-- dump date 20140619_161024 -- class Genbank::CDS -- table cds_note -- id note YP_278806.1 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_278807.1 identified by sequence similarity; ORF located using Blastx; COG0592 YP_278808.1 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_278809.1 identified by sequence similarity; ORF located using Blastx; COG1576 YP_278810.1 identified by sequence similarity; ORF located using Blastx; COG0618 YP_278811.1 identified by sequence similarity; ORF located using Blastx; COG0618 YP_278813.1 identified by sequence similarity; ORF located using Blastx; COG0552 YP_278814.1 identified by sequence similarity; ORF located using Glimmer; GeneMark; Blastx; COG0595 YP_278815.1 Negative regulator of class I heat shock genes (grpE-dnaK-dnaJ and groELS operons). Prevents heat-shock induction of these operons YP_278816.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG0576 YP_278817.1 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_278819.1 identified by sequence similarity; ORF located using Glimmer; GeneMark; Blastx; COG0191 YP_278820.1 identified by sequence similarity; ORF located using Blastx; COG0564 YP_278823.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG1136; TC:3.A.1.123.3 YP_278824.1 identified by sequence similarity; ORF located using Blastx; COG1136; TC:3.A.1.123.3 YP_278825.1 identified by sequence similarity; ORF located using Blastx; COG1136; TC:3.A.1.123.4 YP_278827.1 identified by sequence similarity; ORF located using Blastx; COG0681 YP_278828.1 identified by sequence similarity; ORF located using Blastx; COG0721 YP_278829.1 catalyzes the hydrolysis of a monocarboxylic acid amid to form a monocarboxylate and ammonia YP_278830.1 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_278832.1 identified by sequence similarity; ORF located using Blastx; COG0597 YP_278833.1 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 type 1 subfamily; some organisms carry two different copies of this enzyme YP_278834.1 decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling YP_278835.1 identified by sequence similarity; ORF located using Blastx; COG0187 YP_278836.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG0057 YP_278838.1 identified by sequence similarity; ORF located using Blastx; COG0557 YP_278839.1 identified by sequence similarity; ORF located using Blastx; COG1502 YP_278840.1 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_278841.1 identified by sequence similarity; ORF located using Blastx; COG0510 YP_278842.1 essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication YP_278846.1 identified by sequence similarity; ORF located using Blastx; COG0389 YP_278848.1 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_278849.1 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_278850.1 identified by sequence similarity; ORF located using Blastx; COG0711 YP_278851.1 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_278852.1 produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit YP_278853.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG0224 YP_278854.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit YP_278855.1 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_278856.1 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_278857.1 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_278858.1 identified by sequence similarity; ORF located using Blastx; COG0541; TC:3.A.5.1.1 YP_278859.1 Catalyzes a two-step reaction, first charging a glycine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA YP_278860.1 identified by sequence similarity; ORF located using Blastx; COG0358 YP_278861.1 sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released YP_278862.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG0327 YP_278863.1 Assists in DNA repair by cleaving phosphodiester bonds at apurinic or apyrimidinic sties to produce new 5' ends that are base-free deoxyribose 5-phosphate residues YP_278864.1 identified by sequence similarity; ORF located using Blastx; COG0162 YP_278865.1 identified by sequence similarity; ORF located using Blastx; COG1112 YP_278866.1 identified by sequence similarity; ORF located using Blastx YP_278867.1 identified by sequence similarity; ORF located using Blastx; COG0322 YP_278868.1 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_278869.1 identified by sequence similarity; ORF located using Glimmer; GeneMark; Blastx; COG0484 YP_278870.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG0283 YP_278871.1 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_278872.1 identified by sequence similarity; ORF located using Blastx; COG0776 YP_278873.1 identified by sequence similarity; ORF located using Blastx YP_278874.1 binds to the ribosome on the universally-conserved alpha-sarcin loop YP_278876.1 EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene YP_278877.1 binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit YP_278878.1 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_278880.1 identified by sequence similarity; ORF located using Blastx YP_278881.1 identified by sequence similarity; ORF located using Blastx YP_278882.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG0531; TC:2.A.3.6.1 YP_278883.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG0446; TC:3.D.1.1.1 YP_278884.1 identified by sequence similarity; ORF located using Blastx; COG0213 YP_278885.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG0813 YP_278887.2 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; in some organisms, there are paralogous proteins that have been found to be nonessential but do function in secretion of a subset of exported proteins YP_278888.1 essential GTPase; functions in ribosome assembly; binds a unique part of the 23S rRNA; interacts with ribosomal protein L25(Ctc) YP_278890.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG1404 YP_278892.1 identified by sequence similarity; ORF located using Glimmer; Blastx YP_278893.1 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_278894.1 identified by sequence similarity; ORF located using Blastx; COG0595 YP_278896.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG4487 YP_278898.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG2077 YP_278899.1 transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein YP_278900.1 identified by sequence similarity; ORF located using Glimmer; GeneMark; Blastx; COG0492 YP_278901.1 identified by sequence similarity; ORF located using Blastx YP_278903.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG0542 YP_278904.1 Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate YP_278905.1 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_278907.1 copy 2; identified by sequence similarity; ORF located using Blastx YP_278908.1 copy 2; identified by sequence similarity; ORF located using Blastx YP_278909.1 identified by sequence similarity; ORF located using GeneMark; Blastx; COG0187 YP_278910.1 identified by sequence similarity; ORF located using Blastx; COG0205 YP_278912.1 identified by sequence similarity; ORF located using Blastx; COG0531; TC:2.A.3.8.7 YP_278913.1 catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis YP_278914.1 identified by sequence similarity; ORF located using Glimmer; GeneMark; Blastx; COG1071 YP_278915.1 identified by sequence similarity; ORF located using GeneMark; Blastx; COG0022 YP_278916.1 identified by sequence similarity; ORF located using Glimmer; Blastx YP_278919.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG0542 YP_278921.1 required for 70S ribosome assembly YP_278922.1 binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit YP_278923.2 identified by sequence similarity; ORF located using Blastx; COG0291 YP_278924.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG0290 YP_278925.1 catalyzes the formation of phosphoenolpyruvate from pyruvate YP_278926.1 identified by sequence similarity; ORF located using Blastx YP_278928.1 identified by sequence similarity; ORF located using Blastx; COG1363 YP_278929.1 Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine YP_278930.1 identified by sequence similarity; ORF located using Blastx; COG0261 YP_278931.1 involved in the peptidyltransferase reaction during translation YP_278932.1 identified by sequence similarity; ORF located using Blastx; COG0596 YP_278934.1 identified by sequence similarity; ORF located using Blastx; COG0477 YP_278935.1 identified by sequence similarity; ORF located using Blastx; COG0039 YP_278936.1 identified by sequence similarity; ORF located using Blastx YP_278937.1 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_278938.1 identified by sequence similarity; ORF located using Blastx; COG2890 YP_278939.1 Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation YP_278941.1 identified by sequence similarity; ORF located using Blastx; COG0219 YP_278942.1 identified by sequence similarity; ORF located using Blastx; COG0566 YP_278943.1 identified by sequence similarity; ORF located using Blastx; COG2059; TC:2.A.51.1.2 YP_278944.1 identified by sequence similarity; ORF located using Blastx; COG2059 YP_278945.1 identified by sequence similarity; ORF located using Glimmer; Blastx YP_278946.1 identified by sequence similarity; ORF located using Blastx; COG1281 YP_278947.1 Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer YP_278949.1 catalyzes the interconversion of D-ribulose 5-phosphate to xylulose 5-phosphate YP_278950.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG1162 YP_278951.1 Essential for recycling GMP and indirectly, cGMP YP_278952.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG0742 YP_278953.1 identified by sequence similarity; ORF located using Glimmer; Blastx YP_278954.1 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_278955.1 identified by sequence similarity; ORF located using Blastx; COG0295 YP_278956.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG0319 YP_278958.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG2274; TC:3.A.1.112.4 YP_278959.1 catalyzes the transfer of phosphate between the C1 and C5 carbons of pentose YP_278961.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG1189 YP_278962.1 identified by sequence similarity; ORF located using Blastx; COG0520 YP_278963.1 identified by sequence similarity; ORF located using Blastx; COG0822 YP_278964.1 identified by sequence similarity; ORF located using Blastx; COG1187 YP_278965.1 is a component of the macrolide binding site in the peptidyl transferase center YP_278966.1 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_278967.1 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_278968.1 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_278969.1 smallest protein in the large subunit; similar to what is found with protein L31 and L33 several bacterial genomes contain paralogs which may be regulated by zinc; the protein from Thermus thermophilus has a zinc-binding motif and contains a bound zinc ion; the proteins in this group have the motif YP_278970.1 stimulates the activities of the other two initiation factors, IF-2 and IF-3 YP_278971.1 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_278972.1 identified by sequence similarity; ORF located using Blastx; COG0563 YP_278973.1 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_278974.1 late assembly protein YP_278975.1 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_278976.1 binds 5S rRNA along with protein L5 and L25 YP_278977.1 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_278978.1 binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit YP_278979.1 located in the peptidyl transferase center and involved in assembly of 30S ribosome subunit; similar to what is observed with proteins L31 and L33, some proteins in this family contain CXXC motifs that are involved in zinc binding; if two copies are present in a genome, then the duplicated copy appears to have lost the zinc-binding motif and is instead regulated by zinc; the proteins in this group appear to contain the zinc-binding motif YP_278980.1 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_278981.1 assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel YP_278982.1 binds to the 23S rRNA between the centers for peptidyl transferase and GTPase YP_278983.1 primary binding protein; helps mediate assembly; involved in translation fidelity YP_278984.1 one of the stabilizing components for the large ribosomal subunit YP_278985.1 located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e YP_278986.2 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_278987.1 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_278988.1 protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA YP_278989.1 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_278990.1 binds third domain of 23S rRNA and protein L29; part of exit tunnel YP_278991.1 L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA YP_278992.1 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_278993.1 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_278996.1 copy 1; identified by sequence similarity; ORF located using Blastx YP_278997.1 copy 1; identified by sequence similarity; ORF located using Blastx YP_278998.1 in Escherichia coli RsmE methylates the N3 position of the U1498 base in 16S rRNA; cells lacking this function can grow, but are outcompeted by wild-type; SAM-dependent m(3)U1498 methyltransferase YP_278999.1 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_279000.1 identified by sequence similarity; ORF located using Blastx; COG0816 YP_279002.1 Enables the recycling of peptidyl-tRNAs produced at termination of translation YP_279003.1 identified by sequence similarity; ORF located using Blastx; COG0037 YP_279004.1 identified by sequence similarity; ORF located using Blastx; COG0465 YP_279005.1 class II; LysRS2; catalyzes a two-step reaction, first charging a lysine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; in Methanosarcina barkeri, LysRS2 charges both tRNA molecules for lysine that exist in this organism and in addition can charge the tRNAPyl with lysine in the presence of LysRS1 YP_279006.1 identified by sequence similarity; ORF located using Glimmer; GeneMark; Blastx; COG0561 YP_279007.1 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_279008.1 identified by sequence similarity; ORF located using Blastx; COG0488 YP_279010.1 identified by sequence similarity; ORF located using Blastx; COG0601 YP_279011.1 identified by sequence similarity; ORF located using Blastx; COG1173; TC:3.A.1.5.2 YP_279012.1 identified by sequence similarity; ORF located using Blastx; COG0444; TC:3.A.1.5.2 YP_279013.1 identified by sequence similarity; ORF located using Blastx YP_279014.1 identified by sequence similarity; ORF located using Blastx YP_279015.1 identified by sequence similarity; ORF located using Blastx; COG4166 YP_279017.1 Catalyzes the rate-limiting step in dNTP synthesis YP_279018.1 in Salmonella NrdI has a stimulatory effect on the ribonucleotide reductase activity of NrdH with NrdEF YP_279019.1 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_279020.1 catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate YP_279021.1 identified by sequence similarity; ORF located using Blastx; COG1012 YP_279022.1 identified by sequence similarity; ORF located using Blastx; COG0524 YP_279023.1 identified by sequence similarity; ORF located using Blastx; COG3718 YP_279024.1 identified by sequence similarity; ORF located using Blastx; COG0673 YP_279025.1 identified by sequence similarity; ORF located using GeneMark; Blastx; COG3962 YP_279026.1 identified by sequence similarity; ORF located using Blastx; COG1082 YP_279027.1 identified by sequence similarity; ORF located using Blastx; COG1129 YP_279028.1 identified by sequence similarity; ORF located using Blastx; COG1172; TC:3.A.1.2.1 YP_279029.1 identified by sequence similarity; ORF located using Glimmer; GeneMark; Blastx; COG1879; TC:3.A.2.1.2 YP_279030.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG0673; TC:3.A.2.1.2 YP_279032.2 identified by sequence similarity; ORF located using Blastx YP_279035.1 part of the preprotein secretory system; forms a complex with protein YajC; SecDFyajC stimulates the proton motive force-driven protein translocation, seems to modulate the cycling of SecA by stabilizing its membrane-inserted state and appears to be required for the release of mature proteins from the extracytoplasmic side of the membrane; in some organisms, such as Bacillus subtilis, SecD is fused to SecF YP_279036.1 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_279037.1 identified by sequence similarity; ORF located using Blastx; COG0173 YP_279038.1 identified by sequence similarity; ORF located using Blastx; COG2731 YP_279039.1 binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase YP_279040.1 identified by sequence similarity; ORF located using Blastx; TC:1.C.57.1.2 YP_279041.1 identified by sequence similarity; ORF located using Blastx; COG3451 YP_279043.1 identified by sequence similarity; ORF located using Blastx; COG0758 YP_279044.1 enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis YP_279045.1 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_279046.1 identified by sequence similarity; ORF located using Blastx; COG0693 YP_279047.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG0596 YP_279048.1 identified by sequence similarity; ORF located using Blastx; COG0095 YP_279050.1 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 YP_279051.1 identified by sequence similarity; ORF located using Blastx; COG0718 YP_279052.1 involved in a recombinational process of DNA repair, independent of the recBC complex YP_279053.1 identified by sequence similarity; ORF located using Blastx; COG0125 YP_279054.1 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_279055.1 identified by sequence similarity; ORF located using Blastx; COG0313 YP_279056.1 Catalyzes the salvage synthesis of inosine-5'-monophosphate (IMP) and guanosine-5'-monophosphate (GMP) from the purine bases hypoxanthine and guanine, respectively YP_279057.1 with CbiNQ forms the ABC transporter for cobalt import; Mycoplasmas have two adjacent copies of this gene YP_279058.1 with CbiNQ forms the ABC transporter for cobalt import; Mycoplasmas have two adjacent copies of this gene YP_279059.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG0619 YP_279060.1 identified by sequence similarity; ORF located using Blastx; COG0272 YP_279061.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG1323 YP_279062.1 identified by sequence similarity; ORF located using Blastx; COG0474 YP_279063.1 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_279064.1 identified by sequence similarity; ORF located using Blastx; COG1525 YP_279065.1 identified by sequence similarity; ORF located using Blastx YP_279066.1 identified by sequence similarity; ORF located using Blastx YP_279067.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG0016 YP_279068.1 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_279069.1 some L32 proteins have zinc finger motifs consisting of CXXC while others do not YP_279070.1 catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs YP_279071.1 identified by sequence similarity; ORF located using Blastx; COG0561 YP_279072.1 identified by sequence similarity; ORF located using Blastx; COG0196 YP_279073.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG1737 YP_279074.2 CTP synthase; 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_279075.1 identified by sequence similarity; ORF located using Blastx; COG0558 YP_279077.1 catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity YP_279078.1 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_279079.1 methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA YP_279080.1 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_279082.1 identified by sequence similarity; ORF located using Blastx; TC:3.A.1.106.1 YP_279085.1 identified by sequence similarity; ORF located using Blastx YP_279086.1 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_279087.2 binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit YP_279088.1 identified by sequence similarity; ORF located using Blastx; COG0629 YP_279089.1 binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21 YP_279096.1 identified by sequence similarity; ORF located using Blastx; COG0477 YP_279097.1 identified by sequence similarity; ORF located using Blastx; COG0584; TC:3.A.1.109.1 YP_279098.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG1126; TC:3.A.1.123.3 YP_279099.1 identified by sequence similarity; ORF located using Blastx; TC:3.A.1.123.3 YP_279101.1 identified by sequence similarity; ORF located using Blastx YP_279102.1 identified by sequence similarity; ORF located using Blastx; COG1902 YP_279103.1 identified by sequence similarity; ORF located using Blastx YP_279104.1 identified by sequence similarity; ORF located using Blastx YP_279105.1 identified by sequence similarity; ORF located using Blastx; COG0509 YP_279107.1 identified by sequence similarity; ORF located using Blastx; COG1136; TC:3.A.1.123.3 YP_279108.1 identified by sequence similarity; ORF located using Blastx; COG1136; TC:3.A.1.123.3 YP_279109.1 identified by sequence similarity; ORF located using Blastx YP_279110.1 identified by sequence similarity; ORF located using Blastx YP_279113.1 identified by sequence similarity; ORF located using Blastx YP_279119.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG1002 YP_279124.1 identified by sequence similarity; ORF located using Glimmer; Blastx YP_279126.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG1704 YP_279129.1 identified by sequence similarity; ORF located using Blastx YP_279132.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG1404 YP_279133.1 identified by sequence similarity; ORF located using Blastx; COG1136; TC:3.A.1.3.2 YP_279137.1 identified by sequence similarity; ORF located using Blastx YP_279140.1 identified by sequence similarity; ORF located using Blastx YP_279144.1 identified by sequence similarity; ORF located using Blastx YP_279145.1 identified by sequence similarity; ORF located using Blastx; COG0561 YP_279147.1 identified by sequence similarity; ORF located using Glimmer; Blastx YP_279148.1 identified by sequence similarity; ORF located using Blastx; COG0537 YP_279152.1 identified by sequence similarity; ORF located using Blastx; COG0531; TC:2.A.3.8.5 YP_279153.1 identified by sequence similarity; ORF located using Blastx; COG0580; TC:1.A.8.2.1 YP_279154.1 Converts glycerol and ADP to glycerol-3-phosphate and ADP YP_279155.1 identified by sequence similarity; ORF located using Blastx YP_279156.1 identified by sequence similarity; ORF located using Blastx YP_279157.1 identified by sequence similarity; ORF located using Blastx; COG3639 YP_279159.1 identified by sequence similarity; ORF located using Blastx; COG0658; TC:3.A.11.1.1 YP_279161.1 identified by sequence similarity; ORF located using Blastx YP_279162.1 identified by sequence similarity; ORF located using Blastx YP_279163.1 identified by sequence similarity; ORF located using Blastx; COG1525 YP_279164.2 identified by sequence similarity; ORF located using Blastx YP_279165.1 identified by sequence similarity; ORF located using Blastx; COG1175; TC:3.A.1.1.3 YP_279166.2 identified by sequence similarity; ORF located using Blastx; COG0395; TC:3.A.1.1.4 YP_279167.1 identified by sequence similarity; ORF located using Glimmer; Blastx YP_279168.1 identified by sequence similarity; ORF located using Blastx; COG0419 YP_279169.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG1762 YP_279170.1 identified by sequence similarity; ORF located using Blastx; COG3414 YP_279171.1 membrane component; functions with enzymes IIB (sgaB; ulaB) and IIA (sgaA; ulaC) enzyme I and HPr for anaerobic utilization and uptake of L-ascorbate; sgaTBA are regulated by yifQ as well as Crp and Fnr YP_279172.1 identified by sequence similarity; ORF located using Glimmer; GeneMark; Blastx; COG1735 YP_279173.1 identified by sequence similarity; ORF located using Glimmer; Blastx YP_279174.1 identified by sequence similarity; ORF located using Blastx; COG3839 YP_279175.1 identified by sequence similarity; ORF located using Blastx; COG1175; TC:3.A.1.1.10 YP_279176.1 identified by sequence similarity; ORF located using Blastx; COG0395; TC:3.A.1.1.3 YP_279177.1 identified by sequence similarity; ORF located using Blastx; COG1739 YP_279178.1 identified by sequence similarity; ORF located using Blastx; COG0313; TC:3.A.1.109.1 YP_279179.1 identified by sequence similarity; ORF located using GeneMark; Blastx; COG0526 YP_279180.1 catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro) YP_279181.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG2189 YP_279182.1 identified by sequence similarity; ORF located using Blastx YP_279183.1 identified by sequence similarity; ORF located using Blastx YP_279188.1 identified by sequence similarity; ORF located using Blastx YP_279196.1 identified by sequence similarity; ORF located using Blastx YP_279198.1 identified by sequence similarity; ORF located using Blastx YP_279201.1 MraZ; UPF0040; crystal structure shows similarity to AbrB YP_279202.1 identified by sequence similarity; ORF located using Blastx; COG0275 YP_279203.1 identified by sequence similarity; ORF located using Blastx; COG0206 YP_279204.1 catalyzes the formation of 5-phospho-alpha-D-ribose 1-diphosphate and nicotinate from nicotinate D-ribonucleotide and diphosphate YP_279205.1 identified by sequence similarity; ORF located using Blastx; COG4123 YP_279206.1 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_279207.1 identified by sequence similarity; ORF located using Glimmer; Blastx YP_279208.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG0571 YP_279211.1 catalyzes a two-step reaction, first charging an asparagine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA YP_279213.1 identified by sequence similarity; ORF located using Blastx; COG0210 YP_279215.1 plays an essential role in ATP-dependent branch migration of the Holliday junction YP_279216.1 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_279217.1 identified by sequence similarity; ORF located using Blastx YP_279220.1 identified by sequence similarity; ORF located using Blastx; COG2189 YP_279222.1 Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA YP_279223.1 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 YP_279225.1 catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs YP_279226.1 identified by sequence similarity; ORF located using Blastx; COG1881 YP_279229.1 identified by sequence similarity; ORF located using Blastx YP_279230.1 identified by sequence similarity; ORF located using Blastx; COG0561 YP_279231.1 catalyzes the isomerization of L-ribulose 5-phosphate to D-xylulose 5-phosphate in the anaerobic catabolism of L-ascorbate; links the arabinose metabolic pathway to the pentose phosphate pathway and allows the bacteria to use arabinose as an energy source YP_279232.1 UlaE; catalyzes the epimerization of L-ribulose-5-phosphate into L-xylulose-5-phosphate; part of the anaerobic L-ascorbate degradation pathway YP_279233.1 catalyzes the formation of L-xylulose-5-phosphate from 3-keto-L-gulonate-6-phosphate in anaerobic L-ascorbate utilization YP_279234.1 identified by sequence similarity; ORF located using Blastx YP_279236.1 identified by sequence similarity; ORF located using Blastx YP_279243.1 binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential YP_279244.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG1692 YP_279245.1 methionine adenosyltransferase; catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase YP_279246.1 identified by sequence similarity; ORF located using Blastx; COG1136 YP_279247.1 identified by sequence similarity; ORF located using Blastx YP_279248.1 identified by sequence similarity; ORF located using Blastx; COG1182 YP_279249.1 identified by sequence similarity; ORF located using Blastx; COG1182; TC:3.A.1.1.10 YP_279250.1 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 YP_279251.1 identified by sequence similarity; ORF located using Blastx; COG0783 YP_279252.1 identified by sequence similarity; ORF located using Blastx; COG0564 YP_279253.1 in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA YP_279254.1 binds directly to 23S ribosomal RNA YP_279258.1 identified by sequence similarity; ORF located using Blastx; COG0260 YP_279259.1 tRNA (guanine-N(7)-)-methyltransferase; catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA by transferring the methyl residue from S-adenosyl-L-methionine YP_279261.1 identified by sequence similarity; ORF located using Blastx YP_279262.1 identified by sequence similarity; ORF located using Glimmer; Blastx YP_279263.1 identified by sequence similarity; ORF located using Blastx; COG1131 YP_279264.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG1277 YP_279265.1 identified by sequence similarity; ORF located using Blastx; COG0039 YP_279266.1 identified by sequence similarity; ORF located using Glimmer; GeneMark; Blastx; COG1080; TC:8.A.7.1.1 YP_279267.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG0171; TC:3.A.1.123.4 YP_279268.1 identified by sequence similarity; ORF located using Blastx; COG0217 YP_279269.1 Enables the cleavage of the glycosidic bond in both 5'-methylthioadenosine and S-adenosylhomocysteine YP_279270.2 catalyzes the reversible adenylation of nicotinate mononucleotide to nicotinic acid adenine dinucleotide YP_279271.1 identified by sequence similarity; ORF located using Glimmer; GeneMark; Blastx; COG0561 YP_279272.2 produces ATP from ADP in the presence of a proton gradient across the membrane; the beta chain is a regulatory subunit YP_279273.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a catalytic subunit YP_279274.1 identified by sequence similarity; ORF located using Blastx YP_279276.1 identified by sequence similarity; ORF located using Glimmer; Blastx YP_279277.1 identified by sequence similarity; ORF located using Glimmer; Blastx YP_279279.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG0561 YP_279281.1 identified by sequence similarity; ORF located using Blastx; COG2239; TC:9.A.19.1.1 YP_279282.1 identified by sequence similarity; ORF located using Glimmer; GeneMark; Blastx; COG1624 YP_279284.1 Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway YP_279286.1 identified by sequence similarity; ORF located using Blastx; COG1299; TC:4.A.2.1.1 YP_279288.1 identified by sequence similarity; ORF located using Blastx; COG1482 YP_279289.1 identified by sequence similarity; ORF located using Blastx; COG1057 YP_279290.1 identified by sequence similarity; ORF located using Blastx YP_279291.1 identified by sequence similarity; ORF located using Blastx; TC:1.A.1.5.2 YP_279292.1 identified by sequence similarity; ORF located using Blastx; COG0477; TC:2.A.1.2.5 YP_279294.1 AS-AR; AsnRS2; similar to asparaginyl-tRNA synthetase but lacking the N-terminal anticodon-binding site; the enzyme from Pyrococcus converts aspartic acid into asparagine YP_279295.1 identified by sequence similarity; ORF located using Glimmer; Blastx YP_279296.1 identified by sequence similarity; ORF located using Blastx; COG0444; TC:3.A.1.5.2 YP_279297.1 identified by sequence similarity; ORF located using Blastx; COG1173 YP_279298.1 identified by sequence similarity; ORF located using Blastx; COG0601; TC:3.A.1.5.2 YP_279299.1 identified by sequence similarity; ORF located using Blastx YP_279300.1 unlike PdhC proteins from other organisms, some Mycoplasma lack an N-terminal lipoyl domain; in Mycoplasma hyopneumonia the PdhD proteins contains the lipoyl domain YP_279301.1 identified by sequence similarity; ORF located using Blastx; COG1249; TC:3.D.1.1.1 YP_279302.1 Enables the production of acetyl-CoA by phosphorylating acetate in the presence of ATP and a divalent cation YP_279303.1 in Salmonella this enzyme is required for ethanolamine catabolism; has higher affinity for CoA than Pta YP_279308.1 identified by sequence similarity; ORF located using Blastx; COG4213 YP_279309.1 identified by sequence similarity; ORF located using Blastx; COG1129 YP_279310.1 identified by sequence similarity; ORF located using Blastx; COG4214; TC:3.A.1.2.5 YP_279312.1 identified by sequence similarity; ORF located using Blastx; COG1940 YP_279314.1 identified by sequence similarity; ORF located using Blastx YP_279319.1 identified by sequence similarity; ORF located using Blastx; COG1164 YP_279320.1 identified by sequence similarity; ORF located using Glimmer; Blastx YP_279321.1 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_279322.1 identified by sequence similarity; ORF located using Glimmer; GeneMark; Blastx; COG0466 YP_279323.1 identified by sequence similarity; ORF located using Glimmer; Blastx YP_279324.1 identified by sequence similarity; ORF located using Blastx; COG0035 YP_279325.1 catalyzes the formation of D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-D-ribose-5-phosphate YP_279326.1 negatively supercoils closed circular double-stranded DNA YP_279327.1 this stereospecific enzymes reduces the R isomer of methionine sulfoxide while MsrA reduces the S form; provides protection against oxidative stress YP_279329.1 functions in sugar metabolism in glycolysis and the Embden-Meyerhof pathways (EMP) and in gluconeogenesis; catalyzes reversible isomerization of glucose-6-phosphate to fructose-6-phosphate; member of PGI family YP_279330.1 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 YP_279331.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG0575 YP_279332.1 identified by sequence similarity; ORF located using Blastx; COG0233 YP_279333.1 Catalyzes the phosphorylation of UMP to UDP YP_279335.1 identified by sequence similarity; ORF located using Blastx; COG1214 YP_279336.1 identified by sequence similarity; ORF located using Blastx YP_279337.1 identified by sequence similarity; ORF located using Blastx YP_279338.1 identified by sequence similarity; ORF located using Blastx; COG0687 YP_279339.1 identified by sequence similarity; ORF located using Blastx; COG1177; TC:3.A.1.11.1 YP_279340.1 identified by sequence similarity; ORF located using Blastx; COG1176; TC:3.A.1.11.1 YP_279341.1 identified by sequence similarity; ORF located using GeneMark; Blastx; COG3842 YP_279345.1 identified by sequence similarity; ORF located using Blastx; COG0569 YP_279346.1 identified by sequence similarity; ORF located using Blastx; COG0168; TC:2.A.38.4.1 YP_279347.1 identified by sequence similarity; ORF located using Blastx YP_279348.1 identified by sequence similarity; ORF located using Blastx YP_279349.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG4668 YP_279350.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG0246 YP_279351.1 identified by sequence similarity; ORF located using Blastx; COG2213; TC:4.A.2.1.2 YP_279352.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG1737 YP_279353.1 membrane component; functions with enzymes IIB (sgaB; ulaB) and IIA (sgaA; ulaC) enzyme I and HPr for anaerobic utilization and uptake of L-ascorbate; sgaTBA are regulated by yifQ as well as Crp and Fnr YP_279354.1 identified by sequence similarity; ORF located using Blastx; COG3414 YP_279355.1 identified by sequence similarity; ORF located using Blastx YP_279357.1 identified by sequence similarity; ORF located using Blastx; COG0036 YP_279360.1 identified by sequence similarity; ORF located using Blastx YP_279363.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG0265 YP_279364.1 identified by sequence similarity; ORF located using Blastx; COG1249 YP_279366.1 identified by sequence similarity; ORF located using Glimmer; Blastx YP_279367.1 Catalyzes the oxidation of dihydrolipoamide to lipoamide YP_279368.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG1820 YP_279369.1 identified by sequence similarity; ORF located using Blastx; COG0191 YP_279370.1 identified by sequence similarity; ORF located using Blastx; COG1263; TC:4.A.1.1.2 YP_279371.1 catalyzes the reversible formation of fructose 6-phosphate from glucosamine 6-phosphate YP_279372.1 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_279373.1 catalyzes the interconversion of ribose 5-phosphate to ribulose 5-phosphate; enzyme from E. coli shows allose 6-phosphate isomerase activity YP_279374.1 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_279375.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG0510 YP_279376.1 identified by sequence similarity; ORF located using Blastx YP_279377.1 identified by sequence similarity; ORF located using Blastx; COG0258 YP_279378.1 catalyzes DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time. Proposed to be responsible for the synthesis of the lagging strand. In the low GC gram positive bacteria this enzyme is less processive and more error prone than its counterpart in other bacteria. YP_279379.1 identified by sequence similarity; ORF located using Blastx; COG0858 YP_279380.1 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_279381.1 modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination YP_279382.1 identified by sequence similarity; ORF located using Blastx; COG1523 YP_279383.1 identified by sequence similarity; ORF located using Blastx; COG0579 YP_279384.1 catalyzes the formation of threonyl-tRNA(Thr) from threonine and tRNA(Thr); 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 YP_279385.1 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_279386.1 identified by sequence similarity; ORF located using Blastx; COG1264 YP_279387.1 identified by sequence similarity; ORF located using Blastx; COG1112 YP_279388.1 identified by sequence similarity; ORF located using Blastx; COG1039 YP_279389.1 identified by sequence similarity; ORF located using Blastx; COG3763 YP_279390.1 catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate YP_279398.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG1481 YP_279399.1 identified by sequence similarity; ORF located using Blastx; COG0670 YP_279400.1 catalyzes the hydrolysis of pyrophosphate to phosphate YP_279401.1 identified by sequence similarity; ORF located using Blastx; COG1744 YP_279402.1 identified by sequence similarity; ORF located using Blastx; COG3845 YP_279403.1 identified by sequence similarity; ORF located using Blastx; COG4603; TC:3.A.1.2.6 YP_279404.1 identified by sequence similarity; ORF located using Blastx; COG1079; TC:3.A.1.2.1 YP_279405.1 catalyzes the formation of thymidine 5'-phosphate from thymidine YP_279406.1 identified by sequence similarity; ORF located using GeneMark; Blastx; COG1925 YP_279407.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG2190; TC:9.A.19.1.1 YP_279408.1 identified by sequence similarity; ORF located using Blastx YP_279410.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG0270 YP_279411.1 identified by sequence similarity; ORF located using Blastx; COG0802 YP_279412.1 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_279413.1 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_279414.1 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_279415.2 binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit YP_279416.1 identified by sequence similarity; ORF located using Glimmer; Blastx YP_279417.1 identified by sequence similarity; ORF located using Blastx YP_279418.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG0338 YP_279419.1 identified by sequence similarity; ORF located using Blastx; COG1132; TC:3.A.1.111.2 YP_279420.1 identified by sequence similarity; ORF located using Blastx; COG1132; TC:3.A.1.123.1 YP_279421.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG0286 YP_279422.1 identified by sequence similarity; ORF located using Blastx; COG1132; TC:3.A.1.111.1 YP_279423.1 identified by sequence similarity; ORF located using Blastx; COG1132; TC:3.A.1.112.4 YP_279424.1 identified by sequence similarity; ORF located using Blastx YP_279425.1 identified by sequence similarity; ORF located using Blastx; COG0737 YP_279426.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG0204 YP_279427.1 functions during chromosome segregation; may form a condensin-like structure with SMC and ScpB YP_279428.1 functions during chromosome segregation; may form a condensin-like structure with SMC and ScpA; forms a homodimer YP_279429.1 identified by sequence similarity; ORF located using Blastx; COG0392 YP_279430.1 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_279431.1 Modulates Rho-dependent transcription termination YP_279432.1 forms a complex with SecY and SecG; SecYEG forms a protein-conducting channel to which secA binds and translocates targeted polypeptides across the cytoplasmic membrane, a process driven by ATP and a proton-motive force YP_279434.1 identified by sequence similarity; ORF located using Blastx; COG0566 YP_279435.1 identified by sequence similarity; ORF located using Blastx; COG0215 YP_279436.1 identified by sequence similarity; ORF located using Blastx; COG1451 YP_279437.1 identified by sequence similarity; ORF located using Blastx; COG1253; TC:9.B.37.2.1 YP_279438.1 identified by sequence similarity; ORF located using Blastx; COG0305 YP_279439.1 in Escherichia coli this protein is wrapped around the base of the L1 stalk YP_279440.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG3887 YP_279441.1 identified by sequence similarity; ORF located using Blastx; COG0495 YP_279442.1 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_279443.1 identified by sequence similarity; ORF located using Blastx; COG0009 YP_279444.1 forms a direct contact with the tRNA during translation YP_279445.1 in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit YP_279446.1 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_279447.1 identified by sequence similarity; ORF located using Glimmer; Blastx; COG0084 YP_279448.1 catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP YP_279449.1 glucose-inhibited division protein B; SAM-dependent methyltransferase; methylates the N7 position of guanosine in position 527 of 16S rRNA YP_279450.1 identified by sequence similarity; ORF located using Blastx YP_279451.1 identified by sequence similarity; ORF located using GeneMark; Blastx; COG1196; TC:1.C.57.1.1 YP_279452.1 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 YP_279453.1 identified by sequence similarity; ORF located using Blastx; COG0006 YP_279455.1 identified by sequence similarity; ORF located using Blastx YP_279457.1 identified by sequence similarity; ORF located using Blastx YP_279458.1 identified by sequence similarity; ORF located using Glimmer; Blastx YP_279461.1 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_279462.1 identified by sequence similarity; ORF located using Blastx; COG0534; TC:2.A.66.1.4 YP_279463.1 in some Mycoplasma, this protein is fused to aspartyl/glutamyl-tRNA amidotransferase subunit C domain YP_279465.1 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_279468.1 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_279469.1 identified by sequence similarity; ORF located using Blastx; COG0594 YP_279470.1 in Escherichia coli transcription of this gene is enhanced by polyamines