locus-tag	class	description
YYU_00005	COG0258	In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity
YYU_00005	COG0749	In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity
YYU_00010	COG0036	Belongs to the ribulose-phosphate 3-epimerase family
YYU_00015	COG0767	ABC-type transport system involved in resistance to organic solvents, permease component
YYU_00020	COG1127	ABC transporter
YYU_00035	COG3155	Displays glyoxalase activity, catalyzing the conversion of glyoxal to glycolate
YYU_00040	COG0192	Catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP. The overall synthetic reaction is composed of two sequential steps, AdoMet formation and the subsequent tripolyphosphate hydrolysis which occurs prior to release of AdoMet from the enzyme
YYU_00050	COG0654	COG0654 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases
YYU_00065	COG0752	glycyl-tRNA synthetase alpha subunit
YYU_00075	COG0484	heat shock protein binding
YYU_00085	COG0344	acyl-phosphate glycerol-3-phosphate acyltransferase activity
YYU_00090	COG0817	Nuclease that resolves Holliday junction intermediates in genetic recombination. Cleaves the cruciform structure in supercoiled DNA by nicking to strands with the same polarity at sites symmetrically opposed at the junction in the homologous arms and leaves a 5'-terminal phosphate and a 3'-terminal hydroxyl group
YYU_00095	COG1845	cytochrome c oxidase, subunit III
YYU_00100	COG0407	Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III
YYU_00105	COG1253	flavin adenine dinucleotide binding
YYU_00115	COG4695	Portal protein
YYU_00125	COG0379	Catalyzes the condensation of iminoaspartate with dihydroxyacetone phosphate to form quinolinate
YYU_00165	COG0180	Tryptophanyl-tRNA synthetase
YYU_00170	COG0576	Participates actively in the response to hyperosmotic and heat shock by preventing the aggregation of stress-denatured proteins, in association with DnaK and GrpE. It is the nucleotide exchange factor for DnaK and may function as a thermosensor. Unfolded proteins bind initially to DnaJ
YYU_00175	COG0117	Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)- pyrimidinedione 5'-phosphate
YYU_00175	COG1985	Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)- pyrimidinedione 5'-phosphate
YYU_00180	COG0504	CTP synthase activity
YYU_00190	COG4974	Belongs to the 'phage' integrase family
YYU_00200	COG0280	phosphate acetyltransferase
YYU_00200	COG0281	malic enzyme
YYU_00210	COG0651	ATP synthesis coupled electron transport
YYU_00220	COG1463	ABC-type transport system involved in resistance to organic solvents, periplasmic component
YYU_00230	COG1327	Negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR- boxes
YYU_00250	COG1840	ABC-type Fe3 transport system, periplasmic component
YYU_00255	COG2835	tetraacyldisaccharide 4'-kinase activity
YYU_00265	COG0228	four-way junction DNA binding
YYU_00285	COG0192	Catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP. The overall synthetic reaction is composed of two sequential steps, AdoMet formation and the subsequent tripolyphosphate hydrolysis which occurs prior to release of AdoMet from the enzyme
YYU_00300	COG0292	Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit
YYU_00305	COG0291	Belongs to the bacterial ribosomal protein bL35 family
YYU_00315	COG1158	Facilitates transcription termination by a mechanism that involves Rho binding to the nascent RNA, activation of Rho's RNA-dependent ATPase activity, and release of the mRNA from the DNA template
YYU_00320	COG1249	Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family
YYU_00325	COG0484	heat shock protein binding
YYU_00330	COG0694	Involved in iron-sulfur cluster biogenesis. Binds a 4Fe- 4S cluster, can transfer this cluster to apoproteins, and thereby intervenes in the maturation of Fe S proteins. Could also act as a scaffold chaperone for damaged Fe S proteins
YYU_00355	COG0008	Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu)
YYU_00355	COG1384	Belongs to the class-I aminoacyl-tRNA synthetase family
YYU_00395	COG1722	exodeoxyribonuclease VII activity
YYU_00400	COG3118	belongs to the thioredoxin family
YYU_00410	COG1071	oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
YYU_00415	COG2267	carboxylic ester hydrolase activity
YYU_00430	COG0299	Catalyzes the transfer of a formyl group from 10- formyltetrahydrofolate to 5-phospho-ribosyl-glycinamide (GAR), producing 5-phospho-ribosyl-N-formylglycinamide (FGAR) and tetrahydrofolate
YYU_00435	COG0516	GMP reductase activity
YYU_00435	COG0517	IMP dehydrogenase activity
YYU_00440	COG0061	Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP
YYU_00450	COG4695	Portal protein
YYU_00455	COG0331	[acyl-carrier-protein] S-malonyltransferase activity
YYU_00460	COG0125	Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis
YYU_00480	COG1952	One of the proteins required for the normal export of preproteins out of the cell cytoplasm. It is a molecular chaperone that binds to a subset of precursor proteins, maintaining them in a translocation-competent state. It also specifically binds to its receptor SecA
YYU_00485	COG1651	Required for disulfide bond formation in some periplasmic proteins. Acts by transferring its disulfide bond to other proteins and is reduced in the process
YYU_00495	COG0612	Peptidase, M16
YYU_00510	COG0528	UMP kinase activity
YYU_00525	COG0307	riboflavin synthase, alpha
YYU_00565	COG0528	UMP kinase activity
YYU_00570	COG0233	cytoplasmic translational termination
YYU_00580	COG4589	Belongs to the CDS family
YYU_00605	COG0152	phosphoribosylaminoimidazolesuccinocarboxamide synthase activity
YYU_00610	COG0124	histidyl-tRNA synthetase
YYU_00620	COG1612	heme a metabolic process
YYU_00645	COG0717	Belongs to the dCTP deaminase family
YYU_00675	COG1278	Cold shock
YYU_00680	COG5000	phosphorelay sensor kinase activity
YYU_00685	COG0349	Exonuclease involved in the 3' processing of various precursor tRNAs. Initiates hydrolysis at the 3'-terminus of an RNA molecule and releases 5'-mononucleotides
YYU_00690	COG0272	DNA ligase that 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. It is essential for DNA replication and repair of damaged DNA
YYU_00730	COG0194	GDP metabolic process
YYU_00745	COG0360	Binds together with S18 to 16S ribosomal RNA
YYU_00750	COG0238	Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit
YYU_00755	COG0359	binds to the 23S rRNA
YYU_00760	COG0112	Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine, and other important biomolecules. Also exhibits THF- independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism
YYU_00770	COG1132	(ABC) transporter
YYU_00805	COG2814	Major facilitator Superfamily
YYU_00815	COG0752	glycyl-tRNA synthetase alpha subunit
YYU_00825	COG2255	four-way junction helicase activity
YYU_00830	COG0632	four-way junction helicase activity
YYU_00835	COG0755	Required for the export of heme to the periplasm for the biogenesis of c-type cytochromes
YYU_00840	COG0194	GDP metabolic process
YYU_00860	COG0190	Catalyzes the oxidation of 5,10- methylenetetrahydrofolate to 5,10-methenyltetrahydrofolate and then the hydrolysis of 5,10-methenyltetrahydrofolate to 10- formyltetrahydrofolate
YYU_00885	COG3474	cytochrome
YYU_00890	COG0651	ATP synthesis coupled electron transport
YYU_00895	COG1080	General (non sugar-specific) component of the phosphoenolpyruvate-dependent sugar phosphotransferase system (sugar PTS). This major carbohydrate active-transport system catalyzes the phosphorylation of incoming sugar substrates concomitantly with their translocation across the cell membrane. Enzyme I transfers the phosphoryl group from phosphoenolpyruvate (PEP) to the phosphoryl carrier protein (HPr)
YYU_00895	COG0574	Belongs to the PEP-utilizing enzyme family
YYU_00905	COG0546	phosphoglycolate phosphatase activity
YYU_00920	COG0173	Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Reaction proceeds in two steps L-aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp Asn)
YYU_00940	COG1589	Essential cell division protein. May link together the upstream cell division proteins, which are predominantly cytoplasmic, with the downstream cell division proteins, which are predominantly periplasmic. May control correct divisome assembly
YYU_00945	COG2204	response regulator
YYU_00960	COG0240	glycerol-3-phosphate dehydrogenase [NAD(P)+] activity
YYU_00965	COG4974	Belongs to the 'phage' integrase family
YYU_00975	COG0150	phosphoribosylformylglycinamidine cyclo-ligase activity
YYU_00990	COG0150	phosphoribosylformylglycinamidine cyclo-ligase activity
YYU_01015	COG0150	phosphoribosylformylglycinamidine cyclo-ligase activity
YYU_01025	COG0801	2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
YYU_01030	COG0046	Part of the phosphoribosylformylglycinamidine synthase complex involved in the purines biosynthetic pathway. Catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to yield formylglycinamidine ribonucleotide (FGAM) and glutamate. The FGAM synthase complex is composed of three subunits. PurQ produces an ammonia molecule by converting glutamine to glutamate. PurL transfers the ammonia molecule to FGAR to form FGAM in an ATP-dependent manner. PurS interacts with PurQ and PurL and is thought to assist in the transfer of the ammonia molecule from PurQ to PurL
YYU_01050	COG0502	Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical- based mechanism
YYU_01065	COG4942	peptidase
YYU_01070	COG1494	fructose-1,6-bisphosphatase
YYU_01075	COG0445	tRNA wobble uridine modification
YYU_01080	COG0047	phosphoribosylformylglycinamidine synthase activity
YYU_01080	COG0046	Part of the phosphoribosylformylglycinamidine synthase complex involved in the purines biosynthetic pathway. Catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to yield formylglycinamidine ribonucleotide (FGAM) and glutamate. The FGAM synthase complex is composed of three subunits. PurQ produces an ammonia molecule by converting glutamine to glutamate. PurL transfers the ammonia molecule to FGAR to form FGAM in an ATP-dependent manner. PurS interacts with PurQ and PurL and is thought to assist in the transfer of the ammonia molecule from PurQ to PurL
YYU_01115	COG0299	Catalyzes the transfer of a formyl group from 10- formyltetrahydrofolate to 5-phospho-ribosyl-glycinamide (GAR), producing 5-phospho-ribosyl-N-formylglycinamide (FGAR) and tetrahydrofolate
YYU_01125	COG3485	protocatechuate 3,4-dioxygenase
YYU_01140	COG0542	response to heat
YYU_01165	COG0234	Binds to Cpn60 in the presence of Mg-ATP and suppresses the ATPase activity of the latter
YYU_01170	COG2003	Belongs to the UPF0758 family
YYU_01175	COG0321	lipoyl(octanoyl) transferase activity
YYU_01180	COG0044	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides
YYU_01185	COG0452	Catalyzes two steps in the biosynthesis of coenzyme A. In the first step cysteine is conjugated to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine, in the latter compound is decarboxylated to form 4'-phosphopantotheine
YYU_01190	COG0114	fumarate hydratase activity
YYU_01210	COG0294	Catalyzes the condensation of para-aminobenzoate (pABA) with 6-hydroxymethyl-7,8-dihydropterin diphosphate (DHPt-PP) to form 7,8-dihydropteroate (H2Pte), the immediate precursor of folate derivatives
YYU_01230	COG1074	ATP-dependent DNA helicase activity
YYU_01275	COG0021	Catalyzes the transfer of a two-carbon ketol group from a ketose donor to an aldose acceptor, via a covalent intermediate with the cofactor thiamine pyrophosphate
YYU_01285	COG0776	regulation of translation
YYU_01290	COG0616	signal peptide processing
YYU_01295	COG0539	negative regulation of cytoplasmic translation
YYU_01300	COG0283	belongs to the cytidylate kinase family. Type 1 subfamily
YYU_01305	COG0566	Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase TrmH family
YYU_01320	COG0050	This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis
YYU_01325	COG0051	transcription antitermination factor activity, RNA binding
YYU_01330	COG0087	One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit
YYU_01335	COG0088	Forms part of the polypeptide exit tunnel
YYU_01340	COG0089	rRNA binding
YYU_01345	COG0090	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. It has been suggested to have peptidyltransferase activity
YYU_01350	COG0185	Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA
YYU_01355	COG0091	The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome
YYU_01360	COG0092	Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation
YYU_01365	COG0197	Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs
YYU_01370	COG0255	Belongs to the universal ribosomal protein uL29 family
YYU_01375	COG0186	One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA
YYU_01380	COG0093	Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome
YYU_01385	COG0198	One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit
YYU_01390	COG0094	This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits
YYU_01395	COG0199	Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site
YYU_01400	COG0096	One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit
YYU_01405	COG0097	This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7 L12 stalk, and near the tRNA binding site of the peptidyltransferase center
YYU_01410	COG0256	This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance
YYU_01415	COG0098	Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body
YYU_01425	COG0201	protein transport
YYU_01435	COG0099	Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits
YYU_01440	COG0100	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
YYU_01445	COG0202	RNA polymerase activity
YYU_01450	COG0203	ribosomal protein L17
YYU_01460	COG2333	competence protein COMEC
YYU_01460	COG0658	competence protein
YYU_01475	COG0230	Belongs to the bacterial ribosomal protein bL34 family
YYU_01485	COG1853	conserved protein domain typically associated with flavoprotein oxygenases, DIM6 NTAB family
YYU_01500	COG0343	queuine tRNA-ribosyltransferase activity
YYU_01505	COG0333	Belongs to the bacterial ribosomal protein bL32 family
YYU_01510	COG0416	fatty acid biosynthetic process
YYU_01530	COG0590	tRNA wobble adenosine to inosine editing
YYU_01565	COG0142	geranyltranstransferase activity
YYU_01575	COG0209	Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides
YYU_01580	COG0816	Could be a nuclease involved in processing of the 5'-end of pre-16S rRNA
YYU_01600	COG1198	Involved in the restart of stalled replication forks. Recognizes and binds the arrested nascent DNA chain at stalled replication forks. It can open the DNA duplex, via its helicase activity, and promote assembly of the primosome and loading of the major replicative helicase DnaB onto DNA
YYU_01635	COG2111	Na H antiporter
YYU_01645	COG1530	ribonuclease E activity
YYU_01660	COG1007	ATP synthesis coupled electron transport
YYU_01665	COG0541	Involved in targeting and insertion of nascent membrane proteins into the cytoplasmic membrane. Binds to the hydrophobic signal sequence of the ribosome-nascent chain (RNC) as it emerges from the ribosomes. The SRP-RNC complex is then targeted to the cytoplasmic membrane where it interacts with the SRP receptor FtsY
YYU_01670	COG1159	An essential GTPase that binds both GDP and GTP, with rapid nucleotide exchange. Plays a role in 16S rRNA processing and 30S ribosomal subunit biogenesis and possibly also in cell cycle regulation and energy metabolism
YYU_01690	COG3577	Aspartyl protease
YYU_01720	COG0227	Belongs to the bacterial ribosomal protein bL28 family
YYU_01735	COG0564	pseudouridine synthase activity
YYU_01745	COG0439	Biotin carboxylase
YYU_01760	COG0320	Catalyzes the radical-mediated insertion of two sulfur atoms into the C-6 and C-8 positions of the octanoyl moiety bound to the lipoyl domains of lipoate-dependent enzymes, thereby converting the octanoylated domains into lipoylated derivatives
YYU_01780	COG0581	inorganic phosphate transmembrane transporter activity
YYU_01795	COG3451	type IV secretory pathway VirB4
YYU_01805	COG3704	protein secretion by the type IV secretion system
YYU_01810	COG3704	protein secretion by the type IV secretion system
YYU_01815	COG3704	protein secretion by the type IV secretion system
YYU_01815	COG1340	protein secretion by the type IV secretion system
YYU_01825	COG0756	dUTP diphosphatase activity
YYU_01840	COG0505	Belongs to the CarA family
YYU_01880	COG0696	Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate
YYU_01885	COG1160	GTP binding
YYU_01900	COG1249	Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family
YYU_01910	COG0361	One of the essential components for the initiation of protein synthesis. Stabilizes the binding of IF-2 and IF-3 on the 30S subunit to which N-formylmethionyl-tRNA(fMet) subsequently binds. Helps modulate mRNA selection, yielding the 30S pre- initiation complex (PIC). Upon addition of the 50S ribosomal subunit IF-1, IF-2 and IF-3 are released leaving the mature 70S translation initation complex
YYU_01915	COG0424	maF-like protein
YYU_01920	COG0052	Belongs to the universal ribosomal protein uS2 family
YYU_01925	COG0264	Associates with the EF-Tu.GDP complex and induces the exchange of GDP to GTP. It remains bound to the aminoacyl-tRNA.EF- Tu.GTP complex up to the GTP hydrolysis stage on the ribosome
YYU_01940	COG1108	ABC-type Mn2 Zn2 transport systems permease components
YYU_01950	COG0723	plastoquinol--plastocyanin reductase activity
YYU_01955	COG1290	Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex), which is a respiratory chain that generates an electrochemical potential coupled to ATP synthesis
YYU_01995	COG0008	Catalyzes the attachment of glutamate to tRNA(Glu) in a two-step reaction glutamate is first activated by ATP to form Glu-AMP and then transferred to the acceptor end of tRNA(Glu)
YYU_02010	COG0445	tRNA wobble uridine modification
YYU_02025	COG4799	Acetyl-CoA carboxylase, carboxyltransferase component subunits alpha and beta
YYU_02040	COG0216	Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA
YYU_02050	COG0218	Necessary for normal cell division and for the maintenance of normal septation
YYU_02075	COG0172	Catalyzes the attachment of serine to tRNA(Ser). Is also able to aminoacylate tRNA(Sec) with serine, to form the misacylated tRNA L-seryl-tRNA(Sec), which will be further converted into selenocysteinyl-tRNA(Sec)
YYU_02090	COG0324	Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read codons beginning with uridine, leading to the formation of N6-(dimethylallyl)adenosine (i(6)A)
YYU_02105	COG1894	NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain
YYU_02125	COG0713	ATP synthesis coupled electron transport
YYU_02130	COG1009	NADH ubiquinone oxidoreductase subunit 5 chain L Multisubunit Na H antiporter, MnhA subunit
YYU_02140	COG1007	ATP synthesis coupled electron transport
YYU_02145	COG0743	1-deoxy-D-xylulose-5-phosphate reductoisomerase activity
YYU_02160	COG0805	protein transport
YYU_02170	COG0272	DNA ligase that 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. It is essential for DNA replication and repair of damaged DNA
YYU_02170	COG0195	Participates in both transcription termination and antitermination
YYU_02175	COG0532	One of the essential components for the initiation of protein synthesis. Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex
YYU_02185	COG0480	Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post- translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome
YYU_02190	COG1253	flavin adenine dinucleotide binding
YYU_02260	COG0064	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. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln)
YYU_02270	COG1186	Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA
YYU_02285	COG0629	single-stranded DNA binding
YYU_02290	COG1186	Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA
YYU_02300	COG0064	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. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln)
YYU_02315	COG0623	enoyl-[acyl-carrier-protein] reductase (NADH) activity
YYU_02345	COG0064	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. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln)
YYU_02355	COG1186	Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA
YYU_02360	COG0217	transcriptional regulatory protein
YYU_02370	COG0502	Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical- based mechanism
YYU_02370	COG0161	adenosylmethionine-8-amino-7-oxononanoate transaminase activity
YYU_02405	COG0480	Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post- translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome
YYU_02410	COG0176	Transaldolase is important for the balance of metabolites in the pentose-phosphate pathway
YYU_02420	COG0055	Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits
YYU_02440	COG0293	Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit
YYU_02450	COG0101	tRNA pseudouridine synthase activity
YYU_02455	COG0540	Belongs to the ATCase OTCase family
YYU_02460	COG0293	Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit
YYU_02475	COG0257	Belongs to the bacterial ribosomal protein bL36 family
YYU_02485	COG0852	NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient
YYU_02495	COG1758	RNA polymerase activity
YYU_02510	COG0838	NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient
YYU_02515	COG0377	NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient
YYU_02520	COG0852	NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient
YYU_02530	COG0496	Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates
YYU_02540	COG2332	Heme chaperone required for the biogenesis of c-type cytochromes. Transiently binds heme delivered by CcmC and transfers the heme to apo-cytochromes in a process facilitated by CcmF and CcmH
YYU_02550	COG0084	hydrolase, TatD family'
YYU_02605	COG0054	6,7-dimethyl-8-ribityllumazine synthase activity
YYU_02610	COG0706	membrane insertase activity
YYU_02615	COG0706	membrane insertase activity
YYU_02620	COG1034	ATP synthesis coupled electron transport
YYU_02625	COG1183	phosphatidylcholine synthase activity
YYU_02630	COG0688	phosphatidylethanolamine metabolic process
YYU_02635	COG0543	2 iron, 2 sulfur cluster binding
YYU_02635	COG0493	'glutamate synthase
YYU_02645	COG0231	Involved in peptide bond synthesis. Stimulates efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase
YYU_02650	COG0483	inositol monophosphate 1-phosphatase activity
YYU_02655	COG0564	pseudouridine synthase activity
YYU_02660	COG3706	GGDEF domain
YYU_02660	COG0745	RESPONSE REGULATOR receiver
YYU_02680	COG3932	Exopolysaccharide synthesis, ExoD
YYU_02685	COG0215	cysteine-tRNA ligase activity
YYU_02695	COG0208	Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides
YYU_02705	COG0018	arginyl-trna synthetase
YYU_02740	COG0358	DNA primase activity
YYU_02745	COG0249	that it carries out the mismatch recognition step. This protein has a weak ATPase activity
YYU_02755	COG1947	Catalyzes the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol
YYU_02760	COG0042	Catalyzes the synthesis of 5,6-dihydrouridine (D), a modified base found in the D-loop of most tRNAs, via the reduction of the C5-C6 double bond in target uridines
YYU_02765	COG0568	sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released
YYU_02785	COG1324	tolerance protein
YYU_02810	COG0422	Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction
YYU_02815	COG0063	ADP-dependent NAD(P)H-hydrate dehydratase activity
YYU_02815	COG0062	Bifunctional enzyme that catalyzes the epimerization of the S- and R-forms of NAD(P)HX and the dehydration of the S-form of NAD(P)HX at the expense of ADP, which is converted to AMP. This allows the repair of both epimers of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or heat-dependent hydration
YYU_02845	COG0550	Releases the supercoiling and torsional tension of DNA, which is introduced during the DNA replication and transcription, by transiently cleaving and rejoining one strand of the DNA duplex. Introduces a single-strand break via transesterification at a target site in duplex DNA. The scissile phosphodiester is attacked by the catalytic tyrosine of the enzyme, resulting in the formation of a DNA-(5'-phosphotyrosyl)-enzyme intermediate and the expulsion of a 3'-OH DNA strand. The free DNA strand then undergoes passage around the unbroken strand, thus removing DNA supercoils. Finally, in the religation step, the DNA 3'-OH attacks the covalent intermediate to expel the active-site tyrosine and restore the DNA phosphodiester backbone
YYU_02850	COG0422	Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction
YYU_02880	COG2227	3-demethylubiquinone-9 3-O-methyltransferase activity
YYU_02885	COG1384	Belongs to the class-I aminoacyl-tRNA synthetase family
YYU_02905	COG1214	PFAM Peptidase M22, glycoprotease
YYU_02955	COG0030	16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity
YYU_02965	COG0149	triose-phosphate isomerase activity
YYU_02975	COG0533	Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaE and TsaB. TsaD likely plays a direct catalytic role in this reaction
YYU_02990	COG0039	L-malate dehydrogenase activity
YYU_03055	COG0698	ribose 5-phosphate isomerase
YYU_03070	COG0736	holo-[acyl-carrier-protein] synthase activity
YYU_03075	COG0442	prolyl-tRNA aminoacylation
YYU_03090	COG0669	Reversibly transfers an adenylyl group from ATP to 4'- phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate
YYU_03095	COG0669	Reversibly transfers an adenylyl group from ATP to 4'- phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate
YYU_03130	COG0492	ferredoxin-NADP+ reductase activity
YYU_03135	COG0450	alkyl hydroperoxide reductase
YYU_03175	COG4230	.,Oxidizes proline to glutamate for use as a carbon and nitrogen source
YYU_03175	COG0506	proline dehydrogenase activity
YYU_03175	COG3905	.,Oxidizes proline to glutamate for use as a carbon and nitrogen source
YYU_03185	COG2945	thiolester hydrolase activity
YYU_03195	COG1104	cysteine desulfurase activity
YYU_03200	COG0822	iron-sulfur transferase activity
YYU_03205	COG0316	Belongs to the HesB IscA family
YYU_03215	COG0443	Heat shock 70 kDa protein
YYU_03270	COG0302	gtp cyclohydrolase
YYU_03275	COG0275	rRNA processing
YYU_03295	COG0536	An essential GTPase which binds GTP, GDP and possibly (p)ppGpp with moderate affinity, with high nucleotide exchange rates and a fairly low GTP hydrolysis rate. Plays a role in control of the cell cycle, stress response, ribosome biogenesis and in those bacteria that undergo differentiation, in morphogenesis control
YYU_03300	COG0148	phosphopyruvate hydratase activity
YYU_03310	COG0261	This protein binds to 23S rRNA in the presence of protein L20
YYU_03315	COG0211	Belongs to the bacterial ribosomal protein bL27 family
YYU_03325	COG0018	arginyl-trna synthetase
YYU_03335	COG0312	modulator of DNA gyrase
YYU_03340	COG0302	gtp cyclohydrolase
YYU_03345	COG0224	Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is believed to be important in regulating ATPase activity and the flow of protons through the CF(0) complex
YYU_03360	COG1005	NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. This subunit may bind ubiquinone
YYU_03365	COG1034	ATP synthesis coupled electron transport
YYU_03380	COG0187	DNA topoisomerase II activity
YYU_03440	COG0847	DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. The epsilon subunit contain the editing function and is a proofreading 3'-5' exonuclease
YYU_03445	COG1905	PFAM NADH dehydrogenase (ubiquinone) 24 kDa subunit
YYU_03450	COG0649	NAD binding
YYU_03455	COG0492	ferredoxin-NADP+ reductase activity
YYU_03460	COG0611	Catalyzes the ATP-dependent phosphorylation of thiamine- monophosphate (TMP) to form thiamine-pyrophosphate (TPP), the active form of vitamin B1
YYU_03465	COG1381	Involved in DNA repair and RecF pathway recombination
YYU_03505	COG0812	UDP-N-acetylmuramate dehydrogenase activity
YYU_03510	COG0181	hydroxymethylbilane synthase activity
YYU_03515	COG0285	dihydrofolate synthase activity
YYU_03520	COG0154	amidase activity
YYU_03555	COG0606	chelatase, subunit chli
YYU_03570	COG0568	sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released
YYU_03590	COG0481	GTPase activity
YYU_03600	COG1185	polyribonucleotide nucleotidyltransferase activity
YYU_03605	COG0184	Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome
YYU_03610	COG0130	Responsible for synthesis of pseudouridine from uracil- 55 in the psi GC loop of transfer RNAs
YYU_03660	COG0009	L-threonylcarbamoyladenylate synthase
YYU_03665	COG0470	DNA polymerase III
YYU_03685	COG0854	Catalyzes the complicated ring closure reaction between the two acyclic compounds 1-deoxy-D-xylulose-5-phosphate (DXP) and 3-amino-2-oxopropyl phosphate (1-amino-acetone-3-phosphate or AAP) to form pyridoxine 5'-phosphate (PNP) and inorganic phosphate
YYU_03690	COG1057	Catalyzes the reversible adenylation of nicotinate mononucleotide (NaMN) to nicotinic acid adenine dinucleotide (NaAD)
YYU_03705	COG1385	rRNA (uridine-N3-)-methyltransferase activity
YYU_03710	COG1225	Alkyl hydroperoxide reductase Thiol specific antioxidant Mal allergen
YYU_03730	COG1143	NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient
YYU_03735	COG0681	Belongs to the peptidase S26 family
YYU_03740	COG0316	Belongs to the HesB IscA family
YYU_03785	COG0302	gtp cyclohydrolase
YYU_03935	COG0113	porphobilinogen synthase activity
YYU_03940	COG0388	Catalyzes the ATP-dependent amidation of deamido-NAD to form NAD. Uses L-glutamine as a nitrogen source
YYU_03940	COG0171	NAD+ synthase (glutamine-hydrolyzing) activity
YYU_03955	COG0249	that it carries out the mismatch recognition step. This protein has a weak ATPase activity
YYU_03980	COG0567	Dehydrogenase, E1 component
YYU_03990	COG0015	Belongs to the lyase 1 family. Adenylosuccinate lyase subfamily
YYU_04020	COG0340	biotin-[acetyl-CoA-carboxylase] ligase activity
YYU_04020	COG1654	Acts both as a biotin-- acetyl-CoA-carboxylase ligase and a biotin-operon repressor. In the presence of ATP, BirA activates biotin to form the BirA-biotinyl-5'-adenylate (BirA-bio- 5'-AMP or holoBirA) complex. HoloBirA can either transfer the biotinyl moiety to the biotin carboxyl carrier protein (BCCP) subunit of acetyl-CoA carboxylase, or bind to the biotin operator site and inhibit transcription of the operon
YYU_04040	COG0621	Catalyzes the methylthiolation of N6- (dimethylallyl)adenosine (i(6)A), leading to the formation of 2- methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine
YYU_04065	COG0322	excinuclease ABC activity
YYU_04075	COG0468	Can catalyze 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. It interacts with LexA causing its activation and leading to its autocatalytic cleavage
YYU_04080	COG0326	Molecular chaperone. Has ATPase activity
YYU_04100	COG0177	DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity. The DNA N-glycosylase activity releases various damaged pyrimidines from DNA by cleaving the N- glycosidic bond, leaving an AP (apurinic apyrimidinic) site. The AP-lyase activity cleaves the phosphodiester bond 3' to the AP site by a beta-elimination, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
YYU_04120	COG0210	DNA helicase
YYU_04145	COG0482	sulfurtransferase activity
YYU_04225	COG1495	Required for disulfide bond formation in some periplasmic proteins. Acts by oxidizing the DsbA protein
YYU_04235	COG0267	Belongs to the bacterial ribosomal protein bL33 family
YYU_04255	COG0236	Carrier of the growing fatty acid chain in fatty acid biosynthesis
YYU_04260	COG0304	beta-ketoacyl-acyl-carrier-protein synthase II activity
YYU_04275	COG0758	DNA mediated transformation
YYU_04305	COG0323	This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. May act as a molecular matchmaker , a protein that 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
YYU_04325	COG2205	protein histidine kinase activity
YYU_04325	COG2202	Pas domain
YYU_04330	COG4992	N2-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity
YYU_04370	COG1674	ftsk spoiiie
YYU_04370	COG1674	ftsk spoiiie
YYU_04380	COG4536	flavin adenine dinucleotide binding
YYU_04385	COG0352	thiamine-phosphate diphosphorylase activity
YYU_04390	COG1806	Bifunctional serine threonine kinase and phosphorylase involved in the regulation of the
YYU_04410	COG0223	Attaches a formyl group to the free amino group of methionyl-tRNA(fMet). The formyl group appears to play a dual role in the initiator identity of N-formylmethionyl-tRNA by promoting its recognition by IF2 and preventing the misappropriation of this tRNA by the elongation apparatus
YYU_04425	COG0466	ATP-dependent serine protease that mediates the selective degradation of mutant and abnormal proteins as well as certain short-lived regulatory proteins. Required for cellular homeostasis and for survival from DNA damage and developmental changes induced by stress. Degrades polypeptides processively to yield small peptide fragments that are 5 to 10 amino acids long. Binds to DNA in a double-stranded, site-specific manner
YYU_04430	COG1219	ATP-dependent specificity component of the Clp protease. It directs the protease to specific substrates. Can perform chaperone functions in the absence of ClpP
YYU_04435	COG0740	serine-type endopeptidase activity
YYU_04475	COG0156	8-amino-7-oxononanoate synthase activity
YYU_04500	COG1121	(ABC) transporter
YYU_04505	COG0661	Is probably a protein kinase regulator of UbiI activity which is involved in aerobic coenzyme Q (ubiquinone) biosynthesis
YYU_04515	COG3842	ATPase activity
YYU_04520	COG1826	Part of the twin-arginine translocation (Tat) system that transports large folded proteins containing a characteristic twin-arginine motif in their signal peptide across membranes
YYU_04525	COG0353	May play a role in DNA repair. It seems to be involved in an RecBC-independent recombinational process of DNA repair. It may act with RecF and RecO
YYU_04530	COG0522	One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit
YYU_04540	COG0696	Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate
YYU_04550	COG0351	phosphomethylpyrimidine kinase
YYU_04550	COG0352	thiamine-phosphate diphosphorylase activity
YYU_04560	COG0628	permease
YYU_04575	COG2142	Succinate dehydrogenase hydrophobic membrane anchor
YYU_04580	COG2009	succinate dehydrogenase
YYU_04590	COG0128	3-phosphoshikimate 1-carboxyvinyltransferase activity
YYU_04595	COG0587	DNA-directed DNA polymerase activity
YYU_04625	COG0259	pyridoxamine-phosphate oxidase activity
YYU_04635	COG0400	carboxylic ester hydrolase activity
YYU_04640	COG0242	peptide deformylase activity
YYU_04645	COG0167	dihydroorotate dehydrogenase activity
YYU_04650	COG1521	Catalyzes the phosphorylation of pantothenate (Pan), the first step in CoA biosynthesis
YYU_04660	COG0156	8-amino-7-oxononanoate synthase activity
YYU_04690	COG0164	Endonuclease that specifically degrades the RNA of RNA- DNA hybrids
YYU_04695	COG0086	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates
YYU_04700	COG0085	RNA polymerase activity
YYU_04705	COG0222	ribosome binding
YYU_04710	COG0244	Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors
YYU_04715	COG0081	regulation of translation
YYU_04720	COG0080	Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors
YYU_04725	COG0250	Participates in transcription elongation, termination and antitermination
YYU_04740	COG0050	This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis
YYU_04745	COG0480	Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post- translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome
YYU_04750	COG0049	tRNA binding
YYU_04755	COG0048	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 and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit
YYU_04800	COG1178	ABC-type Fe3 transport system permease component
YYU_04810	COG1999	signal sequence binding
YYU_04820	COG0828	Belongs to the bacterial ribosomal protein bS21 family
YYU_04825	COG0045	succinate-CoA ligase (ADP-forming) activity
YYU_04830	COG0074	Succinyl-CoA synthetase functions in the citric acid cycle (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of either ATP or GTP and thus represents the only step of substrate-level phosphorylation in the TCA. The alpha subunit of the enzyme binds the substrates coenzyme A and phosphate, while succinate binding and nucleotide specificity is provided by the beta subunit
YYU_04855	COG0533	Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaE and TsaB. TsaD likely plays a direct catalytic role in this reaction
YYU_04860	COG0013	Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction alanine is first activated by ATP to form Ala- AMP and then transferred to the acceptor end of tRNA(Ala). Also edits incorrectly charged Ser-tRNA(Ala) and Gly-tRNA(Ala) via its editing domain
YYU_04865	COG0573	inorganic phosphate transmembrane transporter activity
YYU_04910	COG1249	Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family
YYU_04915	COG1158	Facilitates transcription termination by a mechanism that involves Rho binding to the nascent RNA, activation of Rho's RNA-dependent ATPase activity, and release of the mRNA from the DNA template
YYU_04920	COG5405	Protease subunit of a proteasome-like degradation complex believed to be a general protein degrading machinery
YYU_04925	COG1220	this subunit has chaperone activity. The binding of ATP and its subsequent hydrolysis by HslU are essential for unfolding of protein substrates subsequently hydrolyzed by HslV. HslU recognizes the N-terminal part of its protein substrates and unfolds these before they are guided to HslV for hydrolysis
YYU_04930	COG2226	methyltransferase
YYU_04955	COG0143	Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation
YYU_04985	COG0843	Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Subunits 1- 3 form the functional core of the enzyme complex. CO I is the catalytic subunit of the enzyme. Electrons originating in cytochrome c are transferred via the copper A center of subunit 2 and heme A of subunit 1 to the bimetallic center formed by heme A3 and copper B
YYU_04990	COG0109	protoheme IX farnesyltransferase activity
YYU_04995	COG4105	Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane
YYU_05005	COG1862	Preprotein translocase
YYU_05030	COG0533	Required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. Is involved in the transfer of the threonylcarbamoyl moiety of threonylcarbamoyl-AMP (TC-AMP) to the N6 group of A37, together with TsaE and TsaB. TsaD likely plays a direct catalytic role in this reaction
YYU_05035	COG0013	Catalyzes the attachment of alanine to tRNA(Ala) in a two-step reaction alanine is first activated by ATP to form Ala- AMP and then transferred to the acceptor end of tRNA(Ala). Also edits incorrectly charged Ser-tRNA(Ala) and Gly-tRNA(Ala) via its editing domain
YYU_05040	COG0592	DNA-directed DNA polymerase activity
YYU_05050	COG0745	RESPONSE REGULATOR receiver
YYU_05060	COG0221	Catalyzes the hydrolysis of inorganic pyrophosphate (PPi) forming two phosphate ions
YYU_05090	COG0103	maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
YYU_05095	COG0102	This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly
YYU_05110	COG0489	protein tyrosine kinase activity
YYU_05120	COG0721	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. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln)
YYU_05155	COG0026	Catalyzes the ATP-dependent conversion of 5- aminoimidazole ribonucleotide (AIR) and HCO(3)(-) to N5- carboxyaminoimidazole ribonucleotide (N5-CAIR)
YYU_05160	COG2967	ApaG domain
YYU_05285	COG0330	HflC and HflK could
YYU_05290	COG0330	HflC and HflK could
YYU_05295	COG0265	Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain
YYU_05300	COG0571	ribonuclease III activity
YYU_05305	COG3175	Exerts its effect at some terminal stage of cytochrome c oxidase synthesis, probably by being involved in the insertion of the copper B into subunit I
YYU_05350	COG0612	Peptidase, M16
YYU_05355	COG0597	This protein specifically catalyzes the removal of signal peptides from prolipoproteins
YYU_05360	COG0196	riboflavin kinase activity
YYU_05365	COG0695	Has a glutathione-disulfide oxidoreductase activity in the presence of NADPH and glutathione reductase. Reduces low molecular weight disulfides and proteins
YYU_05380	COG4199	Single-strand DNA-specific exonuclease, C terminal domain
YYU_05380	COG0608	single-stranded DNA 5'-3' exodeoxyribonuclease activity
YYU_05385	COG0473	3-isopropylmalate dehydrogenase activity
YYU_05410	COG3346	SURF1 family
YYU_05415	COG0461	Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP)
YYU_05420	COG0476	Involved in molybdopterin and thiamine biosynthesis, family 2
YYU_05425	COG0695	Has a glutathione-disulfide oxidoreductase activity in the presence of NADPH and glutathione reductase. Reduces low molecular weight disulfides and proteins
YYU_05440	COG0653	protein targeting
YYU_05445	COG0465	Acts as a processive, ATP-dependent zinc metallopeptidase for both cytoplasmic and membrane proteins. Plays a role in the quality control of integral membrane proteins
YYU_05460	COG0168	Low-affinity potassium transport system. Interacts with trk system potassium uptake protein TrkA
YYU_05495	COG0636	F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation
YYU_05500	COG0356	it plays a direct role in the translocation of protons across the membrane
YYU_05530	COG0508	dehydrogenase complex catalyzes the overall conversion of
YYU_05535	COG0024	Methionine aminopeptidase
YYU_05540	COG2890	protein-(glutamine-N5) methyltransferase activity
YYU_05555	COG1138	Cytochrome C-type biogenesis protein
YYU_05560	COG0843	Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Subunits 1- 3 form the functional core of the enzyme complex. CO I is the catalytic subunit of the enzyme. Electrons originating in cytochrome c are transferred via the copper A center of subunit 2 and heme A of subunit 1 to the bimetallic center formed by heme A3 and copper B
YYU_05565	COG0558	Belongs to the CDP-alcohol phosphatidyltransferase class-I family
YYU_05570	COG0138	bifunctional purine biosynthesis protein purh
YYU_05575	COG0764	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity
YYU_05585	COG4775	Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane
YYU_05590	COG0750	zinc metalloprotease
YYU_05605	COG1686	Belongs to the peptidase S11 family
YYU_05615	COG0617	tRNA 3'-terminal CCA addition
YYU_05620	COG0105	UTP biosynthetic process
YYU_05625	COG1396	sequence-specific DNA binding
YYU_05645	COG0468	Can catalyze 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. It interacts with LexA causing its activation and leading to its autocatalytic cleavage
YYU_05665	COG0552	protein localization to endoplasmic reticulum
YYU_05670	COG0132	Catalyzes a mechanistically unusual reaction, the ATP- dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA) to form an ureido ring
YYU_05690	COG0372	Belongs to the citrate synthase family
YYU_05695	COG0519	Catalyzes the synthesis of GMP from XMP
YYU_05740	COG0156	8-amino-7-oxononanoate synthase activity
YYU_05745	COG0162	Catalyzes the attachment of tyrosine to tRNA(Tyr) in a two-step reaction tyrosine is first activated by ATP to form Tyr- AMP and then transferred to the acceptor end of tRNA(Tyr)
YYU_05755	COG0174	glutamine synthetase
YYU_05760	COG0142	geranyltranstransferase activity
YYU_05810	COG0508	dehydrogenase complex catalyzes the overall conversion of
YYU_05815	COG1830	Aldolase
YYU_05840	COG0290	IF-3 binds to the 30S ribosomal subunit and shifts the equilibrum between 70S ribosomes and their 50S and 30S subunits in favor of the free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins
YYU_05850	COG1546	Belongs to the CinA family
YYU_05850	COG1058	Belongs to the CinA family
YYU_05860	COG0336	Belongs to the RNA methyltransferase TrmD family
YYU_05865	COG0806	An accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region. Probably interacts with S19. Essential for efficient processing of 16S rRNA. May be needed both before and after RbfA during the maturation of 16S rRNA. It has affinity for free ribosomal 30S subunits but not for 70S ribosomes
YYU_05880	COG1138	Cytochrome C-type biogenesis protein
YYU_05900	COG0245	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity
YYU_05905	COG1211	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity
YYU_05905	COG0245	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity
YYU_05915	COG0041	Catalyzes the conversion of N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) to 4-carboxy-5-aminoimidazole ribonucleotide (CAIR)
YYU_05925	COG0776	regulation of translation
YYU_05945	COG0012	GTP binding
YYU_05960	COG0486	Exhibits a very high intrinsic GTPase hydrolysis rate. Involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA- cmnm(5)s(2)U34
YYU_05965	COG0319	Single strand-specific metallo-endoribonuclease involved in late-stage 70S ribosome quality control and in maturation of the 3' terminus of the 16S rRNA
YYU_05985	COG0817	Nuclease that resolves Holliday junction intermediates in genetic recombination. Cleaves the cruciform structure in supercoiled DNA by nicking to strands with the same polarity at sites symmetrically opposed at the junction in the homologous arms and leaves a 5'-terminal phosphate and a 3'-terminal hydroxyl group
YYU_05995	COG0452	Catalyzes two steps in the biosynthesis of coenzyme A. In the first step cysteine is conjugated to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine, in the latter compound is decarboxylated to form 4'-phosphopantotheine
YYU_06000	COG1200	Critical role in recombination and DNA repair. Helps process Holliday junction intermediates to mature products by catalyzing branch migration. Has a DNA unwinding activity characteristic of a DNA helicase with a 3'- to 5'- polarity. Unwinds branched duplex DNA (Y-DNA)
YYU_06005	COG0451	ADP-glyceromanno-heptose 6-epimerase activity
YYU_06010	COG0034	Catalyzes the formation of phosphoribosylamine from phosphoribosylpyrophosphate (PRPP) and glutamine
YYU_06015	COG0193	aminoacyl-tRNA hydrolase activity
YYU_06020	COG1825	This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance
YYU_06025	COG1040	competence protein
YYU_06045	COG0022	dehydrogenase e1 component
YYU_06060	COG0312	modulator of DNA gyrase
YYU_06090	COG0500	methyltransferase
YYU_06115	COG1570	exodeoxyribonuclease VII activity
YYU_06165	COG0691	Required for rescue of stalled ribosomes mediated by trans-translation. Binds to transfer-messenger RNA (tmRNA), required for stable association of tmRNA with ribosomes. tmRNA and SmpB together mimic tRNA shape, replacing the anticodon stem-loop with SmpB. tmRNA is encoded by the ssrA gene
YYU_06170	COG0807	Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate
YYU_06170	COG0108	Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate
YYU_06175	COG0782	Necessary for efficient RNA polymerase transcription elongation past template-encoded arresting sites. The 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
YYU_06180	COG0056	Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit
YYU_06185	COG0712	F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation
YYU_06210	COG4591	ABC-type transport system involved in lipoprotein release permease component
YYU_06225	COG0802	atpase or kinase
YYU_06230	COG0670	Belongs to the BI1 family
YYU_06235	COG0136	Catalyzes the NADPH-dependent formation of L-aspartate- semialdehyde (L-ASA) by the reductive dephosphorylation of L- aspartyl-4-phosphate
YYU_06245	COG2812	DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity
YYU_06250	COG0057	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
YYU_06270	COG0468	Can catalyze 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. It interacts with LexA causing its activation and leading to its autocatalytic cleavage
YYU_06295	COG0043	3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity
YYU_06320	COG0342	Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. SecDF uses the proton motive force (PMF) to complete protein translocation after the ATP-dependent function of SecA
YYU_06325	COG0556	nucleotide-excision repair
YYU_06350	COG0242	peptide deformylase activity
YYU_06355	COG0204	Acyl-transferase
YYU_06360	COG0268	Binds directly to 16S ribosomal RNA
YYU_06365	COG0242	peptide deformylase activity
YYU_06375	COG0682	Transfers the N-acyl diglyceride group on what will become the N-terminal cysteine of membrane lipoproteins
YYU_06380	COG0728	peptidoglycan biosynthetic process
YYU_06465	COG1230	cation diffusion facilitator family transporter
YYU_06480	COG1734	Transcription factor that acts by binding directly to the RNA polymerase (RNAP). Required for negative regulation of rRNA expression and positive regulation of several amino acid biosynthesis promoters
YYU_06500	COG3505	Type IV secretory pathway VirD4
YYU_06505	COG0630	type IV secretory pathway, VirB11 components, and related ATPases involved in Archaeal flagella biosynthesis
YYU_06510	COG2948	multi-organism process
YYU_06535	COG1195	it is required for DNA replication and normal SOS inducibility. RecF binds preferentially to single-stranded, linear DNA. It also seems to bind ATP