-- dump date 20140619_021307 -- class Genbank::CDS -- table cds_note -- id note YP_001407305.1 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_001407306.1 binds the polymerase to DNA and acts as a sliding clamp YP_001407307.1 negatively supercoils closed circular double-stranded DNA YP_001407310.1 identified by match to protein family HMM PF04323 YP_001407311.1 identified by match to protein family HMM PF00460; match to protein family HMM PF06429 YP_001407312.1 acts as a scaffold for the assembly of hook proteins onto the flagellar basal body rod YP_001407314.1 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_001407316.1 identified by match to protein family HMM PF00384; match to protein family HMM PF01568 YP_001407318.1 identified by match to protein family HMM PF01381 YP_001407319.1 identified by match to protein family HMM PF05973 YP_001407320.1 the hook connects flagellar basal body to the flagellar filament YP_001407321.1 identified by match to protein family HMM PF03553; match to protein family HMM PF03600 YP_001407322.1 identified by glimmer; putative YP_001407324.1 catalyzes the dehydration of 2,3-dihydroxy-3-methylbutanoate to 3-methyl-2-oxobutanoate in valine and isoleucine biosynthesis YP_001407325.1 identified by match to protein family HMM PF00015; match to protein family HMM PF00672; match to protein family HMM PF02743 YP_001407327.1 identified by match to protein family HMM PF02646 YP_001407328.1 identified by match to protein family HMM PF02627 YP_001407329.1 identified by glimmer; putative YP_001407331.1 identified by match to protein family HMM PF00248 YP_001407332.1 identified by match to protein family HMM PF03992 YP_001407333.1 identified by glimmer; putative YP_001407334.1 identified by match to protein family HMM PF00106; match to protein family HMM PF08659 YP_001407335.1 identified by match to protein family HMM PF00248 YP_001407336.1 identified by glimmer; putative YP_001407337.1 identified by glimmer; putative YP_001407338.1 identified by match to protein family HMM PF07883 YP_001407339.1 An electron-transfer protein; flavodoxin binds one FMN molecule, which serves as a redox-active prosthetic group YP_001407340.1 identified by match to protein family HMM PF01073; match to protein family HMM PF01370; match to protein family HMM PF02254; match to protein family HMM PF05368 YP_001407341.1 identified by match to protein family HMM PF00465 YP_001407342.1 identified by glimmer; putative YP_001407343.1 identified by match to protein family HMM PF03063; match to protein family HMM TIGR01702 YP_001407344.1 identified by glimmer; putative YP_001407345.1 identified by match to protein family HMM PF03180 YP_001407346.1 identified by match to protein family HMM PF00528 YP_001407347.1 identified by match to protein family HMM PF00005 YP_001407348.1 identified by match to protein family HMM PF00248 YP_001407349.1 identified by match to protein family HMM PF04055; match to protein family HMM TIGR02495 YP_001407350.1 Catalyzes the reduction of nucleoside 5'-triphosphates to 2'-deoxynucleoside 5'-triphosphates YP_001407351.1 identified by glimmer; putative YP_001407352.1 Catalyzes the rate-limiting step in dNTP synthesis YP_001407353.1 Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide YP_001407354.1 identified by match to protein family HMM PF00849 YP_001407355.1 23S rRNA m2A2503 methyltransferase; methylates the C2 position of the A2530 nucleotide in 23S rRNA; may be involved in antibiotic resistance YP_001407357.1 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_001407358.1 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_001407359.1 identified by match to protein family HMM PF00753; match to protein family HMM PF07521; match to protein family HMM TIGR00649 YP_001407360.1 identified by match to protein family HMM PF00571; match to protein family HMM PF01380; match to protein family HMM TIGR00393 YP_001407361.1 hypothetical RNA pseudouridine synthase jhp_1352; RNA pseudouridylate synthase; identified by match to protein family HMM PF00849; match to protein family HMM PF01479; match to protein family HMM TIGR00093 YP_001407362.1 identified by match to protein family HMM PF04073 YP_001407363.1 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_001407364.1 identified by match to protein family HMM PF00593; match to protein family HMM PF07715 YP_001407365.1 identified by match to protein family HMM PF07366 YP_001407367.1 catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis YP_001407368.1 identified by match to protein family HMM PF01121; match to protein family HMM TIGR00152 YP_001407369.1 involved in lysine biosynthesis; DAP epimerase; produces DL-diaminopimelate from LL-diaminopimelate YP_001407370.1 binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit YP_001407371.1 identified by match to protein family HMM PF01632; match to protein family HMM TIGR00001 YP_001407372.1 identified by match to protein family HMM PF03577 YP_001407373.1 identified by glimmer; putative YP_001407375.1 identified by glimmer; putative YP_001407376.1 catalyzes the transfer of a methyl group from 5-methyltetrahydrofolate to homocysteine to form methionine YP_001407378.1 identified by match to protein family HMM PF01073; match to protein family HMM PF01370 YP_001407379.1 identified by match to protein family HMM PF09335 YP_001407380.1 identified by match to protein family HMM PF00535 YP_001407381.1 identified by match to protein family HMM PF00486 YP_001407383.1 identified by match to protein family HMM PF01988 YP_001407384.1 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_001407385.1 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_001407386.1 Spermidine/spermine N(1)-acetyltransferase 2; Polyamine N-acetyltransferase 2; identified by match to protein family HMM PF00583 YP_001407387.1 identified by glimmer; putative YP_001407388.1 identified by match to protein family HMM PF00696; match to protein family HMM PF01472; match to protein family HMM TIGR01027 YP_001407389.1 Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway YP_001407390.1 identified by match to protein family HMM PF04471 YP_001407391.1 identified by match to protein family HMM PF01210; match to protein family HMM PF03446; match to protein family HMM PF03807; match to protein family HMM TIGR00112 YP_001407394.1 identified by match to protein family HMM PF00561 YP_001407395.1 identified by glimmer; putative YP_001407396.1 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_001407399.1 identified by match to protein family HMM PF03653 YP_001407401.1 lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis YP_001407402.1 catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate YP_001407403.1 binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase YP_001407404.1 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_001407406.1 identified by glimmer; putative YP_001407407.1 identified by match to protein family HMM PF03459; match to protein family HMM TIGR00638 YP_001407409.1 identified by match to protein family HMM PF01219 YP_001407410.1 identified by match to protein family HMM PF00884; match to protein family HMM PF08019 YP_001407411.1 identified by match to protein family HMM PF03372; match to protein family HMM TIGR00195; match to protein family HMM TIGR00633 YP_001407412.1 identified by match to protein family HMM PF02659 YP_001407414.1 identified by match to protein family HMM PF03061 YP_001407416.1 identified by match to protein family HMM PF01297 YP_001407417.1 identified by match to protein family HMM PF03824 YP_001407418.1 identified by match to protein family HMM PF00005 YP_001407419.1 identified by match to protein family HMM PF00950 YP_001407421.1 identified by match to protein family HMM PF07963; match to protein family HMM TIGR02532 YP_001407422.1 identified by match to protein family HMM PF00892 YP_001407423.1 identified by match to protein family HMM PF00892 YP_001407424.1 identified by glimmer; putative YP_001407425.1 identified by match to protein family HMM PF03150 YP_001407426.1 identified by match to protein family HMM PF00563; match to protein family HMM PF00989; match to protein family HMM TIGR00229 YP_001407428.1 Assists in DNA repair by cleaving phosphodiester bonds at apurinic or apyrimidinic sties to produce new 5' ends that are base-free deoxyribose 5-phosphate residues YP_001407429.1 identified by match to protein family HMM PF03349 YP_001407430.1 activates fatty acids by binding to coenzyme A YP_001407431.1 identified by match to protein family HMM PF03595 YP_001407433.1 involved in type III protein export during flagellum assembly YP_001407434.1 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_001407435.1 identified by glimmer; putative YP_001407436.1 Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer YP_001407437.1 hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates YP_001407438.1 identified by match to protein family HMM PF00990; match to protein family HMM TIGR00254 YP_001407439.1 cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+) YP_001407440.1 identified by match to protein family HMM PF01078; match to protein family HMM PF07728; match to protein family HMM TIGR00368 YP_001407441.1 identified by 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_001407442.1 identified by match to protein family HMM PF00551; match to protein family HMM TIGR00639 YP_001407443.1 identified by match to protein family HMM PF03741 YP_001407445.1 identified by match to protein family HMM PF01554; match to protein family HMM TIGR00797 YP_001407447.1 identified by glimmer; putative YP_001407449.1 Catalyzes the transfer of electrons from NADH to quinone YP_001407450.1 Catalyzes the transfer of electrons from NADH to quinone YP_001407451.1 Catalyzes the transfer of electrons from NADH to ubiquinone YP_001407452.1 Catalyzes the transfer of electrons from NADH to quinone YP_001407453.1 Catalyzes the transfer of electrons from NADH to quinone YP_001407454.1 Catalyzes the transfer of electrons from NADH to quinone YP_001407455.1 Catalyzes the transfer of electrons from NADH to quinone YP_001407456.1 Catalyzes the transfer of electrons from NADH to ubiquinone YP_001407459.1 Catalyzes the transfer of electrons from NADH to quinone YP_001407460.1 Catalyzes the transfer of electrons from NADH to ubiquinone YP_001407461.1 The point of entry for the majority of electrons that traverse the respiratory chain eventually resulting in the reduction of oxygen YP_001407462.1 Catalyzes the transfer of electrons from NADH to ubiquinone YP_001407463.1 identified by match to protein family HMM PF00005; match to protein family HMM TIGR01194 YP_001407464.1 identified by glimmer; putative YP_001407465.1 identified by match to protein family HMM PF00561 YP_001407466.1 identified by match to protein family HMM PF00583 YP_001407468.1 catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III YP_001407469.1 putative 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_001407470.1 NADH-dependent hydroxypyruvatereductase; hpr; gdh; hydroxypyruvate dehydrogenase; glyoxylatereductase; hpr-a; identified by match to protein family HMM PF00389; match to protein family HMM PF02826 YP_001407471.1 identified by match to protein family HMM PF03738 YP_001407472.1 identified by glimmer; putative YP_001407474.1 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_001407475.1 identified by match to protein family HMM PF00890 YP_001407476.1 identified by match to protein family HMM PF00512; match to protein family HMM PF02518 YP_001407477.1 identified by match to protein family HMM PF00072; match to protein family HMM PF00486 YP_001407478.1 identified by match to protein family HMM PF00890; match to protein family HMM TIGR01813 YP_001407479.1 identified by match to protein family HMM PF00037; match to protein family HMM TIGR02745 YP_001407480.1 identified by match to protein family HMM PF00440 YP_001407481.1 identified by match to protein family HMM PF00529; match to protein family HMM TIGR01730 YP_001407482.1 identified by match to protein family HMM PF00873; match to protein family HMM TIGR00915 YP_001407484.1 identified by glimmer; putative YP_001407485.1 identified by match to protein family HMM PF01106; match to protein family HMM PF01592; match to protein family HMM PF04324 YP_001407486.1 identified by match to protein family HMM PF00266; match to protein family HMM TIGR03403 YP_001407488.1 identified by match to protein family HMM PF01032 YP_001407489.1 identified by match to protein family HMM PF00005 YP_001407490.1 identified by match to protein family HMM PF01497 YP_001407491.1 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_001407492.1 identified by match to protein family HMM PF01266 YP_001407493.1 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_001407496.1 identified by glimmer; putative YP_001407497.1 together with moaC, is involved in the conversion of a guanosine derivative (GXP) into molybdopterin precursor Z YP_001407498.1 identified by match to protein family HMM PF04055 YP_001407500.1 identified by glimmer; putative YP_001407502.1 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_001407503.1 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_001407504.1 identified by match to protein family HMM PF00590; match to protein family HMM TIGR00096 YP_001407505.1 identified by match to protein family HMM PF00588; match to protein family HMM PF08032 YP_001407508.1 catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate YP_001407509.1 catalyzes the formation of L-aspartate 4-semialdehyde from L-homoserine YP_001407510.1 identified by match to protein family HMM PF00085; match to protein family HMM TIGR01068 YP_001407512.1 identified by match to protein family HMM PF00070; match to protein family HMM PF07992 YP_001407514.1 catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis YP_001407516.1 identified by glimmer; putative YP_001407518.1 identified by match to protein family HMM PF05935 YP_001407519.1 identified by glimmer; putative YP_001407520.1 Catalyzes first step of the de novo purine nucleotide biosynthetic pathway YP_001407521.1 identified by glimmer; putative YP_001407523.1 identified by match to protein family HMM PF00384; match to protein family HMM PF01568; match to protein family HMM TIGR01409 YP_001407524.1 identified by match to protein family HMM PF00989; match to protein family HMM PF02518; match to protein family HMM PF02743; match to protein family HMM TIGR00229 YP_001407525.1 identified by match to protein family HMM PF00072; match to protein family HMM PF00486 YP_001407528.1 identified by match to protein family HMM PF01502; match to protein family HMM PF01503; match to protein family HMM TIGR03188 YP_001407529.1 identified by match to protein family HMM PF01145 YP_001407530.1 catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids YP_001407532.1 identified by match to protein family HMM PF00578; match to protein family HMM PF08534 YP_001407533.1 identified by match to protein family HMM PF01361; match to protein family HMM TIGR00013 YP_001407534.1 identified by glimmer; putative YP_001407535.1 identified by match to protein family HMM PF05359 YP_001407536.1 identified by match to protein family HMM PF02677 YP_001407537.1 identified by glimmer; putative YP_001407538.1 identified by match to protein family HMM PF03062 YP_001407539.1 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_001407540.1 catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis YP_001407541.1 binds and unfolds substrates as part of the ClpXP protease YP_001407542.1 functions in MreBCD complex in some organisms YP_001407543.1 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_001407544.1 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_001407545.1 identified by match to protein family HMM PF06050 YP_001407546.1 identified by match to protein family HMM PF01869; match to protein family HMM TIGR00241 YP_001407547.1 identified by match to protein family HMM PF01554; match to protein family HMM PF03023; match to protein family HMM TIGR00797 YP_001407548.1 identified by match to protein family HMM PF01022 YP_001407549.1 identified by match to protein family HMM PF01370; match to protein family HMM PF07993 YP_001407550.1 identified by glimmer; putative YP_001407551.1 identified by match to protein family HMM PF01408; match to protein family HMM PF02894 YP_001407552.1 identified by match to protein family HMM PF00266; match to protein family HMM PF01041; match to protein family HMM PF01053; match to protein family HMM PF01212 YP_001407553.1 identified by match to protein family HMM PF03783 YP_001407555.1 identified by match to protein family HMM PF05643 YP_001407556.1 identified by glimmer; putative YP_001407557.1 identified by match to protein family HMM PF00892 YP_001407559.1 (NADP-Gdh; NAD(P)H-dependent glutamate dehydrogenase; converts 2-oxoglutarate to glutamate; in Escherichia coli this enzyme plays a role in glutamate synthesis when the cell is under energy restriction; uses NADPH; forms a homohexamer YP_001407560.1 identified by match to protein family HMM PF04909 YP_001407561.1 identified by match to protein family HMM PF00501; match to protein family HMM PF01553; match to protein family HMM PF07690 YP_001407562.1 identified by match to protein family HMM PF00376 YP_001407563.1 identified by match to protein family HMM PF01497 YP_001407564.1 identified by match to protein family HMM PF01032 YP_001407565.1 identified by match to protein family HMM PF00005 YP_001407566.1 identified by glimmer; putative YP_001407567.1 identified by glimmer; putative YP_001407568.1 identified by match to protein family HMM PF04368 YP_001407569.1 catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers YP_001407570.1 identified by glimmer; putative YP_001407572.1 identified by match to protein family HMM PF00989; match to protein family HMM PF02518; match to protein family HMM PF08447; match to protein family HMM TIGR00229 YP_001407573.1 CcoN; FixN YP_001407574.1 CcoO; FixO YP_001407575.1 identified by match to protein family HMM TIGR02736 YP_001407576.1 identified by match to protein family HMM PF00034; match to protein family HMM TIGR00782 YP_001407581.1 identified by match to protein family HMM PF00580 YP_001407582.1 in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit YP_001407583.1 forms a direct contact with the tRNA during translation YP_001407584.1 identified by match to protein family HMM PF00691 YP_001407585.1 identified by match to protein family HMM PF00702; match to protein family HMM TIGR01549 YP_001407586.1 identified by match to protein family HMM PF00037; match to protein family HMM PF01558; match to protein family HMM PF01855; match to protein family HMM TIGR02176 YP_001407588.1 identified by match to protein family HMM PF01177; match to protein family HMM TIGR00035 YP_001407592.1 An electron-transfer protein; flavodoxin binds one FMN molecule, which serves as a redox-active prosthetic group YP_001407593.1 identified by match to protein family HMM PF00496; match to protein family HMM TIGR02294 YP_001407594.1 identified by match to protein family HMM PF00528 YP_001407595.1 with NikABDE is involved in nickel transport into the cell YP_001407596.1 Methionine synthase, vitamin-B12 independent isozyme; Cobalamin-independent methionine synthase; identified by match to protein family HMM PF00005 YP_001407598.1 identified by glimmer; putative YP_001407599.1 identified by match to protein family HMM PF00032; match to protein family HMM PF00033 YP_001407600.1 identified by match to protein family HMM PF00355; match to protein family HMM TIGR01409; match to protein family HMM TIGR01416 YP_001407601.1 identified by match to protein family HMM PF00593 YP_001407602.1 identified by match to protein family HMM PF03929 YP_001407603.1 identified by glimmer; putative YP_001407604.1 airs; phosphoribosyl-aminoimidazole synthetase; air synthase YP_001407606.1 identified by match to protein family HMM PF00072; match to protein family HMM PF00486 YP_001407607.1 identified by match to protein family HMM PF00512; match to protein family HMM PF02518 YP_001407608.1 identified by match to protein family HMM PF00165 YP_001407609.1 identified by match to protein family HMM PF00593; match to protein family HMM PF07715 YP_001407610.1 identified by match to protein family HMM PF03929 YP_001407611.1 identified by glimmer; putative YP_001407613.1 identified by glimmer; putative YP_001407614.1 identified by match to protein family HMM PF01869; match to protein family HMM TIGR00241 YP_001407615.1 identified by match to protein family HMM PF00206; match to protein family HMM TIGR00979 YP_001407616.1 X-Pro dipeptidase; Prolinedipeptidase; Prolidase; Imidodipeptidase; identified by match to protein family HMM PF07690 YP_001407617.1 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_001407618.1 identified by match to protein family HMM PF00037 YP_001407619.1 identified by match to protein family HMM PF00361 YP_001407620.1 identified by match to protein family HMM PF00146 YP_001407621.1 interacts with formate dehydrogenase to produce an active formate hydrogenlyase complex which cleaves formate to dihydrogen and carbon dioxide YP_001407622.1 identified by match to protein family HMM PF00361 YP_001407623.1 identified by match to protein family HMM PF00329; match to protein family HMM PF00346 YP_001407624.1 electron transfer protein for hydrogenase-3; the formate hydrogenlyase complex comprises of a formate dehydrogenase, unidentified electron carriers and hydrogenase-3; in this non-energy conserving pathway, molecular hydrogen and carbodioxide are released from formate YP_001407625.1 identified by match to protein family HMM PF01058 YP_001407627.1 identified by match to protein family HMM PF01750; match to protein family HMM TIGR00072 YP_001407628.1 identified by match to protein family HMM PF01226 YP_001407629.1 identified by glimmer; putative YP_001407630.1 identified by match to protein family HMM PF03061 YP_001407631.1 identified by glimmer; putative YP_001407632.1 identified by match to protein family HMM PF00563; match to protein family HMM PF00990; match to protein family HMM TIGR00254 YP_001407633.1 identified by glimmer; putative YP_001407634.1 identified by match to protein family HMM PF00563; match to protein family HMM PF00990; match to protein family HMM TIGR00254 YP_001407636.1 identified by match to protein family HMM PF08761 YP_001407640.1 identified by glimmer; putative YP_001407642.1 catalyzes the hydrolysis of S-ribosylhomocysteine to homocysteine and autoinducer-2 YP_001407643.1 Cofacial Heme Binding To Chain Of Campylobacter Jejuni; identified by match to protein family HMM PF04187 YP_001407644.1 identified by match to protein family HMM PF00593; match to protein family HMM PF07715 YP_001407645.1 identified by match to protein family HMM PF01618 YP_001407646.1 identified by match to protein family HMM PF02472 YP_001407647.1 identified by match to protein family HMM PF03544; match to protein family HMM TIGR01352 YP_001407648.1 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_001407649.1 First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan YP_001407650.1 catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate YP_001407651.1 Catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis YP_001407652.1 identified by glimmer; putative YP_001407653.1 carries the fatty acid chain in fatty acid biosynthesis YP_001407654.1 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_001407655.1 catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine YP_001407656.1 identified by match to protein family HMM PF02578; match to protein family HMM TIGR00726 YP_001407658.1 identified by match to protein family HMM PF08238 YP_001407659.1 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_001407660.1 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_001407661.1 identified by match to protein family HMM PF00005 YP_001407662.1 identified by glimmer; putative YP_001407663.1 FliR, with proteins FliP and FliQ, forms the core of the central channel in the flagella export apparatus YP_001407665.1 Essential for recycling GMP and indirectly, cGMP YP_001407666.1 identified by match to protein family HMM PF02416; match to protein family HMM TIGR01411 YP_001407667.1 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_001407668.1 identified by match to protein family HMM PF03601; match to protein family HMM TIGR00698 YP_001407670.1 identified by match to protein family HMM PF04228 YP_001407671.1 identified by match to protein family HMM PF01467; match to protein family HMM PF02410; match to protein family HMM TIGR00090; match to protein family HMM TIGR00125; match to protein family HMM TIGR00482 YP_001407672.1 identified by match to protein family HMM PF00044; match to protein family HMM PF02800; match to protein family HMM TIGR01534 YP_001407673.1 Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway YP_001407674.1 Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate YP_001407675.1 identified by glimmer; putative YP_001407676.1 Catalyzes a key regulatory step in fatty acid biosynthesis YP_001407677.1 identified by match to protein family HMM PF00724 YP_001407678.1 identified by match to protein family HMM PF01266; match to protein family HMM PF06039 YP_001407679.1 identified by match to protein family HMM PF03544; match to protein family HMM TIGR01352 YP_001407680.1 identified by match to protein family HMM PF02472; match to protein family HMM TIGR02804 YP_001407681.1 identified by match to protein family HMM PF01618; match to protein family HMM TIGR02805 YP_001407682.1 identified by match to protein family HMM PF00593; match to protein family HMM PF07715 YP_001407683.1 identified by match to protein family HMM PF01075; match to protein family HMM TIGR02195 YP_001407684.1 identified by match to protein family HMM PF00534 YP_001407685.1 identified by match to protein family HMM PF00535 YP_001407687.1 identified by match to protein family HMM PF01522 YP_001407688.1 identified by match to protein family HMM PF00534 YP_001407689.1 identified by match to protein family HMM PF01075; match to protein family HMM TIGR02201 YP_001407690.1 identified by match to protein family HMM PF00535 YP_001407691.1 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_001407692.1 identified by match to protein family HMM PF01075; match to protein family HMM TIGR02193 YP_001407694.1 identified by match to protein family HMM PF01073; match to protein family HMM PF01370; match to protein family HMM PF04321; match to protein family HMM PF07993 YP_001407695.1 catalyzes the formation of a phosphodiester at the site of a single-strand break in duplex DNA YP_001407696.1 identified by match to protein family HMM PF01073; match to protein family HMM PF01370; match to protein family HMM PF02719; match to protein family HMM PF04321; match to protein family HMM PF07993; match to protein family HMM TIGR01179 YP_001407697.1 UDP-glc dehydrogenase; UDP-glcdh; udpgdh; eichuronic acid biosynthesis protein tuad; identified by match to protein family HMM PF00984; match to protein family HMM PF03720; match to protein family HMM PF03721; match to protein family HMM TIGR03026 YP_001407699.1 identified by match to protein family HMM PF00984; match to protein family HMM PF03720; match to protein family HMM PF03721; match to protein family HMM TIGR03026 YP_001407700.1 identified by match to protein family HMM PF02516 YP_001407701.1 identified by match to protein family HMM PF01943 YP_001407702.1 identified by match to protein family HMM PF01755 YP_001407703.1 identified by match to protein family HMM PF00535 YP_001407704.1 identified by match to protein family HMM PF00534 YP_001407705.1 identified by match to protein family HMM PF00534 YP_001407706.1 identified by match to protein family HMM PF00534 YP_001407707.1 identified by match to protein family HMM PF02516 YP_001407708.1 identified by match to protein family HMM PF00534 YP_001407709.1 identified by match to protein family HMM PF02397 YP_001407711.1 identified by match to protein family HMM PF08348 YP_001407712.1 identified by match to protein family HMM PF01042 YP_001407713.1 identified by match to protein family HMM PF03606; match to protein family HMM TIGR00771 YP_001407714.1 identified by match to protein family HMM PF01053 YP_001407715.1 Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide YP_001407716.1 identified by match to protein family HMM PF03972 YP_001407717.1 identified by match to protein family HMM PF01041 YP_001407718.1 identified by match to protein family HMM PF01073; match to protein family HMM PF01370; match to protein family HMM PF02719; match to protein family HMM PF04321 YP_001407720.1 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_001407721.1 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_001407722.1 identified by match to protein family HMM PF00072 YP_001407723.1 methylates ribosomal protein L11 at multiple amino acid positions; mutations of these genes in Escherichia coli or Thermus thermophilus has no apparent phenotype YP_001407724.1 identified by match to protein family HMM PF00004; match to protein family HMM PF01434; match to protein family HMM PF06480; match to protein family HMM PF07728; match to protein family HMM TIGR01241 YP_001407725.1 identified by match to protein family HMM PF02666 YP_001407726.1 identified by match to protein family HMM PF01066; match to protein family HMM TIGR00473 YP_001407727.1 catalyzes the formation of 2-isopropylmalate from acetyl-CoA and 2-oxoisovalerate in leucine biosynthesis YP_001407728.1 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_001407729.1 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_001407731.1 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_001407732.1 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_001407733.1 identified by match to protein family HMM PF01202 YP_001407734.1 unknown function subfamily; 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_001407735.1 catalyzes the formation of 2-dehydro-3-deoxy-D-octonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate in LPS biosynthesis YP_001407736.1 identified by match to protein family HMM PF00893 YP_001407737.1 identified by match to protein family HMM PF00893 YP_001407738.1 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_001407739.1 Regulates rRNA biosynthesis by transcriptional antitermination YP_001407740.1 type 1 subfamily; involved in last step of pyrimidine biosynthesis; converts orotidine 5'-phosphate to UMP and carbon dioxide; OMP decarboxylase; OMPDCase; OMPdecase YP_001407742.1 identified by match to protein family HMM PF01066 YP_001407743.1 identified by match to protein family HMM PF01553 YP_001407744.1 identified by match to protein family HMM PF01148 YP_001407745.1 identified by match to protein family HMM PF00561 YP_001407746.1 identified by match to protein family HMM PF00782; match to protein family HMM PF01569 YP_001407747.1 identified by glimmer; putative YP_001407749.1 identified by match to protein family HMM PF01648 YP_001407750.1 identified by glimmer; putative YP_001407751.1 identified by match to protein family HMM PF00109; match to protein family HMM PF02801 YP_001407753.1 identified by match to protein family HMM PF00106; match to protein family HMM PF08659 YP_001407754.1 identified by match to protein family HMM PF00109; match to protein family HMM PF02801 YP_001407758.1 identified by match to protein family HMM PF01553 YP_001407762.1 5-enolpyruvylshikimate-3-phosphate synthase; epsp synthase; epsps YP_001407763.1 identified by match to protein family HMM PF00535 YP_001407764.1 identified by match to protein family HMM PF03061 YP_001407767.1 identified by match to protein family HMM PF02464; match to protein family HMM TIGR00199 YP_001407768.1 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_001407769.1 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_001407770.1 catalyzes the synthesis of xanthosine monophosphate by the NAD+ dependent oxidation of inosine monophosphate YP_001407771.1 identified by match to protein family HMM PF00561; match to protein family HMM TIGR01392 YP_001407773.1 identified by match to protein family HMM PF00795 YP_001407774.1 DNA-3-methyladenineglycosylase i; 3-methyladenine-dna glycosylase i, constitutive; tagi; DNA-3-methyladenine glycosidase i; identified by match to protein family HMM PF03352 YP_001407775.1 Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis YP_001407776.1 identified by glimmer; putative YP_001407778.1 MutS2; MutS-II; involved in blocking homologous and homeologous recombination; has ATPase activity stimulated by recombination intermediates; inhibits DNA strand exchange YP_001407779.1 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_001407781.1 short form of enzyme; requires HisZ for function; catalyzes the formation of N'-5'-phosphoribosyl-ATP from phosphoribosyl pyrophosphate; crucial role in histidine biosynthesis; forms heteromultimer of HisG and HisZ YP_001407782.1 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_001407783.1 Cysteinyl-tRNA(Sec) selenium transferase; Selenocysteine synthase; Selenocysteinyl-tRNA(Sec) synthase YP_001407785.1 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_001407786.1 identified by match to protein family HMM PF00437; match to protein family HMM TIGR01420 YP_001407787.1 identified by match to protein family HMM PF02674 YP_001407788.1 identified by match to protein family HMM PF01475 YP_001407789.1 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_001407790.1 catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate YP_001407791.1 identified by match to protein family HMM PF08966 YP_001407792.1 identified by match to protein family HMM PF05036 YP_001407793.1 AroE; catalyzes the conversion of shikimate to 3-dehydroshikimate YP_001407794.1 identified by match to protein family HMM PF03480 YP_001407795.1 identified by glimmer; putative YP_001407796.1 identified by match to protein family HMM PF00224; match to protein family HMM PF02887; match to protein family HMM TIGR01064 YP_001407798.1 involved in a recombinational process of DNA repair, independent of the recBC complex YP_001407799.1 identified by match to protein family HMM PF00512; match to protein family HMM PF00672; match to protein family HMM PF02518 YP_001407800.1 identified by match to protein family HMM PF00072; match to protein family HMM PF00486 YP_001407801.1 identified by match to protein family HMM PF01556 YP_001407802.1 identified by glimmer; putative YP_001407803.1 identified by glimmer; putative YP_001407804.1 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_001407806.1 identified by glimmer; putative YP_001407807.1 identified by match to protein family HMM PF03600 YP_001407808.1 contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway YP_001407809.1 identified by match to protein family HMM PF01555 YP_001407810.1 identified by match to protein family HMM TIGR03187 YP_001407812.1 identified by match to protein family HMM PF07883 YP_001407813.1 identified by match to protein family HMM PF01637 YP_001407815.1 identified by match to protein family HMM PF07690; match to protein family HMM TIGR00710 YP_001407816.1 catalyzes the formation of uroporphyrinogen-III from hydroxymethylbilane; functions in tetrapyrrole and heme biosynthesis YP_001407817.1 catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis YP_001407818.1 identified by match to protein family HMM PF06271 YP_001407819.1 identified by match to protein family HMM PF04453 YP_001407821.1 identified by match to protein family HMM PF00013; match to protein family HMM PF00575; match to protein family HMM PF01138; match to protein family HMM PF03725; match to protein family HMM PF03726 YP_001407822.1 identified by match to protein family HMM PF00582 YP_001407824.1 identified by glimmer; putative YP_001407825.1 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_001407826.1 identified by match to protein family HMM PF00209 YP_001407827.1 identified by match to protein family HMM PF00209 YP_001407828.1 identified by match to protein family HMM PF00209 YP_001407829.1 identified by match to protein family HMM PF04290 YP_001407830.1 identified by match to protein family HMM PF06808; match to protein family HMM TIGR00786 YP_001407832.1 identified by match to protein family HMM PF00364; match to protein family HMM PF00682 YP_001407833.1 PEP carboxykinase; PEP carboxylase; PEPCK; catalyzes the phosphorylation and decarboxylation of oxaloacetate to form phosphoenolpyruvate using ATP YP_001407834.1 identified by match to protein family HMM PF00188 YP_001407835.1 identified by match to protein family HMM PF00375 YP_001407836.1 identified by match to protein family HMM PF01177; match to protein family HMM TIGR00035 YP_001407837.1 identified by match to protein family HMM PF00375 YP_001407838.1 identified by match to protein family HMM PF00160 YP_001407839.1 identified by match to protein family HMM PF01709; match to protein family HMM TIGR01033 YP_001407840.1 identified by match to protein family HMM PF00583 YP_001407842.1 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_001407845.1 identified by match to protein family HMM PF07690 YP_001407846.1 identified by match to protein family HMM PF00165; match to protein family HMM PF06719 YP_001407849.1 isopropylmalate isomerase; alpha-ipm isomerase; ipmi YP_001407850.1 catalyzes the formation of arginine from (N-L-arginino)succinate YP_001407851.1 identified by match to protein family HMM PF07656 YP_001407852.1 identified by match to protein family HMM PF00015 YP_001407853.1 identified by match to protein family HMM PF01230 YP_001407854.1 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_001407855.1 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_001407856.1 catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis YP_001407857.1 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_001407858.1 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_001407860.1 catalyzes the formation of 3-phosphonooxypyruvate from 3-phospho-D-glycerate in serine biosynthesis; can also reduce alpha ketoglutarate to form 2-hydroxyglutarate YP_001407861.1 Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA YP_001407862.1 identified by glimmer; putative YP_001407863.1 identified by match to protein family HMM PF01965; match to protein family HMM TIGR01383 YP_001407864.1 identified by match to protein family HMM PF00076 YP_001407865.1 identified by match to protein family HMM PF00749 YP_001407866.1 catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; main replicative polymerase YP_001407867.1 identified by match to protein family HMM PF02525 YP_001407871.1 identified by match to protein family HMM PF00512; match to protein family HMM PF02518 YP_001407872.1 identified by match to protein family HMM PF03008 YP_001407874.1 identified by match to protein family HMM PF02581; match to protein family HMM TIGR00693 YP_001407875.1 identified by match to protein family HMM PF08543; match to protein family HMM TIGR00097 YP_001407876.1 identified by match to protein family HMM PF00497 YP_001407877.1 identified by match to protein family HMM PF00005 YP_001407878.1 identified by match to protein family HMM PF00528; match to protein family HMM TIGR01726 YP_001407879.1 identified by glimmer; putative YP_001407880.1 identified by match to protein family HMM PF00474; match to protein family HMM TIGR00813; match to protein family HMM TIGR02121 YP_001407882.1 identified by match to protein family HMM PF01520 YP_001407883.1 identified by match to protein family HMM PF03060 YP_001407884.1 catalyzes the formation of tyrosyl-tRNA(Tyr) from tyrosine and tRNA(Tyr) YP_001407885.1 identified by match to protein family HMM PF01842; match to protein family HMM PF01966; match to protein family HMM PF02824; match to protein family HMM PF04607; match to protein family HMM TIGR00691 YP_001407886.1 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_001407887.1 Catalyzes the phosphorylation of UMP to UDP YP_001407888.1 identified by match to protein family HMM PF01551 YP_001407889.1 identified by match to protein family HMM PF02687 YP_001407890.1 identified by match to protein family HMM PF00005 YP_001407891.1 rRNA-uridine isomerase D; rRNA pseudouridylate synthase D; identified by match to protein family HMM PF00849; match to protein family HMM PF01479; match to protein family HMM TIGR00005 YP_001407892.1 identified by match to protein family HMM PF01098; match to protein family HMM TIGR02210 YP_001407894.1 identified by match to protein family HMM PF00719 YP_001407895.1 identified by match to protein family HMM PF04076 YP_001407896.1 identified by match to protein family HMM PF01070 YP_001407897.1 identified by match to protein family HMM PF02652; match to protein family HMM TIGR00795 YP_001407898.1 essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP YP_001407899.1 catalyzes the phosphorylation of NAD to NADP YP_001407900.1 identified by match to protein family HMM PF00072; match to protein family HMM PF00990; match to protein family HMM TIGR00254 YP_001407901.1 identified by match to protein family HMM PF01026; match to protein family HMM TIGR00010 YP_001407902.1 identified by match to protein family HMM PF01464; match to protein family HMM PF01476 YP_001407903.1 identified by match to protein family HMM PF03330; match to protein family HMM PF05036; match to protein family HMM TIGR00413 YP_001407904.1 catalyzes the dehydration of D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate to 3-(imidazol-4-yl)-2-oxopropyl phosphate in histidine biosynthesis YP_001407905.1 identified by match to protein family HMM TIGR01670 YP_001407906.1 identified by match to protein family HMM PF06835 YP_001407907.1 identified by match to protein family HMM PF03968; match to protein family HMM TIGR03002 YP_001407908.1 binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential YP_001407909.1 catalyzes the formation of N-acetyl-L-glutamate from acetyl-CoA and L-glutamate YP_001407911.1 identified by match to protein family HMM PF00905; match to protein family HMM PF03717; match to protein family HMM TIGR03423 YP_001407912.1 identified by match to protein family HMM PF02130; match to protein family HMM TIGR00043 YP_001407913.1 identified by match to protein family HMM PF02568; match to protein family HMM PF06508; match to protein family HMM TIGR00364 YP_001407914.1 catalyzes the reduction of hydroxylamine to ammonia and water YP_001407916.1 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_001407918.1 catalyzes the formation of D-fructose 6-phosphate from fructose-1,6-bisphosphate YP_001407919.1 identified by match to protein family HMM PF03205; match to protein family HMM TIGR00176 YP_001407921.1 identified by match to protein family HMM PF01464 YP_001407922.1 identified by match to protein family HMM PF02325 YP_001407923.1 charges one glutamine molecule and pairs it with tRNA(Gln) YP_001407924.1 forms homopentamer; channel that opens in response to pressure or hypoosmotic shock YP_001407925.1 identified by match to protein family HMM PF00027 YP_001407926.1 identified by match to protein family HMM PF03264 YP_001407928.1 identified by match to protein family HMM PF00149 YP_001407929.1 catalyzes the decarboxylaton of phospatidyl-L-sering to phosphatidylethanolamine YP_001407930.1 Methionineadenosyltransferase; AdoMet synthetase; MAT; identified by match to protein family HMM PF07274 YP_001407931.1 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_001407932.1 catalyzes the removal of N-terminal amino acids preferably leucine from various peptides YP_001407934.1 catalyzes a salvage reaction resulting in the formation of AMP which is metabolically less costly than a de novo synthesis YP_001407936.1 identified by match to protein family HMM PF02502; match to protein family HMM TIGR00689; match to protein family HMM TIGR01120 YP_001407939.1 identified by glimmer; putative YP_001407940.1 identified by match to protein family HMM PF05957 YP_001407941.1 identified by glimmer; putative YP_001407942.1 identified by match to protein family HMM PF02163 YP_001407943.1 identified by match to protein family HMM PF00717; match to protein family HMM TIGR02227 YP_001407944.1 catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate YP_001407946.1 Converts (S)-4-amino-5-oxopentanoate to 5-aminolevulinate during the porphyrin biosynthesis pathway YP_001407949.1 identified by match to protein family HMM PF07690 YP_001407951.1 identified by match to protein family HMM TIGR00789 YP_001407952.1 identified by match to protein family HMM PF00015; match to protein family HMM PF00672; match to protein family HMM PF08269 YP_001407953.1 identified by match to protein family HMM PF01339 YP_001407954.1 identified by match to protein family HMM PF01739 YP_001407955.1 identified by match to protein family HMM PF04264 YP_001407956.1 identified by match to protein family HMM PF04332; match to protein family HMM PF07690 YP_001407957.1 identified by glimmer; putative YP_001407959.1 identified by match to protein family HMM PF01957 YP_001407960.1 identified by glimmer; putative YP_001407961.1 identified by glimmer; putative YP_001407962.1 identified by match to protein family HMM PF04055; match to protein family HMM TIGR00423 YP_001407963.1 identified by match to protein family HMM PF00675; match to protein family HMM PF05193 YP_001407964.1 catalyzes branch migration in Holliday junction intermediates YP_001407965.1 identified by match to protein family HMM PF01145 YP_001407966.1 identified by match to protein family HMM PF00005 YP_001407967.1 identified by match to protein family HMM PF01032 YP_001407969.1 identified by match to protein family HMM PF01497 YP_001407970.1 identified by match to protein family HMM PF01497 YP_001407971.1 identified by match to protein family HMM PF00593 YP_001407972.1 identified by glimmer; putative YP_001407974.1 identified by glimmer; putative YP_001407975.1 identified by glimmer; putative YP_001407976.1 identified by match to protein family HMM PF00881 YP_001407979.1 identified by match to protein family HMM PF08238 YP_001407980.1 identified by glimmer; putative YP_001407981.1 identified by glimmer; putative YP_001407982.1 identified by match to protein family HMM PF07509 YP_001407983.1 identified by match to protein family HMM PF07505 YP_001407984.1 identified by match to protein family HMM PF02482; match to protein family HMM TIGR00741 YP_001407986.1 identified by match to protein family HMM PF07963; match to protein family HMM TIGR02532 YP_001407987.1 identified by match to protein family HMM PF07963; match to protein family HMM TIGR02532 YP_001407988.1 identified by glimmer; putative YP_001407989.1 binds to flagellin and appears to stabilize flagellin during flagella assembly YP_001407992.1 identified by match to protein family HMM PF00004; match to protein family HMM PF05362; match to protein family HMM PF07728; match to protein family HMM TIGR00763 YP_001407993.1 pbg; hydroxymethylbilanesynthase; hmbs; pre-uroporphyrinogen synthase YP_001407994.1 binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit YP_001407995.1 identified by match to protein family HMM PF00436; match to protein family HMM TIGR00621 YP_001407996.1 binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21 YP_001407997.1 required for the assembly and function of the DNAX complex which is required for the assembly of the beta subunit onto primed DNA YP_001407998.1 identified by match to protein family HMM PF00773; match to protein family HMM PF08206 YP_001407999.1 identified by match to protein family HMM PF08668 YP_001408000.1 catalyzes the formation of (R)-2,3-dihydroxy-3-methylbutanoate from (S)-2-hydroxy-2-methyl-3-oxobutanoate in valine and isoleucine biosynthesis YP_001408001.1 identified by match to protein family HMM PF04748 YP_001408002.1 identified by match to protein family HMM PF02481; match to protein family HMM TIGR00732 YP_001408003.1 similar to RuvC resolvase with substantial differences; NMR structural information suggests this protein is monomeric; unknown cellular function YP_001408004.1 identified by glimmer; putative YP_001408005.1 Synthesizes oQ from preQ1 in a single S-adenosylmethionine-requiring step YP_001408006.1 identified by match to protein family HMM PF00902; match to protein family HMM TIGR00945 YP_001408007.1 identified by match to protein family HMM PF02416; match to protein family HMM TIGR01410 YP_001408008.1 catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III YP_001408009.1 identified by glimmer; putative YP_001408010.1 hydrolyzes diadenosine polyphosphate YP_001408011.1 catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP, in Bacillus, lysine sensitive; regulated by response to starvation. YP_001408013.1 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_001408014.1 identified by match to protein family HMM PF00809; match to protein family HMM TIGR01496 YP_001408015.1 identified by glimmer; putative YP_001408016.1 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_001408017.1 identified by match to protein family HMM PF01479; match to protein family HMM PF01728 YP_001408018.1 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_001408019.1 identified by match to protein family HMM PF02390; match to protein family HMM PF05175; match to protein family HMM PF08241; match to protein family HMM PF08242; match to protein family HMM TIGR00740 YP_001408021.1 identified by match to protein family HMM PF00593; match to protein family HMM PF07715 YP_001408022.1 identified by match to protein family HMM PF01497 YP_001408024.1 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_001408025.1 identified by match to protein family HMM PF02082 YP_001408026.1 membrane protein involved in the flagellar export apparatus YP_001408029.1 identified by match to protein family HMM PF08238 YP_001408030.1 catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis YP_001408031.1 identified by match to protein family HMM PF01979; match to protein family HMM PF07969; match to protein family HMM TIGR00857 YP_001408032.1 identified by glimmer; putative YP_001408033.1 Acts as a negative regulator of the grpE-dnaK-dnaJ and groELS class I heat shock operons by preventing heat-shock induction YP_001408034.1 identified by match to protein family HMM PF01025 YP_001408035.1 identified by glimmer; putative YP_001408036.1 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_001408037.1 identified by match to protein family HMM PF03976 YP_001408038.1 identified by glimmer; putative YP_001408039.1 identified by match to protein family HMM PF00085; match to protein family HMM PF02683 YP_001408042.1 identified by match to protein family HMM PF00890; match to protein family HMM PF01266; match to protein family HMM PF07992; match to protein family HMM TIGR01409; match to protein family HMM TIGR01813 YP_001408043.1 identified by glimmer; putative YP_001408044.1 identified by match to protein family HMM PF00512; match to protein family HMM PF02518 YP_001408045.1 identified by match to protein family HMM PF00072; match to protein family HMM PF00486 YP_001408048.1 identified by glimmer; putative YP_001408050.1 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_001408051.1 catalyzes the formation of L-threonine from O-phospho-L-homoserine YP_001408052.1 catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate YP_001408053.1 transfers the gamma-phosphate of ATP to the 4' position of a tetraacyldisaccharide 1-phosphate intermediate to form tetraacyldisaccharide 1,4'-bis-phosphate YP_001408054.1 identified by match to protein family HMM PF01041 YP_001408055.1 identified by match to protein family HMM PF02540; match to protein family HMM PF06508; match to protein family HMM TIGR00552 YP_001408056.1 identified by match to protein family HMM PF00753 YP_001408057.1 identified by match to protein family HMM PF05538 YP_001408058.1 identified by match to protein family HMM PF03061 YP_001408059.1 identified by match to protein family HMM PF08003; match to protein family HMM PF08241; match to protein family HMM PF08242 YP_001408061.1 identified by match to protein family HMM PF01841; match to protein family HMM TIGR01409 YP_001408063.1 periplasmic mercury ion-binding protein; Mercury scavenger protein; identified by match to protein family HMM PF00403 YP_001408065.1 identified by match to protein family HMM PF00730; match to protein family HMM TIGR01083 YP_001408066.1 identified by match to protein family HMM PF00639 YP_001408067.1 catalyzes the formation of glycerone phosphate and glyceraldehyde 3-phosphate from fructose 1,6, bisphosphate YP_001408069.1 identified by match to protein family HMM PF00691 YP_001408071.1 catalyzes the oxidation of L-histidinol to L-histidinaldehyde and then to L-histidine in histidine biosynthesis; functions as a dimer YP_001408072.1 identified by match to protein family HMM PF00669 YP_001408073.1 identified by glimmer; putative YP_001408074.1 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_001408075.1 identified by match to protein family HMM PF00460 YP_001408076.1 makes up the distal portion of the flagellar basal body rod YP_001408077.1 identified by glimmer; putative YP_001408078.1 identified by match to protein family HMM PF03591 YP_001408079.1 identified by match to protein family HMM PF05437 YP_001408080.1 identified by match to protein family HMM PF00710; match to protein family HMM TIGR00520 YP_001408081.1 identified by match to protein family HMM PF01810 YP_001408082.1 identified by match to protein family HMM PF00694; match to protein family HMM TIGR02087 YP_001408083.1 catalyzes the oxidation of 3-isopropylmalate to 3-carboxy-4-methyl-2-oxopentanoate in leucine biosynthesis YP_001408086.1 identified by match to protein family HMM PF01743 YP_001408088.1 identified by match to protein family HMM PF00551; match to protein family HMM TIGR00655 YP_001408089.1 identified by match to protein family HMM PF03372 YP_001408090.1 identified by glimmer; putative YP_001408091.1 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_001408092.1 identified by match to protein family HMM PF01729; match to protein family HMM TIGR01334 YP_001408094.1 identified by match to protein family HMM PF00122; match to protein family HMM PF00702; match to protein family HMM TIGR01494; match to protein family HMM TIGR01525 YP_001408100.1 identified by match to protein family HMM PF01475 YP_001408104.1 catalyzes the formation of N-acetyl-l-glutamate 5-semialdehyde from 2-oxoglutarate and N(2)-acetyl-L-ornithine YP_001408105.1 identified by match to protein family HMM PF02636 YP_001408106.1 identified by match to protein family HMM PF04073; match to protein family HMM TIGR00011 YP_001408107.1 interacts with the cytoplasmic MS ring of the basal body and may act to stabilize the MotAB complexes which surround the MS ring YP_001408108.1 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_001408109.1 identified by match to protein family HMM PF03797; match to protein family HMM TIGR01414 YP_001408110.1 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_001408111.1 identified by match to protein family HMM PF04892 YP_001408112.1 identified by match to protein family HMM PF00448; match to protein family HMM TIGR00064 YP_001408113.1 identified by match to protein family HMM PF00085; match to protein family HMM PF00578; match to protein family HMM PF08534 YP_001408114.1 identified by match to protein family HMM PF01812; match to protein family HMM TIGR02727 YP_001408115.1 protein from Staphylococcus aureus has phosphodiesterase activity against 2'-3'-cAMP and 2'-3'-cGMP YP_001408119.1 identified by match to protein family HMM PF00633; match to protein family HMM TIGR00426 YP_001408120.1 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_001408121.1 identified by match to protein family HMM PF00015; match to protein family HMM PF00672; match to protein family HMM PF02743 YP_001408122.1 identified by match to protein family HMM PF00892 YP_001408123.1 identified by match to protein family HMM PF05406 YP_001408124.1 6-O-methylguanine-DNA methyltransferase; mgmt; O-6-methylguanine-DNA-alkyltransferase; identified by match to protein family HMM PF01035; match to protein family HMM PF02870; match to protein family HMM TIGR00589 YP_001408125.1 identified by glimmer; putative YP_001408126.1 catalyzes the conversion of citrate to isocitrate and the conversion of 2-methylaconitate to 2-methylisocitrate YP_001408127.1 identified by match to protein family HMM PF07859 YP_001408129.1 identified by match to protein family HMM PF00023 YP_001408130.1 identified by match to protein family HMM PF00106; match to protein family HMM PF01370; match to protein family HMM PF08659 YP_001408131.1 identified by match to protein family HMM PF03553 YP_001408132.1 catalyzes the formation of 5-methyl-uridine at position 54 in all tRNAs YP_001408133.1 identified by match to protein family HMM PF02629 YP_001408134.1 catalyzes the formation of 2-oxobutanoate from L-threonine YP_001408137.1 mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability YP_001408138.1 identified by match to protein family HMM PF03739 YP_001408139.1 identified by match to protein family HMM PF01478; match to protein family HMM PF06750 YP_001408141.1 catalyzes the conjugation of cysteine to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine, which is then decarboxylated to form 4'-phosphopantotheine YP_001408142.1 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_001408143.1 identified by match to protein family HMM PF01618 YP_001408144.1 identified by match to protein family HMM PF00691 YP_001408145.1 FliP, with proteins FliQ and FliR, forms the core of the central channel in the flagella export apparatus YP_001408148.1 identified by glimmer; putative YP_001408149.1 identified by match to protein family HMM PF00892 YP_001408150.1 identified by glimmer; putative YP_001408151.1 identified by match to protein family HMM PF00171 YP_001408152.1 identified by match to protein family HMM PF00512; match to protein family HMM PF02518 YP_001408153.1 identified by match to protein family HMM PF00072; match to protein family HMM PF00486 YP_001408154.1 identified by glimmer; putative YP_001408155.1 identified by match to protein family HMM PF03547 YP_001408156.1 identified by match to protein family HMM PF03883 YP_001408157.1 identified by glimmer; putative YP_001408158.1 identified by glimmer; putative YP_001408159.1 identified by match to protein family HMM PF01867; match to protein family HMM TIGR00287 YP_001408160.1 identified by match to protein family HMM PF02647; match to protein family HMM TIGR01573 YP_001408161.1 identified by match to protein family HMM PF01930 YP_001408162.1 identified by match to protein family HMM PF00271; match to protein family HMM TIGR01587 YP_001408164.1 identified by match to protein family HMM PF05107; match to protein family HMM TIGR01595; match to protein family HMM TIGR02590 YP_001408165.1 identified by glimmer; putative YP_001408166.1 identified by glimmer; putative YP_001408167.1 with FlgK acts as a hook filament junction protein to join the flagellar filament to the hook YP_001408168.1 identified by match to protein family HMM PF01580 YP_001408169.1 identified by match to protein family HMM PF00589 YP_001408170.1 identified by glimmer; putative YP_001408171.1 identified by glimmer; putative YP_001408174.1 identified by glimmer; putative YP_001408175.1 identified by glimmer; putative YP_001408176.1 identified by glimmer; putative YP_001408177.1 identified by glimmer; putative YP_001408179.1 identified by glimmer; putative YP_001408181.1 identified by glimmer; putative YP_001408182.1 identified by glimmer; putative YP_001408185.1 identified by match to protein family HMM PF03681 YP_001408187.1 identified by glimmer; putative YP_001408188.1 identified by match to protein family HMM PF00271 YP_001408189.1 identified by glimmer; putative YP_001408190.1 identified by match to protein family HMM PF04261; match to protein family HMM TIGR01413 YP_001408192.1 identified by match to protein family HMM PF00384; match to protein family HMM PF01568 YP_001408193.1 identified by match to protein family HMM PF00384; match to protein family HMM PF01568; match to protein family HMM TIGR00509 YP_001408195.1 identified by match to protein family HMM PF00384; match to protein family HMM PF01568 YP_001408196.1 identified by match to protein family HMM PF00015; match to protein family HMM PF02743 YP_001408197.1 identified by match to protein family HMM PF00015; match to protein family HMM PF00672; match to protein family HMM PF02743 YP_001408198.1 identified by match to protein family HMM TIGR00044 YP_001408199.1 identified by match to protein family HMM PF02163; match to protein family HMM TIGR00054 YP_001408200.1 identified by match to protein family HMM PF01066; match to protein family HMM TIGR00560 YP_001408201.1 Acts on the hydroxyl group at position 7 of the steroid frame YP_001408202.1 catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis YP_001408203.1 identified by match to protein family HMM PF00675; match to protein family HMM PF05193 YP_001408204.1 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_001408205.1 identified by match to protein family HMM PF00005; match to protein family HMM PF00664 YP_001408206.1 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_001408207.1 identified by match to protein family HMM PF01554; match to protein family HMM PF03023; match to protein family HMM TIGR01695 YP_001408208.1 identified by match to protein family HMM PF00072 YP_001408209.1 identified by match to protein family HMM PF00512; match to protein family HMM PF02518 YP_001408211.1 identified by match to protein family HMM PF01323 YP_001408212.1 identified by match to protein family HMM PF05935 YP_001408214.1 plays an essential role in ATP-dependent branch migration of the Holliday junction YP_001408215.1 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_001408217.1 identified by match to protein family HMM PF00561 YP_001408218.1 identified by match to protein family HMM PF02875; match to protein family HMM PF08245 YP_001408220.1 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_001408221.1 identified by match to protein family HMM PF01515; match to protein family HMM TIGR00651 YP_001408222.1 part of the flagellar basal body which consists of four rings L,P, S and M mounted on a central rod YP_001408223.1 catalyzes the formation of 2-acetolactate from pyruvate, leucine resistant; also known as acetolactate synthase 3 large subunit YP_001408224.1 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_001408225.1 adds the O-linked and N-linked 3(R)-hydroxy fatty acids to the glucosamine disaccharide during lipid A biosynthesis YP_001408227.1 Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr) YP_001408228.1 identified by match to protein family HMM PF02405; match to protein family HMM TIGR00056 YP_001408229.1 identified by match to protein family HMM PF00005 YP_001408230.1 identified by match to protein family HMM PF02470 YP_001408232.1 identified by match to protein family HMM PF02080 YP_001408233.1 catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis YP_001408234.1 identified by match to protein family HMM PF00924 YP_001408235.1 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_001408236.1 identified by match to protein family HMM PF00004; match to protein family HMM PF01434; match to protein family HMM PF06480 YP_001408237.1 identified by match to protein family HMM PF00994; match to protein family HMM TIGR00177 YP_001408238.1 identified by match to protein family HMM PF09335 YP_001408239.1 identified by match to protein family HMM PF01810 YP_001408240.1 identified by match to protein family HMM PF03180 YP_001408241.1 identified by match to protein family HMM PF03180 YP_001408242.1 identified by match to protein family HMM PF00528 YP_001408243.1 identified by match to protein family HMM PF00005 YP_001408244.1 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_001408245.1 identified by match to protein family HMM PF01835 YP_001408246.1 identified by match to protein family HMM PF00905; match to protein family HMM PF00912 YP_001408247.1 identified by match to protein family HMM PF00593 YP_001408248.1 identified by match to protein family HMM PF00550; match to protein family HMM PF00580; match to protein family HMM TIGR00517 YP_001408249.1 identified by match to protein family HMM PF00529; match to protein family HMM TIGR01730 YP_001408250.1 identified by match to protein family HMM PF00005; match to protein family HMM PF02687 YP_001408251.1 identified by match to protein family HMM PF02321 YP_001408253.1 identified by match to protein family HMM PF00300 YP_001408254.1 identified by match to protein family HMM PF04305 YP_001408255.1 identified by match to protein family HMM PF01694 YP_001408257.1 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_001408258.1 identified by match to protein family HMM PF00994; match to protein family HMM PF03453; match to protein family HMM TIGR00177 YP_001408259.1 required for the assembly of the flagellar basal body P-ring YP_001408260.1 identified by match to protein family HMM PF02441; match to protein family HMM TIGR00421 YP_001408261.1 Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA YP_001408262.1 catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP) YP_001408263.1 identified by match to protein family HMM PF02597; match to protein family HMM TIGR01683 YP_001408264.1 identified by match to protein family HMM PF05690 YP_001408265.1 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_001408266.1 identified by match to protein family HMM PF02581 YP_001408267.1 identified by glimmer; putative YP_001408268.1 identified by match to protein family HMM PF00111; match to protein family HMM TIGR00384 YP_001408269.1 identified by match to protein family HMM PF00890; match to protein family HMM PF01266; match to protein family HMM PF02910; match to protein family HMM PF03486; match to protein family HMM PF07992; match to protein family HMM TIGR01409 YP_001408270.1 identified by glimmer; putative YP_001408271.1 identified by match to protein family HMM PF00258 YP_001408272.1 identified by match to protein family HMM PF01558 YP_001408273.1 identified by match to protein family HMM PF02775 YP_001408274.1 identified by match to protein family HMM PF01855 YP_001408275.1 identified by match to protein family HMM PF00037 YP_001408276.1 identified by match to protein family HMM PF00549; match to protein family HMM PF02629; match to protein family HMM TIGR01019 YP_001408277.1 identified by match to protein family HMM PF00549; match to protein family HMM PF08442; match to protein family HMM TIGR01016 YP_001408278.1 identified by match to protein family HMM PF00056; match to protein family HMM PF02866 YP_001408279.1 identified by match to protein family HMM PF02618 YP_001408281.1 identified by glimmer; putative YP_001408282.1 identified by match to protein family HMM PF01155; match to protein family HMM TIGR00100 YP_001408283.1 identified by match to protein family HMM PF00586; match to protein family HMM PF02769; match to protein family HMM TIGR02124 YP_001408284.1 identified by match to protein family HMM PF01924; match to protein family HMM TIGR00075 YP_001408285.1 identified by match to protein family HMM PF01455; match to protein family HMM TIGR00074 YP_001408286.1 identified by match to protein family HMM PF02492; match to protein family HMM TIGR00073 YP_001408289.1 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_001408290.1 Inhibits transcription at high concentrations of nickel YP_001408291.1 identified by match to protein family HMM PF00708; match to protein family HMM PF01300; match to protein family HMM PF07503; match to protein family HMM TIGR00143 YP_001408293.1 identified by match to protein family HMM PF01750; match to protein family HMM TIGR00072 YP_001408294.1 identified by match to protein family HMM PF01292; match to protein family HMM TIGR02125 YP_001408295.1 Membrane-bound hydrogenase large subunit; Hydrogen:quinoneoxidoreductase; identified by match to protein family HMM PF00374 YP_001408296.1 identified by match to protein family HMM PF01058; match to protein family HMM PF08425; match to protein family HMM TIGR00391; match to protein family HMM TIGR01409 YP_001408297.1 identified by match to protein family HMM PF00004; match to protein family HMM PF02861; match to protein family HMM PF07724; match to protein family HMM PF07728 YP_001408298.1 identified by match to protein family HMM PF00595; match to protein family HMM PF03572; match to protein family HMM TIGR00225 YP_001408299.1 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_001408300.1 identified by match to protein family HMM PF02700; match to protein family HMM TIGR00302 YP_001408301.1 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_001408302.1 1-agpacyltransferase; 1-agpat; lysophosphatidic acid acyltransferase; lpaat; identified by match to protein family HMM PF01553 YP_001408303.1 identified by match to protein family HMM PF00593; match to protein family HMM PF07715; match to protein family HMM TIGR01783 YP_001408304.1 identified by match to protein family HMM PF00593; match to protein family HMM PF07715; match to protein family HMM TIGR01783 YP_001408305.1 identified by match to protein family HMM PF03929 YP_001408306.1 molecular chaperone YP_001408307.1 identified by glimmer; putative YP_001408310.1 identified by glimmer; putative YP_001408311.1 identified by match to protein family HMM PF01177; match to protein family HMM TIGR00067 YP_001408312.1 identified by match to protein family HMM PF00589 YP_001408313.1 S-adenosylmethionine-6-N',N'-adenosyl(rRNA) dimethyltransferase; 16S rRNA dimethylase) (Highlevel kasugamycin resistance protein KsgA; Kasugamycindimethyltransferase; identified by match to protein family HMM PF01098 YP_001408314.1 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_001408315.1 igp synthase cyclase subunit; igp synthase subunit hisf; imgp synthasesubunit hisf; igps subunit hisf YP_001408318.1 Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide YP_001408319.1 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_001408320.1 identified by match to protein family HMM PF00005 YP_001408321.1 identified by match to protein family HMM PF02367; match to protein family HMM TIGR00150 YP_001408322.1 identified by match to protein family HMM PF01479 YP_001408323.1 identified by match to protein family HMM PF00756 YP_001408324.1 identified by match to protein family HMM PF00593 YP_001408325.1 identified by match to protein family HMM PF07715 YP_001408326.1 catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming YP_001408327.1 in Escherichia coli this protein is wrapped around the base of the L1 stalk YP_001408328.1 heat shock protein involved in degradation of misfolded proteins YP_001408329.1 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_001408333.1 identified by match to protein family HMM PF00263; match to protein family HMM PF07655; match to protein family HMM PF07660; match to protein family HMM TIGR02519 YP_001408336.1 identified by glimmer; putative YP_001408337.1 Type II traffic warden ATPase; Cholera toxin secretion protein EpsE; identified by match to protein family HMM PF00437; match to protein family HMM PF05157 YP_001408338.1 identified by match to protein family HMM PF00482 YP_001408339.1 identified by match to protein family HMM PF00989; match to protein family HMM PF08447; match to protein family HMM TIGR00229 YP_001408340.1 identified by match to protein family HMM PF00015 YP_001408341.1 identified by glimmer; putative YP_001408342.1 identified by match to protein family HMM PF02637 YP_001408343.1 identified by match to protein family HMM PF02541 YP_001408344.1 identified by match to protein family HMM PF01384 YP_001408347.1 catalyzes the selenophosphate-dependent transfer of selenium from selenophosphate for conversion of 2-thiouridine to 2-selenouridine at the wobble position in tRNA YP_001408348.1 identified by match to protein family HMM PF01230 YP_001408349.1 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_001408351.1 identified by match to protein family HMM PF03692 YP_001408352.1 identified by match to protein family HMM PF05175 YP_001408354.1 identified by match to protein family HMM PF00070; match to protein family HMM PF07992 YP_001408355.1 identified by glimmer; putative YP_001408357.1 identified by match to protein family HMM TIGR00688 YP_001408358.1 identified by match to protein family HMM PF00892; match to protein family HMM TIGR00688 YP_001408359.1 identified by match to protein family HMM PF00892; match to protein family HMM TIGR00688 YP_001408361.1 identified by match to protein family HMM PF00933 YP_001408362.1 catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate YP_001408363.1 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_001408364.1 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_001408365.1 identified by match to protein family HMM PF01925 YP_001408366.1 identified by match to protein family HMM PF00080 YP_001408367.1 identified by match to protein family HMM TIGR02757 YP_001408368.1 with FlgL acts as a hook filament junction protein to join the flagellar filament to the hook YP_001408372.1 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_001408373.1 identified by match to protein family HMM PF03602; match to protein family HMM TIGR00095 YP_001408375.1 possibly involved in flagella export YP_001408376.1 Also called hook-associated protein 2; involved in flagellin assembly YP_001408377.1 flagellin specific chaperone YP_001408379.1 catalyzes the modification of U13 in tRNA(Glu) YP_001408380.1 catalyzes the formation of thiamine diphosphate from thiamine phosphate ant ATP YP_001408382.1 identified by glimmer; putative YP_001408383.1 identified by match to protein family HMM PF01977; match to protein family HMM TIGR00148 YP_001408384.1 identified by match to protein family HMM PF00515; match to protein family HMM PF00884 YP_001408385.1 identified by glimmer; putative YP_001408386.1 transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis YP_001408388.1 catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro) YP_001408389.1 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_001408390.1 identified by match to protein family HMM PF00348 YP_001408393.1 identified by match to protein family HMM PF00702; match to protein family HMM TIGR01549 YP_001408395.1 identified by match to protein family HMM PF01053; match to protein family HMM TIGR01326 YP_001408396.1 the Vibrio parahaemolyticus gene VP2867 was found to be a potassium/proton antiporter; can rapidly extrude potassium against a potassium gradient at alkaline pH when cloned and expressed in Escherichia coli YP_001408397.1 apparently involved in regulation of cell wall biosynthesis YP_001408398.1 identified by match to protein family HMM PF00512; match to protein family HMM PF00672 YP_001408399.1 identified by match to protein family HMM PF00072; match to protein family HMM PF00486 YP_001408401.1 identified by match to protein family HMM PF00089; match to protein family HMM PF00595; match to protein family HMM TIGR02037 YP_001408402.1 identified by match to protein family HMM PF00226; match to protein family HMM PF01556 YP_001408403.1 identified by match to protein family HMM PF00376 YP_001408404.1 identified by match to protein family HMM PF00999; match to protein family HMM PF02254 YP_001408405.1 identified by match to protein family HMM PF02687 YP_001408406.1 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_001408407.1 participates with LolB in the incorporation of lipoprotein into the outer membrane YP_001408410.1 identified by match to protein family HMM PF00877 YP_001408411.1 identified by glimmer; putative YP_001408412.1 identified by match to protein family HMM PF04463 YP_001408413.1 d-aspartateaminotransferase; d-amino acid aminotransferase; d-amino acidtransaminase; daat; identified by match to protein family HMM PF01063 YP_001408414.1 identified by glimmer; putative YP_001408418.1 identified by match to protein family HMM PF01795; match to protein family HMM TIGR00006 YP_001408419.1 identified by match to protein family HMM PF00596 YP_001408421.1 identified by match to protein family HMM PF02491; match to protein family HMM TIGR01174 YP_001408422.1 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_001408424.1 identified by match to protein family HMM PF01883 YP_001408427.1 identified by match to protein family HMM PF01625; match to protein family HMM PF01641; match to protein family HMM TIGR00357; match to protein family HMM TIGR00401 YP_001408428.1 involved in de novo purine biosynthesis YP_001408429.1 identified by match to protein family HMM PF00226 YP_001408430.1 identified by glimmer; putative YP_001408431.1 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_001408432.1 identified by glimmer; putative YP_001408433.1 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_001408435.1 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_001408436.1 identified by match to protein family HMM PF01809; match to protein family HMM TIGR00278 YP_001408437.1 RNaseP protein; RNaseP protein; Protein C5; identified by match to protein family HMM TIGR00188 YP_001408439.1 identified by match to protein family HMM PF03167 YP_001408442.1 identified by match to protein family HMM PF06738 YP_001408445.1 identified by match to protein family HMM PF01596; match to protein family HMM PF05175; match to protein family HMM TIGR00536 YP_001408446.1 identified by match to protein family HMM PF01435 YP_001408447.1 identified by glimmer; putative YP_001408448.1 identified by match to protein family HMM PF00209 YP_001408450.1 identified by match to protein family HMM PF02525 YP_001408451.1 identified by match to protein family HMM PF08238 YP_001408452.1 identified by glimmer; putative YP_001408453.1 identified by match to protein family HMM PF00005; match to protein family HMM PF02463 YP_001408454.1 identified by match to protein family HMM PF01554; match to protein family HMM TIGR00797 YP_001408455.1 identified by match to protein family HMM PF01863 YP_001408456.1 identified by match to protein family HMM PF08238 YP_001408457.1 identified by match to protein family HMM PF06808; match to protein family HMM TIGR02123 YP_001408458.1 identified by match to protein family HMM TIGR02122 YP_001408459.1 identified by match to protein family HMM PF00795 YP_001408461.1 identified by match to protein family HMM PF01545; match to protein family HMM TIGR01297 YP_001408462.1 identified by match to protein family HMM PF04371 YP_001408464.1 identified by match to protein family HMM PF00034 YP_001408465.1 identified by match to protein family HMM PF00528; match to protein family HMM TIGR01726 YP_001408466.1 identified by match to protein family HMM PF00528; match to protein family HMM TIGR01726 YP_001408467.1 identified by match to protein family HMM PF00005 YP_001408468.1 identified by match to protein family HMM PF00497 YP_001408469.1 identified by match to protein family HMM PF02397; match to protein family HMM TIGR03025 YP_001408470.1 identified by glimmer; putative YP_001408471.1 identified by match to protein family HMM PF00483; match to protein family HMM PF01050; match to protein family HMM PF07883; match to protein family HMM TIGR01479 YP_001408472.1 identified by match to protein family HMM PF00534 YP_001408473.1 identified by match to protein family HMM PF00534 YP_001408474.1 identified by match to protein family HMM PF00534 YP_001408475.1 identified by match to protein family HMM PF00534 YP_001408476.1 identified by match to protein family HMM PF00535 YP_001408477.1 identified by match to protein family HMM PF07021; match to protein family HMM PF08241; match to protein family HMM PF08242 YP_001408478.1 identified by match to protein family HMM PF00534 YP_001408479.1 identified by glimmer; putative YP_001408480.1 identified by match to protein family HMM PF01943 YP_001408481.1 identified by match to protein family HMM PF01041; match to protein family HMM PF01212 YP_001408482.1 identified by match to protein family HMM PF01073; match to protein family HMM PF01370; match to protein family HMM PF02719; match to protein family HMM PF04321; match to protein family HMM PF07993; match to protein family HMM TIGR01181 YP_001408483.1 identified by match to protein family HMM PF00483; match to protein family HMM TIGR01207 YP_001408484.1 identified by match to protein family HMM PF00408; match to protein family HMM PF02878; match to protein family HMM PF02879; match to protein family HMM PF02880 YP_001408485.1 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_001408486.1 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_001408487.1 identified by glimmer; putative YP_001408488.1 identified by glimmer; putative YP_001408489.1 identified by glimmer; putative YP_001408491.1 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_001408494.1 identified by match to protein family HMM PF07963; match to protein family HMM TIGR02532 YP_001408495.1 binding of PriA to forked DNA starts the assembly of the primosome, also possesses 3'-5' helicase activity YP_001408496.1 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_001408497.1 identified by match to protein family HMM PF08238 YP_001408498.1 identified by match to protein family HMM PF03772; match to protein family HMM TIGR00360 YP_001408499.1 identified by match to protein family HMM PF03807 YP_001408500.1 identified by match to protein family HMM PF03631; match to protein family HMM TIGR00765 YP_001408501.1 identified by glimmer; putative YP_001408504.1 identified by match to protein family HMM PF01551 YP_001408505.1 identified by match to protein family HMM PF00571; match to protein family HMM PF01769; match to protein family HMM PF03448; match to protein family HMM TIGR00400 YP_001408506.1 UDPGpyrophosphatase; UGPPase; nucleoside diphosphate-linked moiety xmotif 14; nudix motif 14; identified by match to protein family HMM PF00293; match to protein family HMM TIGR00052 YP_001408507.1 catalyzes the reversible transfer of the terminal phosphate of ATP to form a long chain polyphosphate YP_001408508.1 3'-5' exonuclease of DNA polymerase III YP_001408509.1 identified by glimmer; putative YP_001408510.1 identified by glimmer; putative YP_001408511.1 required for 70S ribosome assembly YP_001408512.1 identified by match to protein family HMM PF02080; match to protein family HMM PF02254; match to protein family HMM PF07885 YP_001408513.1 bifunctional arginine biosynthesis protein ArgJ; functions at the 1st and 5th steps in arginine biosynthesis; involved in synthesis of acetylglutamate from glutamate and acetyl-CoA and ornithine by transacetylation between acetylornithine and glutmate YP_001408514.1 identified by match to protein family HMM PF04325 YP_001408515.1 identified by match to protein family HMM TIGR01172 YP_001408516.1 identified by match to protein family HMM PF00291; match to protein family HMM TIGR01136; match to protein family HMM TIGR01139 YP_001408517.1 identified by match to protein family HMM PF00633; match to protein family HMM PF00730 YP_001408518.1 identified by match to protein family HMM PF05673 YP_001408519.1 identified by match to protein family HMM PF00270; match to protein family HMM PF00271; match to protein family HMM PF02559; match to protein family HMM PF03461; match to protein family HMM PF04851; match to protein family HMM TIGR00580 YP_001408520.1 identified by match to protein family HMM PF08245; match to protein family HMM TIGR01499 YP_001408521.1 identified by match to protein family HMM PF00990; match to protein family HMM TIGR00254 YP_001408523.1 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_001408525.1 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_001408526.1 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_001408527.1 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_001408528.1 Transfers the fatty acyl group on membrane lipoproteins YP_001408530.1 catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase YP_001408531.1 involved in the import of serine and threonine coupled with the import of sodium YP_001408532.1 identified by match to protein family HMM PF01432; match to protein family HMM PF08439; match to protein family HMM TIGR02290 YP_001408534.1 identified by match to protein family HMM PF00580 YP_001408535.1 catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs YP_001408536.1 identified by match to protein family HMM PF02599; match to protein family HMM TIGR00202 YP_001408537.1 catalyzes the phosphorylation of 4-diphosphocytidyl-2-C-methyl-D-erythritol in the nonmevalonate pathway of isoprenoid biosynthesis YP_001408538.1 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_001408539.1 identified by glimmer; putative YP_001408540.1 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_001408541.1 with FlgF and B makes up the proximal portion of the flagellar basal body rod YP_001408542.1 forms a junction between the M-ring and FlgB during flagella biosynthesis YP_001408543.1 identified by match to protein family HMM PF00905; match to protein family HMM PF03717 YP_001408545.1 identified by match to protein family HMM PF01408 YP_001408546.1 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_001408547.1 isopropylmalate isomerase; alpha-ipm isomerase; ipmi YP_001408548.1 Maf; overexpression in Bacillus subtilis inhibits septation in the dividing cell YP_001408549.1 identified by match to protein family HMM PF00905; match to protein family HMM PF00912; match to protein family HMM TIGR02074 YP_001408552.1 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_001408553.1 methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA YP_001408554.1 identified by match to protein family HMM PF01782; match to protein family HMM PF05239; match to protein family HMM TIGR02273 YP_001408555.1 identified by match to protein family HMM PF00886; match to protein family HMM TIGR00002 YP_001408556.1 identified by match to protein family HMM PF00448; match to protein family HMM PF02881; match to protein family HMM PF02978; match to protein family HMM TIGR00959 YP_001408557.1 identified by match to protein family HMM PF00849 YP_001408558.1 catalyzes the transfer of 2-keto-3-deoxy-D-manno-octulosonic acid to lipid A YP_001408559.1 identified by match to protein family HMM PF02591 YP_001408560.1 identified by match to protein family HMM PF01784; match to protein family HMM TIGR00486 YP_001408561.1 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_001408562.1 identified by match to protein family HMM PF06445 YP_001408564.1 identified by match to protein family HMM PF00731; match to protein family HMM TIGR01162 YP_001408565.1 identified by match to protein family HMM PF01136 YP_001408566.1 identified by glimmer; putative YP_001408567.1 identified by glimmer; putative YP_001408568.1 identified by match to protein family HMM PF02811; match to protein family HMM PF03458; match to protein family HMM TIGR01856 YP_001408569.1 identified by match to protein family HMM PF00120; match to protein family HMM PF03951; match to protein family HMM TIGR00653 YP_001408570.1 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_001408571.1 An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes YP_001408572.1 identified by glimmer; putative YP_001408573.1 identified by match to protein family HMM PF01545; match to protein family HMM TIGR01297 YP_001408574.1 identified by match to protein family HMM TIGR01409 YP_001408575.1 identified by match to protein family HMM PF00291 YP_001408576.1 identified by match to protein family HMM PF01042 YP_001408577.1 identified by match to protein family HMM PF00122; match to protein family HMM PF00702; match to protein family HMM TIGR01494; match to protein family HMM TIGR01511; match to protein family HMM TIGR01525 YP_001408578.1 identified by match to protein family HMM TIGR00847 YP_001408579.1 identified by match to protein family HMM TIGR01409 YP_001408580.1 identified by match to protein family HMM PF00126; match to protein family HMM PF03466 YP_001408581.1 modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination YP_001408583.1 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_001408584.1 identified by match to protein family HMM PF04028 YP_001408589.1 identified by match to protein family HMM PF01171; match to protein family HMM TIGR02432 YP_001408590.1 identified by match to protein family HMM PF00919; match to protein family HMM PF04055; match to protein family HMM TIGR00089 YP_001408591.1 catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine YP_001408592.1 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_001408593.1 identified by match to protein family HMM PF08238 YP_001408595.1 identified by match to protein family HMM PF00070; match to protein family HMM PF02852; match to protein family HMM PF07992 YP_001408596.1 identified by match to protein family HMM PF08238 YP_001408597.1 identified by match to protein family HMM PF01380; match to protein family HMM TIGR00441 YP_001408598.1 identified by match to protein family HMM PF00294; match to protein family HMM PF01467; match to protein family HMM TIGR00125; match to protein family HMM TIGR02198; match to protein family HMM TIGR02199 YP_001408599.1 identified by match to protein family HMM PF00106; match to protein family HMM PF01073; match to protein family HMM PF01370; match to protein family HMM PF02719; match to protein family HMM PF04321; match to protein family HMM PF07993; match to protein family HMM TIGR02197 YP_001408600.1 identified by match to protein family HMM PF00034 YP_001408601.1 identified by match to protein family HMM PF00633; match to protein family HMM TIGR00426 YP_001408602.1 identified by match to protein family HMM PF07963; match to protein family HMM TIGR02532 YP_001408604.1 identified by match to protein family HMM PF00156 YP_001408605.1 identified by match to protein family HMM PF00860; match to protein family HMM PF00916 YP_001408606.1 identified by match to protein family HMM PF04055; match to protein family HMM TIGR00423 YP_001408608.1 Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source YP_001408610.1 identified by glimmer; putative YP_001408611.1 identified by glimmer; putative YP_001408615.1 identified by glimmer; putative YP_001408617.1 identified by match to protein family HMM PF03600; match to protein family HMM PF03605; match to protein family HMM TIGR00770 YP_001408618.1 identified by match to protein family HMM PF00206 YP_001408619.1 RppK; phosphoribosylpyrophosphate synthetase; p-rib-pp synthetase; prpp synthetase; identified by match to protein family HMM PF00206 YP_001408620.1 identified by match to protein family HMM PF03972 YP_001408621.1 identified by glimmer; putative YP_001408623.1 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_001408624.1 identified by match to protein family HMM PF00072 YP_001408626.1 identified by match to protein family HMM PF04608 YP_001408628.1 identified by match to protein family HMM PF01578 YP_001408630.1 identified by match to protein family HMM PF05538 YP_001408631.1 identified by glimmer; putative YP_001408634.1 identified by match to protein family HMM PF00210 YP_001408635.1 identified by glimmer; putative YP_001408636.1 EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene YP_001408637.1 binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit YP_001408638.1 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_001408639.1 identified by match to protein family HMM PF01979; match to protein family HMM TIGR01975 YP_001408640.1 identified by match to protein family HMM PF03553; match to protein family HMM TIGR00931 YP_001408641.1 identified by match to protein family HMM PF07681 YP_001408642.1 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_001408643.1 binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit YP_001408644.1 in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA YP_001408645.1 binds directly to 23S ribosomal RNA YP_001408646.1 Modulates Rho-dependent transcription termination YP_001408647.1 forms a complex with SecY and SecG; SecYEG forms a putative protein-conducting channel to which secA binds and translocates targeted polypeptides across the cytoplasmic membrane, a process driven by ATP and a proton-motive force YP_001408648.1 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_001408651.1 identified by match to protein family HMM PF00196 YP_001408653.1 identified by match to protein family HMM PF00529; match to protein family HMM TIGR01843 YP_001408654.1 identified by match to protein family HMM PF00005; match to protein family HMM PF00664; match to protein family HMM TIGR03375 YP_001408655.1 identified by match to protein family HMM PF00563; match to protein family HMM PF00672; match to protein family HMM PF00990; match to protein family HMM TIGR00254 YP_001408657.1 identified by match to protein family HMM PF02321 YP_001408658.1 catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III YP_001408660.1 catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation YP_001408661.1 catalyzes the formation of porphobilinogen from 5-aminolevulinate YP_001408662.1 catalyzes the conversion of GTP to formate and 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine and diphosphate YP_001408663.1 identified by match to protein family HMM PF02527; match to protein family HMM TIGR00138 YP_001408665.1 identified by glimmer; putative YP_001408666.1 identified by match to protein family HMM PF01435 YP_001408667.1 identified by glimmer; putative YP_001408668.1 identified by glimmer; putative YP_001408670.1 converts L-alanine to D-alanine which is used in cell wall biosynthesis; binds one pyridoxal phosphate per monomer; forms a homodimer YP_001408673.1 identified by match to protein family HMM PF04314 YP_001408675.1 identified by match to protein family HMM PF02630 YP_001408676.1 identified by match to protein family HMM PF00581 YP_001408677.1 identified by match to protein family HMM PF00881 YP_001408678.1 identified by match to protein family HMM PF02678; match to protein family HMM PF05726 YP_001408679.1 identified by match to protein family HMM PF01047 YP_001408680.1 identified by glimmer; putative YP_001408681.1 identified by match to protein family HMM PF03927 YP_001408683.1 identified by match to protein family HMM PF00037 YP_001408684.1 identified by match to protein family HMM PF03892 YP_001408685.1 identified by match to protein family HMM PF00037; match to protein family HMM TIGR02163 YP_001408686.1 part of NapHG quinol dehydrogenase; couples electron transfer from ubiquinone-ubiquinol couple via NapC/B to NapA; secreted by twin arginine translocation pathway YP_001408687.1 periplasmic; catalytic subunit; with NapBC catalyzes the reduction of nitrate to nitrite; NapAB receives electrons from NapC YP_001408688.1 identified by glimmer; putative YP_001408689.1 identified by match to protein family HMM PF01627 YP_001408690.1 catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate YP_001408691.1 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_001408692.1 identified by match to protein family HMM PF01594 YP_001408693.1 identified by match to protein family HMM PF01230 YP_001408695.1 identified by match to protein family HMM PF00512; match to protein family HMM PF02518 YP_001408696.1 identified by match to protein family HMM PF00072; match to protein family HMM PF00486 YP_001408697.1 identified by match to protein family HMM PF03916 YP_001408698.1 identified by match to protein family HMM PF00037 YP_001408699.1 identified by 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_001408700.1 identified by glimmer; putative YP_001408701.1 identified by match to protein family HMM PF03605; match to protein family HMM TIGR00770 YP_001408702.1 identified by match to protein family HMM PF00206 YP_001408704.1 identified by match to protein family HMM PF00005 YP_001408705.1 identified by match to protein family HMM PF06940 YP_001408706.1 catalyzes the formation of D-fructose 6-phosphate from D-glucose 6-phosphate YP_001408707.1 identified by match to protein family HMM PF00483; match to protein family HMM TIGR01099 YP_001408708.1 identified by match to protein family HMM PF01205 YP_001408709.1 transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein YP_001408710.1 identified by match to protein family HMM PF02967 YP_001408711.1 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_001408712.1 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_001408713.1 identified by match to protein family HMM PF03573 YP_001408714.1 identified by match to protein family HMM PF00350 YP_001408715.1 identified by match to protein family HMM PF03992; match to protein family HMM TIGR00738 YP_001408716.1 identified by match to protein family HMM PF00903 YP_001408717.1 identified by match to protein family HMM PF00593; match to protein family HMM PF07715 YP_001408718.1 identified by glimmer; putative YP_001408719.1 identified by glimmer; putative YP_001408720.1 identified by match to protein family HMM PF00675; match to protein family HMM PF05193 YP_001408721.1 identified by glimmer; putative YP_001408723.1 identified by match to protein family HMM PF00005 YP_001408724.1 identified by match to protein family HMM TIGR01352 YP_001408725.1 identified by match to protein family HMM PF07715 YP_001408726.1 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_001408727.1 identified by match to protein family HMM PF00589 YP_001408728.1 identified by match to protein family HMM PF01381 YP_001408730.1 identified by match to protein family HMM PF05016; match to protein family HMM TIGR02385 YP_001408732.1 identified by match to protein family HMM PF01420 YP_001408733.1 identified by match to protein family HMM PF00589 YP_001408734.1 identified by match to protein family HMM PF01420 YP_001408735.1 identified by match to protein family HMM PF02384; match to protein family HMM PF05175 YP_001408736.1 identified by match to protein family HMM PF00270; match to protein family HMM PF00271; match to protein family HMM PF04313; match to protein family HMM PF04851; match to protein family HMM PF08463 YP_001408737.1 identified by glimmer; putative YP_001408738.1 identified by match to protein family HMM PF04055 YP_001408739.1 identified by match to protein family HMM PF00015; match to protein family HMM PF00672 YP_001408740.1 catalyzes the formation of coproporphyrinogen from uroporphyrinogen III YP_001408741.1 identified by match to protein family HMM PF03350 YP_001408742.1 identified by glimmer; putative YP_001408745.1 identified by glimmer; putative YP_001408746.1 catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde YP_001408747.1 identified by match to protein family HMM PF00072; match to protein family HMM PF00158; match to protein family HMM PF02954 YP_001408749.1 identified by match to protein family HMM PF04164 YP_001408750.1 negatively supercoils closed circular double-stranded DNA YP_001408752.1 identified by glimmer; putative YP_001408754.1 identified by match to protein family HMM PF01361; match to protein family HMM TIGR00013 YP_001408755.1 binds to the ribosome on the universally-conserved alpha-sarcin loop YP_001408757.1 identified by glimmer; putative YP_001408758.1 identified by match to protein family HMM PF01545; match to protein family HMM TIGR01297 YP_001408759.1 identified by glimmer; putative YP_001408760.1 identified by glimmer; putative YP_001408761.1 identified by match to protein family HMM PF02082 YP_001408762.1 catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP YP_001408763.1 identified by glimmer; putative YP_001408764.1 identified by match to protein family HMM PF04343 YP_001408765.1 identified by glimmer; putative YP_001408766.1 catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs YP_001408767.1 identified by match to protein family HMM PF03641; match to protein family HMM TIGR00730 YP_001408768.1 One of three proteins involved in switching the direction of the flagellar rotation YP_001408769.1 with FliG and FliN makes up the switch complex which is involved in switching the direction of the flagella rotation YP_001408770.1 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_001408772.1 identified by match to protein family HMM PF01656 YP_001408773.1 positive regulator of class III flagellar genes YP_001408774.1 identified by match to protein family HMM PF01288; match to protein family HMM TIGR01498 YP_001408775.1 identified by match to protein family HMM PF00557 YP_001408776.1 catalyzes the formation of 3-dehydroshikimate from 3-dehydroquinate in chorismate biosynthesis YP_001408777.1 identified by glimmer; putative YP_001408778.1 Catalyzes the hydrolytic cleavage of a carbon-halogen bond in N-ethylammeline YP_001408779.1 identified by match to protein family HMM PF01343; match to protein family HMM TIGR00706 YP_001408780.1 identified by match to protein family HMM PF00023 YP_001408781.1 identified by match to protein family HMM PF00383; match to protein family HMM TIGR00326 YP_001408782.1 identified by match to protein family HMM PF01268 YP_001408783.1 identified by match to protein family HMM PF02576 YP_001408784.1 associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock YP_001408785.1 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_001408787.1 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_001408788.1 identified by match to protein family HMM PF01551 YP_001408789.1 catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate YP_001408790.1 identified by match to protein family HMM PF01103; match to protein family HMM PF07244; match to protein family HMM TIGR03303 YP_001408791.1 catalyzes the carboxylation of acetyl-CoA to malonyl-CoA; forms a tetramer of AccA2D2 subunits YP_001408792.1 identified by match to protein family HMM PF02590 YP_001408793.1 identified by match to protein family HMM PF01258 YP_001408795.1 identified by match to protein family HMM PF01207 YP_001408797.1 identified by match to protein family HMM PF00092 YP_001408798.1 identified by match to protein family HMM PF01171; match to protein family HMM PF06508 YP_001408799.1 enables the cleavage of the glycosidic bond in both 5'-methylthioadenosine and S-adenosylhomocysteine YP_001408800.1 identified by match to protein family HMM PF00698; match to protein family HMM TIGR00128 YP_001408801.1 identified by match to protein family HMM PF00254 YP_001408803.1 identified by match to protein family HMM PF00691 YP_001408804.1 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_001408806.1 identified by match to protein family HMM PF02472 YP_001408807.1 identified by match to protein family HMM PF01618 YP_001408808.1 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_001408809.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit YP_001408810.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit YP_001408811.1 produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit YP_001408812.1 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_001408813.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B is part of the membrane proton channel. YP_001408814.1 Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B' is part of the membrane proton channel. YP_001408815.1 identified by match to protein family HMM PF02195; match to protein family HMM TIGR00180 YP_001408816.1 identified by match to protein family HMM PF01656 YP_001408817.1 catalyzes the formation of biotinyl-5'-AMP, also acts as a transcriptional repressor of the biotin operon YP_001408818.1 identified by match to protein family HMM PF00551; match to protein family HMM PF02911; match to protein family HMM TIGR00460 YP_001408819.1 identified by glimmer; putative YP_001408820.1 identified by match to protein family HMM PF00893 YP_001408821.1 essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication YP_001408822.1 involved in the peptidyltransferase reaction during translation YP_001408823.1 identified by match to protein family HMM PF00829; match to protein family HMM TIGR00061 YP_001408825.1 1-deoxyxylulose-5-phosphate synthase; dxp synthase; dxps YP_001408826.1 identified by match to protein family HMM PF03605; match to protein family HMM TIGR00770 YP_001408828.1 identified by match to protein family HMM PF01969; match to protein family HMM TIGR00299 YP_001408829.1 identified by match to protein family HMM PF01171; match to protein family HMM PF06508; match to protein family HMM TIGR00268 YP_001408831.1 Involved in the tartrate degradation pathway YP_001408832.1 Involved in the tartrate degradation pathway YP_001408833.1 identified by glimmer; putative YP_001408834.1 identified by match to protein family HMM PF03600 YP_001408835.1 identified by match to protein family HMM PF00392 YP_001408836.1 identified by match to protein family HMM PF00710 YP_001408837.1 identified by match to protein family HMM PF03600; match to protein family HMM PF06808 YP_001408838.1 identified by glimmer; putative YP_001408839.1 identified by match to protein family HMM PF00106 YP_001408840.1 has 3'-5' exonuclease, 5'-3' exonuclease and 5'-3'polymerase activities, primarily functions to fill gaps during DNA replication and repair YP_001408841.1 identified by glimmer; putative YP_001408842.1 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_001408843.1 catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate YP_001408845.1 involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY YP_001408846.1 3-oxoacyl-[acyl-carrier-protein] synthase III; Beta-ketoacyl-ACP synthase III; KAS III; EcFabH; FabH; beta-ketoacyl-acyl carrier protein synthase III; catalyzes the condensation of acetyl-CoA with malonyl-ACP to initiate cycles of fatty acid elongation; differs from 3-oxoacyl-(acyl carrier protein) synthase I and II in that it utilizes CoA thioesters as primers rather than acyl-ACPs YP_001408847.1 identified by match to protein family HMM PF00578; match to protein family HMM PF08534 YP_001408848.1 identified by match to protein family HMM PF07238 YP_001408850.1 involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsX YP_001408851.1 identified by match to protein family HMM PF02152 YP_001408852.1 identified by match to protein family HMM PF00072; match to protein family HMM PF00486 YP_001408853.1 identified by match to protein family HMM PF00512; match to protein family HMM PF00672; match to protein family HMM PF02518 YP_001408854.1 NDK; NDP kinase; Nucleoside-2-P kinase; identified by match to protein family HMM PF02541 YP_001408856.1 One of three proteins involved in switching the direction of the flagellar rotation YP_001408858.1 catalyzes the formation of indole and glyceraldehyde 3-phosphate from indoleglycerol phosphate in tryptophan biosynthesis YP_001408859.1 catalyzes the formation of L-tryptophan from L-serine and 1-(indol-3-yl)glycerol 3-phosphate YP_001408860.1 identified by match to protein family HMM PF00697 YP_001408861.1 identified by match to protein family HMM PF00117; match to protein family HMM PF00591; match to protein family HMM TIGR00566; match to protein family HMM TIGR01245 YP_001408862.1 identified by match to protein family HMM PF00425 YP_001408863.1 identified by match to protein family HMM PF01925 YP_001408864.1 identified by match to protein family HMM PF02600 YP_001408865.1 identified by glimmer; putative YP_001408866.1 identified by match to protein family HMM PF08241; match to protein family HMM PF08242 YP_001408867.1 identified by match to protein family HMM PF02086 YP_001408868.1 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_001408869.1 bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides YP_001408870.1 Catalyzes the carbon methylation reaction in the biosynthesis of ubiquinone YP_001408871.1 identified by match to protein family HMM PF05235 YP_001408872.1 identified by match to protein family HMM PF01475 YP_001408873.1 catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate YP_001408874.1 One of three proteins involved in switching the direction of the flagellar rotation YP_001408875.1 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_001408876.1 catalyzes the formation of L-histidinol phosphate from imidazole-acetol phosphate and glutamate in histidine biosynthesis YP_001408877.1 identified by 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_001408878.1 identified by match to protein family HMM PF00278; match to protein family HMM PF02784; match to protein family HMM TIGR01048 YP_001408879.1 identified by match to protein family HMM PF03739 YP_001408880.1 Enables the recycling of peptidyl-tRNAs produced at termination of translation YP_001408881.1 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_001408882.1 identified by match to protein family HMM PF00437; match to protein family HMM TIGR01420 YP_001408883.1 Important for the balance of metabolites in the pentose-phosphate pathway YP_001408884.1 identified by match to protein family HMM PF00702; match to protein family HMM TIGR00338; match to protein family HMM TIGR01488 YP_001408885.1 identified by match to protein family HMM PF01584 YP_001408886.1 identified by 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_001408887.1 identified by match to protein family HMM PF00072; match to protein family HMM PF01584 YP_001408889.1 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_001408890.1 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_001408891.1 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_001408893.1 catalyzes the conversion of a phosphate monoester to an alcohol and a phosphate YP_001408894.1 identified by match to protein family HMM PF00899 YP_001408895.1 identified by match to protein family HMM PF00890; match to protein family HMM PF01266; match to protein family HMM TIGR01409; match to protein family HMM TIGR01813 YP_001408896.1 identified by match to protein family HMM PF00890; match to protein family HMM PF01266; match to protein family HMM PF07992; match to protein family HMM TIGR01409; match to protein family HMM TIGR01813 YP_001408897.1 identified by match to protein family HMM PF00126; match to protein family HMM PF03466 YP_001408898.1 5'-methylthioadenosinenucleosidase; S-adenosylhomocysteine nucleosidase YP_001408900.1 catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis YP_001408901.1 May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine YP_001408902.1 identified by match to protein family HMM PF00563; match to protein family HMM PF00990; match to protein family HMM PF08447; match to protein family HMM TIGR00229; match to protein family HMM TIGR00254 YP_001408903.1 identified by match to protein family HMM PF01206 YP_001408904.1 identified by match to protein family HMM PF00126 YP_001408905.1 identified by glimmer; putative YP_001408906.1 identified by match to protein family HMM TIGR01583 YP_001408907.1 identified by match to protein family HMM PF00278; match to protein family HMM TIGR01047 YP_001408908.1 identified by match to protein family HMM PF02597 YP_001408909.1 identified by match to protein family HMM PF00593; match to protein family HMM PF07715; match to protein family HMM TIGR01783 YP_001408910.1 identified by match to protein family HMM PF00005; match to protein family HMM PF05992; match to protein family HMM PF06472 YP_001408912.1 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_001408914.1 identified by match to protein family HMM PF00583; match to protein family HMM TIGR01575 YP_001408915.1 identified by glimmer; putative YP_001408916.1 identified by glimmer; putative YP_001408918.1 identified by match to protein family HMM PF00890; match to protein family HMM PF01266; match to protein family HMM PF03486; match to protein family HMM PF07992 YP_001408919.1 identified by match to protein family HMM PF00083; match to protein family HMM PF07690 YP_001408920.1 identified by glimmer; putative YP_001408921.1 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_001408922.1 identified by match to protein family HMM PF01810 YP_001408923.1 identified by match to protein family HMM PF03435 YP_001408927.1 identified by match to protein family HMM PF05940 YP_001408928.1 identified by match to protein family HMM PF00005 YP_001408929.1 identified by match to protein family HMM PF00528 YP_001408931.1 identified by match to protein family HMM PF00593 YP_001408933.1 identified by match to protein family HMM PF08534 YP_001408934.1 identified by match to protein family HMM PF00005 YP_001408935.1 identified by match to protein family HMM PF02687 YP_001408936.1 identified by match to protein family HMM PF02687 YP_001408937.1 identified by match to protein family HMM PF04945 YP_001408939.1 identified by match to protein family HMM PF03239 YP_001408940.1 identified by match to protein family HMM PF00037 YP_001408941.1 identified by match to protein family HMM PF00384; match to protein family HMM PF01568 YP_001408942.1 identified by match to protein family HMM TIGR01409 YP_001408944.1 identified by match to protein family HMM PF00037 YP_001408945.1 catalyzes the formation of selenocysteinyl-tRNA(Sec) from seryl-tRNA(Sec) and L-selenophosphate in selenoprotein biosynthesis YP_001408946.1 identified by match to protein family HMM PF00009; match to protein family HMM PF03144; match to protein family HMM PF09107; match to protein family HMM TIGR00231; match to protein family HMM TIGR00475 YP_001408948.1 identified by match to protein family HMM PF02621 YP_001408949.1 identified by match to protein family HMM PF02525 YP_001408951.1 Catalyzes the formation of uracil and 5-phospho-alpha-D-ribosy 1-diphosphate from UMP and diphosphate YP_001408952.1 identified by match to protein family HMM PF00390; match to protein family HMM PF03949 YP_001408953.1 Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation YP_001408954.1 identified by match to protein family HMM PF09312 YP_001408955.1 identified by match to protein family HMM PF00528; match to protein family HMM TIGR02141 YP_001408956.1 identified by match to protein family HMM TIGR01256 YP_001408957.1 identified by match to protein family HMM PF00005; match to protein family HMM PF02463 YP_001408958.1 identified by glimmer; putative YP_001408960.1 catalyzes the ATP-dependent transport of cobalt YP_001408962.1 Catalyzes the formation of dUTP from dCTP in thymidylate biosynthesis YP_001408963.1 identified by match to protein family HMM PF00106; match to protein family HMM PF01073; match to protein family HMM PF01370; match to protein family HMM PF02719; match to protein family HMM PF04321; match to protein family HMM PF07993 YP_001408964.1 identified by match to protein family HMM PF00266; match to protein family HMM PF01041; match to protein family HMM PF01053; match to protein family HMM PF01212 YP_001408965.1 identified by match to protein family HMM PF02348 YP_001408967.1 identified by match to protein family HMM PF00583 YP_001408968.1 identified by match to protein family HMM PF03102; match to protein family HMM PF08666 YP_001408969.1 identified by match to protein family HMM PF01973 YP_001408970.1 identified by glimmer; putative YP_001408971.1 FlaB; structural flagella protein; in Helicobacter flagella are composed of flagellin A and flagellin B; the amounts of each seem to be controlled by environmental conditions YP_001408974.1 catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity YP_001408975.1 identified by match to protein family HMM PF00149; match to protein family HMM TIGR00040 YP_001408976.1 catalyzes the formation of biotin from dethiobiotin and sulfur YP_001408977.1 identified by match to protein family HMM PF00999 YP_001408978.1 identified by match to protein family HMM PF00285; match to protein family HMM TIGR01798 YP_001408979.1 identified by match to protein family HMM PF00459 YP_001408980.1 identified by match to protein family HMM PF00999; match to protein family HMM TIGR00831 YP_001408981.1 identified by match to protein family HMM PF08241; match to protein family HMM PF08242 YP_001408982.1 identified by match to protein family HMM PF00578 YP_001408983.1 identified by match to protein family HMM PF00528; match to protein family HMM TIGR02141 YP_001408984.1 identified by match to protein family HMM PF00005 YP_001408985.1 identified by match to protein family HMM PF03459 YP_001408986.1 identified by match to protein family HMM PF01547; match to protein family HMM TIGR01256 YP_001408987.1 identified by match to protein family HMM PF00126; match to protein family HMM PF03459; match to protein family HMM TIGR00638 YP_001408988.1 identified by match to protein family HMM PF04333 YP_001408989.1 identified by match to protein family HMM PF05494 YP_001408991.1 identified by match to protein family HMM PF04972 YP_001408992.1 identified by match to protein family HMM PF00593; match to protein family HMM PF07715; match to protein family HMM TIGR01786 YP_001408993.1 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_001408995.1 identified by match to protein family HMM PF00860; match to protein family HMM TIGR00801 YP_001408996.1 catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate YP_001408997.1 identified by match to protein family HMM PF01148 YP_001409000.1 identified by match to protein family HMM PF05670 YP_001409001.1 identified by match to protein family HMM PF08241; match to protein family HMM PF08242 YP_001409002.1 identified by glimmer; putative YP_001409003.1 identified by match to protein family HMM PF00005 YP_001409004.1 identified by match to protein family HMM PF00950; match to protein family HMM PF01032 YP_001409005.1 identified by match to protein family HMM PF01497 YP_001409006.1 identified by match to protein family HMM PF00593; match to protein family HMM PF07715 YP_001409009.1 identified by match to protein family HMM PF00593; match to protein family HMM PF07715; match to protein family HMM TIGR01783 YP_001409010.1 catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate in leucine biosynthesis YP_001409012.1 identified by match to protein family HMM PF02253 YP_001409013.1 identified by match to protein family HMM PF02447; match to protein family HMM PF03600 YP_001409014.1 identified by match to protein family HMM PF02595; match to protein family HMM TIGR00045 YP_001409016.1 identified by glimmer; putative YP_001409017.1 enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis YP_001409018.1 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_001409019.1 identified by glimmer; putative YP_001409020.1 catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis YP_001409021.1 with proteins FliP and FliR forms the core of the central channel in the flagella export apparatus YP_001409022.1 identified by match to protein family HMM PF02642 YP_001409024.1 catalyzes the formation of 5-phospho-alpha-D-ribose 1-diphosphate and nicotinate from nicotinate D-ribonucleotide and diphosphate YP_001409025.1 identified by match to protein family HMM PF00633; match to protein family HMM TIGR00426 YP_001409027.1 identified by match to protein family HMM PF01042; match to protein family HMM TIGR00004 YP_001409029.1 identified by match to protein family HMM PF03480 YP_001409030.1 identified by match to protein family HMM PF04011 YP_001409033.1 identified by match to protein family HMM PF00672 YP_001409034.1 identified by glimmer; putative YP_001409035.1 identified by match to protein family HMM PF02409 YP_001409036.1 identified by match to protein family HMM PF05940 YP_001409037.1 identified by match to protein family HMM PF00578; match to protein family HMM PF08534 YP_001409038.1 Carbamoyl phosphate-convertingenzyme hypF; (NiFe]-hydrogenase maturation factor hypF; Hydrogenasematuration protein hypF YP_001409039.1 identified by match to protein family HMM PF00571; match to protein family HMM PF01595; match to protein family HMM PF03471 YP_001409040.1 identified by match to protein family HMM PF00209 YP_001409042.1 identified by match to protein family HMM PF04055 YP_001409043.1 identified by match to protein family HMM PF01497 YP_001409044.1 identified by match to protein family HMM PF01032 YP_001409045.1 identified by match to protein family HMM PF00593; match to protein family HMM PF07715 YP_001409046.1 identified by match to protein family HMM PF01243 YP_001409047.1 identified by match to protein family HMM PF04214 YP_001409048.1 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_001409049.1 identified by match to protein family HMM PF01435 YP_001409050.1 identified by glimmer; putative YP_001409053.1 MoaC; along with MoaA is involved in conversion of a guanosine derivative into molybdopterin precursor Z; involved in molybdenum cofactor biosynthesis YP_001409054.1 identified by match to protein family HMM PF07859 YP_001409055.1 identified by match to protein family HMM PF01061 YP_001409056.1 identified by match to protein family HMM PF00005 YP_001409057.1 identified by match to protein family HMM PF00037; match to protein family HMM TIGR02163 YP_001409059.1 identified by glimmer; putative YP_001409060.1 identified by match to protein family HMM PF00037 YP_001409064.1 identified by match to protein family HMM PF00116 YP_001409065.1 identified by glimmer; putative YP_001409067.1 identified by match to protein family HMM PF00581 YP_001409069.1 identified by glimmer; putative YP_001409070.1 identified by glimmer; putative YP_001409071.1 identified by match to protein family HMM PF05838 YP_001409073.1 identified by glimmer; putative YP_001409075.1 identified by glimmer; putative YP_001409076.1 identified by match to protein family HMM PF07087 YP_001409078.1 identified by match to protein family HMM PF01391 YP_001409079.1 identified by glimmer; putative YP_001409080.1 identified by glimmer; putative YP_001409082.1 identified by glimmer; putative YP_001409083.1 identified by glimmer; putative YP_001409086.1 identified by glimmer; putative YP_001409088.1 identified by glimmer; putative YP_001409092.1 identified by glimmer; putative YP_001409093.1 identified by match to protein family HMM PF05866 YP_001409095.1 identified by match to protein family HMM PF03796 YP_001409096.1 identified by glimmer; putative YP_001409097.1 identified by glimmer; putative YP_001409100.1 identified by match to protein family HMM PF00145; match to protein family HMM TIGR00675 YP_001409101.1 identified by glimmer; putative YP_001409102.1 identified by match to protein family HMM PF00717 YP_001409104.1 identified by match to protein family HMM PF02086 YP_001409105.1 identified by match to protein family HMM PF00565 YP_001409107.1 identified by glimmer; putative YP_001409109.1 identified by match to protein family HMM PF03837; match to protein family HMM TIGR01913 YP_001409111.1 identified by match to protein family HMM PF00436; match to protein family HMM TIGR00621 YP_001409113.1 identified by glimmer; putative YP_001409114.1 identified by match to protein family HMM TIGR01671 YP_001409115.1 identified by glimmer; putative YP_001409116.1 identified by glimmer; putative YP_001409117.1 identified by match to protein family HMM PF00589 YP_001409118.1 identified by glimmer; putative YP_001409119.1 BacA; phosphatase activity in Escherichia coli not kinase; involved in bacitracin resistance as bacitracin supposedly sequesters undecaprenyl disphosphate which reduces the pool of lipid carrier available to the cell YP_001409120.1 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_001409121.1 identified by match to protein family HMM PF00348 YP_001409122.1 identified by match to protein family HMM PF00595 YP_001409123.1 identified by match to protein family HMM PF02575; match to protein family HMM TIGR00103 YP_001409124.1 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_001409125.1 UDP-N-acetylmuramyl-tripeptide synthetase; Meso-diaminopimelate-adding enzyme; UDP-MurNAc-tripeptide synthetase; 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_001409127.1 identified by match to protein family HMM PF01106 YP_001409129.1 identified by match to protein family HMM PF02525 YP_001409130.1 is a component of the macrolide binding site in the peptidyl transferase center YP_001409131.1 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_001409132.1 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_001409133.1 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_001409134.1 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_001409135.1 stimulates the activities of the other two initiation factors, IF-2 and IF-3 YP_001409136.1 late assembly protein YP_001409137.1 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_001409138.1 binds 5S rRNA along with protein L5 and L25 YP_001409139.1 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_001409140.1 binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit YP_001409141.1 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_001409142.1 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_001409143.1 assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel YP_001409144.1 binds to the 23S rRNA between the centers for peptidyl transferase and GTPase YP_001409145.1 primary binding protein; helps mediate assembly; involved in translation fidelity YP_001409146.1 one of the stabilizing components for the large ribosomal subunit YP_001409147.1 located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e YP_001409148.1 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_001409149.1 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_001409150.1 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_001409151.1 binds third domain of 23S rRNA and protein L29; part of exit tunnel YP_001409152.1 L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA YP_001409153.1 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_001409154.1 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_001409155.1 identified by glimmer; putative YP_001409158.1 identified by match to protein family HMM PF04909 YP_001409159.1 identified by glimmer; putative YP_001409160.1 identified by match to protein family HMM PF01638 YP_001409162.1 identified by match to protein family HMM PF01177; match to protein family HMM TIGR00035 YP_001409163.1 RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids YP_001409164.1 identified by match to protein family HMM PF00563; match to protein family HMM PF00989; match to protein family HMM PF00990; match to protein family HMM PF08447; match to protein family HMM TIGR00229 YP_001409165.1 identified by match to protein family HMM PF01758 YP_001409166.1 identified by match to protein family HMM PF01053; match to protein family HMM PF01212 YP_001409167.1 identified by match to protein family HMM PF00528; match to protein family HMM TIGR01726 YP_001409168.1 identified by match to protein family HMM PF00497 YP_001409169.1 identified by glimmer; putative YP_001409170.1 identified by match to protein family HMM PF00497 YP_001409172.1 identified by match to protein family HMM PF00155 YP_001409175.1 catalyzes the formation of 4-amino-4-deoxychorismate from chorismate and glutamine YP_001409176.1 identified by match to protein family HMM PF00081; match to protein family HMM PF02777 YP_001409177.1 identified by match to protein family HMM PF03480; match to protein family HMM TIGR00787 YP_001409178.1 identified by match to protein family HMM PF04290 YP_001409179.1 identified by match to protein family HMM PF03600; match to protein family HMM PF06808; match to protein family HMM TIGR00786 YP_001409180.1 identified by match to protein family HMM PF00990; match to protein family HMM TIGR00254 YP_001409181.1 identified by match to protein family HMM PF00990; match to protein family HMM TIGR00254 YP_001409183.1 identified by match to protein family HMM PF00924 YP_001409184.1 identified by match to protein family HMM PF00484 YP_001409185.1 identified by match to protein family HMM PF01027 YP_001409186.1 TMPpyrophosphorylase; TMP-PPase; Thiamine-phosphate synthase YP_001409187.1 identified by match to protein family HMM PF03840; match to protein family HMM TIGR00810 YP_001409188.1 identified by match to protein family HMM PF01522; match to protein family HMM PF03065 YP_001409189.1 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_001409191.1 involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate YP_001409192.1 identified by match to protein family HMM PF06271 YP_001409193.1 identified by match to protein family HMM PF00384; match to protein family HMM PF01568; match to protein family HMM TIGR01409 YP_001409194.1 Tripeptide aminopeptidase; Aminotripeptidase; Tripeptidase; identified by match to protein family HMM PF00037 YP_001409195.1 identified by match to protein family HMM PF06192 YP_001409196.1 identified by match to protein family HMM PF00037 YP_001409197.1 identified by match to protein family HMM PF00165 YP_001409198.1 identified by match to protein family HMM PF04055; match to protein family HMM TIGR00203 YP_001409200.1 identified by match to protein family HMM PF03929 YP_001409201.1 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_001409202.1 identified by match to protein family HMM PF00795 YP_001409203.1 catalyzes the methyl esterification of L-isoaspartyl residues that are formed in damaged proteins YP_001409204.1 identified by glimmer; putative YP_001409205.1 identified by glimmer; putative YP_001409206.1 identified by glimmer; putative YP_001409208.1 identified by match to protein family HMM PF00593; match to protein family HMM PF07715 YP_001409209.1 identified by match to protein family HMM PF01368; match to protein family HMM PF02272; match to protein family HMM TIGR00644 YP_001409210.1 CTP synthase; cytidine triphosphate synthetase; catalyzes the ATP-dependent amination of UTP to CTP with either L-glutamine or ammonia as the source of nitrogen; in Escherichia coli this enzyme forms a homotetramer YP_001409211.1 identified by glimmer; putative YP_001409213.1 identified by match to protein family HMM PF01654 YP_001409214.1 identified by match to protein family HMM PF02322 YP_001409215.1 identified by glimmer; putative YP_001409216.1 identified by glimmer; putative YP_001409217.1 identified by glimmer; putative YP_001409219.1 catalyzes the release of the N-terminal amino acid from a tripeptide YP_001409220.1 identified by match to protein family HMM PF03606; match to protein family HMM TIGR00771 YP_001409221.1 Alpha-aspartyl dipeptidase; Asp-specificdipeptidase; Dipeptidase E; alpha-aspartyl dipeptidase; catalyzes the hydrolysis of dipeptides with an N-terminal aspartate residue; belongs to peptidase S51 family YP_001409222.1 identified by match to protein family HMM PF01546; match to protein family HMM PF07687; match to protein family HMM TIGR01891 YP_001409223.1 identified by match to protein family HMM PF01546; match to protein family HMM PF07687; match to protein family HMM TIGR01879 YP_001409225.1 synthesizes RNA primers at the replication forks YP_001409226.1 identified by match to protein family HMM PF07719 YP_001409227.1 An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids YP_001409228.1 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_001409229.1 catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis YP_001409230.1 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_001409232.1 identified by match to protein family HMM PF04055 YP_001409233.1 identified by match to protein family HMM PF00724 YP_001409235.1 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