locus-tag	class	description
trd_0002	COG0470	DNA polymerase III
trd_0006	COG1171	Catalyzes the anaerobic formation of alpha-ketobutyrate and ammonia from threonine in a two-step reaction. The first step involved a dehydration of threonine and a production of enamine intermediates (aminocrotonate), which tautomerizes to its imine form (iminobutyrate). Both intermediates are unstable and short- lived. The second step is the nonenzymatic hydrolysis of the enamine imine intermediates to form 2-ketobutyrate and free ammonia. In the low water environment of the cell, the second step is accelerated by RidA
trd_0010	COG0284	orotidine-5'-phosphate decarboxylase activity
trd_0011	COG0693	protein deglycase activity
trd_0013	COG1131	(ABC) transporter
trd_0014	COG0566	Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase TrmH family
trd_0020	COG1203	CRISPR-associated helicase, Cas3
trd_0022	COG1518	maintenance of DNA repeat elements
trd_0023	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
trd_0024	COG1343	CRISPR (clustered regularly interspaced short palindromic repeat), is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA). Functions as a ssRNA-specific endoribonuclease. Involved in the integration of spacer DNA into the CRISPR cassette
trd_0025	COG0311	Catalyzes the hydrolysis of glutamine to glutamate and ammonia as part of the biosynthesis of pyridoxal 5'-phosphate. The resulting ammonia molecule is channeled to the active site of PdxS
trd_0026	COG0214	Catalyzes the formation of pyridoxal 5'-phosphate from ribose 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia. The ammonia is provided by the PdxT subunit. Can also use ribulose 5-phosphate and dihydroxyacetone phosphate as substrates, resulting from enzyme-catalyzed isomerization of RBP and G3P, respectively
trd_0027	COG1167	Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain MocR family and their eukaryotic orthologs
trd_0032	COG0462	Involved in the biosynthesis of the central metabolite phospho-alpha-D-ribosyl-1-pyrophosphate (PRPP) via the transfer of pyrophosphoryl group from ATP to 1-hydroxyl of ribose-5-phosphate (Rib-5-P)
trd_0033	COG4535	Mg2 and Co2 transporter CorC
trd_0039	COG1960	acyl-CoA dehydrogenase activity
trd_0040	COG0663	COG0663 Carbonic anhydrases acetyltransferases, isoleucine patch superfamily
trd_0041	COG1024	Enoyl-CoA hydratase
trd_0042	COG2086	electron transfer activity
trd_0043	COG2025	fatty acid beta-oxidation using acyl-CoA dehydrogenase
trd_0044	COG0644	oxidoreductase
trd_0047	COG0456	acetyltransferase
trd_0048	COG5001	Diguanylate cyclase
trd_0049	COG0617	tRNA 3'-terminal CCA addition
trd_0055	COG2001	Belongs to the MraZ family
trd_0056	COG0275	rRNA processing
trd_0058	COG0768	penicillin binding
trd_0059	COG0770	UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase activity
trd_0060	COG0472	First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
trd_0061	COG0771	Cell wall formation. Catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA)
trd_0062	COG0772	Belongs to the SEDS family
trd_0063	COG0773	UDP-N-acetylmuramate-L-alanine ligase activity
trd_0064	COG0812	UDP-N-acetylmuramate dehydrogenase activity
trd_0065	COG1181	Belongs to the D-alanine--D-alanine ligase family
trd_0066	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
trd_0068	COG0206	Essential cell division protein that forms a contractile ring structure (Z ring) at the future cell division site. The regulation of the ring assembly controls the timing and the location of cell division. One of the functions of the FtsZ ring is to recruit other cell division proteins to the septum to produce a new cell wall between the dividing cells. Binds GTP and shows GTPase activity
trd_0069	COG1327	Negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR- boxes
trd_0071	COG3118	belongs to the thioredoxin family
trd_0074	COG1574	metal-dependent hydrolase with the TIM-barrel fold
trd_0075	COG0640	Transcriptional regulator
trd_0080	COG0531	amino acid
trd_0082	COG0366	Alpha amylase catalytic
trd_0084	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)
trd_0085	COG0426	domain, Protein
trd_0085	COG1853	conserved protein domain typically associated with flavoprotein oxygenases, DIM6 NTAB family
trd_0087	COG0438	transferase activity, transferring glycosyl groups
trd_0088	COG0438	transferase activity, transferring glycosyl groups
trd_0089	COG0227	Belongs to the bacterial ribosomal protein bL28 family
trd_0090	COG2890	protein-(glutamine-N5) methyltransferase activity
trd_0091	COG0216	Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA
trd_0096	COG0742	ribosomal rna small subunit methyltransferase
trd_0097	COG0669	Reversibly transfers an adenylyl group from ATP to 4'- phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate
trd_0103	COG0512	Glutamine amidotransferase of anthranilate synthase
trd_0104	COG0547	Catalyzes the transfer of the phosphoribosyl group of 5- phosphorylribose-1-pyrophosphate (PRPP) to anthranilate to yield N-(5'-phosphoribosyl)-anthranilate (PRA)
trd_0105	COG0134	indole-3-glycerol-phosphate synthase activity
trd_0106	COG0135	phosphoribosylanthranilate isomerase activity
trd_0107	COG0133	tryptophan synthase activity
trd_0108	COG0159	tryptophan synthase activity
trd_0110	COG2876	3-deoxy-7-phosphoheptulonate synthase activity
trd_0111	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
trd_0112	COG0140	phosphoribosyl-ATP diphosphatase activity
trd_0112	COG0139	Catalyzes the hydrolysis of the adenine ring of phosphoribosyl-AMP
trd_0113	COG1837	Belongs to the UPF0109 family
trd_0114	COG0228	four-way junction DNA binding
trd_0115	COG0393	Putative heavy-metal-binding
trd_0117	COG0045	succinate-CoA ligase (ADP-forming) activity
trd_0119	COG0687	Required for the activity of the bacterial periplasmic transport system of putrescine
trd_0120	COG0665	tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase activity
trd_0121	COG4638	Rieske (2fe-2S)
trd_0123	COG0665	tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase activity
trd_0127	COG0582	viral genome integration into host DNA
trd_0132	COG1850	ribulose-bisphosphate carboxylase activity
trd_0133	COG0673	inositol 2-dehydrogenase activity
trd_0143	COG0509	glycine decarboxylation via glycine cleavage system
trd_0144	COG0509	glycine decarboxylation via glycine cleavage system
trd_0147	COG0247	lactate metabolic process
trd_0147	COG2181	nitrate reductase activity
trd_0148	COG2025	fatty acid beta-oxidation using acyl-CoA dehydrogenase
trd_0149	COG2086	electron transfer activity
trd_0150	COG2181	nitrate reductase activity
trd_0150	COG0247	lactate metabolic process
trd_0157	COG0509	glycine decarboxylation via glycine cleavage system
trd_0159	COG2210	Belongs to the sulfur carrier protein TusA family
trd_0160	COG0425	Belongs to the sulfur carrier protein TusA family
trd_0164	COG1003	The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor
trd_0165	COG3872	metal-dependent enzyme
trd_0166	COG0165	Argininosuccinate lyase
trd_0167	COG2153	protein acetylation
trd_0168	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
trd_0170	COG0321	lipoyl(octanoyl) transferase activity
trd_0172	COG0611	Catalyzes the ATP-dependent phosphorylation of thiamine- monophosphate (TMP) to form thiamine-pyrophosphate (TPP), the active form of vitamin B1
trd_0174	COG0802	atpase or kinase
trd_0175	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
trd_0177	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
trd_0179	COG0123	including yeast histone deacetylase and acetoin utilization protein
trd_0180	COG0118	IGPS catalyzes the conversion of PRFAR and glutamine to IGP, AICAR and glutamate. The HisH subunit provides the glutamine amidotransferase activity that produces the ammonia necessary to HisF for the synthesis of IGP and AICAR
trd_0181	COG0106	1-(5-phosphoribosyl)-5- 5-phosphoribosylamino)methylideneamino imidazole-4-carboxamide isomerase
trd_0183	COG0107	imidazoleglycerol-phosphate synthase activity
trd_0184	COG0791	NLP P60 protein
trd_0187	COG1131	(ABC) transporter
trd_0188	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
trd_0189	COG3870	Protein conserved in bacteria
trd_0190	COG3845	ABC transporter
trd_0196	COG1381	Involved in DNA repair and RecF pathway recombination
trd_0197	COG0800	Aldolase
trd_0199	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
trd_0200	COG3870	Protein conserved in bacteria
trd_0201	COG0125	Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis
trd_0202	COG3854	ATPases associated with a variety of cellular activities
trd_0204	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
trd_0205	COG1674	ftsk spoiiie
trd_0205	COG4980	gas vesicle protein
trd_0206	COG1573	uracil-dna glycosylase
trd_0207	COG0322	excinuclease ABC activity
trd_0209	COG0461	Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP)
trd_0210	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
trd_0212	COG0458	carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity
trd_0213	COG0505	Belongs to the CarA family
trd_0214	COG0044	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides
trd_0215	COG0424	maF-like protein
trd_0216	COG2265	Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family
trd_0217	COG1586	Catalyzes the decarboxylation of S-adenosylmethionine to S-adenosylmethioninamine (dcAdoMet), the propylamine donor required for the synthesis of the polyamines spermine and spermidine from the diamine putrescine
trd_0218	COG0421	Catalyzes the irreversible transfer of a propylamine group from the amino donor S-adenosylmethioninamine (decarboxy- AdoMet) to putrescine (1,4-diaminobutane) to yield spermidine
trd_0224	COG0577	efflux transmembrane transporter activity
trd_0224	COG1136	(ABC) transporter
trd_0226	COG0336	Belongs to the RNA methyltransferase TrmD family
trd_0232	COG4166	transmembrane transport
trd_0234	COG0082	Catalyzes the anti-1,4-elimination of the C-3 phosphate and the C-6 proR hydrogen from 5-enolpyruvylshikimate-3-phosphate (EPSP) to yield chorismate, which is the branch point compound that serves as the starting substrate for the three terminal pathways of aromatic amino acid biosynthesis. This reaction introduces a second double bond into the aromatic ring system
trd_0236	COG1898	dTDP-4-dehydrorhamnose 3,5-epimerase activity
trd_0237	COG2265	Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family
trd_0238	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
trd_0242	COG1673	EVE domain
trd_0248	COG1028	Short-chain dehydrogenase reductase Sdr
trd_0249	COG0395	ABC-type sugar transport system, permease component
trd_0250	COG1175	transmembrane transport
trd_0252	COG1414	Transcriptional regulator
trd_0260	COG0277	FAD linked oxidase domain protein
trd_0262	COG0247	lactate metabolic process
trd_0264	COG4946	Tricorn protease homolog
trd_0264	COG1506	peptidase
trd_0264	COG0823	Involved in the tonB-independent uptake of proteins
trd_0268	COG0623	enoyl-[acyl-carrier-protein] reductase (NADH) activity
trd_0269	COG1363	Peptidase, m42
trd_0272	COG1136	(ABC) transporter
trd_0283	COG1236	Exonuclease of the beta-lactamase fold involved in RNA processing
trd_0284	COG0484	heat shock protein binding
trd_0293	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
trd_0295	COG0634	Belongs to the purine pyrimidine phosphoribosyltransferase family
trd_0295	COG0037	tRNA processing
trd_0297	COG1028	Short-chain dehydrogenase reductase Sdr
trd_0302	COG2057	Acyl CoA acetate 3-ketoacid CoA transferase beta subunit
trd_0306	COG0574	Belongs to the PEP-utilizing enzyme family
trd_0306	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)
trd_0307	COG0346	lactoylglutathione lyase activity
trd_0314	COG0820	rRNA (adenine-C2-)-methyltransferase activity
trd_0315	COG1641	Involved in the biosynthesis of a nickel-pincer cofactor ((SCS)Ni(II) pincer complex). Binds Ni(2 ), and functions in nickel delivery to pyridinium-3,5-bisthiocarboxylic acid mononucleotide (P2TMN), to form the mature cofactor. Is thus probably required for the activation of nickel-pincer cofactor- dependent enzymes
trd_0318	COG0600	ABC-type nitrate sulfonate bicarbonate transport system permease component
trd_0330	COG0479	Belongs to the succinate dehydrogenase fumarate reductase iron-sulfur protein family
trd_0331	COG1053	succinate dehydrogenase
trd_0333	COG2009	succinate dehydrogenase
trd_0335	COG1199	ATP-dependent helicase activity
trd_0335	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
trd_0337	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
trd_0339	COG0596	Alpha beta hydrolase
trd_0341	COG1385	rRNA (uridine-N3-)-methyltransferase activity
trd_0343	COG2264	protein methyltransferase activity
trd_0344	COG1207	Catalyzes the last two sequential reactions in the de novo biosynthetic pathway for UDP-N-acetylglucosamine (UDP- GlcNAc). The C-terminal domain catalyzes the transfer of acetyl group from acetyl coenzyme A to glucosamine-1-phosphate (GlcN-1-P) to produce N-acetylglucosamine-1-phosphate (GlcNAc-1-P), which is converted into UDP-GlcNAc by the transfer of uridine 5- monophosphate (from uridine 5-triphosphate), a reaction catalyzed by the N-terminal domain
trd_0347	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
trd_0351	COG1803	Methylglyoxal synthase
trd_0351	COG1597	lipid kinase activity
trd_0352	COG1426	Protein conserved in bacteria
trd_0354	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
trd_0358	COG0405	Gamma-glutamyltransferase
trd_0359	COG0746	molybdenum cofactor guanylyltransferase activity
trd_0361	COG2220	Zn-dependent hydrolases of the beta-lactamase fold
trd_0362	COG0726	polysaccharide deacetylase
trd_0365	COG0119	Catalyzes the condensation of the acetyl group of acetyl-CoA with 3-methyl-2-oxobutanoate (2-oxoisovalerate) to form 3-carboxy-3-hydroxy-4-methylpentanoate (2-isopropylmalate)
trd_0367	COG0460	homoserine dehydrogenase
trd_0368	COG2021	Transfers an acetyl group from acetyl-CoA to L- homoserine, forming acetyl-L-homoserine
trd_0370	COG2409	Drug exporters of the RND superfamily
trd_0376	COG2151	metal-sulfur cluster biosynthetic enzyme
trd_0377	COG0822	iron-sulfur transferase activity
trd_0378	COG0520	Catalyzes the removal of elemental sulfur and selenium atoms from L-cysteine, L-cystine, L-selenocysteine, and L- selenocystine to produce L-alanine
trd_0379	COG0719	Fe-S assembly protein
trd_0380	COG0719	Fe-S assembly protein
trd_0381	COG0396	ATPase activity
trd_0382	COG0735	belongs to the Fur family
trd_0386	COG2220	Zn-dependent hydrolases of the beta-lactamase fold
trd_0387	COG1574	metal-dependent hydrolase with the TIM-barrel fold
trd_0391	COG0520	Catalyzes the removal of elemental sulfur and selenium atoms from L-cysteine, L-cystine, L-selenocysteine, and L- selenocystine to produce L-alanine
trd_0394	COG4166	transmembrane transport
trd_0395	COG0601	transmembrane transport
trd_0396	COG1173	ABC-type dipeptide oligopeptide nickel transport systems, permease components
trd_0398	COG0351	phosphomethylpyrimidine kinase
trd_0399	COG2022	thiamine diphosphate biosynthetic process
trd_0400	COG0352	thiamine-phosphate diphosphorylase activity
trd_0401	COG0352	thiamine-phosphate diphosphorylase activity
trd_0402	COG2104	thiamine diphosphate biosynthetic process
trd_0403	COG0350	Involved in the cellular defense against the biological effects of O6-methylguanine (O6-MeG) and O4-methylthymine (O4-MeT) in DNA. Repairs the methylated nucleobase in DNA by stoichiometrically transferring the methyl group to a cysteine residue in the enzyme. This is a suicide reaction the enzyme is irreversibly inactivated
trd_0404	COG2076	Multidrug Resistance protein
trd_0405	COG0653	protein targeting
trd_0406	COG0580	Belongs to the MIP aquaporin (TC 1.A.8) family
trd_0409	COG1999	signal sequence binding
trd_0413	COG0289	4-hydroxy-tetrahydrodipicolinate reductase
trd_0414	COG0329	Catalyzes the condensation of (S)-aspartate-beta- semialdehyde (S)-ASA and pyruvate to 4-hydroxy- tetrahydrodipicolinate (HTPA)
trd_0418	COG0438	transferase activity, transferring glycosyl groups
trd_0421	COG0358	DNA primase activity
trd_0422	COG1921	L-seryl-tRNASec selenium transferase activity
trd_0423	COG0232	Belongs to the dGTPase family. Type 2 subfamily
trd_0424	COG0404	The glycine cleavage system catalyzes the degradation of glycine
trd_0427	COG0322	excinuclease ABC activity
trd_0428	COG0009	L-threonylcarbamoyladenylate synthase
trd_0432	COG2256	atpase related to the helicase subunit of the holliday junction resolvase
trd_0433	COG0689	Phosphorolytic exoribonuclease that removes nucleotide residues following the -CCA terminus of tRNA and adds nucleotides to the ends of RNA molecules by using nucleoside diphosphates as substrates
trd_0434	COG0131	Imidazoleglycerol-phosphate dehydratase
trd_0435	COG0079	Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. Histidinol-phosphate aminotransferase subfamily
trd_0436	COG1686	Belongs to the peptidase S11 family
trd_0437	COG1187	pseudouridine synthase activity
trd_0438	COG0283	belongs to the cytidylate kinase family. Type 1 subfamily
trd_0441	COG1686	Belongs to the peptidase S11 family
trd_0442	COG0789	Transcriptional regulator
trd_0443	COG0542	response to heat
trd_0447	COG0620	Catalyzes the transfer of a methyl group from 5- methyltetrahydrofolate to homocysteine resulting in methionine formation
trd_0449	COG2876	3-deoxy-7-phosphoheptulonate synthase activity
trd_0452	COG0438	transferase activity, transferring glycosyl groups
trd_0455	COG2301	Belongs to the HpcH HpaI aldolase family
trd_0457	COG2344	Modulates transcription in response to changes in cellular NADH NAD( ) redox state
trd_0459	COG0171	NAD+ synthase (glutamine-hydrolyzing) activity
trd_0459	COG0388	Catalyzes the ATP-dependent amidation of deamido-NAD to form NAD. Uses L-glutamine as a nitrogen source
trd_0460	COG0497	DNA recombination
trd_0461	COG0718	Binds to DNA and alters its conformation. May be involved in regulation of gene expression, nucleoid organization and DNA protection
trd_0462	COG2141	COG2141 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases
trd_0468	COG0437	4 iron, 4 sulfur cluster binding
trd_0469	COG0243	molybdopterin cofactor binding
trd_0476	COG3959	Transketolase, thiamine diphosphate binding domain
trd_0477	COG3958	Transketolase
trd_0478	COG0120	Catalyzes the reversible conversion of ribose-5- phosphate to ribulose 5-phosphate
trd_0480	COG1388	LysM domain
trd_0480	COG3942	CHAP domain
trd_0482	COG3288	NAD(P)+ transhydrogenase (AB-specific) activity
trd_0483	COG3288	NAD(P)+ transhydrogenase (AB-specific) activity
trd_0484	COG1282	The transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane
trd_0487	COG0793	Belongs to the peptidase S41A family
trd_0489	COG2120	A mycothiol (MSH, N-acetylcysteinyl-glucosaminyl- inositol) S-conjugate amidase, it recycles conjugated MSH to the N-acetyl cysteine conjugate (AcCys S-conjugate, a mercapturic acid) and the MSH precursor. Involved in MSH-dependent detoxification of a number of alkylating agents and antibiotics
trd_0491	COG1968	undecaprenyl-diphosphatase activity
trd_0492	COG0477	Major facilitator Superfamily
trd_0493	COG0073	Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation
trd_0494	COG1443	Catalyzes the 1,3-allylic rearrangement of the homoallylic substrate isopentenyl (IPP) to its highly electrophilic allylic isomer, dimethylallyl diphosphate (DMAPP)
trd_0502	COG0117	Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)- pyrimidinedione 5'-phosphate
trd_0502	COG1985	Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)- pyrimidinedione 5'-phosphate
trd_0504	COG0807	Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate
trd_0504	COG0108	Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate
trd_0505	COG0054	6,7-dimethyl-8-ribityllumazine synthase activity
trd_0506	COG1686	Belongs to the peptidase S11 family
trd_0509	COG1331	Highly conserved protein containing a thioredoxin domain
trd_0513	COG0260	Presumably involved in the processing and regular turnover of intracellular proteins. Catalyzes the removal of unsubstituted N-terminal amino acids from various peptides
trd_0516	COG2226	methyltransferase
trd_0520	COG0687	Required for the activity of the bacterial periplasmic transport system of putrescine
trd_0521	COG1177	transmembrane transport
trd_0522	COG1176	ABC-type spermidine putrescine transport system, permease component I
trd_0523	COG3842	ATPase activity
trd_0526	COG0489	protein tyrosine kinase activity
trd_0527	COG0304	beta-ketoacyl-acyl-carrier-protein synthase II activity
trd_0530	COG3665	Urea carboxylase-associated protein
trd_0532	COG0832	Belongs to the urease beta subunit family
trd_0532	COG0831	urea catabolic process
trd_0533	COG0831	urea catabolic process
trd_0533	COG0832	Belongs to the urease beta subunit family
trd_0537	COG0828	Belongs to the bacterial ribosomal protein bS21 family
trd_0539	COG0819	Catalyzes an amino-pyrimidine hydrolysis reaction at the C5' of the pyrimidine moiety of thiamine compounds, a reaction that is part of a thiamine salvage pathway
trd_0540	COG0819	Catalyzes an amino-pyrimidine hydrolysis reaction at the C5' of the pyrimidine moiety of thiamine compounds, a reaction that is part of a thiamine salvage pathway
trd_0543	COG0018	arginyl-trna synthetase
trd_0544	COG1316	TRANSCRIPTIONal
trd_0546	COG0717	Belongs to the dCTP deaminase family
trd_0547	COG2096	Adenosyltransferase
trd_0557	COG1622	oxidoreductase activity, acting on a heme group of donors, oxygen as acceptor
trd_0558	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
trd_0561	COG0508	dehydrogenase complex catalyzes the overall conversion of
trd_0562	COG0567	Dehydrogenase, E1 component
trd_0563	COG0644	oxidoreductase
trd_0564	COG2239	Acts as a magnesium transporter
trd_0567	COG1796	DNA polymerase
trd_0567	COG1387	Histidinol phosphatase and related hydrolases of the PHP family
trd_0571	COG0549	Belongs to the carbamate kinase family
trd_0572	COG1304	FMN binding
trd_0573	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
trd_0580	COG1878	Catalyzes the hydrolysis of N-formyl-L-kynurenine to L- kynurenine, the second step in the kynurenine pathway of tryptophan degradation
trd_0596	COG0379	Catalyzes the condensation of iminoaspartate with dihydroxyacetone phosphate to form quinolinate
trd_0597	COG0715	COG0715 ABC-type nitrate sulfonate bicarbonate transport systems periplasmic components
trd_0598	COG0600	ABC-type nitrate sulfonate bicarbonate transport system permease component
trd_0603	COG1234	tRNA 3'-trailer cleavage
trd_0604	COG0405	Gamma-glutamyltransferase
trd_0608	COG0205	6-phosphofructokinase activity
trd_0609	COG0442	prolyl-tRNA aminoacylation
trd_0613	COG0036	Belongs to the ribulose-phosphate 3-epimerase family
trd_0615	COG1716	ATPase activity
trd_0618	COG1872	DUF167
trd_0619	COG0463	Glycosyl transferase, family 2
trd_0620	COG1606	tRNA processing
trd_0623	COG1185	polyribonucleotide nucleotidyltransferase activity
trd_0624	COG0184	Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome
trd_0625	COG0059	Involved in the biosynthesis of branched-chain amino acids (BCAA). Catalyzes an alkyl-migration followed by a ketol- acid reduction of (S)-2-acetolactate (S2AL) to yield (R)-2,3- dihydroxy-isovalerate. In the isomerase reaction, S2AL is rearranged via a Mg-dependent methyl migration to produce 3- hydroxy-3-methyl-2-ketobutyrate (HMKB). In the reductase reaction, this 2-ketoacid undergoes a metal-dependent reduction by NADPH to yield (R)-2,3-dihydroxy-isovalerate
trd_0626	COG0440	acetolactate synthase activity
trd_0627	COG0028	Belongs to the TPP enzyme family
trd_0634	COG0631	protein serine/threonine phosphatase activity
trd_0636	COG0632	four-way junction helicase activity
trd_0637	COG0141	Catalyzes the sequential NAD-dependent oxidations of L- histidinol to L-histidinaldehyde and then to L-histidine
trd_0639	COG0124	histidyl-tRNA synthetase
trd_0640	COG0072	phenylalanine-tRNA ligase activity
trd_0640	COG0073	Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation
trd_0641	COG0016	Belongs to the class-II aminoacyl-tRNA synthetase family. Phe-tRNA synthetase alpha subunit type 1 subfamily
trd_0642	COG0148	phosphopyruvate hydratase activity
trd_0643	COG0696	Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate
trd_0644	COG0129	dihydroxy-acid dehydratase activity
trd_0647	COG0473	3-isopropylmalate dehydrogenase activity
trd_0649	COG0341	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
trd_0650	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
trd_0651	COG1057	Catalyzes the reversible adenylation of nicotinate mononucleotide (NaMN) to nicotinic acid adenine dinucleotide (NaAD)
trd_0652	COG0188	A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner
trd_0655	COG1260	myo-inositol-1-phosphate synthase
trd_0658	COG0438	transferase activity, transferring glycosyl groups
trd_0659	COG0859	PFAM glycosyl transferase family 9
trd_0660	COG0859	PFAM glycosyl transferase family 9
trd_0661	COG0764	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity
trd_0662	COG0104	Plays an important role in the de novo pathway of purine nucleotide biosynthesis. Catalyzes the first committed step in the biosynthesis of AMP from IMP
trd_0663	COG0484	heat shock protein binding
trd_0666	COG1974	Represses a number of genes involved in the response to DNA damage (SOS response), including recA and lexA. In the presence of single-stranded DNA, RecA interacts with LexA causing an autocatalytic cleavage which disrupts the DNA-binding part of LexA, leading to derepression of the SOS regulon and eventually DNA repair
trd_0668	COG1193	negative regulation of DNA recombination
trd_0670	COG1197	Couples transcription and DNA repair by recognizing RNA polymerase (RNAP) stalled at DNA lesions. Mediates ATP-dependent release of RNAP and its truncated transcript from the DNA, and recruitment of nucleotide excision repair machinery to the damaged site
trd_0671	COG1555	photosystem II stabilization
trd_0671	COG1596	polysaccharide export
trd_0676	COG0050	This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis
trd_0677	COG0267	Belongs to the bacterial ribosomal protein bL33 family
trd_0680	COG0250	Participates in transcription elongation, termination and antitermination
trd_0681	COG0080	Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors
trd_0682	COG0081	regulation of translation
trd_0683	COG0244	Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors
trd_0684	COG0222	ribosome binding
trd_0688	COG1624	Catalyzes the condensation of 2 ATP molecules into cyclic di-AMP (c-di-AMP), a second messenger used to regulate differing processes in different bacteria
trd_0690	COG1484	DNA-dependent DNA replication
trd_0692	COG0305	Participates in initiation and elongation during chromosome replication
trd_0693	COG0359	binds to the 23S rRNA
trd_0696	COG0566	Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase TrmH family
trd_0700	COG0258	In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity
trd_0700	COG0749	In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity
trd_0701	COG0714	Associated with various cellular activities
trd_0703	COG1305	Transglutaminase-like
trd_0705	COG3808	pump that utilizes the energy of pyrophosphate hydrolysis as the driving force for
trd_0711	COG0365	Catalyzes the conversion of acetate into acetyl-CoA (AcCoA), an essential intermediate at the junction of anabolic and catabolic pathways. AcsA undergoes a two-step reaction. In the first half reaction, AcsA combines acetate with ATP to form acetyl-adenylate (AcAMP) intermediate. In the second half reaction, it can then transfer the acetyl group from AcAMP to the sulfhydryl group of CoA, forming the product AcCoA
trd_0712	COG0183	Belongs to the thiolase family
trd_0713	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
trd_0714	COG0592	DNA-directed DNA polymerase activity
trd_0716	COG0809	Transfers and isomerizes the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to give epoxyqueuosine (oQ-tRNA)
trd_0717	COG0520	Catalyzes the removal of elemental sulfur and selenium atoms from L-cysteine, L-cystine, L-selenocysteine, and L- selenocystine to produce L-alanine
trd_0718	COG2255	four-way junction helicase activity
trd_0719	COG2835	tetraacyldisaccharide 4'-kinase activity
trd_0726	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
trd_0729	COG0816	Could be a nuclease involved in processing of the 5'-end of pre-16S rRNA
trd_0731	COG3870	Protein conserved in bacteria
trd_0733	COG0190	Catalyzes the oxidation of 5,10- methylenetetrahydrofolate to 5,10-methenyltetrahydrofolate and then the hydrolysis of 5,10-methenyltetrahydrofolate to 10- formyltetrahydrofolate
trd_0739	COG0769	Catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG) in the biosynthesis of bacterial cell-wall peptidoglycan
trd_0739	COG0189	ligase activity
trd_0741	COG0127	Pyrophosphatase that catalyzes the hydrolysis of nucleoside triphosphates to their monophosphate derivatives, with a high preference for the non-canonical purine nucleotides XTP (xanthosine triphosphate), dITP (deoxyinosine triphosphate) and ITP. Seems to function as a house-cleaning enzyme that removes non-canonical purine nucleotides from the nucleotide pool, thus preventing their incorporation into DNA RNA and avoiding chromosomal lesions
trd_0742	COG0084	hydrolase, TatD family'
trd_0743	COG0449	glutamine-fructose-6-phosphate transaminase (isomerizing) activity
trd_0745	COG0015	Belongs to the lyase 1 family. Adenylosuccinate lyase subfamily
trd_0746	COG0152	phosphoribosylaminoimidazolesuccinocarboxamide synthase activity
trd_0747	COG1828	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
trd_0748	COG0047	phosphoribosylformylglycinamidine synthase activity
trd_0749	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
trd_0750	COG0034	Catalyzes the formation of phosphoribosylamine from phosphoribosylpyrophosphate (PRPP) and glutamine
trd_0751	COG0404	The glycine cleavage system catalyzes the degradation of glycine
trd_0753	COG0403	The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor
trd_0754	COG1160	GTP binding
trd_0755	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
trd_0757	COG0661	Is probably a protein kinase regulator of UbiI activity which is involved in aerobic coenzyme Q (ubiquinone) biosynthesis
trd_0760	COG0501	Belongs to the peptidase M48B family
trd_0768	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)
trd_0769	COG0196	riboflavin kinase activity
trd_0770	COG0130	Responsible for synthesis of pseudouridine from uracil- 55 in the psi GC loop of transfer RNAs
trd_0772	COG0858	One of several proteins that assist in the late maturation steps of the functional core of the 30S ribosomal subunit. Associates with free 30S ribosomal subunits (but not with 30S subunits that are part of 70S ribosomes or polysomes). Required for efficient processing of 16S rRNA. May interact with the 5'-terminal helix region of 16S rRNA
trd_0773	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
trd_0774	COG2740	Nucleic-acid-binding protein implicated in transcription termination
trd_0775	COG0195	Participates in both transcription termination and antitermination
trd_0777	COG0391	Required for morphogenesis under gluconeogenic growth conditions
trd_0779	COG0126	phosphoglycerate kinase activity
trd_0780	COG0149	triose-phosphate isomerase activity
trd_0783	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
trd_0788	COG0681	Belongs to the peptidase S26 family
trd_0797	COG0304	beta-ketoacyl-acyl-carrier-protein synthase II activity
trd_0799	COG0568	sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released
trd_0801	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
trd_0802	COG1189	Ribosomal RNA methyltransferase RrmJ FtsJ
trd_0804	COG1884	Catalyzes the reversible interconversion of isobutyryl- CoA and n-butyryl-CoA, using radical chemistry. Also exhibits GTPase activity, associated with its G-protein domain (MeaI) that functions as a chaperone that assists cofactor delivery and proper holo-enzyme assembly
trd_0804	COG2185	Catalyzes the reversible interconversion of isobutyryl- CoA and n-butyryl-CoA, using radical chemistry. Also exhibits GTPase activity, associated with its G-protein domain (MeaI) that functions as a chaperone that assists cofactor delivery and proper holo-enzyme assembly
trd_0807	COG0193	aminoacyl-tRNA hydrolase activity
trd_0808	COG0438	transferase activity, transferring glycosyl groups
trd_0809	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
trd_0811	COG0343	queuine tRNA-ribosyltransferase activity
trd_0812	COG1254	Belongs to the acylphosphatase family
trd_0813	COG1004	Belongs to the UDP-glucose GDP-mannose dehydrogenase family
trd_0814	COG0736	holo-[acyl-carrier-protein] synthase activity
trd_0815	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
trd_0815	COG0063	ADP-dependent NAD(P)H-hydrate dehydratase activity
trd_0816	COG0516	GMP reductase activity
trd_0816	COG0517	IMP dehydrogenase activity
trd_0818	COG1234	tRNA 3'-trailer cleavage
trd_0819	COG0325	Pyridoxal 5'-phosphate (PLP)-binding protein, which is involved in PLP homeostasis
trd_0823	COG1515	deoxyribonuclease V activity
trd_0824	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
trd_0828	COG0291	Belongs to the bacterial ribosomal protein bL35 family
trd_0829	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
trd_0830	COG0566	Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase TrmH family
trd_0831	COG0776	regulation of translation
trd_0832	COG0187	DNA topoisomerase II activity
trd_0835	COG0768	penicillin binding
trd_0837	COG0005	The purine nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the beta- (deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate
trd_0840	COG0451	ADP-glyceromanno-heptose 6-epimerase activity
trd_0848	COG0268	Binds directly to 16S ribosomal RNA
trd_0850	COG0728	peptidoglycan biosynthetic process
trd_0851	COG0481	GTPase activity
trd_0852	COG3956	TIGRFAM MazG family protein
trd_0853	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)
trd_0854	COG3546	catalase activity
trd_0861	COG2262	GTPase that associates with the 50S ribosomal subunit and may have a role during protein synthesis or ribosome biogenesis
trd_0863	COG0150	phosphoribosylformylglycinamidine cyclo-ligase activity
trd_0864	COG1100	Small GTP-binding protein
trd_0865	COG0248	Ppx GppA phosphatase
trd_0867	COG0138	bifunctional purine biosynthesis protein purh
trd_0870	COG2720	vancomycin resistance protein
trd_0871	COG0251	oxidation-reduction process
trd_0873	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
trd_0874	COG1190	Belongs to the class-II aminoacyl-tRNA synthetase family
trd_0875	COG1177	transmembrane transport
trd_0876	COG1176	ABC-type spermidine putrescine transport system, permease component I
trd_0879	COG1473	amidohydrolase
trd_0881	COG3842	ATPase activity
trd_0882	COG0777	Component of the acetyl coenzyme A carboxylase (ACC) complex. Biotin carboxylase (BC) catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the transcarboxylase to acetyl-CoA to form malonyl- CoA
trd_0882	COG0825	malonyl-CoA metabolic process
trd_0887	COG0579	oxidoreductase
trd_0888	COG0517	IMP dehydrogenase activity
trd_0900	COG2759	Belongs to the formate--tetrahydrofolate ligase family
trd_0901	COG0404	The glycine cleavage system catalyzes the degradation of glycine
trd_0904	COG2120	A mycothiol (MSH, N-acetylcysteinyl-glucosaminyl- inositol) S-conjugate amidase, it recycles conjugated MSH to the N-acetyl cysteine conjugate (AcCys S-conjugate, a mercapturic acid) and the MSH precursor. Involved in MSH-dependent detoxification of a number of alkylating agents and antibiotics
trd_0907	COG2843	Capsule synthesis protein
trd_0911	COG4948	Mandelate Racemase Muconate Lactonizing
trd_0912	COG1312	Catalyzes the dehydration of D-mannonate
trd_0914	COG2924	Could be a mediator in iron transactions between iron acquisition and iron-requiring processes, such as synthesis and or repair of Fe-S clusters in biosynthetic enzymes
trd_0917	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
trd_0918	COG0499	May play a key role in the regulation of the intracellular concentration of adenosylhomocysteine
trd_0920	COG0337	Catalyzes the conversion of 3-deoxy-D-arabino- heptulosonate 7-phosphate (DAHP) to dehydroquinate (DHQ)
trd_0921	COG0039	L-malate dehydrogenase activity
trd_0923	COG0303	'Molybdopterin
trd_0924	COG1940	carbohydrate kinase activity
trd_0930	COG0769	Catalyzes the addition of meso-diaminopimelic acid to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanyl-D-glutamate (UMAG) in the biosynthesis of bacterial cell-wall peptidoglycan
trd_0940	COG0639	Hydrolyzes diadenosine 5',5'''-P1,P4-tetraphosphate to yield ADP
trd_0942	COG0799	negative regulation of ribosome biogenesis
trd_0943	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
trd_0944	COG0438	transferase activity, transferring glycosyl groups
trd_0950	COG1234	tRNA 3'-trailer cleavage
trd_0951	COG3191	aminopeptidase activity
trd_0952	COG1082	Xylose isomerase domain protein TIM barrel
trd_0953	COG0103	maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
trd_0954	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
trd_0955	COG0101	tRNA pseudouridine synthase activity
trd_0956	COG0203	ribosomal protein L17
trd_0957	COG0202	RNA polymerase activity
trd_0958	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
trd_0959	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
trd_0960	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
trd_0961	COG0257	Belongs to the bacterial ribosomal protein bL36 family
trd_0962	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
trd_0964	COG0563	adenylate kinase activity
trd_0966	COG0200	Binds to the 23S rRNA
trd_0967	COG1841	ribosomal large subunit assembly
trd_0968	COG0098	Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body
trd_0969	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
trd_0970	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
trd_0971	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
trd_0972	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
trd_0973	COG0198	One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit
trd_0974	COG0093	Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome
trd_0975	COG0186	One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA
trd_0976	COG0255	Belongs to the universal ribosomal protein uL29 family
trd_0977	COG0197	Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs
trd_0978	COG0092	Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation
trd_0979	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
trd_0980	COG0185	Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA
trd_0981	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
trd_0982	COG0089	rRNA binding
trd_0983	COG0088	Forms part of the polypeptide exit tunnel
trd_0984	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
trd_0985	COG0051	transcription antitermination factor activity, RNA binding
trd_0986	COG0050	This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis
trd_0987	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
trd_0988	COG0049	tRNA binding
trd_0989	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
trd_0990	COG0086	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates
trd_0991	COG0085	RNA polymerase activity
trd_0998	COG0052	Belongs to the universal ribosomal protein uS2 family
trd_0999	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
trd_1000	COG0528	UMP kinase activity
trd_1001	COG0233	cytoplasmic translational termination
trd_1003	COG4589	Belongs to the CDS family
trd_1005	COG0743	1-deoxy-D-xylulose-5-phosphate reductoisomerase activity
trd_1014	COG0392	lysyltransferase activity
trd_1014	COG2898	Catalyzes the transfer of a lysyl group from L-lysyl- tRNA(Lys) to membrane-bound phosphatidylglycerol (PG), which produces lysylphosphatidylglycerol (LPG), a major component of the bacterial membrane with a positive net charge. LPG synthesis contributes to bacterial virulence as it is involved in the resistance mechanism against cationic antimicrobial peptides (CAMP) produces by the host's immune system (defensins, cathelicidins) and by the competing microorganisms
trd_1022	COG2071	gamma-glutamyl-gamma-aminobutyrate hydrolase activity
trd_1023	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
trd_1031	COG2379	hydroxypyruvate reductase
trd_1032	COG0564	pseudouridine synthase activity
trd_1033	COG0597	This protein specifically catalyzes the removal of signal peptides from prolipoproteins
trd_1034	COG1066	DNA-dependent ATPase involved in processing of recombination intermediates, plays a role in repairing DNA breaks. Stimulates the branch migration of RecA-mediated strand transfer reactions, allowing the 3' invading strand to extend heteroduplex DNA faster. Binds ssDNA in the presence of ADP but not other nucleotides, has ATPase activity that is stimulated by ssDNA and various branched DNA structures, but inhibited by SSB. Does not have RecA's homology-searching function
trd_1035	COG0542	response to heat
trd_1036	COG0539	negative regulation of cytoplasmic translation
trd_1041	COG2896	Catalyzes the cyclization of GTP to (8S)-3',8-cyclo-7,8- dihydroguanosine 5'-triphosphate
trd_1042	COG2120	A mycothiol (MSH, N-acetylcysteinyl-glucosaminyl- inositol) S-conjugate amidase, it recycles conjugated MSH to the N-acetyl cysteine conjugate (AcCys S-conjugate, a mercapturic acid) and the MSH precursor. Involved in MSH-dependent detoxification of a number of alkylating agents and antibiotics
trd_1043	COG0124	histidyl-tRNA synthetase
trd_1044	COG0521	Mo-molybdopterin cofactor biosynthetic process
trd_1045	COG0624	Catalyzes the hydrolysis of N-succinyl-L,L- diaminopimelic acid (SDAP), forming succinate and LL-2,6- diaminoheptanedioate (DAP), an intermediate involved in the bacterial biosynthesis of lysine and meso-diaminopimelic acid, an essential component of bacterial cell walls
trd_1046	COG0792	nuclease activity
trd_1047	COG0164	Endonuclease that specifically degrades the RNA of RNA- DNA hybrids
trd_1048	COG0335	large ribosomal subunit rRNA binding
trd_1049	COG0685	methylenetetrahydrofolate reductase (NAD(P)H) activity
trd_1049	COG0646	methionine synthase
trd_1053	COG0423	glycine-tRNA ligase activity
trd_1054	COG1475	DNA binding
trd_1055	COG4974	Belongs to the 'phage' integrase family
trd_1056	COG0686	Belongs to the AlaDH PNT family
trd_1057	COG0750	zinc metalloprotease
trd_1058	COG0821	Converts 2C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-2,4cPP) into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate
trd_1060	COG2352	Forms oxaloacetate, a four-carbon dicarboxylic acid source for the tricarboxylic acid cycle
trd_1061	COG1600	Catalyzes the conversion of epoxyqueuosine (oQ) to queuosine (Q), which is a hypermodified base found in the wobble positions of tRNA(Asp), tRNA(Asn), tRNA(His) and tRNA(Tyr)
trd_1062	COG1521	Catalyzes the phosphorylation of pantothenate (Pan), the first step in CoA biosynthesis
trd_1063	COG1363	Peptidase, m42
trd_1064	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
trd_1065	COG0406	alpha-ribazole phosphatase activity
trd_1065	COG0328	RNA-DNA hybrid ribonuclease activity
trd_1067	COG0441	Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr)
trd_1069	COG2227	3-demethylubiquinone-9 3-O-methyltransferase activity
trd_1071	COG0624	Catalyzes the hydrolysis of N-succinyl-L,L- diaminopimelic acid (SDAP), forming succinate and LL-2,6- diaminoheptanedioate (DAP), an intermediate involved in the bacterial biosynthesis of lysine and meso-diaminopimelic acid, an essential component of bacterial cell walls
trd_1072	COG0684	Catalyzes the aldol cleavage of 4-hydroxy-4-methyl-2- oxoglutarate (HMG) into 2 molecules of pyruvate. Also contains a secondary oxaloacetate (OAA) decarboxylase activity due to the common pyruvate enolate transition state formed following C-C bond cleavage in the retro-aldol and decarboxylation reactions
trd_1076	COG1846	Transcriptional regulator
trd_1078	COG0315	cyclic pyranopterin monophosphate synthase activity
trd_1079	COG0482	sulfurtransferase activity
trd_1081	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
trd_1082	COG0442	prolyl-tRNA aminoacylation
trd_1084	COG1847	R3H domain protein
trd_1085	COG0706	membrane insertase activity
trd_1086	COG0759	Could be involved in insertion of integral membrane proteins into the membrane
trd_1087	COG0594	ribonuclease P activity
trd_1088	COG0230	Belongs to the bacterial ribosomal protein bL34 family
trd_1089	COG1680	COG1680 Beta-lactamase class C and other penicillin binding
trd_1093	COG0060	amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile)
trd_1096	COG0205	6-phosphofructokinase activity
trd_1103	COG0161	adenosylmethionine-8-amino-7-oxononanoate transaminase activity
trd_1105	COG0067	glutamate synthase
trd_1105	COG0070	glutamate synthase
trd_1105	COG0069	glutamate synthase activity
trd_1107	COG0004	ammonium transporteR
trd_1113	COG4147	Belongs to the sodium solute symporter (SSF) (TC 2.A.21) family
trd_1114	COG2176	DNA-directed DNA polymerase activity
trd_1117	COG0365	Catalyzes the conversion of acetate into acetyl-CoA (AcCoA), an essential intermediate at the junction of anabolic and catabolic pathways. AcsA undergoes a two-step reaction. In the first half reaction, AcsA combines acetate with ATP to form acetyl-adenylate (AcAMP) intermediate. In the second half reaction, it can then transfer the acetyl group from AcAMP to the sulfhydryl group of CoA, forming the product AcCoA
trd_1118	COG0697	spore germination
trd_1119	COG2366	antibiotic biosynthetic process
trd_1122	COG0373	Catalyzes the NADPH-dependent reduction of glutamyl- tRNA(Glu) to glutamate 1-semialdehyde (GSA)
trd_1123	COG0001	glutamate-1-semialdehyde 2,1-aminomutase activity
trd_1124	COG0113	porphobilinogen synthase activity
trd_1125	COG0181	hydroxymethylbilane synthase activity
trd_1127	COG0302	gtp cyclohydrolase
trd_1128	COG0558	Belongs to the CDP-alcohol phosphatidyltransferase class-I family
trd_1128	COG1213	nucleotidyl transferase
trd_1131	COG0513	Belongs to the DEAD box helicase family
trd_1132	COG0217	transcriptional regulatory protein
trd_1134	COG1921	L-seryl-tRNASec selenium transferase activity
trd_1135	COG3842	ATPase activity
trd_1136	COG0395	ABC-type sugar transport system, permease component
trd_1137	COG1175	transmembrane transport
trd_1139	COG0365	Catalyzes the conversion of acetate into acetyl-CoA (AcCoA), an essential intermediate at the junction of anabolic and catabolic pathways. AcsA undergoes a two-step reaction. In the first half reaction, AcsA combines acetate with ATP to form acetyl-adenylate (AcAMP) intermediate. In the second half reaction, it can then transfer the acetyl group from AcAMP to the sulfhydryl group of CoA, forming the product AcCoA
trd_1141	COG0176	Transaldolase is important for the balance of metabolites in the pentose-phosphate pathway
trd_1142	COG1023	phosphogluconate dehydrogenase (decarboxylating) activity
trd_1143	COG0364	Catalyzes the oxidation of glucose 6-phosphate to 6- phosphogluconolactone
trd_1144	COG3429	Glucose-6-phosphate dehydrogenase subunit
trd_1144	COG3409	Peptidoglycan-binding domain 1 protein
trd_1146	COG0363	glucosamine-6-phosphate deaminase activity
trd_1147	COG2322	membrane
trd_1149	COG1131	(ABC) transporter
trd_1150	COG0842	Transport permease protein
trd_1156	COG1825	This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance
trd_1157	COG2814	Major facilitator Superfamily
trd_1158	COG1309	transcriptional regulator
trd_1159	COG1562	ergosterol biosynthetic process
trd_1160	COG0596	Alpha beta hydrolase
trd_1163	COG1233	COG1233 Phytoene dehydrogenase and related
trd_1164	COG0761	Catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)- butenyl 4-diphosphate (HMBPP) into a mixture of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Acts in the terminal step of the DOXP MEP pathway for isoprenoid precursor biosynthesis
trd_1165	COG0247	lactate metabolic process
trd_1165	COG0277	FAD linked oxidase domain protein
trd_1166	COG0593	it binds specifically double-stranded DNA at a 9 bp consensus (dnaA box) 5'-TTATC CA A CA A-3'. DnaA binds to ATP and to acidic phospholipids
trd_1170	COG0477	Major facilitator Superfamily
trd_1172	COG2897	thiosulfate sulfurtransferase activity
trd_1173	COG0822	iron-sulfur transferase activity
trd_1176	COG0613	PHP domain protein
trd_1177	COG0327	Belongs to the GTP cyclohydrolase I type 2 NIF3 family
trd_1183	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
trd_1184	COG0518	GMP synthase (glutamine-hydrolyzing) activity
trd_1184	COG0519	Catalyzes the synthesis of GMP from XMP
trd_1185	COG2197	response regulator
trd_1186	COG0151	Belongs to the GarS family
trd_1187	COG0494	nUDIX hydrolase
trd_1192	COG0789	Transcriptional regulator
trd_1193	COG0434	BtpA family
trd_1194	COG0608	single-stranded DNA 5'-3' exodeoxyribonuclease activity
trd_1194	COG4199	Single-strand DNA-specific exonuclease, C terminal domain
trd_1196	COG1408	metallophosphoesterase
trd_1199	COG2738	Putative neutral zinc metallopeptidase
trd_1201	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
trd_1202	COG0740	serine-type endopeptidase activity
trd_1203	COG0544	peptidyl-prolyl cis-trans isomerase activity
trd_1212	COG1975	Xanthine and CO dehydrogenases maturation factor, XdhC CoxF family
trd_1212	COG3608	succinylglutamate desuccinylase aspartoacylase
trd_1213	COG1207	Catalyzes the last two sequential reactions in the de novo biosynthetic pathway for UDP-N-acetylglucosamine (UDP- GlcNAc). The C-terminal domain catalyzes the transfer of acetyl group from acetyl coenzyme A to glucosamine-1-phosphate (GlcN-1-P) to produce N-acetylglucosamine-1-phosphate (GlcNAc-1-P), which is converted into UDP-GlcNAc by the transfer of uridine 5- monophosphate (from uridine 5-triphosphate), a reaction catalyzed by the N-terminal domain
trd_1214	COG0494	nUDIX hydrolase
trd_1217	COG0755	Required for the export of heme to the periplasm for the biogenesis of c-type cytochromes
trd_1221	COG3088	subunit of a heme lyase
trd_1223	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
trd_1225	COG0526	COG0526, thiol-disulfide isomerase and thioredoxins
trd_1226	COG0766	Cell wall formation. Adds enolpyruvyl to UDP-N- acetylglucosamine
trd_1227	COG0355	proton-transporting ATP synthase activity, rotational mechanism
trd_1228	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
trd_1229	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
trd_1230	COG0056	Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit
trd_1231	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
trd_1232	COG0711	Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0)
trd_1233	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
trd_1236	COG0504	CTP synthase activity
trd_1237	COG2220	Zn-dependent hydrolases of the beta-lactamase fold
trd_1238	COG2137	regulation of response to DNA damage stimulus
trd_1240	COG0495	leucyl-tRNA aminoacylation
trd_1243	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
trd_1246	COG0760	Chaperone involved in the correct folding and assembly of outer membrane proteins. Recognizes specific patterns of aromatic residues and the orientation of their side chains, which are found more frequently in integral outer membrane proteins. May act in both early periplasmic and late outer membrane-associated steps of protein maturation
trd_1247	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
trd_1248	COG0629	single-stranded DNA binding
trd_1249	COG0360	Binds together with S18 to 16S ribosomal RNA
trd_1251	COG0083	homoserine kinase activity
trd_1252	COG0498	Catalyzes the gamma-elimination of phosphate from L- phosphohomoserine and the beta-addition of water to produce L- threonine
trd_1253	COG1173	ABC-type dipeptide oligopeptide nickel transport systems, permease components
trd_1254	COG0601	transmembrane transport
trd_1258	COG0297	glycogen (starch) synthase activity
trd_1259	COG0448	Catalyzes the synthesis of ADP-glucose, a sugar donor used in elongation reactions on alpha-glucans
trd_1260	COG0777	Component of the acetyl coenzyme A carboxylase (ACC) complex. Biotin carboxylase (BC) catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the transcarboxylase to acetyl-CoA to form malonyl- CoA
trd_1261	COG0825	malonyl-CoA metabolic process
trd_1262	COG0071	Belongs to the small heat shock protein (HSP20) family
trd_1264	COG0540	Belongs to the ATCase OTCase family
trd_1265	COG0568	sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released
trd_1266	COG0419	ATPase involved in DNA repair
trd_1268	COG0330	HflC and HflK could
trd_1269	COG0616	signal peptide processing
trd_1270	COG1806	Bifunctional serine threonine kinase and phosphorylase involved in the regulation of the
trd_1273	COG0745	RESPONSE REGULATOR receiver
trd_1274	COG2205	protein histidine kinase activity
trd_1276	COG1154	Catalyzes the acyloin condensation reaction between C atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-xylulose-5-phosphate (DXP)
trd_1277	COG0357	Ribosomal RNA small subunit methyltransferase G
trd_1279	COG0601	transmembrane transport
trd_1280	COG1173	ABC-type dipeptide oligopeptide nickel transport systems, permease components
trd_1281	COG0747	negative chemotaxis
trd_1282	COG2235	arginine
trd_1283	COG0647	UMP catabolic process
trd_1285	COG0463	Glycosyl transferase, family 2
trd_1288	COG1546	Belongs to the CinA family
trd_1288	COG1058	Belongs to the CinA family
trd_1289	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
trd_1290	COG1480	7TM receptor with intracellular HD hydrolase
trd_1291	COG1610	YqeY-like protein
trd_1295	COG2226	methyltransferase
trd_1300	COG0459	protein refolding
trd_1301	COG0234	Binds to Cpn60 in the presence of Mg-ATP and suppresses the ATPase activity of the latter
trd_1306	COG0030	16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity
trd_1307	COG1947	Catalyzes the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol
trd_1309	COG0476	Involved in molybdopterin and thiamine biosynthesis, family 2
trd_1311	COG1977	Involved in sulfur transfer in the conversion of molybdopterin precursor Z to molybdopterin
trd_1312	COG0031	Belongs to the cysteine synthase cystathionine beta- synthase family
trd_1313	COG2815	serine threonine protein kinase
trd_1313	COG0515	serine threonine protein kinase
trd_1318	COG1878	Catalyzes the hydrolysis of N-formyl-L-kynurenine to L- kynurenine, the second step in the kynurenine pathway of tryptophan degradation
trd_1322	COG1846	Transcriptional regulator
trd_1323	COG0554	Key enzyme in the regulation of glycerol uptake and metabolism. Catalyzes the phosphorylation of glycerol to yield sn- glycerol 3-phosphate
trd_1324	COG0801	2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
trd_1325	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
trd_1329	COG4974	Belongs to the 'phage' integrase family
trd_1331	COG0405	Gamma-glutamyltransferase
trd_1332	COG0730	response to heat
trd_1335	COG0730	response to heat
trd_1336	COG1316	TRANSCRIPTIONal
trd_1340	COG1960	acyl-CoA dehydrogenase activity
trd_1343	COG4948	Mandelate Racemase Muconate Lactonizing
trd_1352	COG2848	UPF0210 protein
trd_1354	COG2120	A mycothiol (MSH, N-acetylcysteinyl-glucosaminyl- inositol) S-conjugate amidase, it recycles conjugated MSH to the N-acetyl cysteine conjugate (AcCys S-conjugate, a mercapturic acid) and the MSH precursor. Involved in MSH-dependent detoxification of a number of alkylating agents and antibiotics
trd_1360	COG2353	YceI-like domain
trd_1362	COG1733	regulation of RNA biosynthetic process
trd_1363	COG0614	abc-type fe3 -hydroxamate transport system, periplasmic component
trd_1364	COG1804	L-carnitine dehydratase bile acid-inducible protein F
trd_1369	COG1235	May be involved in the transport of PQQ or its precursor to the periplasm
trd_1369	COG0321	lipoyl(octanoyl) transferase activity
trd_1372	COG0415	Belongs to the DNA photolyase family
trd_1375	COG0462	Involved in the biosynthesis of the central metabolite phospho-alpha-D-ribosyl-1-pyrophosphate (PRPP) via the transfer of pyrophosphoryl group from ATP to 1-hydroxyl of ribose-5-phosphate (Rib-5-P)
trd_1378	COG1993	acr, cog1993
trd_1379	COG0239	Important for reducing fluoride concentration in the cell, thus reducing its toxicity
trd_1380	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
trd_1383	COG0276	Catalyzes the ferrous insertion into protoporphyrin IX
trd_1384	COG0407	Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III
trd_1389	COG1942	4-Oxalocrotonate Tautomerase
trd_1392	COG0119	Catalyzes the condensation of the acetyl group of acetyl-CoA with 3-methyl-2-oxobutanoate (2-oxoisovalerate) to form 3-carboxy-3-hydroxy-4-methylpentanoate (2-isopropylmalate)
trd_1393	COG4569	acetaldehyde dehydrogenase (acetylating) activity
trd_1394	COG1414	Transcriptional regulator
trd_1398	COG0559	Belongs to the binding-protein-dependent transport system permease family
trd_1404	COG0559	Belongs to the binding-protein-dependent transport system permease family
trd_1405	COG0411	ABC transporter
trd_1406	COG0410	ABC transporter
trd_1409	COG1327	Negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR- boxes
trd_1409	COG0209	Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides
trd_1414	COG2217	Heavy metal translocating P-type atpase
trd_1415	COG1937	Protein conserved in bacteria
trd_1420	COG2200	EAL domain
trd_1421	COG0001	glutamate-1-semialdehyde 2,1-aminomutase activity
trd_1424	COG0254	rRNA binding
trd_1425	COG0211	Belongs to the bacterial ribosomal protein bL27 family
trd_1426	COG0261	This protein binds to 23S rRNA in the presence of protein L20
trd_1429	COG0078	Reversibly catalyzes the transfer of the carbamoyl group from carbamoyl phosphate (CP) to the N(epsilon) atom of ornithine (ORN) to produce L-citrulline
trd_1435	COG0772	Belongs to the SEDS family
trd_1436	COG0635	Involved in the biosynthesis of porphyrin-containing compound
trd_1437	COG1192	Involved in chromosome partitioning
trd_1438	COG0517	IMP dehydrogenase activity
trd_1438	COG0516	GMP reductase activity
trd_1449	COG0474	ATPase, P-type transporting, HAD superfamily, subfamily IC
trd_1451	COG0474	ATPase, P-type transporting, HAD superfamily, subfamily IC
trd_1453	COG0484	heat shock protein binding
trd_1459	COG2195	Cleaves the N-terminal amino acid of tripeptides
trd_1468	COG1012	belongs to the aldehyde dehydrogenase family
trd_1469	COG1027	Aspartate ammonia-lyase
trd_1470	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
trd_1474	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)
trd_1476	COG0334	Belongs to the Glu Leu Phe Val dehydrogenases family
trd_1478	COG0569	domain protein
trd_1479	COG0569	domain protein
trd_1487	COG2814	Major facilitator Superfamily
trd_1493	COG1071	oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
trd_1494	COG0022	dehydrogenase e1 component
trd_1496	COG1285	pathogenesis
trd_1503	COG1131	(ABC) transporter
trd_1505	COG0612	Peptidase, M16
trd_1507	COG1058	Belongs to the CinA family
trd_1507	COG1546	Belongs to the CinA family
trd_1511	COG2094	Belongs to the DNA glycosylase MPG family
trd_1512	COG0525	valine-tRNA ligase activity
trd_1515	COG4992	N2-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity
trd_1516	COG0548	Belongs to the acetylglutamate kinase family. ArgB subfamily
trd_1517	COG2226	methyltransferase
trd_1518	COG0002	Catalyzes the NADPH-dependent reduction of N-acetyl-5- glutamyl phosphate to yield N-acetyl-L-glutamate 5-semialdehyde
trd_1519	COG0189	ligase activity
trd_1520	COG0624	Catalyzes the hydrolysis of N-succinyl-L,L- diaminopimelic acid (SDAP), forming succinate and LL-2,6- diaminoheptanedioate (DAP), an intermediate involved in the bacterial biosynthesis of lysine and meso-diaminopimelic acid, an essential component of bacterial cell walls
trd_1521	COG0189	ligase activity
trd_1523	COG0747	negative chemotaxis
trd_1524	COG0601	transmembrane transport
trd_1528	COG2217	Heavy metal translocating P-type atpase
trd_1530	COG0143	Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation
trd_1531	COG4623	carbon-oxygen lyase activity, acting on polysaccharides
trd_1537	COG2814	Major facilitator Superfamily
trd_1543	COG1132	(ABC) transporter
trd_1549	COG0556	nucleotide-excision repair
trd_1551	COG2197	response regulator
trd_1553	COG0316	Belongs to the HesB IscA family
trd_1557	COG0174	glutamine synthetase
trd_1562	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
trd_1565	COG1077	Cell shape determining protein MreB Mrl
trd_1568	COG0476	Involved in molybdopterin and thiamine biosynthesis, family 2
trd_1569	COG0287	Prephenate dehydrogenase
trd_1574	COG2141	COG2141 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases
trd_1581	COG1982	Orn Lys Arg decarboxylase major
trd_1593	COG0463	Glycosyl transferase, family 2
trd_1599	COG5002	protein histidine kinase activity
trd_1600	COG0745	RESPONSE REGULATOR receiver
trd_1601	COG0758	DNA mediated transformation
trd_1602	COG0662	Cupin 2, conserved barrel domain protein
trd_1602	COG0836	Belongs to the mannose-6-phosphate isomerase type 2 family
trd_1603	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
trd_1604	COG5405	Protease subunit of a proteasome-like degradation complex believed to be a general protein degrading machinery
trd_1605	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
trd_1606	COG1215	transferase activity, transferring glycosyl groups
trd_1607	COG1940	carbohydrate kinase activity
trd_1609	COG4166	transmembrane transport
trd_1610	COG0115	Belongs to the class-IV pyridoxal-phosphate-dependent aminotransferase family
trd_1611	COG0001	glutamate-1-semialdehyde 2,1-aminomutase activity
trd_1612	COG2515	1-aminocyclopropane-1-carboxylate deaminase
trd_1613	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
trd_1614	COG0242	peptide deformylase activity
trd_1617	COG0805	protein transport
trd_1618	COG0236	Carrier of the growing fatty acid chain in fatty acid biosynthesis
trd_1620	COG0439	Biotin carboxylase
trd_1621	COG1028	Short-chain dehydrogenase reductase Sdr
trd_1622	COG0331	[acyl-carrier-protein] S-malonyltransferase activity
trd_1623	COG0332	Catalyzes the condensation reaction of fatty acid synthesis by the addition to an acyl acceptor of two carbons from malonyl-ACP. Catalyzes the first condensation reaction which initiates fatty acid synthesis and may therefore play a role in governing the total rate of fatty acid production. Possesses both acetoacetyl-ACP synthase and acetyl transacylase activities. Its substrate specificity determines the biosynthesis of branched- chain and or straight-chain of fatty acids
trd_1627	COG0115	Belongs to the class-IV pyridoxal-phosphate-dependent aminotransferase family
trd_1628	COG0747	negative chemotaxis
trd_1629	COG0444	Belongs to the ABC transporter superfamily
trd_1630	COG4608	Belongs to the ABC transporter superfamily
trd_1631	COG1994	Peptidase M50
trd_1633	COG1386	Participates in chromosomal partition during cell division. May act via the formation of a condensin-like complex containing Smc and ScpA that pull DNA away from mid-cell into both cell halves
trd_1634	COG1104	cysteine desulfurase activity
trd_1635	COG1959	2 iron, 2 sulfur cluster binding
trd_1638	COG1420	regulation of RNA biosynthetic process
trd_1639	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
trd_1640	COG0443	Heat shock 70 kDa protein
trd_1647	COG5632	N-Acetylmuramoyl-L-alanine amidase
trd_1647	COG3409	Peptidoglycan-binding domain 1 protein
trd_1657	COG3835	regulator
trd_1661	COG0671	phosphoesterase, PA-phosphatase related
trd_1662	COG0761	Catalyzes the conversion of 1-hydroxy-2-methyl-2-(E)- butenyl 4-diphosphate (HMBPP) into a mixture of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Acts in the terminal step of the DOXP MEP pathway for isoprenoid precursor biosynthesis
trd_1663	COG1011	Hydrolase
trd_1666	COG0648	Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic sites (AP sites) to produce new 5'-ends that are base-free deoxyribose 5-phosphate residues. It preferentially attacks modified AP sites created by bleomycin and neocarzinostatin
trd_1668	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
trd_1671	COG0747	negative chemotaxis
trd_1672	COG0601	transmembrane transport
trd_1673	COG1173	ABC-type dipeptide oligopeptide nickel transport systems, permease components
trd_1674	COG1175	transmembrane transport
trd_1675	COG0395	ABC-type sugar transport system, permease component
trd_1677	COG0459	protein refolding
trd_1679	COG0780	Catalyzes the NADPH-dependent reduction of 7-cyano-7- deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1)
trd_1682	COG0511	ligase activity, forming carbon-carbon bonds
trd_1683	COG0511	ligase activity, forming carbon-carbon bonds
trd_1683	COG5016	pyruvate
trd_1684	COG0546	phosphoglycolate phosphatase activity
trd_1685	COG1541	Catalyzes the activation of phenylacetic acid (PA) to phenylacetyl-CoA (PA-CoA)
trd_1690	COG0119	Catalyzes the condensation of the acetyl group of acetyl-CoA with 3-methyl-2-oxobutanoate (2-oxoisovalerate) to form 3-carboxy-3-hydroxy-4-methylpentanoate (2-isopropylmalate)
trd_1691	COG0065	Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate
trd_1692	COG0066	3-isopropylmalate dehydratase activity
trd_1695	COG1388	LysM domain
trd_1695	COG3858	chitin binding
trd_1696	COG0757	Catalyzes a trans-dehydration via an enolate intermediate
trd_1697	COG0006	proline dipeptidase activity
trd_1698	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
trd_1699	COG0511	ligase activity, forming carbon-carbon bonds
trd_1701	COG1722	exodeoxyribonuclease VII activity
trd_1708	COG0314	molybdopterin synthase activity
trd_1709	COG0303	'Molybdopterin
trd_1711	COG0317	In eubacteria ppGpp (guanosine 3'-diphosphate 5-' diphosphate) is a mediator of the stringent response that coordinates a variety of cellular activities in response to changes in nutritional abundance
trd_1712	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
trd_1714	COG0019	diaminopimelate decarboxylase activity
trd_1715	COG0488	(ABC) transporter
trd_1716	COG0237	dephospho-CoA kinase activity
trd_1718	COG0517	IMP dehydrogenase activity
trd_1718	COG1994	Peptidase M50
trd_1722	COG1490	D-aminoacyl-tRNA deacylase activity
trd_1723	COG0245	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity
trd_1724	COG1211	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity
trd_1725	COG4956	integral membrane protein (PIN domain superfamily)
trd_1726	COG0613	PHP domain protein
trd_1727	COG2359	stage V sporulation protein S
trd_1733	COG1071	oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
trd_1734	COG0022	dehydrogenase e1 component
trd_1734	COG0508	dehydrogenase complex catalyzes the overall conversion of
trd_1740	COG0178	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
trd_1742	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)
trd_1744	COG3246	L-lysine catabolic process to acetate
trd_1746	COG1196	nuclear chromosome segregation
trd_1747	COG1087	Belongs to the NAD(P)-dependent epimerase dehydratase family
trd_1754	COG2197	response regulator
trd_1756	COG0154	amidase activity
trd_1757	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)
trd_1759	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
trd_1760	COG0313	Catalyzes the 2'-O-methylation of the ribose of cytidine 1402 (C1402) in 16S rRNA
trd_1761	COG1804	L-carnitine dehydratase bile acid-inducible protein F
trd_1762	COG1024	Enoyl-CoA hydratase
trd_1768	COG2364	Membrane
trd_1770	COG0105	UTP biosynthetic process
trd_1776	COG2217	Heavy metal translocating P-type atpase
trd_1777	COG0111	D-isomer specific 2-hydroxyacid dehydrogenase
trd_1778	COG0297	glycogen (starch) synthase activity
trd_1780	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
trd_1781	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
trd_1784	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
trd_1786	COG0713	ATP synthesis coupled electron transport
trd_1787	COG1009	NADH ubiquinone oxidoreductase subunit 5 chain L Multisubunit Na H antiporter, MnhA subunit
trd_1789	COG1007	ATP synthesis coupled electron transport
trd_1791	COG1092	Specifically methylates the guanine in position 2445 (m2G2445) and the guanine in position 2069 (m7G2069) of 23S rRNA
trd_1792	COG1167	Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain MocR family and their eukaryotic orthologs
trd_1793	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
trd_1795	COG0595	An RNase that has 5'-3' exonuclease and possibly endonuclease activity. Involved in maturation of rRNA and in some organisms also mRNA maturation and or decay
trd_1798	COG0603	Catalyzes the ATP-dependent conversion of 7-carboxy-7- deazaguanine (CDG) to 7-cyano-7-deazaguanine (preQ(0))
trd_1799	COG0012	GTP binding
trd_1803	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
trd_1804	COG0045	succinate-CoA ligase (ADP-forming) activity
trd_1807	COG1071	oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
trd_1808	COG0022	dehydrogenase e1 component
trd_1810	COG2055	Belongs to the LDH2 MDH2 oxidoreductase family
trd_1813	COG5001	Diguanylate cyclase
trd_1818	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
trd_1819	COG0552	protein localization to endoplasmic reticulum
trd_1820	COG2003	Belongs to the UPF0758 family
trd_1825	COG1012	belongs to the aldehyde dehydrogenase family
trd_1827	COG0704	Plays a role in the regulation of phosphate uptake
trd_1828	COG1117	ATPase-coupled phosphate ion transmembrane transporter activity
trd_1829	COG1117	ATPase-coupled phosphate ion transmembrane transporter activity
trd_1830	COG0581	inorganic phosphate transmembrane transporter activity
trd_1831	COG0573	inorganic phosphate transmembrane transporter activity
trd_1832	COG0226	Part of the ABC transporter complex PstSACB involved in phosphate import
trd_1833	COG0745	RESPONSE REGULATOR receiver
trd_1836	COG1670	COG1670 acetyltransferases, including N-acetylases of ribosomal proteins
trd_1839	COG4166	transmembrane transport
trd_1840	COG1173	ABC-type dipeptide oligopeptide nickel transport systems, permease components
trd_1842	COG2870	Catalyzes the ADP transfer from ATP to D-glycero-beta-D- manno-heptose 1-phosphate, yielding ADP-D-glycero-beta-D-manno- heptose
trd_1842	COG0615	ADP-L-glycero-beta-D-manno-heptose biosynthetic process
trd_1843	COG0728	peptidoglycan biosynthetic process
trd_1845	COG0402	S-adenosylhomocysteine deaminase activity
trd_1850	COG2514	catechol 2,3-dioxygenase activity
trd_1851	COG1363	Peptidase, m42
trd_1852	COG0111	D-isomer specific 2-hydroxyacid dehydrogenase
trd_1854	COG0762	integral membrane protein
trd_1857	COG4481	Protein conserved in bacteria
trd_1859	COG2814	Major facilitator Superfamily
trd_1861	COG0601	transmembrane transport
trd_1862	COG0747	negative chemotaxis
trd_1863	COG0068	Along with HypE, it catalyzes the synthesis of the CN ligands of the active site iron of NiFe -hydrogenases using carbamoylphosphate as a substrate. It functions as a carbamoyl transferase using carbamoylphosphate as a substrate and transferring the carboxamido moiety in an ATP-dependent reaction to the thiolate of the C-terminal cysteine of HypE yielding a protein-S-carboxamide
trd_1865	COG0279	D-glycero-D-manno-heptose 7-phosphate biosynthetic process
trd_1871	COG0375	protein maturation
trd_1877	COG0374	Belongs to the NiFe NiFeSe hydrogenase large subunit family
trd_1879	COG1418	mRNA catabolic process
trd_1881	COG1716	ATPase activity
trd_1881	COG0842	Transport permease protein
trd_1881	COG1131	(ABC) transporter
trd_1888	COG0637	HAD-superfamily hydrolase subfamily IA, variant 3
trd_1889	COG2154	pterin-4-alpha-carbinolamine dehydratase
trd_1890	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)
trd_1892	COG0438	transferase activity, transferring glycosyl groups
trd_1894	COG0498	Catalyzes the gamma-elimination of phosphate from L- phosphohomoserine and the beta-addition of water to produce L- threonine
trd_1895	COG0266	class I DNA-(apurinic or apyrimidinic site) endonuclease activity
trd_1896	COG0537	adenosine 5'-monophosphoramidase activity
trd_1904	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
trd_1907	COG5001	Diguanylate cyclase
trd_1909	COG0215	cysteine-tRNA ligase activity
trd_1911	COG1252	NADH dehydrogenase
trd_1917	COG0561	phosphatase activity
trd_1924	COG0851	Prevents the cell division inhibition by proteins MinC and MinD at internal division sites while permitting inhibition at polar sites. This ensures cell division at the proper site by restricting the formation of a division septum at the midpoint of the long axis of the cell
trd_1925	COG2894	cell division
trd_1926	COG0850	regulation of cytokinetic process
trd_1927	COG0768	penicillin binding
trd_1930	COG0366	Alpha amylase catalytic
trd_1933	COG0296	Catalyzes the formation of the alpha-1,6-glucosidic linkages in glycogen by scission of a 1,4-alpha-linked oligosaccharide from growing alpha-1,4-glucan chains and the subsequent attachment of the oligosaccharide to the alpha-1,6 position
trd_1936	COG0770	UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase activity
trd_1938	COG1077	Cell shape determining protein MreB Mrl
trd_1939	COG1196	nuclear chromosome segregation
trd_1939	COG0741	lytic transglycosylase activity
trd_1939	COG0739	heme binding
trd_1940	COG1597	lipid kinase activity
trd_1942	COG1063	alcohol dehydrogenase
trd_1943	COG3653	N-Acyl-D-aspartate D-glutamate deacylase
trd_1944	COG0684	Catalyzes the aldol cleavage of 4-hydroxy-4-methyl-2- oxoglutarate (HMG) into 2 molecules of pyruvate. Also contains a secondary oxaloacetate (OAA) decarboxylase activity due to the common pyruvate enolate transition state formed following C-C bond cleavage in the retro-aldol and decarboxylation reactions
trd_1945	COG4948	Mandelate Racemase Muconate Lactonizing
trd_1948	COG0451	ADP-glyceromanno-heptose 6-epimerase activity
trd_1950	COG1173	ABC-type dipeptide oligopeptide nickel transport systems, permease components
trd_1952	COG0747	negative chemotaxis
trd_1954	COG0444	Belongs to the ABC transporter superfamily
trd_1955	COG4608	Belongs to the ABC transporter superfamily
trd_1956	COG4948	Mandelate Racemase Muconate Lactonizing
trd_1957	COG4948	Mandelate Racemase Muconate Lactonizing
trd_1958	COG4948	Mandelate Racemase Muconate Lactonizing
trd_1963	COG2333	competence protein COMEC
trd_1963	COG0658	competence protein
trd_1965	COG0438	transferase activity, transferring glycosyl groups
trd_1968	COG0744	Peptidoglycan polymerase that catalyzes glycan chain elongation from lipid-linked precursors
trd_1973	COG0437	4 iron, 4 sulfur cluster binding
trd_1976	COG0589	response to stress
trd_1982	COG0668	transmembrane transport
trd_A0004	COG0628	permease
trd_A0007	COG0259	pyridoxamine-phosphate oxidase activity
trd_A0008	COG0537	adenosine 5'-monophosphoramidase activity
trd_A0012	COG1028	Short-chain dehydrogenase reductase Sdr
trd_A0014	COG2084	Dehydrogenase
trd_A0015	COG0778	Nitroreductase
trd_A0017	COG0606	chelatase, subunit chli
trd_A0029	COG1868	FliM is one of three proteins (FliG, FliN, FliM) that forms the rotor-mounted switch complex (C ring), located at the base of the basal body. This complex interacts with the CheY and CheZ chemotaxis proteins, in addition to contacting components of the motor that determine the direction of flagellar rotation
trd_A0032	COG1291	archaeal or bacterial-type flagellum-dependent cell motility
trd_A0034	COG1338	Plays a role in the flagellum-specific transport system
trd_A0036	COG1684	flagellar biosynthetic protein fliR
trd_A0037	COG1377	Required for formation of the rod structure in the basal body of the flagellar apparatus. Together with FliI and FliH, may constitute the export apparatus of flagellin
trd_A0038	COG1298	Required for formation of the rod structure of the flagellar apparatus. Together with FliI and FliH, may constitute the export apparatus of flagellin
trd_A0041	COG1191	sigma factor activity
trd_A0044	COG4786	Flagellar basal body rod
trd_A0045	COG4786	Flagellar basal body rod
trd_A0048	COG4786	Flagellar basal body rod
trd_A0048	COG1256	bacterial-type flagellum assembly
trd_A0049	COG1344	Flagellin is the subunit protein which polymerizes to form the filaments of bacterial flagella
trd_A0050	COG1699	Binds to the C-terminal region of flagellin, which is implicated in polymerization, and participates in the assembly of the flagellum
trd_A0051	COG1551	Could accelerate the degradation of some genes transcripts potentially through selective RNA binding
trd_A0056	COG3383	formate dehydrogenase (NAD+) activity
trd_A0056	COG0243	molybdopterin cofactor binding
trd_A0057	COG3383	formate dehydrogenase (NAD+) activity
trd_A0057	COG0243	molybdopterin cofactor binding
trd_A0058	COG0437	4 iron, 4 sulfur cluster binding
trd_A0063	COG0701	Predicted permease
trd_A0068	COG2080	2 iron, 2 sulfur cluster binding
trd_A0069	COG1529	Aldehyde oxidase and xanthine dehydrogenase
trd_A0075	COG3848	Pyruvate phosphate dikinase
trd_A0075	COG0574	Belongs to the PEP-utilizing enzyme family
trd_A0078	COG5564	TIM-barrel signal transduction protein
trd_A0084	COG0559	Belongs to the binding-protein-dependent transport system permease family
trd_A0087	COG1028	Short-chain dehydrogenase reductase Sdr
trd_A0089	COG1122	ATPase activity
trd_A0097	COG0318	PFAM AMP-dependent synthetase and ligase
trd_A0099	COG1024	Enoyl-CoA hydratase
trd_A0100	COG1649	PFAM Uncharacterised BCR, COG1649
trd_A0100	COG0726	polysaccharide deacetylase
trd_A0109	COG1104	cysteine desulfurase activity
trd_A0117	COG0265	Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain
trd_A0132	COG1595	DNA-templated transcription, initiation
trd_A0137	COG1215	transferase activity, transferring glycosyl groups
trd_A0141	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
trd_A0150	COG1612	heme a metabolic process
trd_A0151	COG1162	GTPase activity
trd_A0153	COG2186	Transcriptional regulator
trd_A0155	COG2197	response regulator
trd_A0156	COG0787	Catalyzes the interconversion of L-alanine and D- alanine. May also act on other amino acids
trd_A0158	COG0028	Belongs to the TPP enzyme family
trd_A0162	COG3938	Belongs to the proline racemase family
trd_A0165	COG0189	ligase activity
trd_A0171	COG1131	(ABC) transporter
trd_A0176	COG2079	MmgE PrpD family protein
trd_A0177	COG2513	Catalyzes the thermodynamically favored C-C bond cleavage of (2R,3S)-2-methylisocitrate to yield pyruvate and succinate
trd_A0182	COG0735	belongs to the Fur family
trd_A0183	COG4531	ABC-type Zn2 transport system, periplasmic component surface adhesin
trd_A0184	COG1121	(ABC) transporter
trd_A0185	COG1108	ABC-type Mn2 Zn2 transport systems permease components
trd_A0192	COG1131	(ABC) transporter
trd_A0197	COG1573	uracil-dna glycosylase
trd_A0200	COG1350	The beta subunit is responsible for the synthesis of L- tryptophan from indole and L-serine
trd_A0202	COG1139	Iron-sulfur cluster binding protein
trd_A0205	COG2508	Transcriptional regulator
trd_A0210	COG2201	protein-glutamate methylesterase activity
trd_A0215	COG2198	Histidine kinase
trd_A0215	COG0643	Histidine kinase
trd_A0217	COG0840	transmembrane signaling receptor activity
trd_A0220	COG1345	Required for morphogenesis and for the elongation of the flagellar filament by facilitating polymerization of the flagellin monomers at the tip of growing filament. Forms a capping structure, which prevents flagellin subunits (transported through the central channel of the flagellum) from leaking out without polymerization at the distal end
trd_A0221	COG1516	flagellar protein fliS
trd_A0228	COG2132	Multicopper oxidase
trd_A0229	COG1028	Short-chain dehydrogenase reductase Sdr
trd_A0230	COG1028	Short-chain dehydrogenase reductase Sdr
trd_A0233	COG1910	domain protein
trd_A0239	COG1914	H( )-stimulated, divalent metal cation uptake system
trd_A0249	COG1116	anion transmembrane transporter activity
trd_A0250	COG0715	COG0715 ABC-type nitrate sulfonate bicarbonate transport systems periplasmic components
trd_A0251	COG0600	ABC-type nitrate sulfonate bicarbonate transport system permease component
trd_A0253	COG0461	Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP)
trd_A0255	COG0285	dihydrofolate synthase activity
trd_A0256	COG1316	TRANSCRIPTIONal
trd_A0258	COG2267	carboxylic ester hydrolase activity
trd_A0259	COG0596	Alpha beta hydrolase
trd_A0261	COG1165	Catalyzes the thiamine diphosphate-dependent decarboxylation of 2-oxoglutarate and the subsequent addition of the resulting succinic semialdehyde-thiamine pyrophosphate anion to isochorismate to yield 2-succinyl-5-enolpyruvyl-6-hydroxy-3- cyclohexene-1-carboxylate (SEPHCHC)
trd_A0263	COG1309	transcriptional regulator
trd_A0265	COG0584	glycerophosphoryl diester phosphodiesterase
trd_A0266	COG1175	transmembrane transport
trd_A0267	COG0395	ABC-type sugar transport system, permease component
trd_A0281	COG0553	Transcription regulator that activates transcription by stimulating RNA polymerase (RNAP) recycling in case of stress conditions such as supercoiled DNA or high salt concentrations. Probably acts by releasing the RNAP, when it is trapped or immobilized on tightly supercoiled DNA. Does not activate transcription on linear DNA. Probably not involved in DNA repair
trd_A0295	COG0840	transmembrane signaling receptor activity
trd_A0299	COG2252	PERMEase
trd_A0302	COG0053	Belongs to the cation diffusion facilitator (CDF) transporter (TC 2.A.4) family
trd_A0304	COG0447	Converts o-succinylbenzoyl-CoA (OSB-CoA) to 1,4- dihydroxy-2-naphthoyl-CoA (DHNA-CoA)
trd_A0306	COG4948	Mandelate Racemase Muconate Lactonizing
trd_A0308	COG0318	PFAM AMP-dependent synthetase and ligase
trd_A0309	COG0281	malic enzyme
trd_A0311	COG2239	Acts as a magnesium transporter
trd_A0315	COG0265	Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain
trd_A0320	COG0265	Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain
trd_A0321	COG1595	DNA-templated transcription, initiation
trd_A0324	COG1173	ABC-type dipeptide oligopeptide nickel transport systems, permease components
trd_A0325	COG0601	transmembrane transport
trd_A0326	COG0492	ferredoxin-NADP+ reductase activity
trd_A0328	COG0028	Belongs to the TPP enzyme family
trd_A0329	COG1116	anion transmembrane transporter activity
trd_A0330	COG0318	PFAM AMP-dependent synthetase and ligase
trd_A0333	COG1024	Enoyl-CoA hydratase
trd_A0340	COG5517	Aromatic-ring-hydroxylating dioxygenase beta subunit
trd_A0341	COG4638	Rieske (2fe-2S)
trd_A0344	COG0492	ferredoxin-NADP+ reductase activity
trd_A0345	COG0168	Low-affinity potassium transport system. Interacts with trk system potassium uptake protein TrkA
trd_A0346	COG0168	Low-affinity potassium transport system. Interacts with trk system potassium uptake protein TrkA
trd_A0347	COG0569	domain protein
trd_A0348	COG0179	Fumarylacetoacetate (FAA) hydrolase
trd_A0350	COG1253	flavin adenine dinucleotide binding
trd_A0355	COG1131	(ABC) transporter
trd_A0356	COG0578	Belongs to the FAD-dependent glycerol-3-phosphate dehydrogenase family
trd_A0358	COG0554	Key enzyme in the regulation of glycerol uptake and metabolism. Catalyzes the phosphorylation of glycerol to yield sn- glycerol 3-phosphate
trd_A0362	COG0160	Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family
trd_A0366	COG0180	Tryptophanyl-tRNA synthetase
trd_A0369	COG1320	monovalent cation:proton antiporter activity
trd_A0370	COG2212	antiporter activity
trd_A0371	COG1863	multisubunit Na H antiporter MnhE subunit
trd_A0374	COG2111	Na H antiporter
trd_A0375	COG2111	Na H antiporter
trd_A0375	COG1009	NADH ubiquinone oxidoreductase subunit 5 chain L Multisubunit Na H antiporter, MnhA subunit
trd_A0390	COG0514	ATP-dependent DNA helicase (RecQ)
trd_A0393	COG1622	oxidoreductase activity, acting on a heme group of donors, oxygen as acceptor
trd_A0395	COG0109	protoheme IX farnesyltransferase activity
trd_A0400	COG1529	Aldehyde oxidase and xanthine dehydrogenase
trd_A0402	COG0351	phosphomethylpyrimidine kinase
trd_A0407	COG3964	amidohydrolase
trd_A0412	COG1067	ATP-dependent peptidase activity
trd_A0421	COG0301	tRNA thio-modification
trd_A0425	COG2268	Band 7 protein
trd_A0428	COG0833	amino acid
trd_A0429	COG1028	Short-chain dehydrogenase reductase Sdr
trd_A0430	COG0174	glutamine synthetase
trd_A0436	COG0024	Methionine aminopeptidase
trd_A0437	COG0697	spore germination
trd_A0439	COG3794	PFAM blue (type 1) copper domain protein
trd_A0442	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
trd_A0446	COG0331	[acyl-carrier-protein] S-malonyltransferase activity
trd_A0447	COG0304	beta-ketoacyl-acyl-carrier-protein synthase II activity
trd_A0448	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
trd_A0449	COG0249	that it carries out the mismatch recognition step. This protein has a weak ATPase activity
trd_A0452	COG0436	Aminotransferase
trd_A0454	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
trd_A0456	COG3336	cytochrome c oxidase
trd_A0457	COG1231	oxidoreductase activity
trd_A0460	COG2084	Dehydrogenase
trd_A0468	COG0395	ABC-type sugar transport system, permease component
trd_A0469	COG1175	transmembrane transport
trd_A0470	COG1653	transport
trd_A0471	COG2186	Transcriptional regulator
trd_A0473	COG1353	crispr-associated protein
trd_A0475	COG0179	Fumarylacetoacetate (FAA) hydrolase
trd_A0479	COG0474	ATPase, P-type transporting, HAD superfamily, subfamily IC
trd_A0482	COG1482	cell wall glycoprotein biosynthetic process
trd_A0485	COG0475	glutathione-regulated potassium exporter activity
trd_A0486	COG1249	Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family
trd_A0488	COG1595	DNA-templated transcription, initiation
trd_A0503	COG0372	Belongs to the citrate synthase family
trd_A0506	COG4867	von Willebrand factor, type A
trd_A0508	COG0095	Lipoate-protein ligase
trd_A0511	COG0388	Catalyzes the ATP-dependent amidation of deamido-NAD to form NAD. Uses L-glutamine as a nitrogen source
trd_A0517	COG1811	Na channel or pump
trd_A0520	COG0277	FAD linked oxidase domain protein
trd_A0521	COG1446	asparaginase
trd_A0525	COG0587	DNA-directed DNA polymerase activity
trd_A0526	COG0389	Poorly processive, error-prone DNA polymerase involved in untargeted mutagenesis. Copies undamaged DNA at stalled replication forks, which arise in vivo from mismatched or misaligned primer ends. These misaligned primers can be extended by PolIV. Exhibits no 3'-5' exonuclease (proofreading) activity. May be involved in translesional synthesis, in conjunction with the beta clamp from PolIII
trd_A0527	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
trd_A0532	COG3842	ATPase activity
trd_A0533	COG1178	ABC-type Fe3 transport system permease component
trd_A0534	COG1840	ABC-type Fe3 transport system, periplasmic component
trd_A0539	COG1063	alcohol dehydrogenase
trd_A0544	COG0259	pyridoxamine-phosphate oxidase activity
trd_A0545	COG0589	response to stress
trd_A0547	COG1764	response to oxidative stress
trd_A0561	COG0612	Peptidase, M16
trd_A0562	COG1048	Catalyzes the isomerization of citrate to isocitrate via cis-aconitate
trd_A0563	COG1975	Xanthine and CO dehydrogenases maturation factor, XdhC CoxF family
trd_A0563	COG3608	succinylglutamate desuccinylase aspartoacylase
trd_A0567	COG1506	peptidase
trd_A0567	COG0823	Involved in the tonB-independent uptake of proteins
trd_A0567	COG4946	Tricorn protease homolog
trd_A0568	COG0746	molybdenum cofactor guanylyltransferase activity
trd_A0582	COG1461	Dihydroxyacetone kinase
trd_A0588	COG1172	Belongs to the binding-protein-dependent transport system permease family
trd_A0589	COG1172	Belongs to the binding-protein-dependent transport system permease family
trd_A0590	COG2220	Zn-dependent hydrolases of the beta-lactamase fold
trd_A0591	COG4948	Mandelate Racemase Muconate Lactonizing
trd_A0592	COG1129	ABC transporter
trd_A0594	COG1414	Transcriptional regulator
trd_A0597	COG1078	dGTPase activity
trd_A0598	COG0506	proline dehydrogenase activity
trd_A0602	COG0310	cobalt ion transport
trd_A0603	COG0619	Transmembrane (T) component of an energy-coupling factor (ECF) ABC-transporter complex. Unlike classic ABC transporters this ECF transporter provides the energy necessary to transport a number of different substrates
trd_A0604	COG1122	ATPase activity
trd_A0607	COG2205	protein histidine kinase activity
trd_A0609	COG2353	YceI-like domain
trd_A0611	COG1595	DNA-templated transcription, initiation
trd_A0619	COG4274	PFAM GYD family protein
trd_A0621	COG0477	Major facilitator Superfamily
trd_A0622	COG0167	dihydroorotate dehydrogenase activity
trd_A0624	COG0546	phosphoglycolate phosphatase activity
trd_A0628	COG0243	molybdopterin cofactor binding
trd_A0630	COG1937	Protein conserved in bacteria
trd_A0638	COG0410	ABC transporter
trd_A0645	COG1815	bacterial-type flagellum-dependent cell motility
trd_A0646	COG0741	lytic transglycosylase activity
trd_A0648	COG1157	protein secretion by the type III secretion system
trd_A0650	COG1536	FliG is one of three proteins (FliG, FliN, FliM) that forms the rotor-mounted switch complex (C ring), located at the base of the basal body. This complex interacts with the CheY and CheZ chemotaxis proteins, in addition to contacting components of the motor that determine the direction of flagellar rotation
trd_A0651	COG1766	The M ring may be actively involved in energy transduction
trd_A0652	COG1677	Flagellar hook-basal body complex protein FliE
trd_A0653	COG1558	bacterial-type flagellum-dependent cell motility
trd_A0657	COG1473	amidohydrolase
trd_A0658	COG2133	pyrroloquinoline quinone binding
trd_A0659	COG0697	spore germination
trd_A0664	COG0586	Pfam SNARE associated Golgi protein
trd_A0672	COG0714	Associated with various cellular activities
trd_A0676	COG2141	COG2141 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases
trd_A0681	COG0846	NAD-dependent lysine deacetylase and desuccinylase that specifically removes acetyl and succinyl groups on target proteins. Modulates the activities of several proteins which are inactive in their acylated form
trd_A0682	COG0665	tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase activity
trd_A0693	COG0035	Catalyzes the conversion of uracil and 5-phospho-alpha- D-ribose 1-diphosphate (PRPP) to UMP and diphosphate
trd_A0699	COG0747	negative chemotaxis
trd_A0700	COG0601	transmembrane transport
trd_A0705	COG0673	inositol 2-dehydrogenase activity
trd_A0706	COG0449	glutamine-fructose-6-phosphate transaminase (isomerizing) activity
trd_A0707	COG1820	Belongs to the metallo-dependent hydrolases superfamily. NagA family
trd_A0708	COG1680	COG1680 Beta-lactamase class C and other penicillin binding
trd_A0709	COG2377	Catalyzes the specific phosphorylation of 1,6-anhydro-N- acetylmuramic acid (anhMurNAc) with the simultaneous cleavage of the 1,6-anhydro ring, generating MurNAc-6-P. Is required for the utilization of anhMurNAc either imported from the medium or derived from its own cell wall murein, and thus plays a role in cell wall recycling
trd_A0712	COG2971	BadF BadG BcrA BcrD
trd_A0713	COG2103	Specifically catalyzes the cleavage of the D-lactyl ether substituent of MurNAc 6-phosphate, producing GlcNAc 6- phosphate and D-lactate
trd_A0715	COG4948	Mandelate Racemase Muconate Lactonizing
trd_A0719	COG1205	dead DEAH box helicase
trd_A0719	COG1111	helicase
trd_A0729	COG0477	Major facilitator Superfamily
trd_A0732	COG0702	epimerase
trd_A0733	COG0702	epimerase
trd_A0735	COG3434	signal transduction protein containing EAL and modified HD-GYP domains
trd_A0737	COG3434	signal transduction protein containing EAL and modified HD-GYP domains
trd_A0739	COG0526	COG0526, thiol-disulfide isomerase and thioredoxins
trd_A0740	COG0665	tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase activity
trd_A0750	COG1522	sequence-specific DNA binding
trd_A0752	COG0001	glutamate-1-semialdehyde 2,1-aminomutase activity
trd_A0767	COG1268	BioY protein
trd_A0768	COG1540	5-oxoprolinase (ATP-hydrolyzing) activity
trd_A0769	COG1984	allophanate hydrolase subunit 2
trd_A0770	COG2049	5-oxoprolinase (ATP-hydrolyzing) activity
trd_A0772	COG1172	Belongs to the binding-protein-dependent transport system permease family
trd_A0773	COG1129	ABC transporter
trd_A0778	COG0439	Biotin carboxylase
trd_A0784	COG0413	3-methyl-2-oxobutanoate hydroxymethyltransferase activity
trd_A0785	COG0414	Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate
trd_A0786	COG2815	serine threonine protein kinase
trd_A0786	COG0515	serine threonine protein kinase
trd_A0787	COG0682	Transfers the N-acyl diglyceride group on what will become the N-terminal cysteine of membrane lipoproteins
trd_A0788	COG0318	PFAM AMP-dependent synthetase and ligase
trd_A0791	COG0028	Belongs to the TPP enzyme family
trd_A0792	COG0404	The glycine cleavage system catalyzes the degradation of glycine
trd_A0797	COG0394	Belongs to the low molecular weight phosphotyrosine protein phosphatase family
trd_A0811	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
trd_A0812	COG0436	Aminotransferase
trd_A0821	COG0489	protein tyrosine kinase activity
trd_A0826	COG0447	Converts o-succinylbenzoyl-CoA (OSB-CoA) to 1,4- dihydroxy-2-naphthoyl-CoA (DHNA-CoA)
trd_A0828	COG0318	PFAM AMP-dependent synthetase and ligase
trd_A0829	COG0477	Major facilitator Superfamily
trd_A0831	COG0640	Transcriptional regulator
trd_A0834	COG0491	Thiolesterase that catalyzes the hydrolysis of S-D- lactoyl-glutathione to form glutathione and D-lactic acid
trd_A0835	COG0607	Catalyzes the ATP-dependent transfer of a sulfur to tRNA to produce 4-thiouridine in position 8 of tRNAs, which functions as a near-UV photosensor. Also catalyzes the transfer of sulfur to the sulfur carrier protein ThiS, forming ThiS-thiocarboxylate. This is a step in the synthesis of thiazole, in the thiamine biosynthesis pathway. The sulfur is donated as persulfide by IscS
trd_A0836	COG1251	Belongs to the nitrite and sulfite reductase 4Fe-4S domain family
trd_A0839	COG1215	transferase activity, transferring glycosyl groups
trd_A0851	COG0154	amidase activity
trd_A0852	COG0717	Belongs to the dCTP deaminase family
trd_A0856	COG0345	Catalyzes the reduction of 1-pyrroline-5-carboxylate (PCA) to L-proline
trd_A0859	COG3387	PFAM Glycoside hydrolase 15-related
trd_A0869	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)
trd_A0870	COG1559	Functions as a peptidoglycan terminase that cleaves nascent peptidoglycan strands endolytically to terminate their elongation
trd_A0871	COG0169	Involved in the biosynthesis of the chorismate, which leads to the biosynthesis of aromatic amino acids. Catalyzes the reversible NADPH linked reduction of 3-dehydroshikimate (DHSA) to yield shikimate (SA)
trd_A0873	COG2719	SpoVR family
trd_A0874	COG2718	Belongs to the UPF0229 family
trd_A0875	COG2766	serine protein kinase
trd_A0877	COG1363	Peptidase, m42
trd_A0888	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
trd_A0892	COG0665	tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase activity
trd_A0895	COG1167	Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain MocR family and their eukaryotic orthologs
trd_A0898	COG0726	polysaccharide deacetylase
trd_A0899	COG1060	Radical SAM enzyme that catalyzes the addition of the adenosyl radical to the double bond of 3- (1- carboxyvinyl)oxy benzoate, leading to aminodeoxyfutalosine (AFL), a key intermediate in the formation of menaquinone (MK, vitamin K2) from chorismate
trd_A0900	COG1060	Radical SAM enzyme that catalyzes the addition of the adenosyl radical to the double bond of 3- (1- carboxyvinyl)oxy benzoate, leading to aminodeoxyfutalosine (AFL), a key intermediate in the formation of menaquinone (MK, vitamin K2) from chorismate
trd_A0908	COG1164	Oligoendopeptidase f
trd_A0909	COG2226	methyltransferase
trd_A0910	COG1881	PFAM PEBP family protein
trd_A0931	COG2368	4-hydroxyphenylacetate
trd_A0932	COG1028	Short-chain dehydrogenase reductase Sdr