-- dump date 20140619_022049 -- class Genbank::CDS -- table cds_note -- id note YP_178030.1 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_178031.1 binds the polymerase to DNA and acts as a sliding clamp YP_178032.1 negatively supercoils closed circular double-stranded DNA YP_178033.1 identified by similarity to GB:AAN53794.1 YP_178034.1 identified by match to protein family HMM PF00174; match to protein family HMM PF03404 YP_178035.1 identified by similarity to GP:28204350; match to protein family HMM PF03553 YP_178036.1 identified by similarity to SP:P39812; match to protein family HMM PF01493; match to protein family HMM PF01645; match to protein family HMM PF04897; match to protein family HMM PF04898; match to protein family HMM TIGR01612 YP_178037.1 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_178038.1 RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids YP_178039.1 identified by similarity to GP:10505056; match to protein family HMM PF00633; match to protein family HMM TIGR00426 YP_178040.1 identified by similarity to GP:22450191; match to protein family HMM PF00301; match to protein family HMM PF02915 YP_178041.1 catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis YP_178042.1 identified by similarity to OMNI:HP0711 YP_178043.1 identified by match to protein family HMM TIGR00364 YP_178044.1 identified by similarity to PIR:D71920; match to protein family HMM PF02600 YP_178046.1 identified by match to protein family HMM PF00015; match to protein family HMM PF00672 YP_178047.1 identified by similarity to SP:P14532; match to protein family HMM PF03150 YP_178048.1 identified by match to protein family HMM PF01557 YP_178049.1 identified by match to protein family HMM PF00849 YP_178050.1 Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide YP_178051.1 Catalyzes the rate-limiting step in dNTP synthesis YP_178052.1 identified by match to protein family HMM PF00375 YP_178053.1 flavin dependent thymidylate synthase; ThyX; thymidylate synthase complementing protein; catalyzes the formation of dTMP and tetrahydrofolate from dUMP and methylenetetrahydrofolate; the enzyme from Mycobacterium tuberculosis forms homotetramers; uses FAD as a cofactor YP_178054.1 CTP synthase; CTP synthase; cytidine triphosphate synthetase; catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen; in Escherichia coli this enzyme forms a homotetramer YP_178055.1 identified by similarity to OMNI:HP0348; match to protein family HMM PF01368; match to protein family HMM PF02272; match to protein family HMM TIGR00644 YP_178056.1 identified by similarity to GP:443453; match to protein family HMM PF00710; match to protein family HMM TIGR00520 YP_178058.1 identified by similarity to PIR:D71810 YP_178060.1 identified by similarity to GP:28805357; match to protein family HMM PF04402 YP_178061.1 identified by match to protein family HMM PF00083; match to protein family HMM TIGR00710 YP_178062.1 identified by similarity to OMNI:NTL01HP01063 YP_178063.1 identified by match to protein family HMM PF00034 YP_178065.1 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_178068.1 acts as a scaffold for the assembly of hook proteins onto the flagellar basal body rod YP_178069.1 identified by similarity to SP:Q44767; match to protein family HMM PF00460 YP_178071.1 identified by similarity to GB:AAP76601.1 YP_178073.1 catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs YP_178074.1 identified by match to protein family HMM PF03641 YP_178079.1 identified by similarity to GP:2909664 YP_178080.1 identified by similarity to GP:2909665; match to protein family HMM PF03412 YP_178081.1 One of three proteins involved in switching the direction of the flagellar rotation YP_178082.1 with FliG and FliN makes up the switch complex which is involved in switching the direction of the flagella rotation YP_178083.1 sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; this sigma factor directs late flagellar biosynthesis genes YP_178085.1 identified by similarity to GP:6952812; match to protein family HMM PF00991 YP_178086.1 positive regulator of class III flagellar genes YP_178087.1 identified by match to protein family HMM PF01288; match to protein family HMM TIGR01498 YP_178088.1 catalyzes the formation of 3-dehydroshikimate from 3-dehydroquinate in chorismate biosynthesis YP_178089.1 Catalyzes the hydrolytic cleavage of a carbon-halogen bond in N-ethylammeline YP_178090.1 identified by similarity to GP:1655731; match to protein family HMM PF01343; match to protein family HMM TIGR00706 YP_178091.1 identified by similarity to OMNI:NTL01CE0721 YP_178093.1 identified by similarity to OMNI:HP0137; match to protein family HMM PF02589 YP_178094.1 identified by match to protein family HMM PF00037; match to protein family HMM TIGR00273 YP_178095.1 identified by match to protein family HMM PF02754 YP_178096.1 identified by similarity to SP:P33231; match to protein family HMM PF02652; match to protein family HMM TIGR00795 YP_178097.1 identified by similarity to OMNI:NTL01CJ00072; match to protein family HMM PF03499 YP_178098.1 identified by similarity to GP:416215; match to protein family HMM PF03372 YP_178099.1 identified by similarity to SP:Q46100; match to protein family HMM PF03498 YP_178100.1 identified by similarity to GP:29338518 YP_178101.1 identified by similarity to SP:P11026; match to protein family HMM PF01654 YP_178102.1 identified by match to protein family HMM PF02322; match to protein family HMM TIGR00203 YP_178104.1 identified by similarity to OMNI:NTL01PH00693; match to protein family HMM PF01177; match to protein family HMM TIGR00035 YP_178105.1 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_178106.1 catalyzes the formation of fumarate from aspartate YP_178107.1 functions in anaerobic transport of C4-dicarboxylate compounds such as fumarate; similar to dcuB YP_178108.1 identified by similarity to OMNI:NTL01HP00016; match to protein family HMM PF04141 YP_178110.1 identified by similarity to OMNI:HP1457 YP_178113.1 identified by similarity to SP:P02422; similarity to EGAD:23167; match to protein family HMM PF00829; match to protein family HMM TIGR00061 YP_178114.1 involved in the peptidyltransferase reaction during translation YP_178115.1 essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication YP_178116.1 catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis YP_178117.1 modifies the free amino group of the aminoacyl moiety of methionyl-tRNA(fMet) which is important in translation initiation; inactivation of this gene in Escherichia coli severely impairs growth YP_178118.1 catalyzes the formation of biotinyl-5'-AMP, also acts as a transcriptional repressor of the biotin operon YP_178119.1 identified by similarity to SP:P37522; match to protein family HMM PF00991 YP_178120.1 identified by similarity to SP:P26497; match to protein family HMM PF02195; match to protein family HMM TIGR00180 YP_178121.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B' is part of the membrane proton channel. YP_178122.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B is part of the membrane proton channel. YP_178123.1 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_178124.1 produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit YP_178125.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit YP_178126.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit YP_178127.1 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_178128.1 identified by match to protein family HMM PF01618 YP_178129.1 identified by similarity to SP:P18784; match to protein family HMM PF02472 YP_178131.1 forms dimers; may be involved in cell envelope integrity; interacts with outer membrane proteins and with the C-terminal domain of inner membrane protein TolA YP_178132.1 identified by similarity to SP:P07176; match to protein family HMM PF00691 YP_178133.1 identified by similarity to OMNI:HP1124 YP_178134.1 identified by similarity to SP:P30856 YP_178135.1 identified by match to protein family HMM PF00698; match to protein family HMM TIGR00128 YP_178136.1 enables the cleavage of the glycosidic bond in both 5'-methylthioadenosine and S-adenosylhomocysteine YP_178137.1 identified by match to protein family HMM PF01171 YP_178138.1 identified by similarity to GB:AAD11442.1 YP_178139.1 identified by similarity to OMNI:HP0951 YP_178140.1 identified by similarity to GP:28974225; match to protein family HMM PF02130; match to protein family HMM TIGR00043 YP_178142.1 identified by similarity to SP:P25717; match to protein family HMM PF01207 YP_178143.1 identified by similarity to OMNI:NTL01HP00875 YP_178144.1 identified by similarity to SP:P18274; match to protein family HMM PF01258 YP_178145.1 identified by similarity to GP:28202370; match to protein family HMM PF02590 YP_178146.1 catalyzes the carboxylation of acetyl-CoA to malonyl-CoA; forms a tetramer of AccA2D2 subunits YP_178147.1 identified by similarity to SP:P22783; match to protein family HMM PF00459 YP_178148.1 identified by similarity to OMNI:NTL01HP00596; match to protein family HMM PF01103 YP_178149.1 catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate YP_178150.1 identified by match to protein family HMM PF01551 YP_178151.1 zinc-dependent; catalyzes the deacetylation of UDP-(3-O-acyl)-N-acetylglucosamine to UDP-3-O-(3-hydroxytetradecanoyl)-glucosamine in the second step of lipid A biosynthesis YP_178152.1 identified by similarity to GP:2314199 YP_178153.1 catalyzes the formation of O-phospho-L-homoserine from L-homoserine in threonine biosynthesis from asparate YP_178154.1 identified by similarity to OMNI:NTL01HP00373; match to protein family HMM PF04296 YP_178155.1 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_178156.1 associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock YP_178157.1 identified by similarity to SP:Q9ZM44; match to protein family HMM PF02576 YP_178158.1 identified by similarity to SP:P15005 YP_178160.1 identified by similarity to PIR:T46653; match to protein family HMM PF00950 YP_178161.1 identified by similarity to SP:Q9XDA6; match to protein family HMM PF00005 YP_178162.1 identified by match to protein family HMM PF01297 YP_178164.1 identified by similarity to OMNI:NTL01CJ01441; match to protein family HMM PF00015; match to protein family HMM PF02743 YP_178165.1 identified by similarity to PIR:G82508; match to protein family HMM PF05787; match to protein family HMM TIGR01409 YP_178166.1 identified by match to protein family HMM PF00070; match to protein family HMM TIGR01292 YP_178167.1 identified by match to protein family HMM PF00085; match to protein family HMM TIGR01068 YP_178168.1 identified by similarity to SP:O25499; match to protein family HMM PF02021 YP_178169.1 catalyzes the formation of L-aspartate 4-semialdehyde from L-homoserine YP_178170.1 catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate YP_178171.1 identified by similarity to OMNI:HP0555 YP_178172.1 identified by similarity to OMNI:HP0554 YP_178173.1 identified by match to protein family HMM PF00588 YP_178174.1 identified by similarity to SP:Q9ZLS8; match to protein family HMM PF00590; match to protein family HMM TIGR00096 YP_178175.1 RpmE; there appears to be two types of ribosomal proteins L31 in bacterial genomes; some contain a CxxC motif while others do not; Bacillus subtilis has both types; the proteins in this cluster have the CXXC motif; RpmE is found in exponentially growing Bacilli while YtiA was found after exponential growth; expression of ytiA is controlled by a zinc-specific transcriptional repressor; RpmE contains one zinc ion and a CxxC motif is responsible for this binding; forms an RNP particle along with proteins L5, L18, and L25 and 5S rRNA; found crosslinked to L2 and L25 and EF-G; may be near the peptidyltransferase site of the 50S ribosome YP_178176.1 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_178178.1 identified by match to protein family HMM PF00034 YP_178180.1 identified by match to protein family HMM PF04055 YP_178181.1 together with moaC, is involved in the conversion of a guanosine derivative (GXP) into molybdopterin precursor Z YP_178182.1 identified by similarity to OMNI:NTL01HP01266 YP_178183.1 identified by similarity to OMNI:HP1359 YP_178184.1 UbiA prenyltransferase family catalyzes the transfer of a prenyl group to various acceptors with hydrophobic ring structures in the biosynthesis of respiratory quinones, hemes, chlorophylls, vitamin E, and shikonin YP_178185.1 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_178186.1 identified by similarity to OMNI:NTL03CP0535; match to protein family HMM PF02659 YP_178188.1 identified by similarity to SP:P09157; match to protein family HMM PF00081; match to protein family HMM PF02777 YP_178189.1 identified by match to protein family HMM PF03435 YP_178190.1 identified by match to protein family HMM PF00005 YP_178191.1 identified by match to protein family HMM PF00528 YP_178192.1 identified by similarity to GP:2125893; match to protein family HMM PF01547 YP_178194.1 identified by similarity to GP:14571873; match to protein family HMM PF04187 YP_178195.1 identified by similarity to GP:14571875; match to protein family HMM PF00593 YP_178196.1 identified by similarity to SP:P18783; match to protein family HMM PF01618 YP_178197.1 identified by similarity to SP:P18784; match to protein family HMM PF02472 YP_178198.1 identified by similarity to GB:AAK67308.1; match to protein family HMM TIGR01352 YP_178199.1 in Escherichia coli SbmA is involved in uptake of microcin J25; functions along with FhuA, TonB, and ExbB/D in this capacity; in Sinorhizobium meliloti, BacA is essential and required for symbiosis; defects appear to affect the cell envelope YP_178200.1 identified by similarity to GP:29895731; match to protein family HMM PF00571; match to protein family HMM PF01595; match to protein family HMM PF03471 YP_178201.1 identified by match to protein family HMM PF00149 YP_178202.1 identified by match to protein family HMM PF03831 YP_178203.1 identified by similarity to SP:P43932; match to protein family HMM PF03741 YP_178204.1 identified by match to protein family HMM PF00551; match to protein family HMM TIGR00639 YP_178205.1 identified by similarity to SP:Q9ZJM4; match to protein family HMM PF01256; match to protein family HMM PF03853; match to protein family HMM TIGR00196; match to protein family HMM TIGR00197 YP_178206.1 identified by similarity to OMNI:CT0467; match to protein family HMM PF01936 YP_178207.1 identified by match to protein family HMM PF01078; match to protein family HMM TIGR00368 YP_178208.1 cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+) YP_178209.1 hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates YP_178210.1 Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer YP_178211.1 involved in the first step of tetrahydrofolate biosynthesis; catalyzes the formation of formate and 2-amino-4-hydroxy-6-(erythro-1,2, 3-trihydroxypropyl)dihydropteridine triphosphate from GTP and water; forms a homopolymer YP_178212.1 involved in type III protein export during flagellum assembly YP_178213.1 Catalyzes first step of the de novo purine nucleotide biosynthetic pathway YP_178214.1 catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis YP_178215.1 identified by match to protein family HMM PF00004 YP_178218.1 identified by similarity to OMNI:PG0424 YP_178220.1 identified by match to protein family HMM PF03169; match to protein family HMM TIGR00728; match to protein family HMM TIGR00733 YP_178221.1 identified by similarity to SP:P31054; match to protein family HMM PF02673; match to protein family HMM TIGR00753 YP_178222.1 catalyzes the formation of threonyl-tRNA(Thr) from threonine and tRNA(Thr); catalyzes a two-step reaction, first charging a threonine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA YP_178223.1 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_178224.1 identified by similarity to SP:P24582; match to protein family HMM PF02086 YP_178231.1 identified by similarity to GB:CAA11507.1 YP_178234.1 identified by similarity to GP:886953 YP_178235.1 identified by similarity to SP:P76017 YP_178238.1 identified by similarity to SP:P14819; match to protein family HMM PF00717 YP_178240.1 identified by similarity to GP:29424997 YP_178243.1 identified by match to protein family HMM PF02086; match to protein family HMM TIGR00571 YP_178244.1 identified by similarity to SP:Q57777 YP_178245.1 identified by similarity to OMNI:WD0570; match to protein family HMM TIGR01369; match to protein family HMM TIGR01760 YP_178248.1 identified by similarity to GP:15278360 YP_178250.1 identified by similarity to SP:P22501 YP_178252.1 identified by similarity to OMNI:NTL03ST1666 YP_178254.1 identified by similarity to GB:AAP04455.1 YP_178255.1 identified by similarity to GB:AAL23025.1 YP_178256.1 identified by similarity to OMNI:PP3054; match to protein family HMM PF04865 YP_178257.1 identified by similarity to GP:8670757; match to protein family HMM PF04965 YP_178259.1 identified by similarity to SP:P31340; match to protein family HMM PF04717; match to protein family HMM TIGR01644 YP_178260.1 identified by similarity to GP:8670755 YP_178267.1 identified by similarity to SP:Q01267 YP_178269.1 identified by similarity to OMNI:PSPTO3407 YP_178270.1 identified by similarity to SP:O60488 YP_178272.1 identified by match to protein family HMM TIGR01630 YP_178274.1 identified by similarity to SP:Q01259; match to protein family HMM PF04233 YP_178275.1 identified by similarity to GB:AAP04463.1 YP_178276.1 identified by similarity to GP:915369; match to protein family HMM PF05489 YP_178277.1 identified by similarity to SP:P21679 YP_178278.1 identified by similarity to SP:Q47588 YP_178279.1 identified by similarity to SP:P39658; match to protein family HMM PF04231 YP_178280.1 identified by similarity to GP:4587560 YP_178281.1 identified by similarity to GB:AAA32406.1 YP_178285.1 identified by similarity to PIR:AI1363; match to protein family HMM TIGR01671 YP_178288.1 identified by similarity to SP:P06023 YP_178289.1 identified by similarity to OMNI:AF2353 YP_178292.1 identified by similarity to SP:P03763 YP_178293.1 identified by match to protein family HMM PF00665 YP_178295.1 identified by similarity to GB:AAL25916.1; match to protein family HMM PF00717; match to protein family HMM PF01381 YP_178297.1 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_178298.1 identified by match to protein family HMM PF00583 YP_178299.1 catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate YP_178300.1 identified by similarity to SP:P18544; match to protein family HMM PF00202; match to protein family HMM TIGR00707 YP_178301.1 catalyzes the methyl esterification of L-isoaspartyl residues that are formed in damaged proteins YP_178302.1 identified by match to protein family HMM PF00132 YP_178303.1 catalyzes the formation of 5-phospho-alpha-D-ribose 1-diphosphate and nicotinate from nicotinate D-ribonucleotide and diphosphate YP_178304.1 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_178305.1 identified by similarity to OMNI:HP1258 YP_178306.1 involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate YP_178307.1 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_178308.1 identified by similarity to SP:P33582; match to protein family HMM PF03840; match to protein family HMM TIGR00810 YP_178309.1 identified by similarity to SP:O25578; match to protein family HMM PF01027 YP_178310.1 identified by similarity to SP:P17582; match to protein family HMM PF00484 YP_178311.1 identified by similarity to SP:P77253; match to protein family HMM PF00924 YP_178312.1 identified by similarity to SP:P05343; match to protein family HMM PF01106; match to protein family HMM PF01592; match to protein family HMM PF04324 YP_178313.1 catalyzes the removal of sulfur from cysteine to form alanine YP_178314.1 identified by similarity to GP:23498399 YP_178315.1 identified by similarity to SP:P55874; match to protein family HMM PF01632; match to protein family HMM TIGR00001 YP_178316.1 binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit YP_178317.1 identified by similarity to GP:27352453 YP_178318.1 identified by similarity to GP:28203787 YP_178320.1 identified by match to protein family HMM PF00083 YP_178322.1 MoaC; along with MoaA is involved in conversion of a guanosine derivative into molybdopterin precursor Z; involved in molybdenum cofactor biosynthesis YP_178323.1 identified by similarity to SP:O25237 YP_178325.1 identified by match to protein family HMM PF03372; match to protein family HMM TIGR00195; match to protein family HMM TIGR00633 YP_178326.1 identified by match to protein family HMM PF00884; match to protein family HMM PF02418 YP_178327.1 identified by similarity to SP:P00556; match to protein family HMM PF01219 YP_178329.1 catalyzes the formation of N-carbamoyl-L-aspartate from (S)-dihydroorotate in pyrimidine biosynthesis YP_178330.1 identified by similarity to OMNI:BBQ67; match to protein family HMM TIGR01612 YP_178332.1 identified by similarity to SP:P39216; match to protein family HMM PF00015; match to protein family HMM PF00672; match to protein family HMM PF02743; match to protein family HMM PF05581 YP_178333.1 identified by similarity to SP:P24198; match to protein family HMM PF02535 YP_178334.1 identified by similarity to OMNI:NTL01CJ00137; match to protein family HMM PF00015 YP_178337.1 identified by similarity to OMNI:NTL01HP00232; match to protein family HMM PF01145 YP_178338.1 catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids YP_178339.1 identified by match to protein family HMM PF01361 YP_178340.1 identified by match to protein family HMM PF00578 YP_178341.1 identified by similarity to OMNI:NTL01AA00490; match to protein family HMM PF02677 YP_178342.1 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_178343.1 catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis YP_178344.1 binds and unfolds substrates as part of the ClpXP protease YP_178345.1 functions in MreBCD complex in some organisms YP_178346.1 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_178347.1 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_178348.1 identified by similarity to OMNI:NTL01HP00845 YP_178349.1 Important for the balance of metabolites in the pentose-phosphate pathway YP_178350.1 identified by match to protein family HMM PF00702; match to protein family HMM TIGR00338; match to protein family HMM TIGR01488 YP_178351.1 identified by similarity to SP:P39802; match to protein family HMM PF01584 YP_178352.1 identified by similarity to GP:3493635; match to protein family HMM PF00072; match to protein family HMM PF01584; match to protein family HMM PF01627; match to protein family HMM PF02518; match to protein family HMM PF02895 YP_178353.1 identified by similarity to SP:P37599; match to protein family HMM PF00072; match to protein family HMM PF01584 YP_178354.1 identified by similarity to OMNI:HP0394 YP_178355.1 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_178356.1 catalyzes the formation of lipid A disaccharide from UDP-2,3-diacylglucosamine and 2,3-diacylglucosamine-1-phosphate, lipid A disaccharide is a precursor of lipid A that anchors LPS to the OM YP_178357.1 identified by similarity to GP:558481; similarity to PIR:C41161 YP_178358.1 catalyzes the conversion of a phosphate monoester to an alcohol and a phosphate YP_178359.1 identified by match to protein family HMM PF00899 YP_178360.1 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_178361.1 catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine YP_178362.1 catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate YP_178363.1 identified by similarity to SP:P14489; match to protein family HMM PF00905 YP_178364.1 identified by similarity to SP:P09833; match to protein family HMM PF00005 YP_178365.1 identified by similarity to SP:P37731; match to protein family HMM PF00528 YP_178366.1 identified by match to protein family HMM PF03459 YP_178367.1 identified by similarity to SP:Q08383; match to protein family HMM PF01547; match to protein family HMM TIGR01256 YP_178368.1 identified by match to protein family HMM TIGR02072 YP_178369.1 identified by similarity to OMNI:NTL01PM1904; match to protein family HMM PF04301 YP_178370.1 identified by similarity to SP:P53556; match to protein family HMM PF00155 YP_178371.1 catalyzes the formation of S-adenosyl-4-methylthionine-2-oxobutanoate and 7,8-diaminononanoate from S-adenosyl-L-methionine and 8-amino-7-oxononanoate YP_178372.1 identified by match to protein family HMM TIGR00347 YP_178373.1 identified by similarity to SP:P14319; match to protein family HMM PF00893 YP_178374.1 identified by match to protein family HMM PF00893 YP_178375.1 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_178376.1 Enables the recycling of peptidyl-tRNAs produced at termination of translation YP_178377.1 identified by similarity to GP:12228593; match to protein family HMM PF03739 YP_178378.1 identified by similarity to SP:P23630; match to protein family HMM PF00278; match to protein family HMM PF02784; match to protein family HMM TIGR01048 YP_178379.1 identified by match to protein family HMM TIGR01460 YP_178380.1 identified by similarity to OMNI:NTL01CJ00292; match to protein family HMM PF00800; match to protein family HMM PF01817; match to protein family HMM PF01842; match to protein family HMM TIGR01807 YP_178381.1 catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis YP_178382.1 the MS-ring anchors the flagellum to the cytoplasmic membrane; part of the flagellar basal body which consists of four rings L, P, S, and M mounted on a central rod YP_178383.1 One of three proteins involved in switching the direction of the flagellar rotation YP_178384.1 binds to and inhibits the function of flagella specific ATPase FliI YP_178385.1 catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate YP_178386.1 identified by match to protein family HMM PF01475 YP_178388.1 Catalyzes the carbon methylation reaction in the biosynthesis of ubiquinone YP_178389.1 bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides YP_178390.1 catalyzes the formation of 3-phosphonooxypyruvate and glutamate from O-phospho-L-serine and 2-oxoglutarate; required both in major phosphorylated pathway of serine biosynthesis and in the biosynthesis of pyridoxine YP_178391.1 identified by match to protein family HMM PF01042 YP_178392.1 FabH; beta-ketoacyl-ACP synthase III; catalyzes the condensation of acetyl-CoA with malonyl-ACP to initiate cycles of fatty acid elongation; differs from 3-oxoacyl-ACP synthase I and II in that it utilizes CoA thioesters as primers rather than acyl-ACPs YP_178393.1 involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY YP_178394.1 some L32 proteins have zinc finger motifs consisting of CXXC while others do not YP_178395.1 identified by similarity to OMNI:HP0199 YP_178396.1 catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate YP_178397.1 identified by similarity to GP:1518927; match to protein family HMM PF00037 YP_178398.1 identified by similarity to OMNI:NTL01CJ00310; match to protein family HMM PF00578 YP_178399.1 membrane protein responsible for substrate specificity switching from rod/hook-type export to filament-type export YP_178400.1 with MotA forms the ion channels that couple flagellar rotation to proton/sodium motive force across the membrane and forms the stator elements of the rotary flagellar machine YP_178401.1 With MotB forms the ion channels that couple flagellar rotation to proton/sodium motive force across the membrane and forms the stator elements of the rotary flagellar machine YP_178402.1 has 3'-5' exonuclease, 5'-3' exonuclease and 5'-3'polymerase activities, primarily functions to fill gaps during DNA replication and repair YP_178403.1 identified by match to protein family HMM PF00083 YP_178404.1 identified by match to protein family HMM PF01156 YP_178405.1 identified by similarity to OMNI:NTL01MM0466 YP_178409.1 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_178410.1 identified by similarity to OMNI:NTL01HP00210; match to protein family HMM PF01925 YP_178413.1 identified by similarity to SP:Q02001; match to protein family HMM PF00425 YP_178414.1 identified by similarity to SP:P00904; match to protein family HMM PF00117; match to protein family HMM PF00591; match to protein family HMM PF02885; match to protein family HMM TIGR00566; match to protein family HMM TIGR01245 YP_178415.1 identified by match to protein family HMM PF00697 YP_178416.1 catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate YP_178417.1 catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis YP_178419.1 One of three proteins involved in switching the direction of the flagellar rotation YP_178420.1 identified by similarity to GB:AAG29563.1 YP_178421.1 identified by match to protein family HMM PF02541 YP_178422.1 identified by similarity to SP:P00208; match to protein family HMM PF00037 YP_178423.1 identified by similarity to OMNI:NTL01HP00378; match to protein family HMM PF00072; match to protein family HMM PF00486 YP_178424.1 identified by match to protein family HMM TIGR00526 YP_178425.1 involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsX YP_178426.1 identified by similarity to SP:P14532; match to protein family HMM PF03150 YP_178428.1 catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate YP_178429.1 lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis YP_178430.1 identified by similarity to SP:Q9ZJD5; match to protein family HMM PF03653; match to protein family HMM TIGR00701 YP_178431.1 catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III YP_178433.1 identified by similarity to GP:18496808; match to protein family HMM PF02321; match to protein family HMM TIGR01845 YP_178434.1 identified by similarity to GP:18496807; match to protein family HMM PF00873; match to protein family HMM TIGR00915 YP_178435.1 identified by similarity to SP:P31223; similarity to GB:AAL74244.1; match to protein family HMM PF00529; match to protein family HMM TIGR01730 YP_178436.1 identified by match to protein family HMM PF00440 YP_178437.1 identified by match to protein family HMM PF00037 YP_178438.1 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_178439.1 identified by similarity to GP:12228587 YP_178440.1 identified by match to protein family HMM PF03738 YP_178441.1 Involved in the metabolism of aromatic amino acids YP_178442.1 nucleotide binding property based on structural studies of Haemophilus influenzae crystallized protein in PDB Accession Number 1IN0 and NMR studies of Escherichia coli YajQ; the YajQ protein from Pseudomonas synringae appears to play a role in activation of bateriophage phi6 segment L transcription YP_178445.1 identified by match to protein family HMM PF00004 YP_178446.1 identified by match to protein family HMM PF05252 YP_178447.1 in Escherichia coli this periplasmic enzyme was found to encode the periplasmic catalytic subunit of an oxidoreductase; sulfite oxidase activity not demonstrated; requires inner membrane anchor protein YedZ YP_178449.1 OMP decarboxylase; OMPDCase; OMPdecase; type 1 subfamily; involved in last step of pyrimidine biosynthesis; converts orotidine 5'-phosphate to UMP and carbon dioxide; OMP decarboxylase; OMPDCase; OMPdecase YP_178450.1 Regulates rRNA biosynthesis by transcriptional antitermination YP_178451.1 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_178452.1 catalyzes the formation of 2-dehydro-3-deoxy-D-octonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate in LPS biosynthesis YP_178453.1 identified by similarity to SP:Q9ZJZ2; match to protein family HMM PF00892 YP_178454.1 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_178455.1 catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis YP_178456.1 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_178457.1 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_178458.1 identified by match to protein family HMM PF00515 YP_178459.1 identified by similarity to GP:25989709 YP_178460.1 identified by match to protein family HMM PF00224; match to protein family HMM PF02887; match to protein family HMM TIGR01064 YP_178462.1 type III; catalyzes the formation of (R)-4'-phosphopantothenate from (R)-pantothenate in coenzyme A biosynthesis; type III pantothenate kinases are not subject to feedback inhibition from coenzyme A and have a high Km for ATP YP_178464.1 identified by similarity to OMNI:NTL01HP00790 YP_178465.1 identified by similarity to OMNI:NTL01HP00791 YP_178466.1 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_178467.1 identified by match to protein family HMM PF02674 YP_178468.1 identified by similarity to SP:P06975; match to protein family HMM PF01475 YP_178469.1 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_178470.1 catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate YP_178471.1 identified by similarity to OMNI:HP0184 YP_178472.1 identified by similarity to GP:12228583 YP_178473.1 AroE; catalyzes the conversion of shikimate to 3-dehydroshikimate YP_178475.1 transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein YP_178476.1 part of three member fumarate reductase enzyme complex FrdABC which catalyzes the reduction of fumarate to succinate during anaerobic respiration; FrdAB are the catalytic subcomplex consisting of a flavoprotein subunit and an iron-sulfur subunit, respectively; FrdC is the cytochrome b-556 subunit YP_178477.1 part of three member fumarate reductase enzyme complex FrdABC which catalyzes the reduction of fumarate to succinate during anaerobic respiration; FrdAB are the catalytic subcomplex consisting of a flavoprotein subunit and an iron-sulfur subunit, respectively; FrdC is the cytochrome b-556 subunit; the catalytic subunits are similar to succinate dehydrogenase SdhAB YP_178478.1 part of three member fumarate reductase enzyme complex FrdABC which catalyzes the reduction of fumarate to succinate during anaerobic respiration; FrdAB are the catalytic subcomplex consisting of a flavoprotein subunit and an iron-sulfur subunit, respectively; FrdC is the cytochrome b-556 subunit; the catalytic subunits are similar to succinate dehydrogenase SdhAB YP_178481.1 identified by similarity to GP:17864805 YP_178482.1 identified by similarity to OMNI:NTL03PA02264 YP_178487.1 identified by match to protein family HMM PF01230 YP_178488.1 identified by similarity to OMNI:HP1286; match to protein family HMM PF04264 YP_178489.1 identified by similarity to OMNI:VCA0560 YP_178494.1 identified by similarity to SP:P75790; match to protein family HMM PF00005 YP_178496.1 identified by similarity to GP:552054 YP_178497.1 identified by similarity to OMNI:HP1485; match to protein family HMM PF01205 YP_178499.1 identified by similarity to OMNI:NTL01HP01148 YP_178501.1 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_178502.1 First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan YP_178503.1 catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate YP_178504.1 Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis YP_178505.1 identified by similarity to OMNI:NTL01FN0973 YP_178507.1 identified by match to protein family HMM PF00890; match to protein family HMM PF02910 YP_178508.1 identified by match to protein family HMM PF00111; match to protein family HMM TIGR00384 YP_178509.1 identified by similarity to GP:3378542; match to protein family HMM PF02754 YP_178510.1 identified by match to protein family HMM PF03070 YP_178512.1 carries the fatty acid chain in fatty acid biosynthesis YP_178513.1 FabF; beta-ketoacyl-ACP synthase II, KASII; catalyzes a condensation reaction in fatty acid biosynthesis: addition of an acyl acceptor of two carbons from malonyl-ACP; required for the elongation of short-chain unsaturated acyl-ACP YP_178514.1 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_178515.1 identified by match to protein family HMM PF00293; match to protein family HMM TIGR00052 YP_178516.1 identified by similarity to GP:1840146; match to protein family HMM PF00015 YP_178517.1 identified by similarity to OMNI:NTL01CJ00422; match to protein family HMM PF04325 YP_178518.1 required for 70S ribosome assembly YP_178519.1 catalyzes the interconversion of D-ribulose 5-phosphate to xylulose 5-phosphate YP_178520.1 3'-5' exonuclease of DNA polymerase III YP_178521.1 required for the synthesis of the hydromethylpyrimidine moiety of thiamine YP_178523.1 identified by similarity to GP:12228461 YP_178525.1 identified by similarity to OMNI:NTL01HP00254; match to protein family HMM PF04028 YP_178526.1 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_178527.1 identified by similarity to OMNI:NTL01HP00252 YP_178528.1 modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination YP_178529.1 identified by similarity to GP:2613096; similarity to OMNI:CT0102; match to protein family HMM PF04332 YP_178530.1 identified by similarity to GB:AAP77588.1; match to protein family HMM PF04055; match to protein family HMM TIGR00423 YP_178531.1 identified by match to protein family HMM PF05193 YP_178532.1 catalyzes branch migration in Holliday junction intermediates YP_178533.1 identified by similarity to GB:AAP76761.1 YP_178534.1 identified by similarity to GP:4585799; match to protein family HMM PF00027 YP_178535.1 identified by match to protein family HMM PF00528; match to protein family HMM TIGR01726 YP_178536.1 identified by match to protein family HMM PF00528; match to protein family HMM TIGR01726 YP_178537.1 identified by similarity to SP:P48243; match to protein family HMM PF00005 YP_178538.1 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_178539.1 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_178540.1 forms a complex with SecY and SecG; SecYEG forms a protein-conducting channel to which secA binds and translocates targeted polypeptides across the cytoplasmic membrane, a process driven by ATP and a proton-motive force YP_178541.1 Modulates Rho-dependent transcription termination YP_178542.1 binds directly to 23S ribosomal RNA YP_178543.1 in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA YP_178544.1 binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit YP_178545.1 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_178546.1 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates; beta subunit is part of the catalytic core which binds with a sigma factor to produce the holoenzyme YP_178547.1 identified by similarity to SP:O83270; match to protein family HMM PF00623; match to protein family HMM PF04983; match to protein family HMM PF04997; match to protein family HMM PF04998; match to protein family HMM PF05000; match to protein family HMM TIGR01369; match to protein family HMM TIGR01612 YP_178548.1 identified by match to protein family HMM PF01614 YP_178550.1 identified by similarity to SP:Q04796; match to protein family HMM PF00701 YP_178551.1 identified by similarity to SP:Q44470; match to protein family HMM PF00083 YP_178552.1 identified by match to protein family HMM PF00106 YP_178553.1 identified by match to protein family HMM PF00083; match to protein family HMM TIGR00885 YP_178554.1 identified by similarity to OMNI:NTL01CJ00461 YP_178555.1 identified by similarity to OMNI:NTL01CJ00462; match to protein family HMM PF05336 YP_178556.1 NAD-linked YP_178557.1 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_178558.1 binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit YP_178559.1 EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene YP_178560.1 identified by match to protein family HMM PF00589 YP_178561.1 identified by match to protein family HMM TIGR01764 YP_178562.1 identified by match to protein family HMM PF00805 YP_178564.1 identified by similarity to GB:AAM53132.1 YP_178566.1 identified by similarity to GB:CAA65779.1; match to protein family HMM PF01555 YP_178567.1 identified by similarity to OMNI:NTL01LI2568 YP_178573.1 identified by similarity to GP:9944309 YP_178578.1 identified by similarity to OMNI:CT1793 YP_178582.1 identified by similarity to GP:27359896; match to protein family HMM PF01223 YP_178584.1 identified by similarity to GP:29337437 YP_178585.1 identified by similarity to GB:AAN53719.1; match to protein family HMM PF00717 YP_178592.1 identified by similarity to SP:Q9T1T1 YP_178593.1 identified by similarity to SP:P27753 YP_178610.1 identified by similarity to OMNI:NTL03ST1666 YP_178619.1 identified by similarity to OMNI:NTL01HP01386 YP_178620.1 identified by similarity to SP:P56132; match to protein family HMM PF03692 YP_178621.1 identified by similarity to OMNI:NTL01HP00259 YP_178622.1 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_178623.1 identified by match to protein family HMM PF01230 YP_178624.1 catalyzes the selenophosphate-dependent transfer of selenium from selenophosphate for conversion of 2-thiouridine to 2-selenouridine at the wobble position in tRNA YP_178625.1 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_178626.1 identified by match to protein family HMM PF01408 YP_178627.1 identified by match to protein family HMM PF01041 YP_178628.1 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_178629.1 Maf; overexpression in Bacillus subtilis inhibits septation in the dividing cell YP_178630.1 identified by similarity to SP:P02918; match to protein family HMM PF00905; match to protein family HMM PF00912 YP_178631.1 identified by similarity to SP:Q9RA63; match to protein family HMM PF00004; match to protein family HMM PF02861 YP_178632.1 identified by similarity to OMNI:NTL01TE1575; match to protein family HMM PF02583 YP_178633.1 identified by similarity to SP:Q44879; match to protein family HMM PF00595; match to protein family HMM PF03572; match to protein family HMM TIGR00225 YP_178634.1 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_178635.1 identified by match to protein family HMM PF02700; match to protein family HMM TIGR00302 YP_178636.1 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_178637.1 identified by similarity to OMNI:NTL01HP01259 YP_178638.1 identified by similarity to SP:O25903; match to protein family HMM PF01553 YP_178639.1 identified by similarity to SP:P37002; match to protein family HMM PF02537; match to protein family HMM TIGR00494 YP_178640.1 molecular chaperone YP_178641.1 identified by similarity to OMNI:NTL01OI2305 YP_178643.1 identified by match to protein family HMM PF02690 YP_178644.1 identified by similarity to SP:P08149; match to protein family HMM PF00905; match to protein family HMM PF03717 YP_178645.1 forms a junction between the M-ring and FlgB during flagella biosynthesis YP_178646.1 with FlgF and B makes up the proximal portion of the flagellar basal body rod YP_178647.1 with FlgF and C makes up the proximal portion of the flagellar basal body rod; Vibrio parahaemolyticus protein is associated with the polar flagella YP_178648.1 identified by similarity to GB:AAP78169.1; match to protein family HMM PF02618 YP_178649.1 identified by similarity to OMNI:HP0586 YP_178650.1 identified by match to protein family HMM PF03971; match to protein family HMM TIGR00178 YP_178651.1 identified by similarity to SP:P49814; match to protein family HMM PF00056; match to protein family HMM PF02866 YP_178652.1 catalyzes the interconversion of succinyl-CoA and succinate YP_178653.1 identified by similarity to SP:P07459; match to protein family HMM PF00549; match to protein family HMM PF02629; match to protein family HMM TIGR01019 YP_178654.1 identified by similarity to GP:2935178; match to protein family HMM PF00037 YP_178655.1 Couples the complete acetyl-CoA oxidation to aromatic ring reduction by the use of the low-potential electron shuttle ferredoxin YP_178656.1 Catalyzes the two-electron reduction of the C2 and C3(1) diene system of 15,16-dihydrobiliverdin YP_178657.1 Catalyzes the ferredoxin-dependent oxidative decarboxylation of arylpyruvates YP_178659.1 identified by similarity to OMNI:NTL01HP00225 YP_178660.1 identified by similarity to SP:Q53479; match to protein family HMM PF00348 YP_178661.1 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_178662.1 catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro) YP_178664.1 transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis YP_178665.1 identified by similarity to SP:P26615; match to protein family HMM PF01977; match to protein family HMM TIGR00148 YP_178666.1 possibly involved in flagella export YP_178667.1 Also called hook-associated protein 2; involved in flagellin assembly YP_178668.1 flagellin specific chaperone YP_178670.1 Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA YP_178671.1 identified by similarity to OMNI:CC1200 YP_178672.1 identified by similarity to PIR:AF0329 YP_178673.1 identified by similarity to OMNI:CC1198 YP_178674.1 identified by similarity to PIR:C95236 YP_178675.1 identified by similarity to OMNI:PP1699 YP_178676.1 identified by similarity to OMNI:EF0906 YP_178677.1 Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway YP_178678.1 identified by match to protein family HMM PF00070 YP_178679.1 identified by similarity to GP:27360586 YP_178680.1 unwinds double stranded DNA YP_178683.1 identified by similarity to GP:4155226 YP_178685.1 identified by similarity to OMNI:NTL01HP00661 YP_178686.1 identified by similarity to SP:P52133 YP_178687.1 bifunctional enzyme DHBP synthase/GTP cyclohydrolase II; functions in riboflavin synthesis; converts GTP to 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine; converts ribulose 5-phopshate to 3,4-dihydroxy-2-butanone 4-phosphate YP_178688.1 identified by match to protein family HMM PF02637 YP_178689.1 catalyzes the formation of 2-acetolactate from pyruvate, leucine resistant; also known as acetolactate synthase 3 large subunit YP_178690.1 with IlvI catalyzes the formation of 2-acetolactate from pyruvate, the small subunit is required for full activity and valine sensitivity; E.coli produces 3 isoenzymes of acetolactate synthase which differ in specificity to substrates, valine sensitivity and affinity for cofactors; also known as acetolactate synthase 3 small subunit YP_178691.1 adds the O-linked and N-linked 3(R)-hydroxy fatty acids to the glucosamine disaccharide during lipid A biosynthesis YP_178692.1 Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step YP_178693.1 identified by similarity to SP:P27857; match to protein family HMM PF00902; match to protein family HMM TIGR00945 YP_178694.1 mediates the export of protein precursors bearing twin-arginine signal peptides YP_178695.1 catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III YP_178696.1 hydrolyzes diadenosine polyphosphate YP_178697.1 catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP, in Bacillus, lysine sensitive; regulated by response to starvation. YP_178698.1 identified by similarity to PIR:F64673 YP_178699.1 catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the delta' subunit seems to interact with the gamma subunit to transfer the beta subunit on the DNA YP_178700.1 identified by match to protein family HMM PF00809; match to protein family HMM TIGR01496 YP_178701.1 this protein catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction; essential for DNA replication and repair of damaged DNA; similar to ligase LigB YP_178703.1 identified by similarity to SP:Q06803; match to protein family HMM PF01479; match to protein family HMM PF01728; match to protein family HMM TIGR00478 YP_178704.1 catalyzes the formation of FMN from riboflavin and the formation of FAD from FMN; in Bacillus the ribC gene has both flavokinase and FAD synthetase activities YP_178705.1 identified by match to protein family HMM TIGR00740 YP_178706.1 identified by similarity to GP:498878 YP_178708.1 identified by similarity to GB:AAP77676.1; match to protein family HMM PF03458 YP_178709.1 identified by similarity to GP:28805682; match to protein family HMM PF01223 YP_178710.1 identified by similarity to SP:P20625; match to protein family HMM PF00730; match to protein family HMM TIGR01083 YP_178711.1 identified by similarity to SP:Q46105; match to protein family HMM PF00639 YP_178712.1 catalyzes the formation of glycerone phosphate and glyceraldehyde 3-phosphate from fructose 1,6, bisphosphate YP_178714.1 identified by similarity to SP:P28612; match to protein family HMM PF00691 YP_178715.1 identified by similarity to OMNI:SO1978 YP_178716.1 identified by similarity to SP:P45320; match to protein family HMM PF00209 YP_178717.1 identified by similarity to GP:29896050; match to protein family HMM PF03473; match to protein family HMM PF03475 YP_178718.1 identified by similarity to SP:P36655; match to protein family HMM PF02683 YP_178719.1 identified by similarity to OMNI:NTL01CE2558; match to protein family HMM PF03976 YP_178720.1 identified by match to protein family HMM PF01546; match to protein family HMM TIGR01891 YP_178721.1 identified by similarity to SP:P75830; match to protein family HMM PF00529; match to protein family HMM TIGR01730 YP_178722.1 identified by similarity to SP:P75831; match to protein family HMM PF00005; match to protein family HMM PF02687 YP_178723.1 identified by match to protein family HMM PF02321 YP_178724.1 identified by similarity to OMNI:NTL01LL1763 YP_178725.1 identified by similarity to OMNI:NMB1274; match to protein family HMM PF04311 YP_178726.1 identified by similarity to GB:AAB09781.1; match to protein family HMM PF03062 YP_178727.1 identified by similarity to SP:P52093; match to protein family HMM PF00210 YP_178728.1 identified by match to protein family HMM PF01547 YP_178729.1 identified by match to protein family HMM PF00528; match to protein family HMM TIGR02138 YP_178730.1 identified by match to protein family HMM PF00528 YP_178731.1 ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation YP_178733.1 identified by match to protein family HMM PF01554; match to protein family HMM TIGR00797 YP_178734.1 identified by similarity to GP:28203619; match to protein family HMM PF01863 YP_178736.1 identified by similarity to SP:Q02987; match to protein family HMM PF00708; match to protein family HMM PF01300; match to protein family HMM TIGR00143 YP_178737.1 identified by similarity to SP:P24190; match to protein family HMM PF01495; match to protein family HMM TIGR00073 YP_178738.1 identified by similarity to GP:15430693; match to protein family HMM PF01455; match to protein family HMM TIGR00074 YP_178739.1 identified by similarity to SP:P24192; match to protein family HMM PF01924; match to protein family HMM TIGR00075 YP_178740.1 identified by similarity to SP:P40595; match to protein family HMM PF00586; match to protein family HMM PF02769 YP_178741.1 identified by similarity to SP:P24189; match to protein family HMM PF01155; match to protein family HMM TIGR00100 YP_178742.1 identified by similarity to SP:P08763; match to protein family HMM PF01555 YP_178743.1 identified by similarity to SP:P08764 YP_178744.1 required for the assembly and function of the DNAX complex which is required for the assembly of the beta subunit onto primed DNA YP_178745.1 identified by match to protein family HMM PF00773 YP_178746.1 catalyzes the formation of (R)-2,3-dihydroxy-3-methylbutanoate from (S)-2-hydroxy-2-methyl-3-oxobutanoate in valine and isoleucine biosynthesis YP_178747.1 identified by similarity to OMNI:BB0770; match to protein family HMM PF04748 YP_178748.1 identified by similarity to OMNI:HP0333; match to protein family HMM PF02481; match to protein family HMM TIGR00732 YP_178749.1 similar to RuvC resolvase with substantial differences; NMR structural information suggests this protein is monomeric; unknown cellular function YP_178750.1 identified by similarity to OMNI:NTL01PH01412; match to protein family HMM PF01189 YP_178751.1 this stereospecific enzymes reduces the S isomer of methionine sulfoxide while MsrB reduces the R form; provides protection against oxidative stress YP_178752.1 catalyzes the hydrolysis of pyrophosphate YP_178753.1 essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP YP_178754.1 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_178755.1 catalyzes the phosphorylation of NAD to NADP YP_178756.1 identified by similarity to SP:O25943; match to protein family HMM TIGR00634 YP_178757.1 identified by similarity to PIR:C97489; match to protein family HMM PF00072; match to protein family HMM PF00990; match to protein family HMM TIGR00254 YP_178758.1 identified by match to protein family HMM PF01026; match to protein family HMM TIGR00010 YP_178759.1 identified by similarity to SP:P23931; match to protein family HMM PF01464; match to protein family HMM PF01476 YP_178760.1 identified by similarity to SP:Q9ZJ38; match to protein family HMM PF03330; match to protein family HMM TIGR00413 YP_178761.1 identified by match to protein family HMM TIGR01662; match to protein family HMM TIGR01670 YP_178762.1 identified by similarity to SP:Q60303 YP_178763.1 identified by match to protein family HMM PF03968 YP_178764.1 binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential YP_178766.1 identified by similarity to SP:P08150; match to protein family HMM PF00905; match to protein family HMM PF03717 YP_178767.1 identified by match to protein family HMM PF00557 YP_178768.1 identified by similarity to SP:P36574; match to protein family HMM PF00854; match to protein family HMM TIGR00924 YP_178772.1 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_178773.1 heat shock protein involved in degradation of misfolded proteins YP_178774.1 heat shock protein involved in degradation of misfolded proteins YP_178775.1 in Escherichia coli this protein is wrapped around the base of the L1 stalk YP_178776.1 catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming YP_178777.1 identified by similarity to OMNI:NTL03CP2478; match to protein family HMM PF01479 YP_178778.1 identified by similarity to OMNI:NTL01HP00650; match to protein family HMM PF02367; match to protein family HMM TIGR00150 YP_178779.1 identified by similarity to OMNI:NMB0356; match to protein family HMM PF00005 YP_178780.1 sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; sigma 54 factor is responsible for the expression of enzymes involved in nitrogen assimilation and metabolism; the rhizobia often have 2 copies of this sigma factor; in Rhizobium etli RpoN1 shown to be involved in the assimilation of several nitrogen and carbon sources during free-living aerobic growth and RpoN2 is involved in symbiotic nitrogen fixation; in Bradyrhizobium both RpoN1 and N2 are functional in free-living and symbiotic conditions, rpoN1 gene was regulated in response to oxygen YP_178781.1 functions in anaerobic transport of C4-dicarboxylate compounds such as fumarate; similar to DcuA; DcuA and DcuB function as independent and mutually redundant C4-dicarboxylate (aspartate, malate, fumarate and succinate) transporters YP_178783.1 identified by similarity to SP:P03961; match to protein family HMM PF02669; match to protein family HMM TIGR00681 YP_178784.1 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_178785.1 identified by similarity to OMNI:HP0385 YP_178786.1 identified by similarity to OMNI:NTL02ST2131 YP_178788.1 binding of PriA to forked DNA starts the assembly of the primosome, also possesses 3'-5' helicase activity YP_178789.1 identified by similarity to GB:AAD50522.1 YP_178790.1 catalyzes the conversion of 2C-methyl-D-erythritol 2,4-cyclodiphosphate into 4-hydroxy-3-methyl-2-en-1-yl diphosphate; involved in isoprenoid synthesis YP_178791.1 part of the flagellar basal body which consists of four rings L,P, S and M mounted on a central rod YP_178792.1 identified by match to protein family HMM PF01515; match to protein family HMM TIGR00651 YP_178793.1 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_178794.1 identified by similarity to OMNI:BBE02; match to protein family HMM PF04313; match to protein family HMM TIGR01612 YP_178797.1 identified by match to protein family HMM PF01795; match to protein family HMM TIGR00006 YP_178798.1 identified by similarity to SP:P77241 YP_178799.1 identified by similarity to SP:P06137; match to protein family HMM PF02491; match to protein family HMM TIGR01174 YP_178800.1 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_178801.1 identified by similarity to SP:P39752; match to protein family HMM PF00460 YP_178802.1 makes up the distal portion of the flagellar basal body rod YP_178803.1 identified by similarity to SP:P06711; match to protein family HMM PF00120; match to protein family HMM PF03951; match to protein family HMM TIGR00653 YP_178805.1 identified by similarity to OMNI:HP0170 YP_178806.1 identified by similarity to SP:P76403; match to protein family HMM PF01136 YP_178807.1 Catalyzes a step in the de novo purine nucleotide biosynthetic pathway YP_178808.1 glycine--tRNA ligase alpha chain; GlyRS; class II aminoacyl tRNA synthetase; tetramer of alpha(2)beta(2); catalyzes a two-step reaction; first charging a glycine molecule by linking its carboxyl group to the alpha-phosphate of ATP; second by transfer of the aminoacyl-adenylate to its tRNA YP_178809.1 identified by similarity to SP:O25613; match to protein family HMM PF01784; match to protein family HMM TIGR00486 YP_178810.1 identified by similarity to OMNI:HP0958; match to protein family HMM PF02591 YP_178811.1 catalyzes the transfer of 2-keto-3-deoxy-D-manno-octulosonic acid to lipid A YP_178812.1 identified by match to protein family HMM PF00849 YP_178813.1 identified by similarity to SP:P37105; 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_178814.1 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_178815.1 identified by similarity to OMNI:HP1150 YP_178816.1 identified by similarity to SP:P21504; match to protein family HMM PF01782; match to protein family HMM PF05239 YP_178817.1 methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA YP_178818.1 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_178819.1 identified by match to protein family HMM PF00576 YP_178820.1 identified by match to protein family HMM PF01474; match to protein family HMM TIGR01358 YP_178821.1 identified by match to protein family HMM PF03960 YP_178822.1 catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; main replicative polymerase YP_178823.1 identified by match to protein family HMM PF01168; match to protein family HMM TIGR00044 YP_178824.1 identified by similarity to GP:1857639; match to protein family HMM PF00669 YP_178825.1 identified by similarity to PIR:B71953 YP_178826.1 identified by match to protein family HMM TIGR00536 YP_178827.1 identified by match to protein family HMM PF01435 YP_178829.1 forms a trimer; related to eukaryotic protein gephyrin; functions during molybdenum cofactor biosynthesis YP_178830.1 identified by similarity to SP:P27841; match to protein family HMM PF01544; match to protein family HMM TIGR00383 YP_178831.1 identified by similarity to SP:P06997; match to protein family HMM PF01547 YP_178832.1 identified by similarity to OMNI:NTL01YP3429 YP_178833.1 identified by similarity to OMNI:NTL03PA03251 YP_178834.1 identified by match to protein family HMM PF00528 YP_178835.1 identified by match to protein family HMM PF00528 YP_178836.1 identified by similarity to PIR:G75124; match to protein family HMM PF00005 YP_178837.1 identified by match to protein family HMM PF00702; match to protein family HMM TIGR01488; match to protein family HMM TIGR01490 YP_178838.1 identified by similarity to SP:Q46125; match to protein family HMM PF00497 YP_178840.1 identified by similarity to OMNI:NTL03PA04082; match to protein family HMM PF05860; match to protein family HMM TIGR01901 YP_178842.1 identified by similarity to GP:26453556 YP_178844.1 identified by similarity to SP:Q04593 YP_178845.1 identified by similarity to GP:9755165 YP_178847.1 identified by similarity to SP:O07650; match to protein family HMM PF03544; match to protein family HMM TIGR01352 YP_178849.1 identified by similarity to GP:2199510; match to protein family HMM PF00593 YP_178850.1 Acts as a negative regulator of the grpE-dnaK-dnaJ and groELS class I heat shock operons by preventing heat-shock induction YP_178851.1 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_178852.1 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_178853.1 identified by similarity to OMNI:NTL01XA0250 YP_178854.1 identified by similarity to OMNI:HP0902 YP_178855.1 catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate YP_178856.1 identified by similarity to SP:Q06750; match to protein family HMM PF00132; match to protein family HMM TIGR01172 YP_178857.1 catalyzes the formation of agmatine from arginine in putrescine and spermidine biosynthesis YP_178858.1 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_178859.1 catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP) YP_178860.1 Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA YP_178861.1 catalyzes the formation of 2-octaprenylphenol from 3-octaprenyl-4-hydroxybenzoate YP_178862.1 required for the assembly of the flagellar basal body P-ring YP_178863.1 identified by similarity to OMNI:PP0112; match to protein family HMM PF03180 YP_178864.1 identified by similarity to GP:28203472; match to protein family HMM PF03180 YP_178865.1 identified by similarity to OMNI:NTL01FN1234; match to protein family HMM PF03180 YP_178866.1 identified by similarity to OMNI:NTL01CA0974; match to protein family HMM PF00528 YP_178867.1 identified by similarity to GB:AAO35916.1; match to protein family HMM PF00005 YP_178868.1 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_178870.1 identified by similarity to SP:P03018; match to protein family HMM PF00580 YP_178871.1 identified by similarity to GP:558481; similarity to PIR:B41161 YP_178872.1 identified by similarity to SP:P37901; match to protein family HMM PF00578 YP_178873.1 periplasmic; catalytic subunit; with NapBC catalyzes the reduction of nitrate to nitrite; NapAB receives electrons from NapC YP_178874.1 part of NapHG quinol dehydrogenase; couples electron transfer from ubiquinone-ubiquinol couple via NapC/B to NapA; secreted by twin arginine translocation pathway YP_178875.1 part of NapHG quinol dehydrogenase; couples electron transfer from ubiquinone-ubiquinol couple via NapC/B to NapA YP_178876.1 identified by similarity to SP:P39186; match to protein family HMM PF03892 YP_178878.1 identified by similarity to SP:P33938; match to protein family HMM PF03927 YP_178880.1 identified by similarity to OMNI:HP0168 YP_178881.1 identified by similarity to OMNI:HP0167 YP_178882.1 identified by match to protein family HMM PF01743 YP_178883.1 produces formate from formyl-tetrahydrofolate which is the major source of formate for PurT in de novo purine nucleotide biosynthesis; has a role in one-carbon metabolism; forms a homohexamer; activated by methionine and inhibited by glycine YP_178885.1 identified by similarity to GB:AAL94332.1; match to protein family HMM PF03008 YP_178886.1 identified by similarity to GP:13359310; match to protein family HMM PF00512; match to protein family HMM PF02518 YP_178888.1 identified by match to protein family HMM PF01225; match to protein family HMM PF02875 YP_178889.1 identified by similarity to OMNI:HP0739 YP_178890.1 identified by match to protein family HMM TIGR01552 YP_178891.1 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_178892.1 plays an essential role in ATP-dependent branch migration of the Holliday junction YP_178893.1 identified by similarity to OMNI:HP0884 YP_178894.1 identified by similarity to SP:O25551; match to protein family HMM PF03023; match to protein family HMM TIGR01695 YP_178895.1 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_178896.1 identified by similarity to SP:P27299; match to protein family HMM PF00005; match to protein family HMM PF00664 YP_178897.1 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_178898.1 identified by match to protein family HMM PF00675; match to protein family HMM PF05193 YP_178899.1 catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis YP_178900.1 Acts on the hydroxyl group at position 7 of the steroid frame YP_178902.1 identified by similarity to OMNI:NTL01HP00742; match to protein family HMM PF00753 YP_178903.1 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_178904.1 transfers the gamma-phosphate of ATP to the 4' position of a tetraacyldisaccharide 1-phosphate intermediate to form tetraacyldisaccharide 1,4'-bis-phosphate YP_178905.1 catalyzes the formation of L-threonine from O-phospho-L-homoserine YP_178906.1 CMP-2-keto-3-deoxyoctulosonic acid synthetase; catalyzes the formation of CMP-3-deoxy-D-manno-octulosonate from CTP and 3-deoxy-D-manno-octulosonate which is incorporated into LPS YP_178908.1 identified by similarity to SP:P10344; similarity to SP:P30859; match to protein family HMM PF00497 YP_178909.1 FliP, with proteins FliQ and FliR, forms the core of the central channel in the flagella export apparatus YP_178910.1 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_178911.1 catalyzes the conjugation of cysteine to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine, which is then decarboxylated to form 4'-phosphopantotheine YP_178912.1 identified by similarity to OMNI:NTL01HP00773 YP_178913.1 identified by match to protein family HMM PF01255; match to protein family HMM TIGR00055 YP_178914.1 identified by similarity to SP:P27717; match to protein family HMM PF01478 YP_178915.1 identified by similarity to OMNI:NTL01HP01010; match to protein family HMM PF03739 YP_178916.1 mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability YP_178917.1 catalyzes the formation of 2-oxobutanoate from L-threonine YP_178918.1 identified by similarity to OMNI:EF1616; match to protein family HMM PF02629 YP_178919.1 identified by similarity to GB:AAP76762.1; match to protein family HMM PF04323 YP_178920.1 catalyzes the formation of 5-methyl-uridine at position 54 in all tRNAs YP_178921.1 identified by similarity to GP:28202739; match to protein family HMM PF03553 YP_178922.1 identified by match to protein family HMM PF00106 YP_178923.1 identified by similarity to OMNI:NTL01CJ00787; match to protein family HMM PF00023 YP_178924.1 catalyzes the conversion of citrate to isocitrate and the conversion of 2-methylaconitate to 2-methylisocitrate YP_178925.1 identified by similarity to SP:P11742; match to protein family HMM PF01035; match to protein family HMM TIGR00589 YP_178926.1 identified by similarity to OMNI:NTL01HP00959 YP_178927.1 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_178928.1 identified by similarity to OMNI:HP1384 YP_178929.1 catalyzes the formation of D-fructose 6-phosphate from fructose-1,6-bisphosphate YP_178930.1 identified by match to protein family HMM PF03205; match to protein family HMM TIGR00176 YP_178931.1 identified by similarity to GP:29341106 YP_178932.1 identified by similarity to SP:P03810; match to protein family HMM PF01464 YP_178933.1 identified by similarity to OMNI:NTL01HP00585; match to protein family HMM PF02325 YP_178934.1 charges one glutamine molecule and pairs it with tRNA(Gln) YP_178935.1 identified by similarity to SP:Q9ZM43; match to protein family HMM PF00149 YP_178936.1 catalyzes the decarboxylaton of phospatidyl-L-sering to phosphatidylethanolamine YP_178937.1 identified by match to protein family HMM TIGR00789 YP_178939.1 identified by similarity to GB:AAN68690.1; match to protein family HMM PF00083 YP_178942.1 Converts (S)-4-amino-5-oxopentanoate to 5-aminolevulinate during the porphyrin biosynthesis pathway YP_178943.1 identified by similarity to PIR:D64549 YP_178944.1 catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate YP_178945.1 identified by similarity to SP:P00803; match to protein family HMM PF00461 YP_178946.1 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_178947.1 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_178949.1 identified by similarity to OMNI:NTL01FN0565; match to protein family HMM PF00892 YP_178950.1 identified by match to protein family HMM PF00117; match to protein family HMM TIGR00566 YP_178951.1 identified by match to protein family HMM PF00425; match to protein family HMM TIGR00553 YP_178952.1 identified by similarity to SP:P21891; match to protein family HMM PF00589 YP_178953.1 identified by similarity to SP:P24991 YP_178954.1 identified by similarity to SP:P30018 YP_178955.1 identified by match to protein family HMM PF01323 YP_178958.1 identified by similarity to SP:Q60375 YP_178959.1 identified by similarity to OMNI:NTL01HP00379 YP_178960.1 membrane protein involved in the flagellar export apparatus YP_178961.1 identified by match to protein family HMM PF02082; match to protein family HMM TIGR00738 YP_178962.1 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_178963.1 identified by similarity to OMNI:NTL01HP00332; match to protein family HMM PF01580 YP_178964.1 with FlgK acts as a hook filament junction protein to join the flagellar filament to the hook YP_178965.1 identified by similarity to GP:28806586; match to protein family HMM PF00005 YP_178966.1 identified by similarity to OMNI:NTL01TT0955; match to protein family HMM PF00512; match to protein family HMM PF02518 YP_178967.1 identified by similarity to OMNI:SA0019; match to protein family HMM PF00072; match to protein family HMM PF00486 YP_178968.1 catalyzes the formation of 3-phosphonooxypyruvate from 3-phospho-D-glycerate in serine biosynthesis; can also reduce alpha ketoglutarate to form 2-hydroxyglutarate YP_178970.1 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_178971.1 catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate into isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP); functions in the nonmevalonate isoprenoid biosynthesis pathway YP_178972.1 catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis YP_178973.1 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_178974.1 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_178975.1 identified by match to protein family HMM PF01230 YP_178976.1 identified by similarity to SP:Q46948; match to protein family HMM PF01965; match to protein family HMM TIGR01383 YP_178978.1 identified by match to protein family HMM PF00528; match to protein family HMM TIGR01726 YP_178979.1 identified by similarity to SP:P27675; match to protein family HMM PF00005 YP_178980.1 identified by match to protein family HMM PF01235; match to protein family HMM TIGR00835 YP_178981.1 identified by match to protein family HMM PF00588 YP_178982.1 converts L-alanine to D-alanine which is used in cell wall biosynthesis; binds one pyridoxal phosphate per monomer; forms a homodimer YP_178983.1 identified by similarity to OMNI:HP0518 YP_178984.1 identified by similarity to GP:28974236 YP_178985.1 identified by similarity to OMNI:VCA0037; match to protein family HMM PF04314 YP_178986.1 identified by similarity to GP:28974236 YP_178987.1 identified by match to protein family HMM PF02630 YP_178988.1 identified by match to protein family HMM PF00291; match to protein family HMM TIGR01136; match to protein family HMM TIGR01139 YP_178989.1 identified by similarity to SP:P02346; match to protein family HMM PF00216 YP_178990.1 identified by similarity to GP:5052311 YP_178991.1 identified by match to protein family HMM PF03061 YP_178992.1 identified by similarity to OMNI:NTL01CJ00861; match to protein family HMM PF04328 YP_178993.1 identified by similarity to SP:P15078; match to protein family HMM PF02554 YP_178994.1 catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP YP_178995.1 identified by similarity to OMNI:NTL01CJ00864; match to protein family HMM PF00528; match to protein family HMM TIGR01726 YP_178996.1 identified by similarity to OMNI:NTL01CJ00865; match to protein family HMM PF00528; match to protein family HMM TIGR01726 YP_178997.1 PEB1 YP_178998.1 identified by similarity to SP:P45677; match to protein family HMM PF00005 YP_178999.1 identified by similarity to SP:P31105; match to protein family HMM PF01739; match to protein family HMM PF03705 YP_179000.1 identified by similarity to SP:P04042; match to protein family HMM PF01339 YP_179001.1 identified by similarity to SP:P37351; match to protein family HMM PF02502; match to protein family HMM TIGR00689 YP_179002.1 identified by similarity to OMNI:HP0573 YP_179003.1 catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis YP_179004.1 identified by match to protein family HMM PF00597 YP_179005.1 catalyzes the removal of N-terminal amino acids preferably leucine from various peptides YP_179006.1 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_179007.1 catalyzes the formation of arginine from (N-L-arginino)succinate YP_179008.1 PEP carboxykinase; PEP carboxylase; PEPCK; catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using ATP YP_179009.1 identified by match to protein family HMM PF00364 YP_179010.1 identified by match to protein family HMM PF00209 YP_179011.1 identified by similarity to SP:P45320; match to protein family HMM PF00209 YP_179012.1 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_179013.1 identified by similarity to OMNI:NTL02LI4054; match to protein family HMM PF03547 YP_179014.1 identified by similarity to SP:P31119; match to protein family HMM PF00501; match to protein family HMM PF01553 YP_179015.1 identified by similarity to OMNI:NTL01HP00357 YP_179016.1 identified by match to protein family HMM PF00528; match to protein family HMM TIGR01726 YP_179017.1 identified by match to protein family HMM PF02687 YP_179018.1 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_179019.2 participates with LolB in the incorporation of lipoprotein into the outer membrane YP_179020.1 identified by similarity to OMNI:BBA60 YP_179021.1 identified by similarity to GP:29341447 YP_179022.1 identified by similarity to OMNI:HP0087 YP_179023.1 identified by match to protein family HMM PF00795 YP_179024.1 identified by match to protein family HMM PF01545; match to protein family HMM TIGR01297 YP_179025.1 identified by match to protein family HMM PF04371 YP_179026.1 identified by similarity to SP:P52644; match to protein family HMM PF03724 YP_179028.1 identified by similarity to OMNI:SO0500; match to protein family HMM PF00015 YP_179029.1 involved in de novo purine biosynthesis YP_179030.1 identified by similarity to SP:Q45885; match to protein family HMM PF00226 YP_179031.1 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_179032.1 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_179033.1 identified by similarity to OMNI:HP1451 YP_179034.1 functions to insert inner membrane proteins into the IM in Escherichia coli; interacts with transmembrane segments; functions in both Sec-dependent and -independent membrane insertion; similar to Oxa1p in mitochondria YP_179035.1 identified by similarity to SP:O25988; match to protein family HMM PF01809; match to protein family HMM TIGR00278 YP_179036.1 identified by match to protein family HMM PF00825; match to protein family HMM TIGR00188 YP_179037.1 in Escherichia coli transcription of this gene is enhanced by polyamines YP_179038.1 identified by match to protein family HMM PF00583 YP_179039.1 identified by similarity to OMNI:NTL01AA01172 YP_179040.1 identified by similarity to OMNI:NTL01HP00711 YP_179041.1 identified by match to protein family HMM PF03061; match to protein family HMM TIGR00051 YP_179048.1 identified by similarity to GP:18389893 YP_179049.1 identified by similarity to GP:29541252 YP_179052.1 identified by similarity to OMNI:NTL01HP00957 YP_179054.1 identified by similarity to SP:P43270; match to protein family HMM PF00565 YP_179055.1 identified by similarity to SP:P15288; match to protein family HMM PF01546 YP_179056.1 identified by similarity to GP:5823681; match to protein family HMM PF00083 YP_179057.1 identified by similarity to GB:AAD26123.1; similarity to GB:CAA71822.1; match to protein family HMM PF00497 YP_179058.1 identified by similarity to GP:11095281 YP_179059.1 identified by similarity to SP:P45491; match to protein family HMM PF03883 YP_179060.1 identified by similarity to GP:535810; match to protein family HMM PF01546; match to protein family HMM TIGR01891 YP_179062.1 identified by similarity to OMNI:PG2044 YP_179064.1 identified by match to protein family HMM PF00037; match to protein family HMM PF02754 YP_179065.1 catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III YP_179066.1 identified by similarity to SP:O25375 YP_179067.1 catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation YP_179068.1 catalyzes the formation of porphobilinogen from 5-aminolevulinate YP_179069.1 catalyzes the conversion of GTP to formate and 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine and diphosphate YP_179070.1 identified by similarity to SP:O25703; match to protein family HMM PF02527; match to protein family HMM TIGR00138 YP_179071.1 identified by similarity to OMNI:NTL01HP00288 YP_179072.1 identified by similarity to OMNI:PP3661; match to protein family HMM PF03601 YP_179073.1 identified by similarity to GP:29898768; match to protein family HMM PF00126; match to protein family HMM PF03466 YP_179074.1 sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; this is the primary sigma factor of bacteria YP_179076.1 identified by match to protein family HMM PF01694 YP_179077.1 identified by similarity to GP:29341996 YP_179078.1 identified by similarity to PIR:F64555; match to protein family HMM PF00004; match to protein family HMM PF01434 YP_179079.1 identified by match to protein family HMM PF00919; match to protein family HMM PF04055; match to protein family HMM TIGR00089; match to protein family HMM TIGR01579 YP_179080.1 identified by similarity to GP:12228607; match to protein family HMM PF00924 YP_179081.1 catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis YP_179082.1 identified by match to protein family HMM PF02080 YP_179083.1 Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr) YP_179086.1 identified by similarity to PIR:A55205 YP_179087.1 identified by similarity to OMNI:HP0675; match to protein family HMM PF00589 YP_179089.1 identified by similarity to GP:4049707 YP_179093.1 identified by match to protein family HMM PF05012 YP_179096.1 identified by similarity to GP:20502858; match to protein family HMM PF03890 YP_179100.1 identified by similarity to GB:BAB93804.1 YP_179108.1 identified by similarity to OMNI:NTL01XA0571 YP_179110.1 identified by similarity to OMNI:NTL01XA0571 YP_179116.1 identified by similarity to OMNI:NTL01CE0348 YP_179129.1 identified by similarity to GB:AAP76852.1 YP_179148.1 identified by match to protein family HMM PF01578 YP_179149.1 identified by similarity to SP:P22731; match to protein family HMM PF00005 YP_179150.1 identified by similarity to SP:P22730; match to protein family HMM PF00005 YP_179151.1 identified by match to protein family HMM PF02653 YP_179152.1 identified by similarity to SP:P08340; match to protein family HMM PF02653 YP_179153.1 identified by similarity to SP:P02917; match to protein family HMM PF01094 YP_179154.1 identified by similarity to SP:P17215; match to protein family HMM PF01094 YP_179155.1 identified by match to protein family HMM PF00034 YP_179156.1 identified by similarity to GP:9965827 YP_179157.1 identified by similarity to OMNI:NTL01AA00210 YP_179158.1 catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde YP_179159.1 identified by match to protein family HMM PF00072; match to protein family HMM PF00158; match to protein family HMM TIGR01199 YP_179161.1 identified by similarity to OMNI:NTL01HP00768; match to protein family HMM PF04164 YP_179162.1 negatively supercoils closed circular double-stranded DNA YP_179163.1 identified by similarity to PIR:A81305 YP_179164.1 identified by similarity to SP:Q46122 YP_179165.1 binds to the ribosome on the universally-conserved alpha-sarcin loop YP_179166.1 identified by similarity to OMNI:HP0606 YP_179167.1 identified by match to protein family HMM PF00873 YP_179168.1 Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide YP_179169.1 Conjugates Arg from its aminoacyl-tRNA to the N-termini of proteins containing an N-terminal aspartate or glutamate YP_179170.1 identified by similarity to GP:19979583 YP_179171.1 biotin carboxylase; catalyses the carboxylation of the carrier protein which then transfers the carboxyl group to form malonyl-CoA, which in turn controls the rate of fatty acid metabolism YP_179172.1 identified by match to protein family HMM PF01098 YP_179173.1 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_179174.1 identified by similarity to SP:P76242 YP_179175.1 identified by similarity to OMNI:NTL02ML3528 YP_179176.1 identified by match to protein family HMM PF00165 YP_179178.1 in Escherichia coli this enzyme functions in thiamine biosynthesis along with thiFSGI and iscS; with ThiFSG catalyzes the formation of thiazole phosphate from tyrosine, cysteine and 1-deoxy-D-xylulose-5-phosphate; forms a complex with ThiG; contains an iron-sulfur center YP_179179.1 functions in thiamine (vitamin B1) biosynthesis; in Bacillus subtilis this enzyme catalyzes the formation of thiazole from dehydroxyglycine and 1-deoxy-D-xylulose-5-phosphate and ThiS-thiocarboxylate YP_179180.1 catalyzes the adenylation of ThiS which is involved in the formation of 5-methyl-4-(beta-hydroxyethyl)thiazole phosphate YP_179181.1 identified by match to protein family HMM PF02597; match to protein family HMM TIGR01683 YP_179182.1 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_179183.1 identified by similarity to OMNI:NTL04PA0868; match to protein family HMM PF01810 YP_179184.1 identified by similarity to SP:P97013; match to protein family HMM PF02146 YP_179185.1 identified by similarity to GP:8572748; match to protein family HMM PF01420 YP_179186.1 MutS2; MutS-II; involved in blocking homologous and homeologous recombination; has ATPase activity stimulated by recombination intermediates; inhibits DNA strand exchange YP_179187.1 identified by similarity to OMNI:HP0622 YP_179188.1 Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis YP_179189.1 identified by match to protein family HMM PF00795 YP_179190.1 identified by similarity to SP:Q9X290 YP_179191.1 catalyzes the synthesis of xanthosine monophosphate by the NAD+ dependent oxidation of inosine monophosphate YP_179192.1 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_179194.1 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_179195.1 identified by similarity to GP:29338222; match to protein family HMM PF02464; match to protein family HMM TIGR00199 YP_179196.1 identified by match to protein family HMM PF00583 YP_179197.1 identified by match to protein family HMM PF00881 YP_179198.1 identified by match to protein family HMM PF01066; match to protein family HMM TIGR00560 YP_179199.1 identified by match to protein family HMM PF02163; match to protein family HMM TIGR00054 YP_179200.1 identified by similarity to OMNI:NTL01CJ01014; match to protein family HMM PF04393 YP_179201.1 binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21 YP_179202.1 binds to single stranded DNA and may facilitate the binding and interaction of other proteins to DNA YP_179203.1 binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit YP_179204.1 identified by similarity to SP:P37945; match to protein family HMM PF00004; match to protein family HMM PF02190; match to protein family HMM PF05362; match to protein family HMM TIGR00763 YP_179205.1 identified by similarity to OMNI:HP1378 YP_179206.1 binds to flagellin and appears to stabilize flagellin during flagella assembly YP_179207.1 catalyzes the formation of L-proline from pyrroline-5-carboxylate YP_179208.1 identified by similarity to PIR:H81310 YP_179210.1 identified by similarity to SP:Q58789 YP_179211.1 catalyzes the formation of uroporphyrinogen-III from hydroxymethylbilane; functions in tetrapyrrole and heme biosynthesis YP_179212.1 identified by match to protein family HMM PF02581; match to protein family HMM TIGR00693 YP_179213.1 identified by match to protein family HMM TIGR00097 YP_179214.1 identified by similarity to GP:14325535; match to protein family HMM PF00633; match to protein family HMM PF00730 YP_179215.1 identified by similarity to OMNI:NTL01CJ01028; match to protein family HMM PF05673 YP_179216.1 identified by similarity to SP:P37474; 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 TIGR00580 YP_179217.1 identified by similarity to OMNI:NTL01CJ01030; match to protein family HMM PF04519 YP_179218.1 identified by match to protein family HMM PF01551 YP_179219.1 identified by match to protein family HMM TIGR01499 YP_179221.1 identified by similarity to OMNI:NTL01HP01442 YP_179222.1 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_179223.1 forms a complex with SecD and 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_179224.1 part of the preprotein secretory system; when complexed with proteins SecF and YajC, SecDFyajC stimulates the proton motive force-driven protein translocation, and appears to be required for the release of mature proteins from the extracytoplasmic side of the membrane YP_179225.1 member of preprotein translocase; forms a heterotrimer with SecD and SecF; links the SecD/SecF/YajC/YidC complex with the SecY/SecE/SecG complex YP_179226.1 Transfers the fatty acyl group on membrane lipoproteins YP_179227.1 methionine adenosyltransferase; catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase YP_179228.1 involved in the import of serine and threonine coupled with the import of sodium YP_179229.1 catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis YP_179230.1 identified by similarity to SP:P94876; match to protein family HMM PF01432; match to protein family HMM TIGR00181 YP_179231.1 identified by similarity to OMNI:HP0469 YP_179232.1 identified by similarity to SP:Q53727; match to protein family HMM PF00580 YP_179233.1 catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs YP_179234.1 identified by match to protein family HMM PF02599; match to protein family HMM TIGR00202 YP_179235.1 catalyzes the phosphorylation of 4-diphosphocytidyl-2-C-methyl-D-erythritol in the nonmevalonate pathway of isoprenoid biosynthesis YP_179236.1 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_179237.1 identified by similarity to GB:AAO81196.1 YP_179238.1 identified by similarity to SP:Q9JZZ5; match to protein family HMM PF02617 YP_179239.1 identified by similarity to SP:P15716; match to protein family HMM PF00004; match to protein family HMM PF02861 YP_179240.1 leucyltransferase; phenylalanyltransferse; functions in the N-end rule pathway; transfers Leu, Phe, Met, from aminoacyl-tRNAs to N-terminal of proteins with Arg or Lys YP_179241.1 identified by similarity to GB:AAQ59129.1; match to protein family HMM PF00015; match to protein family HMM PF00785; match to protein family HMM TIGR00229 YP_179242.1 identified by match to protein family HMM PF01914 YP_179243.1 this stereospecific enzymes reduces the R isomer of methionine sulfoxide while MsrA reduces the S form; a fusion protein of this enzyme with MsrA and thioredoxin provides protection against oxidative stress in Neisseria gonorrhoeae YP_179244.1 identified by similarity to OMNI:NTL01CJ01057; match to protein family HMM PF04305 YP_179245.1 identified by similarity to SP:Q48269; match to protein family HMM PF01066; match to protein family HMM TIGR00473 YP_179247.1 identified by similarity to SP:P71408; match to protein family HMM PF00004; match to protein family HMM PF01434; match to protein family HMM TIGR01241 YP_179248.1 methylates ribosomal protein L11 at multiple amino acid positions; mutations of these genes in Escherichia coli or Thermus thermophilus has no apparent phenotype YP_179249.1 identified by similarity to SP:P06143; match to protein family HMM PF00072 YP_179250.1 identified by similarity to GP:5771416 YP_179251.1 identified by similarity to GP:5771415; match to protein family HMM PF02719 YP_179252.1 identified by similarity to GP:5771414; match to protein family HMM PF01041 YP_179253.1 identified by similarity to GP:5771413 YP_179254.1 identified by similarity to GP:5771412; match to protein family HMM PF02397 YP_179255.1 identified by similarity to GB:AAD51384.1; match to protein family HMM PF00534 YP_179256.1 identified by similarity to GP:5771410; match to protein family HMM PF02516 YP_179257.1 identified by similarity to GP:3413449; match to protein family HMM PF00534 YP_179258.1 identified by similarity to GP:3413448; match to protein family HMM PF00535 YP_179259.1 identified by similarity to GP:3413447; match to protein family HMM PF00534 YP_179260.1 identified by similarity to OMNI:NTL01CJ01074; match to protein family HMM PF00005; match to protein family HMM PF00664 YP_179261.1 identified by similarity to SP:Q59083; match to protein family HMM PF01370; match to protein family HMM TIGR01179 YP_179262.1 identified by similarity to GP:9714080 YP_179263.1 identified by similarity to SP:P24173; match to protein family HMM PF01075 YP_179264.1 acylates the intermediate (KDO)2-lipid IVA to form (KDO)2-(lauroyl)-lipid IVA; essential for survival; plays a role in cell responses to environmental changes YP_179265.1 identified by similarity to GP:15430479; match to protein family HMM PF00535 YP_179266.1 identified by similarity to GP:22086357; match to protein family HMM PF00535 YP_179267.1 identified by similarity to GP:22086358; match to protein family HMM PF00535 YP_179268.1 identified by similarity to GB:AAM90646.1; match to protein family HMM PF00535 YP_179270.1 identified by similarity to GP:22086361; match to protein family HMM PF00535 YP_179271.1 identified by similarity to OMNI:NTL01HP01108; match to protein family HMM PF01075 YP_179272.1 identified by similarity to GP:12802847; match to protein family HMM PF01755 YP_179273.1 catalyzes the isomerization of sedoheptulose 7-phosphate to D-glycero-D-manno-heptose 7-phosphate YP_179274.1 identified by similarity to SP:P76658; match to protein family HMM PF00294; match to protein family HMM PF01467; match to protein family HMM TIGR00125 YP_179275.1 identified by similarity to SP:P17963; match to protein family HMM PF01370 YP_179276.1 identified by match to protein family HMM TIGR00213; match to protein family HMM TIGR01656; match to protein family HMM TIGR01662 YP_179277.1 identified by similarity to SP:P04032; match to protein family HMM PF00034 YP_179278.1 identified by match to protein family HMM PF03597; match to protein family HMM TIGR00847 YP_179279.1 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 TIGR01525 YP_179280.1 An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes YP_179281.1 catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the tau chain serves as a scaffold to help in the dimerizaton of the alpha,epsilon and theta core complex; the gamma chain seems to interact with the delta and delta' subunits to transfer the beta subunit on the DNA YP_179282.1 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_179284.1 identified by similarity to OMNI:NTL02SA2153; match to protein family HMM PF01545; match to protein family HMM TIGR01297 YP_179285.1 identified by similarity to OMNI:NTL04PA0392 YP_179286.1 identified by similarity to GP:29338279 YP_179287.1 identified by similarity to GP:29338280 YP_179288.1 identified by similarity to SP:Q60009; match to protein family HMM PF00056; match to protein family HMM PF02866 YP_179289.1 identified by match to protein family HMM PF00597 YP_179290.1 identified by similarity to GP:29341730 YP_179291.1 identified by similarity to OMNI:SO4143 YP_179292.1 identified by similarity to SP:P35137; match to protein family HMM PF00160 YP_179293.1 identified by similarity to SP:Q9ZMR9; match to protein family HMM PF01709; match to protein family HMM TIGR01033 YP_179294.1 identified by match to protein family HMM PF00893 YP_179295.1 identified by similarity to SP:O31791; match to protein family HMM PF00893 YP_179296.1 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_179297.1 identified by similarity to SP:P25895; match to protein family HMM PF02416; match to protein family HMM TIGR01411 YP_179298.1 Essential for recycling GMP and indirectly, cGMP YP_179299.1 identified by similarity to OMNI:NTL01HP00303 YP_179300.1 FliR, with proteins FliP and FliQ, forms the core of the central channel in the flagella export apparatus YP_179301.1 identified by similarity to OMNI:HP0179; match to protein family HMM PF00005 YP_179302.1 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_179303.1 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_179304.1 identified by match to protein family HMM PF02353 YP_179305.1 identified by match to protein family HMM PF00034 YP_179306.1 identified by similarity to SP:P23134; match to protein family HMM PF00032; match to protein family HMM PF00033 YP_179307.1 identified by match to protein family HMM PF00355; match to protein family HMM TIGR01416 YP_179308.1 identified by similarity to SP:P37310; match to protein family HMM PF02040 YP_179309.1 GidA; glucose-inhibited cell division protein A; involved in the 5-carboxymethylaminomethyl modification (mnm(5)s(2)U) of the wobble uridine base in some tRNAs YP_179310.1 identified by similarity to SP:P50466; match to protein family HMM TIGR00229 YP_179311.1 identified by similarity to PIR:C64532; match to protein family HMM PF00015 YP_179312.1 identified by similarity to SP:P50466; match to protein family HMM TIGR00229 YP_179313.1 identified by similarity to SP:P37312; match to protein family HMM PF00375 YP_179315.1 identified by match to protein family HMM PF01384 YP_179316.1 Catalyzes the reversible hydrolysis of the amide bond within dihydroorotate. This metabolic intermediate is required for the biosynthesis of pyrimidine nucleotides YP_179317.1 catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate YP_179318.1 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_179319.1 catalyzes the hydrolysis of S-ribosylhomocysteine to homocysteine and autoinducer-2 YP_179320.1 identified by match to protein family HMM PF03171 YP_179321.1 identified by similarity to OMNI:PP5165; match to protein family HMM PF03180 YP_179322.1 catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine to form methionine YP_179323.1 identified by similarity to GB:AAF64321.1; match to protein family HMM PF02219 YP_179325.1 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_179326.1 Sms; stabilizes the strand-invasion intermediate during the DNA repair; involved in recombination of donor DNA and plays an important role in DNA damage repair after exposure to mutagenic agents YP_179327.1 identified by similarity to SP:P10121; match to protein family HMM PF00448; match to protein family HMM TIGR00064 YP_179328.1 identified by similarity to GP:14669467 YP_179329.1 identified by similarity to GB:AAP77185.1 YP_179330.1 protein from Staphylococcus aureus has phosphodiesterase activity against 2'-3'-cAMP and 2'-3'-cGMP YP_179331.1 identified by match to protein family HMM PF00597 YP_179332.1 identified by similarity to OMNI:NTL01HP01269; match to protein family HMM PF03772; match to protein family HMM TIGR00360 YP_179333.1 identified by similarity to SP:P32146; match to protein family HMM PF03631; match to protein family HMM TIGR00765 YP_179334.1 identified by similarity to SP:P52075; match to protein family HMM PF01565; match to protein family HMM PF02913 YP_179335.1 identified by similarity to OMNI:NTL01HP00454 YP_179337.1 identified by match to protein family HMM PF01551 YP_179339.1 identified by similarity to SP:P94338; match to protein family HMM PF02578 YP_179340.1 catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine YP_179341.1 identified by similarity to OMNI:NTL01HP01014 YP_179342.1 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_179343.1 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_179344.1 identified by similarity to GP:4104349; match to protein family HMM PF00512; match to protein family HMM PF02518 YP_179345.1 identified by similarity to GP:13177580; match to protein family HMM PF00072; match to protein family HMM PF00486 YP_179346.1 identified by match to protein family HMM PF01814 YP_179347.1 identified by similarity to OMNI:NTL01XF01697 YP_179348.1 identified by similarity to OMNI:NTL01HP00150; match to protein family HMM PF00512; match to protein family HMM PF00672; match to protein family HMM PF02518 YP_179349.1 identified by similarity to OMNI:SA0019; match to protein family HMM PF00072; match to protein family HMM PF00486 YP_179350.1 identified by similarity to SP:P09376; match to protein family HMM PF00089; match to protein family HMM PF00595 YP_179351.1 identified by similarity to SP:P17631; match to protein family HMM PF00226; match to protein family HMM PF01556 YP_179352.1 identified by match to protein family HMM PF00376 YP_179353.1 identified by match to protein family HMM PF00999; match to protein family HMM PF02254 YP_179355.1 identified by match to protein family HMM PF00702; match to protein family HMM TIGR01549 YP_179356.1 glycine--tRNA ligase beta chain; glyS; class II aminoacyl tRNA synthetase; tetramer of alpha(2)beta(2); catalyzes a two-step reaction; first charging a glycine molecule by linking the carboxyl group to the alpha-phosphate of ATP; second by transfer of the aminoacyl-adenylate to its tRNA YP_179357.1 identified by match to protein family HMM PF01551 YP_179358.1 identified by similarity to OMNI:HP0812; match to protein family HMM PF02636 YP_179359.1 identified by match to protein family HMM PF02541 YP_179360.1 involved in the de novo synthesis of pyridoxine (Vitamin B6) YP_179361.1 catalyzes oxidation of 4-(phosphohydroxy)-L-threonine into 2-amino-3-oxo-4-(phosphohydroxy)butyric acid which decarboxylates to form 1-amino-3-(phosphohydroxy)propan-2-one (3-amino-2-oxopropyl phosphate) YP_179364.1 identified by similarity to SP:P77389 YP_179366.1 catalyzes the formation of coproporphyrinogen from uroporphyrinogen III YP_179367.1 identified by match to protein family HMM PF04055 YP_179369.1 The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision YP_179372.1 contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway YP_179374.1 catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis YP_179375.1 identified by similarity to OMNI:VC0842 YP_179376.1 identified by similarity to SP:Q9KUR9; match to protein family HMM PF04453 YP_179377.1 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; match to protein family HMM TIGR01369 YP_179378.1 identified by similarity to OMNI:NTL01OI1065 YP_179380.1 identified by match to protein family HMM PF01451 YP_179381.1 identified by similarity to SP:P80672; match to protein family HMM PF05538 YP_179382.1 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_179383.1 identified by similarity to SP:P30846; match to protein family HMM PF00072; match to protein family HMM PF00486 YP_179384.1 identified by similarity to OMNI:NTL01HP00150; match to protein family HMM PF00512; match to protein family HMM PF00672; match to protein family HMM PF02518 YP_179385.1 involved in a recombinational process of DNA repair, independent of the recBC complex YP_179386.1 identified by similarity to SP:P37182; match to protein family HMM PF01750; match to protein family HMM TIGR00072 YP_179387.1 identified by similarity to SP:P31875; match to protein family HMM PF01292 YP_179388.1 identified by similarity to SP:P31883; match to protein family HMM PF00374 YP_179389.1 identified by similarity to SP:P31884; match to protein family HMM PF01058; match to protein family HMM TIGR00391; match to protein family HMM TIGR01409 YP_179390.1 catalyzes the formation of 5-methylaminomethyl-2-thiouridine in position 34 of the anticodon of tRNA molecules YP_179391.1 identified by similarity to SP:P36548; match to protein family HMM PF01520 YP_179392.1 identified by match to protein family HMM PF03060 YP_179393.1 catalyzes the formation of tyrosyl-tRNA(Tyr) from tyrosine and tRNA(Tyr) YP_179394.1 identified by similarity to SP:O54408; 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_179395.1 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_179396.1 Catalyzes the phosphorylation of UMP to UDP YP_179397.1 identified by match to protein family HMM PF01551 YP_179398.1 identified by similarity to OMNI:NTL01CA2621 YP_179399.1 identified by similarity to SP:P75957; match to protein family HMM PF00005 YP_179400.1 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_179401.1 identified by similarity to OMNI:NTL01CJ01222; match to protein family HMM PF00041 YP_179402.1 identified by match to protein family HMM PF00849; match to protein family HMM PF01479; match to protein family HMM TIGR00005 YP_179403.1 identified by similarity to PIR:C81336; match to protein family HMM PF01098 YP_179404.1 identified by similarity to GB:AAN54532.1; match to protein family HMM PF00589 YP_179407.1 identified by similarity to GB:CAA65779.1; match to protein family HMM PF01555 YP_179415.1 identified by similarity to GP:28203221 YP_179416.1 identified by similarity to GP:23452767 YP_179420.1 identified by similarity to GB:AAL82351.1 YP_179421.1 identified by similarity to GP:13517589; match to protein family HMM PF03374 YP_179426.1 identified by similarity to SP:P41027; match to protein family HMM PF00717 YP_179427.1 identified by similarity to GP:27359896; match to protein family HMM PF01223 YP_179428.1 identified by similarity to OMNI:NT01MC0181 YP_179434.1 identified by similarity to OMNI:NTL03ST1666 YP_179444.1 identified by match to protein family HMM TIGR01554 YP_179454.1 identified by match to protein family HMM TIGR01725 YP_179455.1 identified by match to protein family HMM PF04860; match to protein family HMM TIGR01537 YP_179456.1 identified by similarity to OMNI:NTL02LI2843 YP_179457.1 identified by similarity to OMNI:NTL01SF1096; match to protein family HMM PF03354 YP_179459.1 identified by match to protein family HMM PF01844 YP_179461.1 identified by match to protein family HMM PF02386; match to protein family HMM TIGR00933 YP_179462.1 identified by similarity to GP:3288678; match to protein family HMM PF02254 YP_179463.1 identified by similarity to OMNI:NTL01HP00708; match to protein family HMM PF02621 YP_179464.1 Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate YP_179465.1 identified by similarity to SP:P76558; match to protein family HMM PF00390; match to protein family HMM PF03949 YP_179466.1 Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation YP_179467.1 identified by similarity to GB:AAP77293.1 YP_179468.1 biotin carboxylase; biotin carboxylase catalyzes the carboxylation of the carrier protein and then the transcarboxylase transfers the carboxyl group to form malonyl-CoA; catalyzes the formation of malonyl-CoA, which in turn controls the rate of fatty acid metabolism YP_179469.1 identified by match to protein family HMM PF00364; match to protein family HMM TIGR00531 YP_179470.1 Catalyzes the formation of dUTP from dCTP in thymidylate biosynthesis YP_179471.1 identified by similarity to OMNI:NTL01CJ01235; match to protein family HMM PF02719 YP_179472.1 identified by match to protein family HMM PF01041 YP_179473.1 identified by similarity to PIR:E97170 YP_179475.1 identified by similarity to PIR:F97876 YP_179476.1 identified by similarity to OMNI:NTL03PA02036 YP_179477.1 identified by match to protein family HMM TIGR01681; match to protein family HMM TIGR01686 YP_179478.1 FabH; beta-ketoacyl-ACP synthase III; catalyzes the condensation of acetyl-CoA with malonyl-ACP to initiate cycles of fatty acid elongation; differs from 3-oxoacyl-ACP synthase I and II in that it utilizes CoA thioesters as primers rather than acyl-ACPs; paralogs which do not contain the N-X-R ACP-binding site motif YP_179479.1 identified by similarity to OMNI:NTL01XA1935 YP_179482.1 identified by match to protein family HMM PF00501 YP_179483.1 identified by match to protein family HMM PF00583 YP_179484.1 identified by match to protein family HMM PF00551 YP_179485.1 identified by similarity to GB:AAB41298.1 YP_179486.1 identified by similarity to OMNI:NTL01CA0429; match to protein family HMM PF01522 YP_179487.1 identified by similarity to OMNI:NT01MC2981 YP_179488.1 identified by similarity to SP:P29810 YP_179490.1 identified by similarity to PIR:C81274 YP_179491.1 identified by similarity to OMNI:NTL01CJ01253; match to protein family HMM PF02348 YP_179492.1 identified by similarity to GP:5616173 YP_179493.1 identified by match to protein family HMM PF00583 YP_179494.1 catalyzes the conversion of 5-[(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino]- 1-(5-phosphoribosyl)imidazole-4-carboxamide and glutamine to imidazole-glycerolphosphate, 5-aminoimidazol-4-carboxamideribonucleotide and glutamate; the HisF subunit acts as a cyclase YP_179495.1 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_179496.1 identified by similarity to GP:15559182 YP_179497.1 identified by similarity to GB:AAM76272.1; match to protein family HMM PF01354; match to protein family HMM PF03102 YP_179498.1 identified by similarity to GP:20559811; match to protein family HMM PF01370 YP_179499.1 identified by similarity to OMNI:NTL01CJ01262; match to protein family HMM PF01041 YP_179500.1 identified by similarity to SP:P77398 YP_179501.1 identified by similarity to OMNI:NTL01CJ01269; match to protein family HMM PF01354; match to protein family HMM PF03102 YP_179502.1 identified by similarity to GP:11095582; match to protein family HMM PF02350 YP_179503.1 identified by similarity to OMNI:NTL01CJ01270; match to protein family HMM PF00483; match to protein family HMM PF00571 YP_179504.1 identified by similarity to GP:27354272 YP_179505.1 identified by similarity to SP:Q45982; match to protein family HMM PF02348 YP_179506.1 identified by similarity to SP:Q45983; match to protein family HMM PF00106 YP_179507.1 identified by similarity to PIR:B81277; match to protein family HMM PF01973 YP_179508.1 identified by similarity to PIR:C81277; match to protein family HMM PF01973 YP_179509.1 identified by similarity to PIR:C81275; match to protein family HMM PF01973 YP_179510.1 identified by similarity to PIR:F81277; match to protein family HMM PF01973 YP_179511.1 FlaB; structural flagella protein; in Helicobacter the flagella are composed of flagellin A and flagellin B; the amounts of each seem to be controlled by environmental conditions YP_179513.1 FlaA; structural flagella protein; in Helicobacter the flagella are composed of flagellin A and flagellin B; the amounts of each seem to be controlled by environmental conditions YP_179514.1 identified by similarity to PIR:A81278; match to protein family HMM PF01973 YP_179515.1 identified by similarity to PIR:B81278; match to protein family HMM PF01973 YP_179517.1 identified by similarity to PIR:D81278 YP_179518.1 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_179519.1 identified by similarity to OMNI:NTL01HP00347 YP_179520.1 catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate YP_179521.1 identified by similarity to OMNI:VC2255; match to protein family HMM PF01148 YP_179523.1 identified by similarity to GP:19110786; match to protein family HMM PF05670 YP_179524.1 identified by similarity to SP:P32173 YP_179525.1 identified by similarity to GP:2243138; match to protein family HMM PF02253 YP_179526.1 identified by similarity to GB:CAA61301.1; match to protein family HMM PF01032 YP_179527.1 identified by similarity to GP:1107529; match to protein family HMM PF01032 YP_179528.1 identified by similarity to GP:1107530; match to protein family HMM PF00005 YP_179529.1 identified by similarity to GP:1107532 YP_179530.1 identified by similarity to SP:Q9S1E5; match to protein family HMM PF02335 YP_179531.1 identified by similarity to SP:Q9S1E6; match to protein family HMM PF03264 YP_179532.1 catalyzes the reversible transfer of the terminal phosphate of ATP to form a long chain polyphosphate YP_179536.1 identified by similarity to GP:28974216 YP_179537.1 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_179538.1 identified by match to protein family HMM PF01594 YP_179539.1 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_179540.1 identified by match to protein family HMM PF00082 YP_179541.1 Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source YP_179543.1 identified by match to protein family HMM PF04055; match to protein family HMM TIGR00423 YP_179544.1 identified by match to protein family HMM PF00860 YP_179545.1 identified by similarity to PIR:G64611; match to protein family HMM PF00156 YP_179546.1 identified by match to protein family HMM PF04333 YP_179547.1 identified by similarity to GP:4336801; match to protein family HMM PF05494 YP_179548.1 identified by similarity to OMNI:BB0252 YP_179549.1 HAM1-like protein; Rec-dependent growth; RgdB; yggV; it is suspected that this protein functions to remove misincorporated bases such as xanthine or hypoxanthine YP_179550.1 identified by similarity to SP:P77726; match to protein family HMM PF00083 YP_179551.1 identified by match to protein family HMM PF00037 YP_179552.1 catalyzes the formation of selenocysteinyl-tRNA(Sec) from seryl-tRNA(Sec) and L-selenophosphate in selenoprotein biosynthesis YP_179553.1 identified by similarity to SP:P14081; match to protein family HMM PF00009; match to protein family HMM TIGR00231; match to protein family HMM TIGR00475 YP_179554.1 identified by similarity to OMNI:NTL01AA01434 YP_179556.1 An electron-transfer protein; flavodoxin binds one FMN molecule, which serves as a redox-active prosthetic group YP_179558.1 identified by similarity to OMNI:NTL01BH0516 YP_179559.1 identified by similarity to SP:Q59170; match to protein family HMM PF00199 YP_179560.1 identified by match to protein family HMM PF00023 YP_179561.1 identified by similarity to OMNI:SAG1820 YP_179562.1 identified by match to protein family HMM PF01042; match to protein family HMM TIGR00004 YP_179563.1 identified by similarity to SP:P06721; match to protein family HMM PF01053 YP_179564.1 Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide YP_179565.1 identified by match to protein family HMM PF03972 YP_179566.1 identified by match to protein family HMM PF04023 YP_179567.1 identified by match to protein family HMM PF01058; match to protein family HMM TIGR00391 YP_179568.1 Catalyzes a key regulatory step in fatty acid biosynthesis YP_179569.1 Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate YP_179570.1 Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway YP_179571.1 identified by match to protein family HMM PF00044; match to protein family HMM PF02800; match to protein family HMM TIGR01534 YP_179572.1 identified by match to protein family HMM PF01467; match to protein family HMM TIGR00125; match to protein family HMM TIGR00482 YP_179573.1 identified by similarity to OMNI:HP1414; match to protein family HMM PF02410; match to protein family HMM TIGR00090 YP_179574.1 identified by similarity to OMNI:NTL02YP3559; match to protein family HMM PF06476 YP_179575.1 identified by similarity to SP:P26276; 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_179576.1 interacts with the cytoplasmic MS ring of the basal body and may act to stabilize the MotAB complexes which surround the MS ring YP_179577.1 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_179579.1 identified by match to protein family HMM PF00067 YP_179581.1 identified by similarity to GP:26109934; match to protein family HMM PF05159 YP_179582.1 identified by similarity to SP:Q05013; match to protein family HMM PF05159 YP_179583.1 identified by similarity to GP:29469161 YP_179584.1 identified by similarity to GP:6469930 YP_179585.1 identified by similarity to OMNI:MJ1101 YP_179586.1 identified by similarity to OMNI:NTL01PA0174 YP_179587.1 identified by match to protein family HMM PF00485; match to protein family HMM PF00702 YP_179589.1 identified by similarity to GB:AAK27852.1; match to protein family HMM PF00483 YP_179590.1 identified by similarity to SP:Q9AGY7; match to protein family HMM PF01380; match to protein family HMM TIGR00441 YP_179591.1 identified by match to protein family HMM PF00288 YP_179592.1 identified by similarity to SP:P32054; match to protein family HMM PF01370 YP_179593.1 identified by similarity to SP:P32055 YP_179594.1 identified by similarity to GP:27314628 YP_179596.1 identified by similarity to GP:13446686; match to protein family HMM PF00534 YP_179597.1 identified by similarity to SP:P46918; match to protein family HMM PF04464 YP_179598.1 identified by similarity to EGAD:20643; match to protein family HMM PF00571; match to protein family HMM PF01380; match to protein family HMM TIGR00393 YP_179599.1 identified by similarity to SP:Q03961; match to protein family HMM PF02563 YP_179600.1 identified by similarity to SP:P42214; match to protein family HMM PF02706 YP_179601.1 identified by similarity to SP:P24586; match to protein family HMM PF00005 YP_179602.1 identified by similarity to SP:P23889; match to protein family HMM PF01061 YP_179603.1 identified by similarity to GP:26110162 YP_179606.1 identified by match to protein family HMM PF04401 YP_179607.1 identified by match to protein family HMM PF01171 YP_179608.1 identified by match to protein family HMM PF00919; match to protein family HMM PF04055; match to protein family HMM TIGR00089; match to protein family HMM TIGR01125 YP_179609.1 recognizes the termination signals UGA and UAA during protein translation a specificity which is dependent on amino acid residues residing in loops of the L-shaped tRNA-like molecule of RF2; in some organisms control of PrfB protein levels is maintained through a +1 ribosomal frameshifting mechanism; this protein is similar to release factor 1 YP_179610.1 identified by similarity to SP:Q8ENT9 YP_179612.1 catalyzes the modification of U13 in tRNA(Glu) YP_179613.1 catalyzes the formation of thiamine diphosphate from thiamine phosphate ant ATP YP_179614.1 identified by similarity to OMNI:HP0468 YP_179615.1 identified by similarity to OMNI:HP0811 YP_179616.1 identified by similarity to OMNI:NTL01CJ01398; match to protein family HMM PF03602; match to protein family HMM TIGR00095 YP_179617.1 part of the basal body which consists of four rings L, P, S, and M mounted on a central rod; Vibrio parahaemolyticus, Yersinia, Bradyrhizobium and other bacteria have two copies of this and other flagellar genes; the V. parahaemolyticus protein is associated with the polar flagella and the Bradyrhizobium protein is associated with the thick flagellum YP_179618.1 identified by similarity to SP:O25027 YP_179619.1 identified by similarity to GP:2935678 YP_179620.1 identified by similarity to OMNI:HP1120 YP_179621.1 with FlgL acts as a hook filament junction protein to join the flagellar filament to the hook YP_179622.1 identified by similarity to OMNI:NTL02LI0846 YP_179623.1 identified by similarity to OMNI:NTL01PM0363; match to protein family HMM PF01925 YP_179624.1 identified by similarity to GB:AAP87276.1; match to protein family HMM PF00482 YP_179625.1 identified by similarity to GP:4139237; match to protein family HMM PF00437 YP_179626.1 identified by similarity to PIR:E81293 YP_179627.1 identified by similarity to GB:BAC43933.1 YP_179628.1 identified by similarity to SP:P31780; match to protein family HMM PF00263 YP_179629.1 identified by similarity to GP:27361210 YP_179630.1 identified by match to protein family HMM PF00037; match to protein family HMM PF01558; match to protein family HMM PF01855 YP_179631.1 identified by match to protein family HMM PF00702; match to protein family HMM TIGR01549 YP_179632.1 identified by similarity to GP:2062640; match to protein family HMM PF00691; match to protein family HMM PF01389 YP_179633.1 forms a direct contact with the tRNA during translation YP_179634.1 in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit YP_179635.1 identified by similarity to PIR:A71805; match to protein family HMM PF00580 YP_179636.1 identified by similarity to OMNI:HP1089 YP_179637.1 identified by similarity to GP:23497165 YP_179641.1 identified by match to protein family HMM PF00034; match to protein family HMM TIGR00782 YP_179643.1 CcoO; FixO YP_179644.1 CcoN; FixN YP_179645.1 identified by similarity to GP:29894058; match to protein family HMM PF00072; match to protein family HMM PF00486 YP_179646.1 identified by similarity to OMNI:NT01MC4072; match to protein family HMM PF00785; match to protein family HMM PF02518; match to protein family HMM TIGR00229 YP_179647.1 identified by similarity to OMNI:HP0861 YP_179648.1 catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers YP_179649.1 identified by similarity to OMNI:HP1236; match to protein family HMM PF04368 YP_179650.1 identified by similarity to OMNI:NTL01TT1342 YP_179652.1 catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis YP_179654.1 identified by similarity to SP:P31064; match to protein family HMM PF04143 YP_179655.1 identified by similarity to OMNI:SO0109; match to protein family HMM PF01206 YP_179656.1 identified by similarity to SP:P07117; match to protein family HMM PF00474; match to protein family HMM TIGR00813 YP_179657.1 identified by similarity to SP:P09546; match to protein family HMM PF00171; match to protein family HMM PF01619 YP_179658.1 Selenoprotein. identified by similarity to SP:P16456; match to protein family HMM PF00586; match to protein family HMM PF02769; match to protein family HMM TIGR00476 YP_179659.1 identified by similarity to OMNI:NTL01TT1750; match to protein family HMM PF01206 YP_179660.1 identified by similarity to SP:P42258; match to protein family HMM PF00015 YP_179661.1 identified by match to protein family HMM PF02573 YP_179662.1 involved in the production or activity of formate dehydrogenase-H which is active when nitrate is not present during anaerobic growth YP_179663.1 identified by similarity to GP:48509; match to protein family HMM TIGR01583 YP_179664.1 identified by similarity to SP:P27273; match to protein family HMM PF00037 YP_179665.1 Selenoprotein. identified by similarity to GP:48507; match to protein family HMM PF00384; match to protein family HMM PF01568; match to protein family HMM PF04879; match to protein family HMM TIGR01409 YP_179666.1 identified by match to protein family HMM TIGR01409 YP_179669.1 identified by match to protein family HMM PF00278; match to protein family HMM TIGR01047 YP_179670.1 identified by match to protein family HMM PF00394; match to protein family HMM TIGR01409 YP_179671.1 identified by match to protein family HMM PF02597 YP_179672.1 identified by match to protein family HMM PF02391 YP_179673.1 identified by similarity to OMNI:NTL01LI2517 YP_179674.1 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_179675.1 identified by match to protein family HMM TIGR01573 YP_179676.1 identified by match to protein family HMM TIGR00287 YP_179678.1 catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis YP_179679.1 catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A; involved in coenzyme A biosynthesis YP_179680.1 involved in lysine biosynthesis; DAP epimerase; produces DL-diaminopimelate from LL-diaminopimelate YP_179682.1 identified by similarity to OMNI:NTL01HP01233 YP_179683.1 identified by match to protein family HMM PF00210 YP_179684.1 catalyzes the formation of D-fructose 6-phosphate from D-glucose 6-phosphate YP_179685.1 identified by similarity to GP:1628575; match to protein family HMM PF00483; match to protein family HMM TIGR01099 YP_179686.1 Acs; catalyzes the conversion of acetate and CoA to acetyl-CoA YP_179687.1 identified by similarity to GP:14330290; match to protein family HMM PF00005 YP_179688.1 identified by similarity to GP:14330289; match to protein family HMM PF00528 YP_179689.1 identified by similarity to GP:14330288 YP_179690.1 identified by match to protein family HMM PF03746 YP_179691.1 identified by similarity to OMNI:NTL01TT1494; match to protein family HMM PF02682; match to protein family HMM TIGR00370 YP_179692.1 identified by similarity to OMNI:NTL01OI2676; match to protein family HMM PF02626; match to protein family HMM TIGR00724 YP_179693.1 identified by similarity to OMNI:NTL02LI0514; match to protein family HMM PF00892 YP_179694.1 identified by match to protein family HMM PF02525 YP_179695.1 identified by match to protein family HMM PF01638 YP_179696.1 identified by match to protein family HMM PF00107 YP_179697.1 identified by similarity to GP:19881228 YP_179698.1 identified by similarity to GP:19881229; match to protein family HMM PF02661 YP_179699.1 identified by similarity to SP:Q47282; match to protein family HMM PF02384; match to protein family HMM PF02506 YP_179700.1 identified by similarity to SP:P20370; match to protein family HMM PF02627 YP_179702.1 identified by similarity to OMNI:NTL01BMA0801 YP_179703.1 identified by similarity to SP:P77389 YP_179704.1 identified by similarity to GP:27314600; match to protein family HMM PF03773 YP_179705.1 identified by similarity to SP:P15905; match to protein family HMM PF01022 YP_179706.1 identified by similarity to SP:Q01257; match to protein family HMM PF01451 YP_179707.1 identified by similarity to GP:5802942; match to protein family HMM PF01758 YP_179708.1 identified by similarity to SP:P39215; match to protein family HMM PF00015; match to protein family HMM PF02743 YP_179709.1 identified by similarity to OMNI:NTL01CJ01492 YP_179710.1 identified by similarity to SP:P33608; match to protein family HMM PF00361 YP_179711.1 identified by similarity to SP:P50974; match to protein family HMM PF00361 YP_179712.1 Catalyzes the transfer of electrons from NADH to ubiquinone YP_179713.1 identified by similarity to SP:P50940; match to protein family HMM PF00420 YP_179714.1 Catalyzes the transfer of electrons from NADH to quinone YP_179715.1 Catalyzes the transfer of electrons from NADH to quinone YP_179716.1 Catalyzes the transfer of electrons from NADH to quinone YP_179717.1 Catalyzes the transfer of electrons from NADH to ubiquinone YP_179719.1 identified by similarity to OMNI:HP1264 YP_179720.1 Catalyzes the transfer of electrons from NADH to quinone YP_179721.1 Catalyzes the transfer of electrons from NADH to ubiquinone YP_179722.1 The point of entry for the majority of electrons that traverse the respiratory chain eventually resulting in the reduction of oxygen YP_179723.1 Catalyzes the transfer of electrons from NADH to ubiquinone YP_179724.1 identified by match to protein family HMM PF00005 YP_179725.1 identified by match to protein family HMM PF00005 YP_179726.1 identified by match to protein family HMM PF00528 YP_179727.1 identified by match to protein family HMM PF00528 YP_179728.1 identified by similarity to SP:P42061; match to protein family HMM PF00496 YP_179729.1 identified by match to protein family HMM PF00037; match to protein family HMM PF01565; match to protein family HMM PF02913 YP_179730.1 identified by similarity to SP:P49852; match to protein family HMM PF00042 YP_179731.1 efflux pump for the antibacterial peptide microcin J25 YP_179732.1 identified by similarity to GP:26986249 YP_179733.1 identified by similarity to GP:27902224 YP_179734.1 stimulates the activities of the other two initiation factors, IF-2 and IF-3 YP_179735.1 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_179736.1 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_179737.1 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_179738.1 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_179739.1 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_179740.1 is a component of the macrolide binding site in the peptidyl transferase center YP_179741.1 long form of enzyme; catalyzes the formation of N'-5'-phosphoribosyl-ATP from phosphoribosyl pyrophosphate; crucial role in histidine biosynthesis; forms active dimers and inactive hexamers which is dependent on concentration of substrates and inhibitors YP_179742.1 catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer YP_179743.1 catalyzes the formation of 3-(imidazol-4-yl)-2-oxopropyl phosphate from D-ethythro-1-(imidazol-4-yl)glycerol 3-phosphate and histidinol from histidinol phosphate YP_179744.1 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_179745.1 catalyzes the formation of 5-(5-phospho-1-deoxyribulos-1-ylamino)methylideneamino-l- (5-phosphoribosyl)imidazole-4-carboxamide from 1-(5-phosphoribosyl)-5-[(5- phosphoribosylamino)methylideneamino] imidazole-4-carboxamide YP_179746.1 identified by similarity to GP:28076667; match to protein family HMM PF04373 YP_179747.1 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_179748.1 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_179750.1 identified by similarity to SP:P21590; match to protein family HMM PF01883 YP_179751.1 bifunctional enzyme involved in formation of 4-diphosphocytidyl-2-C-methyl-D-erythritol from CTP and 2-C-methyl-D-erythritol 4-phosphate and 2-C-methyl-D-erythritol 2,4-cyclodiphosphate and CMP from 4-diphosphocytidyl-2-C-methyl-D-erythritol 2-phosphate; involved in isoprenoid and isopentenyl-PP biosynthesis; binds divalent cations YP_179752.1 identified by similarity to OMNI:HP1021; match to protein family HMM PF00072; match to protein family HMM TIGR01199 YP_179754.1 identified by similarity to SP:P18200; match to protein family HMM PF04608 YP_179755.1 binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase YP_179756.1 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_179757.1 identified by similarity to OMNI:NTL01CJ01539; match to protein family HMM PF03774 YP_179758.1 identified by similarity to OMNI:NTL01CJ01540; match to protein family HMM PF00593 YP_179759.1 identified by similarity to SP:Q56992; match to protein family HMM PF01032 YP_179760.1 identified by match to protein family HMM PF00005 YP_179761.1 identified by match to protein family HMM PF01497 YP_179762.1 identified by similarity to SP:P17448; match to protein family HMM PF00083 YP_179763.1 identified by similarity to SP:P17802; match to protein family HMM PF00633; match to protein family HMM PF00730; match to protein family HMM TIGR01084 YP_179764.1 identified by similarity to GB:AAP76658.1 YP_179765.1 identified by similarity to GB:CAB71026.1; match to protein family HMM PF00383 YP_179767.1 identified by match to protein family HMM PF03313; match to protein family HMM PF03315; match to protein family HMM TIGR00720 YP_179768.1 identified by similarity to SP:P36559 YP_179769.1 identified by similarity to GP:29338228 YP_179770.1 identified by similarity to OMNI:NTL01FN0259 YP_179771.1 identified by similarity to SP:P43008; match to protein family HMM PF01618 YP_179772.1 identified by similarity to SP:P43009; match to protein family HMM PF02472 YP_179775.1 identified by similarity to PIR:A71984 YP_179776.1 catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis YP_179777.1 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_179778.1 An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids YP_179779.1 identified by similarity to OMNI:HP0660 YP_179780.1 synthesizes RNA primers at the replication forks YP_179781.1 identified by match to protein family HMM PF01106 YP_179782.1 identified by similarity to OMNI:HP1493 YP_179783.1 involved in cell wall formation; peptidoglycan synthesis; cytoplasmic enzyme; catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-aceylmuramoyl-l-alanyl-d-glutamate YP_179784.1 identified by similarity to SP:O34247; match to protein family HMM PF02575; match to protein family HMM TIGR00103 YP_179785.1 identified by match to protein family HMM PF00595 YP_179786.1 identified by similarity to SP:O66126; match to protein family HMM PF00348 YP_179787.1 catalyzes the formation of ribose 5-phosphate and xylulose 5-phosphate from sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate; can transfer ketol groups between several groups; in Escherichia coli there are two tkt genes, tktA expressed during exponential growth and the tktB during stationary phase YP_179788.1 identified by similarity to GP:28974221; match to protein family HMM PF02405; match to protein family HMM TIGR00056 YP_179789.1 identified by similarity to OMNI:BR1020; match to protein family HMM PF00005 YP_179790.1 identified by similarity to GP:28974223; match to protein family HMM PF02470 YP_179791.1 identified by similarity to SP:P29285 YP_179792.1 identified by similarity to OMNI:NTL01HP00346 YP_179793.1 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_179794.1 converts L-glutamate to D-glutamate, a component of peptidoglycan YP_179795.1 identified by similarity to SP:P23898; match to protein family HMM PF00877 YP_179796.1 exports sodium by using the electrochemical proton gradient to allow protons into the cell; functions in adaptation to high salinity and alkaline pH; activity increases at higher pH; downregulated at acidic pH YP_179797.1 identified by similarity to SP:P13738; match to protein family HMM TIGR00773 YP_179800.1 identified by similarity to GP:12718499; similarity to OMNI:NTL01PM0455; match to protein family HMM PF03239 YP_179801.1 identified by similarity to OMNI:NTL01PM0454 YP_179802.1 identified by similarity to OMNI:NTL01PM0453; match to protein family HMM PF04945 YP_179803.1 identified by similarity to OMNI:NTL01PM0452; match to protein family HMM PF02687 YP_179804.1 identified by similarity to OMNI:NTL01PM0451; match to protein family HMM PF02687 YP_179805.1 identified by similarity to GB:AAK02532.1; match to protein family HMM PF00005 YP_179808.1 identified by similarity to OMNI:NTL01PM1941; match to protein family HMM PF04214 YP_179811.1 catalyzes the formation of a phosphodiester at the site of a single-strand break in duplex DNA YP_179812.1 identified by similarity to OMNI:HP0156 YP_179813.1 identified by similarity to OMNI:HP0155 YP_179814.1 enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis YP_179815.1 catalyzes the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs YP_179816.1 identified by similarity to OMNI:NTL01AA00225; match to protein family HMM PF02642 YP_179817.1 with proteins FliP and FliR forms the core of the central channel in the flagella export apparatus YP_179818.1 catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis YP_179820.1 identified by similarity to SP:P22255; match to protein family HMM PF00459 YP_179821.1 identified by match to protein family HMM PF00285; match to protein family HMM TIGR01798 YP_179822.1 identified by match to protein family HMM PF00999 YP_179823.1 catalyzes the formation of biotin from dethiobiotin and sulfur YP_179824.1 catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity YP_179825.1 identified by similarity to GP:4115707; match to protein family HMM PF00083 YP_179826.1 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_179827.1 late assembly protein YP_179828.1 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_179829.1 binds 5S rRNA along with protein L5 and L25 YP_179830.1 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_179831.1 binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit YP_179832.1 located in the peptidyl transferase center and involved in assembly of 30S ribosome subunit; similar to what is observed with proteins L31 and L33, some proteins in this family contain CXXC motifs that are involved in zinc binding; if two copies are present in a genome, then the duplicated copy appears to have lost the zinc-binding motif and is instead regulated by zinc; the proteins in this group appear to contain the zinc-binding motif YP_179833.1 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_179834.1 assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel YP_179835.1 binds to the 23S rRNA between the centers for peptidyl transferase and GTPase YP_179836.1 primary binding protein; helps mediate assembly; involved in translation fidelity YP_179837.1 one of the stabilizing components for the large ribosomal subunit YP_179838.1 located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e YP_179839.1 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_179840.1 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_179841.1 protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA YP_179842.1 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_179843.1 binds third domain of 23S rRNA and protein L29; part of exit tunnel YP_179844.1 L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA YP_179845.1 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_179846.1 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_179848.1 identified by similarity to SP:P35159; match to protein family HMM PF00849; match to protein family HMM PF01479; match to protein family HMM TIGR00093 YP_179849.1 identified by similarity to GP:28203198; match to protein family HMM PF00753; match to protein family HMM TIGR00649 YP_179850.1 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_179851.1 identified by similarity to OMNI:NTL01HP01407 YP_179852.1 23S rRNA m2A2503 methyltransferase; methylates the C2 position of the A2530 nucleotide in 23S rRNA; may be involved in antibiotic resistance YP_179854.1 identified by similarity to SP:P39907 YP_179855.1 identified by match to protein family HMM PF00583 YP_179856.1 catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis; forms a heterodimer of LeuC/D YP_179857.1 dehydratase component, catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate YP_179858.1 catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis YP_179859.1 catalyzes the formation of 2-isopropylmalate from acetyl-CoA and 2-oxoisovalerate in leucine biosynthesis YP_179861.1 identified by similarity to OMNI:CC0747 YP_179862.1 NADPH-dependent; catalyzes the reduction of 7-cyano-7-deazaguanine to 7-aminomethyl-7-deazaguanine in queuosine biosynthesis YP_179863.1 identified by similarity to OMNI:NTL01AA00295 YP_179864.1 catalyzes the formation of O-succinyl-L-homoserine from succinyl-CoA and L-homoserine in methionine biosynthesis YP_179865.1 identified by similarity to GP:1835113; match to protein family HMM PF01053; match to protein family HMM TIGR01326 YP_179866.1 the hook connects flagellar basal body to the flagellar filament YP_179867.1 endonuclease; resolves Holliday structures; forms a complex of RuvABC; the junction binding protein RuvA forms a hexameric ring along with the RuvB helicase and catalyzes branch migration; RuvC then interacts with RuvAB to resolve the Holliday junction by nicking DNA strands of like polarity