-- dump date   	20140619_000849
-- class       	Genbank::CDS
-- table       	cds_note
-- id	note
YP_988340.1	identified by match to protein family HMM PF01027
YP_988341.1	identified by match to protein family HMM PF03372
YP_988342.1	has 3'-5' exonuclease, 5'-3' exonuclease and 5'-3'polymerase activities, primarily functions to fill gaps during DNA replication and repair
YP_988343.1	identified by match to protein family HMM PF00929; match to protein family HMM TIGR00573; match to protein family HMM TIGR01406
YP_988344.1	catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A; involved in coenzyme A biosynthesis
YP_988345.1	AroE; catalyzes the conversion of shikimate to 3-dehydroshikimate
YP_988346.1	identified by match to protein family HMM PF02545; match to protein family HMM TIGR00172
YP_988347.1	identified by similarity to SP:Q92TF2; match to protein family HMM PF03618
YP_988348.1	An RNA-DNA helicase that actively releases nascent mRNAs from paused transcription complexes
YP_988349.1	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_988350.1	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_988351.1	glucose-inhibited division protein B; SAM-dependent methyltransferase; methylates the N7 position of guanosine in position 527 of 16S rRNA
YP_988352.1	identified by similarity to SP:O05189; match to protein family HMM PF01656
YP_988353.1	identified by similarity to SP:O05190; match to protein family HMM PF02195; match to protein family HMM TIGR00180
YP_988355.1	Involved in cell division; probably involved in intracellular septation
YP_988356.1	identified by match to protein family HMM PF00448; match to protein family HMM PF02881; match to protein family HMM TIGR00064
YP_988357.1	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_988358.1	involved in lysine biosynthesis; DAP epimerase; produces DL-diaminopimelate from LL-diaminopimelate
YP_988360.1	identified by match to protein family HMM PF03969
YP_988361.1	Catalyzes the reversible oxidation of malate to oxaloacetate
YP_988362.1	catalyzes the interconversion of succinyl-CoA and succinate
YP_988363.1	Catalyzes the only substrate-level phosphorylation in the TCA cycle
YP_988364.1	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_988365.1	component of 2-oxoglutarate dehydrogenase complex; catalyzes the transfer of succinyl coenzyme A to form succinyl CoA as part of the conversion of 2-oxoglutarate to succinyl-CoA
YP_988366.1	Catalyzes the oxidation of dihydrolipoamide to lipoamide
YP_988367.1	identified by match to protein family HMM PF03435
YP_988368.1	identified by similarity to GB:BAA06561.1; match to protein family HMM PF00278
YP_988369.1	subunit A of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in S. meliloti it is known to be involved with K+
YP_988370.1	subunit C of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali
YP_988371.1	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_988372.1	subunit E of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in S. meliloti it is known to be involved specifically with K+ transport
YP_988373.1	subunit F of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali; in S. meliloti it is known to be involved specifically with K+ transport
YP_988374.1	subunit G of antiporter complex involved in resistance to high concentrations of Na+, K+, Li+ and/or alkali
YP_988375.1	identified by similarity to RF:YP_032843.1
YP_988376.1	catalyzes the formation of 3-dehydroquinate from 3-deoxy-arabino-heptulonate 7-phosphate; functions in aromatic amino acid biosynthesis
YP_988377.1	catalyzes the formation of shikimate 3-phosphate from shikimate in aromatic amino acid biosynthesis
YP_988378.1	identified by match to protein family HMM PF00589; match to protein family HMM PF02899
YP_988379.1	catalyzes the carboxylation of acetyl-CoA to malonyl-CoA; forms a tetramer composed of two alpha (AccA) and two beta (AccD) subunits; one of the two catalytic subunits that can form the acetyl CoA carboxylase enzyme together with a carrier protein
YP_988380.1	identified by match to protein family HMM PF06104
YP_988381.1	identified by match to protein family HMM PF00768
YP_988382.1	identified by match to protein family HMM PF01553
YP_988385.1	identified by match to protein family HMM PF04392
YP_988386.1	identified by match to protein family HMM PF02653
YP_988387.1	identified by match to protein family HMM PF00005
YP_988388.1	required for the assembly and function of the DNAX complex which are required for the assembly of the beta subunit onto primed DNA
YP_988389.1	identified by match to protein family HMM PF03631
YP_988390.1	identified by match to protein family HMM PF02639
YP_988391.1	identified by match to protein family HMM PF00085; match to protein family HMM PF00578; match to protein family HMM PF08534
YP_988392.1	catalyzes the formation of arginine from (N-L-arginino)succinate
YP_988393.1	identified by similarity to RF:NP_539003.1
YP_988394.1	identified by match to protein family HMM PF00278; match to protein family HMM PF02784; match to protein family HMM TIGR01048
YP_988395.1	identified by match to protein family HMM TIGR02302
YP_988396.1	identified by match to protein family HMM PF08241
YP_988397.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00486
YP_988399.1	identified by similarity to RF:YP_222541.1; match to protein family HMM PF01878
YP_988400.1	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_988402.1	identified by similarity to RF:YP_032822.1; match to protein family HMM PF07219
YP_988403.1	Catalyzes the transfer of the ammonia group from glutamine to a new carbon-nitrogen group
YP_988404.1	identified by match to protein family HMM PF05088
YP_988405.1	identified by similarity to SP:P42737; match to protein family HMM PF00484
YP_988406.1	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_988407.1	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_988408.1	identified by similarity to RF:YP_034294.1; match to protein family HMM PF07896
YP_988409.1	putative metalloprotease
YP_988410.1	identified by match to protein family HMM PF01029; match to protein family HMM PF01189
YP_988411.1	identified by match to protein family HMM PF07940
YP_988412.1	involved in de novo purine biosynthesis
YP_988413.1	identified by match to protein family HMM PF06568
YP_988414.1	identified by match to protein family HMM PF02104
YP_988415.1	required for 70S ribosome assembly
YP_988416.1	identified by match to protein family HMM PF02592; match to protein family HMM TIGR00697
YP_988417.1	identified by match to protein family HMM PF06213; match to protein family HMM TIGR01651
YP_988418.1	identified by match to protein family HMM PF07728; match to protein family HMM TIGR01650
YP_988419.1	identified by match to protein family HMM PF00226
YP_988420.1	identified by match to protein family HMM PF01722
YP_988421.1	site-specific tyrosine recombinase which cuts and rejoins DNA molecules; binds cooperatively to specific DNA consensus sites; forms a heterotetrameric complex with XerC; XerCD exhibit similar sequences; essential to convert chromosome dimers to monomers during cell division and functions during plasmid segregation; cell division protein FtsK may regulate the XerCD complex; enzyme from Streptococcus group has unusual active site motifs
YP_988422.1	identified by match to protein family HMM PF07277
YP_988423.1	Essential for efficient processing of 16S rRNA
YP_988424.1	methylates guanosine-37 in various tRNAs; uses S-adenosyl-L-methionine to transfer methyl group to tRNA
YP_988425.1	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_988426.1	identified by match to protein family HMM PF01127; match to protein family HMM TIGR02970
YP_988427.1	identified by similarity to GB:AAC17941.1; match to protein family HMM PF01127; match to protein family HMM TIGR02968
YP_988428.1	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_988429.1	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_988430.1	identified by match to protein family HMM PF01494; match to protein family HMM TIGR01984; match to protein family HMM TIGR01988
YP_988431.1	identified by match to protein family HMM PF01580
YP_988432.1	identified by match to protein family HMM PF03548
YP_988433.1	identified by match to protein family HMM PF03372; match to protein family HMM TIGR00633
YP_988434.1	identified by similarity to GB:AAV85981.1; match to protein family HMM PF00529; match to protein family HMM TIGR01730
YP_988435.1	identified by similarity to SP:P75831; match to protein family HMM PF00005; match to protein family HMM PF02687
YP_988436.1	identified by match to protein family HMM PF02698
YP_988437.1	identified by similarity to SP:P44872
YP_988438.1	identified by similarity to GB:AAK20881.1; match to protein family HMM PF00005; match to protein family HMM TIGR02673
YP_988439.1	Acs; catalyzes the conversion of acetate and CoA to acetyl-CoA
YP_988440.1	identified by match to protein family HMM PF01168; match to protein family HMM TIGR00044
YP_988442.1	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_988444.1	similar to novel fructose-6-phosphate aldolase from Escherichia coli; enzyme from Methanocaldococcus janaschii shows transaldolase activity
YP_988446.1	binding of PriA to forked DNA starts the assembly of the primosome, also possesses 3'-5' helicase activity
YP_988449.1	identified by match to protein family HMM PF00213; match to protein family HMM TIGR01145
YP_988450.1	produces ATP from ADP in the presence of a proton gradient across the membrane; the alpha chain is a catalytic subunit
YP_988451.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is a regulatory subunit
YP_988452.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. The beta chain is a regulatory subunit
YP_988453.1	identified by match to protein family HMM PF02823; match to protein family HMM TIGR01216
YP_988454.1	identified by match to protein family HMM PF07690
YP_988455.1	identified by match to protein family HMM PF00529
YP_988457.1	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_988458.1	identified by match to protein family HMM PF00348
YP_988459.1	identified by match to protein family HMM PF00912; match to protein family HMM TIGR02070
YP_988460.1	some L32 proteins have zinc finger motifs consisting of CXXC while others do not
YP_988461.1	identified by match to protein family HMM PF02559
YP_988462.1	identified by similarity to GB:AAA85787.1; match to protein family HMM PF00037
YP_988463.1	identified by similarity to GB:CAA90562.1
YP_988464.1	binds with the catalytic core of RNA polymerase to produce the holoenzyme; sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; sigma-32 is responsible for the expression of heat shock promoters; there are paralogs in Rhizobium and Sinorhizobium; the proteins in this cluster act as secondary heat shock sigma factors; the Rhizobium sigma-32 factor may also be involved in exopolysaccharide production
YP_988465.1	identified by match to protein family HMM PF01435
YP_988466.1	identified by match to protein family HMM PF04263; match to protein family HMM TIGR01378
YP_988468.1	identified by match to protein family HMM PF00005; match to protein family HMM PF02463
YP_988469.1	identified by similarity to SP:Q8YIZ8
YP_988472.1	identified by match to protein family HMM PF06282
YP_988473.1	identified by match to protein family HMM PF05164
YP_988475.1	catalyzes the formation of ribose 5-phosphate and xylulose 5-phosphate from sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate; can transfer ketol groups between several groups; in Escherichia coli there are two tkt genes, tktA expressed during exponential growth and the tktB during stationary phase
YP_988476.1	identified by similarity to SP:P51009; match to protein family HMM PF00044; match to protein family HMM PF02800; match to protein family HMM TIGR01534
YP_988478.1	Converts 3-phospho-D-glycerate to 3-phospho-D-glyceroyl phosphate during the glycolysis pathway
YP_988479.1	identified by match to protein family HMM PF00274
YP_988482.1	forms dimers; may be involved in cell envelope integrity; interacts with outer membrane proteins and with the C-terminal domain of inner membrane protein TolA
YP_988484.1	identified by match to protein family HMM PF02472
YP_988485.1	identified by match to protein family HMM PF01618; match to protein family HMM TIGR02796
YP_988486.1	identified by match to protein family HMM PF03061; match to protein family HMM TIGR00051
YP_988487.1	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_988488.1	plays an essential role in ATP-dependent branch migration of the Holliday junction
YP_988489.1	endonuclease; resolves Holliday structures; forms a complex of RuvABC; the junction binding protein RuvA forms a hexameric ring along with the RuvB helicase and catalyzes branch migration; RuvC then interacts with RuvAB to resolve the Holliday junction by nicking DNA strands of like polarity
YP_988493.1	catalyzes the formation of thiamine monophosphate from 2-methyl-4-amino-5-hydroxymethylpyrimidine diphosphate and 4-methyl-5-(2-phosphono-oxyethyl)-thiazole
YP_988494.1	identified by match to protein family HMM PF08238
YP_988496.1	Involved in peptide bond synthesis; alters the affinity of the ribosome for aminoacyl-tRNA
YP_988497.1	identified by match to protein family HMM PF00459
YP_988498.1	identified by match to protein family HMM PF00005; match to protein family HMM PF00664
YP_988499.1	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_988501.1	identified by match to protein family HMM PF01709; match to protein family HMM TIGR01033
YP_988502.1	identified by match to protein family HMM PF06242
YP_988503.1	identified by match to protein family HMM PF00691; match to protein family HMM TIGR02802
YP_988505.1	identified by match to protein family HMM PF01171; match to protein family HMM TIGR02432
YP_988506.1	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 PF07728; match to protein family HMM TIGR01241
YP_988509.1	catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate
YP_988511.1	identified by similarity to SP:P0ABU7; match to protein family HMM PF01618
YP_988512.1	identified by similarity to SP:P0ABV2; match to protein family HMM PF02472
YP_988516.1	catalyzes the formation of dUMP from dUTP
YP_988518.1	identified by match to protein family HMM PF01988
YP_988520.1	identified by similarity to SP:Q7MJN7
YP_988524.1	identified by match to protein family HMM PF01751
YP_988530.1	identified by similarity to RF:YP_032688.1
YP_988531.1	identified by similarity to RF:YP_032687.1
YP_988532.1	identified by similarity to RF:YP_032687.1
YP_988533.1	identified by similarity to SP:P03697
YP_988536.1	identified by similarity to RF:YP_032682.1
YP_988537.1	adds enolpyruvyl to UDP-N-acetylglucosamine as a component of cell wall formation; gram-positive bacteria have 2 copies of MurA which are active
YP_988538.1	identified by match to protein family HMM PF00149; match to protein family HMM TIGR00282
YP_988539.1	identified by match to protein family HMM PF01812; match to protein family HMM TIGR02727
YP_988540.1	identified by match to protein family HMM PF00515; match to protein family HMM PF07719
YP_988541.1	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_988544.1	With PurE catalyzes the conversion of aminoimidazole ribonucleotide to carboxyaminoimidazole ribonucleotide in the de novo purine nucleotide biosynthetic pathway
YP_988545.1	identified by match to protein family HMM PF00731; match to protein family HMM TIGR01162
YP_988547.1	stimulates the activities of the other two initiation factors, IF-2 and IF-3
YP_988548.1	identified by match to protein family HMM PF02545; match to protein family HMM TIGR00172
YP_988549.1	identified by similarity to SP:P67480
YP_988552.1	identified by similarity to SP:Q7CEG6; match to protein family HMM PF00004; match to protein family HMM PF02861; match to protein family HMM PF07724; match to protein family HMM PF07728
YP_988563.1	identified by similarity to RF:YP_032664.1
YP_988571.1	identified by match to protein family HMM PF07484
YP_988573.1	identified by match to protein family HMM PF00959
YP_988582.1	identified by match to protein family HMM PF07536
YP_988583.1	in Caulobacter crescentus, CC3477 is differentially expressed in minimal salts media with glucose as compared to complex media
YP_988587.1	identified by match to protein family HMM PF02518; match to protein family HMM PF07568
YP_988588.1	identified by match to protein family HMM PF01551
YP_988591.1	identified by similarity to SP:P67703
YP_988596.1	catalyzes the formation of 3-phosphonooxypyruvate and glutamate from O-phospho-L-serine and 2-oxoglutarate
YP_988597.1	identified by match to protein family HMM PF00239
YP_988598.1	identified by match to protein family HMM PF04014
YP_988601.1	identified by match to protein family HMM PF05973; match to protein family HMM TIGR02683
YP_988607.1	identified by similarity to SP:P07175
YP_988608.1	catalyzes the formation of N6-(1,2,-dicarboxyethyl)-AMP from L-aspartate, inosine monophosphate and GTP in AMP biosynthesis
YP_988609.1	identified by similarity to RF:YP_033221.1
YP_988610.1	binds with the catalytic core of RNA polymerase to produce the holoenzyme; this sigma factor is responsible for the expression of heat shock promoters
YP_988611.1	identified by match to protein family HMM PF00849; match to protein family HMM PF01479; match to protein family HMM TIGR00005
YP_988612.1	identified by match to protein family HMM PF00171
YP_988614.1	identified by match to protein family HMM PF01580
YP_988615.1	homopentamer; channel that opens in response to pressure or hypoosmotic shock
YP_988616.1	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_988617.1	identified by match to protein family HMM PF00120
YP_988618.1	identified by match to protein family HMM PF01266
YP_988619.1	catalyzes the formation of 5,10-methenyltetrahydrofolate from 5,10-methylenetetrahydrofolate and subsequent formation of 10-formyltetrahydrofolate from 5,10-methenyltetrahydrofolate
YP_988620.1	identified by match to protein family HMM PF05170
YP_988622.1	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_988623.1	identified by match to protein family HMM PF04107; match to protein family HMM TIGR01436
YP_988624.1	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_988626.1	identified by match to protein family HMM TIGR01730
YP_988627.1	identified by match to protein family HMM PF00873
YP_988628.1	functions in sugar metabolism in glycolysis and the Embden-Meyerhof pathways (EMP) and in gluconeogenesis; catalyzes reversible isomerization of glucose-6-phosphate to fructose-6-phosphate; member of PGI family
YP_988629.1	identified by match to protein family HMM PF00829; match to protein family HMM TIGR00061
YP_988630.1	involved in the peptidyltransferase reaction during translation
YP_988631.1	identified by similarity to GB:AAU44778.1; match to protein family HMM PF05658; match to protein family HMM PF05662
YP_988632.1	identified by match to protein family HMM PF06776
YP_988634.1	identified by similarity to GB:AAU44779.1; match to protein family HMM PF03895; match to protein family HMM PF05662
YP_988635.1	identified by match to protein family HMM PF06776
YP_988636.1	identified by match to protein family HMM PF01728
YP_988637.1	essential GTPase; exhibits high exchange rate for GTP/GDP; associates with 50S ribosomal subunit; involved in regulation of chromosomal replication
YP_988638.1	catalyzes the formation of glutamate 5-phosphate from glutamate in proline biosynthesis
YP_988639.1	Catalyzes the phosphorylation of L-glutamate during the proline biosynthesis pathway
YP_988640.1	transfers an adenyl group from ATP to NaMN to form nicotinic acid adenine dinucleotide (NaAD) which is then converted to the ubiquitous compound NAD by NAD synthetase; essential enzyme in bacteria
YP_988641.1	identified by match to protein family HMM PF02410; match to protein family HMM TIGR00090
YP_988642.1	SPOUT methyltransferase family protein; crystal structure shows homodimer; in Escherichia coli this protein methylates pseudouridine at position 1915 of the 23S ribosomal RNA
YP_988643.1	identified by match to protein family HMM PF01551
YP_988644.1	identified by similarity to SP:Q44879; match to protein family HMM PF00595; match to protein family HMM PF03572; match to protein family HMM TIGR00225
YP_988645.1	hydrolyzes diadenosine polyphosphate
YP_988646.1	identified by similarity to SP:P35641; match to protein family HMM PF06776
YP_988647.1	identified by match to protein family HMM PF02325
YP_988648.1	identified by match to protein family HMM PF02594
YP_988649.1	catalyzes the hydrolysis of pyrophosphate to phosphate
YP_988650.1	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_988651.1	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_988652.1	identified by match to protein family HMM PF01432
YP_988653.1	identified by match to protein family HMM PF01471; match to protein family HMM TIGR02283
YP_988654.1	identified by match to protein family HMM PF00483; match to protein family HMM TIGR01099
YP_988655.1	identified by match to protein family HMM PF00571; match to protein family HMM PF01380; match to protein family HMM TIGR00393
YP_988657.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00158; match to protein family HMM PF02954
YP_988660.1	catalyzes the synthesis of xanthosine monophosphate by the NAD+ dependent oxidation of inosine monophosphate
YP_988661.1	identified by match to protein family HMM PF00582
YP_988662.1	identified by match to protein family HMM PF01189
YP_988663.1	contains glutamine-hydrolyzing domain and glutamine amidotransferase; GMP-binding domain; functions to produce GMP from XMP in the IMP pathway
YP_988664.1	identified by match to protein family HMM PF03009
YP_988665.1	part of the UgpABCE glycerol-3-phosphate uptake system
YP_988666.1	identified by similarity to SP:P10906; match to protein family HMM PF00528
YP_988667.1	identified by match to protein family HMM PF00528
YP_988668.1	identified by similarity to SP:P0AG80; match to protein family HMM PF01547
YP_988669.1	identified by match to protein family HMM PF01297
YP_988670.1	identified by match to protein family HMM PF00950
YP_988671.1	identified by match to protein family HMM PF00005
YP_988673.1	identified by similarity to GB:CAA70763.1; match to protein family HMM PF00462; match to protein family HMM TIGR02194
YP_988674.1	in Salmonella NrdI has a stimulatory effect on the ribonucleotide reductase activity of NrdH with NrdEF
YP_988675.1	Catalyzes the rate-limiting step in dNTP synthesis
YP_988676.1	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_988677.1	identified by match to protein family HMM PF05175; match to protein family HMM TIGR00536
YP_988678.1	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_988679.1	identified by similarity to GB:AAL04499.1; match to protein family HMM PF01475
YP_988680.1	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_988681.1	identified by similarity to SP:Q46105; match to protein family HMM PF00639
YP_988682.1	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_988683.1	identified by match to protein family HMM PF00293; match to protein family HMM TIGR00586
YP_988684.1	identified by match to protein family HMM PF00375
YP_988685.1	identified by similarity to RF:NP_698859.1; match to protein family HMM PF08242; match to protein family HMM TIGR02072
YP_988687.1	identified by match to protein family HMM PF00462; match to protein family HMM TIGR02181
YP_988688.1	Involved in ubiquinone biosynthesis
YP_988689.1	catalyzes the formation of 4-phospho-L-aspartate from L-aspartate and ATP, in Bacillus, lysine sensitive; regulated by response to starvation.
YP_988690.1	identified by similarity to SP:P13738; match to protein family HMM PF06965; match to protein family HMM TIGR00773
YP_988693.1	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_988694.1	identified by similarity to RF:YP_033249.1
YP_988695.1	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_988696.1	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_988697.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B' is part of the membrane proton channel.
YP_988698.1	Produces ATP from ADP in the presence of a proton gradient across the membrane. Subunit B is part of the membrane proton channel.
YP_988699.1	glycine--tRNA ligase beta chain; glyS; class II aminoacyl tRNA synthetase; tetramer of alpha(2)beta(2); catalyzes a two-step reaction; first charging a glycine molecule by linking the carboxyl group to the alpha-phosphate of ATP; second by transfer of the aminoacyl-adenylate to its tRNA
YP_988700.1	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_988701.1	identified by match to protein family HMM PF00515; match to protein family HMM PF07719
YP_988702.1	identified by match to protein family HMM PF00348
YP_988703.1	identified by match to protein family HMM PF05175
YP_988704.1	identified by match to protein family HMM PF01343
YP_988706.1	An essential enzyme in the nonmevalonate pathway of isopentenyl diphosphate and dimethylallyl diphosphate biosynthesis
YP_988707.1	RNH2; RNase HII; binds manganese; endonuclease which specifically degrades the RNA of RNA-DNA hybrids
YP_988708.1	identified by match to protein family HMM PF01300; match to protein family HMM PF03481; match to protein family HMM TIGR00057
YP_988709.1	identified by match to protein family HMM PF01565; match to protein family HMM PF02913
YP_988711.1	catalyzes the formation of N(1)-(5-phospho-D-ribosyl)glycinamide from 5-phospho-D-ribosylamine and glycine in purine biosynthesis
YP_988712.1	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_988713.1	catalyzes the formation of pyridoxal 5'-phosphate from pyridoxamine 5'-phosphate
YP_988714.1	identified by match to protein family HMM PF00226; match to protein family HMM PF01556
YP_988715.1	Catalyzes a key regulatory step in fatty acid biosynthesis
YP_988716.1	catalyzes the formation of chorismate from 5-O-(1-carboxyvinyl)-3-phosphoshikimate in aromatic amino acid biosynthesis
YP_988717.1	identified by match to protein family HMM PF00926; match to protein family HMM TIGR00505; match to protein family HMM TIGR00506
YP_988718.1	catalyzes the bidirectional exonucleolytic cleavage of DNA
YP_988719.1	catalyzes the formation of 1-deoxy-D-xylulose 5-phosphate from pyruvate and D-glyceraldehyde 3-phosphate
YP_988720.1	identified by match to protein family HMM PF01479; match to protein family HMM PF01728; match to protein family HMM TIGR00478
YP_988721.1	identified by match to protein family HMM PF05958
YP_988722.1	identified by match to protein family HMM PF01523
YP_988723.1	identified by match to protein family HMM PF06776
YP_988724.1	converts protoheme IX and farnesyl diphosphate to heme O
YP_988725.1	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_988727.1	An endonuclease that specifically degrades the RNA strand of RNA-DNA hybrids
YP_988729.1	identified by match to protein family HMM PF00563; match to protein family HMM PF00990; match to protein family HMM PF07695; match to protein family HMM PF07696; match to protein family HMM PF08447; match to protein family HMM TIGR00229; match to protein family HMM TIGR00254
YP_988730.1	identified by match to protein family HMM PF00675; match to protein family HMM PF05193
YP_988731.1	identified by match to protein family HMM PF00702; match to protein family HMM TIGR01509
YP_988732.1	identified by similarity to SP:Q45971; match to protein family HMM PF01555
YP_988733.1	identified by match to protein family HMM PF00633; match to protein family HMM PF00730; match to protein family HMM TIGR01084
YP_988735.1	identified by match to protein family HMM PF06647
YP_988736.1	identified by match to protein family HMM PF01323
YP_988737.1	catalyzes the formation of phosphoenolpyruvate from pyruvate
YP_988738.1	identified by similarity to SP:P50061; match to protein family HMM PF00081; match to protein family HMM PF02777
YP_988739.1	identified by match to protein family HMM PF00326; match to protein family HMM PF02897
YP_988741.1	identified by similarity to SP:Q04152; match to protein family HMM PF05443
YP_988742.1	identified by match to protein family HMM PF02657
YP_988744.1	identified by match to protein family HMM PF01471
YP_988746.1	identified by similarity to GB:CAA73687.1; match to protein family HMM PF00072; match to protein family HMM PF00486
YP_988747.1	identified by similarity to GB:CAA62009.1; match to protein family HMM PF00512; match to protein family HMM PF02518
YP_988748.1	identified by similarity to SP:P45400
YP_988749.1	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_988750.1	identified by match to protein family HMM PF01578
YP_988751.1	identified by similarity to SP:P45406; match to protein family HMM PF03918
YP_988752.1	identified by match to protein family HMM PF00089; match to protein family HMM PF00595; match to protein family HMM TIGR02037
YP_988753.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00486
YP_988754.1	identified by match to protein family HMM PF00512; match to protein family HMM PF00672; match to protein family HMM PF02518
YP_988756.1	identified by similarity to SP:P37894; match to protein family HMM PF00512; match to protein family HMM PF02518; match to protein family HMM PF08447; match to protein family HMM TIGR00229
YP_988757.1	identified by similarity to SP:P37893; match to protein family HMM PF01433; match to protein family HMM TIGR02414
YP_988758.1	identified by match to protein family HMM PF03167; match to protein family HMM TIGR00758
YP_988759.1	identified by similarity to SP:P56904; match to protein family HMM PF01256; match to protein family HMM PF08543
YP_988760.1	Condenses 4-methyl-5-(beta-hydroxyethyl)-thiazole monophosphate and 4-amino-5-hydroxymethyl pyrimidine pyrophosphate to form thiamine monophosphate
YP_988761.1	functions in thiamine (vitamin B1) biosynthesis; in Bacillus subtilis this enzyme catalyzes the formation of thiazole from dehydroxyglycine and 1-deoxy-D-xylulose-5-phosphate and ThiS-thiocarboxylate
YP_988762.1	with ThiF, ThiG, and ThiO catalyzes the formation of the thiazole moiety of thiamine pyrophosphate
YP_988763.1	identified by match to protein family HMM PF01266; match to protein family HMM TIGR02352
YP_988764.1	required for the synthesis of the hydromethylpyrimidine moiety of thiamine
YP_988765.1	identified by match to protein family HMM PF02530
YP_988769.1	homology to a family of hypothetical proteins in Leptospira interrogans; identified by similarity to RF:NP_711581.1; match to protein family HMM PF07598
YP_988770.1	identified by match to protein family HMM PF01471; match to protein family HMM PF01510
YP_988772.1	with HmuTU is involved in the transport of hemin
YP_988773.1	identified by similarity to GB:CAC34394.1; match to protein family HMM PF01032
YP_988774.1	identified by similarity to GB:CAC34393.1; match to protein family HMM PF01497
YP_988775.1	identified by similarity to GB:CAC34392.1; match to protein family HMM PF05171
YP_988777.1	identified by match to protein family HMM PF00593; match to protein family HMM PF07715; match to protein family HMM TIGR01785; match to protein family HMM TIGR01786
YP_988778.1	identified by match to protein family HMM PF01464
YP_988780.1	catalyzes the formation of dihydrodipicolinate from L-aspartate 4-semialdehyde and pyruvate in lysine and diaminopimelate biosynthesis
YP_988781.1	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_988782.1	identified by match to protein family HMM PF03167
YP_988783.1	Promotes RNA polymerase assembly. Latches the N- and C-terminal regions of the beta' subunit thereby facilitating its interaction with the beta and alpha subunits
YP_988784.1	identified by similarity to SP:O52177; match to protein family HMM PF01842; match to protein family HMM PF01966; match to protein family HMM PF02824; match to protein family HMM PF04607; match to protein family HMM TIGR00691
YP_988785.1	involved in fifth step of pyrimidine biosynthesis; converts orotidine 5'-phosphate and diphosphate to orotate and 5-phospho-alpha-D-ribose 1-diphosphate
YP_988787.1	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_988788.1	identified by match to protein family HMM PF00717; match to protein family HMM TIGR02227
YP_988789.1	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_988790.1	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_988791.1	involved in DNA repair and RecFOR pathway recombination; RecFOR proteins displace ssDNA-binding protein and facilitate the production of RecA-coated ssDNA
YP_988792.1	catalyzes the formation of (R)-pantothenate from pantoate and beta-alanine
YP_988793.1	catalyzes the formation of tetrahydrofolate and 2-dehydropantoate from 5,10-methylenetetrahydrofolate and 3-methyl-2-oxobutanoate
YP_988794.1	identified by match to protein family HMM PF01571; match to protein family HMM PF08669
YP_988795.1	Catalyzes the reversible hydrolysis of the amide bond within dihydroorotate. This metabolic intermediate is required for the biosynthesis of pyrimidine nucleotides
YP_988796.1	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_988797.1	identified by match to protein family HMM PF00005; match to protein family HMM PF00664
YP_988798.1	catalyzes the decarboxylaton of phospatidyl-L-sering to phosphatidylethanolamine
YP_988799.1	identified by match to protein family HMM PF01066
YP_988800.1	identified by match to protein family HMM PF00106; match to protein family HMM PF08659
YP_988801.1	Catalyzes first step of the de novo purine nucleotide biosynthetic pathway
YP_988802.1	identified by match to protein family HMM PF02674
YP_988803.1	identified by match to protein family HMM PF02674
YP_988804.1	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_988805.1	unwinds double stranded DNA
YP_988806.1	identified by match to protein family HMM PF01281; match to protein family HMM PF03948; match to protein family HMM TIGR00158
YP_988808.1	binds as a heterodimer with protein S6 to the central domain of the 16S rRNA; helps stabilize the platform of the 30S subunit
YP_988809.1	binds cooperatively with S18 to the S15-16S complex, allowing platform assembly to continue with S11 and S21
YP_988810.1	identified by match to protein family HMM PF01569
YP_988811.1	identified by match to protein family HMM PF00698; match to protein family HMM TIGR00128
YP_988812.1	catalyzes the first of the two reduction steps in the elongation cycle of fatty acid synthesis
YP_988813.1	identified by match to protein family HMM PF00550; match to protein family HMM TIGR00517
YP_988814.1	FabF; beta-ketoacyl-ACP synthase II, KASII; catalyzes a condensation reaction in fatty acid biosynthesis: addition of an acyl acceptor of two carbons from malonyl-ACP; required for the elongation of short-chain unsaturated acyl-ACP
YP_988816.1	identified by match to protein family HMM PF02618; match to protein family HMM TIGR00247
YP_988817.1	Essential for recycling GMP and indirectly, cGMP
YP_988818.1	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_988819.1	catalyzes oxidation of 4-(phosphohydroxy)-L-threonine into 2-amino-3-oxo-4-(phosphohydroxy)butyric acid which decarboxylates to form 1-amino-3-(phosphohydroxy)propan-2-one (3-amino-2-oxopropyl phosphate)
YP_988820.1	identified by match to protein family HMM PF09312
YP_988821.1	identified by match to protein family HMM PF03968; match to protein family HMM PF04453
YP_988822.1	identified by match to protein family HMM PF03739
YP_988823.1	identified by match to protein family HMM PF03739
YP_988824.1	binds to single-strand binding (SSB) protein and acts as a bridge between the DnaX clamp loader complex and the SSB
YP_988827.1	identified by similarity to GB:AAD41751.1; match to protein family HMM PF03212; match to protein family HMM PF03797; match to protein family HMM TIGR01414
YP_988828.1	identified by similarity to GB:AAD41751.1; match to protein family HMM PF03212; match to protein family HMM PF03797; match to protein family HMM TIGR01414
YP_988829.1	catalyzes the formation of nucleoside triphosphate from ATP and nucleoside diphosphate
YP_988830.1	identified by match to protein family HMM PF01066; match to protein family HMM TIGR00560
YP_988831.1	The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrC both incises the 5' and 3' sides of the lesion. The N-terminal half is responsible for the 3' incision and the C-terminal half is responsible for the 5' incision
YP_988832.1	identified by similarity to SP:P37634; match to protein family HMM PF04378
YP_988834.1	catalyzes a two-step reaction, first charging a serine molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA
YP_988835.1	catalyzes the methyl esterification of L-isoaspartyl residues that are formed in damaged proteins
YP_988836.1	identified by match to protein family HMM PF01476; match to protein family HMM PF01551
YP_988838.1	identified by match to protein family HMM PF02699; match to protein family HMM TIGR00739
YP_988840.1	identified by similarity to PDB:2FVT_A; match to protein family HMM PF04430
YP_988842.1	identified by similarity to RF:YP_033401.1
YP_988843.1	Reversibly isomerizes the ketone sugar dihydroxyacetone phosphate to the aldehyde sugar glyceraldehyde-3-phosphate
YP_988844.1	identified by match to protein family HMM PF03840; match to protein family HMM TIGR00810
YP_988845.1	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_988846.1	catalyzes the formation of 2-dehydro-3-deoxy-D-octonate 8-phosphate from phosphoenolpyruvate and D-arabinose 5-phosphate in LPS biosynthesis
YP_988847.1	enolase; catalyzes the formation of phosphoenolpyruvate from 2-phospho-D-glycerate in glycolysis
YP_988848.1	identified by match to protein family HMM PF04977
YP_988849.1	identified by match to protein family HMM PF00676; match to protein family HMM TIGR03182
YP_988850.1	catalyzes the oxidative decarboxylation of pyruvate with concomitant acetylation of a lipoic acid-containing dihydrolipoamide acetyltransferase within the complex. The E1 component of 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_988851.1	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_988852.1	E3 component of pyruvate complex; catalyzes the oxidation of dihydrolipoamide to lipoamide
YP_988853.1	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_988854.1	identified by match to protein family HMM PF03364
YP_988855.1	identified by match to protein family HMM PF01128; match to protein family HMM PF02542; match to protein family HMM TIGR00151; match to protein family HMM TIGR00453
YP_988857.1	identified by similarity to SP:Q04850; match to protein family HMM PF00512; match to protein family HMM PF00672; match to protein family HMM PF00989; match to protein family HMM PF02518; match to protein family HMM TIGR00229
YP_988858.1	identified by similarity to SP:Q04849; match to protein family HMM PF00072; match to protein family HMM PF00158; match to protein family HMM PF02954
YP_988859.1	involved in potassium uptake; found to be peripherally associated with the inner membrane in Escherichia coli; contains an NAD-binding domain
YP_988860.1	hydrolyzes proteins to small peptides; with the ATPase subunits ClpA or ClpX, ClpP degrades specific substrates
YP_988861.1	binds and unfolds substrates as part of the ClpXP protease
YP_988862.1	identified by match to protein family HMM PF00004; match to protein family HMM PF02190; match to protein family HMM PF05362; match to protein family HMM PF07728; match to protein family HMM TIGR00763
YP_988864.1	identified by similarity to SP:P0ACF4; match to protein family HMM PF00216
YP_988865.1	TrmFO; Gid; glucose-inhibited division protein; similar to GidA; the gene from Bacillus subtilis encodes a tRNA-methyltransferase that utilizes folate as the carbon donor and bound flavin as reductant; modifies tRNA at position 54 (uridine) of the T-psi loop to form a C5-methyluridine
YP_988866.1	Tig; RopA; peptidyl-prolyl cis/trans isomerase; promotes folding of newly synthesized proteins; binds ribosomal 50S subunit; forms a homodimer
YP_988867.1	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_988868.1	Provides the input to the respiratory chain from the NAD-linked dehydrogenases of the citric acid cycle. The complex couples the oxidation of NADH and the reduction of ubiquinone, to the generation of a proton gradient which is then used for ATP synthesis
YP_988871.1	identified by match to protein family HMM PF01694
YP_988872.1	identified by match to protein family HMM PF00588; match to protein family HMM PF08032
YP_988874.1	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_988875.1	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_988876.1	Modulates Rho-dependent transcription termination
YP_988877.1	binds directly to 23S ribosomal RNA
YP_988878.1	in Escherichia coli and Methanococcus, this protein autoregulates expression; the binding site in the mRNA mimics the binding site in the 23S rRNA
YP_988879.1	binds the two ribosomal protein L7/L12 dimers and anchors them to the large ribosomal subunit
YP_988880.1	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_988881.1	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_988882.1	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Subunit beta' binds to sigma factor allowing it to bind to the -10 region of the promoter
YP_988883.1	identified by match to protein family HMM PF00881
YP_988886.1	identified by match to protein family HMM PF00768; match to protein family HMM PF05036
YP_988887.1	involved in the modulation of the specificity of the ClpAP-mediated ATP-dependent protein degradation; binds to the N-terminal domain of the chaperone ClpA
YP_988888.1	identified by match to protein family HMM PF00004; match to protein family HMM PF02861; match to protein family HMM PF07724; match to protein family HMM PF07728; match to protein family HMM TIGR02639
YP_988889.1	identified by match to protein family HMM PF01230
YP_988890.1	identified by match to protein family HMM PF01042
YP_988891.1	identified by similarity to RF:YP_221870.1; match to protein family HMM PF08904
YP_988892.1	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_988893.1	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_988894.1	Catalyzes the phosphorylation of UMP to UDP
YP_988895.1	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_988896.1	identified by match to protein family HMM PF01148
YP_988897.1	identified by match to protein family HMM PF01103; match to protein family HMM PF07244; match to protein family HMM PF08478
YP_988898.1	adds the O-linked and N-linked 3(R)-hydroxy fatty acids to the glucosamine disaccharide during lipid A biosynthesis
YP_988899.1	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_988900.1	catalyzes the addition of (R)-3-hydroxytetradecanoyl to the glucosamine disaccharide in lipid A biosynthesis
YP_988901.1	identified by similarity to RF:YP_221856.1; match to protein family HMM PF06230
YP_988902.1	catalyzes the formation of lipid A disaccharide from UDP-2,3-diacylglucosamine and 2,3-diacylglucosamine-1-phosphate, lipid A disaccharide is a precursor of lipid A that anchors LPS to the OM
YP_988903.1	identified by match to protein family HMM PF00005
YP_988904.1	identified by match to protein family HMM PF00528; match to protein family HMM TIGR01726
YP_988905.1	identified by match to protein family HMM PF00528; match to protein family HMM TIGR01726
YP_988906.1	identified by match to protein family HMM PF00497
YP_988907.1	type II enzyme; in Escherichia coli this enzyme forms a trimer of dimers which is allosterically inhibited by NADH and competitively inhibited by alpha-ketoglutarate; allosteric inhibition is lost when Cys206 is chemically modified which also affects hexamer formation; forms oxaloacetate and acetyl-CoA and water from citrate and coenzyme A; functions in TCA cycle, glyoxylate cycle and respiration; enzyme from Helicobacter pylori is not inhibited by NADH
YP_988908.1	Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation
YP_988909.1	identified by match to protein family HMM PF03772; match to protein family HMM TIGR00360
YP_988910.1	Catalyzes D-ribose 5-phosphate --> D-ribulose 5-phosphate in the nonoxidative branch of the pentose phosphate pathway
YP_988912.1	catalyzes the reduction of 2 glutathione to glutathione disulfide; maintains high levels of reduced glutathione in the cytosol; involved in redox regulation and oxidative defense
YP_988913.1	identified by match to protein family HMM PF01474; match to protein family HMM TIGR01358
YP_988914.1	NH(3)-dependent; catalyzes the formation of nicotinamide adenine dinucleotide (NAD) from nicotinic acid adenine dinucleotide (NAAD) using either ammonia or glutamine as the amide donor and ATP; ammonia-utilizing enzymes include the ones from Bacillus and Escherichia coli while glutamine-utilizing enzymes include the Mycobacterial one; forms homodimers
YP_988915.1	Charges one glutamine molecule and pairs it to its corresponding RNA trinucleotide during protein translation
YP_988916.1	identified by match to protein family HMM PF00270; match to protein family HMM PF00271
YP_988917.1	catalyzes the phosphorylation of NAD to NADP
YP_988918.1	identified by match to protein family HMM PF00072
YP_988920.1	identified by match to protein family HMM PF00011
YP_988921.1	identified by match to protein family HMM PF01521; match to protein family HMM TIGR00049; match to protein family HMM TIGR01997
YP_988922.1	Acylates the intermediate (KDO)2-lipid IVA to form (KDO)2-(lauroyl)-lipid IVA
YP_988923.1	identified by match to protein family HMM PF00107; match to protein family HMM PF08240
YP_988924.1	FabF, beta-Ketoacyl-ACP synthase II, KASII; catalyzes a condensation reaction in fatty acid biosynthesis: addition of an acyl acceptor of two carbons from malonyl-ACP; required for the elongation of short-chain unsaturated acyl-ACP.
YP_988925.1	identified by similarity to RF:NP_770449.1
YP_988926.1	Involved in the biosynthetic pathways of fatty acids, phospholipids, lipopolysaccharides, and oligosaccharides
YP_988927.1	NAD-dependent; catalyzes the oxidative decarboxylation of malate to form pyruvate; does not decarboxylate oxaloacetate
YP_988928.1	identified by similarity to RF:YP_032195.1
YP_988929.1	Stimulates the elongation of poly(A) tails
YP_988930.1	identified by match to protein family HMM PF01926; match to protein family HMM TIGR03156
YP_988931.1	identified by match to protein family HMM PF02628
YP_988932.1	catalyzes the reduction of N-acetyl-5-glutamyl phosphate to N-acetyl-L-glutamate 5-semialdehyde in arginine biosynthesis
YP_988933.1	catalyzes the reaction of glycine with 5,10-methylenetetrahydrofolate to form L-serine and tetrahydrofolate
YP_988934.1	identified by match to protein family HMM PF03477; match to protein family HMM TIGR00244
YP_988935.1	identified by match to protein family HMM PF00383; match to protein family HMM PF01872; match to protein family HMM TIGR00326
YP_988936.1	catalyzes the formation of riboflavin from 6,7-dimethyl-8-(1-D-ribityl)lumazine
YP_988937.1	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_988938.1	Regulates rRNA biosynthesis by transcriptional antitermination
YP_988939.1	identified by match to protein family HMM PF04355
YP_988941.1	involved in acylation of glycerol-3-phosphate to form 1-acyl-glycerol-3 phosphate for use in phospholipid biosynthesis; functions with PlsY
YP_988942.1	FabH; beta-ketoacyl-acyl carrier protein synthase III; catalyzes the condensation of acetyl-CoA with malonyl-ACP to initiate cycles of fatty acid elongation; differs from 3-oxoacyl-(acyl carrier protein) synthase I and II in that it utilizes CoA thioesters as primers rather than acyl-ACPs
YP_988943.1	This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control
YP_988944.1	identified by match to protein family HMM PF00376
YP_988945.1	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_988946.1	identified by similarity to SP:Q8YH92; match to protein family HMM PF01809; match to protein family HMM TIGR00278
YP_988947.1	identified by similarity to RF:YP_570374.1
YP_988948.1	involved in the first step of tetrahydrofolate biosynthesis; catalyzes the formation of formate and 2-amino-4-hydroxy-6-(erythro-1,2, 3-trihydroxypropyl)dihydropteridine triphosphate from GTP and water; forms a homopolymer
YP_988949.1	identified by similarity to RF:YP_033582.1; match to protein family HMM PF05990
YP_988951.1	homology to a family of hypothetical proteins in Leptospira interrogans; identified by similarity to RF:NP_711581.1; match to protein family HMM PF07598
YP_988952.1	identified by match to protein family HMM PF01135
YP_988953.1	identified by match to protein family HMM PF02321; match to protein family HMM TIGR01844
YP_988954.1	identified by similarity to GB:CAC46094.1
YP_988955.1	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_988956.1	identified by similarity to SP:P0AAG3; match to protein family HMM PF00005
YP_988957.1	identified by match to protein family HMM PF00528; match to protein family HMM TIGR01726
YP_988958.1	identified by match to protein family HMM PF00528; match to protein family HMM TIGR01726
YP_988959.1	identified by similarity to SP:P37902; match to protein family HMM TIGR01726
YP_988960.1	identified by similarity to SP:P37902; match to protein family HMM PF00497
YP_988961.1	identified by match to protein family HMM PF03372; match to protein family HMM TIGR00195; match to protein family HMM TIGR00633
YP_988962.1	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_988963.1	binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit
YP_988964.1	EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene
YP_988965.1	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_988966.1	identified by match to protein family HMM PF00338; match to protein family HMM TIGR01049
YP_988967.1	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_988968.1	L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA
YP_988969.1	binds third domain of 23S rRNA and protein L29; part of exit tunnel
YP_988970.1	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_988971.1	protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA
YP_988972.1	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_988973.1	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_988974.1	located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e
YP_988975.1	one of the stabilizing components for the large ribosomal subunit
YP_988976.1	primary binding protein; helps mediate assembly; involved in translation fidelity
YP_988977.1	binds to the 23S rRNA between the centers for peptidyl transferase and GTPase
YP_988978.1	assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel
YP_988979.1	identified by match to protein family HMM PF00281
YP_988982.1	homology to a family of hypothetical proteins in Leptospira interrogans; identified by similarity to RF:NP_711581.1; match to protein family HMM PF07598
YP_988983.1	identified by match to protein family HMM PF01135
YP_988984.1	identified by similarity to GB:CAD13188.1; match to protein family HMM PF02321; match to protein family HMM TIGR01844
YP_988986.1	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_988987.1	identified by similarity to SP:P0AAG3; match to protein family HMM PF00005
YP_988988.1	identified by match to protein family HMM PF00528; match to protein family HMM TIGR01726
YP_988989.1	identified by match to protein family HMM PF00528; match to protein family HMM TIGR01726
YP_988990.1	identified by similarity to SP:P37902; match to protein family HMM PF00497
YP_988991.1	identified by match to protein family HMM PF03372; match to protein family HMM TIGR00195; match to protein family HMM TIGR00633
YP_988992.1	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_988993.1	binds directly to 16S rRNA where it nucleates assembly of the head domain of the 30S subunit
YP_988994.1	EF-G; promotes GTP-dependent translocation of the ribosome during translation; many organisms have multiple copies of this gene
YP_988995.1	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_988996.1	identified by match to protein family HMM PF00338; match to protein family HMM TIGR01049
YP_988997.1	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_988998.1	L4 is important during the early stages of 50S assembly; it initially binds near the 5' end of the 23S rRNA
YP_988999.1	binds third domain of 23S rRNA and protein L29; part of exit tunnel
YP_989000.1	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_989001.1	protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA
YP_989002.1	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_989003.1	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_989004.1	located in the peptidyl transferase center and may be involved in peptidyl transferase activity; similar to archaeal L10e
YP_989005.1	one of the stabilizing components for the large ribosomal subunit
YP_989006.1	primary binding protein; helps mediate assembly; involved in translation fidelity
YP_989007.1	binds to the 23S rRNA between the centers for peptidyl transferase and GTPase
YP_989008.1	assembly initiator protein; binds to 5' end of 23S rRNA and nucleates assembly of the 50S; surrounds polypeptide exit tunnel
YP_989009.1	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_989010.1	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_989011.1	binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit
YP_989012.1	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_989013.1	binds 5S rRNA along with protein L5 and L25
YP_989014.1	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_989015.1	L30 binds domain II of the 23S rRNA and the 5S rRNA; similar to eukaryotic protein L7
YP_989016.1	late assembly protein
YP_989017.1	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_989018.1	essential enzyme that recycles AMP in active cells; converts ATP and AMP to two molecules of ADP
YP_989019.1	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_989020.1	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_989021.1	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_989022.1	is a component of the macrolide binding site in the peptidyl transferase center
YP_989023.1	identified by similarity to SP:P26982; match to protein family HMM PF00089; match to protein family HMM TIGR02037
YP_989024.1	identified by match to protein family HMM PF00004
YP_989026.1	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_989027.1	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_989028.1	responsible for transport of beta-1,2-glucans from the cytoplasm to periplasm; inner membrane ABC transporter permease component; Cgt; ChvA; NdvA
YP_989029.1	identified by match to protein family HMM PF00849; match to protein family HMM TIGR00005
YP_989030.1	identified by match to protein family HMM PF07542
YP_989031.1	identified by similarity to RF:YP_033802.1
YP_989032.1	identified by similarity to SP:Q59747; match to protein family HMM PF00120; match to protein family HMM PF03951; match to protein family HMM TIGR00653
YP_989033.1	The UvrABC repair system catalyzes the recognition and processing of DNA lesions. UvrA is an ATPase and a DNA-binding protein. A damage recognition complex composed of 2 uvrA and 2 uvrB subunits scans DNA for abnormalities. When the presence of a lesion has been verified by uvrB, the uvrA molecules dissociate
YP_989034.1	identified by match to protein family HMM PF00436; match to protein family HMM TIGR00621
YP_989035.1	negatively supercoils closed circular double-stranded DNA
YP_989036.1	Catalyzes the conversion of ATP and pantetheine 4'-phosphate to diphosphate and 3'-dephospho-coA
YP_989037.1	identified by match to protein family HMM PF00160
YP_989038.1	identified by match to protein family HMM PF00160
YP_989039.1	Exchanges the guanine residue with 7-aminomethyl-7-deazaguanine in tRNAs with GU(N) anticodons (tRNA-Asp, -Asn, -His and -Tyr)
YP_989040.1	identified by match to protein family HMM PF07690
YP_989041.1	Converts isocitrate to alpha ketoglutarate
YP_989043.1	type II fructose 1,6-bisphosphatae; in Escherichia coli this protein forms a dimer and binds manganese
YP_989044.1	catalyzes the transamination of the branched-chain amino acids to their respective alpha-keto acids
YP_989045.1	identified by match to protein family HMM PF05036
YP_989046.1	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_989047.1	dGTPase family type 2 subfamily; presumably hydrolyzes dGTP to deoxyguanosine and triphosphate
YP_989048.1	identified by match to protein family HMM PF01521; match to protein family HMM TIGR00049
YP_989049.1	identified by similarity to RF:NP_102613.1
YP_989050.1	identified by similarity to SP:P45706; match to protein family HMM PF02683
YP_989051.1	forms a homotrimer; catalyzes the acetylation of glucosamine-1-phosphate and uridylation of N-acetylglucosamine-1-phosphate to produce UDP-GlcNAc; function in cell wall synthesis
YP_989052.1	Catalyzes the first step in hexosamine metabolism, converting fructose-6P into glucosamine-6P using glutamine as a nitrogen source
YP_989053.1	catalyzes branch migration in Holliday junction intermediates
YP_989054.1	identified by similarity to GB:CAA40813.1; match to protein family HMM PF00583; match to protein family HMM PF02784
YP_989055.1	homology to a family of hypothetical proteins in Leptospira interrogans; identified by similarity to RF:YP_000623.1; match to protein family HMM PF07598
YP_989057.1	an AccC homodimer forms the biotin carboxylase subunit of the acetyl CoA carboxylase, an enzyme that catalyzes the formation of malonyl-CoA, which in turn controls the rate of fatty acid metabolism
YP_989058.1	composes the biotin carboxyl carrier protein subunit of the acetyl-CoA carboxylase complex, the enzyme that catalyzes the carboxylation of acetyl-CoA to malonyl-CoA, which in turn controls the rate of fatty acid metabolism
YP_989059.1	identified by match to protein family HMM PF01323
YP_989060.1	identified by match to protein family HMM PF00551; match to protein family HMM TIGR00639
YP_989061.1	catalyzes the formation of 1-(5-phosphoribosyl)-5-aminoimidazole from 2-(formamido)-N1-(5-phosphoribosyl)acetamidine and ATP in purine biosynthesis
YP_989062.1	identified by match to protein family HMM PF01594
YP_989063.1	identified by similarity to RF:YP_032365.1
YP_989064.1	identified by similarity to SP:Q02375; match to protein family HMM PF04800
YP_989068.1	homology to a family of hypothetical proteins in Leptospira interrogans; identified by similarity to RF:YP_002272.1; match to protein family HMM PF07598
YP_989070.1	Catalyzes the transfer of electrons from NADH to quinone
YP_989071.1	The point of entry for the majority of electrons that traverse the respiratory chain eventually resulting in the reduction of oxygen
YP_989072.1	Catalyzes the transfer of electrons from NADH to quinone
YP_989073.1	Catalyzes the transfer of electrons from NADH to quinone
YP_989074.1	Catalyzes the transfer of electrons from NADH to quinone
YP_989075.1	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_989076.1	Catalyzes the transfer of electrons from NADH to quinone
YP_989077.1	Catalyzes the transfer of electrons from NADH to quinone
YP_989078.1	Catalyzes the transfer of electrons from NADH to quinone
YP_989079.1	Catalyzes the transfer of electrons from NADH to quinone
YP_989080.1	identified by similarity to SP:P50940; match to protein family HMM PF00420
YP_989081.1	Catalyzes the transfer of electrons from NADH to ubiquinone
YP_989082.1	Catalyzes the transfer of electrons from NADH to quinone
YP_989083.1	Catalyzes the transfer of electrons from NADH to quinone
YP_989084.1	identified by match to protein family HMM PF02237; match to protein family HMM PF03099; match to protein family HMM TIGR00121
YP_989085.1	identified by match to protein family HMM PF00753; match to protein family HMM PF07521
YP_989086.1	catalyzes the formation of prolyl-tRNA(Pro) from proline and tRNA(Pro)
YP_989087.1	identified by match to protein family HMM PF02687; match to protein family HMM TIGR02212
YP_989088.1	identified by match to protein family HMM PF00005
YP_989089.1	identified by similarity to RF:YP_032238.1; match to protein family HMM PF03937
YP_989090.1	identified by match to protein family HMM PF00270; match to protein family HMM PF00271; match to protein family HMM PF02559; match to protein family HMM PF03461; match to protein family HMM PF04851; match to protein family HMM TIGR00580
YP_989091.1	identified by match to protein family HMM PF06776
YP_989092.1	identified by match to protein family HMM PF01520
YP_989093.1	identified by match to protein family HMM PF00905; match to protein family HMM PF00912; match to protein family HMM TIGR02074
YP_989094.1	catalyzes the release of newly synthesized polypeptide chains at the stop codons UAA and UGA
YP_989095.1	identified by match to protein family HMM PF00578; match to protein family HMM PF08534
YP_989096.1	catalyzes the formation of tyrosyl-tRNA(Tyr) from tyrosine and tRNA(Tyr)
YP_989099.1	identified by match to protein family HMM PF00266
YP_989100.1	with SufCD activates cysteine desulfurase SufS
YP_989101.1	identified by match to protein family HMM PF00005; match to protein family HMM TIGR01978
YP_989102.1	identified by match to protein family HMM PF01458; match to protein family HMM TIGR01981
YP_989103.1	identified by match to protein family HMM PF00266; match to protein family HMM PF01212; match to protein family HMM TIGR01979
YP_989104.1	identified by match to protein family HMM PF01883; match to protein family HMM TIGR02945
YP_989105.1	identified by match to protein family HMM PF01494; match to protein family HMM TIGR01984; match to protein family HMM TIGR01988
YP_989106.1	identified by similarity to SP:Q9KJY8; match to protein family HMM PF01066
YP_989107.1	identified by match to protein family HMM PF00753
YP_989108.1	identified by match to protein family HMM PF01026; match to protein family HMM TIGR00010
YP_989109.1	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_989110.1	catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the delta' subunit seems to interact with the gamma subunit to transfer the beta subunit on the DNA
YP_989111.1	catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to thymidine monophosphate (dTMP) to form thymidine diphosphate (dTDP)
YP_989112.1	identified by match to protein family HMM PF03330; match to protein family HMM TIGR00413
YP_989113.1	TtcA; YdaO; catalyzes the thiolation of cytosine 32 in specific tRNAs
YP_989114.1	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_989115.1	converts L-glutamate to D-glutamate, a component of peptidoglycan
YP_989116.1	identified by match to protein family HMM PF00588; match to protein family HMM TIGR00050
YP_989117.1	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_989118.1	identified by similarity to SP:P65956; match to protein family HMM PF04002; match to protein family HMM TIGR00608
YP_989120.1	identified by match to protein family HMM PF00561
YP_989121.1	identified by match to protein family HMM PF02643
YP_989122.1	identified by match to protein family HMM PF00313
YP_989123.1	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_989124.1	allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases; reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA; some Mycoplasma proteins contain an N-terminal fusion to an unknown domain
YP_989125.1	identified by match to protein family HMM PF03652; match to protein family HMM TIGR00250
YP_989126.1	identified by match to protein family HMM PF00441
YP_989127.1	catalyzes the transfer of the carbamoyl moiety from carbamoyl phosphate to L- aspartate in pyrimidine biosynthesis
YP_989128.1	Catalyzes the reversible hydrolysis of the amide bond within dihydroorotate. This metabolic intermediate is required for the biosynthesis of pyrimidine nucleotides
YP_989129.1	identified by match to protein family HMM PF02660; match to protein family HMM TIGR00023
YP_989130.1	identified by match to protein family HMM PF02481; match to protein family HMM TIGR00732
YP_989131.1	catalyzes the ATP-dependent breakage of single-stranded DNA followed by passage and rejoining, maintains net negative superhelicity
YP_989132.1	identified by match to protein family HMM PF00575; match to protein family HMM PF00773; match to protein family HMM TIGR00358; match to protein family HMM TIGR02063
YP_989134.1	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_989135.1	identified by match to protein family HMM PF00565
YP_989136.1	identified by similarity to RF:YP_032293.1
YP_989137.1	identified by similarity to SP:P74996; match to protein family HMM PF01037
YP_989138.1	catalyzes the synthesis of alpha-ribazole-5'-phosphate from nicotinate mononucleotide and 5,6-dimethylbenzimidazole
YP_989139.1	identified by similarity to SP:P32695; match to protein family HMM PF01207; match to protein family HMM TIGR00742
YP_989140.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00512; match to protein family HMM PF02518; match to protein family HMM PF08448
YP_989142.1	identified by match to protein family HMM PF01613
YP_989143.1	identified by match to protein family HMM PF00834; match to protein family HMM TIGR01163
YP_989144.1	Catalyzes two discrete reactions in the de novo synthesis of purines: the cleavage of adenylosuccinate and succinylaminoimidazole carboxamide ribotide
YP_989145.1	identified by match to protein family HMM PF06821
YP_989146.1	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_989147.1	identified by match to protein family HMM PF02700; match to protein family HMM TIGR00302
YP_989148.1	catalyzes the formation of 2-(formamido)-N1-(5-phospho-D-ribosyl)acetamidine from N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide and L-glutamine in purine biosynthesis
YP_989150.1	catalyzes the formation of 2-(formamido)-N1-(5-phospho-D-ribosyl)acetamidine from N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide and L-glutamine in purine biosynthesis
YP_989151.1	identified by match to protein family HMM PF01722
YP_989152.1	identified by match to protein family HMM PF00462; match to protein family HMM TIGR00365
YP_989153.1	identified by match to protein family HMM PF07690; match to protein family HMM TIGR00710
YP_989154.1	decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling
YP_989155.1	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_989156.1	identified by match to protein family HMM PF01612; match to protein family HMM TIGR01388
YP_989158.1	catalyzes the formation of catechol from salicylate
YP_989159.1	catalyzes DNA-template-directed extension of the 3'- end of a DNA strand by one nucleotide at a time; main replicative polymerase
YP_989160.1	homology to a family of hypothetical proteins in Leptospira interrogans; identified by similarity to RF:YP_002272.1; match to protein family HMM PF07598
YP_989161.1	identified by match to protein family HMM PF00270; match to protein family HMM PF00271
YP_989164.1	part of the preprotein secretory system; forms a complex with protein YajC; SecDFyajC stimulates the proton motive force-driven protein translocation, seems to modulate the cycling of SecA by stabilizing its membrane-inserted state and appears to be required for the release of mature proteins from the extracytoplasmic side of the membrane; in some organisms, such as Bacillus subtilis, SecD is fused to SecF
YP_989166.1	identified by match to protein family HMM PF00571; match to protein family HMM PF03471; match to protein family HMM PF03741
YP_989172.1	homology to a family of hypothetical proteins in Leptospira interrogans; identified by similarity to RF:YP_000623.1; match to protein family HMM PF07598
YP_989175.1	homology to a family of hypothetical proteins in Leptospira interrogans; identified by similarity to RF:YP_002272.1; match to protein family HMM PF07598
YP_989176.1	identified by similarity to RF:NP_522057.1
YP_989179.1	identified by similarity to RF:NP_522061.1
YP_989180.1	identified by match to protein family HMM PF07690
YP_989181.1	identified by match to protein family HMM PF04011
YP_989182.1	identified by match to protein family HMM PF04536
YP_989183.1	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_989184.1	decatenates newly replicated chromosomal DNA and relaxes positive and negative DNA supercoiling
YP_989185.1	identified by match to protein family HMM PF01368; match to protein family HMM PF02272; match to protein family HMM TIGR00644
YP_989186.1	in Escherichia coli this protein is one of the earliest assembly proteins in the large subunit
YP_989187.1	forms a direct contact with the tRNA during translation
YP_989188.1	identified by similarity to GB:AAA82214.1; match to protein family HMM PF00072
YP_989189.1	identified by match to protein family HMM PF01471; match to protein family HMM PF01510
YP_989194.1	identified by similarity to SP:P22884
YP_989195.1	identified by similarity to GB:AAU44778.1; match to protein family HMM PF05658; match to protein family HMM PF05662
YP_989199.1	identified by similarity to SP:P0AAE0; match to protein family HMM PF00324
YP_989200.1	identified by match to protein family HMM PF01450; match to protein family HMM PF07991; match to protein family HMM TIGR00465
YP_989201.1	involved in the de novo synthesis of pyridoxine (Vitamin B6)
YP_989204.1	identified by match to protein family HMM PF00089; match to protein family HMM PF00595; match to protein family HMM TIGR02037
YP_989205.1	identified by match to protein family HMM PF01145
YP_989206.1	identified by match to protein family HMM PF01145; match to protein family HMM TIGR01933
YP_989207.1	identified by match to protein family HMM PF00186
YP_989208.1	ThyA; catalyzes formation of dTMP and 7,8-dihydrofolate from 5,10-methylenetetrahydrofolate and dUMP; involved in deoxyribonucleotide biosynthesis; there are 2 copies in some Bacilli, one of which appears to be phage-derived
YP_989209.1	identified by similarity to SP:P0AEX3; match to protein family HMM PF00083; match to protein family HMM PF07690
YP_989210.1	identified by similarity to RF:YP_033877.1
YP_989211.1	identified by similarity to RF:YP_033878.1; match to protein family HMM PF07031
YP_989212.1	identified by similarity to RF:YP_033879.1
YP_989213.1	identified by match to protein family HMM PF00580
YP_989214.1	identified by match to protein family HMM PF00132
YP_989215.1	identified by match to protein family HMM PF02630
YP_989216.1	methylates ribosomal protein L11 at multiple amino acid positions; mutations of these genes in Escherichia coli or Thermus thermophilus has no apparent phenotype
YP_989217.1	identified by match to protein family HMM PF00557; match to protein family HMM PF01321
YP_989218.1	this protein catalyzes the formation of phosphodiester linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-stranded DNA using NAD as a coenzyme and as the energy source for the reaction; essential for DNA replication and repair of damaged DNA; similar to ligase LigB
YP_989219.1	identified by match to protein family HMM PF02463; match to protein family HMM TIGR00634
YP_989221.1	zinc-dependent; catalyzes the deacetylation of UDP-(3-O-acyl)-N-acetylglucosamine to UDP-3-O-(3-hydroxytetradecanoyl)-glucosamine in the second step of lipid A biosynthesis
YP_989222.1	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_989223.1	identified by similarity to GB:AAP32281.1; match to protein family HMM PF02491; match to protein family HMM TIGR01174
YP_989224.1	identified by similarity to SP:Q9X5H9; match to protein family HMM PF03799; match to protein family HMM PF08478
YP_989225.1	D-alanine--D-alanine ligase; DdlA; DdlB; cytoplasmic; catalyzes the formation of D-alanyl-D-alanine from two D-alanines in peptidoglycan synthesis; there are two forms of this enzyme in Escherichia coli
YP_989226.1	catalyzes the reduction of UDP-N-acetylglucosamine enolpyruvate to form UDP-N-acetylmuramate in peptidoglycan biosynthesis
YP_989227.1	Catalyzes the formation of UDP-N-acetylmuramoyl-L-alanine from UDP-N-acetylmuramate and L-alanine in peptidoglycan synthesis
YP_989228.1	UDP-N-acetylglucosamine--N-acetylmuramyl- (pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase; involved in cell wall formation; inner membrane-associated; last step of peptidoglycan synthesis
YP_989229.1	identified by match to protein family HMM PF01098; match to protein family HMM TIGR02614
YP_989230.1	UDP-N-acetylmuramoylalanine--D-glutamate ligase; involved in peptidoglycan biosynthesis; cytoplasmic; catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine during cell wall formation
YP_989231.1	First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
YP_989232.1	identified by match to protein family HMM PF01225; match to protein family HMM PF02875; match to protein family HMM PF08245; match to protein family HMM TIGR01143
YP_989233.1	involved in cell wall formation; peptidoglycan synthesis; cytoplasmic enzyme; catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-aceylmuramoyl-l-alanyl-d-glutamate
YP_989234.1	identified by match to protein family HMM PF00905; match to protein family HMM PF03717
YP_989235.1	identified by similarity to RF:YP_033903.1
YP_989236.1	identified by match to protein family HMM PF01795; match to protein family HMM TIGR00006
YP_989237.1	identified by similarity to RF:YP_032508.1
YP_989239.1	ChvD; in Agrobacterium tumefaciens, mutations in both Walker boxes were found to affect virulence
YP_989240.1	identified by match to protein family HMM PF00857
YP_989241.1	identified by match to protein family HMM PF04332
YP_989242.1	identified by match to protein family HMM PF01381
YP_989243.1	identified by similarity to RF:YP_032514.1
YP_989244.1	identified by similarity to GB:AAO39773.1; match to protein family HMM PF04402
YP_989245.1	sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released; this is the primary sigma factor of bacteria
YP_989246.1	synthesizes RNA primers at the replication forks
YP_989247.1	identified by match to protein family HMM PF00924
YP_989248.1	identified by match to protein family HMM PF02690
YP_989249.1	identified by similarity to RF:YP_032521.1; match to protein family HMM PF04226
YP_989250.1	catalyzes the formation of 4-hydroxybenzoate from chorismate
YP_989251.1	catalyzes production of carbamoyl phosphate from bicarbonate and glutamine in pyrimidine and arginine biosynthesis pathways; forms an octamer composed of four CarAB dimers
YP_989252.1	identified by match to protein family HMM PF07690
YP_989254.1	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_989256.1	identified by match to protein family HMM PF00313
YP_989257.1	catalyzes the formation of oxalozcetate and L-glutamate from L-aspartate and 2-oxoglutarate
YP_989259.1	identified by match to protein family HMM PF00126; match to protein family HMM PF03466
YP_989260.1	identified by match to protein family HMM PF00070; match to protein family HMM PF07992; match to protein family HMM TIGR01292
YP_989261.1	identified by similarity to GB:BAA31229.1; match to protein family HMM PF02386
YP_989262.1	identified by similarity to SP:O68547; match to protein family HMM PF00534
YP_989263.1	necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites; arresting sites in DNA have the property of trapping a certain fraction of elongating RNA polymerases that pass through, resulting in locked ternary complexes. Cleavage of the nascent transcript by cleavage factors such as GreA or GreB allows the resumption of elongation from the new 3'terminus
YP_989264.1	The UvrABC repair system catalyzes the recognition and processing of DNA lesions. The beta-hairpin of the Uvr-B subunit is inserted between the strands, where it probes for the presence of a lesion
YP_989265.1	identified by similarity to RF:NP_698511.1
YP_989266.1	identified by match to protein family HMM PF00753
YP_989267.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00486
YP_989268.1	identified by match to protein family HMM PF00512; match to protein family HMM PF00672; match to protein family HMM PF02518
YP_989269.1	identified by similarity to RF:YP_032023.1; match to protein family HMM PF08749
YP_989271.1	identified by similarity to RF:YP_033943.1; match to protein family HMM PF04380
YP_989272.1	transfers the N-acyl diglyceride moiety to the prospective N-terminal cysteine in prolipoprotein
YP_989273.1	identified by match to protein family HMM PF02636
YP_989274.1	identified by similarity to RF:YP_032018.1; match to protein family HMM PF02578; match to protein family HMM TIGR00726
YP_989276.1	catalyzes the formation of 5-phospho-alpha-D-ribose 1-phosphate from D-ribose 5-phosphate and ATP
YP_989277.1	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_989278.1	Enables the recycling of peptidyl-tRNAs produced at termination of translation
YP_989279.1	identified by match to protein family HMM PF03734
YP_989280.1	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_989281.1	identified by match to protein family HMM PF05239
YP_989283.1	identified by match to protein family HMM PF00588
YP_989284.1	identified by similarity to SP:Q8K1J6; match to protein family HMM PF01743
YP_989285.1	identified by match to protein family HMM PF07726; match to protein family HMM PF07728
YP_989286.1	identified by similarity to RF:YP_032538.1
YP_989287.1	identified by match to protein family HMM TIGR02226
YP_989288.1	identified by similarity to RF:YP_222236.1; match to protein family HMM PF07090
YP_989289.1	identified by match to protein family HMM PF00583
YP_989290.1	identified by match to protein family HMM PF00149
YP_989291.1	identified by similarity to GB:CAC83722.1; match to protein family HMM PF01545; match to protein family HMM TIGR01297
YP_989293.1	identified by match to protein family HMM PF00588
YP_989294.1	catalyzes a sulfuration reaction to synthesize 2-thiouridine at the U34 position of tRNAs
YP_989295.1	identified by similarity to RF:YP_032544.1; match to protein family HMM PF06627
YP_989297.1	identified by similarity to SP:Q45994; match to protein family HMM PF00072; match to protein family HMM PF00486
YP_989298.1	identified by similarity to GB:CAC47299.1
YP_989299.1	identified by match to protein family HMM PF06577
YP_989301.1	identified by match to protein family HMM PF00202; match to protein family HMM PF01041
YP_989302.1	identified by match to protein family HMM PF01408; match to protein family HMM PF02894
YP_989303.1	similarity to OppF; identified by similarity to GB:AAG22038.1; match to protein family HMM PF00005
YP_989304.1	identified by match to protein family HMM PF00005
YP_989305.1	similarity to DdpC; identified by similarity to SP:P77463; match to protein family HMM PF00528
YP_989306.1	similarity to DdpB; identified by similarity to SP:P77308; match to protein family HMM PF00528
YP_989307.1	identified by similarity to SP:P76128; match to protein family HMM PF00496
YP_989309.1	identified by match to protein family HMM PF03352
YP_989310.1	bidirectionally degrades single-stranded DNA into large acid-insoluble oligonucleotides
YP_989311.1	identified by similarity to RF:YP_033980.1
YP_989312.1	identified by similarity to SP:P53575; match to protein family HMM PF01012
YP_989313.1	identified by similarity to SP:P38974; match to protein family HMM PF00766; match to protein family HMM PF01012
YP_989314.1	identified by match to protein family HMM PF01266; match to protein family HMM PF05187
YP_989315.1	identified by similarity to GB:CAB64773.1; match to protein family HMM PF00669; match to protein family HMM PF00700
YP_989316.1	catalyzes the formation of L-proline from pyrroline-5-carboxylate
YP_989317.1	identified by match to protein family HMM PF02021
YP_989318.1	identified by match to protein family HMM PF00590; match to protein family HMM TIGR00096
YP_989319.1	type 1 subfamily; involved in last step of pyrimidine biosynthesis; converts orotidine 5'-phosphate to UMP and carbon dioxide; OMP decarboxylase; OMPDCase; OMPdecase
YP_989320.1	identified by similarity to RF:NP_697099.1; match to protein family HMM PF01883
YP_989321.1	identified by match to protein family HMM PF00468; match to protein family HMM TIGR01030
YP_989322.1	protein component of RNaseP which catalyzes the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'terminus; this enzyme also cleaves other RNA substrates
YP_989323.1	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_989324.1	binds guanine nucleotides; in Escherichia coli depletion results in defective cell division and filamentation; in Bacillus subtilis this gene is essential
YP_989325.1	identified by match to protein family HMM PF00043; match to protein family HMM PF02798
YP_989326.1	catalyzes the reduction of 2,3-dihydrodipicolinate to 2,3,4,5-tetrahydrodipicolinate in lysine and diaminopimelate biosynthesis
YP_989327.1	catalyzes the interconversion of 2-phosphoglycerate to 3-phosphoglycerate
YP_989329.1	homology to a family of hypothetical proteins in Leptospira interrogans; identified by similarity to RF:NP_711583.1; match to protein family HMM PF07598
YP_989330.1	identified by match to protein family HMM PF00959
YP_989331.1	identified by similarity to RF:YP_485043.1; match to protein family HMM PF03681
YP_989333.1	identified by similarity to RF:YP_033747.1
YP_989338.1	identified by similarity to RF:YP_211601.1
YP_989339.1	identified by similarity to RF:YP_033517.1
YP_989340.1	identified by match to protein family HMM PF08346
YP_989341.1	identified by similarity to RF:YP_033508.1
YP_989344.1	identified by match to protein family HMM PF00589
YP_989345.1	homology to a family of hypothetical proteins in Leptospira interrogans; identified by similarity to RF:NP_713670.1; match to protein family HMM PF07598
YP_989346.1	homology to a family of hypothetical proteins in Leptospira interrogans; identified by similarity to RF:NP_710801.1; match to protein family HMM PF07598
YP_989350.1	identified by match to protein family HMM PF00529
YP_989351.1	identified by match to protein family HMM PF07690; match to protein family HMM TIGR00711
YP_989352.1	identified by match to protein family HMM PF00278; match to protein family HMM PF02784
YP_989353.1	identified by match to protein family HMM PF00581
YP_989354.1	identified by similarity to SP:Q44532; match to protein family HMM PF00175; match to protein family HMM PF00970
YP_989355.1	identified by match to protein family HMM PF00842; match to protein family HMM PF01168; match to protein family HMM TIGR00492
YP_989356.1	acts in conjunction with GvcH to form H-protein-S-aminomethyldihydrolipoyllysine from glycine
YP_989357.1	part of multienzyme complex composed of H, L, P, and T proteins which catalyzes oxidation of glycine to yield carbon dioxide, ammonia, 5,10-CH2-H4folate and a reduced pyridine nucleotide; protein H is involved in transfer of methylamine group from the P to T protein; covalently bound to a lipoyl cofactor
YP_989358.1	catalyzes the transfer of a methylene carbon from the methylamine-loaded GcvH protein to tetrahydrofolate, causing the release of ammonia and the generation of reduced GcvH protein
YP_989359.1	identified by match to protein family HMM PF02190
YP_989360.1	identified by similarity to RF:YP_034024.1; match to protein family HMM PF03966
YP_989362.1	identified by match to protein family HMM PF03966
YP_989363.1	catalyzes the formation of 4-aspartyl phosphate from aspartate 4-semialdehyde
YP_989364.1	identified by similarity to SP:P28635; match to protein family HMM PF03180; match to protein family HMM TIGR00363
YP_989365.1	identified by match to protein family HMM PF00005
YP_989366.1	identified by match to protein family HMM PF00528
YP_989367.1	identified by similarity to SP:P08634; match to protein family HMM PF01575
YP_989368.1	identified by match to protein family HMM PF01113; match to protein family HMM PF03447; match to protein family HMM PF08666
YP_989369.1	identified by match to protein family HMM PF02633
YP_989371.1	identified by match to protein family HMM PF03797; match to protein family HMM TIGR01414
YP_989373.1	identified by match to protein family HMM PF01497
YP_989374.1	identified by similarity to GB:CAA61301.1; match to protein family HMM PF01032
YP_989375.1	identified by similarity to GB:CAA61302.1; match to protein family HMM PF01032
YP_989376.1	identified by match to protein family HMM PF00005
YP_989377.1	FliQ, with proteins FliP and FliR, forms the core of the central channel in the flagella export apparatus; Bradyrhizobium have one thick flagellum and several thin flagella; the protein in this cluster is associated with the thick flagellum
YP_989378.1	identified by similarity to GB:AAB61250.1; match to protein family HMM PF03963
YP_989379.1	post-transcriptional repressor of flagellum biosynthesis; promotes degradation of fljK mRNA: Bradyrhizobium has one thick flagellum and several thin flagella; the protein in this cluster is associated with the thin flagella
YP_989380.1	acts as an activator or flagellin translation and may be required for filament secretion or assembly; Bradyrhizobium has one thick flagellum and several thin flagella; the protein in this cluster is associated with the thin flagella
YP_989381.1	with FlgK acts as a hook filament junction protein to join the flagellar filament to the hook; Bradyrhizobium has one thick flagellum and several thin flagella; the Bradyrhizobium protein in this cluster is associated with the thin flagella
YP_989382.1	with FlgL acts as a hook filament junction protein to join the flagellar filament to the hook
YP_989383.1	identified by similarity to SP:P75937; match to protein family HMM PF00460; match to protein family HMM PF06429; match to protein family HMM PF07559
YP_989384.1	identified by match to protein family HMM PF00072; match to protein family HMM PF00486
YP_989385.1	identified by match to protein family HMM PF01464
YP_989386.1	identified by similarity to RF:YP_223813.1
YP_989387.1	a periplasmic protein that interacts with and stabilizes MotB; in Rhizobium, interactions between MotB and MotC at the periplasmic surface of the motor control the energy flux or the energy coupling that drives flagellar rotation
YP_989388.1	identified by similarity to GB:AAB81408.1; match to protein family HMM PF00691
YP_989390.1	the MS-ring anchors the flagellum to the cytoplasmic membrane; part of the flagellar basal body which consists of four rings L, P, S, and M mounted on a central rod
YP_989392.1	identified by match to protein family HMM TIGR01414
YP_989393.1	identified by match to protein family HMM TIGR01414
YP_989394.1	FliP, with proteins FliQ and FliR, forms the core of the central channel in the flagella export apparatus
YP_989395.1	identified by match to protein family HMM PF03748
YP_989396.1	part of the flagellar basal body which consists of four rings L,P, S and M mounted on a central rod
YP_989398.1	part of the basal body which consists of four rings L, P, S, and M mounted on a central rod; Vibrio parahaemolyticus, Yersinia, Bradyrhizobium and other bacteria have two copies of this and other flagellar genes; the V. parahaemolyticus protein is associated with the polar flagella and the Bradyrhizobium protein is associated with the thick flagellum
YP_989399.1	required for the assembly of the flagellar basal body P-ring; Bradyrhizobium japonicum has two types of flagella, a single thick flagella and a few thin flagella; the protein in this cluster is associated with the thin flagella
YP_989400.1	makes up the distal portion of the flagellar basal body rod; Bradyrhizobium has one thick flagellum and several thin flagella; the Bradyrhizobium protein in this cluster is associated with the thick flagella
YP_989401.1	identified by match to protein family HMM PF02049; match to protein family HMM TIGR00205
YP_989402.1	with FlgF and B makes up the proximal portion of the flagellar basal body rod; Bradyrhizobium have one thick flagellum and several thin flagella; the protein in this cluster is associated with the thin flagella
YP_989403.1	with FlgF and C makes up the proximal portion of the flagellar basal body rod; Bradyrhizobium have one thick flagellum and several thin flagella; the proteins in this cluster are associated with the thin flagella
YP_989404.1	involved in type III protein export during flagellum assembly
YP_989405.1	identified by match to protein family HMM PF00460
YP_989406.1	identified by match to protein family HMM PF06748
YP_989407.1	identified by similarity to GB:AAF35850.1
YP_989408.1	identified by similarity to GB:AAF35843.1; match to protein family HMM PF01052; match to protein family HMM TIGR01397
YP_989409.1	identified by similarity to RF:YP_222930.1
YP_989410.1	identified by match to protein family HMM PF01052; match to protein family HMM TIGR02480
YP_989411.1	One of three proteins involved in switching the direction of the flagellar rotation
YP_989412.1	membrane protein responsible for substrate specificity switching from rod/hook-type export to filament-type export
YP_989413.1	identified by similarity to RF:NP_104130.1
YP_989414.1	identified by similarity to RF:YP_223799.1
YP_989415.1	identified by similarity to RF:YP_032612.1
YP_989416.1	identified by similarity to RF:YP_223801.1
YP_989418.1	FliR, with proteins FliP and FliQ, forms the core of the central channel in the flagella export apparatus; Bradyrhizobium has one thick and several thin flagella; the Bradyrhizobium protein in this cluster are associated with the thin flagella
YP_989419.1	membrane protein involved in the flagellar export apparatus
YP_989421.1	identified by similarity to RF:YP_032614.1; match to protein family HMM PF04273; match to protein family HMM TIGR01244
YP_989423.1	catalyzes the formation of FMN from riboflavin and the formation of FAD from FMN; in Bacillus the ribC gene has both flavokinase and FAD synthetase activities
YP_989424.1	identified by match to protein family HMM PF00702; match to protein family HMM TIGR01459; match to protein family HMM TIGR01460
YP_989425.1	identified by match to protein family HMM PF03023; match to protein family HMM TIGR01695
YP_989426.1	catalyzes a two-step reaction, first charging a tryptophan molecule by linking its carboxyl group to the alpha-phosphate of ATP, followed by transfer of the aminoacyl-adenylate to its tRNA
YP_989428.1	identified by match to protein family HMM PF01106; match to protein family HMM PF08712
YP_989430.1	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_989431.1	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_989432.1	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_989433.1	catalyzes the interconversion of alpha-D-glucose 1-phosphate to alpha-D-glucose 6-phosphate
YP_989434.1	identified by similarity to SP:P44758; match to protein family HMM PF00578; match to protein family HMM PF08534
YP_989436.1	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_989438.1	homology to a family of hypothetical proteins in Leptospira interrogans; identified by similarity to RF:NP_710801.1; match to protein family HMM PF07598
YP_989441.1	homology to a family of hypothetical proteins in Leptospira interrogans; identified by similarity to RF:NP_711583.1; match to protein family HMM PF07598
YP_989442.1	identified by similarity to RF:YP_033851.1
YP_989445.1	homology to a family of hypothetical proteins in Leptospira interrogans; identified by similarity to RF:YP_000623.1; match to protein family HMM PF07598
YP_989446.1	catalyzes the NAD(P)H-dependent reduction of glycerol 3-phosphate to glycerone phosphate
YP_989447.1	also shows similarity to aroP; identified by similarity to SP:P15993; match to protein family HMM PF00324
YP_989448.1	identified by similarity to GB:AAT52198.1; match to protein family HMM PF02632
YP_989449.1	identified by match to protein family HMM PF02361
YP_989450.1	identified by similarity to GB:AAT52196.1; match to protein family HMM PF00005; match to protein family HMM PF02463
YP_989451.1	also shows similarity to pheP; identified by similarity to SP:P15993; match to protein family HMM PF00324
YP_989453.1	Catalyzes the deamination of dCTP to form dUTP
YP_989454.1	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_989455.1	identified by similarity to RF:YP_031959.1
YP_989456.1	transfers the gamma-phosphate of ATP to the 4' position of a tetraacyldisaccharide 1-phosphate intermediate to form tetraacyldisaccharide 1,4'-bis-phosphate
YP_989457.1	catalyzes the transfer of 2-keto-3-deoxy-D-manno-octulosonic acid to lipid A
YP_989458.1	identified by similarity to RF:YP_223014.1; match to protein family HMM PF04028
YP_989459.1	identified by similarity to RF:YP_033117.1
YP_989460.1	identified by match to protein family HMM PF01523
YP_989461.1	identified by match to protein family HMM PF03602; match to protein family HMM TIGR00095
YP_989462.1	identified by match to protein family HMM PF00849; match to protein family HMM PF01479; match to protein family HMM TIGR00093
YP_989463.1	identified by match to protein family HMM PF00383
YP_989464.1	IleRS; catalyzes the formation of isoleucyl-tRNA(Ile) from isoleucine and tRNA(Ile); since isoleucine and other amino acids such as valine are similar, there are additional editing function in this enzyme; one is involved in hydrolysis of activated valine-AMP and the other is involved in deacylation of mischarged Val-tRNA(Ile); there are two active sites, one for aminoacylation and one for editing; class-I aminoacyl-tRNA synthetase family; some organisms carry two different copies of this enzyme
YP_989465.1	identified by match to protein family HMM PF02530
YP_989466.1	identified by similarity to GB:AAL27289.1; match to protein family HMM PF02530
YP_989467.1	identified by match to protein family HMM PF02530
YP_989468.1	identified by similarity to RF:YP_033106.1
YP_989469.1	homology to a family of hypothetical proteins in Leptospira interrogans; identified by similarity to RF:YP_000623.1; match to protein family HMM PF07598
YP_989471.1	identified by match to protein family HMM PF01612
YP_989472.1	identified by match to protein family HMM PF01546; match to protein family HMM PF07687
YP_989473.1	Involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Acts as DNA glycosylase that recognizes and removes damaged bases
YP_989474.1	identified by similarity to SP:P24828; match to protein family HMM PF02073
YP_989475.1	identified by match to protein family HMM PF07486
YP_989476.1	identified by match to protein family HMM PF01895; match to protein family HMM TIGR02135
YP_989477.1	ATP-binding protein; PstABCS is an ATP dependent phosphate uptake system which is responsible for inorganic phosphate uptake during phosphate starvation
YP_989478.1	identified by match to protein family HMM PF00528; match to protein family HMM TIGR00974
YP_989479.1	identified by match to protein family HMM PF00528; match to protein family HMM TIGR02138
YP_989481.1	catalyzes the second step in the glutathione biosynthesis pathway, where it synthesizes ATP + gamma-L-glutamyl-L-cysteine + glycine = ADP + phosphate + glutathione
YP_989482.1	ATP-dependent adenylate transferase, transfers adenyl moiety to the MoeD subunit of molybdopterin synthase
YP_989484.1	identified by match to protein family HMM PF00034
YP_989485.1	CMP-2-keto-3-deoxyoctulosonic acid synthetase; catalyzes the formation of CMP-3-deoxy-D-manno-octulosonate from CTP and 3-deoxy-D-manno-octulosonate which is incorporated into LPS
YP_989487.1	catalyzes the DNA-template-directed extension of the 3'-end of a DNA strand; the tau chain serves as a scaffold to help in the dimerizaton of the alpha,epsilon and theta core complex; the gamma chain seems to interact with the delta and delta' subunits to transfer the beta subunit on the DNA
YP_989488.1	identified by match to protein family HMM PF02575; match to protein family HMM TIGR00103
YP_989489.1	involved in a recombinational process of DNA repair, independent of the recBC complex
YP_989490.1	identified by match to protein family HMM PF00814
YP_989491.1	identified by match to protein family HMM PF00583; match to protein family HMM TIGR01575
YP_989492.1	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_989493.1	identified by match to protein family HMM PF02562
YP_989494.1	identified by match to protein family HMM PF02130; match to protein family HMM TIGR00043
YP_989495.1	identified by similarity to SP:P0A2L3; match to protein family HMM PF00571; match to protein family HMM PF03471
YP_989496.1	Transfers the fatty acyl group on membrane lipoproteins
YP_989497.1	identified by match to protein family HMM PF01381
YP_989498.1	catalyzes the formation of S-adenosylmethionine from methionine and ATP; methionine adenosyltransferase
YP_989499.1	tRNA (guanine-N(7)-)-methyltransferase; catalyzes the formation of N(7)-methylguanine at position 46 (m7G46) in tRNA by transferring the methyl residue from S-adenosyl-L-methionine
YP_989500.1	in Streptococcus pneumoniae this gene was found to be essential; structure determination of the Streptococcus protein shows that it is similar to a number of other proteins
YP_989501.1	modifies transcription through interactions with RNA polymerase affecting elongation, readthrough, termination, and antitermination
YP_989502.1	identified by similarity to RF:YP_033069.1; match to protein family HMM PF04296
YP_989503.1	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_989504.1	associates with free 30S ribosomal subunits; essential for efficient processing of 16S rRNA; in Escherichia coli rbfA is induced by cold shock
YP_989505.1	catalyzes isomerization of specific uridines in RNA to pseudouridine; responsible for residues in T loops of many tRNAs
YP_989506.1	identified by match to protein family HMM PF00312; match to protein family HMM TIGR00952
YP_989507.1	identified by similarity to OMNI:AFE_2642; 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_989508.1	identified by match to protein family HMM PF05175
YP_989509.1	heat shock protein involved in degradation of misfolded proteins
YP_989510.1	heat shock protein involved in degradation of misfolded proteins
YP_989511.1	identified by match to protein family HMM PF00710
YP_989512.1	catalyzes the formation of (R)-4'-phosphopantothenate in coenzyme A biosynthesis
YP_989513.1	identified by match to protein family HMM PF00883; match to protein family HMM PF02789
YP_989514.1	identified by match to protein family HMM PF00877
YP_989515.1	identified by similarity to RF:YP_031843.1; match to protein family HMM PF06347; match to protein family HMM PF08239
YP_989516.1	identified by similarity to GB:AAO89498.1; match to protein family HMM PF01475
YP_989517.1	catalyzes the dehydration of (3R)-3-hydroxydecanoyl-ACP to 2,3-decenoyl-ACP or 3,4-decenoyl-ACP
YP_989518.1	FabB, beta-Ketoacyl-ACP synthase I, KASI; catalyzes a condensation reaction in fatty acid biosynthesis: addition of an acyl acceptor of two carbons from malonyl-ACP; required for the elongation of short-chain unsaturated acyl-ACP
YP_989519.1	Catalyzes a key regulatory step in fatty acid biosynthesis
YP_989521.1	identified by match to protein family HMM PF03626; match to protein family HMM TIGR02847
YP_989522.1	identified by match to protein family HMM PF00510
YP_989523.1	identified by match to protein family HMM PF00115; match to protein family HMM TIGR02843
YP_989524.1	identified by match to protein family HMM PF00116; match to protein family HMM TIGR01433
YP_989525.1	catalyzes the formation of 3-dehydroshikimate from 3-dehydroquinate in chorismate biosynthesis
YP_989526.1	Required for DNA replication; binds preferentially to single-stranded, linear DNA
YP_989527.1	binds the polymerase to DNA and acts as a sliding clamp
YP_989528.1	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_989530.1	binds directly to the 16S rRNA and is involved in post-translational inhibition of arginine and ornithine decarboxylase
YP_989531.1	Catalyzes the conversion of citrate to isocitrate
YP_989533.1	ATP-binding protein; required for proper cytochrome c maturation
YP_989534.1	identified by similarity to SP:P30964; match to protein family HMM PF03379; match to protein family HMM TIGR01190
YP_989535.1	identified by similarity to SP:P30962; match to protein family HMM PF01578; match to protein family HMM TIGR01191
YP_989536.1	identified by match to protein family HMM TIGR03141
YP_989537.1	identified by similarity to SP:P45409; match to protein family HMM PF00578; match to protein family HMM PF08534; match to protein family HMM TIGR00385
YP_989538.1	identified by match to protein family HMM PF07750
YP_989539.1	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_989540.1	catalyzes the formation of L-citrulline from carbamoyl phosphate and L-ornithine in arginine biosynthesis and degradation
YP_989541.1	becomes active under oxidative stress; four conserved cysteines bind a zinc atom when they are in the reduced state and the enzyme is inactive; oxidative stress results in oxidized cysteines, release of zinc, and binding of Hsp33 to aggregation-prone proteins; forms dimers and higher order oligomers
YP_989542.1	identified by match to protein family HMM PF01713
YP_989543.1	identified by match to protein family HMM PF04280
YP_989544.1	identified by match to protein family HMM PF04186
YP_989545.1	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_989547.1	identified by similarity to SP:O30808; match to protein family HMM PF00390; match to protein family HMM PF03949
YP_989548.1	This protein performs the mismatch recognition step during the DNA repair process
YP_989550.1	identified by match to protein family HMM TIGR02300
YP_989551.1	catalyzes the formation of 5-O-(1-carboxyvinyl)-3-phosphoshikimate from phosphoenolpyruvate and 3-phosphoshikimate in tryptophan biosynthesis
YP_989552.1	Catalyzes the formation of (d)CDP from ATP and (d)CMP
YP_989553.1	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_989554.1	identified by similarity to GB:AAC34747.2; match to protein family HMM PF06165; match to protein family HMM PF06204; match to protein family HMM PF06205
YP_989555.1	catalyzes the formation of nictonate and 5-phospho-alpha-D-ribose 1-diphosphate from nicotinate D-ribonucleotide and diphosphate
YP_989556.1	identified by similarity to GB:AAU94305.1; match to protein family HMM PF00950
YP_989557.1	similarity to yfeC of Yersinia pestis; identified by similarity to GB:AAU94304.1; match to protein family HMM PF00950; match to protein family HMM PF01032
YP_989558.1	similarity to yfeB of Yersinia pestis; identified by similarity to GB:AAU94303.1; match to protein family HMM PF00005
YP_989559.1	similarity to yfeA of Yersinia pestis; identified by similarity to GB:AAU94302.1; match to protein family HMM PF01297
YP_989560.1	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_989561.1	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_989562.1	binds directly to 23S ribosomal RNA prior to in vitro assembly of the 50S ribosomal subunit
YP_989563.1	identified by match to protein family HMM PF01632; match to protein family HMM TIGR00001
YP_989564.1	identified by match to protein family HMM PF00633; match to protein family HMM PF00730; match to protein family HMM TIGR01083
YP_989566.1	identified by match to protein family HMM PF02646
YP_989567.1	cleaves off formyl group from N-terminal methionine residues of newly synthesized proteins; binds iron(2+)
YP_989568.1	identified by match to protein family HMM PF00551; match to protein family HMM PF02911; match to protein family HMM TIGR00460
YP_989569.1	mediates pseudouridylation (positions 38, 39, 40) at the tRNA anticodon region which contributes to the structural stability
YP_989570.1	identified by match to protein family HMM PF03641
YP_989571.1	catalyzes the formation of N-succinyl-2-amino-6-ketopimelate from succinyl-CoA and tetrahydrodipicolinate in the lysine biosynthetic pathway
YP_989572.1	binds to the ribosome on the universally-conserved alpha-sarcin loop
YP_989573.1	identified by match to protein family HMM PF00892
YP_989574.1	catalyzes the phosphorylation of N-acetyl-L-glutamate to form N-acetyl-L-glutamate 5-phosphate
YP_989575.1	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_989576.1	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_989578.1	identified by similarity to RF:NP_104456.1; match to protein family HMM PF04314
YP_989580.1	identified by similarity to GB:AAC28777.1; match to protein family HMM PF00072; match to protein family HMM PF00486
YP_989581.1	identified by similarity to GB:AAC28778.1; match to protein family HMM PF00512; match to protein family HMM PF00672; match to protein family HMM PF02518
YP_989582.1	with DnaK and DnaJ acts in response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins; may act as a thermosensor
YP_989583.1	HAM1-like protein; Rec-dependent growth; RgdB; yggV; it is suspected that this protein functions to remove misincorporated bases such as xanthine or hypoxanthine
YP_989584.1	catalyzes the oxygen-independent formation of protoporphyrinogen-IX from coproporphyrinogen-III
YP_989585.1	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_989586.1	identified by similarity to RF:YP_031771.1; match to protein family HMM PF01863
YP_989587.1	identified by similarity to RF:NP_699091.1
YP_989588.1	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_989589.1	identified by match to protein family HMM PF00005; match to protein family HMM PF00664
YP_989590.1	identified by match to protein family HMM PF04357
YP_989591.1	identified by match to protein family HMM PF01103; match to protein family HMM PF07244
YP_989592.1	identified by match to protein family HMM PF01078; match to protein family HMM TIGR00368
YP_989593.1	negatively supercoils closed circular double-stranded DNA
YP_989594.1	Catalyzes the carbon methylation reaction in the biosynthesis of ubiquinone
YP_989595.1	identified by match to protein family HMM PF03109; match to protein family HMM TIGR01982
YP_989596.1	catalyzes the conjugation of cysteine to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine, which is then decarboxylated to form 4'-phosphopantotheine
YP_989597.1	putative role in sulfur assimilation
YP_989598.1	catalyzes the carboxylation of acetyl-CoA to malonyl-CoA; forms a tetramer of AccA2D2 subunits
YP_989599.1	identified by match to protein family HMM PF08245; match to protein family HMM TIGR01499
YP_989600.1	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_989601.1	identified by match to protein family HMM PF00512; match to protein family HMM PF02518
YP_989602.1	identified by match to protein family HMM PF01636; match to protein family HMM PF02367; match to protein family HMM PF02958; match to protein family HMM TIGR00150
YP_989603.1	identified by match to protein family HMM TIGR02786
YP_989604.1	identified by match to protein family HMM PF00580; match to protein family HMM TIGR02784
YP_989605.1	identified by match to protein family HMM PF00085; match to protein family HMM TIGR01068
YP_989606.1	identified by match to protein family HMM PF00009; match to protein family HMM PF03144; match to protein family HMM TIGR00231; match to protein family HMM TIGR00503
YP_989607.1	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_989608.1	catalyzes the formation of 2-N(omega)-(L-arginino)succinate from L-citrulline and L-aspartate in arginine biosynthesis, AMP-forming
YP_989609.1	identified by match to protein family HMM PF01810
YP_989610.1	identified by match to protein family HMM PF04055; match to protein family HMM TIGR00048
YP_989611.1	identified by similarity to RF:YP_031747.1
YP_989612.1	identified by similarity to SP:P69829; match to protein family HMM PF00359; match to protein family HMM TIGR01419
YP_989615.1	identified by match to protein family HMM PF00005
YP_989616.1	identified by match to protein family HMM PF03968
YP_989617.1	identified by similarity to RF:YP_031743.1; match to protein family HMM PF06835
YP_989618.1	This protein is one of the two subunits of integration host factor, a specific DNA-binding protein that functions in genetic recombination as well as in transcriptional and translational control
YP_989619.1	identified by similarity to RF:YP_032885.1
YP_989620.1	Identification is based on SCOP SUPERFAMILY HMM SSF53335.
YP_989621.1	identified by match to protein family HMM PF00588; match to protein family HMM PF08032
YP_989622.1	lipoprotein signal peptidase; integral membrane protein that removes signal peptides from prolipoproteins during lipoprotein biosynthesis