-- dump date   	20140619_223957
-- class       	Genbank::CDS
-- table       	cds_note
-- id	note
YP_809660.1	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_809667.1	binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit
YP_809707.1	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_809799.1	Catalyzes the rate-limiting step in dNTP synthesis
YP_809800.1	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_809812.1	catalyzes the hydrolysis of both purine and pyrimidine ribonucleosides
YP_809817.1	Catalyzes D-ribose 5-phosphate --> D-ribulose 5-phosphate in the nonoxidative branch of the pentose phosphate pathway
YP_809873.1	required for cellobiose uptake and metabolism
YP_809905.1	catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis
YP_809910.1	involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate
YP_809911.1	catalyzes the conversion of dihydroorotate to orotate in the pyrimidine biosynthesis pathway; subclass 1A is a dimer formed by two identical PyrD subunits each containing an FMN group
YP_809924.1	catalyzes the formation of 1,4-dihydroxy-2-naphthoate from O-succinylbenzoyl-CoA
YP_809944.1	catalyzes the formation of alpha-D-glucose 1-phosphate and UDP-galactose from UDP-glucose and alpha-D-galactose 1-phosphate in galactose metabolism
YP_809945.1	catalyzes the formation of alpha-D-galactose 1-phosphate from D-galactose in galactose metabolism
YP_809959.1	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_809962.1	Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation
YP_809971.1	E3 component of pyruvate complex; catalyzes the oxidation of dihydrolipoamide to lipoamide
YP_810004.1	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_810017.1	catalyzes the formation of succinate semialdehyde and glutamate from 4-aminobutanoate and 2-oxoglutarate
YP_810045.1	acyl carrier protein; with CitE and CitF catalyzes the formation of oxaloacetate from citrate
YP_810049.1	catalyzes the reversible formation of 2'-(5''-triphosphoribosyl)-3'dephospho-CoA from 3-dephospho-CoA
YP_810057.1	IF-2; GTPase; 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_810068.1	required for 70S ribosome assembly
YP_810071.1	catalyzes branch migration in Holliday junction intermediates
YP_810075.1	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_810141.1	similar to zinc-dependent eukaryotic ADH enzymes and distinct from fermentative ADHs
YP_810164.1	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_810186.1	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_810189.1	binds to the ribosome on the universally-conserved alpha-sarcin loop
YP_810198.1	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_810205.1	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_810207.1	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_810209.1	located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e
YP_810212.1	binds to the 23S rRNA between the centers for peptidyl transferase and GTPase
YP_810214.1	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_810219.1	L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7
YP_810223.1	IF-1
YP_810225.1	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_810226.1	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_810233.1	mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability
YP_810235.1	in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit
YP_810242.1	Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source
YP_810259.1	catalyzes the formation of pyruvate from serine
YP_810265.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit
YP_810267.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit
YP_810274.1	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_810324.1	same as uCOG01554
YP_810362.1	some L32 proteins have zinc finger motifs consisting of CXXC while others do not
YP_810373.1	ThyA; catalyzes formation of dTMP and 7,8-dihydrofolate from 5,10-methylenetetrahydrofolate and dUMP; involved in deoxyribonucleotide biosynthesis; there are 2 copies in some Bacilli, one of which appears to be phage-derived
YP_810383.1	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_810392.1	methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA
YP_810393.1	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_810396.1	cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+)
YP_810424.1	catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase
YP_810425.1	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_810434.1	BacA; phosphatase activity in Escherichia coli not kinase; involved in bacitracin resistance as bacitracin supposedly sequesters undecaprenyl disphosphate which reduces the pool of lipid carrier available to the cell
YP_810472.1	catalyzes the formation of 5-phospho-alpha-D-ribose 1-diphosphate and nicotinate from nicotinate D-ribonucleotide and diphosphate
YP_810488.1	in Bacillus subtilis this enzyme appears to be involved in 30S ribosomal RNA subunit biogenesis
YP_810499.1	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_810517.1	catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming
YP_810521.1	ACT domain-containing protein
YP_810525.1	Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway
YP_810534.1	involved in the peptidyltransferase reaction during translation
YP_810550.1	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_810558.1	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_810566.1	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_810572.1	catalyzes the release of the N-terminal amino acid from a tripeptide
YP_810600.1	decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling
YP_810603.1	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_810609.1	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_810613.1	forms a homotetramer; hydrolyzes lactose disaccharide to galactose and glucose; converts lactose to allolactose which is the natural inducer of the lac operon
YP_810636.1	catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis
YP_810640.1	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_810658.1	functions in homologous recombination, DNA repair, and chromosome segregation; binds preferentially to three- and four-stranded DNA intermediates; introduces specific nick sites in four-stranded DNA substrates; functions similarly to Escherichia coli RuvC
YP_810667.1	catalyzes the isomerization of isopentenyl pyrophosphate to dimethylallyl diphosphate
YP_810680.1	Catalyzes the reduction of nucleoside 5'-triphosphates to 2'-deoxynucleoside 5'-triphosphates
YP_810686.1	contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway
YP_810689.1	catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis
YP_810691.1	involved in de novo purine biosynthesis
YP_810694.1	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_810697.1	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_810698.1	With PurE catalyzes the conversion of aminoimidazole ribonucleotide to carboxyaminoimidazole ribonucleotide in the de novo purine nucleotide biosynthetic pathway
YP_810709.1	First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
YP_810713.1	MraZ; UPF0040; crystal structure shows similarity to AbrB
YP_810720.1	catalyzes the phosphorylation of NAD to NADP
YP_810728.1	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_810807.1	Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis
YP_810818.1	IF-3
YP_810833.1	catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids
YP_810851.1	EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene
YP_810852.1	binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit
YP_810853.1	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_810866.1	catalyzes the formation of 2-dehydro-3-deoxy-D-octonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate in LPS biosynthesis
YP_810901.1	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_810909.1	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_810920.1	acts to negatively regulates ftsZ ring formation by modulating the frequency and position of the ftsZ ring formation
YP_810925.1	modulates transcription in response to the NADH/NAD(+) redox state
YP_810936.1	involved in a recombinational process of DNA repair, independent of the recBC complex
YP_810938.1	catalyzes the removal of N-terminal dipeptides when proline is the penultimate residue
YP_810943.1	binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit
YP_810964.1	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_811045.1	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_811065.1	catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP; lysine and threonine sensitive
YP_811066.1	catalyzes the formation of L-threonine from O-phospho-L-homoserine
YP_811079.1	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_811082.1	catalyzes the hydrolysis of S-ribosylhomocysteine to homocysteine and autoinducer-2
YP_811084.1	malic enzyme; oxaloacetate-decarboxylating; NAD-dependent; catalyzes the formation of pyruvate form malate
YP_811120.1	catalyzes the formation of (R)-4'-phosphopantothenate in coenzyme A biosynthesis
YP_811128.1	Catalyzes D-ribose 5-phosphate --> D-ribulose 5-phosphate in the nonoxidative branch of the pentose phosphate pathway
YP_811130.1	cytoplasmic mutarotase that catalyzes the conversion between beta-pyran and beta-furan forms of D-ribose; RbsD is required for efficient ribose utilization in E. coli; rbsD-mutant E. coli strains are unable to use ribose as a sole carbon source
YP_811189.1	similar to YegS from E. coli
YP_811214.1	catalyzes the formation of 2-acetolactate from pyruvate in stationary phase
YP_811225.1	in group A Streptococci this protein was found to cross react with anti myosin antibodies and may play a role in rheumatic fever
YP_811238.1	binds and unfolds substrates as part of the ClpXP protease
YP_811290.1	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_811302.1	catalyzes the formation of oxaloacetate from phosphoenolpyruvate
YP_811304.1	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_811319.1	catalyzes the formation of acetyl phosphate from pyruvate