-- dump date   	20140619_070354
-- class       	Genbank::CDS
-- table       	cds_note
-- id	note
YP_506836.1	identified by match to protein family HMM PF02195; match to protein family HMM TIGR00180
YP_506837.1	Essential for efficient processing of 16S rRNA
YP_506838.1	methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA
YP_506839.1	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_506840.1	identified by match to protein family HMM PF02464; match to protein family HMM TIGR00199
YP_506841.1	catalyzes a two-step reaction, first charging a threonine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA; catalyzes the formation of threonyl-tRNA(Thr) from threonine and tRNA(Thr)
YP_506842.1	IF-3 has several functions that are required and promote translation initiation including; preventing association of 70S by binding to 30S; monitoring codon-anticodon interactions by promoting disassociation of fMet-tRNA(fMet) from initiation complexes formed on leaderless mRNAs or incorrectly bound noninitiatior tRNAs and complexes with noncanonical start sites; stimulates codon-anticodon interactions at P-site; involved in moving mRNA to the P-site; and in recycling subunits
YP_506843.1	identified by match to protein family HMM PF02367; match to protein family HMM TIGR00150
YP_506844.1	identified by match to protein family HMM PF01027
YP_506846.1	identified by similarity to SP:O34425; match to protein family HMM PF00044; match to protein family HMM PF02800; match to protein family HMM TIGR01534
YP_506847.1	identified by similarity to SP:P26428; match to protein family HMM PF01965
YP_506848.1	identified by similarity to GB:AAG27705.1; match to protein family HMM PF03807
YP_506849.1	identified by match to protein family HMM PF00004; match to protein family HMM TIGR02397
YP_506850.1	identified by similarity to GB:AAS14718.1
YP_506851.1	identified by match to protein family HMM PF01118; match to protein family HMM PF02774; match to protein family HMM TIGR01296
YP_506853.1	catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase
YP_506854.1	identified by match to protein family HMM PF01494; match to protein family HMM TIGR01988
YP_506855.1	identified by similarity to GB:AAS14514.1
YP_506856.1	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_506857.1	identified by similarity to SP:P45651; match to protein family HMM PF02092; match to protein family HMM PF05746; match to protein family HMM TIGR00211
YP_506858.1	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_506859.1	identified by similarity to SP:P30011; match to protein family HMM PF01729; match to protein family HMM PF02749; match to protein family HMM TIGR00078
YP_506860.1	identified by match to protein family HMM PF02660; match to protein family HMM TIGR00023
YP_506861.1	identified by similarity to SP:P24239; match to protein family HMM PF02075; match to protein family HMM TIGR00228
YP_506862.1	identified by match to protein family HMM PF00510
YP_506863.1	identified by similarity to SP:P29680; match to protein family HMM PF01208; match to protein family HMM TIGR01464
YP_506864.1	identified by similarity to GB:AAC62436.1; match to protein family HMM PF00571; match to protein family HMM PF03471
YP_506865.1	identified by match to protein family HMM PF04586; match to protein family HMM TIGR01543
YP_506866.1	identified by match to protein family HMM PF04860; match to protein family HMM TIGR01537
YP_506868.1	identified by similarity to SP:P12999; match to protein family HMM PF01209
YP_506869.1	3 different subfamilies; catalyzes the formation of quinolinate from iminoaspartate and dihydroxyacetone phosphate
YP_506870.1	identified by similarity to GB:AAA85787.1; match to protein family HMM PF00037
YP_506871.1	identified by similarity to PIR:JC6174; match to protein family HMM TIGR02202
YP_506872.1	identified by similarity to GB:AAM00416.1; match to protein family HMM PF02534
YP_506873.1	identified by similarity to GB:AAM00414.1; match to protein family HMM PF00437
YP_506874.1	identified by similarity to GB:AAM00413.1; match to protein family HMM PF03743
YP_506875.1	identified by similarity to GB:AAM00415.1; match to protein family HMM PF03524
YP_506876.1	identified by similarity to GB:AAM00411.1; match to protein family HMM PF04335
YP_506877.1	identified by match to protein family HMM PF00925
YP_506879.1	identified by match to protein family HMM PF00515; match to protein family HMM PF07719
YP_506881.1	identified by match to protein family HMM PF01678; match to protein family HMM TIGR00652
YP_506886.1	Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway
YP_506887.1	identified by similarity to SP:P04994; match to protein family HMM PF01336; match to protein family HMM PF02601; match to protein family HMM TIGR00237
YP_506888.1	identified by match to protein family HMM TIGR02098
YP_506889.1	catalyzes the formation of N-succinyl-2-amino-6-ketopimelate from succinyl-CoA and tetrahydrodipicolinate in the lysine biosynthetic pathway
YP_506891.1	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_506892.1	decarboxylates 4-phosphopantothenoylcysteine to form 4'-phosphopantotheine.
YP_506893.1	identified by match to protein family HMM PF00270; match to protein family HMM PF00271; match to protein family HMM PF01336; match to protein family HMM PF04851
YP_506894.1	identified by match to protein family HMM PF01073; match to protein family HMM PF01370; match to protein family HMM PF04321; match to protein family HMM PF05368; match to protein family HMM PF07993
YP_506895.1	identified by similarity to SP:P18274
YP_506896.1	identified by similarity to SP:P33930; match to protein family HMM PF03379
YP_506897.1	identified by match to protein family HMM PF01545; match to protein family HMM TIGR01297
YP_506899.1	identified by similarity to GB:AAK25655.1
YP_506901.1	binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase
YP_506902.1	identified by match to protein family HMM PF01553
YP_506903.1	identified by match to protein family HMM PF01327; match to protein family HMM TIGR00079
YP_506904.1	identified by match to protein family HMM PF03167; match to protein family HMM TIGR00758
YP_506906.1	Required for DNA replication; binds preferentially to single-stranded, linear DNA
YP_506907.1	catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation
YP_506910.1	identified by similarity to SP:P00582; match to protein family HMM PF00476; match to protein family HMM PF01367; match to protein family HMM PF02739; match to protein family HMM TIGR00593
YP_506912.1	identified by match to protein family HMM PF00834; match to protein family HMM TIGR01163
YP_506914.1	identified by similarity to GB:AAS14650.1; match to protein family HMM PF02405
YP_506915.1	identified by match to protein family HMM PF00005
YP_506918.1	identified by similarity to SP:P19641; match to protein family HMM PF00348
YP_506919.1	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_506920.1	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_506921.1	catalyzes the formation of 5-aminolevulinate from succinyl-CoA and glycine
YP_506922.1	identified by similarity to SP:Q8XJQ1; match to protein family HMM PF02021
YP_506924.1	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_506925.2	catalyzes the formation of glycerone phosphate and D-glyceraldehyde 3-phosphate from D-fructose 1,6-bisphosphate
YP_506926.1	identified by similarity to SP:Q9R9N3; match to protein family HMM PF00198; match to protein family HMM PF00364; match to protein family HMM PF02817; match to protein family HMM TIGR01349
YP_506951.1	contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway
YP_506952.1	identified by similarity to SP:P51033; match to protein family HMM PF00285; match to protein family HMM TIGR01798
YP_506953.1	identified by similarity to GB:AAB41630.1; match to protein family HMM TIGR02049
YP_506954.1	identified by similarity to GB:AAS14093.1; match to protein family HMM PF06144; match to protein family HMM TIGR01128
YP_506955.1	identified by match to protein family HMM PF02687; match to protein family HMM TIGR02212
YP_506958.1	identified by similarity to GB:BAC50165.1
YP_506959.1	identified by similarity to SP:Q02849; match to protein family HMM PF00213; match to protein family HMM TIGR01145
YP_506960.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit
YP_506961.1	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_506962.1	identified by match to protein family HMM PF00926; match to protein family HMM TIGR00506
YP_506963.1	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_506964.1	valine--tRNA ligase; ValRS; converts valine ATP and tRNA(Val) to AMP PPi and valyl-tRNA(Val); class-I aminoacyl-tRNA synthetase type 1 subfamily; has a posttransfer editing process to hydrolyze mischarged Thr-tRNA(Val) which is done by the editing domain
YP_506965.1	identified by match to protein family HMM PF01578
YP_506966.1	identified by match to protein family HMM PF01571
YP_506967.1	Catalyzes first step of the de novo purine nucleotide biosynthetic pathway
YP_506968.1	identified by similarity to GB:AAM00401.1
YP_506969.1	Enables the recycling of peptidyl-tRNAs produced at termination of translation
YP_506970.1	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_506971.1	identified by similarity to SP:P31773
YP_506972.1	dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase (DapE), catalyzes the hydrolysis of N-succinyl-L,Ldiaminopimelate L,L-SDAP to L,L-diaminopimelate and succinate. It is a metalloprotease containing dinuclear active sites. Its structure is similar to the carboxypeptidase G2 from Pseudomonas sp. strain RS-16 and the aminopeptidase from Aeromonas proteolytica.
YP_506974.1	identified by similarity to SP:P45522; match to protein family HMM PF00999; match to protein family HMM PF02254
YP_506975.1	identified by similarity to GB:AAS14896.1
YP_506976.1	identified by match to protein family HMM PF03653
YP_506977.1	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_506979.1	identified by similarity to SP:P46473; match to protein family HMM PF01523
YP_506981.1	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_506983.1	identified by similarity to SP:P36663; match to protein family HMM PF02542; match to protein family HMM TIGR00151
YP_506984.1	identified by similarity to GB:AAF61714.1; match to protein family HMM PF01128
YP_506987.1	identified by similarity to SP:P09028; match to protein family HMM PF00731; match to protein family HMM TIGR01162
YP_506989.1	identified by similarity to SP:P30787; match to protein family HMM PF00216
YP_506990.1	identified by match to protein family HMM PF00376
YP_506991.1	identified by similarity to GB:AAL08844.1
YP_506992.1	identified by match to protein family HMM PF00579; match to protein family HMM TIGR00233
YP_506993.1	identified by match to protein family HMM PF01025
YP_506994.1	identified by match to protein family HMM PF00383; match to protein family HMM PF01872; match to protein family HMM TIGR00326
YP_506995.1	identified by similarity to GB:AAQ82755.1; match to protein family HMM PF07122
YP_506996.1	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_506997.1	identified by similarity to SP:P33582; match to protein family HMM PF03840; match to protein family HMM TIGR00810
YP_506998.1	identified by similarity to SP:P21891; match to protein family HMM PF00589; match to protein family HMM PF02899
YP_506999.1	identified by match to protein family HMM PF00005
YP_507000.1	NADP-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; decarboxylates oxaloacetate
YP_507001.1	identified by similarity to GB:AAS14671.1
YP_507003.1	identified by match to protein family HMM PF00795; match to protein family HMM TIGR00546
YP_507004.1	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_507008.1	identified by match to protein family HMM PF02470
YP_507009.1	identified by match to protein family HMM PF05071
YP_507010.1	identified by similarity to GB:BAC44856.1; match to protein family HMM PF03477; match to protein family HMM TIGR00244
YP_507012.1	identified by similarity to GB:AAD32553.1
YP_507013.1	identified by similarity to GB:AAD03802.1; match to protein family HMM PF01547
YP_507016.1	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_507017.1	identified by match to protein family HMM PF00083; match to protein family HMM PF07690
YP_507018.1	identified by similarity to PIR:AF3011; match to protein family HMM PF03966
YP_507019.1	identified by match to protein family HMM PF00106
YP_507020.1	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_507021.1	binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit
YP_507022.1	identified by match to protein family HMM PF01632; match to protein family HMM TIGR00001
YP_507023.1	identified by similarity to PIR:G97712; match to protein family HMM PF06242
YP_507024.1	An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes
YP_507025.1	identified by match to protein family HMM PF00226
YP_507026.1	identified by match to protein family HMM PF01106
YP_507028.1	identified by match to protein family HMM PF02597; match to protein family HMM TIGR01683
YP_507030.2	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_507031.1	identified by similarity to PIR:AF3507
YP_507032.1	Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation
YP_507033.1	identified by similarity to SP:P21202
YP_507034.1	identified by match to protein family HMM PF03602; match to protein family HMM TIGR00095
YP_507035.1	identified by similarity to GB:AAS13992.1; match to protein family HMM PF03547
YP_507036.1	identified by match to protein family HMM PF04800
YP_507040.1	identified by match to protein family HMM PF00919; match to protein family HMM PF04055; match to protein family HMM TIGR00089; match to protein family HMM TIGR01579
YP_507041.1	identified by similarity to SP:P06544; match to protein family HMM PF00085; match to protein family HMM TIGR01068
YP_507042.1	identified by match to protein family HMM PF03524
YP_507043.1	identified by similarity to SP:Q9R9N5; match to protein family HMM PF00676
YP_507044.1	identified by match to protein family HMM PF00561
YP_507045.1	identified by match to protein family HMM PF00478; match to protein family HMM PF00571; match to protein family HMM TIGR01302
YP_507046.1	catalyzes the phosphorylation of NAD to NADP
YP_507047.1	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_507048.1	identified by similarity to SP:P71019; match to protein family HMM PF00698; match to protein family HMM TIGR00128
YP_507050.1	catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP)
YP_507051.1	identified by match to protein family HMM PF07690
YP_507053.1	identified by similarity to GB:AAS13862.1; match to protein family HMM PF04280
YP_507054.1	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_507055.1	identified by similarity to GB:AAS14712.1
YP_507056.1	identified by match to protein family HMM PF00675; match to protein family HMM PF05193
YP_507058.1	identified by similarity to GB:AAS13931.1; match to protein family HMM PF03060
YP_507060.2	catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine
YP_507068.1	identified by similarity to GB:AAO05891.1
YP_507071.1	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 TIGR00580
YP_507084.1	An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids
YP_507085.1	identified by similarity to GB:AAS14039.1
YP_507087.1	Catalyzes the phosphorylation of UMP to UDP
YP_507088.1	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_507090.1	identified by similarity to SP:P76091; match to protein family HMM PF01148
YP_507096.1	identified by similarity to GB:AAL08846.1
YP_507098.1	responsible for recognizing base lesions in the genome and initiating base excision DNA repair
YP_507111.1	catalyzes the formation of (S)-2-(5-amino-1-(5-phospho-D-ribosyl)imidazole-4- carboxamido)succinate from 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate and L-aspartate in purine biosynthesis; SAICAR synthase
YP_507112.1	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_507113.1	identified by similarity to GB:AAL08832.1
YP_507114.1	identified by similarity to GB:AAM22615.1; match to protein family HMM PF01323
YP_507115.1	identified by match to protein family HMM PF02628
YP_507116.1	ATP-binding protein; required for proper cytochrome c maturation
YP_507117.1	Catalyzes the formation of dUTP from dCTP in thymidylate biosynthesis
YP_507118.1	identified by similarity to GB:AAS14665.1
YP_507119.1	identified by similarity to SP:Q47130; match to protein family HMM PF00313
YP_507120.1	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_507121.1	identified by similarity to SP:P09155; match to protein family HMM PF01612
YP_507122.1	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_507123.1	identified by match to protein family HMM PF00462; match to protein family HMM TIGR00365
YP_507124.1	identified by match to protein family HMM PF01722
YP_507125.1	identified by similarity to SP:P33926
YP_507126.1	Sms; stabilizes the strand-invasion intermediate during the DNA repair; involved in recombination of donor DNA and plays an important role in DNA damage repair after exposure to mutagenic agents
YP_507127.1	identified by match to protein family HMM PF06808; match to protein family HMM TIGR02123
YP_507128.1	identified by match to protein family HMM PF02674
YP_507129.1	binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21
YP_507130.1	binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit
YP_507131.1	in Escherichia coli this protein is wrapped around the base of the L1 stalk
YP_507132.1	catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate
YP_507133.1	identified by similarity to SP:P27838
YP_507134.1	identified by match to protein family HMM PF00005; match to protein family HMM PF00664
YP_507136.1	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_507137.1	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_507138.1	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_507139.1	identified by match to protein family HMM PF07690; match to protein family HMM TIGR00710
YP_507140.1	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_507141.1	plays an essential role in ATP-dependent branch migration of the Holliday junction
YP_507142.1	identified by similarity to SP:P33929; match to protein family HMM PF01578; match to protein family HMM TIGR01191
YP_507143.1	identified by similarity to SP:P24234; match to protein family HMM PF00625
YP_507145.1	catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate
YP_507146.1	identified by match to protein family HMM PF00561
YP_507147.1	identified by similarity to SP:P30323; match to protein family HMM PF00034
YP_507148.1	identified by match to protein family HMM PF00361
YP_507150.1	catalyzes the formation of phosphoenolpyruvate from pyruvate
YP_507151.1	identified by match to protein family HMM PF06271
YP_507152.1	identified by match to protein family HMM PF00702; match to protein family HMM TIGR01549
YP_507153.1	identified by similarity to SP:P00477
YP_507154.1	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_507155.1	identified by similarity to SP:P27291; match to protein family HMM PF04972
YP_507156.1	catalyzes the second step in the glutathione biosynthesis pathway, where it synthesizes ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione
YP_507157.1	identified by similarity to SP:P06136; match to protein family HMM PF03799
YP_507159.1	identified by similarity to SP:Q04849; 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_507160.1	catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate
YP_507161.1	identified by similarity to SP:P46352; match to protein family HMM PF00589; match to protein family HMM PF02899
YP_507162.1	catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis
YP_507163.1	identified by similarity to PIR:F97652
YP_507165.1	identified by similarity to GB:AAS13843.1
YP_507166.1	identified by match to protein family HMM PF02410; match to protein family HMM TIGR00090
YP_507167.1	identified by match to protein family HMM PF01435
YP_507168.1	identified by similarity to GB:AAL08839.1
YP_507170.1	identified by similarity to SP:P26281; match to protein family HMM PF01288; match to protein family HMM TIGR01498
YP_507171.1	identified by similarity to SP:P35852; match to protein family HMM PF00586; match to protein family HMM PF02769
YP_507172.1	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_507174.1	identified by similarity to GB:AAS14547.1
YP_507175.1	identified by match to protein family HMM PF01551
YP_507176.1	type II fructose 1,6-bisphosphatae; in Escherichia coli this protein forms a dimer and binds manganese
YP_507179.1	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_507182.1	identified by similarity to SP:P15254
YP_507183.1	identified by similarity to SP:P25531; match to protein family HMM PF00633; match to protein family HMM PF04002; match to protein family HMM TIGR00608
YP_507184.1	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_507185.1	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_507186.1	identified by match to protein family HMM PF00106
YP_507187.1	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_507188.1	identified by match to protein family HMM PF00775
YP_507189.1	catalyzes the removal of N-terminal amino acids preferably leucine from various peptides
YP_507190.1	identified by match to protein family HMM PF00551; match to protein family HMM TIGR00639
YP_507191.1	lipoyl/octanoyltransferase; catalyzes the transfer of the lipoyl/octanoyl moiety of lipoyl/octanoyl-ACP onto lipoate-dependent enzymes like pyruvate dehydrogenase and the glycine cleavage system H protein
YP_507193.1	identified by similarity to SP:P48795; match to protein family HMM PF01979; match to protein family HMM TIGR00857
YP_507194.1	identified by match to protein family HMM PF04127
YP_507196.1	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_507197.1	identified by similarity to PIR:T27606
YP_507198.1	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_507201.1	identified by match to protein family HMM PF00809; match to protein family HMM TIGR01496
YP_507202.1	identified by similarity to PIR:D97734
YP_507203.1	identified by similarity to GB:AAD09853.1; match to protein family HMM PF00005; match to protein family HMM TIGR01842
YP_507205.1	identified by similarity to SP:P28304; match to protein family HMM PF00107
YP_507207.1	identified by match to protein family HMM PF00580
YP_507210.1	identified by match to protein family HMM PF01145
YP_507211.1	identified by similarity to GB:AAS14513.1
YP_507212.1	identified by match to protein family HMM PF03969
YP_507215.1	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_507217.1	identified by similarity to GB:AAS14830.1
YP_507218.1	identified by similarity to GB:AAS14743.1
YP_507219.1	identified by similarity to GB:BAB50572.1
YP_507220.1	identified by similarity to SP:Q06607; match to protein family HMM PF00216
YP_507221.1	identified by match to protein family HMM PF01343; match to protein family HMM TIGR00706
YP_507222.1	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_507223.1	identified by match to protein family HMM PF02224; match to protein family HMM TIGR00017
YP_507224.1	identified by match to protein family HMM PF00588; match to protein family HMM PF08032; match to protein family HMM TIGR00186
YP_507225.1	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_507226.1	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_507227.1	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_507228.1	L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA
YP_507229.1	binds third domain of 23S rRNA and protein L29; part of exit tunnel
YP_507230.1	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_507231.1	protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA
YP_507232.1	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_507233.1	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_507234.1	located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e
YP_507235.1	one of the stabilizing components for the large ribosomal subunit
YP_507236.1	primary binding protein; helps mediate assembly; involved in translation fidelity
YP_507237.1	binds to the 23S rRNA between the centers for peptidyl transferase and GTPase
YP_507238.1	assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel
YP_507239.1	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_507240.1	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_507241.1	binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit
YP_507242.1	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_507243.1	binds 5S rRNA along with protein L5 and L25
YP_507244.1	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_507245.1	late assembly protein
YP_507246.1	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_507247.1	identified by similarity to SP:P16304; match to protein family HMM PF00406
YP_507248.1	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_507249.1	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_507250.1	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_507251.1	is a component of the macrolide binding site in the peptidyl transferase center
YP_507252.1	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_507253.1	identified by match to protein family HMM PF03772; match to protein family HMM TIGR00360
YP_507256.1	identified by match to protein family HMM PF01235
YP_507258.1	in Escherichia coli transcription of this gene is enhanced by polyamines
YP_507259.1	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_507260.1	identified by similarity to GB:BAB18470.1; match to protein family HMM PF01613
YP_507261.1	catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis
YP_507262.1	ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation
YP_507263.1	identified by similarity to SP:P28720; match to protein family HMM PF01702; match to protein family HMM TIGR00430; match to protein family HMM TIGR00449
YP_507264.1	some L32 proteins have zinc finger motifs consisting of CXXC while others do not
YP_507265.1	involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY
YP_507266.1	identified by similarity to SP:P24249; match to protein family HMM TIGR00747
YP_507267.1	identified by match to protein family HMM PF00383
YP_507268.1	identified by similarity to GB:AAS14136.1
YP_507269.1	unwinds double stranded DNA
YP_507270.1	identified by match to protein family HMM PF01266
YP_507272.1	identified by similarity to GB:AAS14837.1
YP_507273.1	identified by similarity to SP:Q08291; match to protein family HMM PF00348
YP_507276.1	Catalyzes the rate-limiting step in dNTP synthesis
YP_507277.1	identified by similarity to GB:AAS13897.1; match to protein family HMM PF03652; match to protein family HMM TIGR00250
YP_507278.1	catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis
YP_507279.1	identified by match to protein family HMM PF00691
YP_507281.1	identified by similarity to SP:P42663
YP_507282.1	identified by match to protein family HMM PF00456; match to protein family HMM PF02779; match to protein family HMM PF02780; match to protein family HMM TIGR00232
YP_507283.1	subunit F of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali
YP_507284.1	subunit G of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali
YP_507285.1	subunit C of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali
YP_507286.1	identified by match to protein family HMM PF00575; match to protein family HMM TIGR00757
YP_507287.1	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_507289.1	identified by similarity to GB:AAS14711.1; match to protein family HMM PF03364
YP_507290.1	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_507291.1	identified by match to protein family HMM PF00448; match to protein family HMM PF02881; match to protein family HMM PF02978; match to protein family HMM TIGR00959
YP_507292.1	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_507293.1	identified by similarity to GB:AAS14435.1
YP_507294.1	identified by similarity to GB:AAS13980.1; match to protein family HMM TIGR02281
YP_507295.1	identified by match to protein family HMM PF00557
YP_507296.1	identified by match to protein family HMM PF02602
YP_507299.1	identified by similarity to SP:P17888; 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_507300.1	required for 70S ribosome assembly
YP_507301.1	identified by match to protein family HMM PF00278; match to protein family HMM PF02784; match to protein family HMM TIGR01048
YP_507302.1	identified by match to protein family HMM PF00849; match to protein family HMM PF01479; match to protein family HMM TIGR00005
YP_507303.1	identified by similarity to GB:AAL66189.1; 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_507306.1	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_507307.1	identified by match to protein family HMM PF00528
YP_507308.1	identified by similarity to SP:P37369; match to protein family HMM PF00081; match to protein family HMM PF02777
YP_507309.1	identified by similarity to GB:AAM00402.1; match to protein family HMM PF05101
YP_507310.1	identified by similarity to GB:AAM00400.1; match to protein family HMM PF03135; match to protein family HMM TIGR00929
YP_507311.1	identified by similarity to GB:AAM00403.1; match to protein family HMM PF04610
YP_507312.1	identified by similarity to GB:AAM00403.1; match to protein family HMM PF04610
YP_507313.1	identified by match to protein family HMM PF04610
YP_507314.1	identified by match to protein family HMM PF04610
YP_507315.1	identified by similarity to GB:AAS14953.1; match to protein family HMM TIGR02217
YP_507316.1	identified by match to protein family HMM PF00692; match to protein family HMM TIGR00576
YP_507317.1	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_507318.1	catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers
YP_507319.1	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_507320.1	catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate
YP_507324.1	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_507325.1	identified by match to protein family HMM TIGR01730
YP_507326.1	identified by match to protein family HMM TIGR00008
YP_507327.1	Maf; overexpression in Bacillus subtilis inhibits septation in the dividing cell
YP_507329.1	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_507330.1	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_507331.1	identified by similarity to GB:AAS14090.1; match to protein family HMM PF04635
YP_507332.1	identified by similarity to GB:AAK33470.1; match to protein family HMM PF00950
YP_507335.1	identified by similarity to SP:P23136; match to protein family HMM PF00355; match to protein family HMM TIGR01416
YP_507336.1	identified by similarity to SP:P23134; match to protein family HMM PF00032; match to protein family HMM PF00033
YP_507337.1	identified by similarity to SP:P23135; match to protein family HMM PF02167
YP_507338.1	identified by similarity to GB:AAS14436.1
YP_507340.1	identified by similarity to GB:AAS14436.1
YP_507341.1	identified by similarity to GB:AAS14436.1
YP_507342.1	identified by similarity to SP:P77785; match to protein family HMM PF02769; match to protein family HMM TIGR01379
YP_507343.1	identified by match to protein family HMM PF03631; match to protein family HMM TIGR00765
YP_507346.1	identified by similarity to SP:P45049; match to protein family HMM PF01078; match to protein family HMM TIGR00368
YP_507347.1	identified by similarity to GB:AAS13832.1; match to protein family HMM PF01728
YP_507349.1	involved in DNA repair and RecFOR pathway recombination; RecFOR proteins displace ssDNA-binding protein and facilitate the production of RecA-coated ssDNA
YP_507350.1	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_507351.2	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_507352.1	identified by match to protein family HMM PF00578
YP_507353.1	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_507354.1	identified by match to protein family HMM PF01812
YP_507355.1	identified by match to protein family HMM PF01795; match to protein family HMM TIGR00006
YP_507356.1	essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication
YP_507357.1	enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis
YP_507358.1	identified by match to protein family HMM PF00829; match to protein family HMM TIGR00061
YP_507359.1	involved in the peptidyltransferase reaction during translation
YP_507360.1	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_507364.1	identified by match to protein family HMM PF00499
YP_507365.1	identified by similarity to SP:P50940; match to protein family HMM PF00420
YP_507366.1	identified by similarity to SP:P29924; match to protein family HMM PF00361; match to protein family HMM PF00662; match to protein family HMM PF06455; match to protein family HMM TIGR01974
YP_507367.1	identified by similarity to SP:P29925; match to protein family HMM PF00361; match to protein family HMM TIGR01972
YP_507368.1	identified by similarity to SP:P50973; match to protein family HMM PF00361; match to protein family HMM TIGR01770
YP_507369.1	catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate
YP_507371.1	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_507372.1	identified by match to protein family HMM PF00902; match to protein family HMM TIGR00945
YP_507373.1	identified by match to protein family HMM PF00873
YP_507374.1	modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination
YP_507375.1	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_507376.1	identified by match to protein family HMM PF02033
YP_507378.1	identified by match to protein family HMM PF03741
YP_507379.1	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_507383.1	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_507384.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit
YP_507385.1	identified by similarity to SP:P37812; match to protein family HMM PF02823; match to protein family HMM TIGR01216
YP_507386.1	similar to novel fructose-6-phosphate aldolase from Escherichia coli; enzyme from Methanocaldococcus janaschii shows transaldolase activity
YP_507387.1	identified by similarity to SP:O05113
YP_507388.1	identified by match to protein family HMM PF02646
YP_507390.1	identified by similarity to GB:AAS14504.1
YP_507392.1	identified by match to protein family HMM PF00375
YP_507395.2	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_507398.1	identified by similarity to GB:AAS14508.1
YP_507399.1	identified by similarity to SP:P38436; match to protein family HMM PF01715; match to protein family HMM TIGR00174
YP_507402.1	catalyzes the conversion of the propionic acid groups of rings I and III to vinyl groups during heme synthesis
YP_507403.1	identified by similarity to SP:P72848
YP_507404.1	identified by similarity to GB:AAS13842.1
YP_507405.1	catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate
YP_507406.1	binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential
YP_507408.1	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_507410.1	identified by similarity to GB:AAB28900.1; match to protein family HMM PF01039
YP_507413.1	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_507415.1	Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation
YP_507423.1	identified by similarity to GB:AAQ95406.1
YP_507425.1	Catalyzes the transfer of electrons from NADH to quinone
YP_507426.1	Catalyzes the transfer of electrons from NADH to quinone
YP_507427.1	Catalyzes the transfer of electrons from NADH to quinone
YP_507428.1	Catalyzes the transfer of electrons from NADH to quinone
YP_507429.1	identified by similarity to GB:AAS13913.1
YP_507430.1	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_507431.1	catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis
YP_507432.1	mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability
YP_507433.1	identified by similarity to GB:AAS14501.1; match to protein family HMM PF01648
YP_507434.1	identified by similarity to SP:P75000
YP_507436.1	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_507437.1	identified by similarity to GB:AAS14400.1
YP_507438.1	identified by match to protein family HMM PF00266; match to protein family HMM PF01212; match to protein family HMM PF02082; match to protein family HMM TIGR00738
YP_507439.1	catalyzes the removal of elemental sulfur from cysteine to produce alanine; involved in NAD biosynthesis
YP_507440.1	identified by match to protein family HMM PF01592; match to protein family HMM TIGR01999
YP_507441.1	identified by match to protein family HMM PF01521; match to protein family HMM TIGR00049
YP_507442.1	identified by similarity to SP:P36540; match to protein family HMM PF00226; match to protein family HMM PF07743
YP_507443.1	identified by similarity to SP:P36541; match to protein family HMM PF00012
YP_507444.1	identified by match to protein family HMM PF00111
YP_507446.1	identified by match to protein family HMM PF03918
YP_507447.1	Involved in ubiquinone biosynthesis
YP_507448.1	identified by match to protein family HMM PF02502; match to protein family HMM TIGR00689; match to protein family HMM TIGR01120
YP_507451.1	Catalyzes the reversible oxidation of malate to oxaloacetate
YP_507452.1	identified by match to protein family HMM PF02152; match to protein family HMM TIGR00526
YP_507453.1	identified by match to protein family HMM PF06271
YP_507454.1	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_507455.1	identified by similarity to SP:P12920; match to protein family HMM TIGR02122
YP_507456.1	Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate
YP_507457.1	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_507458.1	identified by match to protein family HMM PF00070; match to protein family HMM PF07992
YP_507459.1	identified by similarity to SP:P24231; match to protein family HMM PF01523
YP_507460.1	identified by similarity to SP:Q54769; match to protein family HMM PF01227
YP_507461.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit
YP_507462.1	identified by match to protein family HMM PF00023
YP_507463.1	identified by match to protein family HMM PF02482; match to protein family HMM TIGR00741
YP_507464.1	identified by similarity to SP:P48194; match to protein family HMM PF04542; match to protein family HMM PF04545
YP_507465.1	smallest protein in the large subunit; similar to what is found with protein L31 and L33 several bacterial genomes contain paralogs which may be regulated by zinc; the protein from Thermus thermophilus has a zinc-binding motif and contains a bound zinc ion; the proteins in this group do not have the motif
YP_507467.1	identified by similarity to GB:AAS13835.1
YP_507468.1	identified by similarity to GB:AAS13837.1; match to protein family HMM TIGR02215
YP_507469.1	identified by similarity to GB:AAS13838.1
YP_507470.1	identified by similarity to GB:AAS13839.1
YP_507471.1	identified by similarity to GB:AAS13840.1
YP_507473.1	identified by match to protein family HMM TIGR01630
YP_507474.1	identified by similarity to SP:P12995; match to protein family HMM PF00202; match to protein family HMM TIGR00508
YP_507475.1	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_507477.1	identified by similarity to SP:P25716; match to protein family HMM PF00106; match to protein family HMM PF01370
YP_507482.1	identified by match to protein family HMM PF03372; match to protein family HMM TIGR00195; match to protein family HMM TIGR00633
YP_507483.1	bifunctional arginine biosynthesis protein ArgJ; functions at the 1st and 5th steps in arginine biosynthesis; involved in synthesis of acetylglutamate from glutamate and acetyl-CoA and ornithine by transacetylation between acetylornithine and glutmate
YP_507487.1	catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming
YP_507490.1	identified by match to protein family HMM PF00023
YP_507493.1	identified by match to protein family HMM PF01966; match to protein family HMM TIGR01353
YP_507494.1	identified by match to protein family HMM PF01521; match to protein family HMM TIGR00049
YP_507495.1	identified by similarity to SP:P26844; match to protein family HMM PF00717; match to protein family HMM TIGR02227
YP_507496.1	Catalyzes the transfer of electrons from NADH to quinone
YP_507498.1	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_507506.1	transformation of porphobilinogen to hydroxymethylbilane in porphyrin biosynthesis
YP_507507.1	identified by similarity to SP:Q05865; match to protein family HMM TIGR01499
YP_507508.1	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_507509.1	identified by similarity to GB:AAS14201.1; match to protein family HMM PF01709; match to protein family HMM TIGR01033
YP_507510.1	identified by similarity to SP:P28353; match to protein family HMM PF00472; match to protein family HMM PF03462; match to protein family HMM TIGR00020
YP_507511.1	identified by similarity to GB:AAS14116.1
YP_507513.1	identified by similarity to GB:AAS14116.1
YP_507516.1	identified by similarity to GB:AAS14116.1
YP_507527.1	binds to the ribosome on the universally-conserved alpha-sarcin loop
YP_507528.1	identified by similarity to GB:AAK22816.1
YP_507529.1	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_507530.1	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_507531.1	identified by similarity to SP:P09171; match to protein family HMM PF01509; match to protein family HMM TIGR00431
YP_507532.1	identified by match to protein family HMM PF00814
YP_507533.1	identified by similarity to SP:P77241; match to protein family HMM PF00639
YP_507534.1	identified by similarity to SP:Q02635; match to protein family HMM PF00155
YP_507536.1	identified by match to protein family HMM PF00578
YP_507537.1	identified by match to protein family HMM PF00070; match to protein family HMM PF07992; match to protein family HMM TIGR01292
YP_507539.1	Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA
YP_507541.1	catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro)
YP_507542.1	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_507543.1	identified by similarity to PIR:F71632; match to protein family HMM PF07031
YP_507544.1	identified by similarity to GB:CAE27354.1
YP_507545.1	identified by similarity to SP:P73810; match to protein family HMM PF01396
YP_507548.1	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_507549.1	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_507551.1	identified by similarity to GB:AAS14713.1
YP_507552.1	identified by match to protein family HMM PF01596
YP_507553.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00512; match to protein family HMM PF02518
YP_507554.1	identified by match to protein family HMM PF03091
YP_507555.1	An essential enzyme in the nonmevalonate pathway of isopentenyl diphosphate and dimethylallyl diphosphate biosynthesis
YP_507556.1	identified by match to protein family HMM PF01207; match to protein family HMM TIGR00737
YP_507557.1	identified by similarity to GB:AAW70773.1
YP_507558.1	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 PF04546; match to protein family HMM TIGR02393
YP_507559.1	identified by similarity to SP:P02923; match to protein family HMM PF01751; match to protein family HMM PF01807; match to protein family HMM TIGR01391
YP_507560.1	identified by similarity to GB:AAS14410.1; match to protein family HMM PF02636
YP_507561.1	identified by similarity to GB:AAS14409.1
YP_507562.1	identified by similarity to GB:AAS14408.1
YP_507564.1	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_507565.1	identified by similarity to GB:AAL08817.1
YP_507566.1	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_507567.1	identified by match to protein family HMM PF06055
YP_507569.1	identified by match to protein family HMM PF05088
YP_507571.1	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_507572.1	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_507574.1	identified by similarity to SP:P22783
YP_507575.1	identified by match to protein family HMM PF01132; match to protein family HMM TIGR00038
YP_507576.1	identified by similarity to PIR:E97700; match to protein family HMM PF00175
YP_507577.1	catalyzes the decarboxylaton of phospatidyl-L-sering to phosphatidylethanolamine
YP_507578.1	identified by similarity to SP:Q48269; match to protein family HMM PF01066
YP_507579.1	identified by match to protein family HMM PF01235; match to protein family HMM TIGR00835
YP_507580.1	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_507581.1	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_507582.1	identified by similarity to GB:AAS13983.1
YP_507583.1	identified by match to protein family HMM PF00005; match to protein family HMM TIGR00630
YP_507584.1	identified by similarity to SP:O84969; match to protein family HMM PF00507
YP_507585.1	The point of entry for the majority of electrons that traverse the respiratory chain eventually resulting in the reduction of oxygen
YP_507586.1	identified by similarity to SP:O84971; match to protein family HMM PF00329; match to protein family HMM TIGR01961
YP_507587.1	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_507588.1	identified by similarity to GB:AAS14633.1
YP_507589.1	identified by similarity to SP:P36664; match to protein family HMM PF01975; match to protein family HMM TIGR00087
YP_507590.1	identified by similarity to SP:P08244; match to protein family HMM PF00215; match to protein family HMM TIGR01740
YP_507591.1	identified by match to protein family HMM PF01026; match to protein family HMM TIGR00010
YP_507592.1	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_507593.1	identified by similarity to GB:AAS14946.1
YP_507594.1	identified by similarity to SP:P08374; match to protein family HMM PF01192; match to protein family HMM TIGR00690
YP_507595.1	identified by match to protein family HMM PF01713
YP_507596.1	required for the synthesis of the hydromethylpyrimidine moiety of thiamine
YP_507599.1	identified by similarity to SP:P36679; match to protein family HMM PF01121; match to protein family HMM TIGR00152
YP_507600.1	identified by match to protein family HMM PF01300; match to protein family HMM TIGR00057
YP_507602.1	identified by match to protein family HMM PF00216
YP_507603.1	involved in the de novo synthesis of pyridoxine (Vitamin B6)
YP_507604.1	identified by similarity to SP:P54455; match to protein family HMM PF01467; match to protein family HMM TIGR00125
YP_507606.1	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_507608.1	identified by similarity to SP:Q05069
YP_507609.1	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_507610.1	identified by similarity to GB:AAD48994.1; match to protein family HMM PF05292
YP_507611.1	identified by similarity to SP:P02339; match to protein family HMM PF00436; match to protein family HMM TIGR00621
YP_507612.1	identified by match to protein family HMM PF00083; match to protein family HMM PF07690
YP_507614.1	identified by match to protein family HMM PF00083; match to protein family HMM PF07690
YP_507616.1	identified by similarity to GB:AAS14586.1
YP_507617.1	catalyzes the formation of porphobilinogen from 5-aminolevulinate
YP_507618.1	identified by similarity to SP:Q03638; match to protein family HMM PF02540; match to protein family HMM TIGR00552
YP_507620.1	This protein performs the mismatch recognition step during the DNA repair process
YP_507622.1	identified by match to protein family HMM PF01230
YP_507624.1	catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis
YP_507626.1	identified by similarity to SP:P49861; match to protein family HMM PF05065; match to protein family HMM TIGR01554
YP_507627.1	identified by similarity to PIR:D90427
YP_507628.1	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_507631.1	identified by similarity to GB:AAS14439.1; match to protein family HMM TIGR02218
YP_507632.1	identified by similarity to GB:AAS14108.1
YP_507633.1	catalyzes the formation of 2-methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine from N6-(dimethylallyl)adenosine (i(6)A)
YP_507634.1	identified by similarity to GB:AAS13819.1; match to protein family HMM PF07690
YP_507636.1	identified by similarity to SP:P27854; match to protein family HMM PF03109; match to protein family HMM TIGR01982
YP_507637.1	identified by similarity to SP:P52648; match to protein family HMM PF00005
YP_507638.1	identified by similarity to SP:P39172; match to protein family HMM PF01297
YP_507639.1	involved in a recombinational process of DNA repair, independent of the recBC complex
YP_507640.1	identified by match to protein family HMM PF02416; match to protein family HMM TIGR01411
YP_507641.1	identified by match to protein family HMM PF00005
YP_507642.1	identified by similarity to GB:BAA36355.1
YP_507643.1	identified by match to protein family HMM PF02798
YP_507644.1	identified by match to protein family HMM PF02237; match to protein family HMM PF03099; match to protein family HMM TIGR00121
YP_507647.1	Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide
YP_507648.1	molecular chaperone
YP_507649.1	identified by similarity to PIR:B95982
YP_507651.1	fragment; identified by similarity to SP:P20625
YP_507652.1	identified by similarity to SP:P20625; match to protein family HMM PF00730; match to protein family HMM TIGR01083
YP_507653.1	negatively supercoils closed circular double-stranded DNA
YP_507655.1	identified by match to protein family HMM PF00580
YP_507666.1	identified by similarity to SP:P24559
YP_507667.1	catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs
YP_507669.1	identified by match to protein family HMM PF02600
YP_507671.1	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_507672.1	identified by match to protein family HMM PF00023
YP_507676.1	identified by similarity to SP:P80643; match to protein family HMM PF00550
YP_507677.1	identified by similarity to SP:P39435; match to protein family HMM PF00109; match to protein family HMM PF02801
YP_507678.1	identified by similarity to SP:P43862; match to protein family HMM PF02481; match to protein family HMM TIGR00732
YP_507679.1	This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. Promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of a final effector complex
YP_507680.1	identified by match to protein family HMM PF00512; match to protein family HMM PF02518
YP_507681.1	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_507685.1	identified by similarity to SP:P46889; match to protein family HMM PF01580
YP_507687.1	identified by match to protein family HMM PF00571; match to protein family HMM PF01595; match to protein family HMM PF03471
YP_507688.1	identified by similarity to SP:P30137; match to protein family HMM PF02581; match to protein family HMM TIGR00693
YP_507689.1	identified by similarity to SP:Q92TF2
YP_507690.1	identified by similarity to GB:AAS14071.1; match to protein family HMM PF03618
YP_507691.1	identified by match to protein family HMM PF00581
YP_507692.1	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_507693.1	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_507694.1	binds and unfolds substrates as part of the ClpXP protease
YP_507695.1	hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates
YP_507696.1	identified by match to protein family HMM PF00254; match to protein family HMM PF05697; match to protein family HMM TIGR00115
YP_507697.1	identified by similarity to SP:P18200; match to protein family HMM PF04608
YP_507698.1	identified by match to protein family HMM PF00583
YP_507699.1	identified by similarity to GB:AAS14420.1
YP_507700.1	identified by similarity to GB:AAS14115.1
YP_507702.1	identified by similarity to GB:AAS14795.1; match to protein family HMM PF01594
YP_507703.1	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_507704.1	identified by similarity to PIR:F71668
YP_507705.1	identified by match to protein family HMM TIGR00097
YP_507708.1	identified by similarity to SP:P10445
YP_507709.1	identified by match to protein family HMM PF01127
YP_507710.1	identified by similarity to SP:Q9R4E4; match to protein family HMM PF00275
YP_507712.1	identified by match to protein family HMM PF02811; match to protein family HMM PF07733; match to protein family HMM TIGR00594
YP_507720.1	identified by similarity to SP:P15298
YP_507721.1	identified by match to protein family HMM PF01243; match to protein family HMM TIGR00558
YP_507724.1	identified by match to protein family HMM PF02230
YP_507726.1	catalyzes the formation of arginine from (N-L-arginino)succinate
YP_507728.1	identified by similarity to SP:P27251; match to protein family HMM PF01327
YP_507729.1	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_507730.1	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_507733.1	identified by match to protein family HMM PF01899
YP_507734.1	identified by similarity to GB:AAS09484.1
YP_507735.1	RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids
YP_507736.1	identified by similarity to GB:AAS13900.1
YP_507738.1	identified by similarity to SP:P53556; match to protein family HMM PF00155
YP_507739.1	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_507740.1	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_507741.1	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_507742.1	binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit
YP_507743.1	in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA
YP_507744.1	binds directly to 23S ribosomal RNA
YP_507745.1	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_507746.1	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_507747.1	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_507748.1	EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene
YP_507749.1	binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit
YP_507750.1	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_507751.1	identified by match to protein family HMM PF00149
YP_507753.1	identified by match to protein family HMM PF00753; match to protein family HMM PF07521
YP_507754.1	identified by similarity to GB:AAS14534.1; match to protein family HMM TIGR02396
YP_507757.1	identified by match to protein family HMM PF00529; match to protein family HMM TIGR01843
YP_507759.1	identified by match to protein family HMM PF00528
YP_507760.1	identified by match to protein family HMM PF01292
YP_507761.1	identified by similarity to GB:AAF98273.1; match to protein family HMM PF00478; match to protein family HMM PF03060
YP_507763.1	identified by similarity to GB:AAD40620.1; match to protein family HMM PF02630
YP_507764.1	identified by similarity to GB:BAB83861.1
YP_507765.1	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_507766.1	catalyzes the interconversion of succinyl-CoA and succinate
YP_507767.1	identified by similarity to SP:O08371; match to protein family HMM PF00549; match to protein family HMM PF02629; match to protein family HMM TIGR01019
YP_507768.1	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_507769.1	identified by match to protein family HMM PF00528; match to protein family HMM TIGR02138
YP_507770.1	identified by similarity to SP:P78061; match to protein family HMM PF00120
YP_507772.1	identified by match to protein family HMM PF00753
YP_507775.1	identified by similarity to GB:AAS14461.1
YP_507776.1	identified by similarity to GB:AAS14460.1
YP_507779.1	identified by similarity to GB:AAA21748.1; 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_507781.1	An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes
YP_507783.1	heat shock protein involved in degradation of misfolded proteins
YP_507784.1	heat shock protein involved in degradation of misfolded proteins
YP_507785.1	identified by similarity to SP:P27851; match to protein family HMM PF01209; match to protein family HMM TIGR01934
YP_507787.1	methionine--tRNA ligase; MetRS; adds methionine to tRNA(Met) with cleavage of ATP to AMP and diphosphate; some MetRS enzymes form dimers depending on a C-terminal domain that is also found in other proteins such as Trbp111 in Aquifex aeolicus and the cold-shock protein CsaA from Bacillus subtilis while others do not; four subfamilies exist based on sequence motifs and zinc content
YP_507788.1	catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP, in Bacillus, lysine sensitive; regulated by response to starvation.
YP_507789.1	identified by match to protein family HMM PF00116; match to protein family HMM PF02790
YP_507790.1	identified by similarity to SP:P31833; match to protein family HMM PF00115
YP_507791.1	converts protoheme IX and farnesyl diphosphate to heme O
YP_507792.1	identified by similarity to SP:Q50985
YP_507793.1	catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis
YP_507794.1	identified by match to protein family HMM PF02699; match to protein family HMM TIGR00739
YP_507795.1	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_507796.1	identified by similarity to SP:P00583; match to protein family HMM PF02767
YP_507797.1	identified by match to protein family HMM PF01612
YP_507798.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00486
YP_507799.1	identified by match to protein family HMM PF00717; match to protein family HMM PF01381
YP_507800.1	identified by similarity to SP:P17288; match to protein family HMM PF00719
YP_507803.1	catalyzes the reduction of N-acetyl-5-glutamyl phosphate to N-acetyl-L-glutamate 5-semialdehyde in arginine biosynthesis and the reduction of N-acetyl-gamma-aminoadipyl-phosphate to N-acetyl-L-aminoadipate-semialdehyde in lysine biosynthesis; involved in both the arginine and lysine biosynthetic pathways; lysine is produced via the AAA pathway, lysine from alpha-aminoadipate
YP_507804.1	forms a direct contact with the tRNA during translation
YP_507805.1	in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit
YP_507806.1	identified by similarity to SP:P02930; match to protein family HMM PF02321
YP_507809.1	identified by similarity to GB:AAS13928.1; match to protein family HMM PF01883
YP_507810.1	identified by similarity to SP:P08330; match to protein family HMM PF00156; match to protein family HMM TIGR01251
YP_507811.1	identified by match to protein family HMM PF02686; match to protein family HMM TIGR00135
YP_507817.1	Catalyzes the conversion of citrate to isocitrate
YP_507819.1	protein associated with Co2+ and Mg2+ efflux
YP_507820.1	identified by similarity to SP:P12045; match to protein family HMM PF02222; match to protein family HMM TIGR01161
YP_507821.1	identified by similarity to GB:AAK31315.1
YP_507826.1	identified by similarity to GB:AAM00400.1; match to protein family HMM PF03135
YP_507827.1	identified by similarity to GB:AAO41095.1
YP_507828.1	identified by similarity to GB:AAO41095.1
YP_507829.1	identified by similarity to GB:AAO41092.1
YP_507832.1	identified by similarity to GB:AAN05086.1
YP_507835.1	identified by similarity to SP:P25662; match to protein family HMM PF01145; match to protein family HMM TIGR01933
YP_507836.1	identified by similarity to SP:P25661; match to protein family HMM PF01145; match to protein family HMM TIGR01932
YP_507837.1	identified by match to protein family HMM PF00089; match to protein family HMM PF00595; match to protein family HMM TIGR02037
YP_507838.1	identified by similarity to PIR:G97866; match to protein family HMM PF03548
YP_507839.1	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_507840.1	involved in the insertion of copper into subunit I of cytochrome C oxidase
YP_507842.1	identified by match to protein family HMM PF00675; match to protein family HMM PF05193
YP_507843.1	identified by match to protein family HMM PF00675; match to protein family HMM PF05193
YP_507844.1	identified by similarity to GB:AAO15317.1
YP_507845.1	identified by match to protein family HMM PF01252; match to protein family HMM TIGR00077
YP_507846.1	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_507847.1	identified by similarity to SP:P37687; match to protein family HMM PF00462; match to protein family HMM TIGR02181
YP_507848.1	identified by match to protein family HMM TIGR00536
YP_507849.1	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_507850.1	identified by similarity to SP:P07016; match to protein family HMM PF00198; match to protein family HMM PF00364; match to protein family HMM PF02817; match to protein family HMM TIGR01347
YP_507852.1	identified by similarity to SP:P08506; match to protein family HMM PF00768; match to protein family HMM PF07943
YP_507853.1	identified by match to protein family HMM PF02683
YP_507854.1	identified by match to protein family HMM PF03937
YP_507855.1	identified by match to protein family HMM PF02163; match to protein family HMM TIGR00054
YP_507856.1	identified by match to protein family HMM PF01103; match to protein family HMM PF07244
YP_507857.1	identified by match to protein family HMM PF03938
YP_507858.1	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_507859.1	identified by match to protein family HMM PF01808; match to protein family HMM PF02142; match to protein family HMM TIGR00355
YP_507863.1	identified by similarity to SP:P06978; match to protein family HMM PF01066; match to protein family HMM TIGR00560
YP_507868.1	identified by match to protein family HMM PF00805
YP_507869.1	identified by similarity to GB:AAL08818.1
YP_507871.1	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_507872.1	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_507873.1	identified by similarity to SP:P15015; match to protein family HMM PF00430
YP_507874.1	identified by similarity to GB:CAA72984.1
YP_507875.1	identified by similarity to SP:P06137; match to protein family HMM PF02491; match to protein family HMM TIGR01174
YP_507878.1	identified by similarity to GB:BAA31229.1; match to protein family HMM PF02386
YP_507881.1	identified by match to protein family HMM PF01171; match to protein family HMM TIGR02432
YP_507882.1	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_507885.1	transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein
YP_507887.1	identified by similarity to GB:AAS14447.1
YP_507889.1	identified by similarity to GB:AAS14237.1
YP_507890.1	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_507891.1	identified by similarity to SP:P30138; match to protein family HMM PF00899; match to protein family HMM PF05237
YP_507892.1	involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate
YP_507893.1	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_507894.1	identified by similarity to SP:P53558; match to protein family HMM TIGR00347
YP_507895.1	identified by match to protein family HMM PF00448; match to protein family HMM PF02881; match to protein family HMM TIGR00064
YP_507898.1	catalyzes the formation of 2-oxoglutarate from isocitrate
YP_507899.1	identified by match to protein family HMM PF01368; match to protein family HMM PF02272; match to protein family HMM TIGR00644
YP_507900.1	identified by similarity to SP:P42977; match to protein family HMM PF01743
YP_507901.1	catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate
YP_507902.1	identified by similarity to GB:AAC02808.2; match to protein family HMM PF01381
YP_507903.1	identified by similarity to GB:AAK28658.1; match to protein family HMM PF01617
YP_507905.1	identified by similarity to GB:AAK28659.1; match to protein family HMM PF01617
YP_507906.1	identified by similarity to GB:AAK28660.1
YP_507907.1	identified by similarity to GB:AAK28661.1; match to protein family HMM PF01617
YP_507908.1	identified by similarity to GB:AAK28662.1; match to protein family HMM PF01617
YP_507909.1	identified by similarity to GB:AAK28663.1; match to protein family HMM PF01617
YP_507910.1	identified by similarity to GB:AAK28664.1; match to protein family HMM PF01617
YP_507911.1	identified by similarity to GB:AAK28665.1; match to protein family HMM PF01617
YP_507912.1	identified by similarity to GB:AAK28666.1
YP_507913.1	identified by similarity to GB:AAK28667.1; match to protein family HMM PF01617
YP_507914.1	identified by similarity to GB:AAK28668.1; match to protein family HMM PF01617
YP_507915.1	identified by similarity to GB:AAK28669.1; match to protein family HMM PF01617
YP_507916.1	identified by similarity to GB:AAK28670.1; match to protein family HMM PF01617
YP_507917.1	identified by similarity to GB:AAK28671.1; match to protein family HMM PF01617
YP_507918.1	identified by similarity to GB:AAK28672.1; match to protein family HMM PF01617
YP_507919.1	identified by similarity to GB:AAC02935.2; match to protein family HMM PF01617
YP_507920.1	identified by similarity to GB:AAC02936.1; match to protein family HMM PF01617
YP_507921.1	identified by similarity to GB:AAC02937.1; match to protein family HMM PF01617
YP_507923.1	identified by similarity to GB:AAC02938.1; match to protein family HMM PF01617
YP_507924.1	identified by similarity to GB:AAC02939.1; match to protein family HMM PF01617
YP_507926.1	identified by similarity to GB:AAC02940.1; match to protein family HMM PF01617
YP_507927.1	identified by similarity to GB:AAK28673.1; match to protein family HMM PF01617
YP_507928.1	identified by similarity to GB:AAK28674.1; match to protein family HMM PF01617
YP_507930.1	identified by similarity to GB:AAK28675.1; match to protein family HMM PF01617
YP_507931.1	identified by similarity to GB:AAK28676.1
YP_507932.1	identified by similarity to GB:AAK28677.1
YP_507933.1	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_507937.1	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_507938.1	identified by match to protein family HMM PF04543
YP_507939.1	identified by similarity to GB:AAS14418.1; match to protein family HMM PF02130; match to protein family HMM TIGR00043
YP_507940.1	identified by match to protein family HMM PF01656