-- dump date   	20140620_033907
-- class       	Genbank::CDS
-- table       	cds_note
-- id	note
YP_001498901.1	similar to related oxidoreductases; undetermined function
YP_001498902.1	catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis
YP_001498903.1	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_001498904.1	adds the O-linked and N-linked 3(R)-hydroxy fatty acids to the glucosamine disaccharide during lipid A biosynthesis
YP_001498909.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B is part of the membrane proton channel.
YP_001498910.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B' is part of the membrane proton channel.
YP_001498911.1	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_001498912.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit A is part of the membrane proton channel F0
YP_001498917.1	Required for DNA replication; binds preferentially to single-stranded, linear DNA
YP_001498926.1	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_001498928.1	binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21
YP_001498929.1	binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit
YP_001498930.1	in Escherichia coli this protein is wrapped around the base of the L1 stalk
YP_001498933.1	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_001498935.1	transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein
YP_001498937.1	functions to insert inner membrane proteins into the IM in Escherichia coli; interacts with transmembrane segments; functions in both Sec-dependent and -independent membrane insertion; similar to Oxa1p in mitochondria
YP_001498945.1	catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate
YP_001498946.1	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_001498947.1	glucose-inhibited division protein B; SAM-dependent methyltransferase; methylates the N7 position of guanosine in position 527 of 16S rRNA
YP_001498950.1	ChvD; in Agrobacterium tumefaciens, mutations in both Walker boxes were found to affect virulence
YP_001498952.1	catalyzes the formation of 2-dehydro-3-deoxy-D-octonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate in LPS biosynthesis
YP_001498954.1	dGTPase family type 2 subfamily; presumably hydrolyzes dGTP to deoxyguanosine and triphosphate
YP_001498955.1	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_001498957.1	decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling
YP_001498959.1	Catalyzes the formation of dUTP from dCTP in thymidylate biosynthesis
YP_001498960.1	molecular chaperone that is required for the normal export of envelope proteins out of the cell cytoplasm; in Escherichia coli this proteins forms a homotetramer in the cytoplasm and delivers proteins to be exported to SecA
YP_001498962.1	catalyzes the NADPH-dependent reduction of 7-cyano-7-deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1) in queuosine biosynthesis
YP_001498971.1	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_001498972.1	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_001498973.1	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_001498974.1	catalyzes the transfer of 2-keto-3-deoxy-D-manno-octulosonic acid to lipid A
YP_001498976.1	catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate
YP_001498981.1	related to toluene tolerance
YP_001498983.1	converts L-alanine to D-alanine which is used in cell wall biosynthesis; binds one pyridoxal phosphate per monomer; forms a homodimer
YP_001498989.1	required for 70S ribosome assembly
YP_001498990.1	RpmE; 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; 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_001498991.1	binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential
YP_001498999.1	methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA
YP_001499000.1	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_001499002.1	forms a complex with SecD and YajC; SecDFyajC stimulates the proton motive force-driven protein translocation; seems to modulate the cycling of SecA by stabilizing its membrane-inserted state and appears to be required for the release of mature proteins from the extracytoplasmic side of the membrane; in some organisms, such as Bacillus subtilis, SecD is fused to SecF
YP_001499003.1	part of NADH-ubiquinone oxidoreductase complex I; shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain; NuoF is part of the soluble NADH dehydrogenase fragment, which represents the electron input part of NADH dehydrogenase
YP_001499005.1	cytoplasmic enzyme involved in processing rRNA and some mRNAs; substrates typically have dsRNA regions; forms a homodimer; have N-terminal nuclease and C-terminal RNA-binding domains; requires magnesium as preferred ion for activity
YP_001499006.1	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_001499007.1	endonuclease; resolves Holliday structures; forms a complex of RuvABC; the junction binding protein RuvA forms a hexameric ring along with the RuvB helicase and catalyzes branch migration; RuvC then interacts with RuvAB to resolve the Holliday junction by nicking DNA strands of like polarity
YP_001499019.1	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_001499021.1	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_001499022.1	binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit
YP_001499023.1	EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene
YP_001499024.1	forms a complex with SecY and SecG; SecYEG forms a putative protein-conducting channel to which secA binds and translocates targeted polypeptides across the cytoplasmic membrane, a process driven by ATP and a proton-motive force
YP_001499025.1	Modulates Rho-dependent transcription termination
YP_001499026.1	binds directly to 23S ribosomal RNA
YP_001499027.1	in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA
YP_001499028.1	binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit
YP_001499029.1	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_001499030.1	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_001499031.1	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_001499033.1	catalyzes the removal of N-terminal amino acids preferably leucine from various peptides
YP_001499036.1	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_001499039.1	catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis
YP_001499042.1	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_001499043.1	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_001499044.1	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_001499045.1	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_001499046.1	Catalyzes the phosphorylation of UMP to UDP
YP_001499047.1	subunit E of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali
YP_001499053.1	Regulates rRNA biosynthesis by transcriptional antitermination
YP_001499059.2	in Escherichia coli RsmE methylates the N3 position of the U1498 base in 16S rRNA; cells lacking this function can grow, but are outcompeted by wild-type; SAM-dependent m(3)U1498 methyltransferase
YP_001499063.1	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_001499065.1	catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III
YP_001499069.1	component of 2-oxoglutarate dehydrogenase complex; catalyzes the transfer of succinyl coenzyme A to form succinyl CoA as part of the conversion of 2-oxoglutarate to succinyl-CoA
YP_001499070.1	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_001499073.1	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_001499074.1	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_001499078.1	required for the assembly and function of the DNAX complex which are required for the assembly of the beta subunit onto primed DNA
YP_001499083.1	catalyzes the formation of N-succinyl-2-amino-6-ketopimelate from succinyl-CoA and tetrahydrodipicolinate in the lysine biosynthetic pathway
YP_001499085.1	similar to related nucleotide-binding proteins
YP_001499089.1	involved in the maturation of iron-sulfur cluster-containing proteins
YP_001499090.1	J-type co-chaperone that regulates the ATPase and peptide-binding activity of Hsc66 chaperone; may function in biogenesis of iron-sulfur proteins
YP_001499091.1	RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids
YP_001499092.1	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_001499095.1	negatively supercoils closed circular double-stranded DNA
YP_001499097.1	cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+)
YP_001499098.1	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_001499110.1	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_001499112.1	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_001499118.1	decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling
YP_001499124.1	in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit
YP_001499125.1	forms a direct contact with the tRNA during translation
YP_001499129.1	hydrolyzes diadenosine polyphosphate
YP_001499130.1	involved in swarmer-to-stalked cell differentiation in Caulobacter crescentus; catalyzes the condensation of two GTP molecules to form the secondary messenger cyclic di-GMP (c-di-GMP); upon phosphorylation of domain D1 the protein dimerizes; presumably this allows the two GTP-bound GGDEF (diguanylate cyclase) domains to catalyze the condensation reaction; allosterically inhibited by c-di-GMP
YP_001499131.1	Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA
YP_001499134.1	catalyzes the decarboxylaton of phospatidyl-L-sering to phosphatidylethanolamine
YP_001499141.1	Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis
YP_001499142.1	catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis
YP_001499143.1	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_001499149.1	zinc-dependent; catalyzes the deacetylation of UDP-(3-O-acyl)-N-acetylglucosamine to UDP-3-O-(3-hydroxytetradecanoyl)-glucosamine in the second step of lipid A biosynthesis
YP_001499157.1	catalyzes the oxidative decarboxylation of pyruvate with concomitant acetylation of a lipoic acid-containing dihydrolipoamide acyltransferase within the complex. The pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2); it contains multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2) and lipoamide dehydrogenase
YP_001499160.1	catalyzes the formation of 2-oxoglutarate from isocitrate
YP_001499161.1	subunit G of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in S. meliloti it is known to be involved specifically with K+ transport
YP_001499162.1	subunit B of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali
YP_001499172.1	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_001499173.1	binds to the ribosome on the universally-conserved alpha-sarcin loop
YP_001499178.1	subunit D of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; contains an oxidoreductase domain; catalyzes the transfer of electrons from NADH to ubiquinone
YP_001499181.1	subunit D of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; contains an oxidoreductase domain; catalyzes the transfer of electrons from NADH to ubiquinone
YP_001499182.1	subunit D of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; contains an oxidoreductase domain; catalyzes the transfer of electrons from NADH to ubiquinone
YP_001499183.1	subunit C of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali
YP_001499197.1	This protein performs the mismatch recognition step during the DNA repair process
YP_001499198.1	catalyzes the interconversion of ribose 5-phosphate to ribulose 5-phosphate; enzyme from E. coli shows allose 6-phosphate isomerase activity
YP_001499200.1	flavin dependent thymidylate synthase; ThyX; thymidylate synthase complementing protein; catalyzes the formation of dTMP and tetrahydrofolate from dUMP and methylenetetrahydrofolate; the enzyme from Mycobacterium tuberculosis forms homotetramers; uses FAD as a cofactor
YP_001499201.1	forms dimers; may be involved in cell envelope integrity; interacts with outer membrane proteins and with the C-terminal domain of inner membrane protein TolA
YP_001499202.1	binds with the catalytic core of RNA polymerase to produce the holoenzyme; this sigma factor is responsible for the expression of heat shock promoters
YP_001499203.1	involved in the insertion of copper into subunit I of cytochrome C oxidase
YP_001499205.1	catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs
YP_001499207.1	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_001499211.1	links inner and outer membranes
YP_001499216.1	catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde
YP_001499219.1	heat shock protein involved in degradation of misfolded proteins
YP_001499220.1	heat shock protein involved in degradation of misfolded proteins
YP_001499222.1	catalyzes the formation of lipid A disaccharide from UDP-2,3-diacylglucosamine and 2,3-diacylglucosamine-1-phosphate, lipid A disaccharide is a precursor of lipid A that anchors LPS to the OM
YP_001499225.1	defects in the mitochondrial frataxin protein cause Friedreich ataxis which is an autosomal recessive neurodegenerative disease; based on phylogenomic distribution this protein may have a role in iron-sulfur cluster protein assembly
YP_001499230.1	Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation
YP_001499231.1	catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity
YP_001499235.1	similar to RuvC resolvase with substantial differences; NMR structural information suggests this protein is monomeric; unknown cellular function
YP_001499248.1	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_001499249.1	converts protoheme IX and farnesyl diphosphate to heme O
YP_001499252.1	Essential for efficient processing of 16S rRNA
YP_001499254.1	catalyzes the bidirectional exonucleolytic cleavage of DNA
YP_001499255.1	responsible for recognizing base lesions in the genome and initiating base excision DNA repair
YP_001499257.1	Catalyzes the transfer of electrons from NADH to quinone
YP_001499258.1	Catalyzes the transfer of electrons from NADH to quinone
YP_001499259.1	Catalyzes the transfer of electrons from NADH to quinone
YP_001499260.1	The point of entry for the majority of electrons that traverse the respiratory chain eventually resulting in the reduction of oxygen
YP_001499261.1	Catalyzes the transfer of electrons from NADH to quinone
YP_001499264.1	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; XerD specifically exchanges the bottom strands; cell division protein FtsK may regulate the XerCD complex; enzyme from Streptococcus group has unusual active site motifs
YP_001499267.1	Catalyzes a key regulatory step in fatty acid biosynthesis
YP_001499268.1	Transfers the fatty acyl group on membrane lipoproteins
YP_001499271.1	class I; LysRS1; catalyzes a two-step reaction, first charging a lysine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; in Methanosarcina barkeri this enzyme charges both tRNA molecules for lysine that exist in this organism (but the tRNALysUUU very poorly) and in the presence of LysRS2 can charge tRNAPyl with lysine
YP_001499273.1	NADP-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; decarboxylates oxaloacetate
YP_001499277.1	Catalyzes the reversible oxidation of malate to oxaloacetate
YP_001499281.1	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_001499282.1	CMP-2-keto-3-deoxyoctulosonic acid synthetase; catalyzes the formation of CMP-3-deoxy-D-manno-octulosonate from CTP and 3-deoxy-D-manno-octulosonate which is incorporated into LPS
YP_001499285.1	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_001499286.1	catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro)
YP_001499289.1	plays an essential role in ATP-dependent branch migration of the Holliday junction
YP_001499290.1	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_001499296.1	Involved in cell division; probably involved in intracellular septation
YP_001499303.1	catalyzes the formation of dUMP from dUTP
YP_001499313.1	lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis
YP_001499315.1	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_001499317.1	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_001499322.1	involved in lysine biosynthesis; DAP epimerase; produces DL-diaminopimelate from LL-diaminopimelate
YP_001499324.1	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_001499325.1	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_001499326.1	binds the polymerase to DNA and acts as a sliding clamp
YP_001499328.1	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_001499335.1	catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids
YP_001499336.1	catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis
YP_001499337.1	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_001499339.1	Catalyzes the only substrate-level phosphorylation in the TCA cycle
YP_001499340.1	catalyzes the interconversion of succinyl-CoA and succinate
YP_001499344.1	associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock
YP_001499347.1	involved in a recombinational process of DNA repair, independent of the recBC complex
YP_001499348.1	catalyzes the phosphorylation of NAD to NADP
YP_001499350.1	catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate
YP_001499360.1	catalyzes the formation of 2-oxobutanoate from L-threonine
YP_001499364.1	catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate
YP_001499367.1	Catalyzes the rate-limiting step in dNTP synthesis
YP_001499368.1	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_001499370.1	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_001499377.1	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_001499378.1	catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs; proteins in this cluster have Rickettsial repeat elements (RPE) inserts
YP_001499389.1	catalyzes the formation of phosphoenolpyruvate from pyruvate
YP_001499402.1	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_001499404.1	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_001499407.1	An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes
YP_001499448.1	Catalyzes the formation of (d)CDP from ATP and (d)CMP
YP_001499449.1	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_001499450.1	hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates
YP_001499451.1	catalyzes the isomerization of isopentenyl pyrophosphate to dimethylallyl diphosphate
YP_001499458.1	smallest protein in the large subunit; similar to what is found with protein L31 and L33 several bacterial genomes contain paralogs which may be regulated by zinc; the protein from Thermus thermophilus has a zinc-binding motif and contains a bound zinc ion; the proteins in this group do not have the motif
YP_001499464.1	Catalyzes the oxidation of dihydrolipoamide to lipoamide
YP_001499468.1	related to GcvT
YP_001499471.1	transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis
YP_001499472.1	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_001499487.1	catalyzes the removal of elemental sulfur from cysteine to produce alanine; involved in NAD biosynthesis
YP_001499491.1	Catalyzes the transfer of electrons from NADH to quinone
YP_001499493.1	catalyzes the formation of porphobilinogen from 5-aminolevulinate
YP_001499495.1	binding of PriA to forked DNA starts the assembly of the primosome, also possesses 3'-5' helicase activity
YP_001499497.1	unwinds double stranded DNA
YP_001499501.1	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_001499503.1	involved in DNA repair and RecFOR pathway recombination; RecFOR proteins displace ssDNA-binding protein and facilitate the production of RecA-coated ssDNA
YP_001499506.1	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_001499507.1	modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination
YP_001499508.1	in Streptococcus pneumoniae this gene was found to be essential; structure determination of the Streptococcus protein shows that it is similar to a number of other proteins
YP_001499511.1	catalyzes the formation of tyrosyl-tRNA(Tyr) from tyrosine and tRNA(Tyr)
YP_001499521.1	Oxygenase that introduces the hydroxyl group at carbon four of 2-octaprenyl-6-methoxyphenol resulting in the formation of 2-octaprenyl-6-methoxy-1,4-benzoquinone
YP_001499522.1	subunit F of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali
YP_001499531.1	MraZ; UPF0040; crystal structure shows similarity to AbrB
YP_001499534.1	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_001499538.1	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_001499540.1	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_001499541.1	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_001499542.1	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_001499543.1	negatively supercoils closed circular double-stranded DNA
YP_001499548.1	member of preprotein translocase; forms a heterotrimer with SecD and SecF; links the SecD/SecF/YajC/YidC complex with the SecY/SecE/SecG complex
YP_001499549.1	part of the preprotein secretory system; when complexed with proteins SecF and YajC, SecDFyajC stimulates the proton motive force-driven protein translocation, and appears to be required for the release of mature proteins from the extracytoplasmic side of the membrane
YP_001499552.1	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_001499553.1	catalyzes the hydrolysis of pyrophosphate to phosphate
YP_001499561.1	First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
YP_001499563.1	involved in cell wall formation; peptidoglycan synthesis; cytoplasmic enzyme; catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-aceylmuramoyl-l-alanyl-d-glutamate
YP_001499567.1	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_001499569.1	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_001499570.1	Enables the recycling of peptidyl-tRNAs produced at termination of translation
YP_001499571.1	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_001499574.1	binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit
YP_001499575.1	in Escherichia coli transcription of this gene is enhanced by polyamines
YP_001499576.1	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_001499583.1	a small basic protein that is one of the last in the subunit assembly; omission does not prevent assembly but the subunit is inactive; binds central domain of 16S rRNA
YP_001499585.1	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_001499589.1	Synthesizes thioester adducts of fatty acids enzymatically to the phosphopantetheine group of acyl carrier protein
YP_001499592.1	Involved in ubiquinone biosynthesis
YP_001499593.1	Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation
YP_001499598.1	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_001499599.1	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_001499600.1	RNase PH; tRNA nucleotidyltransferase; forms hexamers in Bacillus subtilis; phosphoroltic 3'-5' exoribonuclease; involved in maturation of tRNA precursors and removes terminal nucleotides near CCA acceptor arms of mature tRNAs
YP_001499601.1	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_001499604.1	binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase
YP_001499605.1	is a component of the macrolide binding site in the peptidyl transferase center
YP_001499606.1	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_001499607.1	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_001499608.1	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_001499609.1	essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP
YP_001499610.1	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_001499611.1	late assembly protein
YP_001499612.1	L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7
YP_001499613.1	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_001499614.1	binds 5S rRNA along with protein L5 and L25
YP_001499615.1	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_001499616.1	binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit
YP_001499617.1	located in the peptidyl transferase center and involved in assembly of 30S ribosome subunit; similar to what is observed with proteins L31 and L33, some proteins in this family contain CXXC motifs that are involved in zinc binding; if two copies are present in a genome, then the duplicated copy appears to have lost the zinc-binding motif and is instead regulated by zinc; the proteins in this group do not appear to have the zinc-binding motif
YP_001499618.1	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_001499619.1	assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel
YP_001499620.1	binds to the 23S rRNA between the centers for peptidyl transferase and GTPase
YP_001499621.1	primary binding protein; helps mediate assembly; involved in translation fidelity
YP_001499622.1	one of the stabilizing components for the large ribosomal subunit
YP_001499623.1	located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e
YP_001499624.1	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_001499625.1	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_001499626.1	protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA
YP_001499627.1	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_001499628.1	binds third domain of 23S rRNA and protein L29; part of exit tunnel
YP_001499629.1	L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA
YP_001499630.1	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_001499631.1	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_001499632.1	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_001499635.1	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_001499638.1	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_001499644.1	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_001499647.1	bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides
YP_001499650.1	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_001499652.1	Catalyzes the carbon methylation reaction in the biosynthesis of ubiquinone
YP_001499653.1	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_001499657.1	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_001499658.1	catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP)
YP_001499660.1	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_001499661.1	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_001499666.1	binds and unfolds substrates as part of the ClpXP protease
YP_001499685.1	Acylates the intermediate (KDO)2-lipid IVA to form (KDO)2-(lauroyl)-lipid IVA
YP_001499686.1	transfers the gamma-phosphate of ATP to the 4' position of a tetraacyldisaccharide 1-phosphate intermediate to form tetraacyldisaccharide 1,4'-bis-phosphate
YP_001499688.1	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_001499689.1	Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr)
YP_001499693.1	An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids
YP_001499696.1	catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A; involved in coenzyme A biosynthesis
YP_001499697.1	3'-5' exonuclease of DNA polymerase III
YP_001499707.1	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_001499708.1	catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate
YP_001499717.1	TatA; similar to TatE that is found in some proteobacteria; part of system that translocates proteins with a conserved twin arginine motif across the inner membrane; capable of translocating folded substrates typically those with bound cofactors; similar to a protein import system in thylakoid membranes
YP_001499720.1	involved in the peptidyltransferase reaction during translation
YP_001499721.1	catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP, in Bacillus, lysine sensitive; regulated by response to starvation.
YP_001499730.1	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_001499733.1	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_001499734.1	Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis
YP_001499735.1	carries the fatty acid chain in fatty acid biosynthesis
YP_001499736.1	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_001499740.1	Essential for recycling GMP and indirectly, cGMP
YP_001499742.1	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_001499743.1	functions in MreBCD complex in some organisms
YP_001499746.1	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_001499747.1	some L32 proteins have zinc finger motifs consisting of CXXC while others do not
YP_001499750.1	has 3'-5' exonuclease, 5'-3' exonuclease and 5'-3'polymerase activities, primarily functions to fill gaps during DNA replication and repair
YP_001499751.1	catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; main replicative polymerase
YP_001499756.1	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_001499762.1	Catalyzes the transfer of electrons from NADH to quinone
YP_001499763.1	Catalyzes the transfer of electrons from NADH to quinone
YP_001499764.1	Catalyzes the transfer of electrons from NADH to ubiquinone
YP_001499765.1	Catalyzes the transfer of electrons from NADH to quinone
YP_001499766.1	ATP-binding protein; required for proper cytochrome c maturation
YP_001499767.1	Catalyzes the transfer of electrons from NADH to quinone
YP_001499768.1	Catalyzes the transfer of electrons from NADH to quinone
YP_001499769.1	Catalyzes the transfer of electrons from NADH to quinone
YP_001499771.1	Catalyzes the conversion of citrate to isocitrate
YP_001499772.1	part of catalytic core of ATP synthase; alpha(3)beta(3)gamma(1)delta(1)epsilon(1); involved in producing ATP from ADP in the presence of the proton motive force across the membrane
YP_001499773.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit
YP_001499774.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit
YP_001499775.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit
YP_001499776.1	Produces ATP from ADP in the presence of a proton gradient across the membrane; the delta subunit is part of the catalytic core of the ATP synthase complex
YP_001499777.1	Catalyzes the oxidation of dihydrolipoamide to lipoamide
YP_001499779.1	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_001499786.1	stimulates the activities of the other two initiation factors, IF-2 and IF-3
YP_001499787.1	Maf; overexpression in Bacillus subtilis inhibits septation in the dividing cell
YP_001499789.1	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_001499796.1	catalyzes the removal of N-terminal amino acids from peptides and arylamides; generally Co(II) however activity has been shown for some methionine aminopeptidases with Zn, Fe, or Mn
YP_001499808.1	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_001499809.1	binds to single stranded DNA and may facilitate the binding and interaction of other proteins to DNA
YP_001499813.1	molecular chaperone
YP_001499814.1	catalyzes the formation of 5-aminolevulinate from succinyl-CoA and glycine
YP_001499815.1	Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer
YP_001499816.1	essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication
YP_001499817.1	type II enzyme; in Escherichia coli this enzyme forms a trimer of dimers which is allosterically inhibited by NADH and competitively inhibited by alpha-ketoglutarate; allosteric inhibition is lost when Cys206 is chemically modified which also affects hexamer formation; forms oxaloacetate and acetyl-CoA and water from citrate and coenzyme A; functions in TCA cycle, glyoxylate cycle and respiration; enzyme from Helicobacter pylori is not inhibited by NADH
YP_001499821.1	fusion of hemK/trmB; N-terminal HemK domain transfers a methyl group from S-adenosylmethionine to amide nitrogen of specific glutamine residues in protein chain release factors PrfA and PrfB; C-terminal
YP_001499823.1	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_001499824.1	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_001499829.1	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_001499830.1	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_001499831.1	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_001499833.1	lipoyl/octanoyltransferase; catalyzes the transfer of the lipoyl/octanoyl moiety of lipoyl/octanoyl-ACP onto lipoate-dependent enzymes like pyruvate dehydrogenase and the glycine cleavage system H protein
YP_001499836.1	dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE), catalyzes the hydrolysis of N-succinyl-L,Ldiaminopimelate L,L-SDAP to L,L-diaminopimelate and succinate. It is a metalloprotease containing dinuclear active sites. Its structure is similar to the carboxypeptidase G2 from Pseudomonas sp. strain RS-16 and the aminopeptidase from Aeromonas proteolytica.
YP_001499837.1	binds to single-strand binding (SSB) protein and acts as a bridge between the DnaX clamp loader complex and the SSB
YP_001499847.1	catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; rhe 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_001499851.1	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_001499853.1	synthesizes RNA primers at the replication forks
YP_001499854.1	sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; this is the primary sigma factor of bacteria
YP_001499855.1	mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability
YP_001499856.1	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_001499861.1	catalyzes the conversion of the propionic acid groups of rings I and III to vinyl groups during heme synthesis
YP_001499863.1	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_001499864.1	catalyzes the formation of coproporphyrinogen from uroporphyrinogen III