-- dump date 20140618_193055 -- class Genbank::CDS -- table cds_note -- id note NP_355038.1 similar to inner mitochondrial membrane protein NP_357528.2 allantoate amidohydrolase and N-carbamoyl-L-amino acid amidohydrolase are very similar; the allantoate amidohydrolase from Escherichia coli forms a dimer and binds zinc ions for catalytic activity and catalyzes the conversion of allantoate to (S)-ureidoglycolate and ammonia; carbamoyl amidohydrolase from Bacillus sp. converts N-carbamoyl amino acids to amino acids, ammonia, and carbon dioxide NP_357514.2 Member of the extracytoplasmic function sigma factors which are active under specific conditions; binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription NP_357508.1 3'-5' exonuclease of DNA polymerase III NP_357499.2 part of the UgpABCE glycerol-3-phosphate uptake system NP_533623.1 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 NP_357461.2 catalyzes the formation of 2,5-dioxopentanoate from 5-dehydro-4-deoxy-D-glucarate NP_357459.2 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase; catalyzes the interconversion of 4-deoxy-L-threo-5-hexosulose uronate to 3-deoxy-D-glycero-2,5-hexodiulosonate NP_357437.2 Converts D-sorbitol to L-sorbose NP_357413.1 part of the UgpABCE glycerol-3-phosphate uptake system NP_357385.1 catalyzes the formation of 3-methyl-2-oxobutanoate from 2,3,-dihydroxy-3-methylbutanoate NP_357379.1 membrane component of a sugar ABC transporter system NP_357357.1 works in conjunction with MinC and MinD to enable cell division at the midpoint of the long axis of the cell NP_357355.2 blocks the formation of polar Z-ring septums NP_357348.1 catalyzes the formation of 2-dehydro-3-deoxy-D-gluconate from mannonate NP_357339.2 Catalyzes the reversible hydrolysis of the amide bond within dihydroorotate. This metabolic intermediate is required for the biosynthesis of pyrimidine nucleotides NP_357317.1 catalyzes the formation of 4-methyl-5-(2-phosphoethyl)-thiazole and ADP from 4-methyl-5-(2-hydroxyethyl)-thiazole and ATP NP_357312.1 catalyzes the oxidative deamination of D-amino acids NP_357307.1 involved in the transport of C4-dicarboxylates across the membrane NP_357277.1 catalyzes the formation of pyruvate and beta-alanine from L-alanine and 3-oxopropanoate NP_357273.1 Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis NP_357271.2 responsible for recognizing base lesions in the genome and initiating base excision DNA repair NP_357249.1 NADP-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; decarboxylates oxaloacetate NP_357207.1 catalyzes the formation of L-ornithine from N(2)-acetyl-L-ornithine NP_357203.2 catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis NP_357140.1 catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate NP_357128.2 Catalyzes the reversible hydration of unsaturated fatty acyl-CoA to beta-hydroxyacyl-CoA NP_357127.2 catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine NP_357126.1 catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate NP_357105.2 catalyzes the formation of 3-hydroxy-2-methylpropanoate from 3-hydroxy-2-methylpropanoyl-CoA NP_357102.1 Involved in ubiquinone biosynthesis NP_357093.1 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 NP_357091.2 functions in protein export; can interact with acidic membrane phospholipids and the SecYEG protein complex; binds to preproteins; binds to ATP and undergoes a conformational change to promote membrane insertion of SecA/bound preprotein; ATP hydrolysis appears to drive release of the preprotein from SecA and deinsertion of SecA from the membrane; additional proteins SecD/F/YajC aid SecA recycling; exists in an equilibrium between monomers and dimers; may possibly form higher order oligomers; proteins in this cluster correspond SecA1; SecA2 is not essential and seems to play a role in secretion of a subset of proteins NP_357089.2 required for the transfer of succinyl residues to the glucan backbone NP_357083.1 catalyzes the formation of 2-dehydro-3-deoxy-D-gluconate from mannonate NP_357070.1 in some organisms the DhaK and DhaL subunits are encoded by separate genes; in others they are fused; functions along with DhaM to phosphorylate dihydroxyacetone NP_357050.2 activates RNA polymerase to cleave back-tracked RNA during elongational pausing NP_357034.2 in Escherichia coli this homodimeric enzyme is expressed under aerobic conditions; anaerobic expression is repressed by the arcAB system; converts sn-glycerol-3-phosphate and ubiquinone-8 to dihydroxy acetone phosphate and ubiquinol-8; associates with the cytoplasmic membrane NP_357032.1 MDM; functions in conversion of succinate to propionate NP_357027.2 YghU; B2989; one of eight glutathione transferases from E. coli NP_357023.1 this tRNA synthetase lacks the tRNA anticodon interaction domain; instead this enzyme modifies tRNA(Asp) with glutamate by esterifying glutamate to the 2-amino-5-(4,5-dihydroxy-2-cyclopenten-1-yl) moiety of queosine generating a modified nucleoside at the first anticodon position of tRNAAsp; the modified tRNA does not bind elongation factor Tu NP_357015.2 converts (S)-3-hydroxybutanoyl-CoA to 3-acetoacetyl-CoA NP_357013.2 catalyzes the formation of arginine from (N-L-arginino)succinate NP_357000.2 dual function enzyme catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate and the formation of tyrosine from arogenate NP_356999.1 catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis NP_356994.2 required for 70S ribosome assembly NP_356986.1 catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis NP_356985.2 catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis NP_356983.1 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 NP_356982.1 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 NP_356975.2 a small basic protein that is one of the last in the subunit assembly; omission does not prevent assembly but the subunit is inactive; binds central domain of 16S rRNA NP_356949.1 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) NP_356917.2 catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs NP_356914.1 catalyzes the formation of 3-phosphonooxypyruvate from 3-phospho-D-glycerate in serine biosynthesis; can also reduce alpha ketoglutarate to form 2-hydroxyglutarate NP_356913.1 catalyzes the formation of 3-phosphonooxypyruvate and glutamate from O-phospho-L-serine and 2-oxoglutarate NP_356911.2 catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate NP_356906.2 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 NP_356898.1 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 NP_356897.1 plays an essential role in ATP-dependent branch migration of the Holliday junction NP_356896.1 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 NP_356885.1 catalyzes the formation of ribose 5-phosphate and xylulose 5-phosphate from sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate; can transfer ketol groups between several groups; in Escherichia coli there are two tkt genes, tktA expressed during exponential growth and the tktB during stationary phase NP_356883.2 the Vibrio parahaemolyticus gene VP2867 was found to be a potassium/proton antiporter; can rapidly extrude potassium against a potassium gradient at alkaline pH when cloned and expressed in Escherichia coli NP_356882.2 Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway NP_356878.1 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 NP_356876.1 proposed role in polysaccahride synthesis NP_356871.2 catalyzes the formation of thiamine monophosphate from 2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate and 4-methyl-5-(2-phosphono-oxyethyl)-thiazole NP_356867.2 With PurE catalyzes the conversion of aminoimidazole ribonucleotide to carboxyaminoimidazole ribonucleotide in the de novo purine nucleotide biosynthetic pathway YP_001542598.1 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 NP_356860.1 catalyzes the formation of phosphoenolpyruvate from pyruvate NP_356851.2 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 NP_356840.1 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 NP_356834.2 One of the components of the high-affinity ATP-driven potassium transport (or KDP) system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions NP_356833.1 catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions NP_356829.1 catalyzes the formation of fumarate from aspartate NP_356816.1 catalyzes the formation of methanethiol and 2-ocobutanoate from L-methionine NP_356800.1 catalyzes the formation of tetrahydropteroyl-L-glutamate and methionine from L-homocysteine and 5-methyltetrahydropteroyltri-L-glutamate NP_356737.1 in Escherichia coli this homodimeric enzyme is expressed under aerobic conditions; anaerobic expression is repressed by the arcAB system; converts sn-glycerol-3-phosphate and ubiquinone-8 to dihydroxy acetone phosphate and ubiquinol-8; associates with the cytoplasmic membrane NP_356720.2 converts 1,4-alpha-D-glucans to maltodextrin NP_356704.2 catalyzes the formation of 4-imidazolone-5-propanoate from urocanate during histidine metabolism NP_356702.1 catalyzes the degradation of histidine to urocanate and ammmonia NP_356701.2 catalyzing the hydrolysis of 4-imidazolone-5-propionate to N-formimidoyl-L-glutamate, the third step in the histidine degradation pathway NP_356700.2 catalyzes the deimination of N-formimino-L-glutamate to ammonia and N-formyl-L-glutamate NP_356670.1 catalyzes the formation of 3-methyl-2-oxobutanoate from 2,3,-dihydroxy-3-methylbutanoate NP_356656.1 catalyzes the formation of L-proline from pyrroline-5-carboxylate NP_356642.1 catalyzes the formation of 8-amino-7-oxononanoate from 6-carboxyhexanoyl-CoA and L-alanine NP_356641.1 DTB synthetase; dethiobiotin synthase; involved in production of dethiobiotin from ATP and 7,8-diaminononanoate and carbon dioxide; contains magnesium NP_356640.1 catalyzes the formation of S-adenosyl-4-methylthionine-2-oxobutanoate and 7,8-diaminononanoate from S-adenosyl-L-methionine and 8-amino-7-oxononanoate NP_356639.2 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 NP_356618.1 part of the FhuBCD ATP-dependent iron (III) hydroxamate transporter involved in the high-affinity transport of Fe(3+)-ferrichrome NP_356614.2 binds RecA and inhibits RecA-mediated DNA strand exchange and ATP hydrolysis and coprotease activities NP_356579.1 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 NP_356570.2 catalyzes the interconversion of alpha-D-glucose 1-phosphate to alpha-D-glucose 6-phosphate NP_356569.1 catalyzes the formation of alpha-1,4-glucan chains from ADP-glucose NP_356568.1 catalyzes the formation of ADP-glucose and diphosphate from ATP and alpha-D-glucose 1-phosphate NP_356567.1 catalyzes the transfer of a segment of a 1,4-alpha-D-glucan chain to a primary hydroxy group in a similar glucan chain NP_356560.2 catalyzes the formation of 5-dehydro-D-gluconate from D-gluconate NP_356550.2 catalyzes the formation of pyridine-2,3-dicarboxylate and 5-phospho-alpha-D-ribose 1-diphosphate from nictinate D-ribonucleotide NP_356549.1 catalyzes the formation of oxaloacetate from L-aspartate NP_356548.1 3 different subfamilies; catalyzes the formation of quinolinate from iminoaspartate and dihydroxyacetone phosphate NP_356543.1 Catalyzes the formation of (d)CDP from ATP and (d)CMP NP_356542.2 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 NP_356517.1 AcsA; in Sinorhizobium meliloti this enzyme is required for acetoacetate activation; similar to acetyl-CoA synthase NP_356501.2 The second step in the glutathione biosynthesis pathway, where it synthesizes ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione NP_356492.1 proline utilization protein A; multifunctional protein that functions in proline catabolism in the first two enzymatic steps resulting in the conversion of proline to glutamate; in Escherichia coli this protein self regulates transcription via a DNA-binding domain at the N-terminus but the protein from Pseudomonas does not have this domain NP_356490.2 Bacteria have multiple sigma factors which are active under specific conditions; the sigma factor binds with the catalytic core of RNA polymerase to produce the holoenzyme and directs bacterial core RNA polymerase to specific promoter elements to initiate transcription NP_356488.2 in Caulobacter crescentus, CC3477 is differentially expressed in minimal salts media with glucose as compared to complex media NP_356477.2 catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP, in Bacillus, lysine sensitive; regulated by response to starvation. NP_356475.1 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 NP_356438.2 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. NP_356423.2 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 NP_356375.2 catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate NP_356340.1 catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate NP_356339.2 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 NP_356261.1 catalyzes the formation of 2-octaprenylphenol from 3-octaprenyl-4-hydroxybenzoate NP_356246.1 periplasmic; catalytic subunit; with NapBC catalyzes the reduction of nitrate to nitrite; NapAB receives electrons from NapC NP_356228.2 unwinds double stranded DNA NP_356226.1 Involved in nucleotide synthesis and salvage NP_356214.1 catalyzes the hydrolysis of a monocarboxylic acid amid to form a monocarboxylate and ammonia NP_356200.1 role in sulfur assimilation NP_356184.1 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 NP_356183.2 Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation NP_356174.2 catalyzes the interconversion of D-xylose to D-xylulose NP_356163.2 catalyzes the formation of pyruvate and glyoxylate from 4-hydroxy-2-oxoglutarate; or pyruvate and D-glyceraldehyde 3-phosphate from 2-dehydro-3-deoxy-D-glyconate 6-phosphate NP_356127.2 catalyzes the formation of 3-dehydroshikimate from 3-dehydroquinate in chorismate biosynthesis NP_356126.1 AroE; catalyzes the conversion of shikimate to 3-dehydroshikimate NP_356120.1 Catalyzes the cycloisomerization of cis,cis-muconate NP_356114.2 catalyzes the formation of protocatechuate from 4-hydroxybenzoate NP_356109.2 catalyzes the thiolytic cleavage of beta-ketoadipyl-CoA to succinate and acetyl-CoA NP_355992.2 LovR from Caulobacter crescentus is a response regulator part of a two-component signaling system that regulates photosensitive bacterial cell-surface and cell-cell attachment NP_355991.1 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 NP_355967.2 Catalyzes the deamination of cytosine to uracil and ammonia NP_355966.2 Catalyzes the hydrolytic cleavage of a carbon-halogen bond in N-ethylammeline NP_355959.2 catalyzes the oxidation of formate to carbon dioxide and hydrogen using NAD or NADP as the acceptor NP_355930.2 catalyzes the conversion of citrate to isocitrate and the conversion of 2-methylaconitate to 2-methylisocitrate NP_355907.1 cyclodeaminase NP_355906.2 catalyzes the formation of 2-oxobutanoate from L-threonine; involved in ectoine utilization NP_355861.2 catalyzes the formation of 5-aminovulinate from (S)-4-amino-5-oxopentanoate NP_355840.1 activates fatty acids by binding to coenzyme A NP_355839.1 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 NP_355830.1 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 NP_355829.1 catalyzes the formation of D-glucono-1,5-lactone 6-phosphate from D-glucose 6-phosphate NP_395989.2 catalyzes the ATP dependent formation of a phosphodiester at the site of a single-strand break in duplex DNA NP_396043.1 VirD4 family NP_396055.1 Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis NP_396056.1 catalyzes the formation of 2-acetolactate from pyruvate, leucine sensitive; catalytic NP_396149.1 with ProVW, part of the high-affinity transport system for the osmoprotectant glycine betaine NP_396183.1 Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis NP_396239.2 forms citrate from oxaloacetate and acetyl-CoA; functions in TCA cycle NP_396276.2 Converts (S)-3-hydroxyacyl-CoA to 3-oxyacyl-CoA; may also act as a thioesterase NP_396294.1 porin involved in osmoregulation allowing water to move into and out of the cell in response to osmotic pressure NP_396403.1 involved in translesion DNA polymerization with beta clamp of polymerase III; belongs to Y family of polymerases; does not contain proofreading function NP_396474.1 Enables the enzymatic reduction of mercuric ions to elemental mercury NP_396527.1 catalyzes the formation of indole-3-acetic acid from indole-3-acetamide NP_396533.3 catalyzes the formation of L-proline from L-ornithine NP_396555.1 type IV secretion system ATPase; VirB4 family NP_396558.2 VirB11 family protein; ATPase NP_396583.2 catalyzes the cleavage of carbon-halogen bonds in aliphatic compounds forming a primary alcohol and a halide NP_396622.2 ParB family NP_396647.1 VirD4 family NP_396650.2 conjugal transfer system TraA; oriT nicking enzyme NP_396657.1 quorum-sensing transcriptional regulator NP_396498.2 ATPase NP_396505.2 coupling protein TraG/VirD4 family NP_396509.1 in Agrobacterium tumefaciens plasmid Ti this protein binds VirE2