-- dump date   	20140618_204347
-- class       	Genbank::CDS
-- table       	cds_note
-- id	note
YP_504640.1	has 3'-5' exonuclease, 5'-3' exonuclease and 5'-3'polymerase activities, primarily functions to fill gaps during DNA replication and repair
YP_504641.1	identified by match to protein family HMM PF00834; match to protein family HMM TIGR01163
YP_504642.1	identified by similarity to GB:AAS14650.1; match to protein family HMM PF02405
YP_504643.1	identified by match to protein family HMM PF00005
YP_504645.1	identified by similarity to SP:P26428; match to protein family HMM PF01965
YP_504646.1	catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase
YP_504647.1	identified by match to protein family HMM PF01494; match to protein family HMM TIGR01988
YP_504650.1	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_504651.1	identified by similarity to SP:P00961; match to protein family HMM PF02092; match to protein family HMM PF05746; match to protein family HMM TIGR00211
YP_504652.1	chaperone Hsp40; co-chaperone with DnaK; Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins and by disaggregating proteins, also in an autonomous, dnaK-independent fashion
YP_504653.1	identified by similarity to SP:P39666; match to protein family HMM PF01729; match to protein family HMM PF02749; match to protein family HMM TIGR00078
YP_504654.1	identified by match to protein family HMM PF02660; match to protein family HMM TIGR00023
YP_504655.1	identified by similarity to SP:P24239; match to protein family HMM PF02075; match to protein family HMM TIGR00228
YP_504656.1	identified by match to protein family HMM PF00510
YP_504657.1	identified by similarity to SP:P42503; match to protein family HMM PF01208; match to protein family HMM TIGR01464
YP_504658.1	identified by similarity to SP:Q54318; match to protein family HMM PF00571; match to protein family HMM PF03471
YP_504659.1	identified by similarity to SP:P49860; match to protein family HMM PF04586; match to protein family HMM TIGR01543
YP_504660.2	identified by match to protein family HMM PF04860; match to protein family HMM TIGR01537
YP_504662.1	identified by similarity to SP:P12999
YP_504663.1	3 different subfamilies; catalyzes the formation of quinolinate from iminoaspartate and dihydroxyacetone phosphate
YP_504664.1	identified by similarity to GB:AAA85787.1; match to protein family HMM PF00037
YP_504669.1	identified by match to protein family HMM PF00579; match to protein family HMM TIGR00233
YP_504670.1	identified by match to protein family HMM PF01025
YP_504671.1	identified by similarity to SP:P25539; match to protein family HMM PF00383; match to protein family HMM PF01872; match to protein family HMM TIGR00326
YP_504672.1	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_504673.1	identified by match to protein family HMM PF03840; match to protein family HMM TIGR00810
YP_504674.1	identified by similarity to SP:P21891; match to protein family HMM PF00589; match to protein family HMM PF02899
YP_504675.1	identified by match to protein family HMM PF00005
YP_504676.1	NADP-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; decarboxylates oxaloacetate
YP_504677.1	identified by similarity to GB:AAS14671.1
YP_504678.1	subunit D of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; contains an oxidoreductase domain; catalyzes the transfer of electrons from NADH to ubiquinone
YP_504679.1	identified by match to protein family HMM PF02470
YP_504681.1	identified by match to protein family HMM PF03477; match to protein family HMM TIGR00244
YP_504684.1	identified by similarity to GB:AAD03802.1; match to protein family HMM PF01547
YP_504685.1	identified by similarity to GB:CAC47765.1; match to protein family HMM PF03966
YP_504686.1	identified by match to protein family HMM PF00083; match to protein family HMM PF07690
YP_504687.1	binds to lower part of 30S body where it stabilizes two domains; required for efficient assembly of 30S; in Escherichia coli this protein has nuclease activity
YP_504689.1	identified by match to protein family HMM PF00106
YP_504691.1	catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase
YP_504692.1	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_504693.1	binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit
YP_504694.1	identified by match to protein family HMM PF01632; match to protein family HMM TIGR00001
YP_504695.1	identified by similarity to GB:AAL02641.1; match to protein family HMM PF06242
YP_504697.1	An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes
YP_504698.1	identified by similarity to SP:P54533; match to protein family HMM PF00070; match to protein family HMM PF02852; match to protein family HMM PF07992; match to protein family HMM TIGR01350
YP_504699.1	identified by match to protein family HMM PF00226
YP_504700.1	identified by match to protein family HMM PF01106
YP_504702.1	identified by match to protein family HMM PF02597; match to protein family HMM TIGR01683
YP_504703.1	functions in thiamine (vitamin B1) biosynthesis; in Bacillus subtilis this enzyme catalyzes the formation of thiazole from dehydroxyglycine and 1-deoxy-D-xylulose-5-phosphate and ThiS-thiocarboxylate
YP_504704.1	identified by similarity to GB:AAL02970.1
YP_504705.1	Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation
YP_504706.1	identified by similarity to GB:AAS14910.1
YP_504707.1	identified by match to protein family HMM PF03602
YP_504708.1	identified by match to protein family HMM PF03547
YP_504709.1	identified by match to protein family HMM PF04800
YP_504710.1	identified by similarity to SP:P22938; match to protein family HMM PF02609
YP_504711.1	identified by similarity to SP:P00274; match to protein family HMM PF00085; match to protein family HMM TIGR01068
YP_504712.1	identified by similarity to GB:AAM00421.1; match to protein family HMM PF03524
YP_504713.1	identified by similarity to SP:Q9R9N5; match to protein family HMM PF00676
YP_504714.1	identified by match to protein family HMM PF00561
YP_504715.1	identified by similarity to SP:Q64737; match to protein family HMM PF00551
YP_504716.1	identified by similarity to SP:P06981; match to protein family HMM PF00478; match to protein family HMM PF00571; match to protein family HMM TIGR01302
YP_504717.1	catalyzes the phosphorylation of NAD to NADP
YP_504718.1	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 do not have the CXXC motif; RpmE is found in exponentially growing Bacilli while YtiA was found after exponential growth; expression of ytiA is controlled by a zinc-specific transcriptional repressor; RpmE contains one zinc ion and a CxxC motif is responsible for this binding; forms an RNP particle along with proteins L5, L18, and L25 and 5S rRNA; found crosslinked to L2 and L25 and EF-G; may be near the peptidyltransferase site of the 50S ribosome
YP_504720.1	identified by similarity to SP:P71019; match to protein family HMM PF00698; match to protein family HMM TIGR00128
YP_504721.1	catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP)
YP_504722.1	identified by match to protein family HMM PF07690
YP_504724.1	identified by match to protein family HMM PF04280
YP_504725.1	molecular chaperone that is required for the normal export of envelope proteins out of the cell cytoplasm; in Escherichia coli this proteins forms a homotetramer in the cytoplasm and delivers proteins to be exported to SecA
YP_504726.1	identified by similarity to GB:AAS14712.1
YP_504729.1	identified by match to protein family HMM PF00675; match to protein family HMM PF05193
YP_504731.1	identified by similarity to GB:AAS13931.1; match to protein family HMM PF03060
YP_504732.1	identified by similarity to SP:P29464
YP_504734.1	catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine
YP_504735.1	identified by similarity to SP:P30958; 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_504737.1	identified by similarity to SP:P00647; match to protein family HMM PF00075
YP_504739.1	identified by match to protein family HMM PF00696; match to protein family HMM TIGR02075
YP_504740.1	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_504741.1	identified by match to protein family HMM PF01148
YP_504746.1	identified by similarity to SP:P12046; match to protein family HMM PF01259; match to protein family HMM TIGR00081
YP_504747.1	catalyzes a two-step reaction, first charging a histidine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; class II aminoacyl-tRNA synthetase; forms homodimers; some organisms have a paralogous gene, hisZ, that is similar to hisS and produces a protein that performs the first step in histidine biosynthesis along with HisG
YP_504749.1	identified by similarity to GB:AAM22615.1; match to protein family HMM PF01323
YP_504750.1	identified by match to protein family HMM PF02628
YP_504752.1	ATP-binding protein; required for proper cytochrome c maturation
YP_504756.1	identified by match to protein family HMM PF03953
YP_504757.1	Catalyzes the formation of dUTP from dCTP in thymidylate biosynthesis
YP_504760.1	identified by match to protein family HMM PF00313
YP_504761.1	identified by similarity to SP:Q04850; match to protein family HMM PF00512; match to protein family HMM PF00672; match to protein family HMM PF02518
YP_504762.1	identified by similarity to SP:P09155; match to protein family HMM PF01612
YP_504763.1	identified by similarity to SP:P15042; match to protein family HMM PF00533; match to protein family HMM PF01653; match to protein family HMM PF03119; match to protein family HMM PF03120; match to protein family HMM TIGR00575
YP_504764.1	identified by match to protein family HMM PF00462; match to protein family HMM TIGR00365
YP_504765.1	identified by match to protein family HMM PF01722
YP_504766.1	identified by similarity to SP:P33926
YP_504767.1	identified by similarity to GB:AAK69697.1; match to protein family HMM PF01617
YP_504768.1	identified by similarity to GB:AAO30104.1
YP_504769.1	identified by match to protein family HMM PF01617
YP_504771.1	identified by similarity to SP:P60548
YP_504773.1	identified by match to protein family HMM PF06808; match to protein family HMM TIGR02123
YP_504774.1	identified by match to protein family HMM PF02674
YP_504775.1	binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21
YP_504776.1	binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit
YP_504777.1	in Escherichia coli this protein is wrapped around the base of the L1 stalk
YP_504778.1	catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate
YP_504781.1	identified by match to protein family HMM PF00005; match to protein family HMM PF00664
YP_504782.1	part of four member succinate dehydrogenase enzyme complex that forms a trimeric complex (trimer of tetramers); SdhA/B are the catalytic subcomplex and can exhibit succinate dehydrogenase activity in the absence of SdhC/D which are the membrane components and form cytochrome b556; SdhC binds ubiquinone; oxidizes succinate to fumarate while reducing ubiquinone to ubiquinol
YP_504783.1	part of four member succinate dehydrogenase enzyme complex that forms a trimeric complex (trimer of tetramers); SdhA/B are the catalytic subcomplex and can exhibit succinate dehydrogenase activity in the absence of SdhC/D which are the membrane components and form cytochrome b556; SdhC binds ubiquinone; oxidizes succinate to fumarate while reducing ubiquinone to ubiquinol; the catalytic subunits are similar to fumarate reductase
YP_504784.1	identified by similarity to GB:AAU03772.1
YP_504785.1	part of four member succinate dehydrogenase enzyme complex that forms a trimeric complex (trimer of tetramers); SdhA/B are the catalytic subcomplex and can exhibit succinate dehydrogenase activity in the absence of SdhC/D which are the membrane components and form cytochrome b556; SdhC binds ubiquinone; oxidizes succinate to fumarate while reducing ubiquinone to ubiquinol
YP_504786.1	part of four member succinate dehydrogenase enzyme complex that forms a trimeric complex (trimer of tetramers); SdhA/B are the catalytic subcomplex and can exhibit succinate dehydrogenase activity in the absence of SdhC/D which are the membrane components and form cytochrome b556; SdhC binds ubiquinone; oxidizes succinate to fumarate while reducing ubiquinone to ubiquinol; the catalytic subunits are similar to fumarate reductase
YP_504787.1	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_504788.1	identified by similarity to SP:P28246; match to protein family HMM PF00083; match to protein family HMM PF07690; match to protein family HMM TIGR00710
YP_504789.1	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_504790.1	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_504791.1	plays an essential role in ATP-dependent branch migration of the Holliday junction
YP_504792.1	identified by match to protein family HMM PF01578; match to protein family HMM TIGR01191
YP_504794.1	identified by similarity to SP:P60548; match to protein family HMM PF00625
YP_504795.1	identified by match to protein family HMM PF01617
YP_504798.1	identified by match to protein family HMM PF01617
YP_504799.1	identified by similarity to SP:P54382; match to protein family HMM PF00763; match to protein family HMM PF02882
YP_504801.1	identified by match to protein family HMM PF00561
YP_504802.1	identified by similarity to PIR:A71691; match to protein family HMM PF00561
YP_504803.1	identified by similarity to SP:P30323; match to protein family HMM PF00034
YP_504804.1	identified by match to protein family HMM PF00361
YP_504808.1	catalyzes the formation of phosphoenolpyruvate from pyruvate
YP_504810.1	identified by match to protein family HMM PF00702; match to protein family HMM TIGR01549
YP_504813.1	catalyzes a two-step reaction, first charging an aspartate molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; contains discriminating and non-discriminating subtypes
YP_504815.1	identified by similarity to SP:P27291; match to protein family HMM PF04972
YP_504816.1	catalyzes the second step in the glutathione biosynthesis pathway, where it synthesizes ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione
YP_504818.1	identified by match to protein family HMM PF03799
YP_504819.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00158; match to protein family HMM PF02954; match to protein family HMM TIGR01199
YP_504821.1	identified by similarity to SP:P37606; match to protein family HMM PF01210; match to protein family HMM PF03807; match to protein family HMM PF07479
YP_504822.1	identified by match to protein family HMM PF00589; match to protein family HMM PF02899
YP_504823.1	identified by similarity to GB:AAL08839.1
YP_504824.1	catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis
YP_504827.1	identified by similarity to GB:AAS13843.1
YP_504828.1	identified by match to protein family HMM PF02410; match to protein family HMM TIGR00090
YP_504829.1	identified by match to protein family HMM PF01435; match to protein family HMM PF07719
YP_504830.1	identified by similarity to GB:AAL08839.1
YP_504831.1	catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis
YP_504832.1	identified by similarity to SP:P15254
YP_504833.1	identified by similarity to SP:P29252; match to protein family HMM PF01288; match to protein family HMM TIGR01498
YP_504834.1	identified by match to protein family HMM PF00586; match to protein family HMM PF02769
YP_504837.1	identified by similarity to SP:P12996; match to protein family HMM PF04055; match to protein family HMM PF06968; match to protein family HMM TIGR00433
YP_504839.1	identified by similarity to GB:AAS14547.1
YP_504840.1	identified by similarity to SP:P33648; match to protein family HMM PF01551
YP_504841.1	type II fructose 1,6-bisphosphatae; in Escherichia coli this protein forms a dimer and binds manganese
YP_504843.1	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_504844.1	identified by similarity to SP:P15254
YP_504847.1	identified by match to protein family HMM PF00551; match to protein family HMM TIGR00639
YP_504848.1	catalyzes the removal of N-terminal amino acids preferably leucine from various peptides
YP_504849.1	identified by similarity to SP:P15110; match to protein family HMM PF00775
YP_504852.1	identified by similarity to SP:P03815; match to protein family HMM PF00004; match to protein family HMM PF02861; match to protein family HMM PF07724
YP_504853.1	identified by match to protein family HMM PF00106
YP_504857.1	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_504858.1	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_504859.1	identified by similarity to SP:P25531; match to protein family HMM PF04002; match to protein family HMM TIGR00608
YP_504860.1	lipoyl-[acyl-carrier protein]-protein-N-lipoyltransferse; lipoate-protein ligase B; transfers lipoate to apolipoproteins; involved in lipoate metabolism
YP_504862.1	identified by similarity to SP:P25995; match to protein family HMM PF01979; match to protein family HMM PF07969; match to protein family HMM TIGR00857
YP_504863.1	identified by similarity to SP:P24285; match to protein family HMM PF04127
YP_504864.1	class II family (does not require metal); tetrameric enzyme; fumarase C; reversibly converts (S)-malate to fumarate and water; functions in the TCA cycle
YP_504866.1	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_504867.1	identified by similarity to SP:O26861
YP_504869.1	identified by match to protein family HMM PF00809; match to protein family HMM TIGR01496
YP_504871.1	identified by match to protein family HMM PF00005; match to protein family HMM TIGR01842
YP_504872.1	identified by similarity to SP:P28304; match to protein family HMM PF00107
YP_504873.1	identified by match to protein family HMM PF00580
YP_504874.1	identified by match to protein family HMM PF00023
YP_504875.1	identified by match to protein family HMM PF01145
YP_504876.1	identified by similarity to GB:AAS14513.1
YP_504877.1	identified by match to protein family HMM PF03969
YP_504878.1	protoheme ferro-lyase; catalyzes the insertion of a ferrous ion into protoporphyrin IX to form protoheme; involved in protoheme biosynthesis; in some organisms this protein is membrane-associated while in others it is cytosolic
YP_504881.1	identified by similarity to GB:AAS14743.1
YP_504882.1	identified by similarity to GB:BAB50572.1
YP_504885.1	identified by similarity to SP:Q06607; match to protein family HMM PF00216
YP_504886.1	identified by match to protein family HMM PF01343; match to protein family HMM TIGR00706
YP_504887.1	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_504888.1	identified by match to protein family HMM PF02224
YP_504889.1	identified by match to protein family HMM PF00588; match to protein family HMM PF08032; match to protein family HMM TIGR00186
YP_504890.1	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_504891.1	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_504892.1	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_504893.1	L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA
YP_504894.1	binds third domain of 23S rRNA and protein L29; part of exit tunnel
YP_504895.1	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_504896.1	protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA
YP_504897.1	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_504898.1	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_504899.1	located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e
YP_504900.1	one of the stabilizing components for the large ribosomal subunit
YP_504901.1	primary binding protein; helps mediate assembly; involved in translation fidelity
YP_504902.1	binds to the 23S rRNA between the centers for peptidyl transferase and GTPase
YP_504903.1	assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel
YP_504904.1	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_504905.1	located in the peptidyl transferase center and involved in assembly of 30S ribosome subunit; similar to what is observed with proteins L31 and L33, some proteins in this family contain CXXC motifs that are involved in zinc binding; if two copies are present in a genome, then the duplicated copy appears to have lost the zinc-binding motif and is instead regulated by zinc; the proteins in this group do not appear to have the zinc-binding motif
YP_504906.1	binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit
YP_504907.1	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_504908.1	binds 5S rRNA along with protein L5 and L25
YP_504909.1	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_504910.1	late assembly protein
YP_504911.1	forms heterotrimeric complex in the membrane; in bacteria the complex consists of SecY which forms the channel pore and SecE and SecG; the SecG subunit is not essential; in bacteria translocation is driven via the SecA ATPase
YP_504912.1	identified by similarity to SP:P27142; match to protein family HMM PF00406
YP_504913.1	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_504914.1	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_504915.1	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_504916.1	is a component of the macrolide binding site in the peptidyl transferase center
YP_504917.1	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_504918.1	identified by match to protein family HMM PF03772; match to protein family HMM TIGR00360
YP_504919.1	identified by match to protein family HMM PF01235
YP_504920.1	identified by similarity to SP:P25814; match to protein family HMM PF00825; match to protein family HMM TIGR00188
YP_504921.1	in Escherichia coli transcription of this gene is enhanced by polyamines
YP_504922.1	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_504923.1	identified by match to protein family HMM PF01613
YP_504925.1	ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation
YP_504926.1	identified by similarity to SP:P19675; match to protein family HMM PF01702; match to protein family HMM TIGR00430; match to protein family HMM TIGR00449
YP_504927.1	some L32 proteins have zinc finger motifs consisting of CXXC while others do not
YP_504928.1	involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY
YP_504929.1	identified by similarity to SP:P24249; match to protein family HMM TIGR00747
YP_504931.1	identified by match to protein family HMM PF00383
YP_504932.1	identified by similarity to GB:AAS14136.1
YP_504933.1	unwinds double stranded DNA
YP_504935.1	identified by match to protein family HMM PF01266
YP_504938.1	identified by similarity to SP:Q08291; match to protein family HMM PF00348
YP_504939.1	Catalyzes the rate-limiting step in dNTP synthesis
YP_504940.1	identified by similarity to GB:AAS13897.1; match to protein family HMM PF03652; match to protein family HMM TIGR00250
YP_504944.1	catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis
YP_504946.1	identified by similarity to SP:P07176; match to protein family HMM PF00691
YP_504947.1	identified by similarity to SP:P42663
YP_504948.1	identified by similarity to SP:P29277; match to protein family HMM PF00456; match to protein family HMM PF02779; match to protein family HMM PF02780; match to protein family HMM TIGR00232
YP_504949.1	subunit F of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali
YP_504950.1	subunit G of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali
YP_504951.1	subunit C of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali
YP_504952.1	identified by similarity to SP:P21513; match to protein family HMM PF00575; match to protein family HMM TIGR00757
YP_504953.1	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_504954.1	identified by match to protein family HMM PF03364
YP_504955.1	subunit D of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; contains an oxidoreductase domain; catalyzes the transfer of electrons from NADH to ubiquinone
YP_504956.1	identified by similarity to SP:P07019; 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_504957.1	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_504958.1	identified by similarity to GB:AAS14435.1
YP_504959.1	identified by similarity to GB:AAS13980.1; match to protein family HMM TIGR02281
YP_504960.1	identified by match to protein family HMM PF00557
YP_504962.1	identified by similarity to GB:AAS14235.1
YP_504963.1	identified by similarity to SP:P94461; match to protein family HMM PF00270; match to protein family HMM PF00271; match to protein family HMM PF04851; match to protein family HMM TIGR00595
YP_504966.1	required for 70S ribosome assembly
YP_504969.1	identified by match to protein family HMM PF00849; match to protein family HMM PF01479; match to protein family HMM TIGR00005
YP_504971.1	identified by similarity to SP:P05165; match to protein family HMM PF00289; match to protein family HMM PF00364; match to protein family HMM PF02785; match to protein family HMM PF02786
YP_504974.1	catalyzes the radical-mediated insertion of two sulfur atoms into an acyl carrier protein (ACP) bound to an octanoyl group to produce a lipoyl group
YP_504976.1	identified by match to protein family HMM PF00528; match to protein family HMM TIGR00974
YP_504977.1	identified by similarity to GB:AAM00410.1; match to protein family HMM PF00081; match to protein family HMM PF02777
YP_504978.1	identified by similarity to GB:AAM00406.1; match to protein family HMM PF05101
YP_504979.1	identified by similarity to GB:AAM00407.1; match to protein family HMM PF03135; match to protein family HMM TIGR00929
YP_504980.1	identified by similarity to GB:AAM00403.1; match to protein family HMM PF04610
YP_504981.1	identified by match to protein family HMM PF04610
YP_504982.1	identified by match to protein family HMM PF04610
YP_504983.1	identified by match to protein family HMM PF04610
YP_504984.1	identified by similarity to GB:AAS14953.1; match to protein family HMM TIGR02217
YP_504985.1	identified by match to protein family HMM PF00692; match to protein family HMM TIGR00576
YP_504986.1	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_504987.1	catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers
YP_504988.1	identified by similarity to GB:AAK69700.1
YP_504990.1	identified by similarity to GB:AAK69700.1
YP_504991.1	identified by similarity to GB:AAK69700.1
YP_504992.1	identified by similarity to GB:AAK69700.1
YP_504994.1	catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate
YP_504995.1	EngA; essential Neisserial GTPase; synchronizes cellular events by interacting with multiple targets with tandem G-domains; overexpression in Escherichia coli suppresses rrmJ mutation; structural analysis of the Thermotoga maritima ortholog shows different nucleotide binding affinities in the two binding domains
YP_504998.1	identified by match to protein family HMM PF00070; match to protein family HMM PF01134; match to protein family HMM PF02852; match to protein family HMM PF03486; match to protein family HMM PF07992; match to protein family HMM TIGR01350
YP_504999.1	identified by match to protein family HMM TIGR01730
YP_505000.1	identified by match to protein family HMM PF00575; match to protein family HMM TIGR00008
YP_505001.1	Maf; overexpression in Bacillus subtilis inhibits septation in the dividing cell
YP_505002.1	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_505003.1	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_505004.1	identified by match to protein family HMM PF00950
YP_505006.1	identified by similarity to SP:P23136; match to protein family HMM PF00355; match to protein family HMM TIGR01416
YP_505007.1	identified by similarity to SP:P23134; match to protein family HMM PF00032; match to protein family HMM PF00033
YP_505008.1	identified by similarity to SP:P23135; match to protein family HMM PF02167
YP_505013.1	Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation
YP_505015.1	identified by similarity to SP:P05523; match to protein family HMM PF01149; match to protein family HMM PF06831; match to protein family HMM TIGR00577
YP_505018.1	identified by similarity to SP:P05166; match to protein family HMM PF01039
YP_505020.1	identified by similarity to GB:AAM00407.1
YP_505022.1	identified by similarity to GB:AAM00407.1
YP_505023.1	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_505024.1	binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential
YP_505025.1	catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate
YP_505026.1	catalyzes the conversion of the propionic acid groups of rings I and III to vinyl groups during heme synthesis
YP_505027.1	identified by match to protein family HMM PF00375
YP_505030.1	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_505031.1	identified by similarity to SP:P27850; match to protein family HMM PF02646
YP_505034.1	identified by similarity to SP:P38436; match to protein family HMM PF01715; match to protein family HMM TIGR00174
YP_505035.1	identified by similarity to GB:AAS14508.1
YP_505037.1	part of NADH-ubiquinone oxidoreductase complex I; shuttles electrons from NADH, via FMN and iron-sulfur (Fe-S) centers, to quinones in the respiratory chain; NuoF is part of the soluble NADH dehydrogenase fragment, which represents the electron input part of NADH dehydrogenase
YP_505038.1	identified by similarity to SP:P50975; match to protein family HMM PF00499
YP_505039.1	identified by similarity to SP:P50940; match to protein family HMM PF00420
YP_505040.1	identified by similarity to SP:P29924; match to protein family HMM PF00361; match to protein family HMM PF00662; match to protein family HMM TIGR01974
YP_505041.1	identified by similarity to SP:P29925; match to protein family HMM PF00361; match to protein family HMM TIGR01972
YP_505042.1	identified by similarity to SP:P29926; match to protein family HMM PF00361
YP_505043.1	catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate
YP_505045.1	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_505046.1	identified by match to protein family HMM PF00902; match to protein family HMM TIGR00945
YP_505047.1	identified by match to protein family HMM PF00873
YP_505048.1	modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination
YP_505049.1	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_505050.1	identified by match to protein family HMM PF02033; match to protein family HMM TIGR00082
YP_505052.1	identified by match to protein family HMM PF03741
YP_505053.1	identified by similarity to SP:P15716; match to protein family HMM PF00004; match to protein family HMM PF02861; match to protein family HMM PF07724
YP_505054.1	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_505055.1	identified by similarity to GB:AAK69700.1
YP_505056.1	identified by similarity to GB:AAK69700.1
YP_505057.1	identified by similarity to GB:AAK69700.1
YP_505059.1	identified by similarity to GB:AAK69700.1
YP_505064.1	identified by similarity to SP:P28367
YP_505066.1	identified by match to protein family HMM PF00436; match to protein family HMM TIGR00621
YP_505069.1	identified by similarity to SP:P07012; match to protein family HMM PF03462
YP_505070.1	identified by similarity to GB:AAD48994.1; match to protein family HMM PF05292
YP_505071.1	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_505072.1	identified by match to protein family HMM PF03372; match to protein family HMM TIGR00633
YP_505073.1	identified by similarity to SP:P54616
YP_505074.1	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_505078.1	identified by similarity to SP:P07012; match to protein family HMM PF00472; match to protein family HMM PF03462; match to protein family HMM TIGR00020
YP_505079.1	identified by similarity to GB:AAS14201.1; match to protein family HMM PF01709; match to protein family HMM TIGR01033
YP_505080.1	identified by match to protein family HMM PF03631; match to protein family HMM TIGR00765
YP_505081.1	identified by similarity to SP:P12995; match to protein family HMM PF00202; match to protein family HMM TIGR00508
YP_505091.1	similar to novel fructose-6-phosphate aldolase from Escherichia coli; enzyme from Methanocaldococcus janaschii shows transaldolase activity
YP_505092.1	identified by match to protein family HMM PF02823
YP_505093.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit
YP_505094.1	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_505097.1	mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability
YP_505098.1	catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis
YP_505099.1	identified by similarity to SP:P28692; match to protein family HMM PF01728
YP_505100.1	identified by match to protein family HMM PF03372; match to protein family HMM TIGR00195; match to protein family HMM TIGR00633
YP_505103.1	identified by match to protein family HMM TIGR01022
YP_505106.1	identified by similarity to SP:O84971; match to protein family HMM PF00329
YP_505108.1	identified by match to protein family HMM PF01713
YP_505109.1	identified by similarity to SP:P08374; match to protein family HMM PF01192; match to protein family HMM TIGR00690
YP_505110.1	identified by similarity to GB:AAS14946.1
YP_505114.1	identified by similarity to SP:O84969; match to protein family HMM PF00507
YP_505115.1	The point of entry for the majority of electrons that traverse the respiratory chain eventually resulting in the reduction of oxygen
YP_505116.1	identified by similarity to SP:O84971; match to protein family HMM PF00329; match to protein family HMM TIGR01961
YP_505119.1	identified by similarity to SP:P36664; match to protein family HMM PF01975; match to protein family HMM TIGR00087
YP_505121.1	CycJ; periplasmic heme chaperone that binds heme transiently via a histidine residue and delivers it to newly synthesized and exported c-type cytochromes; requires the ATP hydrolysis activity of the CcmA protein in order to transfer the heme to the apocytochrome; part of the cytochrome c maturation system; periplasmic protein anchored to the inner membrane
YP_505122.1	identified by similarity to SP:Q59654; match to protein family HMM PF00215; match to protein family HMM TIGR01740
YP_505123.1	identified by similarity to SP:P37346; match to protein family HMM PF01026; match to protein family HMM TIGR00010
YP_505125.1	identified by similarity to SP:P37346
YP_505129.1	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_505130.1	identified by similarity to SP:O34863; match to protein family HMM PF00005; match to protein family HMM TIGR00630
YP_505131.1	identified by match to protein family HMM PF01029
YP_505132.1	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_505133.1	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_505134.1	identified by match to protein family HMM PF02096
YP_505135.1	identified by match to protein family HMM PF01066; match to protein family HMM TIGR00473
YP_505136.1	catalyzes the decarboxylaton of phospatidyl-L-sering to phosphatidylethanolamine
YP_505137.1	identified by similarity to GB:CAD84769.1; match to protein family HMM PF00175; match to protein family HMM PF00970
YP_505139.1	identified by match to protein family HMM PF01132; match to protein family HMM TIGR00038
YP_505141.1	identified by similarity to SP:P23851; match to protein family HMM PF00849; match to protein family HMM PF01479; match to protein family HMM TIGR00005
YP_505143.1	involved in swarmer-to-stalked cell differentiation in Caulobacter crescentus; catalyzes the condensation of two GTP molecules to form the secondary messenger cyclic di-GMP (c-di-GMP); upon phosphorylation of domain D1 the protein dimerizes; presumably this allows the two GTP-bound GGDEF (diguanylate cyclase) domains to catalyze the condensation reaction; allosterically inhibited by c-di-GMP
YP_505144.1	identified by similarity to SP:O69415; match to protein family HMM PF02416
YP_505145.1	identified by match to protein family HMM PF05088
YP_505146.1	identified by similarity to SP:Q52923; match to protein family HMM PF06055
YP_505147.1	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_505152.1	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_505153.1	identified by similarity to SP:P35160
YP_505156.1	identified by similarity to GB:AAS14408.1
YP_505157.1	identified by similarity to GB:AAS14410.1; match to protein family HMM PF02636
YP_505162.1	identified by similarity to SP:O33470; match to protein family HMM PF01751; match to protein family HMM PF01807; match to protein family HMM TIGR01391
YP_505163.1	identified by match to protein family HMM PF00488
YP_505165.1	An essential enzyme in the nonmevalonate pathway of isopentenyl diphosphate and dimethylallyl diphosphate biosynthesis
YP_505166.1	identified by match to protein family HMM PF01207; match to protein family HMM TIGR00737
YP_505167.1	identified by similarity to SP:Q59753; match to protein family HMM PF00140; match to protein family HMM PF03979; match to protein family HMM PF04539; match to protein family HMM PF04542; match to protein family HMM PF04545; match to protein family HMM TIGR02393
YP_505171.1	identified by similarity to SP:P36654; match to protein family HMM PF03091
YP_505172.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00512; match to protein family HMM PF02518
YP_505174.1	identified by match to protein family HMM PF01596
YP_505175.1	identified by similarity to GB:AAS14713.1
YP_505176.1	identified by similarity to SP:P30136
YP_505178.1	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_505187.1	identified by similarity to SP:P39814; match to protein family HMM PF01131; match to protein family HMM PF01396; match to protein family HMM PF01751; match to protein family HMM TIGR01051
YP_505190.1	required for the synthesis of the hydromethylpyrimidine moiety of thiamine
YP_505191.1	identified by similarity to GB:AAS13958.1
YP_505196.1	Involved in ubiquinone biosynthesis
YP_505197.1	class I; LysRS1; 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 this enzyme charges both tRNA molecules for lysine that exist in this organism (but the tRNALysUUU very poorly) and in the presence of LysRS2 can charge tRNAPyl with lysine
YP_505198.1	identified by similarity to SP:P77241
YP_505200.1	identified by match to protein family HMM PF00814
YP_505203.1	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_505205.1	identified by similarity to GB:AAS14116.1
YP_505210.1	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_505211.1	Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate
YP_505212.1	identified by similarity to SP:P12920; match to protein family HMM TIGR02122
YP_505213.1	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_505214.1	identified by match to protein family HMM PF06271
YP_505215.1	identified by similarity to SP:P46362; match to protein family HMM PF02152; match to protein family HMM TIGR00526
YP_505216.1	Catalyzes the reversible oxidation of malate to oxaloacetate
YP_505220.1	identified by match to protein family HMM TIGR02215
YP_505222.1	identified by similarity to GB:AAS13839.1
YP_505227.1	identified by similarity to SP:P37351; match to protein family HMM PF02502; match to protein family HMM TIGR00689; match to protein family HMM TIGR01120
YP_505230.1	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_505231.1	catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro)
YP_505232.1	identified by similarity to GB:AAS14235.1
YP_505233.1	Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA
YP_505240.1	identified by similarity to SP:P09625; match to protein family HMM PF00070; match to protein family HMM PF07992; match to protein family HMM TIGR01292
YP_505241.1	identified by match to protein family HMM PF00578
YP_505242.1	identified by similarity to SP:Q02635; match to protein family HMM PF00155
YP_505244.1	identified by match to protein family HMM PF01617
YP_505245.1	identified by match to protein family HMM PF01617
YP_505246.1	identified by match to protein family HMM PF01617
YP_505250.1	identified by similarity to SP:P25716; match to protein family HMM PF00106; match to protein family HMM TIGR01830
YP_505251.1	proline utilization protein A; multifunctional protein that functions in proline catabolism in the first two enzymatic steps resulting in the conversion of proline to glutamate; in Escherichia coli this protein self regulates transcription via a DNA-binding domain at the N-terminus but the proteins from this group do not and in addition appear to have a truncated C-terminal domain
YP_505253.1	identified by similarity to PIR:A97789
YP_505255.1	identified by similarity to GB:AAL10759.1; match to protein family HMM PF00266; match to protein family HMM PF01212; match to protein family HMM PF02082
YP_505256.1	catalyzes the removal of elemental sulfur from cysteine to produce alanine; involved in NAD biosynthesis
YP_505257.1	identified by similarity to SP:P77310; match to protein family HMM PF01592; match to protein family HMM TIGR01999
YP_505258.1	identified by match to protein family HMM PF01521; match to protein family HMM TIGR00049
YP_505259.1	identified by similarity to SP:P36540; match to protein family HMM PF00226
YP_505260.1	identified by similarity to SP:P36541; match to protein family HMM PF00012
YP_505261.1	identified by match to protein family HMM PF00111
YP_505265.1	identified by similarity to GB:AAS14108.1
YP_505270.1	identified by match to protein family HMM TIGR02218
YP_505272.1	identified by match to protein family HMM PF01795; match to protein family HMM TIGR00006
YP_505275.1	identified by match to protein family HMM PF01812; match to protein family HMM TIGR02727
YP_505276.1	essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication
YP_505277.1	enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis
YP_505279.1	identified by match to protein family HMM PF00829; match to protein family HMM TIGR00061
YP_505280.1	involved in the peptidyltransferase reaction during translation
YP_505281.1	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_505286.1	identified by similarity to SP:P24231; match to protein family HMM PF01523
YP_505287.1	identified by similarity to SP:P19465; match to protein family HMM PF01227
YP_505288.1	identified by match to protein family HMM PF00231
YP_505290.1	identified by similarity to GB:AAP34830.1; match to protein family HMM PF00023
YP_505292.1	Catalyzes the transfer of electrons from NADH to quinone
YP_505293.1	Catalyzes the transfer of electrons from NADH to quinone
YP_505294.1	identified by similarity to GB:AAS13913.1
YP_505297.1	identified by similarity to SP:P06982; match to protein family HMM PF00204; match to protein family HMM PF00986; match to protein family HMM PF01751; match to protein family HMM PF02518; match to protein family HMM TIGR01059
YP_505310.1	identified by similarity to SP:P03007; match to protein family HMM PF00929; match to protein family HMM TIGR00573; match to protein family HMM TIGR01406
YP_505311.1	Catalyzes the transfer of electrons from NADH to quinone
YP_505312.1	Catalyzes the transfer of electrons from NADH to quinone
YP_505314.1	identified by match to protein family HMM PF00070; match to protein family HMM PF03486; match to protein family HMM PF07992
YP_505315.1	identified by similarity to SP:P77785; match to protein family HMM PF02769; match to protein family HMM TIGR01379
YP_505316.1	involved in DNA repair and RecFOR pathway recombination; RecFOR proteins displace ssDNA-binding protein and facilitate the production of RecA-coated ssDNA
YP_505319.1	identified by similarity to GB:AAF42723.1; match to protein family HMM PF00023
YP_505324.1	identified by similarity to SP:P18579; match to protein family HMM PF01565; match to protein family HMM PF02873; match to protein family HMM TIGR00179
YP_505325.1	transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis
YP_505326.1	identified by similarity to SP:Q05865; match to protein family HMM TIGR01499
YP_505327.1	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_505328.1	identified by similarity to SP:P09550; match to protein family HMM PF02441; match to protein family HMM TIGR00421
YP_505333.1	identified by match to protein family HMM PF01078; match to protein family HMM TIGR00368
YP_505338.1	identified by similarity to SP:P48194; match to protein family HMM PF04542; match to protein family HMM PF04545
YP_505340.1	identified by match to protein family HMM TIGR01630
YP_505344.1	binds to the ribosome on the universally-conserved alpha-sarcin loop
YP_505345.1	identified by similarity to GB:AAK22816.1
YP_505346.1	identified by similarity to SP:P05055; 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_505347.1	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_505348.1	identified by match to protein family HMM PF01509; match to protein family HMM TIGR00431
YP_505349.1	identified by similarity to SP:Q01465; match to protein family HMM PF06723; match to protein family HMM TIGR00904
YP_505354.1	identified by similarity to PIR:E97838; match to protein family HMM PF07031
YP_505357.1	identified by match to protein family HMM PF01121; match to protein family HMM TIGR00152
YP_505359.1	identified by match to protein family HMM PF01300; match to protein family HMM TIGR00057
YP_505361.1	identified by similarity to SP:P02346; match to protein family HMM PF00216
YP_505367.1	involved in the de novo synthesis of pyridoxine (Vitamin B6)
YP_505368.1	identified by match to protein family HMM PF01467; match to protein family HMM TIGR00125
YP_505371.1	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_505372.1	identified by match to protein family HMM PF00578
YP_505373.2	IleRS; catalyzes the formation of isoleucyl-tRNA(Ile) from isoleucine and tRNA(Ile); since isoleucine and other amino acids such as valine are similar, there are additional editing function in this enzyme; one is involved in hydrolysis of activated valine-AMP and the other is involved in deacylation of mischarged Val-tRNA(Ile); there are two active sites, one for aminoacylation and one for editing; class-I aminoacyl-tRNA synthetase family type 2 subfamily; some organisms carry two different copies of this enzyme; in some organisms, the type 2 subfamily is associated with resistance to the antibiotic pseudomonic acid (mupirocin)
YP_505378.1	Catalyzes the transfer of electrons from NADH to quinone
YP_505379.1	identified by similarity to SP:P26844; match to protein family HMM PF00717; match to protein family HMM TIGR02227
YP_505380.1	identified by match to protein family HMM PF01521; match to protein family HMM TIGR00049
YP_505390.1	identified by match to protein family HMM PF00231
YP_505391.1	identified by similarity to SP:Q54769; match to protein family HMM PF01227
YP_505425.1	identified by match to protein family HMM PF00083
YP_505426.1	identified by similarity to GB:AAS14586.1
YP_505428.1	catalyzes the formation of porphobilinogen from 5-aminolevulinate
YP_505429.1	identified by similarity to SP:Q03638; match to protein family HMM PF00733; match to protein family HMM PF02540; match to protein family HMM TIGR00552
YP_505433.1	identified by similarity to GB:AAS14632.1
YP_505434.1	This protein performs the mismatch recognition step during the DNA repair process
YP_505437.1	identified by match to protein family HMM PF01230
YP_505438.1	identified by match to protein family HMM PF05065; match to protein family HMM TIGR01554
YP_505440.1	SucA; E1 component of the oxoglutarate dehydrogenase complex which catalyzes the formation of succinyl-CoA from 2-oxoglutarate; SucA catalyzes the reaction of 2-oxoglutarate with dihydrolipoamide succinyltransferase-lipoate to form dihydrolipoamide succinyltransferase-succinyldihydrolipoate and carbon dioxide
YP_505443.1	Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide
YP_505452.1	identified by match to protein family HMM PF03099; match to protein family HMM TIGR00121
YP_505456.1	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 TIGR01574
YP_505460.1	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_505468.1	molecular chaperone
YP_505469.1	identified by similarity to GB:AAS14866.1
YP_505472.1	identified by similarity to SP:P20625; match to protein family HMM PF00633; match to protein family HMM PF00730; match to protein family HMM TIGR01083
YP_505474.1	negatively supercoils closed circular double-stranded DNA
YP_505476.1	identified by match to protein family HMM PF00580
YP_505482.1	identified by similarity to GB:AAB30824.1
YP_505483.1	catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs
YP_505496.1	identified by match to protein family HMM PF02600
YP_505498.1	in Escherichia coli BM108, a mutation that results in lack of L33 synthesis had no effect on ribosome synthesis or function; there are paralogous genes in several bacterial genomes, and a CXXC motif for zinc binding and an upstream regulation region of the paralog lacking this motif that are regulated by zinc similar to other ribosomal proteins like L31; the proteins in this group lack the CXXC motif
YP_505501.1	identified by match to protein family HMM PF00023
YP_505502.1	identified by match to protein family HMM PF00550
YP_505503.1	identified by similarity to SP:P39435; match to protein family HMM PF00109; match to protein family HMM PF02801
YP_505506.1	identified by match to protein family HMM PF02481; match to protein family HMM TIGR00732
YP_505509.1	identified by match to protein family HMM PF01119; match to protein family HMM PF02518; match to protein family HMM TIGR00585
YP_505510.1	identified by similarity to SP:P05828; match to protein family HMM PF01618
YP_505514.1	identified by match to protein family HMM PF00512; match to protein family HMM PF02518
YP_505515.1	DapATase; functions in arginine biosynthetic pathway; catalyzes the formation of N-acetyl-L-glutamate 5-semialdehyde from 2-oxoglutarate and N(2)-acetyl-L-ornithine
YP_505523.1	identified by match to protein family HMM PF01580
YP_505524.1	identified by match to protein family HMM PF02325
YP_505525.1	identified by match to protein family HMM PF00571; match to protein family HMM PF01595; match to protein family HMM PF03471
YP_505528.1	identified by match to protein family HMM PF02581; match to protein family HMM TIGR00693
YP_505529.1	identified by similarity to GB:AAS14071.1; match to protein family HMM PF03618
YP_505530.1	identified by match to protein family HMM PF00581
YP_505532.1	identified by match to protein family HMM PF01391
YP_505533.1	identified by similarity to SP:P23882; match to protein family HMM PF00551; match to protein family HMM PF02911; match to protein family HMM TIGR00460
YP_505535.1	identified by similarity to SP:P08177; match to protein family HMM PF00004; match to protein family HMM PF02190; match to protein family HMM PF05362; match to protein family HMM TIGR00763
YP_505536.1	binds and unfolds substrates as part of the ClpXP protease
YP_505537.1	hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates
YP_505538.1	identified by match to protein family HMM PF00254; match to protein family HMM PF05697
YP_505539.1	identified by similarity to SP:P18200; match to protein family HMM PF04608
YP_505540.1	identified by match to protein family HMM PF00583
YP_505541.1	identified by similarity to GB:AAS14420.1
YP_505544.1	identified by similarity to SP:P53556; match to protein family HMM PF00155
YP_505545.1	identified by similarity to SP:P39172; match to protein family HMM PF01297
YP_505546.1	identified by similarity to SP:P52648; match to protein family HMM PF00005
YP_505547.1	identified by similarity to SP:P27854; match to protein family HMM PF03109; match to protein family HMM TIGR01982
YP_505549.1	identified by match to protein family HMM PF00005
YP_505550.1	identified by match to protein family HMM PF02416; match to protein family HMM TIGR01411
YP_505551.1	involved in a recombinational process of DNA repair, independent of the recBC complex
YP_505552.1	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_505555.1	identified by match to protein family HMM TIGR00097
YP_505556.1	identified by similarity to GB:AAS14796.1
YP_505557.1	identified by match to protein family HMM PF01594
YP_505560.1	identified by similarity to GB:AAC17941.1
YP_505561.1	identified by match to protein family HMM PF01127
YP_505562.1	identified by similarity to GB:AAD45819.1
YP_505564.1	identified by match to protein family HMM PF02811; match to protein family HMM PF07733; match to protein family HMM TIGR00594
YP_505565.1	identified by similarity to SP:P15298; match to protein family HMM PF01722
YP_505569.1	identified by match to protein family HMM PF01243; match to protein family HMM TIGR00558
YP_505571.1	identified by match to protein family HMM PF02230
YP_505573.1	identified by match to protein family HMM PF01327
YP_505574.1	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_505575.1	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_505576.1	identified by match to protein family HMM PF01899
YP_505577.1	identified by similarity to SP:P53556; match to protein family HMM PF00155; match to protein family HMM PF00202
YP_505578.1	identified by match to protein family HMM PF01617
YP_505580.1	identified by similarity to GB:AAS13900.1
YP_505581.1	RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids
YP_505582.1	identified by similarity to SP:P00577; match to protein family HMM PF00623; match to protein family HMM PF04983; match to protein family HMM PF04997; match to protein family HMM PF04998; match to protein family HMM PF05000; match to protein family HMM TIGR02386
YP_505583.1	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates; beta subunit is part of the catalytic core which binds with a sigma factor to produce the holoenzyme
YP_505584.1	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_505585.1	binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit
YP_505586.1	in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA
YP_505587.1	binds directly to 23S ribosomal RNA
YP_505588.1	identified by similarity to SP:P16921; match to protein family HMM PF00467; match to protein family HMM PF02357; match to protein family HMM TIGR00922
YP_505589.1	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_505590.1	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_505591.1	EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene
YP_505592.1	binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit
YP_505593.1	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_505594.1	identified by match to protein family HMM PF00753; match to protein family HMM PF07521
YP_505595.1	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_505599.1	identified by similarity to GB:AAS14534.1; match to protein family HMM TIGR02396
YP_505600.1	identified by match to protein family HMM PF00529; match to protein family HMM TIGR01843
YP_505602.1	identified by match to protein family HMM PF00528
YP_505605.1	identified by similarity to GB:AAF98273.1; match to protein family HMM PF03060
YP_505606.1	identified by similarity to PIR:A49213; match to protein family HMM PF02630
YP_505608.1	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_505609.1	catalyzes the interconversion of succinyl-CoA and succinate
YP_505610.1	identified by similarity to SP:P80865; match to protein family HMM PF00549; match to protein family HMM PF02629; match to protein family HMM TIGR01019
YP_505615.1	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_505616.1	identified by match to protein family HMM PF00528; match to protein family HMM TIGR02138
YP_505617.1	identified by similarity to SP:P78061; match to protein family HMM PF00120
YP_505618.1	identified by match to protein family HMM PF00753
YP_505620.1	identified by similarity to GB:AAS14461.1
YP_505621.1	identified by similarity to GB:AAS14460.1
YP_505623.1	identified by match to protein family HMM PF00070; match to protein family HMM PF02852; match to protein family HMM PF07992; match to protein family HMM TIGR01350
YP_505624.1	An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes
YP_505626.1	heat shock protein involved in degradation of misfolded proteins
YP_505627.1	heat shock protein involved in degradation of misfolded proteins
YP_505628.1	identified by similarity to SP:P27851; match to protein family HMM PF01209; match to protein family HMM TIGR01934
YP_505629.1	identified by similarity to GB:AAD41482.1
YP_505630.1	identified by similarity to SP:P23920; match to protein family HMM PF00133; match to protein family HMM TIGR00398
YP_505632.1	identified by similarity to SP:Q03736; match to protein family HMM PF00116; match to protein family HMM PF02790
YP_505633.1	identified by similarity to SP:P31833; match to protein family HMM PF00115
YP_505634.1	converts protoheme IX and farnesyl diphosphate to heme O
YP_505635.1	identified by similarity to SP:Q50985
YP_505636.1	catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis
YP_505638.1	identified by similarity to SP:P19677; match to protein family HMM PF02699; match to protein family HMM TIGR00739
YP_505645.1	identified by similarity to SP:P00583; match to protein family HMM PF00712; match to protein family HMM PF02767; match to protein family HMM PF02768; match to protein family HMM TIGR00663
YP_505646.1	identified by similarity to SP:O67779; match to protein family HMM PF01612
YP_505647.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00486
YP_505648.1	identified by match to protein family HMM PF01381
YP_505649.1	identified by similarity to SP:O34955; match to protein family HMM PF00719
YP_505655.1	forms a direct contact with the tRNA during translation
YP_505656.1	in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit
YP_505658.1	identified by match to protein family HMM PF02321
YP_505659.1	identified by similarity to SP:P21590
YP_505660.1	identified by similarity to SP:P08330; match to protein family HMM PF00156; match to protein family HMM TIGR01251
YP_505661.1	identified by match to protein family HMM PF02686; match to protein family HMM TIGR00135
YP_505662.1	identified by match to protein family HMM PF01617
YP_505664.1	Catalyzes the conversion of citrate to isocitrate
YP_505665.1	identified by similarity to SP:P12045; match to protein family HMM PF02222; match to protein family HMM TIGR01161
YP_505666.1	protein associated with Co2+ and Mg2+ efflux
YP_505671.1	identified by similarity to GB:AAM00400.1
YP_505672.1	identified by similarity to GB:AAO41101.1
YP_505673.1	identified by similarity to GB:AAO41092.1
YP_505674.1	identified by similarity to GB:AAO41101.1
YP_505675.1	identified by similarity to GB:AAN05086.1
YP_505676.1	identified by similarity to GB:AAN05086.1
YP_505678.1	identified by similarity to GB:AAO41098.1
YP_505686.1	identified by similarity to GB:AAO41101.1
YP_505688.1	identified by similarity to SP:P25662; match to protein family HMM PF01145; match to protein family HMM TIGR01933
YP_505689.1	identified by match to protein family HMM PF01145; match to protein family HMM TIGR01932
YP_505690.1	identified by match to protein family HMM PF00089; match to protein family HMM PF00595; match to protein family HMM TIGR02037
YP_505691.1	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_505692.1	involved in the insertion of copper into subunit I of cytochrome C oxidase
YP_505695.1	identified by similarity to GB:AAN15212.2; match to protein family HMM PF01617
YP_505698.1	identified by match to protein family HMM PF00675; match to protein family HMM PF05193
YP_505699.1	identified by match to protein family HMM PF00675; match to protein family HMM PF05193
YP_505700.1	lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis
YP_505701.1	identified by similarity to SP:P54575; match to protein family HMM PF01687; match to protein family HMM PF06574; match to protein family HMM TIGR00083
YP_505702.1	identified by similarity to SP:P37687; match to protein family HMM PF00462; match to protein family HMM TIGR02181
YP_505703.1	identified by similarity to SP:P06137; match to protein family HMM PF02491; match to protein family HMM TIGR01174
YP_505704.1	identified by similarity to SP:P21893; match to protein family HMM PF01368; match to protein family HMM PF02272; match to protein family HMM TIGR00644
YP_505705.1	catalyzes the formation of 2-oxoglutarate from isocitrate
YP_505707.1	identified by similarity to GB:AAC31309.1; match to protein family HMM PF01617
YP_505708.1	identified by match to protein family HMM PF01617
YP_505709.1	identified by match to protein family HMM PF00805
YP_505710.1	identified by similarity to GB:AAS14894.1
YP_505712.1	involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate
YP_505713.1	identified by similarity to SP:P30138; match to protein family HMM PF00899; match to protein family HMM PF05237
YP_505714.1	identified by similarity to SP:P37687
YP_505715.1	alternate gene name: p44-2b. Infect. Immun. 70 (3), 1175-1184 (2002); identified by similarity to GB:AAL38044.1; match to protein family HMM PF01617
YP_505716.1	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_505717.1	identified by similarity to GB:CAB51029.1; match to protein family HMM PF00004; match to protein family HMM PF01434; match to protein family HMM PF06480; match to protein family HMM TIGR01241
YP_505718.1	identified by match to protein family HMM PF01171; match to protein family HMM TIGR02432
YP_505719.1	identified by similarity to GB:BAA31229.1; match to protein family HMM PF02386; match to protein family HMM PF07723
YP_505720.1	identified by similarity to SP:P06137; match to protein family HMM PF02491; match to protein family HMM TIGR01174
YP_505725.1	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_505726.1	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_505727.1	identified by similarity to SP:P94527; match to protein family HMM PF01761
YP_505728.1	identified by match to protein family HMM PF01617
YP_505731.1	identified by match to protein family HMM PF00198; match to protein family HMM PF00364; match to protein family HMM TIGR01347
YP_505732.1	catalyzes the removal of N-terminal amino acids from peptides and arylamides; generally Co(II) however activity has been shown for some methionine aminopeptidases with Zn, Fe, or Mn
YP_505733.1	identified by similarity to SP:P37186; match to protein family HMM TIGR00536
YP_505735.1	identified by similarity to SP:P45403
YP_505737.1	identified by similarity to SP:P06978; match to protein family HMM PF01066; match to protein family HMM TIGR00560
YP_505738.1	identified by similarity to SP:P12048; match to protein family HMM PF01808; match to protein family HMM PF02142; match to protein family HMM TIGR00355
YP_505739.1	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_505740.1	identified by similarity to GB:AAS14739.1
YP_505741.1	identified by match to protein family HMM PF01103; match to protein family HMM PF07244
YP_505742.1	identified by match to protein family HMM PF00595; match to protein family HMM PF02163; match to protein family HMM TIGR00054
YP_505743.1	identified by match to protein family HMM PF03937
YP_505744.1	identified by similarity to GB:AAM35423.1
YP_505745.1	identified by match to protein family HMM PF00768; match to protein family HMM PF07943
YP_505746.1	identified by match to protein family HMM PF01617
YP_505747.1	identified by similarity to SP:P42977; match to protein family HMM PF01743
YP_505748.1	catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate
YP_505749.1	identified by similarity to GB:AAN15209.1; match to protein family HMM PF01381
YP_505750.1	identified by similarity to GB:AAN15210.1; match to protein family HMM PF01617
YP_505751.1	identified by similarity to GB:AAN15211.1
YP_505752.1	identified by match to protein family HMM PF01617
YP_505754.1	identified by similarity to SP:Q04761
YP_505755.1	identified by similarity to SP:Q58413; match to protein family HMM PF00133; match to protein family HMM TIGR00422
YP_505757.1	identified by match to protein family HMM PF00448; match to protein family HMM PF02881; match to protein family HMM TIGR00064
YP_505758.1	identified by similarity to SP:P53558; match to protein family HMM TIGR00347
YP_505759.1	identified by match to protein family HMM PF01617
YP_505760.1	identified by similarity to GB:AAB41630.1; match to protein family HMM TIGR02049
YP_505761.1	identified by similarity to SP:P20901; match to protein family HMM PF00285; match to protein family HMM TIGR01798
YP_505762.1	contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway
YP_505767.1	alternate name:major surface protein-2C.Infect Immun. 1998 Aug;66(8):3711-8.; identified by similarity to GB:AAC31309.1; match to protein family HMM PF01617
YP_505768.1	identified by similarity to SP:Q07408; match to protein family HMM PF01617
YP_505769.1	catalyzes the formation of 5-aminolevulinate from succinyl-CoA and glycine
YP_505770.1	identified by similarity to SP:P00951; match to protein family HMM PF00579; match to protein family HMM PF01479; match to protein family HMM TIGR00234
YP_505771.1	identified by similarity to SP:P05457; match to protein family HMM PF00120; match to protein family HMM PF03951; match to protein family HMM TIGR00653
YP_505772.1	identified by similarity to SP:P19641; match to protein family HMM PF00348
YP_505773.1	identified by match to protein family HMM PF01617
YP_505775.1	identified by similarity to GB:AAS14093.1; match to protein family HMM PF06144
YP_505777.1	identified by match to protein family HMM PF01617
YP_505778.1	identified by match to protein family HMM PF00198; match to protein family HMM PF00364; match to protein family HMM PF02817
YP_505779.1	catalyzes the formation of glycerone phosphate and D-glyceraldehyde 3-phosphate from D-fructose 1,6-bisphosphate
YP_505782.1	identified by match to protein family HMM PF00707; match to protein family HMM PF05198; match to protein family HMM TIGR00168
YP_505783.1	identified by similarity to SP:P00955; match to protein family HMM PF00587; match to protein family HMM PF03129; match to protein family HMM PF07973; match to protein family HMM TIGR00418
YP_505784.1	identified by match to protein family HMM PF02464; match to protein family HMM TIGR00199
YP_505785.1	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_505786.1	methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA
YP_505787.1	Essential for efficient processing of 16S rRNA
YP_505788.1	identified by similarity to GB:AAO30106.1; match to protein family HMM PF01617
YP_505789.1	identified by match to protein family HMM PF01571
YP_505790.1	identified by similarity to SP:P45403; match to protein family HMM PF01578
YP_505791.1	identified by similarity to GB:AAD41482.1
YP_505792.1	identified by match to protein family HMM PF01617
YP_505793.1	identified by similarity to SP:P36663; match to protein family HMM PF02542; match to protein family HMM TIGR00151
YP_505794.1	identified by match to protein family HMM PF01128
YP_505796.1	identified by similarity to SP:P09028; match to protein family HMM PF00731; match to protein family HMM TIGR01162
YP_505798.1	identified by similarity to SP:P06984; match to protein family HMM PF00216
YP_505799.1	identified by match to protein family HMM PF00376
YP_505800.1	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_505802.1	identified by match to protein family HMM PF01617
YP_505803.1	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_505804.1	identified by similarity to GB:AAS14418.1; match to protein family HMM PF02130; match to protein family HMM TIGR00043
YP_505805.1	identified by similarity to GB:AAS14416.1; match to protein family HMM PF04543
YP_505806.1	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_505811.1	decarboxylates 4-phosphopantothenoylcysteine to form 4'-phosphopantotheine.
YP_505812.1	identified by match to protein family HMM PF00270; match to protein family HMM PF00271
YP_505813.1	identified by similarity to SP:P34943; match to protein family HMM PF01073; match to protein family HMM PF01370; match to protein family HMM PF04321; match to protein family HMM PF05368; match to protein family HMM PF07993
YP_505814.1	Catalyzes first step of the de novo purine nucleotide biosynthetic pathway
YP_505815.1	Enables the recycling of peptidyl-tRNAs produced at termination of translation
YP_505816.1	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_505819.1	identified by similarity to SP:P45522; match to protein family HMM PF00999; match to protein family HMM PF02254
YP_505820.1	identified by similarity to GB:AAS14896.1
YP_505821.1	identified by similarity to GB:AAS14141.1; match to protein family HMM PF03653
YP_505822.1	catalyzes the oxidative decarboxylation of pyruvate with concomitant acetylation of a lipoic acid-containing dihydrolipoamide acyltransferase within the complex. The pyruvate dehydrogenase complex catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2); it contains multiple copies of three enzymatic components: pyruvate dehydrogenase (E1), dihydrolipoamide acetyltransferase (E2) and lipoamide dehydrogenase
YP_505823.1	identified by similarity to SP:P46473; match to protein family HMM PF01523
YP_505824.1	identified by match to protein family HMM PF01617
YP_505825.1	identified by similarity to SP:P43525; match to protein family HMM PF00925
YP_505826.1	identified by match to protein family HMM PF00515; match to protein family HMM PF07719
YP_505829.1	identified by similarity to GB:AAS14454.1
YP_505830.1	Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway
YP_505831.1	identified by match to protein family HMM PF01336; match to protein family HMM PF02601; match to protein family HMM TIGR00237
YP_505832.1	identified by match to protein family HMM TIGR02098
YP_505833.1	identified by match to protein family HMM PF01617
YP_505834.1	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_505836.1	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_505837.1	identified by match to protein family HMM PF00926; match to protein family HMM TIGR00506
YP_505838.1	identified by similarity to SP:P21346; match to protein family HMM PF01272; match to protein family HMM PF03449; match to protein family HMM TIGR01462
YP_505839.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit
YP_505840.1	identified by match to protein family HMM PF00213; match to protein family HMM TIGR01145
YP_505842.1	identified by similarity to GB:CAE28374.1
YP_505846.1	identified by match to protein family HMM PF02687; match to protein family HMM TIGR02212
YP_505847.1	identified by similarity to GB:AAL02551.1; match to protein family HMM PF02367; match to protein family HMM TIGR00150
YP_505848.1	identified by match to protein family HMM PF01027
YP_505849.1	identified by match to protein family HMM PF01118; match to protein family HMM PF02774
YP_505850.1	identified by similarity to GB:AAS14718.1
YP_505851.1	identified by similarity to GB:AAB61695.1; match to protein family HMM PF00004; match to protein family HMM TIGR02397
YP_505852.1	identified by similarity to SP:O34425; match to protein family HMM PF00044; match to protein family HMM PF02800
YP_505854.1	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_505855.1	identified by match to protein family HMM PF01617
YP_505857.1	identified by similarity to GB:AAK28689.1; match to protein family HMM PF01617
YP_505858.1	identified by match to protein family HMM PF01617
YP_505859.1	identified by similarity to SP:P26615; match to protein family HMM PF01977; match to protein family HMM TIGR00148
YP_505860.1	identified by match to protein family HMM PF01617
YP_505865.1	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_505866.1	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_505870.1	identified by match to protein family HMM PF03167; match to protein family HMM TIGR00758
YP_505871.1	identified by similarity to SP:P27251; match to protein family HMM PF01327; match to protein family HMM TIGR00079
YP_505872.1	identified by match to protein family HMM PF01553
YP_505873.1	binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase
YP_505874.1	identified by similarity to SP:P27251; match to protein family HMM PF01327
YP_505875.1	transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein
YP_505876.1	identified by match to protein family HMM PF03023; match to protein family HMM TIGR01695
YP_505877.1	identified by similarity to GB:AAS14447.1
YP_505888.1	identified by match to protein family HMM PF01617
YP_505891.1	identified by similarity to SP:P75757; match to protein family HMM PF01545; match to protein family HMM TIGR01297
YP_505893.1	identified by similarity to SP:P18274; match to protein family HMM PF01258
YP_505894.1	identified by similarity to GB:AAM00422.1; match to protein family HMM PF02534
YP_505895.1	identified by similarity to GB:AAM00419.1; match to protein family HMM PF00437
YP_505896.1	identified by similarity to GB:AAM00418.1; match to protein family HMM PF03743
YP_505897.1	identified by similarity to GB:AAM00421.1; match to protein family HMM PF03524
YP_505898.1	identified by similarity to GB:AAM00420.1; match to protein family HMM PF04335
YP_505900.1	Required for DNA replication; binds preferentially to single-stranded, linear DNA