-- dump date 20140619_160546 -- class Genbank::CDS -- table cds_note -- id note NP_072661.2 identified by sequence similarity NP_072662.2 identified by sequence similarity NP_072663.1 negatively supercoils closed circular double-stranded DNA NP_072664.1 negatively supercoils closed circular double-stranded DNA NP_072665.1 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 NP_072666.1 identified by sequence similarity NP_072667.1 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 NP_072668.1 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 NP_072669.1 identified by sequence similarity NP_072670.1 identified by sequence similarity NP_072671.1 identified by sequence similarity NP_072672.1 identified by sequence similarity NP_072673.2 identified by sequence similarity NP_072674.1 identified by sequence similarity NP_072675.1 identified by sequence similarity NP_072678.2 identified by sequence similarity NP_072679.1 identified by sequence similarity NP_072680.1 identified by sequence similarity NP_072681.1 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 NP_072682.1 participates in both the initiation and recycling phases of transcription; in the presence of the delta subunit, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling NP_072683.1 identified by sequence similarity NP_072684.1 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 NP_072685.1 identified by sequence similarity NP_072686.1 Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA NP_072687.1 identified by sequence similarity NP_072688.1 identified by sequence similarity NP_072689.1 identified by sequence similarity NP_072690.1 Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate NP_072691.1 catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; required for leading strand synthesis; PolC exhibits 3' to 5' exonuclease activity NP_072692.1 identified by sequence similarity NP_072693.1 identified by sequence similarity NP_072694.1 catalyzes the formation of thymidine 5'-phosphate from thymidine NP_072695.1 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 NP_072696.1 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 NP_072697.1 identified by sequence similarity NP_072698.1 Converts glycerol and ADP to glycerol-3-phosphate and ADP NP_072699.1 identified by sequence similarity NP_072700.1 identified by sequence similarity NP_072701.1 identified by sequence similarity NP_072702.1 identified by sequence similarity NP_072703.1 identified by sequence similarity NP_072704.1 identified by sequence similarity NP_072705.1 identified by sequence similarity NP_072706.1 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 NP_072707.1 methionine adenosyltransferase; catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase NP_072708.1 identified by sequence similarity NP_072709.2 catalyzes the reversible phosphorolysis of ribonucleosides and 2'- deoxyribonucleosides to the free base and (2'-deoxy)ribose-1- phosphate NP_072710.1 catalyzes the formation of D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-D-ribose-5-phosphate NP_072711.1 Catalyzes the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate NP_072712.1 identified by sequence similarity NP_072713.1 identified by sequence similarity NP_072714.1 identified by sequence similarity NP_072715.1 forms a complex with SecY and SecG; SecYEG forms a protein-conducting channel to which secA binds and translocates targeted polypeptides across the cytoplasmic membrane, a process driven by ATP and a proton-motive force NP_072716.1 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 have the CXXC motif NP_072717.1 identified by sequence similarity NP_072718.1 identified by sequence similarity NP_072719.1 identified by sequence similarity NP_072720.2 catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP NP_072721.1 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 NP_072722.1 identified by sequence similarity NP_072723.2 identified by sequence similarity NP_072724.1 identified by sequence similarity NP_072725.2 identified by sequence similarity NP_072726.1 identified by sequence similarity NP_072727.1 identified by sequence similarity NP_072728.1 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_072729.1 identified by sequence similarity NP_072730.1 identified by sequence similarity NP_072731.1 identified by sequence similarity NP_072732.1 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 NP_072733.1 identified by sequence similarity NP_072734.1 functions in protein export; can interact with acidic membrane phospholipids and the SecYEG protein complex; binds to preproteins; binds to ATP and undergoes a conformational change to promote membrane insertion of SecA/bound preprotein; ATP hydrolysis appears to drive release of the preprotein from SecA and deinsertion of SecA from the membrane; additional proteins SecD/F/YajC aid SecA recycling; exists in an equilibrium between monomers and dimers; may possibly form higher order oligomers; in some organisms, there are paralogous proteins that have been found to be nonessential but do function in secretion of a subset of exported proteins NP_072735.1 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 NP_072736.1 identified by sequence similarity NP_072737.1 identified by sequence similarity NP_072738.1 identified by sequence similarity NP_072739.1 identified by sequence similarity NP_072740.1 identified by sequence similarity NP_072741.1 identified by sequence similarity NP_072742.1 identified by sequence similarity NP_072743.1 binds directly to 23S ribosomal RNA NP_072744.1 in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA NP_072745.1 Enables the recycling of peptidyl-tRNAs produced at termination of translation NP_072746.1 identified by sequence similarity NP_072747.1 catalyzes the phosphorylation of the phosphocarrier protein HPr of the bacterial phosphotransferase system NP_072748.1 transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein NP_072749.1 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 NP_072750.1 binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit NP_072751.1 EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene NP_072752.1 binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21 NP_072753.1 identified by sequence similarity NP_072754.1 binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit NP_072755.1 in Escherichia coli this protein is wrapped around the base of the L1 stalk NP_072756.2 identified by sequence similarity NP_072757.1 identified by sequence similarity NP_072758.1 identified by sequence similarity NP_072759.1 Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine NP_072760.1 contains unknown domain at the N-terminus that is found by itself in some proteins by in others is fused to GatC at the C-terminus NP_072761.1 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 NP_072762.1 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 NP_072763.1 identified by sequence similarity NP_072764.1 identified by sequence similarity NP_072765.1 identified by sequence similarity NP_072766.1 identified by sequence similarity NP_072767.2 identified by sequence similarity NP_072768.2 cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+) NP_072769.1 identified by sequence similarity NP_072770.1 identified by sequence similarity NP_072771.2 identified by sequence similarity NP_072772.1 identified by sequence similarity NP_072773.2 functions in sugar metabolism in glycolysis and the Embden-Meyerhof pathways (EMP) and in gluconeogenesis; catalyzes reversible isomerization of glucose-6-phosphate to fructose-6-phosphate; member of PGI family NP_072774.1 catalyzes the interconversion of D-ribulose 5-phosphate to xylulose 5-phosphate NP_072775.1 catalyzes a two-step reaction, first charging an asparagine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA NP_072776.1 identified by sequence similarity NP_072777.1 identified by sequence similarity NP_072778.1 identified by sequence similarity NP_072779.1 identified by sequence similarity NP_072780.1 identified by sequence similarity NP_072781.1 identified by sequence similarity NP_072782.1 identified by sequence similarity NP_072783.1 identified by sequence similarity NP_072784.1 catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity NP_072785.1 identified by sequence similarity NP_072786.1 identified by sequence similarity NP_072787.1 identified by sequence similarity NP_072788.1 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 NP_072789.1 identified by sequence similarity NP_072790.1 catalyzes the phosphorylation of NAD to NADP NP_072791.1 identified by sequence similarity NP_072792.1 identified by sequence similarity NP_072794.1 identified by sequence similarity NP_072795.2 identified by sequence similarity NP_072796.1 identified by sequence similarity NP_072797.1 identified by sequence similarity NP_072798.1 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_072799.1 identified by sequence similarity NP_072800.1 binds to the ribosome on the universally-conserved alpha-sarcin loop NP_072801.1 identified by sequence similarity NP_072802.1 identified by sequence similarity NP_072803.1 modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination NP_072804.1 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 NP_072805.1 identified by sequence similarity NP_072806.1 identified by sequence similarity NP_072807.1 identified by sequence similarity NP_072808.1 identified by sequence similarity NP_072809.2 identified by sequence similarity NP_072810.1 identified by sequence similarity NP_072811.1 identified by sequence similarity NP_072812.2 identified by sequence similarity NP_072813.1 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 NP_072814.1 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 NP_072815.1 L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA NP_072816.1 binds third domain of 23S rRNA and protein L29; part of exit tunnel NP_072817.1 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 NP_072818.1 protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA NP_072819.1 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 NP_072820.1 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 NP_072821.1 located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e NP_072822.1 one of the stabilizing components for the large ribosomal subunit NP_072823.1 primary binding protein; helps mediate assembly; involved in translation fidelity NP_072824.1 binds to the 23S rRNA between the centers for peptidyl transferase and GTPase NP_072825.1 assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel NP_072826.1 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 NP_072827.1 located in the peptidyl transferase center and involved in assembly of 30S ribosome subunit; similar to what is observed with proteins L31 and L33, some proteins in this family contain CXXC motifs that are involved in zinc binding; if two copies are present in a genome, then the duplicated copy appears to have lost the zinc-binding motif and is instead regulated by zinc; the proteins in this group appear to contain the zinc-binding motif NP_072828.1 binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit NP_072829.1 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 NP_072830.1 binds 5S rRNA along with protein L5 and L25 NP_072831.1 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 NP_072832.1 late assembly protein NP_072833.1 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 NP_072834.1 identified by sequence similarity NP_072835.1 identified by sequence similarity NP_072836.1 identified by sequence similarity NP_072837.1 smallest protein in the large subunit; similar to what is found with protein L31 and L33 several bacterial genomes contain paralogs which may be regulated by zinc; the protein from Thermus thermophilus has a zinc-binding motif and contains a bound zinc ion; the proteins in this group have the motif NP_072838.1 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 NP_072839.2 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 NP_072840.1 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 NP_072841.1 is a component of the macrolide binding site in the peptidyl transferase center NP_072842.1 with CbiNQ forms the ABC transporter for cobalt import; Mycoplasmas have two adjacent copies of this gene NP_072843.1 with CbiNQ forms the ABC transporter for cobalt import; Mycoplasmas have two adjacent copies of this gene NP_072844.1 identified by sequence similarity NP_072845.1 mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability NP_072846.1 identified by sequence similarity NP_072847.1 identified by sequence similarity NP_072848.1 identified by sequence similarity NP_072849.1 identified by sequence similarity NP_072850.1 identified by sequence similarity NP_072851.1 identified by sequence similarity NP_072852.2 identified by sequence similarity NP_072853.2 identified by sequence similarity NP_072854.1 identified by sequence similarity NP_072855.2 identified by sequence similarity NP_072856.1 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 NP_072857.1 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 NP_072858.1 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 NP_072859.1 identified by sequence similarity NP_072860.1 binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit NP_072862.1 identified by sequence similarity NP_072863.1 identified by sequence similarity NP_072864.1 identified by sequence similarity NP_072865.1 identified by sequence similarity NP_072866.1 identified by sequence similarity NP_072867.1 Negative regulator of class I heat shock genes (grpE-dnaK-dnaJ and groELS operons). Prevents heat-shock induction of these operons NP_072868.1 identified by sequence similarity NP_072869.1 identified by sequence similarity NP_072870.1 identified by sequence similarity NP_072871.1 identified by sequence similarity NP_072872.1 lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis NP_072873.1 identified by sequence similarity NP_072874.1 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_072875.1 identified by sequence similarity NP_072876.1 Catalyzes the formation of holo-ACP, which mediates the essential transfer of acyl fatty acid intermediates during the biosynthesis of fatty acids and lipids NP_072877.1 identified by sequence similarity NP_072878.1 functions during chromosome segregation; may form a condensin-like structure with SMC and ScpB NP_072879.1 functions during chromosome segregation; may form a condensin-like structure with SMC and ScpA; forms a homodimer NP_072880.1 catalyzes the formation of D-fructose 1,6-bisphosphate from D-fructose 6-phosphate in glycolysis NP_072881.1 catalyzes the formation of phosphoenolpyruvate from pyruvate NP_072882.1 identified by sequence similarity NP_072883.1 identified by sequence similarity NP_072884.1 identified by sequence similarity NP_072885.1 hypothetical protein; identified by GeneMark NP_072886.2 identified by sequence similarity NP_072887.2 MraZ; UPF0040; crystal structure shows similarity to AbrB NP_072888.1 identified by sequence similarity NP_072889.1 identified by sequence similarity NP_072890.1 identified by sequence similarity NP_072891.1 identified by sequence similarity NP_072892.2 identified by sequence similarity NP_072893.1 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 NP_072894.1 identified by sequence similarity NP_072895.1 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 NP_072896.1 in Salmonella NrdI has a stimulatory effect on the ribonucleotide reductase activity of NrdH with NrdEF NP_072897.1 Catalyzes the rate-limiting step in dNTP synthesis NP_072898.1 identified by sequence similarity NP_072899.1 identified by sequence similarity NP_072900.1 involved in the peptidyltransferase reaction during translation NP_072901.1 identified by sequence similarity NP_072902.1 identified by sequence similarity NP_072903.1 identified by sequence similarity NP_072904.1 identified by sequence similarity NP_072905.1 identified by sequence similarity NP_072906.2 catalyzes the reversible adenylation of nicotinate mononucleotide to nicotinic acid adenine dinucleotide NP_072907.1 identified by sequence similarity NP_072908.1 identified by sequence similarity NP_072909.1 identified by sequence similarity NP_072910.1 identified by sequence similarity NP_072911.1 identified by sequence similarity NP_072912.1 involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsX NP_072913.1 identified by sequence similarity NP_072914.1 sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released NP_072915.1 identified by sequence similarity NP_072916.1 Catalyzes a two-step reaction, first charging a glycine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA NP_072917.1 identified by sequence similarity NP_072918.1 identified by sequence similarity NP_072919.1 identified by sequence similarity NP_072920.1 identified by sequence similarity NP_072922.1 identified by sequence similarity NP_072923.1 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 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_072924.1 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_072925.1 identified by sequence similarity NP_072926.1 identified by sequence similarity NP_072927.1 identified by sequence similarity NP_072928.1 identified by sequence similarity NP_072929.1 Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases NP_072930.1 identified by sequence similarity NP_072931.1 identified by sequence similarity NP_072932.1 identified by sequence similarity NP_072933.1 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 NP_072934.1 identified by sequence similarity NP_072935.1 identified by sequence similarity NP_072936.1 identified by sequence similarity NP_072937.1 identified by sequence similarity NP_072938.1 identified by sequence similarity NP_072939.1 Catalyzes the transfer of acetyl from acetyldihydrolipoamide to coenzyme A to form acetyl CoA NP_072940.1 identified by sequence similarity NP_072941.1 identified by sequence similarity NP_072942.2 identified by sequence similarity NP_072943.1 catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis NP_072944.1 identified by sequence similarity NP_072945.1 identified by sequence similarity NP_072946.1 identified by sequence similarity NP_072947.2 identified by sequence similarity NP_072948.1 identified by sequence similarity NP_072949.1 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 NP_072950.1 catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro) NP_072951.1 identified by sequence similarity NP_072952.1 identified by sequence similarity NP_072953.1 identified by sequence similarity NP_072954.1 carries the fatty acid chain in fatty acid biosynthesis NP_072955.1 identified by sequence similarity NP_072956.1 identified by sequence similarity NP_072957.1 identified by sequence similarity NP_072958.1 identified by sequence similarity NP_072959.1 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 NP_072960.1 identified by sequence similarity NP_072961.1 identified by sequence similarity NP_072962.1 catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs NP_072963.1 identified by sequence similarity NP_072964.1 identified by sequence similarity NP_072965.1 identified by sequence similarity NP_072966.1 in Salmonella this enzyme is required for ethanolamine catabolism; has higher affinity for CoA than Pta NP_072967.2 Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway NP_072968.1 catalyzes the formation of 3-phospho-D-glyceroyl phosphate from D-glyceraldehyde 3-phosphate NP_072969.1 identified by sequence similarity NP_072970.1 identified by sequence similarity NP_072971.2 identified by sequence similarity NP_072972.1 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 NP_072973.1 identified by sequence similarity NP_072974.1 identified by sequence similarity NP_072975.1 identified by sequence similarity NP_072976.2 identified by sequence similarity NP_072977.1 identified by sequence similarity NP_072978.1 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 NP_072979.1 identified by sequence similarity NP_072980.1 identified by sequence similarity NP_072981.1 identified by sequence similarity NP_072982.1 identified by sequence similarity NP_072983.1 identified by sequence similarity NP_072984.1 identified by sequence similarity NP_072985.1 identified by sequence similarity NP_072986.1 identified by sequence similarity NP_072987.1 identified by sequence similarity NP_072989.1 identified by sequence similarity NP_072990.1 identified by sequence similarity NP_072991.1 identified by sequence similarity NP_072992.1 identified by sequence similarity NP_072993.1 identified by sequence similarity NP_072994.1 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 have the CXXC motif NP_072995.1 identified by sequence similarity NP_072996.1 identified by sequence similarity NP_072997.1 identified by sequence similarity NP_072998.1 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 NP_072999.1 identified by sequence similarity NP_073000.1 identified by sequence similarity NP_073001.1 identified by sequence similarity NP_073002.1 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 NP_073003.1 binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential NP_073004.1 hypothetical protein; identified by GeneMark NP_073005.1 identified by sequence similarity NP_073006.1 identified by sequence similarity NP_073007.1 identified by sequence similarity NP_073008.2 identified by sequence similarity NP_073009.1 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 NP_073010.2 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 NP_073011.1 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 NP_073012.1 identified by sequence similarity NP_073013.1 identified by sequence similarity NP_073014.1 identified by sequence similarity NP_073015.2 IleRS; catalyzes the formation of isoleucyl-tRNA(Ile) from isoleucine and tRNA(Ile); since isoleucine and other amino acids such as valine are similar, there are additional editing function in this enzyme; one is involved in hydrolysis of activated valine-AMP and the other is involved in deacylation of mischarged Val-tRNA(Ile); there are two active sites, one for aminoacylation and one for editing; class-I aminoacyl-tRNA synthetase family type 1 subfamily; some organisms carry two different copies of this enzyme NP_073016.1 identified by sequence similarity NP_073017.1 identified by sequence similarity NP_073018.1 identified by sequence similarity NP_073019.1 identified by sequence similarity NP_073020.1 identified by sequence similarity NP_073021.1 identified by sequence similarity NP_073022.1 catalyzes the hydrolysis of pyrophosphate to phosphate NP_073023.1 identified by sequence similarity NP_073024.1 identified by sequence similarity NP_073025.1 identified by sequence similarity NP_073026.1 identified by sequence similarity NP_073027.1 identified by sequence similarity NP_073028.1 AckA utilizes acetate and can acetylate CheY which increases signal strength during flagellar rotation; utilizes magnesium and ATP; also involved in conversion of acetate to aceyl-CoA NP_073029.2 plays an essential role in ATP-dependent branch migration of the Holliday junction NP_073030.1 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_073031.1 identified by sequence similarity NP_073032.1 binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit NP_073033.1 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 NP_073034.1 some L32 proteins have zinc finger motifs consisting of CXXC while others do not NP_073035.1 binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase NP_073036.1 identified by sequence similarity NP_073037.1 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 NP_073038.1 identified by sequence similarity NP_073039.1 identified by sequence similarity NP_073040.1 involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY NP_073041.1 identified by sequence similarity NP_073042.1 identified by sequence similarity NP_073043.1 identified by sequence similarity NP_073044.1 Required for the synthesis of the thiazole moiety NP_073045.1 identified by sequence similarity NP_073046.1 identified by sequence similarity NP_073047.1 identified by sequence similarity NP_073048.1 identified by sequence similarity NP_073049.1 identified by sequence similarity NP_073050.1 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 NP_073051.1 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 NP_073052.1 identified by sequence similarity NP_073053.1 identified by sequence similarity NP_073054.1 functions in pyrimidine salvage; pyrimidine ribonucleoside kinase; phosphorylates nucleosides or dinucleosides to make UMP or CMP using ATP or GTP as the donor NP_073055.1 identified by sequence similarity NP_073056.1 essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication NP_073057.1 identified by sequence similarity NP_073058.1 identified by sequence similarity NP_073059.1 identified by sequence similarity NP_073060.1 identified by sequence similarity NP_073061.2 identified by sequence similarity NP_073062.1 identified by sequence similarity NP_073063.1 identified by sequence similarity NP_073064.1 catalyzes the removal of N-terminal amino acids preferably leucine from various peptides NP_073065.2 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 NP_073066.1 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 NP_073067.1 catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate NP_073068.1 identified by sequence similarity NP_073069.1 catalyzes the interconversion of ribose 5-phosphate to ribulose 5-phosphate; enzyme from E. coli shows allose 6-phosphate isomerase activity NP_073070.1 identified by sequence similarity NP_073071.1 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 NP_073072.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit NP_073073.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit NP_073074.1 produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit NP_073075.1 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 NP_073076.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B is part of the membrane proton channel. NP_073077.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit C is part of the membrane proton channel F0 NP_073078.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit A is part of the membrane proton channel F0 NP_073079.2 identified by sequence similarity NP_073080.1 enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis NP_073081.1 this stereospecific enzymes reduces the S isomer of methionine sulfoxide while MsrB reduces the R form; provides protection against oxidative stress NP_073082.1 identified by sequence similarity NP_073083.1 identified by sequence similarity NP_073084.1 identified by sequence similarity NP_073085.1 identified by sequence similarity NP_073086.1 identified by sequence similarity NP_073087.2 identified by sequence similarity NP_073088.1 forms a direct contact with the tRNA during translation NP_073089.1 in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit NP_073090.2 catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the tau chain serves as a scaffold to help in the dimerizaton of the alpha,epsilon and theta core complex; the gamma chain seems to interact with the delta and delta' subunits to transfer the beta subunit on the DNA NP_073092.1 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 NP_073093.1 identified by sequence similarity NP_073094.1 identified by sequence similarity NP_073095.1 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 NP_073096.1 identified by sequence similarity NP_073097.1 required for 70S ribosome assembly NP_073098.1 identified by sequence similarity NP_073099.1 identified by sequence similarity NP_073100.1 identified by sequence similarity NP_073101.2 catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate NP_073102.1 Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate NP_073103.1 identified by sequence similarity NP_073104.1 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 NP_073105.1 identified by sequence similarity NP_073106.1 identified by sequence similarity NP_073107.2 hypothetical protein; identified by GeneMark NP_073108.1 identified by sequence similarity NP_073109.1 identified by sequence similarity NP_073110.1 identified by sequence similarity NP_073111.1 identified by sequence similarity NP_073112.1 essential GTPase; functions in ribosome assembly; binds a unique part of the 23S rRNA; interacts with ribosomal protein L25(Ctc) NP_073113.1 identified by sequence similarity NP_073114.1 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 NP_073115.1 methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA NP_073116.2 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 NP_073117.1 identified by sequence similarity NP_073118.1 this stereospecific enzymes reduces the R isomer of methionine sulfoxide while MsrA reduces the S form; provides protection against oxidative stress NP_073120.2 identified by sequence similarity NP_073121.1 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 NP_073122.1 identified by sequence similarity NP_073123.1 identified by sequence similarity NP_073124.1 identified by sequence similarity NP_073125.2 identified by sequence similarity NP_073126.1 identified by sequence similarity NP_073127.1 identified by sequence similarity NP_073128.1 identified by sequence similarity NP_073129.1 identified by sequence similarity NP_073130.1 identified by sequence similarity NP_073131.2 identified by sequence similarity NP_073132.1 Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation NP_073133.1 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 NP_073134.1 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 NP_073135.1 identified by sequence similarity NP_073136.1 in Escherichia coli transcription of this gene is enhanced by polyamines NP_073137.1 identified by sequence similarity NP_073138.1 identified by sequence similarity NP_073139.1 identified by sequence similarity NP_073140.1 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. NP_073141.1 identified by sequence similarity