-- dump date 20140620_075520 -- class Genbank::CDS -- table cds_note -- id note YP_492679.1 identified by match to protein family HMM PF01446 YP_492681.1 identified by similarity to GB:BAB78430.1 YP_492684.1 identified by similarity to SP:P23054; match to protein family HMM PF07690 YP_492685.1 identified by similarity to SP:P03864; match to protein family HMM PF01076 YP_492686.1 identified by match to protein family HMM PF02486 YP_492687.1 identified by match to protein family HMM PF06970 YP_492688.1 identified by match to protein family HMM PF00665 YP_492689.1 IleRS; catalyzes the formation of isoleucyl-tRNA(Ile) from isoleucine and tRNA(Ile); since isoleucine and other amino acids such as valine are similar, there are additional editing function in this enzyme; one is involved in hydrolysis of activated valine-AMP and the other is involved in deacylation of mischarged Val-tRNA(Ile); there are two active sites, one for aminoacylation and one for editing; class-I aminoacyl-tRNA synthetase family type 2 subfamily; some organisms carry two different copies of this enzyme; in some organisms, the type 2 subfamily is associated with resistance to the antibiotic pseudomonic acid (mupirocin) YP_492690.1 hypothetical protein in ileS 3'region (ORF C), see GenBank Accession X75439 YP_492691.1 identified by match to protein family HMM PF00665 YP_492692.1 identified by match to protein family HMM PF05732 YP_492693.1 identified by match to protein family HMM PF00398 YP_492694.1 identified by match to protein family HMM PF00665 YP_492698.1 identified by similarity to GB:AAC61955.1 YP_492702.1 identified by match to protein family HMM PF05257 YP_492703.1 identified by similarity to GB:AAC61960.1 YP_492704.1 identified by match to protein family HMM PF01131; match to protein family HMM PF01751; match to protein family HMM TIGR01056 YP_492706.1 identified by match to protein family HMM PF02534 YP_492708.1 identified by match to protein family HMM PF00436; match to protein family HMM TIGR00621 YP_492710.1 identified by match to protein family HMM PF00665 YP_492713.1 identical to VRA0046 in plasmid pLW1043 YP_492714.1 identified by match to protein family HMM PF00239; match to protein family HMM PF02796 YP_492717.1 identical to pSK41 LtrC protein; similar to Lactococcus lactis pRS01 LtrC protein YP_492718.1 an authenticated frameshift results in a truncated nickase protein; identified by match to protein family HMM PF03389 YP_492722.1 identified by match to protein family HMM PF01381 YP_492723.1 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_492724.1 binds the polymerase to DNA and acts as a sliding clamp YP_492726.1 Required for DNA replication; binds preferentially to single-stranded, linear DNA YP_492727.1 identified by match to protein family HMM PF00204; match to protein family HMM PF00986; match to protein family HMM PF01751; match to protein family HMM PF02518; match to protein family HMM TIGR01059 YP_492728.1 Ser-84->Leu (ciprofloxacin resistant mutation); identified by match to protein family HMM PF00521; match to protein family HMM PF03989; match to protein family HMM TIGR01063 YP_492729.1 identified by match to protein family HMM PF01256; match to protein family HMM TIGR00196 YP_492730.1 catalyzes the degradation of histidine to urocanate and ammmonia YP_492731.1 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_492732.1 identified by match to protein family HMM PF03591 YP_492733.1 identified by match to protein family HMM PF05437 YP_492734.1 identified by match to protein family HMM PF00561 YP_492736.1 identified by match to protein family HMM PF01368; match to protein family HMM PF02272 YP_492737.1 in Escherichia coli this protein is wrapped around the base of the L1 stalk YP_492738.1 identified by match to protein family HMM PF00772; match to protein family HMM PF03796; match to protein family HMM TIGR00665 YP_492739.1 catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis YP_492740.1 identified by match to protein family HMM PF00072; match to protein family HMM PF00486 YP_492741.1 identified by match to protein family HMM PF00512; match to protein family HMM PF00672; match to protein family HMM PF00989; match to protein family HMM PF02518; match to protein family HMM TIGR00229 YP_492742.1 identified by match to protein family HMM PF07435 YP_492744.1 identified by match to protein family HMM PF00753 YP_492745.1 identified by match to protein family HMM PF00149; match to protein family HMM PF02872; match to protein family HMM TIGR01167 YP_492746.1 SPOUT methyltransferase family protein; crystal structure shows homodimer; in Escherichia coli this protein methylates pseudouridine at position 1915 of the 23S ribosomal RNA YP_492748.1 identified by match to protein family HMM PF00665 YP_492750.1 identified by match to protein family HMM PF03009 YP_492751.1 identified by match to protein family HMM PF01575 YP_492752.1 identified by match to protein family HMM PF00905; match to protein family HMM PF03717; match to protein family HMM PF05223 YP_492753.1 identified by match to protein family HMM PF05569 YP_492754.1 similar to type I restriction-modification system endonuclease YP_492755.1 identified by match to protein family HMM PF01609 YP_492756.1 identified by match to protein family HMM PF07799 YP_492757.1 identified by match to protein family HMM PF00239; match to protein family HMM PF04606; match to protein family HMM PF07508 YP_492758.1 identified by match to protein family HMM PF00239; match to protein family HMM PF07508 YP_492759.1 identified by match to protein family HMM PF06048 YP_492760.1 identified by match to protein family HMM PF07205 YP_492762.1 identified by match to protein family HMM PF04326 YP_492764.1 identified by match to protein family HMM PF00753 YP_492765.1 identified by match to protein family HMM PF01844 YP_492772.1 identified by match to protein family HMM PF00583 YP_492774.1 alkaliphilic; identified by match to protein family HMM PF00107 YP_492775.1 identified by match to protein family HMM PF07799 YP_492776.1 identified by match to protein family HMM PF06124 YP_492778.1 identified by match to protein family HMM PF06106 YP_492779.1 identified by similarity to GB:CAC98906.1; match to protein family HMM PF00665 YP_492780.1 catalyzes the reversible synthesis of carbamate and ATP from carbamoyl phosphate and ADP YP_492781.1 catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation YP_492782.1 identified by match to protein family HMM PF00027 YP_492783.1 identified by match to protein family HMM PF00324; match to protein family HMM TIGR00905 YP_492784.1 catalyzes the degradation of arginine to citruline and ammonia YP_492785.1 identified by match to protein family HMM PF02863 YP_492787.1 identified by similarity to GB:CAB96929.1 YP_492788.1 identified by match to protein family HMM PF00561 YP_492789.1 identified by match to protein family HMM PF02371 YP_492791.1 identified by similarity to GB:AAU24316.1; match to protein family HMM PF00496 YP_492792.1 identified by match to protein family HMM PF00528 YP_492793.1 identified by similarity to GB:AAL94601.1; match to protein family HMM PF00528 YP_492794.1 identified by match to protein family HMM PF00005 YP_492795.1 identified by match to protein family HMM PF00005 YP_492796.1 identified by match to protein family HMM PF00122; match to protein family HMM PF00702; match to protein family HMM TIGR01494; match to protein family HMM TIGR01511; match to protein family HMM TIGR01525 YP_492797.1 identified by match to protein family HMM PF07563 YP_492801.1 identified by match to protein family HMM PF01925 YP_492802.1 identified by match to protein family HMM PF02583 YP_492803.1 identified by match to protein family HMM PF00581; match to protein family HMM PF01206 YP_492804.1 identified by match to protein family HMM PF00581; match to protein family HMM PF00753 YP_492806.1 identified by match to protein family HMM PF01207 YP_492807.1 identified by match to protein family HMM PF04993 YP_492808.1 identified by match to protein family HMM PF07690 YP_492810.1 identified by match to protein family HMM PF00126; match to protein family HMM PF03466 YP_492812.1 identified by match to protein family HMM PF00126 YP_492816.1 identified by match to protein family HMM PF00388 YP_492817.1 identified by match to protein family HMM PF04507; match to protein family HMM TIGR01742 YP_492818.1 identified by match to protein family HMM PF04507; match to protein family HMM TIGR01742 YP_492819.1 identified by match to protein family HMM PF04507; match to protein family HMM TIGR01742 YP_492820.1 identified by match to protein family HMM PF04507; match to protein family HMM TIGR01742 YP_492821.1 identified by match to protein family HMM PF00165 YP_492822.1 identified by match to protein family HMM PF01546; match to protein family HMM PF07687; match to protein family HMM TIGR01891 YP_492823.1 identified by match to protein family HMM PF07690 YP_492824.1 identified by match to protein family HMM PF02690; match to protein family HMM TIGR00704 YP_492825.1 in group A Streptococci this protein was found to cross react with anti myosin antibodies and may play a role in rheumatic fever YP_492826.1 identified by match to protein family HMM PF00892 YP_492827.1 identified by match to protein family HMM PF00155; match to protein family HMM PF00392 YP_492828.1 identified by match to protein family HMM PF07853 YP_492829.1 identified by match to protein family HMM PF02652; match to protein family HMM TIGR00795 YP_492830.1 identified by match to protein family HMM PF00746; match to protein family HMM PF01476; match to protein family HMM PF02216; match to protein family HMM PF03373; match to protein family HMM PF04650; match to protein family HMM TIGR01167; match to protein family HMM TIGR01168 YP_492831.1 identified by match to protein family HMM PF01047; match to protein family HMM TIGR01889 YP_492832.1 identified by match to protein family HMM PF01032 YP_492833.1 identified by match to protein family HMM PF01032 YP_492834.1 identified by match to protein family HMM PF01497 YP_492835.1 identified by match to protein family HMM PF00291 YP_492836.1 identified by match to protein family HMM PF02423 YP_492837.1 identified by match to protein family HMM PF04183 YP_492838.1 identified by match to protein family HMM PF07690 YP_492839.1 identified by match to protein family HMM PF04183 YP_492840.1 identified by match to protein family HMM PF04183 YP_492841.1 identified by match to protein family HMM PF03328 YP_492842.1 identified by match to protein family HMM PF00278; match to protein family HMM PF02784 YP_492843.1 identified by match to protein family HMM PF02195 YP_492846.1 identified by match to protein family HMM PF00106; match to protein family HMM TIGR02415 YP_492847.1 identified by match to protein family HMM PF01073; match to protein family HMM PF01370; match to protein family HMM PF04321; match to protein family HMM PF07993 YP_492848.1 identified by match to protein family HMM PF02397 YP_492849.1 identified by match to protein family HMM PF00534 YP_492850.1 identified by match to protein family HMM PF04932 YP_492851.1 identified by match to protein family HMM PF01943 YP_492852.1 identified by match to protein family HMM PF00081; match to protein family HMM PF02777 YP_492853.1 identified by match to protein family HMM PF00746; match to protein family HMM TIGR01167 YP_492854.1 identified by match to protein family HMM PF00392 YP_492855.1 catalyzes the reversible phosphorolysis of ribonucleosides and 2'- deoxyribonucleosides to the free base and (2'-deoxy)ribose-1- phosphate YP_492856.1 identified by match to protein family HMM PF07690 YP_492857.1 catalyzes the formation of D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-D-ribose-5-phosphate YP_492858.1 catalyzes the transfer of phosphate between the C1 and C5 carbons of pentose YP_492859.1 identified by match to protein family HMM PF00528; match to protein family HMM TIGR01097 YP_492860.1 identified by match to protein family HMM PF00528; match to protein family HMM TIGR01097 YP_492861.1 identified by match to protein family HMM PF00005; match to protein family HMM TIGR02315 YP_492862.1 identified by match to protein family HMM TIGR01098 YP_492864.1 identified by match to protein family HMM PF00149; match to protein family HMM PF02872 YP_492866.1 identified by match to protein family HMM PF00171; match to protein family HMM PF00465 YP_492867.1 identified by match to protein family HMM PF02706; match to protein family HMM TIGR01006 YP_492868.1 identified by match to protein family HMM TIGR01007 YP_492869.1 identified by match to protein family HMM PF02811 YP_492870.1 identified by match to protein family HMM PF01073; match to protein family HMM PF01370; match to protein family HMM PF02719; match to protein family HMM PF07993 YP_492871.1 identified by match to protein family HMM PF01370; match to protein family HMM PF07993 YP_492872.1 identified by match to protein family HMM PF02350; match to protein family HMM TIGR00236 YP_492873.1 identified by match to protein family HMM PF00132 YP_492874.1 identified by match to protein family HMM PF00534 YP_492875.1 identified by match to protein family HMM PF04932 YP_492877.1 identified by match to protein family HMM PF00534 YP_492878.1 identified by match to protein family HMM PF02397 YP_492879.1 identified by match to protein family HMM PF01073; match to protein family HMM PF01370; match to protein family HMM PF07993 YP_492880.1 identified by match to protein family HMM PF00984; match to protein family HMM PF03720; match to protein family HMM PF03721 YP_492881.1 identified by match to protein family HMM PF02350; match to protein family HMM PF04007; match to protein family HMM TIGR00236 YP_492882.1 iron regulated; catalyzes the release of heme from hemoglobin allowing bacterial pathogens to use the host heme as an iron source YP_492883.1 identified by match to protein family HMM PF04304 YP_492884.1 identified by match to protein family HMM PF00171 YP_492885.1 identified by match to protein family HMM PF01545; match to protein family HMM TIGR01297 YP_492888.1 identified by match to protein family HMM PF00005 YP_492890.1 identified by match to protein family HMM PF00528 YP_492893.1 Catalyzes the reversible two-electron oxidation of formate to carbon dioxide. It allows the assimilation of carbon dioxide and provides energy for growth through oxidative phosphorylation coupled to the reduction of oxygen, nitrate, sulphate or fumarate YP_492894.1 identified by match to protein family HMM PF07690 YP_492895.1 identified by match to protein family HMM PF00501; match to protein family HMM PF00550; match to protein family HMM PF00668; match to protein family HMM PF01073; match to protein family HMM PF01370; match to protein family HMM PF04321; match to protein family HMM PF07993; match to protein family HMM TIGR01733; match to protein family HMM TIGR01746 YP_492896.1 identified by match to protein family HMM PF01648 YP_492897.1 identified by match to protein family HMM PF07274 YP_492898.1 identified by match to protein family HMM PF00696; match to protein family HMM TIGR00761 YP_492899.1 bifunctional arginine biosynthesis protein ArgJ; functions at the 1st and 5th steps in arginine biosynthesis; involved in synthesis of acetylglutamate from glutamate and acetyl-CoA and ornithine by transacetylation between acetylornithine and glutmate YP_492900.1 catalyzes the reduction of N-acetyl-5-glutamyl phosphate to N-acetyl-L-glutamate 5-semialdehyde in arginine biosynthesis and the reduction of N-acetyl-gamma-aminoadipyl-phosphate to N-acetyl-L-aminoadipate-semialdehyde in lysine biosynthesis; involved in both the arginine and lysine biosynthetic pathways; lysine is produced via the AAA pathway, lysine from alpha-aminoadipate YP_492901.1 identified by match to protein family HMM PF00202; match to protein family HMM TIGR01885 YP_492902.1 identified by match to protein family HMM PF05525; match to protein family HMM TIGR00796 YP_492903.1 identified by match to protein family HMM PF00857 YP_492904.1 identified by match to protein family HMM PF00205; match to protein family HMM PF02775; match to protein family HMM PF02776 YP_492905.1 identified by match to protein family HMM PF00358; match to protein family HMM PF00367; match to protein family HMM PF02378; match to protein family HMM TIGR00826; match to protein family HMM TIGR00830; match to protein family HMM TIGR02002 YP_492906.1 identified by match to protein family HMM PF05913 YP_492907.1 catalyzes the cleavage of the lactyl ether moiety of N-acetylmuramic acid-6-phosphate (MurNAc-6-P) to form N-acetylglucosamine-6-phosphate (GlcNAc-6-P) and lactate; involved in MurNAc dissimilation pathway YP_492908.1 identified by match to protein family HMM PF00367; match to protein family HMM PF02378 YP_492909.1 identified by match to protein family HMM PF01380; match to protein family HMM PF01418 YP_492910.1 identified by match to protein family HMM PF00270; match to protein family HMM PF04313; match to protein family HMM PF04851; match to protein family HMM TIGR00348 YP_492914.1 identified by match to protein family HMM PF00005 YP_492915.1 identified by match to protein family HMM PF00528 YP_492916.1 identified by match to protein family HMM PF00528 YP_492918.1 identified by match to protein family HMM PF01019; match to protein family HMM TIGR00066 YP_492919.1 identified by match to protein family HMM PF04507; match to protein family HMM TIGR01742 YP_492920.1 FMN-dependent; requires NADH; catalyzes the cleavage of azo bond in aromatic azo compounds YP_492921.1 identified by match to protein family HMM PF01551 YP_492922.1 identified by match to protein family HMM PF00005; match to protein family HMM PF03459 YP_492923.1 identified by match to protein family HMM PF01547 YP_492924.1 identified by match to protein family HMM PF00528; match to protein family HMM PF05154 YP_492925.1 identified by match to protein family HMM PF00528 YP_492926.1 identified by match to protein family HMM PF01408; match to protein family HMM PF02894 YP_492927.1 identified by match to protein family HMM PF01408; match to protein family HMM PF02894 YP_492928.1 identified by match to protein family HMM PF01261; match to protein family HMM PF07582 YP_492929.1 identified by match to protein family HMM PF04140 YP_492930.1 cytoplasmic membrane protein that functions as a monomer; catalyzes the active transport of sugar-phosphates such as glucose-6-phosphate with the obligatory exchange of inorganic phosphate or organophosphate YP_492931.1 identified by match to protein family HMM PF00072; match to protein family HMM PF00165 YP_492932.1 identified by match to protein family HMM PF06580 YP_492933.1 identified by similarity to GB:AAW37499.1 YP_492934.1 identified by match to protein family HMM PF01228; match to protein family HMM PF02901; match to protein family HMM TIGR01255 YP_492935.1 identified by match to protein family HMM PF04055; match to protein family HMM TIGR02493 YP_492936.1 identified by match to protein family HMM PF03009 YP_492939.1 identified by match to protein family HMM PF00108; match to protein family HMM PF02803; match to protein family HMM TIGR01930 YP_492940.1 identified by match to protein family HMM PF00378; match to protein family HMM PF00725; match to protein family HMM PF02737 YP_492941.1 identified by match to protein family HMM PF00441; match to protein family HMM PF02770; match to protein family HMM PF08028 YP_492942.1 identified by match to protein family HMM PF00501 YP_492945.1 identified by match to protein family HMM PF00496 YP_492946.1 identified by match to protein family HMM PF04343 YP_492948.1 identified by match to protein family HMM PF00042; match to protein family HMM PF00175; match to protein family HMM PF00970 YP_492949.1 identified by match to protein family HMM PF00056; match to protein family HMM PF02866; match to protein family HMM TIGR01771 YP_492950.1 identified by match to protein family HMM PF00367; match to protein family HMM PF02378; match to protein family HMM TIGR00826 YP_492951.1 identified by match to protein family HMM PF01156 YP_492952.1 identified by match to protein family HMM PF00359; match to protein family HMM PF00874; match to protein family HMM PF05043 YP_492953.1 identified by match to protein family HMM PF00359 YP_492954.1 identified by match to protein family HMM PF02302 YP_492955.1 identified by match to protein family HMM PF03611; match to protein family HMM TIGR00827 YP_492956.1 identified by match to protein family HMM PF00107 YP_492958.1 identified by match to protein family HMM PF00107 YP_492959.1 4-diphosphocytidyl-2C-methyl-D-erythritol synthase; MEP cytidylyltransferase; MCT; catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate; involved in isoprenoid and isopentenyl-PP biosynthesis; forms homodimers YP_492961.1 identified by match to protein family HMM PF04464 YP_492962.1 identified by match to protein family HMM PF04464 YP_492963.1 4-diphosphocytidyl-2C-methyl-D-erythritol synthase; MEP cytidylyltransferase; MCT; catalyzes the formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate; involved in isoprenoid and isopentenyl-PP biosynthesis; forms homodimers YP_492965.1 identified by match to protein family HMM PF04464 YP_492966.1 identified by match to protein family HMM PF00535 YP_492967.1 involved in peptidoglycan cross-linking YP_492968.1 identified by match to protein family HMM PF02518; match to protein family HMM PF06580; match to protein family HMM PF07694 YP_492969.1 identified by match to protein family HMM PF00072; match to protein family HMM PF04397 YP_492970.1 negatively regulates murein hydrolase activity YP_492971.1 in conjunction with LrgA this protein inhibits the expression or activity of extracellular murein hydrolases YP_492972.1 identified by match to protein family HMM PF00392; match to protein family HMM PF07702 YP_492973.1 identified by match to protein family HMM PF00358; match to protein family HMM TIGR00830 YP_492974.1 identified by match to protein family HMM PF00232 YP_492975.1 identified by match to protein family HMM PF01209 YP_492976.1 identified by match to protein family HMM PF00294; match to protein family HMM TIGR02152 YP_492977.1 cytoplasmic mutarotase that catalyzes the conversion between beta-pyran and beta-furan forms of D-ribose; RbsD is required for efficient ribose utilization in E. coli; rbsD-mutant E. coli strains are unable to use ribose as a sole carbon source YP_492978.1 identified by match to protein family HMM PF06800 YP_492979.1 identified by match to protein family HMM PF00356; match to protein family HMM PF00532 YP_492982.1 identified by match to protein family HMM PF07690 YP_492983.1 identified by match to protein family HMM PF02275 YP_492984.1 identified by match to protein family HMM PF01551 YP_492985.1 identified by match to protein family HMM PF00005 YP_492991.1 identified by match to protein family HMM PF05257 YP_492992.1 identified by match to protein family HMM PF06013 YP_492997.1 identified by similarity to SP:P0C048; match to protein family HMM PF01580 YP_493003.1 identified by match to protein family HMM PF04634; match to protein family HMM TIGR01741 YP_493007.1 identified by match to protein family HMM PF04634; match to protein family HMM TIGR01741 YP_493008.2 identified by match to protein family HMM PF04634; match to protein family HMM TIGR01741 YP_493009.1 authenticated frameshift, not result of sequencing error; same frameshift also found in COL; identified by match to protein family HMM PF04634; match to protein family HMM TIGR01741 YP_493010.1 identified by match to protein family HMM PF04634; match to protein family HMM TIGR01741 YP_493012.1 identified by match to protein family HMM PF04634; match to protein family HMM TIGR01741 YP_493013.1 identified by match to protein family HMM PF04634; match to protein family HMM TIGR01741 YP_493014.1 identified by match to protein family HMM PF04634; match to protein family HMM TIGR01741 YP_493015.1 identified by match to protein family HMM PF04634; match to protein family HMM TIGR01741 YP_493016.1 identified by match to protein family HMM PF04634; match to protein family HMM TIGR01741 YP_493019.1 authenticated frameshift; identified by match to protein family HMM PF01226 YP_493020.1 identified by match to protein family HMM PF05525; match to protein family HMM TIGR00796 YP_493021.1 identified by match to protein family HMM PF03767; match to protein family HMM TIGR01533 YP_493022.1 identified by match to protein family HMM PF02687 YP_493023.1 identified by match to protein family HMM PF00005 YP_493025.1 identified by match to protein family HMM PF00294 YP_493026.1 identified by match to protein family HMM PF04227 YP_493027.1 identified by match to protein family HMM PF01773; match to protein family HMM PF07662; match to protein family HMM PF07670 YP_493028.1 identified by match to protein family HMM PF00474; match to protein family HMM TIGR00813 YP_493029.1 catalyzes the formation of pyruvate and N-acetylmannosamine from N-acetylneuraminic acid YP_493030.1 identified by match to protein family HMM PF00480 YP_493031.1 identified by match to protein family HMM PF01380; match to protein family HMM PF01418 YP_493032.1 Converts N-acetylmannosamine-6-phosphate to N-acetylglucosamine-6-phosphate YP_493033.1 identified by match to protein family HMM PF07670 YP_493034.1 identified by match to protein family HMM PF04650; match to protein family HMM TIGR01168 YP_493036.1 identified by match to protein family HMM PF00724 YP_493038.1 identified by match to protein family HMM PF00296 YP_493039.1 identified by match to protein family HMM PF01597 YP_493040.1 identified by match to protein family HMM PF01661 YP_493042.1 identified by match to protein family HMM PF03099; match to protein family HMM TIGR00545 YP_493043.1 identified by match to protein family HMM PF01073; match to protein family HMM PF01370; match to protein family HMM PF05368; match to protein family HMM PF07993 YP_493044.1 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_493045.1 identified by match to protein family HMM PF02302 YP_493046.1 identified by match to protein family HMM PF00359 YP_493047.1 identified by match to protein family HMM PF00359; match to protein family HMM PF00874; match to protein family HMM PF05043 YP_493048.1 identified by match to protein family HMM PF01047 YP_493049.1 identified by match to protein family HMM PF01554; match to protein family HMM TIGR00797 YP_493051.1 identified by match to protein family HMM PF07690; match to protein family HMM TIGR00712; match to protein family HMM TIGR00881 YP_493052.1 identified by match to protein family HMM PF00903 YP_493053.1 identified by match to protein family HMM PF00296 YP_493054.1 identified by match to protein family HMM PF03358 YP_493055.1 identified by match to protein family HMM PF03601 YP_493057.1 identified by match to protein family HMM PF00583 YP_493058.1 identified by match to protein family HMM PF04302 YP_493059.1 identified by match to protein family HMM PF04261; match to protein family HMM TIGR01409; match to protein family HMM TIGR01412; match to protein family HMM TIGR01413 YP_493061.1 identified by match to protein family HMM PF00902; match to protein family HMM TIGR00945 YP_493062.1 identified by match to protein family HMM PF02416; match to protein family HMM TIGR01411 YP_493064.1 identified by match to protein family HMM PF01381 YP_493066.1 identified by match to protein family HMM PF00005 YP_493068.1 identified by match to protein family HMM PF06772 YP_493069.1 identified by match to protein family HMM PF00108; match to protein family HMM PF02803; match to protein family HMM TIGR01930 YP_493070.1 identified by match to protein family HMM PF04199 YP_493071.1 catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine to form methionine YP_493072.1 catalyzes the formation of 5,10-methylenetetrahydrofolate from 5-methyltetrahydrofolate and S-adenosyl-L-homocysteine and methionine from S-adenosyl-L-methionine and L-homocysteine; expressed in B. subtilis under methionine starvation conditions YP_493073.1 identified by match to protein family HMM PF01053 YP_493074.1 identified by match to protein family HMM PF01053 YP_493075.1 identified by match to protein family HMM PF02195; match to protein family HMM TIGR00180 YP_493076.1 identified by match to protein family HMM PF00924 YP_493077.1 identified by match to protein family HMM PF06107 YP_493078.1 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_493080.1 binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21 YP_493081.1 identified by match to protein family HMM PF00436; match to protein family HMM TIGR00621 YP_493082.1 binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit YP_493083.1 identified by match to protein family HMM PF07751 YP_493085.1 identified by match to protein family HMM PF06486; match to protein family HMM TIGR01655 YP_493086.1 identified by match to protein family HMM PF03413 YP_493088.1 identified by match to protein family HMM PF04226 YP_493089.1 identified by match to protein family HMM PF00300 YP_493093.1 identified by match to protein family HMM PF00070; match to protein family HMM PF07992 YP_493094.1 identified by match to protein family HMM PF00578 YP_493095.1 identified by match to protein family HMM PF00881 YP_493096.1 identified by match to protein family HMM PF00375 YP_493100.1 Catalyzes the transfer of the phosphoribosyl moiety from 5-phospho--D-ribosyl-1-pyrophosphate (PRib-PP) to the 6-oxo-guanine and -xanthine YP_493101.1 identified by match to protein family HMM PF00860; match to protein family HMM TIGR00801 YP_493102.1 identified by match to protein family HMM PF00478; match to protein family HMM PF00571; match to protein family HMM TIGR01302 YP_493103.1 contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway YP_493107.1 identified by match to protein family HMM PF06993 YP_493108.1 identified by match to protein family HMM PF01073; match to protein family HMM PF01370; match to protein family HMM PF05368 YP_493109.1 these proteins share structural homology to known superantigen proteins but do not exhibit any of the properties expected such as histocompatibility complex class II binding or broad T-cell activation YP_493110.1 these proteins share structural homology to known superantigen proteins but do not exhibit any of the properties expected such as histocompatibility complex class II binding or broad T-cell activation YP_493111.1 these proteins share structural homology to known superantigen proteins but do not exhibit any of the properties expected such as histocompatibility complex class II binding or broad T-cell activation YP_493112.1 these proteins share structural homology to known superantigen proteins but do not exhibit any of the properties expected such as histocompatibility complex class II binding or broad T-cell activation YP_493113.1 SSL5, SET3, SET10; bind P-selectin glycoprotein ligand-1 and inhibit P-selectin-mediated neutrophil rolling along the endothelium; these proteins share structural homology to known superantigens but do not exhibit any of the properties expected such as histocompatibility complex class II binding or broad T-cell activation YP_493114.1 these proteins share structural homology to known superantigen proteins but do not exhibit any of the properties expected such as histocompatibility complex class II binding or broad T-cell activation YP_493115.1 SSL7, SET1; blocks IgA-FcR interactions and inhibits complement, leading to increased survival of a sensitive bacterium in blood YP_493116.1 these proteins share structural homology to known superantigen proteins but do not exhibit any of the properties expected such as histocompatibility complex class II binding or broad T-cell activation YP_493117.1 these proteins share structural homology to known superantigen proteins but do not exhibit any of the properties expected such as histocompatibility complex class II binding or broad T-cell activation YP_493118.1 these proteins share structural homology to known superantigen proteins but do not exhibit any of the properties expected such as histocompatibility complex class II binding or broad T-cell activation YP_493119.1 identified by match to protein family HMM PF02384; match to protein family HMM TIGR00497 YP_493120.1 identified by match to protein family HMM PF01420 YP_493121.1 these proteins share structural homology to known superantigen proteins but do not exhibit any of the properties expected such as histocompatibility complex class II binding or broad T-cell activation YP_493122.1 identified by match to protein family HMM TIGR01168 YP_493124.1 identified by match to protein family HMM PF04507; match to protein family HMM TIGR01742 YP_493125.1 identified by match to protein family HMM PF04507; match to protein family HMM TIGR01742 YP_493126.1 identified by match to protein family HMM PF04507; match to protein family HMM TIGR01742 YP_493127.1 identified by match to protein family HMM PF04507; match to protein family HMM TIGR01742 YP_493128.1 identified by match to protein family HMM PF04507; match to protein family HMM TIGR01742 YP_493129.1 identified by match to protein family HMM PF04507; match to protein family HMM TIGR01742 YP_493130.1 identified by match to protein family HMM PF04507; match to protein family HMM TIGR01742 YP_493131.1 identified by match to protein family HMM PF04507; match to protein family HMM TIGR01742 YP_493132.1 identified by match to protein family HMM PF04507; match to protein family HMM TIGR01742 YP_493137.1 identified by match to protein family HMM PF02492; match to protein family HMM PF07683 YP_493138.1 Catalyzes the transfer of electrons from NADH to ubiquinone YP_493142.1 identified by match to protein family HMM PF01569 YP_493145.1 identified by match to protein family HMM PF00209 YP_493146.1 identified by match to protein family HMM PF00291 YP_493147.1 identified by match to protein family HMM PF00266; match to protein family HMM PF01053 YP_493148.1 identified by match to protein family HMM PF00005 YP_493149.1 identified by match to protein family HMM PF00528 YP_493150.1 identified by match to protein family HMM PF03180 YP_493151.1 identified by match to protein family HMM PF01476; match to protein family HMM PF05257 YP_493153.1 identified by match to protein family HMM PF00293 YP_493154.1 identified by match to protein family HMM PF00583 YP_493155.1 identified by match to protein family HMM PF07907 YP_493156.1 identified by match to protein family HMM PF07907 YP_493157.1 identified by match to protein family HMM PF00126 YP_493158.1 identified by match to protein family HMM PF00310; match to protein family HMM PF01493; match to protein family HMM PF01645; match to protein family HMM PF04898 YP_493159.1 glutamate synthase is composed of subunits alpha and beta; beta subunit is a flavin adenine dinucleotide-NADPH dependent oxidoreductase; provides electrons to the alpha subunit, which binds L-glutamine and 2-oxoglutarate and forms L-glutamate YP_493160.1 identified by match to protein family HMM PF00367; match to protein family HMM PF02378; match to protein family HMM TIGR00826; match to protein family HMM TIGR01992 YP_493161.1 identified by match to protein family HMM PF00128; match to protein family HMM TIGR02403 YP_493162.1 identified by match to protein family HMM PF00392; match to protein family HMM PF07702; match to protein family HMM TIGR02404 YP_493163.1 identified by match to protein family HMM PF00583 YP_493164.1 identified by match to protein family HMM PF00004; match to protein family HMM TIGR02397 YP_493165.1 identified by match to protein family HMM PF02575; match to protein family HMM TIGR00103 YP_493166.1 involved in a recombinational process of DNA repair, independent of the recBC complex YP_493167.1 identified by match to protein family HMM PF01276; match to protein family HMM PF03711 YP_493168.1 catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP) YP_493169.1 identified by match to protein family HMM PF06153 YP_493171.1 identified by match to protein family HMM PF04468 YP_493172.2 in Bacillus subtilis this protein is involved in the negative regulation of DNA replication initiation; interacts with DnaN and DnaA YP_493173.1 identified by match to protein family HMM PF05175 YP_493174.1 identified by match to protein family HMM PF01541 YP_493175.1 identified by match to protein family HMM PF00590; match to protein family HMM TIGR00096 YP_493176.1 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_493177.1 identified by match to protein family HMM PF01026; match to protein family HMM PF04909; match to protein family HMM TIGR00010 YP_493178.1 identified by match to protein family HMM PF01751; match to protein family HMM TIGR00334 YP_493179.1 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_493180.1 identified by similarity to SP:P37466; match to protein family HMM PF06257 YP_493181.1 An essential enzyme in the nonmevalonate pathway of isopentenyl diphosphate and dimethylallyl diphosphate biosynthesis YP_493182.1 identified by match to protein family HMM PF00156; match to protein family HMM TIGR01743 YP_493183.1 identified by match to protein family HMM PF01042; match to protein family HMM TIGR00004 YP_493184.1 stage V sporulation protein G; essential for spore formation and a negative regulator of asymmetric septation in Bacillus; involved in methicillin-resistance, biofilm formation and capsular polysaccharide synthesis in Staphylococcus YP_493186.1 forms a homotrimer; catalyzes the acetylation of glucosamine-1-phosphate and uridylation of N-acetylglucosamine-1-phosphate to produce UDP-GlcNAc; function in cell wall synthesis YP_493187.1 catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP YP_493188.1 the Ctc family of proteins consists of two types, one that contains the N-terminal ribosomal protein L25 domain only which in Escherichia coli binds the 5S rRNA while a subset of proteins contain a C-terminal extension that is involved in the stress response YP_493189.1 Enables the recycling of peptidyl-tRNAs produced at termination of translation YP_493190.1 identified by match to protein family HMM PF00270; match to protein family HMM PF00271; match to protein family HMM PF02559; match to protein family HMM PF03461; match to protein family HMM PF04851; match to protein family HMM TIGR00580 YP_493191.1 identified by match to protein family HMM PF01943 YP_493192.1 identified by match to protein family HMM PF00590; match to protein family HMM PF03819 YP_493193.1 identified by match to protein family HMM PF01479 YP_493194.1 identified by match to protein family HMM PF04977 YP_493195.1 identified by match to protein family HMM PF00575 YP_493196.1 identified by match to protein family HMM PF01171; match to protein family HMM TIGR02432; match to protein family HMM TIGR02433 YP_493197.1 identified by match to protein family HMM PF00156; match to protein family HMM TIGR01203 YP_493198.1 identified by match to protein family HMM PF00004; match to protein family HMM PF01434; match to protein family HMM PF06480; match to protein family HMM PF07728; match to protein family HMM TIGR01241 YP_493199.1 becomes active under oxidative stress; four conserved cysteines bind a zinc atom when they are in the reduced state and the enzyme is inactive; oxidative stress results in oxidized cysteines, release of zinc, and binding of Hsp33 to aggregation-prone proteins; forms dimers and higher order oligomers YP_493200.1 identified by match to protein family HMM PF00291; match to protein family HMM TIGR01136; match to protein family HMM TIGR01139 YP_493201.1 identified by match to protein family HMM PF00809; match to protein family HMM TIGR01496 YP_493202.1 identified by match to protein family HMM PF02152; match to protein family HMM TIGR00525; match to protein family HMM TIGR00526 YP_493203.1 identified by match to protein family HMM PF01288; match to protein family HMM TIGR01498 YP_493205.1 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_493206.1 identified by match to protein family HMM PF00392 YP_493207.1 with PdxT forms pyridoxal 5'-phosphate from glutamine, either ribose 5-phosphate or ribulose 5-phosphate, and either glyceraldehyde 3-phosphate or dihydroxyacetone phosphate YP_493208.1 with PdxST is involved in the biosynthesis of pyridoxal 5'-phosphate; PdxT catalyzes the hydrolysis of glutamine to glutamate and ammonia; PdxS utilizes the ammonia to synthesize pyridoxal 5'-phosphate YP_493209.1 identified by match to protein family HMM PF01773; match to protein family HMM PF07662; match to protein family HMM PF07670 YP_493210.1 identified by match to protein family HMM PF05848 YP_493211.1 identified by match to protein family HMM PF02151 YP_493212.1 identified by match to protein family HMM PF00217 YP_493213.1 identified by match to protein family HMM PF00004; match to protein family HMM PF02151; match to protein family HMM PF02861; match to protein family HMM PF07724; match to protein family HMM PF07728 YP_493214.2 Sms; stabilizes the strand-invasion intermediate during the DNA repair; involved in recombination of donor DNA and plays an important role in DNA damage repair after exposure to mutagenic agents YP_493215.1 identified by match to protein family HMM PF01850; match to protein family HMM PF01938 YP_493216.1 Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation YP_493217.1 identified by match to protein family HMM PF00132; match to protein family HMM TIGR01172 YP_493218.1 catalyzes a two-step reaction; charges a cysteine by linking its carboxyl group to the alpha-phosphate of ATP then transfers the aminoacyl-adenylate to its tRNA YP_493219.1 identified by match to protein family HMM PF00636 YP_493220.1 identified by match to protein family HMM PF00588; match to protein family HMM PF08032; match to protein family HMM TIGR00186 YP_493221.1 identified by match to protein family HMM PF05991 YP_493222.1 identified by match to protein family HMM PF04542 YP_493223.1 forms a complex with SecY and SecG; SecYEG forms a putative protein-conducting channel to which secA binds and translocates targeted polypeptides across the cytoplasmic membrane, a process driven by ATP and a proton-motive force YP_493224.1 identified by match to protein family HMM PF00467; match to protein family HMM PF02357; match to protein family HMM TIGR00922 YP_493225.1 binds directly to 23S ribosomal RNA YP_493226.1 in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA YP_493227.1 binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit YP_493228.1 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_493229.1 identified by match to protein family HMM PF05175 YP_493230.2 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_493231.1 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_493232.1 in Bacillus subtilis this non-essential protein associates with the ribosome YP_493233.1 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_493234.1 truncated; authenticated frameshift; identified by match to protein family HMM PF00177; match to protein family HMM TIGR01029 YP_493235.1 EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene YP_493236.1 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_493237.1 identified by match to protein family HMM PF01546; match to protein family HMM PF07687; match to protein family HMM TIGR01891 YP_493238.1 catalyzes the formation of 2-amino-3-oxobutanoate from acetyl-CoA and glycine YP_493239.1 Hsp31 stabilizes early unfolding protein intermediates under severe heat stress YP_493240.1 catalyzes the phosphorylation of ribulose to ribulose 5-phosphate YP_493241.1 identified by match to protein family HMM PF01370; match to protein family HMM PF02719; match to protein family HMM PF07993 YP_493242.1 catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids YP_493243.1 identified by match to protein family HMM PF00702; match to protein family HMM TIGR01549 YP_493244.1 identified by match to protein family HMM PF01712 YP_493245.1 identified by match to protein family HMM PF01712 YP_493246.1 identified by match to protein family HMM PF00383 YP_493247.1 identified by match to protein family HMM PF00702; match to protein family HMM PF05116; match to protein family HMM TIGR00099; match to protein family HMM TIGR01484 YP_493248.1 identified by match to protein family HMM PF02525; match to protein family HMM PF03358 YP_493249.1 identified by match to protein family HMM PF00746; match to protein family HMM PF04650; match to protein family HMM PF05738; match to protein family HMM TIGR01167; match to protein family HMM TIGR01168 YP_493250.1 identified by match to protein family HMM PF00746; match to protein family HMM PF04650; match to protein family HMM PF05738; match to protein family HMM TIGR01167; match to protein family HMM TIGR01168 YP_493251.1 identified by match to protein family HMM PF00746; match to protein family HMM PF04650; match to protein family HMM PF05738; match to protein family HMM TIGR01167; match to protein family HMM TIGR01168 YP_493252.1 identified by match to protein family HMM PF00534 YP_493253.1 identified by match to protein family HMM PF00534 YP_493254.1 similar protein in Methanocaldococcus converts GTP to 7,8-dihydro-D-neopterin 2',3'-cyclic phosphate as the first step in methanopterin biosynthesis YP_493255.1 identified by match to protein family HMM PF02585 YP_493257.1 identified by match to protein family HMM PF01182 YP_493258.1 identified by match to protein family HMM PF00215 YP_493259.2 identified by match to protein family HMM PF01380 YP_493260.1 identified by match to protein family HMM PF00702; match to protein family HMM TIGR01549 YP_493261.1 identified by match to protein family HMM PF00083; match to protein family HMM PF07690 YP_493262.1 identified by match to protein family HMM PF00501 YP_493263.1 identified by match to protein family HMM PF00108; match to protein family HMM PF02803; match to protein family HMM TIGR01930 YP_493265.1 identified by match to protein family HMM TIGR00097 YP_493266.1 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_493268.1 identified by match to protein family HMM PF04241 YP_493269.1 identified by match to protein family HMM PF00324 YP_493271.1 identified by match to protein family HMM PF06738 YP_493272.1 identified by match to protein family HMM PF06778 YP_493273.1 in Salmonella this enzyme is required for ethanolamine catabolism; has higher affinity for CoA than Pta YP_493275.1 identified by match to protein family HMM PF00288; match to protein family HMM TIGR00549 YP_493276.1 identified by match to protein family HMM PF00288; match to protein family HMM TIGR01240 YP_493277.1 identified by match to protein family HMM PF00288; match to protein family HMM TIGR01220 YP_493279.1 identified by match to protein family HMM PF00070; match to protein family HMM PF02852; match to protein family HMM PF07992 YP_493280.1 identified by match to protein family HMM PF02082 YP_493283.1 identified by match to protein family HMM PF04276; match to protein family HMM TIGR01218 YP_493284.1 identified by match to protein family HMM PF04276; match to protein family HMM TIGR01218 YP_493285.1 identified by match to protein family HMM PF04276; match to protein family HMM TIGR01218 YP_493286.1 identified by match to protein family HMM PF04276; match to protein family HMM TIGR01218 YP_493287.1 identified by match to protein family HMM PF04276; match to protein family HMM TIGR01218 YP_493288.1 identified by match to protein family HMM PF04276; match to protein family HMM TIGR01218 YP_493289.1 identified by match to protein family HMM PF04276; match to protein family HMM TIGR01218 YP_493290.1 identified by match to protein family HMM PF04276; match to protein family HMM TIGR01218 YP_493291.1 identified by match to protein family HMM PF04276; match to protein family HMM TIGR01218 YP_493292.1 identified by match to protein family HMM PF00248 YP_493293.1 identified by match to protein family HMM PF03358 YP_493294.1 identified by match to protein family HMM PF00583 YP_493295.1 identified by match to protein family HMM PF01966 YP_493297.1 similar to zinc-dependent eukaryotic ADH enzymes and distinct from fermentative ADHs YP_493299.1 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_493301.1 identified by match to protein family HMM PF01497 YP_493302.1 identified by match to protein family HMM PF01032 YP_493303.1 identified by match to protein family HMM PF00702; match to protein family HMM TIGR01509; match to protein family HMM TIGR01549 YP_493304.1 identified by match to protein family HMM PF00561 YP_493307.1 identified by match to protein family HMM PF00561 YP_493308.1 identified by match to protein family HMM TIGR01889 YP_493309.1 identified by match to protein family HMM PF04657 YP_493312.1 identified by match to protein family HMM PF00589 YP_493313.1 subunit A of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali YP_493314.1 subunit B of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali YP_493315.1 subunit C of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali YP_493316.1 subunit D of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; contains an oxidoreductase domain; catalyzes the transfer of electrons from NADH to ubiquinone; in S. meliloti it is known to be involved specifically with K+ transport YP_493317.1 subunit E of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in S. meliloti it is known to be involved specifically with K+ transport YP_493318.1 subunit F of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali YP_493319.1 subunit G of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali YP_493320.1 identified by match to protein family HMM PF00999 YP_493321.1 identified by match to protein family HMM PF01297 YP_493322.1 identified by match to protein family HMM PF00950 YP_493323.1 identified by match to protein family HMM PF00005 YP_493324.1 identified by match to protein family HMM PF01325; match to protein family HMM PF02742; match to protein family HMM PF04023 YP_493326.1 identified by match to protein family HMM PF03808; match to protein family HMM TIGR00696 YP_493327.1 with TagG is involved in the export of teichoic acids YP_493328.1 identified by match to protein family HMM PF01061 YP_493329.1 identified by match to protein family HMM PF04464 YP_493330.1 identified by match to protein family HMM PF00535 YP_493331.1 identified by match to protein family HMM PF01467; match to protein family HMM TIGR00125; match to protein family HMM TIGR01518 YP_493332.1 identified by match to protein family HMM PF00144; match to protein family HMM PF00768 YP_493333.1 identified by match to protein family HMM PF00005; match to protein family HMM PF00664 YP_493334.1 identified by match to protein family HMM PF01773; match to protein family HMM PF07662 YP_493335.1 identified by match to protein family HMM PF02588 YP_493336.1 identified by match to protein family HMM PF00005 YP_493337.1 identified by match to protein family HMM PF01032 YP_493338.1 identified by match to protein family HMM PF01032 YP_493339.1 with DhaL and DhaM forms dihydroxyacetone kinase, which is responsible for phosphorylating dihydroxyacetone; DhaK is the dihydroxyacetone binding subunit of the dihydroxyacetone kinase YP_493340.1 identified by match to protein family HMM PF02734; match to protein family HMM TIGR02365 YP_493341.1 identified by match to protein family HMM PF03610; match to protein family HMM TIGR02364 YP_493343.1 identified by match to protein family HMM PF05525 YP_493344.1 identified by match to protein family HMM PF07859 YP_493346.1 identified by match to protein family HMM PF00583 YP_493348.1 identified by match to protein family HMM PF00072; match to protein family HMM PF00486 YP_493349.1 identified by match to protein family HMM PF00512; match to protein family HMM PF02518 YP_493350.1 identified by match to protein family HMM PF00005 YP_493352.1 identified by match to protein family HMM PF01865 YP_493353.1 identified by match to protein family HMM PF01384 YP_493354.1 identified by match to protein family HMM PF01476; match to protein family HMM PF05257 YP_493356.1 two frameshifts, both authenticated; identified by match to protein family HMM PF00165 YP_493357.1 identified by match to protein family HMM TIGR01889 YP_493358.1 identified by match to protein family HMM PF01709; match to protein family HMM TIGR01033 YP_493359.1 identified by match to protein family HMM PF06172 YP_493360.1 identified by match to protein family HMM PF04167 YP_493361.1 identified by match to protein family HMM PF00126; match to protein family HMM PF03466 YP_493362.1 identified by match to protein family HMM PF07690 YP_493363.1 identified by match to protein family HMM PF04306 YP_493365.1 identified by match to protein family HMM PF00583 YP_493368.1 identified by match to protein family HMM PF00583 YP_493369.1 identified by match to protein family HMM PF03641; match to protein family HMM TIGR00730 YP_493370.1 identified by match to protein family HMM PF02639 YP_493372.1 BacA; phosphatase activity in Escherichia coli not kinase; involved in bacitracin resistance as bacitracin supposedly sequesters undecaprenyl disphosphate which reduces the pool of lipid carrier available to the cell YP_493373.1 identified by match to protein family HMM PF00005; match to protein family HMM PF00664 YP_493374.1 identified by match to protein family HMM PF00005 YP_493375.1 identified by match to protein family HMM PF01047 YP_493376.1 identified by match to protein family HMM PF02492; match to protein family HMM PF07683 YP_493377.1 identified by match to protein family HMM PF00248 YP_493379.1 identified by match to protein family HMM PF00939; match to protein family HMM PF03600; match to protein family HMM TIGR00785 YP_493380.1 identified by match to protein family HMM PF03441 YP_493381.1 identified by match to protein family HMM PF07099 YP_493382.1 identified by match to protein family HMM PF03479 YP_493383.1 identified by match to protein family HMM PF07690; match to protein family HMM TIGR00880 YP_493385.1 identified by match to protein family HMM PF04073; match to protein family HMM TIGR00011 YP_493386.1 identified by match to protein family HMM PF00455; match to protein family HMM PF08220 YP_493387.1 identified by match to protein family HMM PF00294 YP_493388.1 identified by match to protein family HMM PF00359; match to protein family HMM PF02378; match to protein family HMM PF02379; match to protein family HMM TIGR00829; match to protein family HMM TIGR00848; match to protein family HMM TIGR01427 YP_493389.1 identified by match to protein family HMM PF01979; match to protein family HMM TIGR00221 YP_493390.1 identified by match to protein family HMM PF00571; match to protein family HMM PF01595; match to protein family HMM PF03471 YP_493391.1 identified by match to protein family HMM PF00248 YP_493392.1 identified by match to protein family HMM PF00535 YP_493393.1 identified by match to protein family HMM PF00512; match to protein family HMM PF00672; match to protein family HMM PF02518 YP_493394.1 identified by match to protein family HMM PF00072; match to protein family HMM PF00486 YP_493395.1 identified by match to protein family HMM PF07681 YP_493398.1 identified by match to protein family HMM PF04055 YP_493399.1 identified by match to protein family HMM PF01242 YP_493400.1 identified by match to protein family HMM PF06508; match to protein family HMM TIGR00364 YP_493401.1 identified by match to protein family HMM PF00117; match to protein family HMM TIGR00566 YP_493402.1 identified by match to protein family HMM PF00425 YP_493404.1 identified by match to protein family HMM PF02682 YP_493405.1 identified by match to protein family HMM PF02626 YP_493406.1 identified by match to protein family HMM PF00884 YP_493407.1 identified by match to protein family HMM PF00005 YP_493408.1 identified by match to protein family HMM PF00270; match to protein family HMM PF00271; match to protein family HMM PF00570; match to protein family HMM TIGR00614; match to protein family HMM TIGR01389 YP_493409.1 identified by match to protein family HMM PF00005 YP_493410.1 identified by match to protein family HMM PF00528; match to protein family HMM PF04069 YP_493411.1 catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis YP_493412.1 identified by match to protein family HMM PF06941 YP_493414.1 identified by match to protein family HMM PF00781; match to protein family HMM TIGR00147 YP_493415.1 identified by match to protein family HMM PF00854; match to protein family HMM PF07690; match to protein family HMM TIGR00924 YP_493416.1 NADPH-dependent; catalyzes the reduction of 7-cyano-7-deazaguanine to 7-aminomethyl-7-deazaguanine in queuosine biosynthesis YP_493417.1 identified by match to protein family HMM PF00892 YP_493418.1 in Salmonella NrdI has a stimulatory effect on the ribonucleotide reductase activity of NrdH with NrdEF YP_493419.1 Catalyzes the rate-limiting step in dNTP synthesis YP_493420.1 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_493421.1 identified by match to protein family HMM PF01032 YP_493422.1 identified by match to protein family HMM PF01032 YP_493423.1 identified by match to protein family HMM PF00005 YP_493424.1 identified by match to protein family HMM PF01497 YP_493425.1 catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis YP_493426.1 identified by match to protein family HMM PF04229 YP_493429.1 identified by match to protein family HMM PF02595; match to protein family HMM TIGR00045 YP_493430.1 catalyzes the release of the N-terminal amino acid from a tripeptide YP_493432.1 identified by match to protein family HMM PF06738 YP_493433.1 identified by match to protein family HMM PF00990; match to protein family HMM PF07694; match to protein family HMM TIGR00254 YP_493434.1 identified by match to protein family HMM PF00953 YP_493435.1 identified by match to protein family HMM PF01205; match to protein family HMM TIGR00257 YP_493436.1 identified by match to protein family HMM PF02645; match to protein family HMM TIGR00762 YP_493437.1 identified by match to protein family HMM PF00271; match to protein family HMM PF04851 YP_493439.1 identified by match to protein family HMM PF02482; match to protein family HMM TIGR00741 YP_493440.1 functions in protein export; can interact with acidic membrane phospholipids and the SecYEG protein complex; binds to preproteins; binds to ATP and undergoes a conformational change to promote membrane insertion of SecA/bound preprotein; ATP hydrolysis appears to drive release of the preprotein from SecA and deinsertion of SecA from the membrane; additional proteins SecD/F/YajC aid SecA recycling; exists in an equilibrium between monomers and dimers; may possibly form higher order oligomers; proteins in this cluster correspond SecA1; SecA2 is not essential and seems to play a role in secretion of a subset of proteins YP_493441.1 identified by match to protein family HMM PF01476; match to protein family HMM PF05257 YP_493443.1 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_493444.1 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_493445.1 catalyzes the phosphorylation of the phosphocarrier protein HPr of the bacterial phosphotransferase system YP_493446.1 transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein YP_493447.1 identified by match to protein family HMM PF00132 YP_493448.1 identified by match to protein family HMM PF00515; match to protein family HMM PF07719 YP_493449.1 identified by match to protein family HMM PF00070; match to protein family HMM PF07992; match to protein family HMM TIGR01292 YP_493450.1 identified by match to protein family HMM PF03668 YP_493451.1 identified by match to protein family HMM PF01933; match to protein family HMM TIGR01826 YP_493452.1 identified by match to protein family HMM PF02650; match to protein family HMM TIGR00647 YP_493453.1 hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates YP_493454.1 identified by match to protein family HMM PF01370; match to protein family HMM PF07993; match to protein family HMM TIGR01777 YP_493456.1 identified by match to protein family HMM PF04198 YP_493457.1 identified by match to protein family HMM PF00044; match to protein family HMM PF02800; match to protein family HMM TIGR01534 YP_493458.1 Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway YP_493459.1 Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate YP_493460.1 catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate YP_493461.1 enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis YP_493463.2 identified by match to protein family HMM PF03840; match to protein family HMM TIGR00810 YP_493465.1 identified by match to protein family HMM PF00575; match to protein family HMM PF00773; match to protein family HMM PF08206; match to protein family HMM TIGR00358; match to protein family HMM TIGR02063 YP_493466.1 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_493471.1 identified by match to protein family HMM PF00583 YP_493472.1 identified by match to protein family HMM PF00746; match to protein family HMM PF04650; match to protein family HMM TIGR01167; match to protein family HMM TIGR01168 YP_493473.1 identified by similarity to SP:P07767 YP_493476.1 identified by match to protein family HMM PF00565 YP_493477.1 identified by match to protein family HMM PF00313 YP_493481.1 identified by match to protein family HMM PF06855 YP_493483.1 identified by match to protein family HMM PF00300 YP_493484.1 identified by match to protein family HMM PF01810 YP_493486.1 identified by match to protein family HMM PF02566 YP_493487.1 catalyzes the dehydration of 3-dehydroquinate to form 3-dehydroshikimate in aromatic amino acid biosynthesis YP_493488.1 identified by match to protein family HMM PF00881 YP_493489.1 identified by match to protein family HMM PF00085 YP_493490.1 identified by match to protein family HMM PF03960; match to protein family HMM TIGR01617 YP_493491.1 part of multienzyme complex composed of H, L, P, and T proteins which catalyzes oxidation of glycine to yield carbon dioxide, ammonia, 5,10-CH2-H4folate and a reduced pyridine nucleotide; protein H is involved in transfer of methylamine group from the P to T protein; covalently bound to a lipoyl cofactor YP_493494.1 identified by match to protein family HMM PF01751 YP_493496.1 identified by match to protein family HMM PF00005 YP_493497.1 identified by match to protein family HMM PF00528 YP_493498.1 identified by match to protein family HMM PF03180 YP_493499.1 Staphylococcus aureus pathogenicity island; identified by match to protein family HMM PF00589 YP_493500.1 Staphylococcus aureus pathogenicity island; identified by match to protein family HMM PF01123; match to protein family HMM PF02876 YP_493501.1 Staphylococcus aureus pathogenicity island; identified by match to protein family HMM PF01123; match to protein family HMM PF02876 YP_493502.1 Staphylococcus aureus pathogenicity island; identified by match to protein family HMM PF06114 YP_493503.1 Staphylococcus aureus pathogenicity island; identified by match to protein family HMM PF00356; match to protein family HMM PF01381 YP_493504.1 identified by match to protein family HMM PF01381 YP_493505.1 Staphylococcus aureus pathogenicity island YP_493506.1 Staphylococcus aureus pathogenicity island YP_493507.1 Staphylococcus aureus pathogenicity island; identified by similarity to GB:AAG29614.1 YP_493508.1 Staphylococcus aureus pathogenicity island; identified by match to protein family HMM PF07342 YP_493509.1 Staphylococcus aureus pathogenicity island; identified by match to protein family HMM PF03288; match to protein family HMM TIGR01613 YP_493510.1 Staphylococcus aureus pathogenicity island YP_493511.1 Staphylococcus aureus pathogenicity island YP_493512.1 Staphylococcus aureus pathogenicity island YP_493513.1 Staphylococcus aureus pathogenicity island YP_493514.1 Staphylococcus aureus pathogenicity island; identified by match to protein family HMM PF07751 YP_493515.1 Staphylococcus aureus pathogenicity island YP_493516.1 identified by match to protein family HMM PF05532 YP_493517.1 identified by match to protein family HMM PF04018 YP_493518.1 identified by match to protein family HMM PF00005; match to protein family HMM TIGR01978 YP_493519.1 identified by match to protein family HMM PF01458; match to protein family HMM TIGR01981 YP_493520.1 identified by match to protein family HMM PF00266; match to protein family HMM PF01212; match to protein family HMM TIGR01979 YP_493521.1 identified by match to protein family HMM PF01592; match to protein family HMM TIGR01994 YP_493522.1 identified by match to protein family HMM PF01458; match to protein family HMM TIGR01980 YP_493524.1 identified by match to protein family HMM PF00571; match to protein family HMM PF01595 YP_493525.1 identified by match to protein family HMM PF01180; match to protein family HMM PF03060 YP_493526.1 identified by match to protein family HMM PF01904 YP_493527.1 identified by match to protein family HMM PF01925 YP_493528.1 identified by match to protein family HMM PF00149 YP_493529.1 catalyzes the radical-mediated insertion of two sulfur atoms into an acyl carrier protein (ACP) bound to an octanoyl group to produce a lipoyl group YP_493530.1 identified by match to protein family HMM PF06265 YP_493532.1 identified by match to protein family HMM PF01934 YP_493533.1 identified by match to protein family HMM PF00702; match to protein family HMM TIGR01457; match to protein family HMM TIGR01460 YP_493534.1 identified by match to protein family HMM PF00389; match to protein family HMM PF02826 YP_493535.1 transfers D-alanine to the D-alanyl carrier protein during the incorporation of D-alanine into lipoteichoic acid YP_493536.1 identified by match to protein family HMM PF03062 YP_493537.1 D-alanyl carrier protein subunit; involved in the incorporation of D-alanine into membrane-associated D-alanyl-lipoteichoic acid; D-alanyl carrier protein is the acceptor of activated D-alanine which it donates to a membrane acceptor(D-alanyl transferase) for incorporation into membrane lipoteichoic acid YP_493538.1 identified by match to protein family HMM PF04914; match to protein family HMM PF04915; match to protein family HMM PF04918 YP_493539.1 identified by match to protein family HMM PF01106 YP_493540.1 identified by match to protein family HMM PF07315 YP_493541.1 identified by match to protein family HMM PF00070; match to protein family HMM PF07992 YP_493542.1 identified by match to protein family HMM PF07293 YP_493543.1 identified by match to protein family HMM PF01521; match to protein family HMM TIGR00049 YP_493544.1 identified by match to protein family HMM PF00070; match to protein family HMM PF07992 YP_493545.1 identified by match to protein family HMM PF00883; match to protein family HMM PF02789 YP_493546.1 authenticated frameshift YP_493547.1 identified by match to protein family HMM PF03061; match to protein family HMM TIGR00369 YP_493549.1 subunit G of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali YP_493550.1 subunit F of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali YP_493551.1 subunit E of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali YP_493552.1 subunit D of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; contains an oxidoreductase domain; catalyzes the transfer of electrons from NADH to ubiquinone YP_493553.1 subunit C of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali YP_493554.1 subunit B of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in the case of S. meliloti it was proved to be involved specifically with K+ transport YP_493555.1 subunit A of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali YP_493557.1 identified by match to protein family HMM PF00160 YP_493558.1 identified by match to protein family HMM PF00575 YP_493559.1 identified by match to protein family HMM PF00724 YP_493560.1 identified by match to protein family HMM PF00202; match to protein family HMM TIGR01885 YP_493561.1 identified by match to protein family HMM PF00208; match to protein family HMM PF02812 YP_493562.1 identified by match to protein family HMM PF03009 YP_493563.1 catalyzes the formation of arginine from (N-L-arginino)succinate YP_493564.1 catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming YP_493565.1 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_493567.1 identified by match to protein family HMM PF00717; match to protein family HMM TIGR02227 YP_493568.1 identified by match to protein family HMM PF00717; match to protein family HMM TIGR02227 YP_493569.1 identified by match to protein family HMM TIGR02773 YP_493570.1 identified by match to protein family HMM PF00580; match to protein family HMM TIGR02785 YP_493571.1 identified by match to protein family HMM PF01557 YP_493572.1 identified by match to protein family HMM PF07457 YP_493573.1 NADPH-dependent; catalyzes the reduction of coenzyme A disulfide YP_493574.1 identified by match to protein family HMM PF00702; match to protein family HMM PF05116; match to protein family HMM TIGR00099; match to protein family HMM TIGR01484 YP_493575.1 identified by match to protein family HMM PF01883 YP_493576.1 identified by match to protein family HMM PF01757 YP_493577.1 identified by match to protein family HMM PF00004; match to protein family HMM PF02861; match to protein family HMM PF07724; match to protein family HMM PF07728 YP_493578.1 identified by match to protein family HMM PF00126; match to protein family HMM PF03466 YP_493579.1 identified by match to protein family HMM PF00682 YP_493580.1 identified by match to protein family HMM PF01300 YP_493582.1 identified by match to protein family HMM TIGR00481 YP_493583.1 identified by match to protein family HMM PF03642 YP_493585.1 FabH; beta-ketoacyl-acyl carrier protein synthase III; catalyzes the condensation of acetyl-CoA with malonyl-ACP to initiate cycles of fatty acid elongation; differs from 3-oxoacyl-(acyl carrier protein) synthase I and II in that it utilizes CoA thioesters as primers rather than acyl-ACPs YP_493586.1 identified by match to protein family HMM PF00109; match to protein family HMM PF02801 YP_493587.1 identified by match to protein family HMM PF00528 YP_493588.1 identified by match to protein family HMM PF00528 YP_493589.1 identified by match to protein family HMM PF00005; match to protein family HMM TIGR01727 YP_493590.1 identified by match to protein family HMM PF00005 YP_493591.1 identified by match to protein family HMM PF00496 YP_493592.1 identified by match to protein family HMM PF00496 YP_493593.1 identified by match to protein family HMM PF00005; match to protein family HMM TIGR01727 YP_493594.1 identified by match to protein family HMM PF00005; match to protein family HMM TIGR01727 YP_493595.1 identified by match to protein family HMM PF00528 YP_493596.1 identified by match to protein family HMM PF00528 YP_493597.1 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_493598.1 the anti-alpha factor Spx interacts with RNA polymerase alpha subunit C-terminal domain in a region that interacts with the sigma 70 subunit and may interfere with activation of promoters; in Bacillus subtilis this protein is a substrate for ClpXP protease; blocks transcription of the competence regulatory gene encoded by the srf operon; regulates a number of genes involved in thiol homeostasis including trxA and trxB; monomeric member of ArsC family of proteins; does not bind DNA; contains a disulfide bond between C10 and C13 which may sense disulfide stress YP_493599.1 enables recognition and targeting of proteins for proteolysis, involved in negative regulation of competence YP_493600.1 authenticated frameshift YP_493601.1 authenticated frameshift; identified by match to protein family HMM PF06054 YP_493602.1 identified by match to protein family HMM PF01432; match to protein family HMM TIGR00181 YP_493604.1 identified by match to protein family HMM PF01152 YP_493605.1 identified by match to protein family HMM PF01928 YP_493607.1 identified by match to protein family HMM PF04607 YP_493608.1 catalyzes the phosphorylation of NAD to NADP YP_493609.1 identified by match to protein family HMM PF00849; match to protein family HMM TIGR00005 YP_493610.1 identified by match to protein family HMM PF00571; match to protein family HMM PF01769; match to protein family HMM PF03448; match to protein family HMM TIGR00400 YP_493611.1 identified by match to protein family HMM PF00999; match to protein family HMM PF02080; match to protein family HMM PF02254 YP_493612.1 Catalyzes a key regulatory step in fatty acid biosynthesis YP_493613.1 identified by match to protein family HMM PF01594 YP_493614.1 identified by match to protein family HMM PF00324; match to protein family HMM PF01235; match to protein family HMM TIGR00835 YP_493615.1 identified by match to protein family HMM PF00756 YP_493616.1 similar to 2'-5' RNA ligase YP_493617.1 identified by match to protein family HMM PF07690 YP_493618.1 processive; catalyzes the formation of mono-, di- and tri-glucosyldiacylglycerol by the progressive transfer of glucosyl residues to diacylglycerol; involved in the formation of membrane glycolipids YP_493619.1 involved in cell wall formation; peptidoglycan synthesis; cytoplasmic enzyme; catalyzes the addition of lysine to UDP-N-acetylmuramoyl-L-alanyl-D-glutamate forming UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-L-lysine YP_493621.1 stimulates the release of release factors 1 and 2 from the ribosome after hydrolysis of the ester bond in peptidyl-tRNA has occurred; GDP/GTP-binding protein YP_493622.1 identified by match to protein family HMM PF03741 YP_493623.1 identified by match to protein family HMM PF00089 YP_493624.1 identified by match to protein family HMM PF02386 YP_493625.1 identified by match to protein family HMM PF02872 YP_493626.1 identified by match to protein family HMM PF06338 YP_493628.1 identified by match to protein family HMM PF03099; match to protein family HMM TIGR00545 YP_493630.1 identified by match to protein family HMM PF02517 YP_493632.1 identified by match to protein family HMM TIGR01654 YP_493633.1 identified by match to protein family HMM TIGR01655 YP_493634.1 identified by match to protein family HMM PF00005 YP_493637.1 identified by match to protein family HMM PF00534 YP_493638.1 identified by match to protein family HMM PF07681 YP_493639.1 identified by match to protein family HMM PF01497 YP_493640.1 identified by match to protein family HMM PF05154 YP_493641.1 identified by match to protein family HMM PF00583 YP_493642.1 catalyzes the formation of dimethylmenaquinone from 1,4-dihydroxy-2-naphthoate and octaprenyl diphosphate YP_493643.1 identified by match to protein family HMM PF00425; match to protein family HMM TIGR00543 YP_493644.1 identified by match to protein family HMM PF02776; match to protein family HMM TIGR00173 YP_493645.1 identified by match to protein family HMM PF00561 YP_493646.1 catalyzes the formation of 1,4-dihydroxy-2-naphthoate from O-succinylbenzoyl-CoA YP_493649.1 identified by match to protein family HMM PF00089 YP_493650.1 identified by match to protein family HMM PF00155 YP_493651.1 identified by match to protein family HMM PF01757 YP_493652.1 identified by match to protein family HMM PF01047 YP_493653.1 identified by match to protein family HMM PF01510; match to protein family HMM PF01832 YP_493654.1 identified by match to protein family HMM PF00583 YP_493656.1 identified by match to protein family HMM PF03816; match to protein family HMM TIGR00350 YP_493657.1 identified by match to protein family HMM PF00144 YP_493658.1 identified by match to protein family HMM PF03626 YP_493659.1 identified by match to protein family HMM PF00510 YP_493660.1 identified by match to protein family HMM PF00115 YP_493661.1 identified by match to protein family HMM PF00116; match to protein family HMM PF02790; match to protein family HMM PF06481; match to protein family HMM TIGR01432 YP_493663.1 catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate YP_493664.1 identified by match to protein family HMM PF00731; match to protein family HMM TIGR01162 YP_493665.1 With PurE catalyzes the conversion of aminoimidazole ribonucleotide to carboxyaminoimidazole ribonucleotide in the de novo purine nucleotide biosynthetic pathway YP_493666.1 catalyzes the formation of (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4- carboxamido)succinate from 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate and L-aspartate in purine biosynthesis; SAICAR synthase YP_493667.1 identified by match to protein family HMM PF02700; match to protein family HMM TIGR00302 YP_493668.1 catalyzes the formation of 2-(formamido)-N1-(5-phospho-D-ribosyl)acetamidine from N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide and L-glutamine in purine biosynthesis YP_493669.1 catalyzes the formation of 2-(formamido)-N1-(5-phospho-D-ribosyl)acetamidine from N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide and L-glutamine in purine biosynthesis YP_493670.1 Catalyzes first step of the de novo purine nucleotide biosynthetic pathway YP_493671.1 catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis YP_493672.1 identified by match to protein family HMM PF00551; match to protein family HMM TIGR00639 YP_493673.1 involved in de novo purine biosynthesis YP_493674.1 catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis YP_493675.1 identified by match to protein family HMM PF02361 YP_493676.1 identified by match to protein family HMM PF00005 YP_493681.1 identified by match to protein family HMM PF00381; match to protein family HMM TIGR01003 YP_493682.1 identified by match to protein family HMM PF00391; match to protein family HMM PF02896; match to protein family HMM PF05524; match to protein family HMM TIGR01417 YP_493683.1 identified by match to protein family HMM PF00462 YP_493684.1 identified by match to protein family HMM PF01654 YP_493686.1 identified by match to protein family HMM PF02080; match to protein family HMM PF02254 YP_493687.1 identified by match to protein family HMM PF00753; match to protein family HMM PF07521; match to protein family HMM TIGR00649 YP_493688.1 identified by match to protein family HMM PF07288 YP_493689.1 cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+) YP_493691.1 identified by match to protein family HMM PF00676 YP_493692.1 identified by match to protein family HMM PF02779; match to protein family HMM PF02780 YP_493693.1 identified by similarity to GB:CAA37630.1; match to protein family HMM PF00198; match to protein family HMM PF00364; match to protein family HMM PF02817 YP_493694.1 E3 component of pyruvate complex; catalyzes the oxidation of dihydrolipoamide to lipoamide YP_493695.1 identified by match to protein family HMM PF05256 YP_493696.1 identified by match to protein family HMM PF01381; match to protein family HMM PF07883 YP_493697.1 identified by match to protein family HMM PF00005 YP_493698.1 identified by match to protein family HMM PF00528 YP_493699.1 identified by match to protein family HMM PF00528 YP_493700.1 identified by match to protein family HMM PF01547 YP_493703.1 identified by match to protein family HMM PF01566; match to protein family HMM TIGR01197 YP_493704.1 identified by match to protein family HMM PF06335 YP_493705.1 identified by match to protein family HMM PF00459 YP_493707.1 identified by match to protein family HMM PF00009; match to protein family HMM PF00679; match to protein family HMM PF03144; match to protein family HMM TIGR00231; match to protein family HMM TIGR01394 YP_493710.1 depletion of this protein in Bacillus subtilis results in defects in cell morphology; crystal structure of Staphylococcus protein shows homodimer; putative ligand binding protein YP_493711.1 identified by match to protein family HMM PF01098 YP_493712.1 biotin-containing enzyme that catalyzes a two step carboxylation of pyruvate to oxaloacetate YP_493713.1 identified by match to protein family HMM PF02628 YP_493714.1 converts protoheme IX and farnesyl diphosphate to heme O YP_493715.1 identified by match to protein family HMM PF04238 YP_493716.1 identified by match to protein family HMM PF00188 YP_493717.1 identified by match to protein family HMM PF07050 YP_493718.1 identified by match to protein family HMM PF03009 YP_493721.1 identified by match to protein family HMM PF03602; match to protein family HMM PF05175; match to protein family HMM TIGR00095 YP_493722.1 Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA YP_493723.1 identified by match to protein family HMM PF05636 YP_493724.1 identified by match to protein family HMM PF02620 YP_493725.1 some L32 proteins have zinc finger motifs consisting of CXXC while others do not YP_493726.1 identified by match to protein family HMM PF00746; match to protein family HMM PF04650; match to protein family HMM PF05031; match to protein family HMM TIGR01167; match to protein family HMM TIGR01168 YP_493727.1 identified by match to protein family HMM PF00746; match to protein family HMM PF05031; match to protein family HMM TIGR01167 YP_493728.1 identified by match to protein family HMM PF05031 YP_493730.1 identified by match to protein family HMM PF01497 YP_493731.1 identified by match to protein family HMM PF01032; match to protein family HMM PF02653 YP_493732.1 identified by match to protein family HMM PF07170 YP_493733.1 iron regulated; catalyzes the release of heme from hemoglobin allowing bacterial pathogens to use the host heme as an iron source YP_493734.1 identified by match to protein family HMM PF00588; match to protein family HMM PF08032 YP_493735.1 catalyzes a two-step reaction, first charging a phenylalanine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; forms a heterotetramer of alpha(2)beta(2); binds two magnesium ions per tetramer; type 1 subfamily YP_493736.1 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_493737.1 An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids YP_493738.1 identified by match to protein family HMM PF05164 YP_493739.1 identified by match to protein family HMM PF02674 YP_493740.1 identified by match to protein family HMM PF02811 YP_493741.1 MutS2; MutS-II; involved in blocking homologous and homeologous recombination; has ATPase activity stimulated by recombination intermediates; inhibits DNA strand exchange YP_493742.1 identified by match to protein family HMM PF00085; match to protein family HMM TIGR01068 YP_493743.2 The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision YP_493744.1 identified by match to protein family HMM TIGR02046 YP_493745.1 part of four member succinate dehydrogenase enzyme complex that forms a trimeric complex (trimer of tetramers); SdhA/B are the catalytic subcomplex and can exhibit succinate dehydrogenase activity in the absence of SdhC/D which are the membrane components and form cytochrome b556; SdhC binds ubiquinone; oxidizes succinate to fumarate while reducing ubiquinone to ubiquinol YP_493746.1 part of four member succinate dehydrogenase enzyme complex that forms a trimeric complex (trimer of tetramers); SdhA/B are the catalytic subcomplex and can exhibit succinate dehydrogenase activity in the absence of SdhC/D which are the membrane components and form cytochrome b556; SdhC binds ubiquinone; oxidizes succinate to fumarate while reducing ubiquinone to ubiquinol; the catalytic subunits are similar to fumarate reductase YP_493747.1 converts L-glutamate to D-glutamate, a component of peptidoglycan YP_493748.1 hydrolyzes non-standard nucleotides such as xanthine and inosine YP_493749.1 identified by match to protein family HMM TIGR00040 YP_493751.1 FLIPr; secreted protein that blocks the formyl peptide receptor-like 1 (FPRL1) found in neutrophils, monocytes, B cells, and NK cells; inhibits the binding of chemoattractants (such as formylated peptides) to FPRL1, which initiates the phagocyte mobilization towards the infection site YP_493756.1 identified by match to protein family HMM PF07968; match to protein family HMM TIGR01002 YP_493757.1 these proteins share structural homology to known superantigen proteins but do not exhibit any of the properties expected such as histocompatibility complex class II binding or broad T-cell activation YP_493758.1 these proteins share structural homology to known superantigen proteins but do not exhibit any of the properties expected such as histocompatibility complex class II binding or broad T-cell activation YP_493759.1 these proteins share structural homology to known superantigen proteins but do not exhibit any of the properties expected such as histocompatibility complex class II binding or broad T-cell activation YP_493760.1 catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation YP_493761.1 catalyzes the reversible synthesis of carbamate and ATP from carbamoyl phosphate and ADP YP_493762.1 identified by match to protein family HMM PF03600; match to protein family HMM PF03606; match to protein family HMM PF06808 YP_493763.1 identified by match to protein family HMM PF03595 YP_493764.1 identified by match to protein family HMM PF05480 YP_493765.1 identified by match to protein family HMM PF05480 YP_493766.1 identified by match to protein family HMM PF00702; match to protein family HMM TIGR01549; match to protein family HMM TIGR02254 YP_493767.1 identified by match to protein family HMM PF00583 YP_493769.1 MraZ; UPF0040; crystal structure shows similarity to AbrB YP_493770.1 identified by match to protein family HMM PF01795; match to protein family HMM TIGR00006 YP_493771.1 identified by match to protein family HMM PF04977; match to protein family HMM TIGR02209 YP_493772.1 identified by match to protein family HMM PF00905; match to protein family HMM PF03717; match to protein family HMM PF03793 YP_493773.1 First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan YP_493774.1 UDP-N-acetylmuramoylalanine--D-glutamate ligase; involved in peptidoglycan biosynthesis; cytoplasmic; catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine during cell wall formation YP_493775.1 identified by match to protein family HMM PF03799 YP_493776.1 identified by match to protein family HMM PF02491; match to protein family HMM TIGR01174 YP_493777.1 GTPase; similar structure to tubulin; forms ring-shaped polymers at the site of cell division; other proteins such as FtsA, ZipA, and ZapA, interact with and regulate FtsZ function YP_493778.1 identified by match to protein family HMM PF02578 YP_493779.1 identified by match to protein family HMM PF01168; match to protein family HMM TIGR00044 YP_493780.1 identified by match to protein family HMM PF04472 YP_493781.1 identified by match to protein family HMM PF02325 YP_493782.1 identified by match to protein family HMM PF01479 YP_493783.1 identified by match to protein family HMM PF05103 YP_493784.1 IleRS; catalyzes the formation of isoleucyl-tRNA(Ile) from isoleucine and tRNA(Ile); since isoleucine and other amino acids such as valine are similar, there are additional editing function in this enzyme; one is involved in hydrolysis of activated valine-AMP and the other is involved in deacylation of mischarged Val-tRNA(Ile); there are two active sites, one for aminoacylation and one for editing; class-I aminoacyl-tRNA synthetase family type 1 subfamily; some organisms carry two different copies of this enzyme YP_493785.1 identified by match to protein family HMM PF00903 YP_493786.1 lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis YP_493787.1 identified by match to protein family HMM PF00849; match to protein family HMM PF01479; match to protein family HMM TIGR00005 YP_493788.1 regulates pyrimidine biosynthesis by binding to the mRNA of the pyr genes, also has been shown to have uracil phosphoribosyltransferase activity YP_493789.1 identified by match to protein family HMM PF00860; match to protein family HMM TIGR00801 YP_493790.1 catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis YP_493791.1 catalyzes the formation of N-carbamoyl-L-aspartate from (S)-dihydroorotate in pyrimidine biosynthesis YP_493792.1 catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers YP_493793.1 four CarB-CarA dimers form the carbamoyl phosphate synthetase holoenzyme that catalyzes the production of carbamoyl phosphate; CarB is responsible for the amidotransferase activity YP_493794.1 type 1 subfamily; involved in last step of pyrimidine biosynthesis; converts orotidine 5'-phosphate to UMP and carbon dioxide; OMP decarboxylase; OMPDCase; OMPdecase YP_493795.1 involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate YP_493797.1 identified by match to protein family HMM PF06983 YP_493798.1 identified by match to protein family HMM PF05670; match to protein family HMM PF05833 YP_493799.1 Essential for recycling GMP and indirectly, cGMP YP_493800.1 Promotes RNA polymerase assembly; latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits YP_493801.1 identified by match to protein family HMM PF02441; match to protein family HMM PF04127; match to protein family HMM TIGR00521 YP_493802.1 identified by match to protein family HMM PF00270; match to protein family HMM PF00271; match to protein family HMM PF04851; match to protein family HMM TIGR00595 YP_493804.1 identified by match to protein family HMM PF05154 YP_493805.1 cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+) YP_493806.1 identified by match to protein family HMM PF00551; match to protein family HMM PF02911; match to protein family HMM TIGR00460 YP_493807.1 identified by match to protein family HMM PF01029; match to protein family HMM PF01189; match to protein family HMM TIGR00563 YP_493808.1 23S rRNA m2A2503 methyltransferase; methylates the C2 position of the A2530 nucleotide in 23S rRNA; may be involved in antibiotic resistance YP_493809.1 identified by match to protein family HMM PF00481 YP_493810.1 identified by match to protein family HMM PF00069; match to protein family HMM PF03793 YP_493811.2 identified by match to protein family HMM PF03193; match to protein family HMM TIGR00157 YP_493812.1 identified by match to protein family HMM PF00834; match to protein family HMM TIGR01163 YP_493813.1 identified by match to protein family HMM PF04263; match to protein family HMM PF04265; match to protein family HMM TIGR01378 YP_493814.1 required for 70S ribosome assembly YP_493815.1 identified by match to protein family HMM PF03780 YP_493816.1 identified by match to protein family HMM PF02734 YP_493817.1 catalyzes branch migration in Holliday junction intermediates YP_493818.1 negative regulator of genes involved in fatty acid and phospholipid biosynthesis for gram positive bacteria YP_493819.1 involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY YP_493820.1 identified by match to protein family HMM PF00698; match to protein family HMM TIGR00128 YP_493821.1 identified by match to protein family HMM PF00106; match to protein family HMM TIGR01830 YP_493822.1 carries the fatty acid chain in fatty acid biosynthesis YP_493823.1 cytoplasmic enzyme involved in processing rRNA and some mRNAs; substrates typically have dsRNA regions; forms a homodimer; have N-terminal nuclease and C-terminal RNA-binding domains; requires magnesium as preferred ion for activity YP_493824.1 identified by match to protein family HMM PF02463; match to protein family HMM PF06470; match to protein family HMM TIGR00650; match to protein family HMM TIGR02168 YP_493825.1 identified by match to protein family HMM PF00448; match to protein family HMM PF02881; match to protein family HMM TIGR00064 YP_493826.1 identified by match to protein family HMM PF04297 YP_493827.1 identified by match to protein family HMM PF00448; match to protein family HMM PF02881; match to protein family HMM PF02978; match to protein family HMM TIGR00959 YP_493828.1 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_493829.1 Essential for efficient processing of 16S rRNA YP_493830.1 methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA YP_493831.1 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_493833.1 essential GTPase; functions in ribosome assembly; binds a unique part of the 23S rRNA; interacts with ribosomal protein L25(Ctc) YP_493834.1 RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids YP_493835.1 catalyzes the interconversion of succinyl-CoA and succinate YP_493836.1 Catalyzes the only substrate-level phosphorylation in the TCA cycle YP_493837.1 identified by match to protein family HMM PF01476; match to protein family HMM PF04650; match to protein family HMM PF05257; match to protein family HMM TIGR01168 YP_493838.1 identified by match to protein family HMM PF02388 YP_493839.1 identified by match to protein family HMM PF02481; match to protein family HMM TIGR00732 YP_493840.1 catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity YP_493841.1 TrmFO; Gid; glucose-inhibited division protein; similar to GidA; the gene from Bacillus subtilis encodes a tRNA-methyltransferase that utilizes folate as the carbon donor and bound flavin as reductant; modifies tRNA at position 54 (uridine) of the T-psi loop to form a C5-methyluridine YP_493842.1 identified by match to protein family HMM PF00589; match to protein family HMM PF02899; match to protein family HMM TIGR02224 YP_493843.1 heat shock protein involved in degradation of misfolded proteins YP_493844.1 heat shock protein involved in degradation of misfolded proteins YP_493845.1 CodY; DNA-binding protein that represses the expression of many genes that are induced as cells make the transition from rapid exponential growth to stationary phase (By similarity). It is a GTP-binding protein that senses the intracellular GTP concentration as an indicator of nutritional limitations. At low GTP concentration it no longer binds GTP and stop to act as a transcriptional repressor YP_493846.1 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_493847.1 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_493848.1 Catalyzes the phosphorylation of UMP to UDP YP_493849.1 Rrf; Frr; ribosome-recycling factor; release factor 4; RF4; recycles ribosomes upon translation termination along with release factor RF-3 and elongation factor EF-G; A GTPase-dependent process results in release of 50S from 70S; inhibited by release factor RF-1; essential for viability; structurally similar to tRNAs YP_493850.1 catalyzes the formation of undecaprenyl pyrophosphate from isopentenyl pyrophosphate YP_493851.1 identified by match to protein family HMM PF01148 YP_493852.1 identified by match to protein family HMM PF02163 YP_493853.1 catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro) YP_493854.1 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_493855.1 in Streptococcus pneumoniae this gene was found to be essential; structure determination of the Streptococcus protein shows that it is similar to a number of other proteins YP_493856.1 modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination YP_493857.1 identified by match to protein family HMM PF04296 YP_493858.1 identified by match to protein family HMM PF01248 YP_493859.1 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_493860.1 associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock YP_493861.1 catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs YP_493862.1 identified by match to protein family HMM PF01687; match to protein family HMM PF06574; match to protein family HMM TIGR00083 YP_493863.1 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_493864.1 identified by match to protein family HMM PF00013; match to protein family HMM PF00575; match to protein family HMM PF01138; match to protein family HMM PF03725; match to protein family HMM PF03726 YP_493865.1 identified by match to protein family HMM PF00753; match to protein family HMM PF07521 YP_493866.1 identified by match to protein family HMM PF01580 YP_493867.1 identified by match to protein family HMM PF00392; match to protein family HMM PF07702 YP_493868.1 identified by match to protein family HMM PF05193 YP_493869.1 identified by match to protein family HMM PF00675; match to protein family HMM PF05193 YP_493870.1 identified by match to protein family HMM PF00106; match to protein family HMM PF01073 YP_493873.1 identified by match to protein family HMM PF01066; match to protein family HMM TIGR00560 YP_493874.1 identified by match to protein family HMM PF00994; match to protein family HMM TIGR00200 YP_493875.2 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_493876.1 protein from Staphylococcus aureus has phosphodiesterase activity against 2'-3'-cAMP and 2'-3'-cGMP YP_493878.1 identified by match to protein family HMM PF00149; match to protein family HMM TIGR00282 YP_493879.1 identified by match to protein family HMM PF01558; match to protein family HMM PF01855 YP_493880.1 catalyzes the coenzyme A dependent formation of succinyl-CoA from 2-oxoglutarate and ferredoxin YP_493882.1 catalyzes the formation of 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine from N6-(dimethylallyl)adenosine (i(6)A) YP_493884.1 identified by match to protein family HMM TIGR02359 YP_493885.1 This protein performs the mismatch recognition step during the DNA repair process YP_493886.1 This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. Promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of a final effector complex YP_493887.1 identified by match to protein family HMM PF04309 YP_493888.1 identified by match to protein family HMM PF00230; match to protein family HMM TIGR00861 YP_493889.1 Converts glycerol and ADP to glycerol-3-phosphate and ADP YP_493890.1 identified by match to protein family HMM PF01266 YP_493891.1 identified by match to protein family HMM PF00561 YP_493892.1 IPP transferase; isopentenyltransferase; involved in tRNA modification; in Escherichia coli this enzyme catalyzes the addition of a delta2-isopentenyl group from dimethylallyl diphosphate to the N6-nitrogen of adenosine adjacent to the anticodon of tRNA species that read codons starting with uracil; further tRNA modifications may occur; mutations in miaA result in defects in translation efficiency and fidelity YP_493893.1 identified by match to protein family HMM PF01423; match to protein family HMM TIGR02383 YP_493894.1 identified by match to protein family HMM PF00255 YP_493895.1 identified by match to protein family HMM PF01926; match to protein family HMM PF04471 YP_493896.1 identified by match to protein family HMM PF01053; match to protein family HMM PF06838 YP_493897.1 identified by match to protein family HMM PF00376 YP_493898.1 identified by match to protein family HMM PF00120; match to protein family HMM PF03951; match to protein family HMM TIGR00653 YP_493904.1 identified by match to protein family HMM TIGR01641 YP_493911.1 identified by match to protein family HMM PF01212 YP_493913.1 identified by match to protein family HMM PF00614 YP_493914.1 identified by match to protein family HMM PF00005 YP_493915.1 identified by match to protein family HMM PF01061 YP_493916.1 identified by match to protein family HMM PF02518; match to protein family HMM PF07730 YP_493917.1 identified by match to protein family HMM PF00072; match to protein family HMM PF00196 YP_493919.1 identified by match to protein family HMM PF00565 YP_493922.1 catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP; lysine and threonine sensitive YP_493923.1 catalyzes the formation of L-aspartate 4-semialdehyde from L-homoserine YP_493924.1 catalyzes the formation of L-threonine from O-phospho-L-homoserine YP_493925.1 catalyzes the formation of O-phospho-L-homoserine from L-homoserine in threonine biosynthesis from asparate YP_493926.1 identified by match to protein family HMM PF00702; match to protein family HMM PF05116; match to protein family HMM TIGR00099; match to protein family HMM TIGR01484 YP_493928.1 identified by match to protein family HMM PF00324 YP_493929.1 identified by match to protein family HMM PF00199 YP_493930.2 in Escherichia coli BM108, a mutation that results in lack of L33 synthesis had no effect on ribosome synthesis or function; there are paralogous genes in several bacterial genomes, and a CXXC motif for zinc binding and an upstream regulation region of the paralog lacking this motif that are regulated by zinc similar to other ribosomal proteins like L31; the proteins in this group lack the CXXC motif YP_493931.1 located in the peptidyl transferase center and involved in assembly of 30S ribosome subunit; similar to what is observed with proteins L31 and L33, some proteins in this family contain CXXC motifs that are involved in zinc binding; if two copies are present in a genome, then the duplicated copy appears to have lost the zinc-binding motif and is instead regulated by zinc; the proteins in this group do not appear to have the zinc-binding motif YP_493932.1 identified by match to protein family HMM PF00478; match to protein family HMM TIGR01306 YP_493933.1 identified by match to protein family HMM PF00188 YP_493934.1 Represses a number of genes involved in the response to DNA damage YP_493935.1 identified by match to protein family HMM PF05979 YP_493936.1 identified by match to protein family HMM PF00456; match to protein family HMM PF02779; match to protein family HMM PF02780; match to protein family HMM TIGR00232 YP_493937.1 identified by match to protein family HMM PF03672 YP_493938.1 identified by match to protein family HMM PF07301 YP_493939.1 identified by match to protein family HMM PF00149; match to protein family HMM TIGR00619 YP_493941.1 forms homopentamer; channel that opens in response to pressure or hypoosmotic shock YP_493942.1 identified by match to protein family HMM PF02028; match to protein family HMM TIGR00842 YP_493943.1 Catalyzes the conversion of citrate to isocitrate YP_493944.1 identified by match to protein family HMM PF03061; match to protein family HMM TIGR00051 YP_493945.1 identified by match to protein family HMM PF01521 YP_493946.1 identified by match to protein family HMM PF02660; match to protein family HMM TIGR00023 YP_493947.1 decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling YP_493948.1 decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling YP_493949.1 identified by match to protein family HMM PF01235; match to protein family HMM TIGR00835 YP_493950.1 identified by match to protein family HMM PF00874; match to protein family HMM PF03123 YP_493951.1 identified by match to protein family HMM PF01594 YP_493952.1 identified by match to protein family HMM PF04329; match to protein family HMM PF04330; match to protein family HMM PF04331 YP_493953.1 this stereospecific enzymes reduces the S isomer of methionine sulfoxide while MsrB reduces the R form; provides protection against oxidative stress YP_493954.1 identified by match to protein family HMM PF03816; match to protein family HMM TIGR00350 YP_493955.1 identified by match to protein family HMM PF01361; match to protein family HMM TIGR00013 YP_493956.1 identified by match to protein family HMM PF00817 YP_493957.1 catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate YP_493958.1 identified by match to protein family HMM PF05343 YP_493959.1 with component II, the glutamine amidotransferase, catalyzes the formation of anthranilate from chorismate and glutamine YP_493960.1 identified by match to protein family HMM PF00117; match to protein family HMM TIGR00566 YP_493961.1 Catalyzes the conversion of N-(5-phospho-D-ribosyl)-anthranilate and diphosphate to anthranilate and 5-phospho-alpha-D-ribose 1-diphosphate YP_493962.1 involved in tryptophan biosynthesis; amino acid biosynthesis; converts 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate to C(1)-(3-indolyl)-glycerol 3-phosphate and carbon dioxide and water YP_493963.1 catalyzes the formation of 1-(2-carboxyphenylamino)-1-deoxy-D-ribulose 5-phosphate from N-(5-phospho-beta-D-ribosyl)-anthranilate in tryptophan biosynthesis YP_493964.1 catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate YP_493965.1 catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis YP_493966.1 identified by match to protein family HMM PF02388 YP_493967.1 identified by match to protein family HMM PF02388 YP_493968.1 identified by match to protein family HMM TIGR00099; match to protein family HMM TIGR01484 YP_493969.1 identified by match to protein family HMM PF04434 YP_493970.1 identified by match to protein family HMM PF00005 YP_493971.1 identified by match to protein family HMM PF00005 YP_493972.1 identified by match to protein family HMM PF00528 YP_493973.1 identified by match to protein family HMM PF00528 YP_493975.1 identified by match to protein family HMM PF01432; match to protein family HMM TIGR00181 YP_493976.1 identified by match to protein family HMM PF01895; match to protein family HMM TIGR02135 YP_493977.1 ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation YP_493978.1 identified by match to protein family HMM PF00528; match to protein family HMM TIGR00974 YP_493979.1 identified by match to protein family HMM PF00528; match to protein family HMM TIGR02138 YP_493980.1 identified by match to protein family HMM PF01547; match to protein family HMM TIGR02136 YP_493982.1 identified by match to protein family HMM PF00005 YP_493983.1 catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP, in Bacillus, lysine sensitive; regulated by response to starvation. YP_493984.1 identified by match to protein family HMM PF01118; match to protein family HMM PF02774; match to protein family HMM TIGR01296 YP_493985.1 catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis YP_493986.1 catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis YP_493987.1 identified by match to protein family HMM PF00132 YP_493988.1 identified by match to protein family HMM PF01546; match to protein family HMM TIGR01891 YP_493989.1 identified by match to protein family HMM PF00842; match to protein family HMM PF01168 YP_493990.1 identified by match to protein family HMM PF00278; match to protein family HMM PF02784; match to protein family HMM TIGR01048 YP_493992.1 identified by match to protein family HMM PF00313 YP_493994.1 catalyzes the hydrolysis of acylphosphate YP_493996.1 identified by match to protein family HMM PF05816 YP_493997.1 identified by match to protein family HMM PF05525; match to protein family HMM TIGR00796 YP_493999.1 identified by match to protein family HMM PF07726; match to protein family HMM PF07728 YP_494001.1 identified by match to protein family HMM PF00903 YP_494002.1 component of 2-oxoglutarate dehydrogenase complex; catalyzes the transfer of succinyl coenzyme A to form succinyl CoA as part of the conversion of 2-oxoglutarate to succinyl-CoA YP_494003.1 SucA; E1 component of the oxoglutarate dehydrogenase complex which catalyzes the formation of succinyl-CoA from 2-oxoglutarate; SucA catalyzes the reaction of 2-oxoglutarate with dihydrolipoamide succinyltransferase-lipoate to form dihydrolipoamide succinyltransferase-succinyldihydrolipoate and carbon dioxide YP_494004.1 identified by match to protein family HMM PF00512; match to protein family HMM PF00672; match to protein family HMM PF02518 YP_494005.1 identified by match to protein family HMM PF00072; match to protein family HMM PF00486 YP_494006.1 identified by match to protein family HMM PF01797 YP_494007.1 identified by match to protein family HMM PF01569 YP_494008.1 UDP-N-acetylglucosamine--N-acetylmuramyl- (pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase; involved in cell wall formation; inner membrane-associated; last step of peptidoglycan synthesis YP_494009.1 identified by match to protein family HMM PF00583 YP_494010.1 identified by match to protein family HMM PF00595; match to protein family HMM PF01471; match to protein family HMM PF03572; match to protein family HMM TIGR00225 YP_494011.1 identified by match to protein family HMM PF06855 YP_494012.1 identified by match to protein family HMM PF00358; match to protein family HMM TIGR00830 YP_494013.1 this stereospecific enzymes reduces the R isomer of methionine sulfoxide while MsrA reduces the S form; provides protection against oxidative stress YP_494014.1 this stereospecific enzymes reduces the S isomer of methionine sulfoxide while MsrB reduces the R form; provides protection against oxidative stress YP_494015.1 identified by match to protein family HMM PF02645; match to protein family HMM TIGR00762 YP_494016.1 identified by match to protein family HMM PF00186 YP_494017.1 ThyA; catalyzes formation of dTMP and 7,8-dihydrofolate from 5,10-methylenetetrahydrofolate and dUMP; involved in deoxyribonucleotide biosynthesis; there are 2 copies in some Bacilli, one of which appears to be phage-derived YP_494018.1 identified by match to protein family HMM PF06491 YP_494019.1 identified by match to protein family HMM PF03130 YP_494021.1 identified by match to protein family HMM PF02592; match to protein family HMM TIGR00697 YP_494024.1 identified by similarity to GB:AAW37659.1; match to protein family HMM PF01468; match to protein family HMM PF04650; match to protein family HMM PF07554; match to protein family HMM PF07564; match to protein family HMM TIGR01168 YP_494025.1 identified by match to protein family HMM PF07690 YP_494026.1 identified by match to protein family HMM PF00324 YP_494027.1 catalyzes the formation of 2-oxobutanoate from L-threonine; catabolic YP_494028.1 identified by match to protein family HMM PF01262; match to protein family HMM PF03949; match to protein family HMM PF05222; match to protein family HMM TIGR00518 YP_494029.1 identified by match to protein family HMM PF01367; match to protein family HMM PF02739 YP_494030.1 identified by match to protein family HMM PF00350; match to protein family HMM PF01926 YP_494031.1 identified by match to protein family HMM PF03413; match to protein family HMM PF03929 YP_494033.1 identified by match to protein family HMM PF01170 YP_494034.1 identified by match to protein family HMM PF05103 YP_494035.1 identified by match to protein family HMM PF06908 YP_494037.1 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_494038.1 identified by match to protein family HMM PF00905; match to protein family HMM PF00912 YP_494040.1 identified by match to protein family HMM PF00633; match to protein family HMM PF00730; match to protein family HMM TIGR01083 YP_494041.1 identified by match to protein family HMM PF04271; match to protein family HMM TIGR01446 YP_494042.1 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_494043.1 identified by match to protein family HMM PF00929; match to protein family HMM TIGR00573; match to protein family HMM TIGR01407 YP_494044.1 identified by match to protein family HMM PF03099; match to protein family HMM TIGR00121 YP_494045.2 catalyzes the addition and repair of the 3'-terminal CCA sequence in tRNA; these proteins belong to the CCA-adding enzyme subfamily 2 which does not have phosphohydrolase activity YP_494046.1 identified by match to protein family HMM PF00534 YP_494047.1 identified by match to protein family HMM PF03819 YP_494048.1 identified by match to protein family HMM PF04298 YP_494049.1 identified by match to protein family HMM PF07187 YP_494051.1 identified by match to protein family HMM PF07719 YP_494052.1 catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis YP_494053.1 catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis YP_494054.1 catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis YP_494055.1 catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate YP_494056.1 identified by match to protein family HMM PF00348 YP_494057.1 Catalyzes the carbon methylation reaction in the biosynthesis of ubiquinone YP_494059.1 identified by match to protein family HMM PF00216 YP_494060.1 catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate YP_494061.1 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_494062.1 in Escherichia coli this protein is involved in binding to the leader sequence of mRNAs and is itself bound to the 30S subunit; autoregulates expression via a C-terminal domain; in most gram negative organisms this protein is composed of 6 repeats of the S1 domain while in gram positive there are 4 repeats; the S1 nucleic acid-binding domain is found associated with other proteins YP_494064.2 Catalyzes the formation of (d)CDP from ATP and (d)CMP YP_494065.1 identified by match to protein family HMM PF00710 YP_494066.1 identified by match to protein family HMM PF00070; match to protein family HMM PF07992 YP_494067.1 identified by match to protein family HMM PF01476 YP_494068.1 identified by match to protein family HMM PF00270; match to protein family HMM PF00271; match to protein family HMM PF04851; match to protein family HMM TIGR00614 YP_494073.1 identified by match to protein family HMM PF07901 YP_494075.1 identified by match to protein family HMM PF07901 YP_494076.1 identified by match to protein family HMM PF07901 YP_494078.1 identified by match to protein family HMM PF07968; match to protein family HMM TIGR01002 YP_494079.1 identified by match to protein family HMM PF07968; match to protein family HMM TIGR01002 YP_494080.1 identical to Staphylococcus aureus temperate phage phiSLT; identified by match to protein family HMM PF01520; match to protein family HMM PF05257 YP_494081.1 identical to holin in Staphylococcus aureus temperate phage phiSLT; identified by match to protein family HMM PF04688; match to protein family HMM TIGR01592 YP_494083.1 identified by match to protein family HMM TIGR01669 YP_494088.1 identified by match to protein family HMM PF06605 YP_494089.1 identified by match to protein family HMM PF06997 YP_494090.1 identified by match to protein family HMM PF01464; match to protein family HMM PF01551; match to protein family HMM TIGR01760 YP_494093.1 identified by match to protein family HMM PF02368 YP_494094.1 identified by match to protein family HMM PF04630; match to protein family HMM TIGR01603 YP_494097.1 identified by match to protein family HMM TIGR01560 YP_494098.1 identified by match to protein family HMM PF05065 YP_494099.1 identified by match to protein family HMM PF00574 YP_494100.1 identified by match to protein family HMM PF04860; match to protein family HMM TIGR01537 YP_494101.1 identified by match to protein family HMM PF03354 YP_494102.1 identified by match to protein family HMM PF05119 YP_494103.1 identified by match to protein family HMM PF01844 YP_494104.1 identified by match to protein family HMM TIGR01636 YP_494105.1 identified by match to protein family HMM PF00176 YP_494107.1 identified by match to protein family HMM PF05272 YP_494108.1 identified by match to protein family HMM PF07438 YP_494109.1 similar to transcriptional activator rinB; identified by match to protein family HMM PF06116 YP_494113.1 identified by match to protein family HMM PF07129 YP_494115.1 identified by match to protein family HMM PF06260 YP_494116.1 identified by match to protein family HMM PF06194 YP_494118.1 identified by match to protein family HMM PF07768 YP_494120.1 identified by match to protein family HMM PF00476 YP_494124.1 identified by match to protein family HMM PF06531 YP_494130.1 identified by match to protein family HMM PF01381 YP_494131.1 identified by match to protein family HMM PF01381 YP_494132.1 identified by match to protein family HMM PF06114 YP_494135.1 identified by match to protein family HMM PF00589 YP_494136.1 identified by match to protein family HMM PF07901 YP_494137.1 identified by match to protein family HMM PF00512; match to protein family HMM PF00672; match to protein family HMM PF02518 YP_494138.1 identified by match to protein family HMM PF00072; match to protein family HMM PF00486 YP_494139.1 identified by match to protein family HMM PF00849; match to protein family HMM PF01479; match to protein family HMM TIGR00093 YP_494140.1 identified by match to protein family HMM PF04079; match to protein family HMM TIGR00281 YP_494141.1 identified by match to protein family HMM PF02616 YP_494142.1 identified by match to protein family HMM PF03745 YP_494143.1 identified by match to protein family HMM PF00589; match to protein family HMM PF02899; match to protein family HMM TIGR02225 YP_494144.1 identified by match to protein family HMM PF01475 YP_494145.1 identified by match to protein family HMM PF00293 YP_494146.1 identified by match to protein family HMM PF00248 YP_494147.1 identified by match to protein family HMM PF00106 YP_494148.1 identified by match to protein family HMM PF03807; match to protein family HMM TIGR00112 YP_494149.1 identified by match to protein family HMM TIGR02651 YP_494150.1 catalyzes the formation of D-glucono-1,5-lactone 6-phosphate from D-glucose 6-phosphate YP_494151.1 identified by match to protein family HMM PF00165; match to protein family HMM PF06445 YP_494152.1 identified by match to protein family HMM PF00128 YP_494153.1 identified by match to protein family HMM PF00356; match to protein family HMM PF00532 YP_494154.1 identified by match to protein family HMM PF00903 YP_494155.1 catalyzes the formation of D-ribulose 5-phosphate from 6-phospho-D-gluconate YP_494156.1 identified by match to protein family HMM PF01546; match to protein family HMM PF05343; match to protein family HMM PF07687; match to protein family HMM TIGR01883 YP_494158.1 identified by match to protein family HMM PF06081 YP_494159.1 identified by match to protein family HMM PF06491 YP_494160.1 identified by match to protein family HMM PF00198; match to protein family HMM PF00364; match to protein family HMM PF02817 YP_494161.1 identified by match to protein family HMM PF02779; match to protein family HMM PF02780 YP_494162.1 identified by match to protein family HMM PF00676 YP_494163.1 identified by match to protein family HMM PF00070; match to protein family HMM PF01134; match to protein family HMM PF02852; match to protein family HMM PF07992; match to protein family HMM TIGR01350 YP_494164.1 identified by match to protein family HMM PF02463; match to protein family HMM TIGR00634 YP_494165.1 regulates arginine biosynthesis when complexed with arginine by binding at site that overlap the promotors of the arginine biosynthesis genes YP_494166.1 identified by match to protein family HMM PF00348 YP_494167.1 catalyzes the bidirectional exonucleolytic cleavage of DNA YP_494168.1 bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides YP_494169.1 Regulates rRNA biosynthesis by transcriptional antitermination YP_494170.1 identified by match to protein family HMM PF03780 YP_494171.1 an AccC homodimer forms the biotin carboxylase subunit of the acetyl CoA carboxylase, an enzyme that catalyzes the formation of malonyl-CoA, which in turn controls the rate of fatty acid metabolism YP_494172.1 identified by match to protein family HMM PF00364; match to protein family HMM TIGR00531 YP_494175.1 identified by match to protein family HMM PF05257 YP_494177.1 identified by match to protein family HMM PF01580 YP_494182.1 identified by match to protein family HMM PF02486 YP_494185.1 Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA YP_494186.1 identified by match to protein family HMM PF00557 YP_494189.1 identified by match to protein family HMM PF03099 YP_494190.1 identified by match to protein family HMM PF00581 YP_494191.1 acts in conjunction with GvcH to form H-protein-S-aminomethyldihydrolipoyllysine from glycine; forms a heterodimer with subunit 1 to form the P protein YP_494192.1 acts in conjunction with GvcH to form H-protein-S-aminomethyldihydrolipoyllysine from glycine; forms a heterodimer with subunit 2 to form the P protein YP_494193.1 catalyzes the transfer of a methylene carbon from the methylamine-loaded GcvH protein to tetrahydrofolate, causing the release of ammonia and the generation of reduced GcvH protein YP_494194.1 identified by match to protein family HMM PF01202 YP_494195.1 identified by match to protein family HMM PF07963; match to protein family HMM TIGR02532 YP_494196.1 identified by match to protein family HMM PF07963; match to protein family HMM TIGR02532 YP_494197.1 identified by match to protein family HMM PF07963; match to protein family HMM TIGR02532 YP_494198.1 identified by match to protein family HMM PF00482 YP_494199.1 identified by match to protein family HMM PF00437 YP_494200.1 identified by match to protein family HMM PF00753 YP_494201.1 identified by match to protein family HMM PF01910; match to protein family HMM TIGR00106 YP_494202.1 identified by match to protein family HMM PF00480; match to protein family HMM TIGR00744 YP_494203.1 identified by match to protein family HMM PF06014 YP_494204.1 identified by match to protein family HMM PF01694; match to protein family HMM PF07719 YP_494205.1 identified by match to protein family HMM PF01812; match to protein family HMM TIGR02727 YP_494206.1 in Escherichia coli BM108, a mutation that results in lack of L33 synthesis had no effect on ribosome synthesis or function; there are paralogous genes in several bacterial genomes, and a CXXC motif for zinc binding and an upstream regulation region of the paralog lacking this motif that are regulated by zinc similar to other ribosomal proteins like L31; the proteins in this group lack the CXXC motif YP_494207.1 identified by match to protein family HMM PF00905; match to protein family HMM PF03717 YP_494208.1 identified by match to protein family HMM PF00081; match to protein family HMM PF02777 YP_494209.1 identified by match to protein family HMM PF01475 YP_494210.1 identified by match to protein family HMM PF00950; match to protein family HMM PF01032 YP_494211.1 identified by match to protein family HMM PF00005 YP_494212.1 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_494213.1 identified by match to protein family HMM PF00270; match to protein family HMM PF00271 YP_494214.1 identified by match to protein family HMM PF01784; match to protein family HMM TIGR00486 YP_494215.1 identified by match to protein family HMM PF04816 YP_494216.1 sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; primary sigma factor of bacterium YP_494217.1 identified by match to protein family HMM PF01751; match to protein family HMM PF01807; match to protein family HMM TIGR01391 YP_494218.1 identified by match to protein family HMM PF03618 YP_494219.1 identified by match to protein family HMM PF00571 YP_494220.1 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_494221.1 identified by match to protein family HMM PF02565; match to protein family HMM TIGR00613 YP_494222.1 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_494223.1 identified by match to protein family HMM PF00383; match to protein family HMM TIGR01354 YP_494224.1 identified by match to protein family HMM PF01219 YP_494225.1 identified by match to protein family HMM PF02130; match to protein family HMM TIGR00043 YP_494226.1 identified by match to protein family HMM PF00013; match to protein family HMM PF02562 YP_494228.1 identified by match to protein family HMM PF07251 YP_494229.1 identified by match to protein family HMM PF01957 YP_494230.1 a small basic protein that is one of the last in the subunit assembly; omission does not prevent assembly but the subunit is inactive; binds central domain of 16S rRNA YP_494231.1 identified by match to protein family HMM PF00919; match to protein family HMM PF01938; match to protein family HMM PF04055; match to protein family HMM TIGR00089; match to protein family HMM TIGR01579 YP_494232.1 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_494233.1 methylates ribosomal protein L11 at multiple amino acid positions; mutations of these genes in Escherichia coli or Thermus thermophilus has no apparent phenotype YP_494234.1 chaperone Hsp40; co-chaperone with DnaK; Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, dnaK-independent fashion YP_494235.1 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_494236.1 with DnaK and DnaJ acts in response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins; may act as a thermosensor YP_494237.1 identified by match to protein family HMM PF01628; match to protein family HMM TIGR00331 YP_494238.1 catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III YP_494239.1 binds to the ribosome on the universally-conserved alpha-sarcin loop YP_494240.1 binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase YP_494241.1 required for the assembly and function of the DNAX complex which is required for the assembly of the beta subunit onto primed DNA YP_494242.1 identified by match to protein family HMM PF00753; match to protein family HMM PF03772; match to protein family HMM TIGR00360; match to protein family HMM TIGR00361 YP_494243.1 identified by match to protein family HMM PF00383; match to protein family HMM TIGR02571 YP_494244.1 identified by match to protein family HMM PF00633; match to protein family HMM TIGR00426 YP_494246.1 identified by match to protein family HMM PF02410; match to protein family HMM TIGR00090 YP_494247.1 identified by match to protein family HMM PF01966; match to protein family HMM TIGR00488 YP_494248.1 identified by match to protein family HMM PF01467; match to protein family HMM TIGR00125; match to protein family HMM TIGR00482 YP_494249.1 identified by match to protein family HMM PF01985; match to protein family HMM TIGR00253 YP_494250.1 identified by match to protein family HMM PF01488; match to protein family HMM TIGR00507 YP_494251.1 in Bacillus subtilis this enzyme appears to be involved in 30S ribosomal RNA subunit biogenesis YP_494252.1 identified by match to protein family HMM TIGR01662; match to protein family HMM TIGR01668 YP_494253.1 identified by match to protein family HMM PF01048; match to protein family HMM TIGR01704 YP_494254.1 identified by match to protein family HMM PF01123; match to protein family HMM PF02876 YP_494255.1 identified by match to protein family HMM PF02661 YP_494257.1 identified by match to protein family HMM PF03746 YP_494258.1 identified by match to protein family HMM PF00289; match to protein family HMM PF01071; match to protein family HMM PF02222; match to protein family HMM PF02785; match to protein family HMM PF02786 YP_494259.1 identified by match to protein family HMM PF00364 YP_494260.1 identified by match to protein family HMM PF02626 YP_494261.1 identified by match to protein family HMM PF02682; match to protein family HMM TIGR00370 YP_494262.1 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_494263.1 functions in pyrimidine salvage; pyrimidine ribonucleoside kinase; phosphorylates nucleosides or dinucleosides to make UMP or CMP using ATP or GTP as the donor YP_494264.1 identified by match to protein family HMM PF01136 YP_494265.1 identified by match to protein family HMM PF01136 YP_494266.1 identified by match to protein family HMM PF01596 YP_494267.1 identified by match to protein family HMM PF06949 YP_494268.1 similar to RuvC resolvase with substantial differences; NMR structural information suggests this protein is monomeric; unknown cellular function YP_494269.1 identified by match to protein family HMM PF06135 YP_494270.1 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_494271.1 identified by match to protein family HMM TIGR01448 YP_494272.1 identified by match to protein family HMM PF00515; match to protein family HMM PF07719; match to protein family HMM PF07720 YP_494273.1 catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs YP_494274.1 identified by match to protein family HMM PF00266; match to protein family HMM PF00282 YP_494275.1 identified by match to protein family HMM PF00296 YP_494277.1 identified by match to protein family HMM PF05532 YP_494278.1 identified by match to protein family HMM PF02082; match to protein family HMM TIGR00738 YP_494279.2 identified by match to protein family HMM PF00004 YP_494280.1 identified by match to protein family HMM PF00899 YP_494281.1 catalyzes a two-step reaction, first charging an aspartate molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; contains discriminating and non-discriminating subtypes YP_494282.1 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_494283.1 identified by match to protein family HMM PF01520 YP_494284.1 hydrolyzes D-tyrosyl-tRNA(Tyr) into D-tyrosine and free tRNA(Tyr); possible defense mechanism against a harmful effect of D-tyrosine YP_494285.1 identified by match to protein family HMM PF01842; match to protein family HMM PF01966; match to protein family HMM PF02824; match to protein family HMM PF04607; match to protein family HMM TIGR00691 YP_494286.1 catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis YP_494287.1 identified by match to protein family HMM PF01368; match to protein family HMM PF02272; match to protein family HMM TIGR00644 YP_494288.2 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_494289.1 identified by match to protein family HMM PF02699; match to protein family HMM TIGR00739 YP_494290.1 Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr) YP_494291.1 Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step YP_494292.1 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_494293.1 plays an essential role in ATP-dependent branch migration of the Holliday junction YP_494294.1 identified by match to protein family HMM PF01842 YP_494295.1 essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication YP_494296.1 involved in the peptidyltransferase reaction during translation YP_494297.1 identified by match to protein family HMM PF04327 YP_494298.1 identified by match to protein family HMM PF00829; match to protein family HMM TIGR00061 YP_494299.1 identified by match to protein family HMM PF04093 YP_494300.1 in some organisms this protein is a transmembrane protein while in others it is periplasmic; involved in some organisms with other components of the MreBCD complex and with penicillin binding proteins in the periplasm or cell wall YP_494303.1 Involved in DNA double-strand break repair and recombination. Promotes the annealing of complementary single-stranded DNA and by simulation of RAD51 recombinase YP_494304.1 identified by match to protein family HMM PF01478; match to protein family HMM PF06750 YP_494305.1 identified by match to protein family HMM PF02875; match to protein family HMM TIGR01499 YP_494306.1 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_494307.1 identified by match to protein family HMM PF03352 YP_494308.1 identified by match to protein family HMM PF05145 YP_494309.1 Converts (S)-4-amino-5-oxopentanoate to 5-aminolevulinate during the porphyrin biosynthesis pathway YP_494310.1 catalyzes the formation of porphobilinogen from 5-aminolevulinate YP_494311.1 identified by match to protein family HMM PF02602 YP_494312.1 transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis YP_494313.1 identified by match to protein family HMM PF01578 YP_494314.1 catalyzes the formation of glutamate-1-semialdehyde from glutamyl-tRNA(Glu) and NADPH; the second step of the pathway is catalyzed by glutamate-1-semialdehyde aminomutase which results in the formation of 5-aminolevulinic acid; functions in porphyrin (tetrapyrroles) biosynthesis; the crystal structure showed a C-terminal dimerization domain that appears to be absent in Chlamydial proteins YP_494315.1 binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential YP_494316.1 binds and unfolds substrates as part of the ClpXP protease YP_494317.1 Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer YP_494319.1 identified by match to protein family HMM PF00293 YP_494320.1 binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit YP_494321.1 identified by match to protein family HMM PF01632; match to protein family HMM TIGR00001 YP_494322.1 IF-3 has several functions that are required and promote translation initiation including; preventing association of 70S by binding to 30S; monitoring codon-anticodon interactions by promoting disassociation of fMet-tRNA(fMet) from initiation complexes formed on leaderless mRNAs or incorrectly bound noninitiatior tRNAs and complexes with noncanonical start sites; stimulates codon-anticodon interactions at P-site; involved in moving mRNA to the P-site; and in recycling subunits YP_494323.1 identified by match to protein family HMM PF00324 YP_494324.1 catalyzes a two-step reaction, first charging a threonine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; catalyzes the formation of threonyl-tRNA(Thr) from threonine and tRNA(Thr) YP_494325.1 Primosomal protein that may act to load helicase DnaC during DNA replication YP_494326.1 identified by match to protein family HMM PF07261 YP_494327.1 identified by match to protein family HMM PF03477; match to protein family HMM TIGR00244 YP_494328.1 identified by match to protein family HMM PF00044; match to protein family HMM PF02800; match to protein family HMM TIGR01534 YP_494329.1 catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A; involved in coenzyme A biosynthesis YP_494330.1 identified by match to protein family HMM PF01149; match to protein family HMM PF06831; match to protein family HMM TIGR00577 YP_494331.1 identified by match to protein family HMM PF00476; match to protein family HMM PF01367; match to protein family HMM PF02739; match to protein family HMM TIGR00593 YP_494334.1 identified by match to protein family HMM PF00072; match to protein family HMM PF00486 YP_494335.1 Converts isocitrate to alpha ketoglutarate YP_494336.1 catalyzes the formation of citrate from acetyl-CoA and oxaloacetate YP_494337.1 identified by match to protein family HMM PF00324 YP_494338.1 identified by match to protein family HMM PF00224; match to protein family HMM PF00391; match to protein family HMM PF02887; match to protein family HMM TIGR01064 YP_494339.1 catalyzes the formation of D-fructose 1,6-bisphosphate from D-fructose 6-phosphate in glycolysis YP_494340.1 catalyzes the carboxylation of acetyl-CoA to malonyl-CoA; forms a tetramer composed of two alpha (AccA) and two beta (AccD) subunits; one of the two catalytic subunits that can form the acetyl CoA carboxylase enzyme together with a carrier protein YP_494341.1 catalyzes the carboxylation of acetyl-CoA to malonyl-CoA; forms a tetramer of AccA2D2 subunits YP_494342.1 identified by match to protein family HMM PF00390; match to protein family HMM PF03949 YP_494343.1 identified by match to protein family HMM PF01336; match to protein family HMM PF02811; match to protein family HMM PF07733; match to protein family HMM TIGR00594 YP_494344.1 identified by match to protein family HMM PF01368; match to protein family HMM PF02272 YP_494345.1 identified by match to protein family HMM PF00571; match to protein family HMM PF07085 YP_494346.1 identified by match to protein family HMM PF00582 YP_494347.1 catalyzes the opening and hydrolysis of the beta-lactam ring of beta-lactam antibiotics such as penicillins and cephalosporins YP_494348.1 identified by match to protein family HMM PF00557 YP_494349.1 identified by match to protein family HMM PF01262; match to protein family HMM PF01488; match to protein family HMM PF05222; match to protein family HMM TIGR00518 YP_494350.1 identified by match to protein family HMM PF00582 YP_494351.1 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 YP_494353.1 antioxidant activity; thioredoxin-dependent thiol peroxidase; forms homodimers in solution; shows substrate specificity to alkyl hydroperoxides; periplasmic protein YP_494354.1 identified by match to protein family HMM PF01925 YP_494355.1 Required for the synthesis of the thiazole moiety YP_494356.1 identified by match to protein family HMM PF00266 YP_494358.1 acts to negatively regulates ftsZ ring formation by modulating the frequency and position of the ftsZ ring formation YP_494359.1 identified by match to protein family HMM PF01590 YP_494360.1 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_494361.1 identified by match to protein family HMM PF03009 YP_494362.1 identified by match to protein family HMM PF02566 YP_494363.1 identified by match to protein family HMM PF00266 YP_494364.1 catalyzes the formation of 3-phosphonooxypyruvate from 3-phospho-D-glycerate in serine biosynthesis; can also reduce alpha ketoglutarate to form 2-hydroxyglutarate YP_494366.1 identified by match to protein family HMM PF00367; match to protein family HMM PF02378; match to protein family HMM TIGR01998 YP_494367.1 identified by match to protein family HMM PF01553; match to protein family HMM TIGR00530 YP_494368.1 identified by match to protein family HMM PF00089 YP_494369.1 identified by match to protein family HMM PF00579; match to protein family HMM PF01479; match to protein family HMM TIGR00234 YP_494370.1 identified by match to protein family HMM PF00912 YP_494371.1 identified by match to protein family HMM PF04650; match to protein family HMM PF05031; match to protein family HMM TIGR01167; match to protein family HMM TIGR01168 YP_494372.1 catalyzes the formation of 10-formyltetrahydrofolate from formate and tetrahydrofolate YP_494373.1 Acs; catalyzes the conversion of acetate and CoA to acetyl-CoA YP_494375.1 identified by match to protein family HMM PF00850 YP_494376.1 identified by match to protein family HMM PF00356; match to protein family HMM PF00532; match to protein family HMM TIGR01481 YP_494377.1 catalyzes the formation of 3-deoxy-D-aribino-hept-2-ulosonate 7-phosphate from phosphoenolpyruvate and D-erythrose 4-phosphate and the formation of prephenate from chorismate YP_494379.1 identified by match to protein family HMM PF06103 YP_494380.1 Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis YP_494381.1 identified by match to protein family HMM PF01580 YP_494382.1 identified by match to protein family HMM PF01588 YP_494383.1 identified by match to protein family HMM PF07285 YP_494384.1 identified by match to protein family HMM PF00085 YP_494385.1 identified by match to protein family HMM PF05343 YP_494386.1 identified by match to protein family HMM PF03413 YP_494387.1 identified by match to protein family HMM PF00753 YP_494388.1 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_494389.1 identified by match to protein family HMM PF01636 YP_494390.1 identified by match to protein family HMM PF01063; match to protein family HMM TIGR01121 YP_494391.1 divalent metal ion-dependent extracellular dipeptidase; able to hydrolyze a broad range of dipeptides but no tri-, tetra-, or larger oligopeptides; differences in the amino acid specificity of the cleavage site varies between species; similar to succinyl-diaminopimelate desuccinylases YP_494393.1 identified by match to protein family HMM PF00849; match to protein family HMM PF01479; match to protein family HMM TIGR00093 YP_494394.1 identified by match to protein family HMM PF01943 YP_494395.1 identified by match to protein family HMM PF00890; match to protein family HMM PF01266; match to protein family HMM PF03486; match to protein family HMM PF07992; match to protein family HMM TIGR00275 YP_494396.1 identified by match to protein family HMM PF04650; match to protein family HMM PF07564; match to protein family HMM TIGR01167; match to protein family HMM TIGR01168 YP_494397.1 identified by match to protein family HMM PF00581 YP_494398.1 leucine--tRNA ligase; LeuRS; class-I aminoacyl-tRNA synthetase; charges leucine by linking carboxyl group to alpha-phosphate of ATP and then transfers aminoacyl-adenylate to its tRNA; due to the large number of codons that tRNA(Leu) recognizes, the leucyl-tRNA synthetase does not recognize the anticodon loop of the tRNA, but instead recognition is dependent on a conserved discriminator base A37 and a long arm; an editing domain hydrolyzes misformed products; in Methanothermobacter thermautotrophicus this enzyme associates with prolyl-tRNA synthetase YP_494399.1 identified by match to protein family HMM PF07690 YP_494400.1 identified by match to protein family HMM PF04055; match to protein family HMM TIGR01212 YP_494401.1 identified by match to protein family HMM PF06962 YP_494402.1 identified by similarity to GB:AAF22306.1; match to protein family HMM PF01047; match to protein family HMM TIGR01889 YP_494403.1 identified by match to protein family HMM PF00561 YP_494404.1 identified by match to protein family HMM PF01619 YP_494405.1 RibE; 6,7-diimethyl-8-ribityllumazine synthase; DMRL synthase; lumazine synthase; beta subunit of riboflavin synthase; condenses 5-amino-6-(1'-D)-ribityl-amino-2,4(1H,3H)-pyrimidinedione with L-3,4-dihydrohy-2-butanone-4-phosphate to generate 6,6-dimethyl-8-lumazine (DMRL); riboflavin synthase then uses 2 molecules of DMRL to produce riboflavin (vitamin B12); involved in the last steps of riboflavin biosynthesis; forms a 60mer (icosahedral shell) in both Bacillus subtilis and Escherichia coli; in Bacillus subtilis this 60mer is associated with the riboflavin synthase subunit (alpha) while in Escherichia coli it is not YP_494406.1 identified by match to protein family HMM PF00925; match to protein family HMM PF00926; match to protein family HMM TIGR00505; match to protein family HMM TIGR00506 YP_494407.1 catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine YP_494408.1 identified by match to protein family HMM PF00383; match to protein family HMM PF01872; match to protein family HMM TIGR00326 YP_494410.1 identified by match to protein family HMM PF01022 YP_494411.1 identified by match to protein family HMM PF02040; match to protein family HMM PF03600; match to protein family HMM TIGR00935 YP_494412.1 catalyzes the reduction of arsenate to arsenite; also can dephosphorylate tyrosine phosphorylated proteins, aryl phosphates, and acyl phosphates YP_494413.1 identified by match to protein family HMM PF01832 YP_494415.1 identified by match to protein family HMM PF04542 YP_494417.1 identified by match to protein family HMM PF02517 YP_494418.1 similar to novel fructose-6-phosphate aldolase from Escherichia coli; enzyme from Methanocaldococcus janaschii shows transaldolase activity YP_494419.1 identified by match to protein family HMM PF02537 YP_494420.1 identified by match to protein family HMM PF00248 YP_494422.1 catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase YP_494423.1 PEP carboxykinase; PEP carboxylase; PEPCK; catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using ATP YP_494426.1 identified by match to protein family HMM PF00293; match to protein family HMM TIGR02705 YP_494427.1 identified by match to protein family HMM PF01809; match to protein family HMM TIGR00278 YP_494428.1 identified by match to protein family HMM TIGR01928 YP_494429.1 identified by match to protein family HMM PF00501; match to protein family HMM TIGR01923 YP_494431.1 identified by match to protein family HMM PF05901 YP_494437.1 identified by match to protein family HMM PF06114 YP_494440.1 identified by match to protein family HMM PF07252 YP_494442.1 identified by match to protein family HMM PF01420 YP_494443.1 identified by match to protein family HMM PF02384; match to protein family HMM TIGR00497 YP_494444.1 identified by match to protein family HMM PF00089 YP_494445.1 identified by match to protein family HMM PF00089 YP_494446.1 identified by match to protein family HMM PF00089 YP_494447.1 identified by match to protein family HMM PF00089 YP_494448.1 identified by match to protein family HMM PF00089 YP_494449.1 identified by match to protein family HMM PF00089 YP_494453.1 identified by match to protein family HMM PF00005 YP_494454.1 identified by match to protein family HMM PF00082 YP_494455.1 identified by match to protein family HMM PF02441 YP_494456.1 identified by match to protein family HMM PF05147 YP_494457.1 identified by match to protein family HMM PF04737; match to protein family HMM PF04738 YP_494458.1 identified by match to protein family HMM PF02052 YP_494459.1 identified by match to protein family HMM PF07968; match to protein family HMM TIGR01002 YP_494460.1 identified by match to protein family HMM PF07968; match to protein family HMM TIGR01002 YP_494463.1 identified by match to protein family HMM PF06821 YP_494464.1 catalyzes the formation of protoporphyrin IX from protoporphyrinogen IX YP_494465.1 protoheme ferro-lyase; catalyzes the insertion of a ferrous ion into protoporphyrin IX to form protoheme; involved in protoheme biosynthesis; in some organisms this protein is membrane-associated while in others it is cytosolic YP_494466.1 catalyzes the formation of coproporphyrinogen from uroporphyrinogen III YP_494468.1 identified by match to protein family HMM PF05975 YP_494469.1 identified by match to protein family HMM PF00005 YP_494470.1 identified by match to protein family HMM PF01230 YP_494473.1 identified by match to protein family HMM PF00639 YP_494474.1 catalyzes the exonucleic cleavage of mRNA yielding nucleioside 5'-phosphates YP_494476.1 identified by match to protein family HMM PF00149 YP_494478.1 identified by match to protein family HMM PF06133 YP_494479.1 identified by match to protein family HMM PF04286 YP_494481.1 identified by match to protein family HMM PF00072; match to protein family HMM PF00196 YP_494482.1 identified by match to protein family HMM PF02518; match to protein family HMM PF07730 YP_494483.1 identified by match to protein family HMM PF00849 YP_494484.1 class II family (does not require metal); tetrameric enzyme; fumarase C; reversibly converts (S)-malate to fumarate and water; functions in the TCA cycle YP_494488.1 identified by match to protein family HMM PF00588; match to protein family HMM TIGR00185 YP_494489.1 identified by match to protein family HMM PF00037; match to protein family HMM TIGR00276 YP_494490.1 identified by match to protein family HMM PF00005 YP_494491.1 identified by match to protein family HMM PF00497; match to protein family HMM PF00528; match to protein family HMM TIGR01726 YP_494492.1 identified by match to protein family HMM PF02378 YP_494493.1 identified by match to protein family HMM PF01610 YP_494494.1 identified by match to protein family HMM PF01475 YP_494495.1 identified by match to protein family HMM PF00389; match to protein family HMM PF02826 YP_494496.1 identified by match to protein family HMM PF00578 YP_494497.1 converts (S)-4-amino-5-oxopentanoate to 5-aminolevulinate YP_494498.1 identified by match to protein family HMM PF06081 YP_494499.1 identified by match to protein family HMM PF00005; match to protein family HMM PF00664 YP_494500.1 identified by match to protein family HMM PF04167 YP_494501.1 identified by match to protein family HMM PF00633; match to protein family HMM PF00730; match to protein family HMM TIGR01084 YP_494502.1 identified by match to protein family HMM PF04307 YP_494506.1 binds RecA and inhibits RecA-mediated DNA strand exchange and ATP hydrolysis and coprotease activities YP_494507.1 monofunctional; catalyzes the elongation of glycan strands in cell wall biosynthesis YP_494508.1 identified by match to protein family HMM PF01965; match to protein family HMM TIGR01382 YP_494510.1 identified by match to protein family HMM PF04055 YP_494511.1 identified by match to protein family HMM PF03061 YP_494512.1 identified by match to protein family HMM PF02073 YP_494513.1 identified by match to protein family HMM PF06569 YP_494514.1 identified by match to protein family HMM PF01451 YP_494516.1 identified by match to protein family HMM PF03631; match to protein family HMM TIGR00765 YP_494517.1 identified by match to protein family HMM PF00072; match to protein family HMM PF00196 YP_494518.1 identified by match to protein family HMM PF02518; match to protein family HMM PF07730 YP_494521.1 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_494524.1 identified by match to protein family HMM PF07685 YP_494526.1 identified by match to protein family HMM PF00210 YP_494527.1 identified by match to protein family HMM PF00929 YP_494528.1 involved in translesion DNA polymerization with beta clamp of polymerase III; belongs to Y family of polymerases; does not contain proofreading function YP_494530.1 identified by match to protein family HMM PF02475; match to protein family HMM PF05958; match to protein family HMM TIGR00479 YP_494531.1 similar to YegS from E. coli YP_494532.1 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_494533.1 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_494534.1 allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA; some Mycoplasma proteins contain an N-terminal fusion to an unknown domain YP_494535.1 identified by match to protein family HMM PF00474; match to protein family HMM TIGR00813; match to protein family HMM TIGR02121 YP_494536.1 identified by match to protein family HMM PF07537 YP_494537.1 identified by match to protein family HMM PF00533; match to protein family HMM PF01653; match to protein family HMM PF03119; match to protein family HMM PF03120; match to protein family HMM TIGR00575 YP_494538.1 identified by match to protein family HMM PF00580; match to protein family HMM TIGR01073 YP_494539.1 PcrB-like protein; GGGP synthase; member of prenyltransferases that transfer isoprenoid groups to nonisoprenoid acceptors; functions in form GGGP from glycerol-1-phosphate (G-1-P) and geranylgeranyl pyrophosphate (GGPP); important in lipid metabolism and especially important as the ether linkages in archaea are different than those in bacteria; GGGP synthase lies at the branch point for membrane lipid biosynthesis; cytosolic; T acidophilum protein acts as a homodimer while M thermoautotrophicum protein has been reported to function as a pentamer YP_494540.1 identified by match to protein family HMM PF01371; match to protein family HMM TIGR02531 YP_494541.1 Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide YP_494542.1 identified by match to protein family HMM PF05543 YP_494545.1 catalyzes the formation of nicotinamide adenine dinucleotide (NAD) from nicotinic acid adenine dinucleotide (NAAD) using either ammonia or glutamine as the amide donor and ATP; ammonia-utilizing enzymes include the ones from Bacillus and Escherichia coli while glutamine-utilizing enzymes include the Mycobacterial one; forms homodimers YP_494546.1 catalyzes the formation of 5-phospho-alpha-D-ribose 1-diphosphate and nicotinate from nicotinate D-ribonucleotide and diphosphate YP_494547.1 identified by match to protein family HMM PF02898 YP_494548.1 identified by match to protein family HMM PF00800; match to protein family HMM PF01842 YP_494549.1 identified by match to protein family HMM PF00939; match to protein family HMM PF03600; match to protein family HMM TIGR00785 YP_494551.1 identified by match to protein family HMM PF00857 YP_494552.1 catalyzes the hydrolysis of pyrophosphate to phosphate YP_494553.1 identified by match to protein family HMM PF00171 YP_494557.1 identified by match to protein family HMM PF02275; match to protein family HMM PF03417 YP_494559.1 identified by match to protein family HMM PF08006 YP_494563.1 identified by match to protein family HMM PF00005 YP_494565.1 identified by match to protein family HMM PF00005 YP_494566.1 identified by match to protein family HMM PF00392 YP_494568.1 identified by match to protein family HMM PF00155 YP_494571.1 secreted protein that specifically inhibits the activation of neutrophils and monocytes by binding to the formylated peptide receptor and the C5a receptor; blocks neutrophil migration towards the infection site and hinders the establishment of the initial defense against the infection YP_494573.1 identified by match to protein family HMM PF02821 YP_494574.1 identified by match to protein family HMM PF05257 YP_494575.1 identified by similarity to PIR:A89984; match to protein family HMM PF04531; match to protein family HMM TIGR01598 YP_494579.1 identified by match to protein family HMM TIGR01665 YP_494581.1 identified by match to protein family HMM PF01464; match to protein family HMM PF01551; match to protein family HMM TIGR01760 YP_494585.1 identified by match to protein family HMM TIGR01603 YP_494587.1 identical to SA1771 (N315); identified by match to protein family HMM TIGR01563 YP_494590.1 identified by match to protein family HMM PF00574 YP_494591.1 identified by match to protein family HMM PF04860; match to protein family HMM TIGR01537 YP_494592.1 identified by match to protein family HMM PF03354 YP_494594.1 identified by match to protein family HMM PF01844 YP_494596.1 identified by match to protein family HMM PF07438 YP_494597.1 identified by match to protein family HMM PF06116 YP_494599.1 identified by match to protein family HMM PF07129 YP_494600.1 identified by match to protein family HMM PF00692; match to protein family HMM TIGR00576 YP_494604.1 identified by match to protein family HMM PF06194 YP_494605.1 identified by match to protein family HMM PF07768 YP_494606.1 identified by match to protein family HMM PF05866 YP_494608.1 identified by match to protein family HMM PF04271; match to protein family HMM TIGR01446 YP_494609.1 identified by match to protein family HMM PF00436; match to protein family HMM TIGR00621 YP_494611.1 identified by match to protein family HMM PF03837; match to protein family HMM TIGR00616 YP_494613.1 identified by match to protein family HMM PF06531 YP_494615.1 identified by match to protein family HMM PF05595 YP_494617.1 identified by match to protein family HMM PF03374 YP_494619.1 identified by match to protein family HMM PF01381 YP_494620.1 identified by match to protein family HMM PF00717; match to protein family HMM PF01381 YP_494621.1 identified by match to protein family HMM PF00929 YP_494623.1 identified by match to protein family HMM PF00589 YP_494624.1 identified by match to protein family HMM PF03372 YP_494625.1 identified by match to protein family HMM PF07968; match to protein family HMM TIGR01002 YP_494626.1 identified by match to protein family HMM PF07968 YP_494627.1 dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE), catalyzes the hydrolysis of N-succinyl-L,Ldiaminopimelate L,L-SDAP to L,L-diaminopimelate and succinate. It is a metalloprotease containing dinuclear active sites. Its structure is similar to the carboxypeptidase G2 from Pseudomonas sp. strain RS-16 and the aminopeptidase from Aeromonas proteolytica. YP_494629.1 identified by match to protein family HMM PF01497 YP_494630.1 identified by match to protein family HMM PF02386 YP_494631.1 identified by match to protein family HMM PF00583 YP_494632.1 identified by match to protein family HMM PF03592 YP_494633.1 60 kDa chaperone family; promotes refolding of misfolded polypeptides especially under stressful conditions; forms two stacked rings of heptamers to form a barrel-shaped 14mer; ends can be capped by GroES; misfolded proteins enter the barrel where they are refolded when GroES binds; many bacteria have multiple copies of the groEL gene which are active under different environmental conditions; the B.japonicum protein in this cluster is expressed constitutively; in Rhodobacter, Corynebacterium and Rhizobium this protein is essential for growth YP_494634.1 10 kDa chaperonin; Cpn10; GroES; forms homoheptameric ring; binds to one or both ends of the GroEL double barrel in the presence of adenine nucleotides capping it; folding of unfolded substrates initiates in a GroEL-substrate bound and capped by GroES; release of the folded substrate is dependent on ATP binding and hydrolysis in the trans ring YP_494635.1 identified by match to protein family HMM PF02517 YP_494637.1 identified by match to protein family HMM PF00881 YP_494638.1 identified by match to protein family HMM PF00795 YP_494639.1 Lyses erythrocytes and other mammalian cells YP_494640.1 identified by match to protein family HMM PF04647 YP_494641.1 identified by match to protein family HMM PF05931 YP_494643.1 identified by match to protein family HMM PF00072; match to protein family HMM PF04397 YP_494644.1 identified by match to protein family HMM PF00294 YP_494645.1 identified by match to protein family HMM PF00251; match to protein family HMM TIGR01322 YP_494646.1 identified by match to protein family HMM PF00356; match to protein family HMM PF00532 YP_494647.1 identified by match to protein family HMM PF00909; match to protein family HMM TIGR00836 YP_494648.1 identified by match to protein family HMM PF01206 YP_494649.1 identified by match to protein family HMM PF04143 YP_494650.1 modulates transcription in response to the NADH/NAD(+) redox state YP_494651.1 identified by match to protein family HMM PF00005 YP_494652.1 identified by match to protein family HMM PF00488 YP_494653.1 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_494654.1 identified by match to protein family HMM PF00583; match to protein family HMM TIGR01575 YP_494655.1 identified by match to protein family HMM PF00814 YP_494656.1 identified by match to protein family HMM PF02367; match to protein family HMM TIGR00150 YP_494657.1 catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis YP_494658.1 identified by match to protein family HMM PF00205; match to protein family HMM PF02775; match to protein family HMM PF02776; match to protein family HMM TIGR00118 YP_494659.1 with IlvI catalyzes the formation of 2-acetolactate from pyruvate, this subunit subunit is required for full activity and valine sensitivity; also known as acetolactate synthase small YP_494660.1 catalyzes the formation of (R)-2,3-dihydroxy-3-methylbutanoate from (S)-2-hydroxy-2-methyl-3-oxobutanoate in valine and isoleucine biosynthesis YP_494661.1 catalyzes the formation of 2-isopropylmalate from acetyl-CoA and 2-oxoisovalerate in leucine biosynthesis YP_494662.1 catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis YP_494663.1 dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate YP_494664.1 catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis; forms a heterodimer of LeuC/D YP_494665.1 catalyzes the formation of 2-oxobutanoate from L-threonine; biosynthetic YP_494666.1 identified by match to protein family HMM PF03926 YP_494667.1 identified by match to protein family HMM PF00575 YP_494668.1 sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; sigma B is not essential for sporulation; rather it is required for maximal expression of ctc and csbA which are transcribed in the early stationary phase under conditions inimical to sporulation; induced by heat shock, salt stress, oxidative stress, glucose limitation, oxygen limitation and entry into stationary phase YP_494669.1 binds to sigma-B preventing the formation of an RNA polymerase holoenzyme YP_494670.1 identified by match to protein family HMM PF01740; match to protein family HMM TIGR00377 YP_494671.1 identified by match to protein family HMM PF07228 YP_494672.1 identified by match to protein family HMM PF02452 YP_494673.1 identified by match to protein family HMM PF00842; match to protein family HMM PF01168; match to protein family HMM TIGR00492 YP_494674.1 Catalyzes the formation of holo-ACP, which mediates the essential transfer of acyl fatty acid intermediates during the biosynthesis of fatty acids and lipids YP_494675.1 identified by match to protein family HMM PF03703 YP_494676.1 identified by match to protein family HMM PF03703 YP_494678.1 one of the components of the high-affinity ATP-driven potassium transport (or KDP)system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions; the C subunit may be involved in assembly of the KDP complex YP_494679.1 One of the components of the high-affinity ATP-driven potassium transport (or KDP) system, which catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions YP_494680.1 catalyzes the hydrolysis of ATP coupled with the exchange of hydrogen and potassium ions YP_494681.1 identified by match to protein family HMM PF00512; match to protein family HMM PF02518; match to protein family HMM PF02702 YP_494682.1 identified by match to protein family HMM PF00072; match to protein family HMM PF00486 YP_494683.1 identified by match to protein family HMM PF00270; match to protein family HMM PF00271 YP_494684.1 identified by match to protein family HMM PF01225; match to protein family HMM PF02875; match to protein family HMM TIGR01143 YP_494685.1 D-alanine--D-alanine ligase; DdlA; DdlB; cytoplasmic; catalyzes the formation of D-alanyl-D-alanine from two D-alanines in peptidoglycan synthesis; there are two forms of this enzyme in Escherichia coli YP_494686.1 identified by match to protein family HMM PF01098 YP_494689.1 identified by match to protein family HMM PF02583 YP_494690.1 identified by match to protein family HMM PF00614 YP_494691.1 identified by match to protein family HMM PF01966 YP_494692.1 identified by match to protein family HMM PF02096 YP_494693.1 Condenses 4-methyl-5-(beta-hydroxyethyl)-thiazole monophosphate and 4-amino-5-hydroxymethyl pyrimidine pyrophosphate to form thiamine monophosphate YP_494694.1 catalyzes the formation of 4-methyl-5-(2-phosphoethyl)-thiazole and ADP from 4-methyl-5-(2-hydroxyethyl)-thiazole and ATP YP_494695.1 catalyzes the formation of 4-amino-2-methyl-5-diphosphomethylpyrimidine YP_494696.1 identified by match to protein family HMM PF03070 YP_494697.1 identified by match to protein family HMM PF06737 YP_494698.1 identified by match to protein family HMM PF00436 YP_494700.1 in Pseudomonas aeruginosa this enzyme is a trimer of dimers; essential for membrane formation; performs third step of type II fatty acid biosynthesis; catalyzes dehydration of (3R)-hydroxyacyl-ACP to trans-2-acyl-ACP YP_494701.1 adds enolpyruvyl to UDP-N-acetylglucosamine as a component of cell wall formation; gram-positive bacteria have 2 copies of MurA which are active YP_494702.1 identified by match to protein family HMM PF06612; match to protein family HMM TIGR02327 YP_494703.1 part of catalytic core of ATP synthase; alpha(3)beta(3)gamma(1)delta(1)epsilon(1); involved in producing ATP from ADP in the presence of the proton motive force across the membrane YP_494704.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit YP_494705.2 Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit YP_494706.1 produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit YP_494707.1 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_494708.1 produces ATP from ADP in the presence of a proton gradient across the membrane; subunit B is part of the membrane proton channel YP_494709.1 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_494710.1 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_494711.1 identified by match to protein family HMM PF02350; match to protein family HMM TIGR00236 YP_494712.1 Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate YP_494713.1 catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate YP_494714.1 identified by match to protein family HMM PF04260; match to protein family HMM TIGR01440 YP_494715.1 identified by match to protein family HMM PF01451 YP_494716.1 identified by match to protein family HMM PF01300; match to protein family HMM PF03481; match to protein family HMM TIGR00057 YP_494717.1 identified by match to protein family HMM PF05175; match to protein family HMM TIGR00536 YP_494718.1 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_494719.1 catalyzes the formation of thymidine 5'-phosphate from thymidine YP_494720.1 RpmE2; there appears to be two types of ribosomal proteins L31 in bacterial genomes; some contain a CxxC motif while others do not; Bacillus subtilis has both types; the proteins in this cluster do not have the CXXC motif; RpmE is found in exponentially growing Bacilli while YtiA was found after exponential growth; expression of ytiA is controlled by a zinc-specific transcriptional repressor; RpmE contains one zinc ion and a CxxC motif is responsible for this binding; forms an RNP particle along with proteins L5, L18, and L25 and 5S rRNA; found crosslinked to L2 and L25 and EF-G; may be near the peptidyltransferase site of the 50S ribosome YP_494721.1 An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes YP_494722.1 identified by match to protein family HMM PF00171 YP_494723.1 identified by match to protein family HMM PF01638 YP_494724.1 adds enolpyruvyl to UDP-N-acetylglucosamine as a component of cell wall formation; gram-positive bacteria have 2 copies of MurA which are active YP_494725.1 catalyzes the formation of glycerone phosphate and glyceraldehyde 3-phosphate from fructose 1,6, bisphosphate; induced by anaerobic conditions in Bacillus subtilis YP_494727.1 CTP synthase; cytidine triphosphate synthetase; catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen; in Escherichia coli this enzyme forms a homotetramer YP_494728.1 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 YP_494729.1 identified by match to protein family HMM PF00583 YP_494730.1 catalyzes the formation of (R)-4'-phosphopantothenate from (R)-pantothenate in coenzyme A biosynthesis; type II pantothenate kinases are not regulated by feedback inhibition by coenzyme A YP_494733.1 identified by match to protein family HMM PF01546; match to protein family HMM PF07687; match to protein family HMM TIGR01891 YP_494734.1 catalyzes the hydrolysis of S-ribosylhomocysteine to homocysteine and autoinducer-2 YP_494735.2 Catalyzes the reversible phosphorolysis of pyrimidines in the nucleotide synthesis salvage pathway YP_494736.1 catalyzes the formation of D-glyceraldehyde 3-phosphate and acetaldehyde from 2-deoxy-D-ribose-5-phosphate YP_494737.1 catalyzes the reversible phosphorolysis of ribonucleosides and 2'- deoxyribonucleosides to the free base and (2'-deoxy)ribose-1- phosphate YP_494738.1 identified by match to protein family HMM PF00210 YP_494739.1 identified by match to protein family HMM PF04134 YP_494742.1 identified by match to protein family HMM PF01238; match to protein family HMM TIGR00218 YP_494743.1 identified by match to protein family HMM PF01370 YP_494744.1 identified by match to protein family HMM PF01022 YP_494745.1 identified by match to protein family HMM PF01545; match to protein family HMM TIGR01297 YP_494748.1 identified by match to protein family HMM PF00702; match to protein family HMM PF05116; match to protein family HMM TIGR00099; match to protein family HMM TIGR01484 YP_494749.1 identified by match to protein family HMM PF00005 YP_494750.1 Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source YP_494751.1 identified by match to protein family HMM PF02302; match to protein family HMM PF02378; match to protein family HMM TIGR00851 YP_494752.1 identified by match to protein family HMM PF00874; match to protein family HMM PF05043 YP_494753.1 identified by match to protein family HMM PF00359 YP_494754.1 identified by match to protein family HMM PF01232; match to protein family HMM PF08125 YP_494755.1 identified by match to protein family HMM PF07564; match to protein family HMM TIGR01167 YP_494756.1 identified by match to protein family HMM PF04650; match to protein family HMM PF07564; match to protein family HMM TIGR01168 YP_494757.1 catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate YP_494758.1 identified by match to protein family HMM PF07949 YP_494759.1 identified by match to protein family HMM PF02457; match to protein family HMM TIGR00159 YP_494760.1 identified by match to protein family HMM PF00491; match to protein family HMM TIGR01229 YP_494761.1 identified by match to protein family HMM PF01610 YP_494763.1 identified by match to protein family HMM PF07690; match to protein family HMM TIGR00711 YP_494765.1 identified by match to protein family HMM PF07690 YP_494766.1 identified by match to protein family HMM PF03006; match to protein family HMM TIGR01065 YP_494767.1 identified by match to protein family HMM PF01704 YP_494768.1 identified by match to protein family HMM PF04307 YP_494770.1 identified by match to protein family HMM PF07670 YP_494771.1 identified by match to protein family HMM PF01032 YP_494772.1 identified by match to protein family HMM PF01032 YP_494773.1 identified by match to protein family HMM PF01497 YP_494774.1 identified by match to protein family HMM PF01168 YP_494775.1 identified by match to protein family HMM PF04183 YP_494776.1 identified by match to protein family HMM PF05977; match to protein family HMM PF07690 YP_494777.1 identified by match to protein family HMM PF04183 YP_494778.1 identified by match to protein family HMM PF03780 YP_494781.1 identified by match to protein family HMM PF02028; match to protein family HMM TIGR00842 YP_494782.1 identified by match to protein family HMM PF00107 YP_494783.1 identified by match to protein family HMM PF00107 YP_494784.1 identified by match to protein family HMM PF06028 YP_494785.1 catalyzes the formation of 6-phospho-galactose from a 6-phospho-beta-galactoside YP_494786.1 identified by match to protein family HMM PF02302; match to protein family HMM PF02378; match to protein family HMM TIGR00394; match to protein family HMM TIGR00410; match to protein family HMM TIGR00853 YP_494787.1 identified by match to protein family HMM PF02255; match to protein family HMM TIGR00823 YP_494788.1 catalyzes the reversible reaction of dihydroxyacetone phosphate with glyceraldehyde 3-phosphate to produce tagatose 1,6-bisphosphate; in Streptococcus pyogenes there are two paralogs of tagatose-bisphosphate aldolase, encoded by lacD1 and lacD2; expression of lacD1 is highly regulated by environmental conditions while lacD2 specializes in an efficient utilization of carbohydrate sources YP_494789.1 catalyzes the formation of tagatose 1,6-bisphosphate from tagatose 6-phosphate and ATP YP_494790.1 catalyzes the interconversion of galactose 6-phosphate to tagatose 6-phosphate YP_494791.1 catalyzes the interconversion of galactose 6-phosphate to tagatose 6-phosphate; tagatose pathway for galactose utilization YP_494792.1 identified by match to protein family HMM PF00455; match to protein family HMM PF08220 YP_494793.1 Modulates the activities of several enzymes which are inactive in their acetylated form YP_494795.1 identified by match to protein family HMM PF00248 YP_494796.1 identified by match to protein family HMM PF00376 YP_494797.1 identified by match to protein family HMM PF02278; match to protein family HMM PF02884; match to protein family HMM PF08124 YP_494798.1 identified by match to protein family HMM PF01551 YP_494799.1 identified by match to protein family HMM PF05116; match to protein family HMM TIGR01484 YP_494800.1 identified by match to protein family HMM PF03642 YP_494801.1 identified by match to protein family HMM PF03306; match to protein family HMM TIGR01252 YP_494802.1 catalyzes the formation of 2-acetolactate from pyruvate in stationary phase YP_494804.1 identified by match to protein family HMM PF07724 YP_494806.1 forms a direct contact with the tRNA during translation YP_494807.1 in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit YP_494808.1 mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability YP_494809.1 identified by match to protein family HMM PF02361 YP_494810.1 with CbiNQ forms the ABC transporter for cobalt import; Staphylococcus has two adjacent copies of this gene YP_494811.1 with CbiNQ forms the ABC transporter for cobalt import; Staphylococcus has two adjacent copies of this gene YP_494812.1 is a component of the macrolide binding site in the peptidyl transferase center YP_494813.1 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_494814.1 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_494815.1 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_494816.1 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_494817.1 stimulates the activities of the other two initiation factors, IF-2 and IF-3 YP_494818.1 essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP YP_494819.1 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_494820.1 late assembly protein YP_494821.1 L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7 YP_494822.1 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_494823.1 binds 5S rRNA along with protein L5 and L25 YP_494824.1 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_494825.1 binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit YP_494826.2 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_494827.1 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_494828.1 assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel YP_494829.1 binds to the 23S rRNA between the centers for peptidyl transferase and GTPase YP_494830.1 primary binding protein; helps mediate assembly; involved in translation fidelity YP_494831.1 one of the stabilizing components for the large ribosomal subunit YP_494832.1 located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e YP_494833.1 forms a complex with S10 and S14; binds the lower part of the 30S subunit head and the mRNA in the complete ribosome to position it for translation YP_494834.1 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_494835.1 protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA YP_494836.1 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_494837.1 binds third domain of 23S rRNA and protein L29; part of exit tunnel YP_494838.1 L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA YP_494839.1 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_494840.1 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_494842.1 identified by match to protein family HMM PF00860; match to protein family HMM PF00916 YP_494843.1 decatenates replicating daughter chromosomes YP_494844.1 identified by match to protein family HMM PF00583 YP_494845.1 identified by match to protein family HMM PF06800 YP_494846.1 identified by match to protein family HMM PF03547 YP_494848.1 identified by match to protein family HMM PF00873 YP_494849.1 identified by match to protein family HMM PF02388 YP_494851.1 identified by match to protein family HMM PF01047 YP_494852.1 identified by match to protein family HMM PF07690 YP_494853.1 identified by match to protein family HMM PF01047; match to protein family HMM TIGR01889 YP_494854.1 identified by match to protein family HMM PF04055; match to protein family HMM PF06463; match to protein family HMM TIGR02666 YP_494855.1 in Escherichia coli MobA links a guanosine 5'-phosphate to molydopterin to form molybdopterin guanine dinucleotide during molybdenum cofactor biosynthesis YP_494856.1 identified by match to protein family HMM PF02597; match to protein family HMM TIGR01682 YP_494857.1 identified by match to protein family HMM PF02391 YP_494858.1 identified by match to protein family HMM PF03205; match to protein family HMM TIGR00176 YP_494859.1 identified by match to protein family HMM PF00994; match to protein family HMM PF03453; match to protein family HMM PF03454; match to protein family HMM TIGR00177 YP_494860.1 MoaC; along with MoaA is involved in conversion of a guanosine derivative into molybdopterin precursor Z; involved in molybdenum cofactor biosynthesis YP_494861.1 identified by match to protein family HMM PF00994; match to protein family HMM TIGR00177 YP_494862.1 identified by match to protein family HMM PF00899; match to protein family HMM PF05237 YP_494863.1 identified by match to protein family HMM PF00005 YP_494864.1 identified by match to protein family HMM PF00528; match to protein family HMM TIGR02141 YP_494865.1 identified by match to protein family HMM PF01547; match to protein family HMM TIGR01256 YP_494866.1 involved in the production or activity of formate dehydrogenase-H which is active when nitrate is not present during anaerobic growth YP_494867.1 identified by match to protein family HMM PF00583 YP_494868.1 identified by match to protein family HMM PF02632 YP_494869.1 identified by match to protein family HMM PF01156 YP_494870.1 identified by match to protein family HMM PF01497 YP_494871.1 identified by match to protein family HMM PF02770; match to protein family HMM PF08028 YP_494872.1 identified by match to protein family HMM PF03253 YP_494873.1 UreA, with UreB and UreC catalyzes the hydrolysis of urea into ammonia and carbon dioxide; nickel metalloenzyme; accessory proteins UreD, UreE, UreF, and UreG are necessary for assembly of the metallocenter YP_494874.1 ureases catalyze the hydrolysis of urea into ammonia and carbon dioxide; in Helicobacter pylori and Yersinia enterocolitica the ammonia released plays a key role in bacterial survival by neutralizing acids when colonizing the gastric mucosa; the holoenzyme is composed of 3 UreC (alpha) and 3 UreAB (gamma/beta); in Staphylococcus saprophyticus plays a role in bladder invasiveness and may induce the formation of kidney and bladder stones due to the alkalization of urine YP_494875.1 ureases catalyze the hydrolysis of urea into ammonia and carbon dioxide; in Helicobacter pylori the ammonia released plays a key role in bacterial survival by neutralizing acids when colonizing the gastric mucosa; the holoenzyme is composed of 3 ureC (alpha) and 3 ureAB (gamma/beta) subunits YP_494876.1 involved in the assembly of the urease metallocenter; possible nickel donor YP_494877.1 identified by match to protein family HMM PF01730 YP_494878.1 identified by match to protein family HMM PF02492; match to protein family HMM TIGR00101 YP_494879.1 identified by match to protein family HMM PF01774 YP_494880.1 identified by match to protein family HMM TIGR01889 YP_494882.1 identified by match to protein family HMM TIGR01889 YP_494883.1 identified by match to protein family HMM PF00165 YP_494884.1 identified by match to protein family HMM PF05257 YP_494885.1 identified by match to protein family HMM PF03553; match to protein family HMM TIGR00931 YP_494886.1 identified by match to protein family HMM PF01210; match to protein family HMM PF02317 YP_494888.1 identified by match to protein family HMM PF05257 YP_494889.1 identified by match to protein family HMM PF00389; match to protein family HMM PF02826 YP_494890.1 identified by match to protein family HMM PF01494 YP_494891.1 identified by match to protein family HMM PF01832 YP_494892.1 identified by match to protein family HMM PF07849 YP_494893.1 identified by match to protein family HMM PF00037; match to protein family HMM PF00111; match to protein family HMM PF00384; match to protein family HMM PF01568; match to protein family HMM PF04879; match to protein family HMM TIGR01591 YP_494894.1 identified by match to protein family HMM PF03816; match to protein family HMM TIGR00350 YP_494895.1 identified by match to protein family HMM PF00459 YP_494896.1 identified by match to protein family HMM PF08220 YP_494898.1 identified by match to protein family HMM PF02517 YP_494899.1 contains one authenticated frameshift mutation YP_494900.1 identified by match to protein family HMM PF00324 YP_494902.1 identified by match to protein family HMM PF00702; match to protein family HMM TIGR01509; match to protein family HMM TIGR01549 YP_494903.1 identified by match to protein family HMM PF01758 YP_494904.1 identified by similarity to PIR:E90031 YP_494905.1 identified by match to protein family HMM PF00367; match to protein family HMM PF02378; match to protein family HMM TIGR00826; match to protein family HMM TIGR02005 YP_494906.1 identified by match to protein family HMM PF01380; match to protein family HMM PF01418 YP_494908.1 identified by match to protein family HMM PF03553 YP_494910.1 identified by match to protein family HMM PF00106 YP_494911.1 identified by match to protein family HMM PF01546; match to protein family HMM PF07687; match to protein family HMM TIGR01891 YP_494912.1 catalyzing the hydrolysis of 4-imidazolone-5-propionate to N-formimidoyl-L-glutamate, the third step in the histidine degradation pathway YP_494913.1 catalyzes the formation of 4-imidazolone-5-propanoate from urocanate during histidine metabolism YP_494914.1 identified by match to protein family HMM PF00126; match to protein family HMM PF03466 YP_494915.1 catalyzes resistance to fosfomycin by the addition of a thiol cofactor YP_494916.1 catalyzes the formation of glutamate and formamide from N-formimidoyl-L-glutamate YP_494917.1 identified by match to protein family HMM PF02517 YP_494918.1 catalyzes D-ribose 5-phosphate --> D-ribulose 5-phosphate in the nonoxidative branch of the pentose phosphate pathway YP_494919.1 identified by match to protein family HMM PF03473; match to protein family HMM PF03475 YP_494920.1 identified by match to protein family HMM PF01263 YP_494921.1 identified by match to protein family HMM PF02694 YP_494923.1 identified by match to protein family HMM PF00005 YP_494924.1 identified by match to protein family HMM PF05656 YP_494925.1 identified by match to protein family HMM PF02245; match to protein family HMM TIGR00567 YP_494926.1 identified by match to protein family HMM PF03616; match to protein family HMM TIGR00210 YP_494927.1 catalyzes the isomerization of isopentenyl pyrophosphate to dimethylallyl diphosphate YP_494928.1 identified by match to protein family HMM PF01544 YP_494931.1 identified by match to protein family HMM PF07859 YP_494933.1 identified by match to protein family HMM PF07690; match to protein family HMM TIGR00711 YP_494935.1 identified by match to protein family HMM PF00440 YP_494936.1 identified by match to protein family HMM PF07690; match to protein family HMM TIGR00710 YP_494938.1 identified by match to protein family HMM PF01047 YP_494939.1 identified by match to protein family HMM PF02698 YP_494940.1 identified by similarity to GB:AAO04226.1 YP_494941.1 identified by match to protein family HMM PF00005 YP_494942.1 identified by match to protein family HMM PF02687 YP_494943.1 identified by match to protein family HMM PF00072; match to protein family HMM PF00486 YP_494944.1 identified by match to protein family HMM PF00512; match to protein family HMM PF00672; match to protein family HMM PF02518 YP_494945.1 identified by match to protein family HMM PF04397 YP_494947.1 malate dehydrogenase; catalyzes the oxidation of malate to oxaloacetate YP_494948.1 identified by match to protein family HMM PF02652; match to protein family HMM TIGR00795 YP_494951.1 identified by match to protein family HMM PF00583 YP_494952.1 identified by match to protein family HMM PF00107 YP_494953.1 identified by match to protein family HMM PF00583 YP_494954.1 identified by match to protein family HMM PF00070; match to protein family HMM PF03486; match to protein family HMM PF07992 YP_494956.1 identified by match to protein family HMM PF01061 YP_494957.1 identified by match to protein family HMM PF00440 YP_494958.1 identified by match to protein family HMM PF01544 YP_494959.1 identified by match to protein family HMM PF00367; match to protein family HMM PF02378; match to protein family HMM TIGR00826; match to protein family HMM TIGR01996 YP_494961.1 identified by match to protein family HMM PF00165 YP_494962.1 identified by match to protein family HMM PF01243 YP_494964.1 identified by match to protein family HMM PF00375 YP_494966.1 identified by match to protein family HMM PF01047 YP_494967.1 identified by match to protein family HMM PF00011 YP_494968.1 identified by match to protein family HMM PF07690 YP_494970.1 authenticated frameshift mutation resulting in a premature stop--the same authenticated frameshift mutation was found in COL YP_494971.1 identified by match to protein family HMM PF00376; match to protein family HMM PF07739 YP_494972.1 identified by match to protein family HMM PF00072; match to protein family HMM PF00196 YP_494973.1 identified by match to protein family HMM PF02518; match to protein family HMM PF07730 YP_494975.1 identified by match to protein family HMM PF02665; match to protein family HMM TIGR00351 YP_494976.1 identified by match to protein family HMM PF02613; match to protein family HMM TIGR00684 YP_494977.1 identified by match to protein family HMM TIGR01660 YP_494978.1 identified by match to protein family HMM PF00384; match to protein family HMM PF01568; match to protein family HMM TIGR01580 YP_494979.1 identified by match to protein family HMM PF00590; match to protein family HMM TIGR01469 YP_494980.1 identified by match to protein family HMM PF00355; match to protein family HMM TIGR02378 YP_494981.1 identified by match to protein family HMM PF00070; match to protein family HMM PF01077; match to protein family HMM PF03460; match to protein family HMM PF04324; match to protein family HMM PF07992; match to protein family HMM TIGR02374 YP_494982.1 identified by match to protein family HMM PF01903 YP_494983.1 identified by match to protein family HMM PF00583 YP_494984.1 identified by match to protein family HMM PF01226 YP_494986.1 identified by match to protein family HMM PF01297 YP_494987.1 identified by match to protein family HMM PF06769; match to protein family HMM TIGR02116 YP_494988.1 identified by match to protein family HMM PF02604; match to protein family HMM TIGR01552 YP_494991.1 identified by match to protein family HMM PF02388 YP_494992.1 identified by match to protein family HMM PF00005 YP_494993.1 identified by match to protein family HMM PF00528; match to protein family HMM TIGR01726 YP_494994.1 identified by match to protein family HMM PF00497 YP_494995.1 identified by match to protein family HMM PF07690; match to protein family HMM TIGR00711 YP_494997.1 2,3-bisphosphoglycerate-dependent; catalyzes the interconversion of 2-phosphoglycerate to 3-phosphoglycerate YP_494998.1 identified by match to protein family HMM PF01545; match to protein family HMM TIGR01297 YP_494999.1 identified by match to protein family HMM PF02216 YP_495000.1 identified by match to protein family HMM PF07968; match to protein family HMM TIGR01002 YP_495001.1 identified by match to protein family HMM PF07968; match to protein family HMM TIGR01002 YP_495002.1 identified by match to protein family HMM PF07968; match to protein family HMM TIGR01002 YP_495004.1 catalyzes the formation of pimeloyl-CoA from pimelate and coenzyme A YP_495005.1 identified by match to protein family HMM PF00155; match to protein family HMM PF00266 YP_495006.1 catalyzes the formation of biotin from dethiobiotin and sulfur 2 S-adenosyl-L-methionine YP_495007.1 identified by match to protein family HMM PF00202; match to protein family HMM TIGR00508 YP_495008.1 identified by match to protein family HMM TIGR00347 YP_495009.1 identified by match to protein family HMM PF00005 YP_495010.1 identified by match to protein family HMM PF00005; match to protein family HMM PF00664 YP_495011.1 identified by match to protein family HMM PF04138 YP_495012.1 identified by match to protein family HMM PF02595; match to protein family HMM TIGR00045 YP_495014.1 identified by match to protein family HMM PF07690; match to protein family HMM TIGR00710 YP_495015.1 identified by match to protein family HMM PF06445 YP_495017.1 identified by match to protein family HMM PF00149 YP_495018.1 identified by match to protein family HMM PF00324 YP_495019.1 identified by match to protein family HMM PF00999 YP_495020.1 identified by match to protein family HMM PF00324 YP_495021.1 identified by match to protein family HMM PF00144 YP_495022.1 identified by match to protein family HMM PF01073; match to protein family HMM PF01370; match to protein family HMM PF02719; match to protein family HMM PF04321 YP_495023.1 ketopantoate reductase; catalyzes the NADPH reduction of ketopantoate to pantoate; functions in pantothenate (vitamin B5) biosynthesis YP_495024.1 identified by match to protein family HMM PF07690 YP_495025.1 identified by match to protein family HMM PF00528 YP_495026.1 identified by match to protein family HMM PF04069 YP_495027.1 identified by match to protein family HMM PF00528 YP_495028.1 identified by match to protein family HMM PF00005; match to protein family HMM PF00571; match to protein family HMM TIGR01186 YP_495030.1 identified by match to protein family HMM PF00324 YP_495031.1 identified by match to protein family HMM PF00135 YP_495032.1 identified by match to protein family HMM PF07690 YP_495033.1 identified by match to protein family HMM PF03649; match to protein family HMM TIGR00245 YP_495034.1 identified by match to protein family HMM PF00005 YP_495035.1 identified by match to protein family HMM PF05343 YP_495036.1 identified by match to protein family HMM PF05016; match to protein family HMM PF06769; match to protein family HMM TIGR02116 YP_495037.1 identified by match to protein family HMM PF02604; match to protein family HMM TIGR01552 YP_495038.1 identified by match to protein family HMM PF06998 YP_495039.1 identified by similarity to GB:CAA75550.1; match to protein family HMM PF01645 YP_495040.1 identified by similarity to GB:AAW38558.1 YP_495041.1 identified by match to protein family HMM PF07690 YP_495042.1 identified by match to protein family HMM PF00005 YP_495043.1 identified by match to protein family HMM PF00005 YP_495044.1 identified by match to protein family HMM PF00528 YP_495045.1 identified by match to protein family HMM PF00528 YP_495046.1 identified by match to protein family HMM PF00496; match to protein family HMM TIGR02294 YP_495049.1 identified by similarity to GB:BAB05790.1 YP_495052.1 identified by match to protein family HMM PF03606; match to protein family HMM PF03806 YP_495053.1 identified by match to protein family HMM PF02627; match to protein family HMM TIGR00778 YP_495054.1 identified by match to protein family HMM PF07252 YP_495055.1 identified by match to protein family HMM PF07252 YP_495056.1 identified by match to protein family HMM PF07252 YP_495057.1 identified by match to protein family HMM PF00106; match to protein family HMM PF01370 YP_495059.1 identified by match to protein family HMM PF04507; match to protein family HMM TIGR01742 YP_495063.1 identified by match to protein family HMM PF04507; match to protein family HMM TIGR01742 YP_495064.1 identified by match to protein family HMM PF04507; match to protein family HMM TIGR01742 YP_495065.1 identified by match to protein family HMM PF00270; match to protein family HMM PF00271; match to protein family HMM PF04851 YP_495066.1 identified by match to protein family HMM PF00293 YP_495067.1 identified by match to protein family HMM PF00408; match to protein family HMM PF02878; match to protein family HMM PF02879; match to protein family HMM PF02880 YP_495068.1 identified by match to protein family HMM PF07690 YP_495069.1 identified by similarity to GB:BAB58658.2; match to protein family HMM PF00746; match to protein family HMM PF07501; match to protein family HMM TIGR01167 YP_495070.1 identified by match to protein family HMM PF04650; match to protein family HMM TIGR01168 YP_495071.1 identified by match to protein family HMM TIGR01889 YP_495072.1 identified by match to protein family HMM PF01047; match to protein family HMM TIGR01889 YP_495073.1 identified by match to protein family HMM PF00483; match to protein family HMM TIGR01099 YP_495074.1 identified by match to protein family HMM PF00746; match to protein family HMM PF02986; match to protein family HMM PF04650; match to protein family HMM TIGR01167; match to protein family HMM TIGR01168 YP_495075.1 identified by match to protein family HMM PF00746; match to protein family HMM PF02986; match to protein family HMM PF04650; match to protein family HMM TIGR01167; match to protein family HMM TIGR01168 YP_495076.1 identified by match to protein family HMM PF02447; match to protein family HMM PF03600; match to protein family HMM TIGR00791 YP_495077.1 identified by match to protein family HMM PF00370; match to protein family HMM PF02782; match to protein family HMM TIGR01314 YP_495078.1 identified by match to protein family HMM PF00392; match to protein family HMM PF07729 YP_495079.1 identified by match to protein family HMM PF00376 YP_495080.1 identified by match to protein family HMM PF04607 YP_495082.1 identified by match to protein family HMM PF05976 YP_495083.1 identified by match to protein family HMM PF07690 YP_495085.1 identified by match to protein family HMM PF00083; match to protein family HMM PF07690 YP_495086.1 identified by match to protein family HMM PF01047 YP_495087.1 identified by match to protein family HMM PF00005 YP_495089.1 identified by match to protein family HMM PF06874 YP_495091.1 identified by match to protein family HMM PF02230 YP_495092.1 identified by match to protein family HMM PF00903 YP_495093.1 identified by match to protein family HMM PF01047; match to protein family HMM PF01978 YP_495095.1 identified by match to protein family HMM PF00903 YP_495096.1 identified by match to protein family HMM PF00881 YP_495097.1 catalyzes the formation of pyruvate from lactate YP_495098.1 identified by match to protein family HMM PF05116; match to protein family HMM TIGR00099; match to protein family HMM TIGR01484 YP_495099.1 identified by match to protein family HMM PF00005 YP_495101.1 identified by match to protein family HMM PF04203; match to protein family HMM TIGR01076 YP_495102.1 identified by match to protein family HMM PF00583 YP_495103.1 identified by match to protein family HMM PF03313; match to protein family HMM TIGR00718 YP_495104.1 identified by match to protein family HMM PF03315; match to protein family HMM TIGR00719 YP_495106.1 identified by match to protein family HMM PF00892 YP_495107.1 identified by match to protein family HMM PF07859 YP_495108.1 identified by similarity to GB:BAE03833.1 YP_495110.1 identified by match to protein family HMM PF00358; match to protein family HMM PF00367; match to protein family HMM PF02378; match to protein family HMM TIGR00826; match to protein family HMM TIGR00830; match to protein family HMM TIGR02002 YP_495111.1 catalyzes the formation of acetyl phosphate from pyruvate YP_495112.1 identified by match to protein family HMM PF04172 YP_495113.1 identified by match to protein family HMM PF03788 YP_495114.1 identified by match to protein family HMM PF00126; match to protein family HMM PF03466 YP_495115.1 identified by match to protein family HMM PF06855 YP_495116.1 identified by match to protein family HMM PF05257 YP_495117.1 identified by match to protein family HMM TIGR00532 YP_495118.1 identified by match to protein family HMM PF01154; match to protein family HMM TIGR01835 YP_495119.1 identified by match to protein family HMM PF01035; match to protein family HMM PF02870; match to protein family HMM TIGR00589 YP_495120.1 identified by match to protein family HMM PF00004; match to protein family HMM PF02151; match to protein family HMM PF07724 YP_495121.1 identified by match to protein family HMM PF01926; match to protein family HMM PF02421; match to protein family HMM PF07664; match to protein family HMM PF07670; match to protein family HMM TIGR00231; match to protein family HMM TIGR00437 YP_495122.1 identified by match to protein family HMM PF04023 YP_495123.1 identified by match to protein family HMM PF03176 YP_495124.1 identified by match to protein family HMM PF00440 YP_495125.1 catalyzes the conversion of 1-proline-5-carboxylate dehydrogenase to L-glutamate YP_495126.1 identified by match to protein family HMM PF00132 YP_495128.1 identified by match to protein family HMM PF00122; match to protein family HMM PF00403; match to protein family HMM PF00702; match to protein family HMM TIGR01494; match to protein family HMM TIGR01511; match to protein family HMM TIGR01525 YP_495129.1 identified by match to protein family HMM PF00403; match to protein family HMM TIGR00003 YP_495130.1 catalyzes the formation of pyruvate from lactate YP_495131.1 identified by match to protein family HMM PF00155 YP_495132.1 identified by match to protein family HMM PF01266; match to protein family HMM PF01593; match to protein family HMM TIGR02734 YP_495133.1 identified by match to protein family HMM PF00494 YP_495134.1 identified by match to protein family HMM PF00535 YP_495135.1 identified by match to protein family HMM PF01266; match to protein family HMM PF01593; match to protein family HMM TIGR02734 YP_495137.1 identified by match to protein family HMM PF05257 YP_495138.1 identified by match to protein family HMM PF01757 YP_495139.1 identified by match to protein family HMM PF00583 YP_495140.1 identified by match to protein family HMM PF06737 YP_495143.1 identified by match to protein family HMM PF00440 YP_495145.1 identified by match to protein family HMM PF05979 YP_495146.1 identified by match to protein family HMM PF00903 YP_495147.1 identified by match to protein family HMM PF05368 YP_495149.1 identified by match to protein family HMM PF00440 YP_495150.1 identified by match to protein family HMM PF00106 YP_495151.1 identified by match to protein family HMM PF04909 YP_495152.1 identified by match to protein family HMM PF00561 YP_495153.1 identified by match to protein family HMM PF02492; match to protein family HMM PF07683 YP_495154.1 identified by match to protein family HMM PF07670 YP_495155.1 identified by match to protein family HMM PF07992 YP_495159.1 identified by match to protein family HMM PF01636; match to protein family HMM PF03881 YP_495160.1 catalyzes the conversion of dihydroorotate to orotate in the pyrimidine biosynthesis pathway; uses a flavin nucleotide as an essential cofactor; class 2 enzymes are monomeric and compared to the class 1 class 2 possess an extended N terminus, which plays a role in the membrane association of the enzyme and provides the binding site for the respiratory quinones that serve as physiological electron acceptors YP_495162.1 identified by match to protein family HMM PF02677 YP_495163.1 identified by match to protein family HMM PF00903; match to protein family HMM PF06983 YP_495165.1 identified by match to protein family HMM PF02129; match to protein family HMM TIGR00976 YP_495166.1 Converts L-aspartate to beta-alanine and provides the major route of beta-alanine production in bacteria. Beta-alanine is essential for the biosynthesis of pantothenate (vitamin B5) YP_495167.1 catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine YP_495168.1 catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate YP_495169.1 identified by match to protein family HMM PF01210; match to protein family HMM PF02558; match to protein family HMM TIGR00745 YP_495170.1 identified by match to protein family HMM PF03306; match to protein family HMM TIGR01252 YP_495171.1 identified by match to protein family HMM PF00056; match to protein family HMM PF02866; match to protein family HMM TIGR01771 YP_495172.1 identified by match to protein family HMM PF00324 YP_495173.1 catalyzes the formation of succinate semialdehyde and glutamate from 4-aminobutanoate and 2-oxoglutarate YP_495174.1 catalyzes the formation of glycerone phosphate and D-glyceraldehyde 3-phosphate from D-fructose 1,6-bisphosphate in glycolysis YP_495175.1 malate dehydrogenase; catalyzes the oxidation of malate to oxaloacetate YP_495176.1 identified by match to protein family HMM PF00501 YP_495177.1 identified by match to protein family HMM PF03992 YP_495178.1 identified by match to protein family HMM PF06855 YP_495179.1 catalyzes the oxidation of choline to betaine aldehyde and betain aldehyde to glycine betaine YP_495180.1 identified by match to protein family HMM PF00171; match to protein family HMM TIGR01804 YP_495183.1 identified by match to protein family HMM PF02028; match to protein family HMM TIGR00842 YP_495184.1 identified by match to protein family HMM TIGR02491 YP_495185.1 Catalyzes the reduction of nucleoside 5'-triphosphates to 2'-deoxynucleoside 5'-triphosphates YP_495186.1 identified by match to protein family HMM PF03600; match to protein family HMM PF06808; match to protein family HMM TIGR00784 YP_495187.1 catalyzes the formation of siroheme from precorrin-2 YP_495188.1 identified by match to protein family HMM PF00175; match to protein family HMM PF00258; match to protein family HMM PF00667; match to protein family HMM TIGR01931 YP_495189.1 identified by match to protein family HMM PF00255 YP_495190.1 identified by match to protein family HMM PF02687 YP_495191.1 identified by match to protein family HMM PF00005 YP_495192.1 identified by match to protein family HMM PF02518 YP_495193.1 identified by match to protein family HMM PF00072; match to protein family HMM PF00486 YP_495195.1 identified by match to protein family HMM PF00245 YP_495198.1 identified by match to protein family HMM PF00756 YP_495199.1 identified by match to protein family HMM PF00746; match to protein family HMM PF04650; match to protein family HMM TIGR01167; match to protein family HMM TIGR01168 YP_495200.1 identified by match to protein family HMM PF00027 YP_495201.1 catalyzes the reversible synthesis of carbamate and ATP from carbamoyl phosphate and ADP YP_495202.1 identified by match to protein family HMM PF00324; match to protein family HMM TIGR00905 YP_495203.1 catalyzes the formation of ornithine and carbamylphosphate from citrulline in the arginine catabolic pathway YP_495204.1 catalyzes the degradation of arginine to citruline and ammonia YP_495205.1 identified by match to protein family HMM PF02863 YP_495206.1 identified by match to protein family HMM PF01447; match to protein family HMM PF02868; match to protein family HMM PF03413; match to protein family HMM PF07504 YP_495209.1 identified by match to protein family HMM PF00359; match to protein family HMM PF00874 YP_495210.1 identified by match to protein family HMM PF00359; match to protein family HMM PF02378; match to protein family HMM PF02379; match to protein family HMM TIGR00829; match to protein family HMM TIGR00848; match to protein family HMM TIGR01427 YP_495211.1 identified by match to protein family HMM PF01238; match to protein family HMM TIGR00218 YP_495212.1 identified by match to protein family HMM PF01061 YP_495213.1 identified by match to protein family HMM PF01832; match to protein family HMM PF05257 YP_495214.1 identified by match to protein family HMM PF00857 YP_495217.1 identified by match to protein family HMM PF00534 YP_495218.1 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, especially gram positive pathogens, have paralogs that have been found to be nonessential but do function in secretion of a subset of exported proteins YP_495222.1 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_495223.1 identified by match to protein family HMM PF00746; match to protein family HMM PF05345; match to protein family HMM TIGR01167 YP_495228.1 this stereospecific enzymes reduces the S isomer of methionine sulfoxide while MsrB reduces the R form; a fusion protein of this enzyme with MsrB provides protection against oxidative stress in Neisseria gonorrhoeae YP_495229.1 identified by match to protein family HMM PF00583 YP_495230.1 identified by match to protein family HMM PF02811 YP_495231.1 identified by match to protein family HMM TIGR01007 YP_495232.1 identified by match to protein family HMM PF02706 YP_495233.1 identified by match to protein family HMM PF00440 YP_495234.1 predicted polysaccharide polymerase involved in biofilm formation; required for the synthesis of the beta-1,6-N-acetylglucosamine polysaccharide; PgaC; in Yersinia the HmsR protein is an inner membrane protein YP_495235.1 identified by match to protein family HMM PF01522 YP_495237.1 identified by match to protein family HMM PF04650; match to protein family HMM TIGR01168 YP_495239.1 catalyzes the formation of 1-(5-phosphoribosyl)-AMP from 1-(5-phosphoribosyl)-ATP and the subsequent formation of 1-(5-phosphoribosyl)-5-((5- phosphoribosylamino)methylideneamino)imidazole-4- carboxamide from 1-(5-phosphoribosyl)-AMP in histidine biosynthesis YP_495240.1 catalyzes the conversion of 5-[(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino]- 1-(5-phosphoribosyl)imidazole-4-carboxamideand glutamine to imidazole-glycerol phosphate, 5-aminoimidazol-4-carboxamideribonucleotide and glutamate; the HisF subunit acts as a cyclase YP_495241.1 catalyzes the formation of 5-(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino-l- (5-hosphoribosyl)imidazole-4-carboxamide from 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide YP_495242.1 with HisF IGPS catalyzes the conversion of phosphoribulosyl-formimino-5-aminoimidazole-4-carboxamide ribonucleotide phosphate and glutamine to imidazole-glycerol phosphate, 5-aminoimidazol-4-carboxamide ribonucleotide, and glutamate in histidine biosynthesis; the HisH subunit provides the glutamine amidotransferase activity that produces the ammonia necessary to HisF for the synthesis of imidazole-glycerol phosphate and 5-aminoimidazol-4-carboxamide ribonucleotide YP_495243.1 catalyzes the dehydration of D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate to 3-(imidazol-4-yl)-2-oxopropyl phosphate in histidine biosynthesis YP_495244.1 identified by match to protein family HMM PF00155 YP_495245.1 catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer YP_495246.1 short form of enzyme; requires HisZ for function; catalyzes the formation of N'-5'-phosphoribosyl-ATP from phosphoribosyl pyrophosphate; crucial role in histidine biosynthesis; forms heteromultimer of HisG and HisZ YP_495247.1 May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine YP_495248.1 identified by match to protein family HMM PF01522 YP_495250.1 identified by match to protein family HMM PF02361 YP_495251.1 identified by match to protein family HMM PF00005 YP_495252.1 identified by match to protein family HMM PF07155 YP_495253.1 identified by match to protein family HMM PF01887 YP_495254.1 identified by match to protein family HMM PF04264 YP_495255.1 identified by similarity to GB:AAW53218.1 YP_495256.1 identified by match to protein family HMM PF00581 YP_495257.1 catalyzes the removal of 5-oxoproline from various penultimate amino acid residues except L-proline YP_495259.1 identified by match to protein family HMM PF03551 YP_495261.1 identified by match to protein family HMM PF00939; match to protein family HMM PF06808; match to protein family HMM TIGR00785 YP_495262.1 identified by match to protein family HMM PF00892; match to protein family HMM TIGR00688 YP_495264.1 identified by match to protein family HMM PF03824; match to protein family HMM TIGR00802 YP_495265.1 identified by match to protein family HMM PF00797 YP_495267.1 identified by match to protein family HMM PF00005 YP_495268.1 identified by match to protein family HMM PF02687 YP_495270.1 identified by match to protein family HMM PF00665 YP_495273.1 identified by match to protein family HMM PF00313 YP_495274.1 identified by match to protein family HMM PF01381 YP_495277.1 identified by match to protein family HMM PF02195; match to protein family HMM TIGR00180 YP_495278.1 glucose-inhibited division protein B; SAM-dependent methyltransferase; methylates the N7 position of guanosine in position 527 of 16S rRNA YP_495279.2 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_495280.1 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_495281.1 protein component of RNaseP which catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'terminus; this enzyme also cleaves other RNA substrates YP_495282.1 in Escherichia coli transcription of this gene is enhanced by polyamines