YP_001201446.1	catalyzes the formation of 2-oxobutanoate from L-threonine; biosynthetic
YP_001201447.1	catalyzes the formation of (R)-2,3-dihydroxy-3-methylbutanoate from (S)-2-hydroxy-2-methyl-3-oxobutanoate in valine and isoleucine biosynthesis
YP_001201448.1	with IlvI catalyzes the formation of 2-acetolactate from pyruvate, the small subunit is required for full activity and valine sensitivity; E.coli produces 3 isoenzymes of acetolactate synthase which differ in specificity to substrates, valine sensitivity and affinity for cofactors; also known as acetolactate synthase 3 small subunit
YP_001201449.1	catalyzes the formation of 2-acetolactate from pyruvate; also known as acetolactate synthase large subunit
YP_001201452.1	catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis
YP_001201457.1	forms a direct contact with the tRNA during translation
YP_001201458.1	in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit
YP_001201487.1	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_001201507.1	cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+)
YP_001201509.1	catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis; forms a heterodimer of LeuC/D
YP_001201511.1	catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis
YP_001201512.1	catalyzes the formation of 2-isopropylmalate from acetyl-CoA and 2-oxoisovalerate in leucine biosynthesis
YP_001201517.1	catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; required for leading strand synthesis; PolC exhibits 3' to 5' exonuclease activity
YP_001201518.1	similar to DhaK; in Lactococcus lactis this protein froms a stable complex with DhaS and activates transcription of the dha operon in the presence of dihydroxyacetone
YP_001201520.1	with DhaL and DhaM forms dihydroxyacetone kinase, which is responsible for phosphorylating dihydroxyacetone; DhaK is the dihydroxyacetone binding subunit of the dihydroxyacetone kinase
YP_001201524.1	catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro)
YP_001201527.1	catalyzes the formation of undecaprenyl pyrophosphate from isopentenyl pyrophosphate
YP_001201530.1	Synthesizes glutathione from L-glutamate and L-cysteine via gamma-L-glutamyl-L-cysteine
YP_001201532.1	becomes active under oxidative stress; four conserved cysteines bind a zinc atom when they are in the reduced state and the enzyme is inactive; oxidative stress results in oxidized cysteines, release of zinc, and binding of Hsp33 to aggregation-prone proteins; forms dimers and higher order oligomers
YP_001201541.1	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_001201542.1	one of the last subunits in the assembly of the 30S subunit; absence of S2 does not inhibit assembly but results in an inactive subunit
YP_001201545.1	Modulates Rho-dependent transcription termination
YP_001201546.1	forms a complex with SecY and SecG; SecYEG forms a protein-conducting channel to which secA binds and translocates targeted polypeptides across the cytoplasmic membrane, a process driven by ATP and a proton-motive force
YP_001201557.1	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_001201563.1	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_001201572.1	in Escherichia coli transcription of this gene is enhanced by polyamines
YP_001201575.1	protein component of RNaseP which catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'terminus; this enzyme also cleaves other RNA substrates
YP_001201576.1	catalyzes the formation of arginine from (N-L-arginino)succinate
YP_001201577.1	catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming
YP_001201583.1	converts homocysteine and S-adenosyl-methionine to methionine and S-adenosyl-homocysteine or S-methyl-methionine and homocysteine to two methionines
YP_001201585.1	Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation
YP_001201592.1	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_001201594.1	catalyzes the formation of dUMP from dUTP
YP_001201598.1	catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate
YP_001201600.1	homolog of Drosophila rhomboid
YP_001201603.1	Similar to several hippurate hydrolases and amino acid amidohydrolases; can be a peptidase too
YP_001201609.1	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_001201613.1	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_001201619.1	catalyzes the formation of D-xylulose 5-phosphate from L-ribulose 5-phosphate in the L-arabinose and L-ascorbate degradation pathways
YP_001201620.1	L-xylulose 5-phosphate 3-epimerase activity not yet demonstrated; may be involved in the utilization of 2,3-diketo-L-gulonate
YP_001201621.1	catalyzes the formation of L-xylulose-5-phosphate from 3-keto-L-gulonate-6-phosphate in anaerobic L-ascorbate utilization
YP_001201624.1	membrane component; functions with enzymes IIB (sgaB; ulaB) and IIA (sgaA; ulaC) enzyme I and HPr for anaerobic utilization and uptake of L-ascorbate; sgaTBA are regulated by yifQ as well as Crp and Fnr
YP_001201642.1	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_001201646.1	unknown pir||T45470
YP_001201654.1	hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr); possible defense mechanism against a harmful effect of D-tyrosine
YP_001201656.1	in Escherichia coli this is a periplasmic enzyme while in gram positive organisms it may be anchored at the cell surface; functions during ribonucleic acid degradation; 2',3'-cyclic nucleotides are first converted to 3'-nucleotide and then cleaved to yield a ribonucleotide and a phosphate
YP_001201669.1	similar to CG18331-PA
YP_001201671.1	in Escherichia coli RsmE methylates the N3 position of the U1498 base in 16S rRNA; cells lacking this function can grow, but are outcompeted by wild-type; SAM-dependent m(3)U1498 methyltransferase
YP_001201672.1	methylates ribosomal protein L11 at multiple amino acid positions; mutations of these genes in Escherichia coli or Thermus thermophilus has no apparent phenotype
YP_001201682.1	Catalyzes the reduction of nucleoside 5'-triphosphates to 2'-deoxynucleoside 5'-triphosphates
YP_001201683.1	FOG: Transposase and inactivated derivative
YP_001201686.1	This protein performs the mismatch recognition step during the DNA repair process
YP_001201688.1	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_001201692.1	amylomaltase; acts to release glucose from maltodextrins
YP_001201701.1	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_001201707.1	Butyrivibrio fibrisolvens sp|P16084|BGLS_BUTFI Beta-glucosidase A (Gentiobiase) (Cellobiase) (Beta-D-glucoside glucohydrolase) gb|AAA23008.1| beta-glucosidase
YP_001201712.1	Reduces fumarate to succinate in anaerobic bacterial respiration
YP_001201714.1	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_001201716.1	unwinds double stranded DNA
YP_001201717.1	in Escherichia coli this protein is wrapped around the base of the L1 stalk
YP_001201719.1	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_001201726.1	catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs
YP_001201729.1	FOG: LysM repeat
YP_001201731.1	with CbiNQ forms the ABC transporter for cobalt import; Streptococcus has two adjacent copies of this gene
YP_001201732.1	with CbiNQ forms the ABC transporter for cobalt import; Streptococcus has two adjacent copies of this gene
YP_001201738.1	Required for DNA replication; binds preferentially to single-stranded, linear DNA
YP_001201739.1	catalyzes the synthesis of xanthosine monophosphate by the NAD+ dependent oxidation of inosine monophosphate
YP_001201740.1	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