-- dump date   	20120504_143152
-- class       	Genbank::CDS
-- table       	cds_note
-- id	note
YP_002784551.2	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_002784553.1	enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis
YP_002784555.1	catalyzes the formation of tyrosyl-tRNA(Tyr) from tyrosine and tRNA(Tyr)
YP_002784559.1	in Escherichia coli this protein is wrapped around the base of the L1 stalk
YP_002784560.1	binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit
YP_002784562.1	binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21
YP_002784578.2	An essential enzyme in the nonmevalonate pathway of isopentenyl diphosphate and dimethylallyl diphosphate biosynthesis
YP_002784591.1	functions in pyrimidine salvage; pyrimidine ribonucleoside kinase; phosphorylates nucleosides or dinucleosides to make UMP or CMP using ATP or GTP as the donor
YP_002784624.1	four CarB-CarA dimers form the carbamoyl phosphate synthetase holoenzyme that catalyzes the production of carbamoyl phosphate; CarB is responsible for the amidotransferase activity
YP_002784626.1	catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming
YP_002784630.1	catalyzes the formation of arginine from (N-L-arginino)succinate
YP_002784633.1	catalyzes the formation of N-acetyl-L-glutamate from acetyl-CoA and L-glutamate
YP_002784635.1	catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers
YP_002784637.1	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_002784642.1	Enables the recycling of peptidyl-tRNAs produced at termination of translation
YP_002784653.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the A subunit is part of the catalytic core of the ATP synthase complex
YP_002784654.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the B subunit is part of the catalytic core of the ATP synthase complex
YP_002784669.1	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_002784675.1	primary rRNA binding protein; helps nucleate assembly of 30S; binds directly to the 16S rRNA and an intersubunit bridge to the 23S rRNA; autoregulates translation through interactions with the mRNA leader sequence
YP_002784684.1	catalyzes the formation of O-phospho-L-homoserine from L-homoserine in threonine biosynthesis from asparate
YP_002784688.1	lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis
YP_002784689.1	catalyzes the hydrolysis of S-ribosylhomocysteine to homocysteine and autoinducer-2
YP_002784693.1	some L32 proteins have zinc finger motifs consisting of CXXC while others do not
YP_002784714.1	transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis
YP_002784733.1	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_002784747.1	catalyzes the formation of pyridoxal 5'-phosphate from pyridoxal
YP_002784760.1	catalyzes the formation of undecaprenyl pyrophosphate from isopentenyl pyrophosphate
YP_002784786.1	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_002784788.1	catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine
YP_002784821.1	promotes RNA polymerase assembly or stability; latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits
YP_002784832.1	catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis
YP_002784833.1	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_002784847.1	orfB of ISDds1 - IS3 family member
YP_002784848.1	orfA of ISDds1 - IS3 family member
YP_002784886.1	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_002784890.1	E1 component; part of pyruvate dehydrogenase; forms a complex with DlaT and LpdC
YP_002784906.1	Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA
YP_002784907.1	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_002784916.1	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_002784952.1	catalyzes the transfer of phosphate between the C1 and C5 carbons of pentose
YP_002784965.1	in Escherichia coli transcription of this gene is enhanced by polyamines
YP_002784983.1	Catalyzes the transfer of the phosphoribosyl moiety from 5-phospho--D-ribosyl-1-pyrophosphate (PRib-PP) to the 6-oxo-guanine and -xanthine
YP_002784985.1	this stereospecific enzymes reduces the R isomer of methionine sulfoxide while MsrA reduces the S form; provides protection against oxidative stress
YP_002784994.1	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_002785016.1	threonine deaminase; threonine dehydratase; in Escherichia coli, IlvA is part of the isoleucine biosynthetic pathway
YP_002785024.1	catalyzes the formation of agmatine from arginine in putrescine and spermidine biosynthesis
YP_002785029.1	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_002785034.1	required for the synthesis of the hydromethylpyrimidine moiety of thiamine
YP_002785037.1	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_002785040.1	with PaaBCDE catalyzes the hydroxylation of phenylacetyl-CoA
YP_002785044.1	catalyzes the ring cleavage reaction in phenylacetate degradation and the formation of 3-hydroxyacyl-CoA from crotonyl-CoA
YP_002785055.1	catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate
YP_002785083.1	acts in conjunction with GvcH to form H-protein-S-aminomethyldihydrolipoyllysine from glycine
YP_002785084.1	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_002785093.1	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_002785100.1	The point of entry for the majority of electrons that traverse the respiratory chain eventually resulting in the reduction of oxygen
YP_002785119.1	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_002785125.1	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_002785126.1	catalyzes a two-step reaction, first charging a serine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA
YP_002785136.1	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_002785143.1	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_002785146.1	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_002785148.1	Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis
YP_002785150.1	contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway
YP_002785155.1	catalyzes the formation of 3-deoxy-D-aribino-hept-2-ulosonate 7-phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate and the formation of prephenate from chorismate
YP_002785162.1	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_002785166.1	carries the fatty acid chain in fatty acid biosynthesis
YP_002785171.1	catalyzes the reversible transfer of the terminal phosphate of ATP to form a long chain polyphosphate
YP_002785172.1	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_002785182.1	catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro)
YP_002785186.1	binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit
YP_002785194.1	Acs; catalyzes the conversion of acetate and CoA to acetyl-CoA
YP_002785198.1	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_002785201.1	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_002785202.1	binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit
YP_002785203.1	in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA
YP_002785204.1	binds directly to 23S ribosomal RNA
YP_002785206.1	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_002785207.1	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_002785209.1	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_002785233.1	involved in a recombinational process of DNA repair, independent of the recBC complex
YP_002785237.1	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_002785240.1	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_002785258.1	ISDds2 - IS4 family member
YP_002785262.1	ISDds7 - IS4 family member
YP_002785269.1	catalyzes the formation of 2-phospho-D-glyceroyl phosphate from ATP and 2-phospho-D-glycerate
YP_002785274.1	catalyzes the formation of thymidine 5'-phosphate from thymidine
YP_002785276.1	RpmE; there appears to be two types of ribosomal proteins L31 in bacterial genomes; some contain a CxxC motif while others do not; Bacillus subtilis has both types; the proteins in this cluster do not have the CXXC motif; RpmE is found in exponentially growing Bacilli while YtiA was found after exponential growth; expression of ytiA is controlled by a zinc-specific transcriptional repressor; RpmE contains one zinc ion and a CxxC motif is responsible for this binding; forms an RNP particle along with proteins L5, L18, and L25 and 5S rRNA; found crosslinked to L2 and L25 and EF-G; may be near the peptidyltransferase site of the 50S ribosome
YP_002785281.1	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_002785307.1	catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A; involved in coenzyme A biosynthesis
YP_002785315.1	catalyzes the formation of L-histidinol from L-histidinol phosphate
YP_002785317.2	catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation
YP_002785319.1	catalyzes the reduction of N-acetyl-5-glutamyl phosphate to N-acetyl-L-glutamate 5-semialdehyde in arginine biosynthesis
YP_002785321.1	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_002785332.1	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_002785336.1	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_002785343.1	forms a direct contact with the tRNA during translation
YP_002785344.1	in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit
YP_002785346.1	required for 70S ribosome assembly
YP_002785348.1	type II fructose 1,6-bisphosphatae; in Escherichia coli this protein forms a dimer and binds manganese
YP_002785349.1	catalyzes the interconversion of alpha-D-glucose 1-phosphate to alpha-D-glucose 6-phosphate
YP_002785361.2	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_002785362.1	transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein
YP_002785373.1	converts threonine and NAD to 1,2-amino-3-oxobutanoate and NADH; functions in threonine catabolism
YP_002785374.1	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_002785375.1	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_002785380.2	catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine
YP_002785401.1	catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate
YP_002785410.1	Catalyzes the conversion of citrate to isocitrate
YP_002785426.1	catalyzes the formation of 5-phospho-alpha-D-ribose 1-diphosphate and nicotinate from nicotinate D-ribonucleotide and diphosphate
YP_002785427.1	NadM-Nudix subfamily; involved in creation of nicotanimide adenine dinucleotide NAD from either biosynthetic or salvage pathways
YP_002785429.1	functions in transport of arginine/ornithine; inner membrane ATPase that cleaves ATP and phosphorylates two periplasmic proteins that function as two distinct transport systems, the AO (arginine and ornithine) and LAO (lysine, arginine, and ornithine) periplasmic binding proteins
YP_002785431.1	MDM; functions in conversion of succinate to propionate
YP_002785433.1	catalyzes the formation of (2R)-3-sulfolactate from (2R)-2-phospho-3-sulfolactate
YP_002785444.1	Converts L-aspartate to beta-alanine and provides the major route of beta-alanine production in bacteria. Beta-alanine is essential for the biosynthesis of pantothenate (vitamin B5)
YP_002785453.1	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_002785490.1	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_002785491.1	catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs
YP_002785495.1	MraZ; UPF0040; crystal structure shows similarity to AbrB
YP_002785503.1	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_002785506.1	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_002785520.1	unknown function; YciI from Haemophilus influenzae presents crystal structure similarity to a muconolactone isomerase, but does not seem to catalyze any of the predicted reactions based on sequence and structure similarity
YP_002785524.1	catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis
YP_002785530.1	TrpG; with TrpE catalyzes the formation of anthranilate and glutamate from chorismate and glutamine; TrpG provides the glutamine amidotransferase activity
YP_002785531.1	Catalyzes the conversion of N-(5-phospho-D-ribosyl)-anthranilate and diphosphate to anthranilate and 5-phospho-alpha-D-ribose 1-diphosphate
YP_002785534.1	catalyzes the formation of succinate semialdehyde and glutamate from 4-aminobutanoate and 2-oxoglutarate
YP_002785550.1	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_002785551.1	catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids
YP_002785552.1	catalyzes the transfer of a segment of a 1,4-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain
YP_002785565.1	catalyzes the isomerization of isopentenyl pyrophosphate to dimethylallyl diphosphate
YP_002785567.1	plays an essential role in ATP-dependent branch migration of the Holliday junction
YP_002785573.1	Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway
YP_002785575.1	catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate
YP_002785585.1	catalyzes the reversible phosphorolysis of ribonucleosides and 2'- deoxyribonucleosides to the free base and (2'-deoxy)ribose-1- phosphate
YP_002785594.1	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_002785599.1	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_002785601.1	catalyzes the formation of 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine from N6-(dimethylallyl)adenosine (i(6)A)
YP_002785610.1	hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr); possible defense mechanism against a harmful effect of D-tyrosine
YP_002785613.1	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_002785614.1	catalyzes the formation of 3-phosphonooxypyruvate from 3-phospho-D-glycerate in serine biosynthesis; can also reduce alpha ketoglutarate to form 2-hydroxyglutarate
YP_002785631.1	catalyzes branch migration in Holliday junction intermediates
YP_002785637.1	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_002785656.1	bifunctional arginine biosynthesis protein ArgJ; functions at the 1st and 5th steps in arginine biosynthesis; involved in synthesis of acetylglutamate from glutamate and acetyl-CoA and ornithine by transacetylation between acetylornithine and glutmate
YP_002785677.1	catalyzes the reduction of N-acetyl-5-glutamyl phosphate to N-acetyl-L-glutamate 5-semialdehyde in arginine biosynthesis and the reduction of N-acetyl-gamma-aminoadipyl-phosphate to N-acetyl-L-aminoadipate-semialdehyde in lysine biosynthesis; involved in both the arginine and lysine biosynthetic pathways; lysine is produced via the AAA pathway, lysine from alpha-aminoadipate
YP_002785678.1	part of the preprotein secretory system; forms a complex with protein 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_002785680.1	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_002785682.1	modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination
YP_002785688.1	catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate and N-acetyl-L-aminoadipate to form N-acetyl-L-aminoadipate 5-phosphate in arginine and lysine biosynthesis
YP_002785695.1	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_002785701.1	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_002785705.1	catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis
YP_002785709.1	methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA
YP_002785710.1	Essential for efficient processing of 16S rRNA
YP_002785712.1	binds to lower part of 30S body where it stabilizes two domains; required for efficient assembly of 30S; in Escherichia coli this protein has nuclease activity
YP_002785720.1	ISDds8 - IS630 family member
YP_002785737.1	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_002785738.1	Maf; overexpression in Bacillus subtilis inhibits septation in the dividing cell
YP_002785743.2	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_002785755.1	catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis
YP_002785765.1	one of two methionine synthases in Escherichia coli; MetH catalyzes a methyl transfer reaction from methyltetrahydrofolate to homocysteine to create methionine; requires zinc for activity
YP_002785788.1	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_002785797.1	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_002785798.1	Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate
YP_002785800.1	Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway
YP_002785802.1	catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP
YP_002785804.1	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_002785805.1	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_002785806.1	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_002785820.1	with PdxST is involved in the biosynthesis of pyridoxal 5'-phosphate; PdxT catalyzes the hydrolysis of glutamine to glutamate and ammonia; PdxS utilizes the ammonia to synthesize pyridoxal 5'-phosphate
YP_002785821.1	with PdxT forms pyridoxal 5'-phosphate from glutamine, either ribose 5-phosphate or ribulose 5-phosphate, and either glyceraldehyde 3-phosphate or dihydroxyacetone phosphate
YP_002785824.1	An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes
YP_002785825.1	similar to novel fructose-6-phosphate aldolase from Escherichia coli; enzyme from Methanocaldococcus janaschii shows transaldolase activity
YP_002785826.1	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 2 subfamily; some organisms carry two different copies of this enzyme; in some organisms, the type 2 subfamily is associated with resistance to the antibiotic pseudomonic acid (mupirocin)
YP_002785831.1	catalyzes the interconversion of succinyl-CoA and succinate
YP_002785836.1	catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis
YP_002785837.2	catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate
YP_002785851.1	Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate
YP_002785863.1	Catalyzes the aldol condensation of glyoxylate with acetyl-CoA to form malate as part of the second step of the glyoxylate bypass and an alternative to the tricarboxylic acid cycle
YP_002785882.1	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_002785895.1	catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate
YP_002785903.1	PEP carboxykinase; PEP carboxylase; PEPCK; catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using ATP
YP_002785905.1	binds RecA and inhibits RecA-mediated DNA strand exchange and ATP hydrolysis and coprotease activities
YP_002785906.1	binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase
YP_002785910.1	catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis
YP_002785911.1	catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis
YP_002785913.1	catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis
YP_002785918.1	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_002785919.1	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_002785921.1	catalyzes the formation of porphobilinogen from 5-aminolevulinate
YP_002785939.1	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_002785950.1	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_002785959.1	catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs
YP_002785965.1	May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine
YP_002785966.1	short form of enzyme; requires HisZ for function; catalyzes the formation of N'-5'-phosphoribosyl-ATP from phosphoribosyl pyrophosphate; crucial role in histidine biosynthesis; forms heteromultimer of HisG and HisZ
YP_002786009.2	one of the last subunits in the assembly of the 30S subunit; absence of S2 does not inhibit assembly but results in an inactive subunit
YP_002786010.1	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_002786011.1	Catalyzes the phosphorylation of UMP to UDP
YP_002786012.1	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_002786014.1	catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate
YP_002786024.1	catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis
YP_002786028.1	Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis
YP_002786039.1	catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis
YP_002786040.1	catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis
YP_002786051.1	3 different subfamilies; catalyzes the formation of quinolinate from iminoaspartate and dihydroxyacetone phosphate
YP_002786061.1	catalyzes the conversion of 1-proline-5-carboxylate dehydrogenase to L-glutamate
YP_002786074.1	methylates ribosomal protein L11 at multiple amino acid positions; mutations of these genes in Escherichia coli or Thermus thermophilus has no apparent phenotype
YP_002786075.1	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_002786081.1	catalyzes the conversion of 1-proline-5-carboxylate dehydrogenase to L-glutamate
YP_002786083.1	UbiA prenyltransferase family catalyzes the transfer of a prenyl group to various acceptors with hydrophobic ring structures in the biosynthesis of respiratory quinones, hemes, chlorophylls, vitamin E, and shikonin
YP_002786084.1	Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis
YP_002786085.1	Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis
YP_002786088.1	converts ATP and adenylyl sulfate to ADP and 3'-phosphoadenylyl sulfate; in Escherichia coli this enzyme functions in cysteine biosynthesis
YP_002786090.1	ATP sulfurylase; ATPS; converts ATP and sulfate to 5'phosphosulfate and pyrophosphate; in some organisms this enzyme is involved in the incorporation of inorganic sulfate while in others it is involved in the production of ATP in the reverse direction; the enzyme from Thermus thermophilus is dimeric and binds a zinc ion that is coordinated by cysteine and histidine residues that are not found in all related proteins but is found in some thermophilic organisms
YP_002786098.1	23S rRNA m2A2503 methyltransferase; methylates the C2 position of the A2530 nucleotide in 23S rRNA; may be involved in antibiotic resistance
YP_002786101.1	modulates transcription in response to the NADH/NAD(+) redox state
YP_002786103.1	periplasmic enzyme; 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_002786112.1	catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis
YP_002786115.1	involved in tryptophan biosynthesis; amino acid biosynthesis; converts 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate to C(1)-(3-indolyl)-glycerol 3-phosphate and carbon dioxide and water
YP_002786118.1	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_002786127.1	Required for DNA replication; binds preferentially to single-stranded, linear DNA
YP_002786154.1	cleaves the the RNA-DNA junction of a RNA-DNA/DNA heteroduplex; does not have RNase H activity
YP_002786155.1	binds to the ribosome on the universally-conserved alpha-sarcin loop
YP_002786163.1	catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis
YP_002786166.1	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_002786168.1	catalyzes the formation of D-fructose 1,6-bisphosphate from D-fructose 6-phosphate in glycolysis
YP_002786175.1	First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
YP_002786204.1	Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step
YP_002786224.1	catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate
YP_002786227.1	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_002786235.1	catalyzes the degradation of histidine to urocanate and ammmonia
YP_002786236.1	catalyzing the hydrolysis of 4-imidazolone-5-propionate to N-formimidoyl-L-glutamate, the third step in the histidine degradation pathway
YP_002786238.1	catalyzes the formation of 4-imidazolone-5-propanoate from urocanate during histidine metabolism
YP_002786250.1	Bordetella uptake gene bug product
YP_002786267.1	catalyzes the cleavage of carbon-halogen bonds in aliphatic compounds forming a primary alcohol and a halide
YP_002786273.1	This protein performs the mismatch recognition step during the DNA repair process
YP_002786283.1	Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation
YP_002786309.1	Converts (S)-4-amino-5-oxopentanoate to 5-aminolevulinate during the porphyrin biosynthesis pathway
YP_002786312.1	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_002786318.1	involved in de novo purine biosynthesis
YP_002786330.1	catalyzes the hydrolysis of acylphosphate
YP_002786345.1	CTP synthase; cytidine triphosphate synthetase; catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen; in Escherichia coli this enzyme forms a homotetramer
YP_002786346.1	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_002786347.1	catalyzes the removal of 5-oxoproline from various penultimate amino acid residues except L-proline
YP_002786366.1	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_002786370.1	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_002786371.1	catalyzes the formation of D-glucono-1,5-lactone 6-phosphate from D-glucose 6-phosphate
YP_002786390.1	Catalyzes the formation of dUTP from dCTP in thymidylate biosynthesis
YP_002786408.1	catalyzes the formation of (R)-2,3-dihydroxy-3-methylbutanoate from (S)-2-hydroxy-2-methyl-3-oxobutanoate in valine and isoleucine biosynthesis
YP_002786410.1	orfA of ISDds1 - IS3 family member
YP_002786411.1	orfB of ISDds1 - IS3 family member
YP_002786413.1	catalyzes the formation of 2-isopropylmalate from acetyl-CoA and 2-oxoisovalerate in leucine biosynthesis
YP_002786417.1	catalyzes the formation of N-acetyl-l-glutamate 5-semialdehyde from 2-oxoglutarate and N(2)-acetyl-L-ornithine
YP_002786423.1	amylomaltase; acts to release glucose from maltodextrins
YP_002786431.1	catalyzes the formation of phosphoenolpyruvate from pyruvate
YP_002786433.1	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_002786441.1	catalyzes the phosphorylation of 2-butanoate to butanoyl phosphate
YP_002786444.1	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_002786445.1	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; in some organisms, there are paralogous proteins that have been found to be nonessential but do function in secretion of a subset of exported proteins
YP_002786469.1	protein associated with Co2+ and Mg2+ efflux
YP_002786475.1	Catalyzes a two-step reaction, first charging a glycine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA
YP_002786493.1	catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis
YP_002786494.1	catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis
YP_002786496.1	catalyzes the formation of 3-dehydroshikimate from 3-dehydroquinate in chorismate biosynthesis
YP_002786525.1	catalyzes the conversion of 5-[(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino]- 1-(5-phosphoribosyl)imidazole-4-carboxamideand glutamine to imidazole-glycerol phosphate, 5-aminoimidazol-4-carboxamideribonucleotide and glutamate; the HisF subunit acts as a cyclase
YP_002786526.1	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_002786536.2	catalyzes N(2)-acetyl-L-lysine + H(2)O = acetate + L-lysine
YP_002786542.1	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_002786551.1	regulates pyrimidine biosynthesis by binding to the mRNA of the pyr genes, also has been shown to have uracil phosphoribosyltransferase activity
YP_002786552.1	catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis
YP_002786553.1	catalyzes the formation of N-carbamoyl-L-aspartate from (S)-dihydroorotate in pyrimidine biosynthesis
YP_002786560.1	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_002786569.1	catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate
YP_002786572.1	converts protoheme IX and farnesyl diphosphate to heme O
YP_002786576.1	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_002786589.1	catalyzes the formation of 3-deoxy-D-arabino-hept-2-ulosonate 7 phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate, phenylalanine sensitive
YP_002786592.1	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_002786599.1	involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY
YP_002786604.1	is a component of the macrolide binding site in the peptidyl transferase center
YP_002786605.1	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_002786606.1	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_002786607.1	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_002786608.1	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_002786609.1	smallest protein in the large subunit; similar to what is found with protein L31 and L33 several bacterial genomes contain paralogs which may be regulated by zinc; the protein from Thermus thermophilus has a zinc-binding motif and contains a bound zinc ion; the proteins in this group have the motif
YP_002786610.1	stimulates the activities of the other two initiation factors, IF-2 and IF-3
YP_002786616.1	essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP
YP_002786617.1	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_002786618.1	late assembly protein
YP_002786619.1	L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7
YP_002786620.1	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_002786621.1	binds 5S rRNA along with protein L5 and L25
YP_002786622.1	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_002786623.1	binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit
YP_002786624.1	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 appear to contain the zinc-binding motif
YP_002786625.1	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_002786626.1	assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel
YP_002786627.1	binds to the 23S rRNA between the centers for peptidyl transferase and GTPase
YP_002786628.1	primary binding protein; helps mediate assembly; involved in translation fidelity
YP_002786629.1	one of the stabilizing components for the large ribosomal subunit
YP_002786630.1	located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e
YP_002786631.1	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_002786632.1	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_002786633.1	protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA
YP_002786634.1	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_002786635.1	binds third domain of 23S rRNA and protein L29; part of exit tunnel
YP_002786636.1	L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA
YP_002786637.1	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_002786638.1	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_002786639.1	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_002786641.1	EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene
YP_002786642.1	binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit
YP_002786655.1	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_002786678.1	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_002786686.1	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_002786690.1	regulator of RNase E; increases half-life and abundance of RNAs; interacts with RNase E possibly inhibiting catalytic activity
YP_002786695.1	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_002786712.1	hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates
YP_002786713.1	binds and unfolds substrates as part of the ClpXP protease
YP_002786724.1	catalyzes the opening and hydrolysis of the beta-lactam ring of beta-lactam antibiotics such as penicillins and cephalosporins
YP_002786734.1	Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA
YP_002786735.1	catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase
YP_002786741.1	involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate
YP_002786763.1	NadM-Nudix subfamily; involved in creation of nicotanimide adenine dinucleotide NAD from either biosynthetic or salvage pathways
YP_002786766.1	catalyzes the formation of methylglyoxal from glycerone phosphate
YP_002786774.1	malic enzyme; oxaloacetate-decarboxylating; NAD-dependent; catalyzes the formation of pyruvate form malate
YP_002786783.1	catalyzes the oxidation of malate to oxaloacetate
YP_002786784.1	Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA
YP_002786803.1	degenerated IS - IS982 family
YP_002786804.1	degenerated IS - IS982 family
YP_002786807.1	in Escherichia coli this inner membrane protein was found to anchor the periplasmic catalytic oxidoreductase YedY; sulfite oxidase activity not demonstrated; contains heme
YP_002786808.1	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_002786824.1	E3 component of 2-oxoglutarate dehydrogenase complex; catalyzes the oxidation of dihydrolipoamide to lipoamide
YP_002786826.1	MoaC; along with MoaA is involved in conversion of a guanosine derivative into molybdopterin precursor Z; involved in molybdenum cofactor biosynthesis
YP_002786832.1	catalyzes the hydrolysis of pyrophosphate to phosphate
YP_002786834.2	Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr)
YP_002786859.1	partial IS - IS30 family
YP_002786860.1	partial ISDds7 - IS4 family
YP_002786861.1	partial ISDds7 - IS4 family
YP_002786863.1	degenerated IS - IS5 family
YP_002786864.1	degenerated IS - IS5 family
YP_002786865.1	degenerated IS - IS5 family
YP_002786867.1	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_002786869.1	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_002786872.1	catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate
YP_002786873.1	glutamate synthase is composed of subunits alpha and beta; beta subunit is a flavin adenine dinucleotide-NADPH dependent oxidoreductase; provides electrons to the alpha subunit, which binds L-glutamine and 2-oxoglutarate and forms L-glutamate
YP_002786889.1	catalyzes the methylthiolation of an aspartic acid residue of the S12 protein of the 30S ribosomal subunit
YP_002786904.1	shows similarity to CbiX(S)
YP_002786905.1	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_002786908.1	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_002786910.1	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_002786923.1	SucA; E1 component of the oxoglutarate dehydrogenase complex which catalyzes the formation of succinyl-CoA from 2-oxoglutarate; SucA catalyzes the reaction of 2-oxoglutarate with dihydrolipoamide succinyltransferase-lipoate to form dihydrolipoamide succinyltransferase-succinyldihydrolipoate and carbon dioxide
YP_002786925.1	Zn-dependent Hydrolase, including glyoxylases
YP_002786932.1	Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source
YP_002786981.1	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_002786991.1	converts L-glutamate to D-glutamate, a component of peptidoglycan
YP_002787002.1	involved in the peptidyltransferase reaction during translation
YP_002787003.1	essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication
YP_002787042.1	10 kDa chaperonin; Cpn10; GroES; forms homoheptameric ring; binds to one or both ends of the GroEL double barrel in the presence of adenine nucleotides capping it; folding of unfolded substrates initiates in a GroEL-substrate bound and capped by GroES; release of the folded substrate is dependent on ATP binding and hydrolysis in the trans ring
YP_002787043.1	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_002787050.2	catalyzes the interconversion of 3-phosphoglycerate and 2-phosphoglycerate; this enzyme does not require the cofactor 2,3-bisphosphoglycerate as a phosphate donor; BPG-independent PGAM; aPGAM
YP_002787083.2	catalyzes the conversion of a phosphate monoester to an alcohol and a phosphate
YP_002787087.1	bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides
YP_002787094.1	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_002787100.1	cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+)
YP_002787107.2	Essential for recycling GMP and indirectly, cGMP
YP_002787110.1	AckA utilizes acetate and can acetylate CheY which increases signal strength during flagellar rotation; utilizes magnesium and ATP; also involved in conversion of acetate to aceyl-CoA
YP_002787111.1	catalyzes the synthesis of acetylphosphate or propionylphosphate from acetyl-CoA or propionyl-CoA and inorganic phosphate; when using propionyl-CoA the enzyme is functioning in the anaerobic pathway catabolizing threonine to propionate
YP_002787117.1	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_002787124.1	EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene
YP_002787130.1	glucose-inhibited division protein B; SAM-dependent methyltransferase; methylates the N7 position of guanosine in position 527 of 16S rRNA
YP_002787132.1	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_002787153.1	exports sodium by using the electrochemical proton gradient to allow protons into the cell; functions in adaptation to high salinity and alkaline pH; activity increases at higher pH; downregulated at acidic pH
YP_002787166.1	Enables the enzymatic reduction of mercuric ions to elemental mercury
YP_002787188.1	partial IS - IS5 family
YP_002787189.1	partial IS - IS5 family
YP_002787190.1	orfA of ISDds1 - IS3 family member
YP_002787191.1	orfB of ISDds1 - IS3 family member
YP_002787264.1	ISDds3 - IS4 family member
YP_002787268.1	partial IS - IS701 family
YP_002787276.1	partial ISDds3 - IS4 family
YP_002787318.1	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_002787337.1	AroE; catalyzes the conversion of shikimate to 3-dehydroshikimate
YP_002787382.1	ISDds9 - IS5 family member
YP_002787383.1	ISDds9 - IS5 family member
YP_002787429.1	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_002787455.1	catalyzes the formation of pyruvate from D-cysteine
YP_002787456.1	degenerated IS - IS630 family
YP_002787457.1	degenerated IS - IS630 family
YP_002787475.1	Bordetella uptake gene bug product
YP_002787476.1	catalyzes the oxidation of tricarballylate to cis-aconitate; FAD-dependent; required for the utilization of tricarballylate as a carbon and energy source by S. enterica
YP_002787478.1	partial ISDds3 - IS4 family
YP_002787490.1	ISDds6 - IS701 family member
YP_002787522.1	partial IS - IS630 family
YP_002787524.1	partial IS OrfB - IS200/IS605 family
YP_002787534.1	partial IS - IS982 family
YP_002787555.1	Converts N-acetylmannosamine-6-phosphate to N-acetylglucosamine-6-phosphate
YP_002787585.1	Bordetella uptake gene bug product
YP_002787652.1	ISDds4 - IS982 family member
YP_002787710.1	ISDds5 - IS982 family member
YP_002787732.1	partial IS - IS5 family
YP_002787788.1	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_002787789.1	catalyzes the cleavage of the lactyl ether moiety of N-acetylmuramic acid-6-phosphate (MurNAc-6-P) to form N-acetylglucosamine-6-phosphate (GlcNAc-6-P) and lactate; involved in MurNAc dissimilation pathway
YP_002787813.1	partial IS - IS982 family
YP_002787837.1	orfA of ISDds1 - IS3 family member
YP_002787838.1	orfB of ISDds1 - IS3 family member
YP_002787839.1	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_002787841.1	partial IS - IS5family
YP_002787842.1	partial IS - IS5family
YP_002787856.1	orfB of ISDds1 - IS3 family member
YP_002787857.1	orfA of ISDds1 - IS3 family member
YP_002787930.1	catalyzes the methylation of C-5 in cobalt-precorrin-6Y to form cobalt-precorrin-7W-a
YP_002787935.1	catalyzes the formation of cobalt-precorrin 4 from cobalt-precorrin 3
YP_002787963.1	ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation
YP_002787965.1	activates fatty acids by binding to coenzyme A
YP_002787974.1	Involved in the nonphosphorylative, ketogenic oxidation of glucose and oxidizes gluconate to 5-ketogluconate