locus-tag	class	description
D3M96_00010	COG0592	DNA-directed DNA polymerase activity
D3M96_00050	COG1593	TRAP-type C4-dicarboxylate transport system, large permease component
D3M96_00070	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
D3M96_00075	COG0583	DNA-binding transcription factor activity
D3M96_00085	COG4663	Part of the tripartite ATP-independent periplasmic (TRAP) transport system
D3M96_00095	COG0559	Belongs to the binding-protein-dependent transport system permease family
D3M96_00110	COG0318	PFAM AMP-dependent synthetase and ligase
D3M96_00120	COG0508	dehydrogenase complex catalyzes the overall conversion of
D3M96_00120	COG0596	Alpha beta hydrolase
D3M96_00125	COG1167	Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain MocR family and their eukaryotic orthologs
D3M96_00140	COG3181	Tripartite tricarboxylate transporter family receptor
D3M96_00150	COG0697	spore germination
D3M96_00155	COG0583	DNA-binding transcription factor activity
D3M96_00165	COG3842	ATPase activity
D3M96_00185	COG0523	cobalamin synthesis protein
D3M96_00245	COG1846	Transcriptional regulator
D3M96_00265	COG0179	Fumarylacetoacetate (FAA) hydrolase
D3M96_00270	COG0388	Catalyzes the ATP-dependent amidation of deamido-NAD to form NAD. Uses L-glutamine as a nitrogen source
D3M96_00275	COG1878	Catalyzes the hydrolysis of N-formyl-L-kynurenine to L- kynurenine, the second step in the kynurenine pathway of tryptophan degradation
D3M96_00285	COG4638	Rieske (2fe-2S)
D3M96_00310	COG1028	Short-chain dehydrogenase reductase Sdr
D3M96_00340	COG1028	Short-chain dehydrogenase reductase Sdr
D3M96_00350	COG1853	conserved protein domain typically associated with flavoprotein oxygenases, DIM6 NTAB family
D3M96_00365	COG1853	conserved protein domain typically associated with flavoprotein oxygenases, DIM6 NTAB family
D3M96_00385	COG4608	Belongs to the ABC transporter superfamily
D3M96_00390	COG0444	Belongs to the ABC transporter superfamily
D3M96_00395	COG1173	ABC-type dipeptide oligopeptide nickel transport systems, permease components
D3M96_00405	COG0747	negative chemotaxis
D3M96_00410	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
D3M96_00415	COG4992	N2-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity
D3M96_00460	COG4149	molybdate abc transporter
D3M96_00475	COG2225	Involved in the glycolate utilization. Catalyzes the condensation and subsequent hydrolysis of acetyl-coenzyme A (acetyl-CoA) and glyoxylate to form malate and CoA
D3M96_00485	COG0775	Catalyzes the irreversible cleavage of the glycosidic bond in both 5'-methylthioadenosine (MTA) and S- adenosylhomocysteine (SAH AdoHcy) to adenine and the corresponding thioribose, 5'-methylthioribose and S-ribosylhomocysteine, respectively
D3M96_00495	COG1593	TRAP-type C4-dicarboxylate transport system, large permease component
D3M96_00510	COG0028	Belongs to the TPP enzyme family
D3M96_00515	COG1638	TRAP-type C4-dicarboxylate transport system periplasmic component
D3M96_00540	COG0551	DNA topoisomerase type I activity
D3M96_00540	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
D3M96_00550	COG2922	Belongs to the Smg family
D3M96_00565	COG4799	Acetyl-CoA carboxylase, carboxyltransferase component subunits alpha and beta
D3M96_00570	COG0183	Belongs to the thiolase family
D3M96_00575	COG4579	[isocitrate dehydrogenase (NADP+)] phosphatase activity
D3M96_00580	COG1960	acyl-CoA dehydrogenase activity
D3M96_00600	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
D3M96_00610	COG0018	arginyl-trna synthetase
D3M96_00640	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)
D3M96_00650	COG1508	bacterial-type RNA polymerase transcriptional activator activity, sequence-specific DNA binding
D3M96_00655	COG4774	siderophore transport
D3M96_00675	COG4108	Increases the formation of ribosomal termination complexes and stimulates activities of RF-1 and RF-2. It binds guanine nucleotides and has strong preference for UGA stop codons. It may interact directly with the ribosome. The stimulation of RF- 1 and RF-2 is significantly reduced by GTP and GDP, but not by GMP
D3M96_00680	COG1280	lysine exporter protein (LysE YggA)
D3M96_00685	COG0513	Belongs to the DEAD box helicase family
D3M96_00695	COG1512	COG1512 Beta-propeller domains of methanol dehydrogenase type
D3M96_00710	COG0486	Exhibits a very high intrinsic GTPase hydrolysis rate. Involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA- cmnm(5)s(2)U34
D3M96_00725	COG0154	amidase activity
D3M96_00770	COG0767	ABC-type transport system involved in resistance to organic solvents, permease component
D3M96_00775	COG1127	ABC transporter
D3M96_00795	COG0637	HAD-superfamily hydrolase subfamily IA, variant 3
D3M96_00800	COG1638	TRAP-type C4-dicarboxylate transport system periplasmic component
D3M96_00810	COG1593	TRAP-type C4-dicarboxylate transport system, large permease component
D3M96_00850	COG0583	DNA-binding transcription factor activity
D3M96_00880	COG1254	Belongs to the acylphosphatase family
D3M96_00900	COG0564	pseudouridine synthase activity
D3M96_00905	COG0252	asparaginase activity
D3M96_00930	COG0334	Belongs to the Glu Leu Phe Val dehydrogenases family
D3M96_00935	COG0325	Pyridoxal 5'-phosphate (PLP)-binding protein, which is involved in PLP homeostasis
D3M96_00940	COG3181	Tripartite tricarboxylate transporter family receptor
D3M96_00955	COG0411	ABC transporter
D3M96_00960	COG0559	Belongs to the binding-protein-dependent transport system permease family
D3M96_00985	COG0834	ABC-type amino acid transport signal transduction systems periplasmic component domain
D3M96_01000	COG0758	DNA mediated transformation
D3M96_01005	COG0242	peptide deformylase activity
D3M96_01010	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
D3M96_01015	COG0697	spore germination
D3M96_01030	COG1593	TRAP-type C4-dicarboxylate transport system, large permease component
D3M96_01045	COG4336	lyase activity
D3M96_01050	COG0583	DNA-binding transcription factor activity
D3M96_01055	COG0859	PFAM glycosyl transferase family 9
D3M96_01065	COG1278	Cold shock
D3M96_01070	COG1210	Utp--glucose-1-phosphate uridylyltransferase
D3M96_01075	COG1521	Catalyzes the phosphorylation of pantothenate (Pan), the first step in CoA biosynthesis
D3M96_01080	COG1654	Acts both as a biotin-- acetyl-CoA-carboxylase ligase and a biotin-operon repressor. In the presence of ATP, BirA activates biotin to form the BirA-biotinyl-5'-adenylate (BirA-bio- 5'-AMP or holoBirA) complex. HoloBirA can either transfer the biotinyl moiety to the biotin carboxyl carrier protein (BCCP) subunit of acetyl-CoA carboxylase, or bind to the biotin operator site and inhibit transcription of the operon
D3M96_01080	COG0340	biotin-[acetyl-CoA-carboxylase] ligase activity
D3M96_01090	COG1686	Belongs to the peptidase S11 family
D3M96_01100	COG2921	Belongs to the UPF0250 family
D3M96_01105	COG0321	lipoyl(octanoyl) transferase activity
D3M96_01110	COG1024	Enoyl-CoA hydratase
D3M96_01115	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
D3M96_01125	COG0692	Excises uracil residues from the DNA which can arise as a result of misincorporation of dUMP residues by DNA polymerase or due to deamination of cytosine
D3M96_01205	COG0134	indole-3-glycerol-phosphate synthase activity
D3M96_01210	COG0547	Catalyzes the transfer of the phosphoribosyl group of 5- phosphorylribose-1-pyrophosphate (PRPP) to anthranilate to yield N-(5'-phosphoribosyl)-anthranilate (PRA)
D3M96_01215	COG0512	Glutamine amidotransferase of anthranilate synthase
D3M96_01225	COG0546	phosphoglycolate phosphatase activity
D3M96_01240	COG2967	ApaG domain
D3M96_01250	COG0654	COG0654 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases
D3M96_01255	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
D3M96_01265	COG0840	transmembrane signaling receptor activity
D3M96_01275	COG1028	Short-chain dehydrogenase reductase Sdr
D3M96_01280	COG1535	isochorismatase
D3M96_01280	COG3433	isochorismatase activity
D3M96_01285	COG1169	isochorismate synthase
D3M96_01300	COG1020	D-alanine [D-alanyl carrier protein] ligase activity
D3M96_01305	COG3433	isochorismatase activity
D3M96_01305	COG1535	isochorismatase
D3M96_01310	COG1021	2,3-dihydroxybenzoate-AMP ligase
D3M96_01320	COG0410	ABC transporter
D3M96_01325	COG0411	ABC transporter
D3M96_01340	COG0683	leucine binding
D3M96_01355	COG0600	ABC-type nitrate sulfonate bicarbonate transport system permease component
D3M96_01390	COG4559	Part of the ABC transporter complex HmuTUV involved in hemin import. Responsible for energy coupling to the transport system
D3M96_01395	COG0609	Belongs to the binding-protein-dependent transport system permease family. FecCD subfamily
D3M96_01400	COG2819	hydrolase of the alpha beta superfamily
D3M96_01405	COG0513	Belongs to the DEAD box helicase family
D3M96_01410	COG2814	Major facilitator Superfamily
D3M96_01420	COG0583	DNA-binding transcription factor activity
D3M96_01430	COG1253	flavin adenine dinucleotide binding
D3M96_01455	COG0115	Belongs to the class-IV pyridoxal-phosphate-dependent aminotransferase family
D3M96_01460	COG2311	Membrane
D3M96_01485	COG1853	conserved protein domain typically associated with flavoprotein oxygenases, DIM6 NTAB family
D3M96_01505	COG0600	ABC-type nitrate sulfonate bicarbonate transport system permease component
D3M96_01510	COG4525	Part of the ABC transporter complex TauABC involved in taurine import. Responsible for energy coupling to the transport system
D3M96_01520	COG0583	DNA-binding transcription factor activity
D3M96_01525	COG0834	ABC-type amino acid transport signal transduction systems periplasmic component domain
D3M96_01530	COG1126	abc transporter atp-binding protein
D3M96_01535	COG0765	amino acid transport
D3M96_01540	COG0765	amino acid transport
D3M96_01550	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
D3M96_01565	COG3391	amine dehydrogenase activity
D3M96_01575	COG1225	Alkyl hydroperoxide reductase Thiol specific antioxidant Mal allergen
D3M96_01600	COG0407	Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III
D3M96_01605	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
D3M96_01610	COG0210	DNA helicase
D3M96_01630	COG0069	glutamate synthase activity
D3M96_01630	COG0067	glutamate synthase
D3M96_01630	COG0070	glutamate synthase
D3M96_01635	COG1024	Enoyl-CoA hydratase
D3M96_01645	COG1804	L-carnitine dehydratase bile acid-inducible protein F
D3M96_01650	COG1250	3-hydroxyacyl-CoA dehydrogenase
D3M96_01675	COG2918	glutathione biosynthetic process
D3M96_01685	COG2197	response regulator
D3M96_01690	COG2021	Transfers an acetyl group from acetyl-CoA to L- homoserine, forming acetyl-L-homoserine
D3M96_01700	COG2223	nitrite transmembrane transporter activity
D3M96_01705	COG2860	membrane
D3M96_01710	COG1346	cytolysis
D3M96_01725	COG0251	oxidation-reduction process
D3M96_01760	COG1280	lysine exporter protein (LysE YggA)
D3M96_01770	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
D3M96_01785	COG0161	adenosylmethionine-8-amino-7-oxononanoate transaminase activity
D3M96_01800	COG2096	Adenosyltransferase
D3M96_01815	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
D3M96_01820	COG5405	Protease subunit of a proteasome-like degradation complex believed to be a general protein degrading machinery
D3M96_01825	COG0583	DNA-binding transcription factor activity
D3M96_01830	COG1028	Short-chain dehydrogenase reductase Sdr
D3M96_01840	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
D3M96_01845	COG0523	cobalamin synthesis protein
D3M96_01850	COG0735	belongs to the Fur family
D3M96_01860	COG1108	ABC-type Mn2 Zn2 transport systems permease components
D3M96_01865	COG0803	Belongs to the bacterial solute-binding protein 9 family
D3M96_01870	COG4973	Belongs to the 'phage' integrase family. XerC subfamily
D3M96_01880	COG0253	Catalyzes the stereoinversion of LL-2,6- diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso- DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan
D3M96_01885	COG1560	Kdo2-lipid A biosynthetic process
D3M96_01895	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
D3M96_01900	COG0499	May play a key role in the regulation of the intracellular concentration of adenosylhomocysteine
D3M96_01905	COG1950	PFAM Membrane protein of
D3M96_01940	COG0275	rRNA processing
D3M96_01945	COG0730	response to heat
D3M96_01950	COG2352	Forms oxaloacetate, a four-carbon dicarboxylic acid source for the tricarboxylic acid cycle
D3M96_01955	COG0129	dihydroxy-acid dehydratase activity
D3M96_01965	COG1638	TRAP-type C4-dicarboxylate transport system periplasmic component
D3M96_01975	COG1593	TRAP-type C4-dicarboxylate transport system, large permease component
D3M96_01990	COG0171	NAD+ synthase (glutamine-hydrolyzing) activity
D3M96_02010	COG3181	Tripartite tricarboxylate transporter family receptor
D3M96_02020	COG0628	permease
D3M96_02165	COG3181	Tripartite tricarboxylate transporter family receptor
D3M96_02170	COG1846	Transcriptional regulator
D3M96_02185	COG4774	siderophore transport
D3M96_02190	COG4607	ABC-type enterochelin transport system periplasmic component
D3M96_02195	COG4604	ABC transporter, ATP-binding protein
D3M96_02200	COG4605	iron ion homeostasis
D3M96_02205	COG4606	Belongs to the binding-protein-dependent transport system permease family. FecCD subfamily
D3M96_02220	COG0277	FAD linked oxidase domain protein
D3M96_02225	COG1304	FMN binding
D3M96_02230	COG2186	Transcriptional regulator
D3M96_02245	COG2188	Transcriptional regulator
D3M96_02250	COG1522	sequence-specific DNA binding
D3M96_02255	COG3844	kynureninase activity
D3M96_02260	COG1113	amino acid transport
D3M96_02265	COG1574	metal-dependent hydrolase with the TIM-barrel fold
D3M96_02270	COG1349	DNA-binding transcription factor activity
D3M96_02290	COG0395	ABC-type sugar transport system, permease component
D3M96_02305	COG0861	Integral membrane protein TerC family
D3M96_02310	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
D3M96_02325	COG1671	Belongs to the UPF0178 family
D3M96_02335	COG1418	mRNA catabolic process
D3M96_02345	COG4948	Mandelate Racemase Muconate Lactonizing
D3M96_02370	COG0154	amidase activity
D3M96_02380	COG0583	DNA-binding transcription factor activity
D3M96_02405	COG0326	Molecular chaperone. Has ATPase activity
D3M96_02425	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
D3M96_02440	COG3328	transposase activity
D3M96_02445	COG1652	LysM domain
D3M96_02460	COG0220	tRNA (guanine-N7-)-methyltransferase activity
D3M96_02470	COG0582	viral genome integration into host DNA
D3M96_02485	COG0583	DNA-binding transcription factor activity
D3M96_02525	COG1459	type II secretion system
D3M96_02565	COG2165	general secretion pathway protein
D3M96_02620	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
D3M96_02690	COG0667	Aldo Keto reductase
D3M96_02775	COG2003	Belongs to the UPF0758 family
D3M96_02830	COG3177	Filamentation induced by cAMP protein fic
D3M96_02975	COG0270	DNA (cytosine-5-)-methyltransferase activity
D3M96_02985	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
D3M96_03005	COG0629	single-stranded DNA binding
D3M96_03040	COG1192	Involved in chromosome partitioning
D3M96_03055	COG0582	viral genome integration into host DNA
D3M96_03070	COG1192	Involved in chromosome partitioning
D3M96_03105	COG0629	single-stranded DNA binding
D3M96_03110	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
D3M96_03300	COG2003	Belongs to the UPF0758 family
D3M96_03355	COG1180	Activation of pyruvate formate-lyase under anaerobic conditions by generation of an organic free radical, using S- adenosylmethionine and reduced flavodoxin as cosubstrates to produce 5'-deoxy-adenosine
D3M96_03360	COG0542	response to heat
D3M96_03410	COG3177	Filamentation induced by cAMP protein fic
D3M96_03455	COG0583	DNA-binding transcription factor activity
D3M96_03500	COG0583	DNA-binding transcription factor activity
D3M96_03505	COG0387	Pfam Sodium calcium exchanger
D3M96_03510	COG0745	RESPONSE REGULATOR receiver
D3M96_03510	COG3706	GGDEF domain
D3M96_03520	COG0477	Major facilitator Superfamily
D3M96_03525	COG0235	Class ii aldolase
D3M96_03535	COG3391	amine dehydrogenase activity
D3M96_03540	COG0590	tRNA wobble adenosine to inosine editing
D3M96_03550	COG3257	ureidoglycine aminohydrolase activity
D3M96_03555	COG0583	DNA-binding transcription factor activity
D3M96_03560	COG0053	Belongs to the cation diffusion facilitator (CDF) transporter (TC 2.A.4) family
D3M96_03575	COG0489	protein tyrosine kinase activity
D3M96_03590	COG0717	Belongs to the dCTP deaminase family
D3M96_03595	COG1982	Orn Lys Arg decarboxylase major
D3M96_03600	COG2081	HI0933 family
D3M96_03605	COG0509	glycine decarboxylation via glycine cleavage system
D3M96_03615	COG0207	Catalyzes the reductive methylation of 2'-deoxyuridine- 5'-monophosphate (dUMP) to 2'-deoxythymidine-5'-monophosphate (dTMP) while utilizing 5,10-methylenetetrahydrofolate (mTHF) as the methyl donor and reductant in the reaction, yielding dihydrofolate (DHF) as a by-product. This enzymatic reaction provides an intracellular de novo source of dTMP, an essential precursor for DNA biosynthesis
D3M96_03620	COG1765	OsmC-like protein
D3M96_03625	COG3278	Belongs to the heme-copper respiratory oxidase family
D3M96_03650	COG2941	Oxygenase that introduces the hydroxyl group at carbon five of 2-nonaprenyl-3-methyl-6-methoxy-1,4-benzoquinol resulting in the formation of 2-nonaprenyl-3-methyl-5-hydroxy-6-methoxy-1,4- benzoquinol
D3M96_03655	COG0469	pyruvate kinase activity
D3M96_03660	COG3193	protein, possibly involved in utilization of glycolate and propanediol
D3M96_03670	COG2084	Dehydrogenase
D3M96_03675	COG3622	Belongs to the hyi family
D3M96_03680	COG3960	tartronate-semialdehyde synthase activity
D3M96_03685	COG0583	DNA-binding transcription factor activity
D3M96_03695	COG2233	PERMEase
D3M96_03700	COG1942	4-Oxalocrotonate Tautomerase
D3M96_03705	COG0235	Class ii aldolase
D3M96_03715	COG3648	Uricase
D3M96_03715	COG3195	allantoin biosynthetic process
D3M96_03725	COG0472	First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
D3M96_03730	COG0677	UDP-N-acetyl-D-mannosamine dehydrogenase activity
D3M96_03745	COG0438	transferase activity, transferring glycosyl groups
D3M96_03755	COG0438	transferase activity, transferring glycosyl groups
D3M96_03765	COG0277	FAD linked oxidase domain protein
D3M96_03775	COG0179	Fumarylacetoacetate (FAA) hydrolase
D3M96_03780	COG3508	Involved in the catabolism of homogentisate (2,5- dihydroxyphenylacetate or 2,5-OH-PhAc), a central intermediate in the degradation of phenylalanine and tyrosine. Catalyzes the oxidative ring cleavage of the aromatic ring of homogentisate to yield maleylacetoacetate
D3M96_03790	COG0654	COG0654 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases
D3M96_03800	COG0266	class I DNA-(apurinic or apyrimidinic site) endonuclease activity
D3M96_03810	COG3017	Plays a critical role in the incorporation of lipoproteins in the outer membrane after they are released by the LolA protein
D3M96_03825	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)
D3M96_03830	COG1825	This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance
D3M96_03835	COG0193	aminoacyl-tRNA hydrolase activity
D3M96_03845	COG0012	GTP binding
D3M96_03890	COG0488	(ABC) transporter
D3M96_03905	COG0288	reversible hydration of carbon dioxide
D3M96_03910	COG0583	DNA-binding transcription factor activity
D3M96_03930	COG0755	Required for the export of heme to the periplasm for the biogenesis of c-type cytochromes
D3M96_03940	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
D3M96_03950	COG0526	COG0526, thiol-disulfide isomerase and thioredoxins
D3M96_03955	COG3088	subunit of a heme lyase
D3M96_03960	COG4235	cytochrome complex assembly
D3M96_03965	COG0785	Cytochrome C biogenesis protein
D3M96_03975	COG2169	Transcriptional regulator
D3M96_03975	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
D3M96_03995	COG0559	Belongs to the binding-protein-dependent transport system permease family
D3M96_04005	COG0411	ABC transporter
D3M96_04010	COG0410	ABC transporter
D3M96_04015	COG1858	cytochrome C peroxidase
D3M96_04020	COG0111	D-isomer specific 2-hydroxyacid dehydrogenase
D3M96_04025	COG1959	2 iron, 2 sulfur cluster binding
D3M96_04030	COG2346	COG2346, Truncated hemoglobins
D3M96_04035	COG0463	Glycosyl transferase, family 2
D3M96_04070	COG1526	Required for formate dehydrogenase (FDH) activity. Acts as a sulfur carrier protein that transfers sulfur from IscS to the molybdenum cofactor prior to its insertion into FDH
D3M96_04075	COG3383	formate dehydrogenase (NAD+) activity
D3M96_04090	COG1910	domain protein
D3M96_04095	COG2896	Catalyzes the cyclization of GTP to (8S)-3',8-cyclo-7,8- dihydroguanosine 5'-triphosphate
D3M96_04105	COG0303	'Molybdopterin
D3M96_04110	COG0521	Mo-molybdopterin cofactor biosynthetic process
D3M96_04115	COG0314	molybdopterin synthase activity
D3M96_04125	COG0315	cyclic pyranopterin monophosphate synthase activity
D3M96_04155	COG0678	peroxiredoxin activity
D3M96_04165	COG0697	spore germination
D3M96_04170	COG0502	Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical- based mechanism
D3M96_04190	COG0845	Belongs to the membrane fusion protein (MFP) (TC 8.A.1) family
D3M96_04235	COG0815	Transfers the fatty acyl group on membrane lipoproteins
D3M96_04240	COG4535	Mg2 and Co2 transporter CorC
D3M96_04245	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
D3M96_04250	COG1702	phosphate starvation-inducible protein PhoH
D3M96_04255	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
D3M96_04265	COG0024	Methionine aminopeptidase
D3M96_04270	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
D3M96_04275	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
D3M96_04280	COG1862	Preprotein translocase
D3M96_04285	COG0343	queuine tRNA-ribosyltransferase activity
D3M96_04290	COG0809	Transfers and isomerizes the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to give epoxyqueuosine (oQ-tRNA)
D3M96_04295	COG2027	D-alanyl-D-alanine carboxypeptidase
D3M96_04300	COG0035	Catalyzes the conversion of uracil and 5-phospho-alpha- D-ribose 1-diphosphate (PRPP) to UMP and diphosphate
D3M96_04310	COG4575	ribosome binding
D3M96_04325	COG0583	DNA-binding transcription factor activity
D3M96_04340	COG0451	ADP-glyceromanno-heptose 6-epimerase activity
D3M96_04365	COG0477	Major facilitator Superfamily
D3M96_04390	COG0043	3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity
D3M96_04400	COG0436	Aminotransferase
D3M96_04410	COG0280	phosphate acetyltransferase
D3M96_04410	COG0281	malic enzyme
D3M96_04420	COG2732	(Barnase) inhibitor
D3M96_04425	COG1385	rRNA (uridine-N3-)-methyltransferase activity
D3M96_04430	COG0021	Catalyzes the transfer of a two-carbon ketol group from a ketose donor to an aldose acceptor, via a covalent intermediate with the cofactor thiamine pyrophosphate
D3M96_04435	COG0057	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
D3M96_04440	COG0126	phosphoglycerate kinase activity
D3M96_04465	COG0521	Mo-molybdopterin cofactor biosynthetic process
D3M96_04475	COG0152	phosphoribosylaminoimidazolesuccinocarboxamide synthase activity
D3M96_04480	COG0041	Catalyzes the conversion of N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) to 4-carboxy-5-aminoimidazole ribonucleotide (CAIR)
D3M96_04485	COG0026	Catalyzes the ATP-dependent conversion of 5- aminoimidazole ribonucleotide (AIR) and HCO(3)(-) to N5- carboxyaminoimidazole ribonucleotide (N5-CAIR)
D3M96_04490	COG0009	L-threonylcarbamoyladenylate synthase
D3M96_04500	COG1012	belongs to the aldehyde dehydrogenase family
D3M96_04500	COG2030	dehydratase
D3M96_04505	COG1960	acyl-CoA dehydrogenase activity
D3M96_04515	COG0405	Gamma-glutamyltransferase
D3M96_04525	COG0579	oxidoreductase
D3M96_04530	COG1853	conserved protein domain typically associated with flavoprotein oxygenases, DIM6 NTAB family
D3M96_04535	COG0259	pyridoxamine-phosphate oxidase activity
D3M96_04545	COG1179	involved in molybdopterin and THIamine biosynthesis family 1
D3M96_04560	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
D3M96_04565	COG1215	transferase activity, transferring glycosyl groups
D3M96_04575	COG0488	(ABC) transporter
D3M96_04595	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
D3M96_04600	COG2894	cell division
D3M96_04610	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)
D3M96_04620	COG1294	oxidase, subunit
D3M96_04625	COG0038	chloride channel
D3M96_04635	COG0514	ATP-dependent DNA helicase (RecQ)
D3M96_04640	COG0209	Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides
D3M96_04645	COG0208	Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides
D3M96_04650	COG0633	Ferredoxin
D3M96_04665	COG2001	Belongs to the MraZ family
D3M96_04670	COG0275	rRNA processing
D3M96_04675	COG3116	cell division
D3M96_04685	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
D3M96_04690	COG0472	First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
D3M96_04705	COG0707	Cell wall formation. Catalyzes the transfer of a GlcNAc subunit on undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide (lipid intermediate I) to form undecaprenyl-pyrophosphoryl-MurNAc- (pentapeptide)GlcNAc (lipid intermediate II)
D3M96_04710	COG0773	UDP-N-acetylmuramate-L-alanine ligase activity
D3M96_04715	COG1181	Belongs to the D-alanine--D-alanine ligase family
D3M96_04720	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
D3M96_04735	COG0774	UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase activity
D3M96_04745	COG0739	heme binding
D3M96_04745	COG0741	lytic transglycosylase activity
D3M96_04745	COG1196	nuclear chromosome segregation
D3M96_04750	COG0653	protein targeting
D3M96_04760	COG2239	Acts as a magnesium transporter
D3M96_04765	COG1607	acyl-coa hydrolase
D3M96_04770	COG1473	amidohydrolase
D3M96_04775	COG0318	PFAM AMP-dependent synthetase and ligase
D3M96_04785	COG0665	tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase activity
D3M96_04785	COG4121	Catalyzes the last two steps in the biosynthesis of 5- methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at the wobble position (U34) in tRNA. Catalyzes the FAD-dependent demodification of cmnm(5)s(2)U34 to nm(5)s(2)U34, followed by the transfer of a methyl group from S-adenosyl-L-methionine to nm(5)s(2)U34, to form mnm(5)s(2)U34
D3M96_04800	COG1135	Part of the ABC transporter complex MetNIQ involved in methionine import. Responsible for energy coupling to the transport system
D3M96_04805	COG2011	ABC-type metal ion transport system permease component
D3M96_04815	COG0834	ABC-type amino acid transport signal transduction systems periplasmic component domain
D3M96_04820	COG0765	amino acid transport
D3M96_04825	COG1126	abc transporter atp-binding protein
D3M96_04835	COG1208	COG1208 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis translation initiation factor 2B, gamma epsilon subunits eIF-2Bgamma eIF-2Bepsilon
D3M96_04850	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
D3M96_04855	COG0030	16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity
D3M96_04860	COG0700	Nucleoside recognition
D3M96_04875	COG0204	Acyl-transferase
D3M96_04880	COG0241	D,D-heptose 1,7-bisphosphate phosphatase
D3M96_04885	COG0751	glycine-tRNA ligase activity
D3M96_04890	COG0752	glycyl-tRNA synthetase alpha subunit
D3M96_04910	COG1309	transcriptional regulator
D3M96_04930	COG0801	2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
D3M96_04935	COG0617	tRNA 3'-terminal CCA addition
D3M96_04945	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
D3M96_04950	COG0150	phosphoribosylformylglycinamidine cyclo-ligase activity
D3M96_04955	COG1953	Uracil, thiamine, allantoin
D3M96_04960	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)
D3M96_04965	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
D3M96_04970	COG0586	Pfam SNARE associated Golgi protein
D3M96_04975	COG1477	protein flavinylation
D3M96_04995	COG0860	N-Acetylmuramoyl-L-alanine amidase
D3M96_05000	COG0802	atpase or kinase
D3M96_05010	COG3181	Tripartite tricarboxylate transporter family receptor
D3M96_05015	COG0281	malic enzyme
D3M96_05015	COG0280	phosphate acetyltransferase
D3M96_05020	COG0583	DNA-binding transcription factor activity
D3M96_05025	COG1012	belongs to the aldehyde dehydrogenase family
D3M96_05030	COG0329	Catalyzes the condensation of (S)-aspartate-beta- semialdehyde (S)-ASA and pyruvate to 4-hydroxy- tetrahydrodipicolinate (HTPA)
D3M96_05070	COG1733	regulation of RNA biosynthetic process
D3M96_05075	COG2910	NAD(P)H-binding
D3M96_05085	COG2223	nitrite transmembrane transporter activity
D3M96_05095	COG2606	Belongs to the prolyl-tRNA editing family. YbaK EbsC subfamily
D3M96_05100	COG4974	Belongs to the 'phage' integrase family
D3M96_05105	COG0725	ABC transporter, periplasmic molybdate-binding protein
D3M96_05110	COG4149	molybdate abc transporter
D3M96_05115	COG4148	Part of the ABC transporter complex ModABC involved in molybdenum import. Responsible for energy coupling to the transport system
D3M96_05150	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
D3M96_05165	COG0600	ABC-type nitrate sulfonate bicarbonate transport system permease component
D3M96_05185	COG3391	amine dehydrogenase activity
D3M96_05190	COG0176	Transaldolase is important for the balance of metabolites in the pentose-phosphate pathway
D3M96_05195	COG0505	Belongs to the CarA family
D3M96_05200	COG0458	carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity
D3M96_05220	COG2233	PERMEase
D3M96_05225	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
D3M96_05230	COG1534	Rna-binding protein
D3M96_05235	COG0293	Specifically methylates the uridine in position 2552 of 23S rRNA at the 2'-O position of the ribose in the fully assembled 50S ribosomal subunit
D3M96_05240	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
D3M96_05245	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
D3M96_05250	COG1109	Catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate
D3M96_05265	COG0248	Ppx GppA phosphatase
D3M96_05270	COG0855	Catalyzes the reversible transfer of the terminal phosphate of ATP to form a long-chain polyphosphate (polyP)
D3M96_05290	COG1117	ATPase-coupled phosphate ion transmembrane transporter activity
D3M96_05300	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
D3M96_05315	COG0745	RESPONSE REGULATOR receiver
D3M96_05320	COG2205	protein histidine kinase activity
D3M96_05335	COG0583	DNA-binding transcription factor activity
D3M96_05355	COG1368	sulfuric ester hydrolase activity
D3M96_05385	COG4147	Belongs to the sodium solute symporter (SSF) (TC 2.A.21) family
D3M96_05405	COG3328	transposase activity
D3M96_05425	COG3327	negative regulation of DNA-templated transcription, initiation
D3M96_05445	COG0009	L-threonylcarbamoyladenylate synthase
D3M96_05450	COG1994	Peptidase M50
D3M96_05455	COG0329	Catalyzes the condensation of (S)-aspartate-beta- semialdehyde (S)-ASA and pyruvate to 4-hydroxy- tetrahydrodipicolinate (HTPA)
D3M96_05460	COG3317	Gram-negative-bacterium-type cell outer membrane assembly
D3M96_05475	COG0132	Catalyzes a mechanistically unusual reaction, the ATP- dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA) to form an ureido ring
D3M96_05485	COG0156	8-amino-7-oxononanoate synthase activity
D3M96_05490	COG2124	cytochrome p450
D3M96_05495	COG3135	benzoate transporter
D3M96_05500	COG2850	peptidyl-arginine hydroxylation
D3M96_05505	COG0249	that it carries out the mismatch recognition step. This protein has a weak ATPase activity
D3M96_05510	COG0582	viral genome integration into host DNA
D3M96_05545	COG0477	Major facilitator Superfamily
D3M96_05550	COG2003	Belongs to the UPF0758 family
D3M96_05600	COG0811	peptide transport
D3M96_05630	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
D3M96_05650	COG0431	NADPH-dependent FMN reductase
D3M96_05655	COG0798	PFAM Bile acid sodium symporter
D3M96_05660	COG0394	Belongs to the low molecular weight phosphotyrosine protein phosphatase family
D3M96_05665	COG0640	Transcriptional regulator
D3M96_05670	COG2003	Belongs to the UPF0758 family
D3M96_05675	COG0653	protein targeting
D3M96_05695	COG0530	calcium, potassium:sodium antiporter activity
D3M96_05710	COG1475	DNA binding
D3M96_05780	COG3620	sequence-specific DNA binding
D3M96_05800	COG3609	addiction module antidote protein, CC2985 family
D3M96_05840	COG4962	Type ii secretion system protein e
D3M96_05855	COG3451	type IV secretory pathway VirB4
D3M96_05885	COG2948	multi-organism process
D3M96_05965	COG3391	amine dehydrogenase activity
D3M96_06020	COG1538	Outer membrane efflux protein
D3M96_06025	COG0363	glucosamine-6-phosphate deaminase activity
D3M96_06030	COG1132	(ABC) transporter
D3M96_06050	COG2141	COG2141 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases
D3M96_06060	COG0668	transmembrane transport
D3M96_06105	COG0154	amidase activity
D3M96_06110	COG2031	fatty acid transporter
D3M96_06130	COG1253	flavin adenine dinucleotide binding
D3M96_06135	COG1968	undecaprenyl-diphosphatase activity
D3M96_06150	COG2908	Hydrolyzes the pyrophosphate bond of UDP-2,3- diacylglucosamine to yield 2,3-diacylglucosamine 1-phosphate (lipid X) and UMP by catalyzing the attack of water at the alpha-P atom. Involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell
D3M96_06165	COG0215	cysteine-tRNA ligase activity
D3M96_06175	COG0825	malonyl-CoA metabolic process
D3M96_06180	COG0037	tRNA processing
D3M96_06200	COG0330	HflC and HflK could
D3M96_06210	COG4977	sequence-specific DNA binding
D3M96_06215	COG0388	Catalyzes the ATP-dependent amidation of deamido-NAD to form NAD. Uses L-glutamine as a nitrogen source
D3M96_06240	COG4208	sulfate ABC transporter
D3M96_06245	COG3842	ATPase activity
D3M96_06250	COG3288	NAD(P)+ transhydrogenase (AB-specific) activity
D3M96_06255	COG3288	NAD(P)+ transhydrogenase (AB-specific) activity
D3M96_06260	COG1282	The transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane
D3M96_06280	COG1304	FMN binding
D3M96_06285	COG0435	Glutathione S-transferase
D3M96_06290	COG0655	NAD(P)H dehydrogenase (quinone) activity
D3M96_06305	COG2094	Belongs to the DNA glycosylase MPG family
D3M96_06315	COG2363	Small membrane protein
D3M96_06320	COG0598	Magnesium transport protein CorA
D3M96_06325	COG1960	acyl-CoA dehydrogenase activity
D3M96_06335	COG0747	negative chemotaxis
D3M96_06345	COG1173	ABC-type dipeptide oligopeptide nickel transport systems, permease components
D3M96_06350	COG4172	Belongs to the ABC transporter superfamily
D3M96_06360	COG3284	Transcriptional regulator
D3M96_06365	COG1012	belongs to the aldehyde dehydrogenase family
D3M96_06370	COG1454	alcohol dehydrogenase
D3M96_06375	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
D3M96_06400	COG4663	Part of the tripartite ATP-independent periplasmic (TRAP) transport system
D3M96_06430	COG3829	transcription factor binding
D3M96_06435	COG0477	Major facilitator Superfamily
D3M96_06445	COG0039	L-malate dehydrogenase activity
D3M96_06450	COG2188	Transcriptional regulator
D3M96_06455	COG2009	succinate dehydrogenase
D3M96_06465	COG1053	succinate dehydrogenase
D3M96_06470	COG0479	Belongs to the succinate dehydrogenase fumarate reductase iron-sulfur protein family
D3M96_06475	COG2938	An FAD assembly protein, which accelerates covalent attachment of the cofactor into other proteins. Plays an essential role in the assembly of succinate dehydrogenase (SDH, respiratory complex II), an enzyme complex that is a component of both the tricarboxylic acid cycle and the electron transport chain, and which couples the oxidation of succinate to fumarate with the reduction of ubiquinone (coenzyme Q) to ubiquinol. Required for flavinylation (covalent attachment of FAD) of the flavoprotein subunit SdhA of SDH
D3M96_06480	COG0372	Belongs to the citrate synthase family
D3M96_06485	COG2186	Transcriptional regulator
D3M96_06490	COG1620	l-lactate permease
D3M96_06495	COG0280	phosphate acetyltransferase
D3M96_06495	COG0281	malic enzyme
D3M96_06500	COG0567	Dehydrogenase, E1 component
D3M96_06505	COG0508	dehydrogenase complex catalyzes the overall conversion of
D3M96_06510	COG1249	Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family
D3M96_06515	COG1485	Reduces the stability of FtsZ polymers in the presence of ATP
D3M96_06535	COG2183	response to ionizing radiation
D3M96_06540	COG1199	ATP-dependent helicase activity
D3M96_06545	COG0659	secondary active sulfate transmembrane transporter activity
D3M96_06585	COG0564	pseudouridine synthase activity
D3M96_06595	COG3243	poly(R)-hydroxyalkanoic acid synthase
D3M96_06600	COG1028	Short-chain dehydrogenase reductase Sdr
D3M96_06605	COG5394	Polyhydroxyalkanoate synthesis repressor PhaR
D3M96_06630	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
D3M96_06635	COG1187	pseudouridine synthase activity
D3M96_06640	COG0779	Required for maturation of 30S ribosomal subunits
D3M96_06645	COG2251	uridine kinase activity
D3M96_06645	COG0195	Participates in both transcription termination and antitermination
D3M96_06655	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
D3M96_06660	COG0130	Responsible for synthesis of pseudouridine from uracil- 55 in the psi GC loop of transfer RNAs
D3M96_06670	COG0446	pyridine nucleotide-disulphide oxidoreductase
D3M96_06680	COG4160	amino acid transport
D3M96_06685	COG4215	(ABC) transporter
D3M96_06695	COG1611	Belongs to the LOG family
D3M96_06705	COG1283	sodium-dependent phosphate transmembrane transporter activity
D3M96_06710	COG0501	Belongs to the peptidase M48B family
D3M96_06725	COG1722	exodeoxyribonuclease VII activity
D3M96_06730	COG0142	geranyltranstransferase activity
D3M96_06735	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)
D3M96_06740	COG1469	GTP cyclohydrolase I activity
D3M96_06745	COG0360	Binds together with S18 to 16S ribosomal RNA
D3M96_06750	COG2965	DNA replication, synthesis of RNA primer
D3M96_06755	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
D3M96_06760	COG0359	binds to the 23S rRNA
D3M96_06765	COG0305	Participates in initiation and elongation during chromosome replication
D3M96_06775	COG1995	Catalyzes the NAD(P)-dependent oxidation of 4- (phosphohydroxy)-L-threonine (HTP) into 2-amino-3-oxo-4- (phosphohydroxy)butyric acid which spontaneously decarboxylates to form 3-amino-2-oxopropyl phosphate (AHAP)
D3M96_06780	COG1875	ATPase related to phosphate starvation-inducible protein PhoH
D3M96_06785	COG1225	Alkyl hydroperoxide reductase Thiol specific antioxidant Mal allergen
D3M96_06795	COG0436	Aminotransferase
D3M96_06815	COG1670	COG1670 acetyltransferases, including N-acetylases of ribosomal proteins
D3M96_06820	COG3349	Catalyzes the conversion of zeta-carotene to lycopene via the intermediary of neurosporene. It carries out two consecutive desaturations (introduction of double bonds) at positions C-7 and C-7'
D3M96_06825	COG1562	ergosterol biosynthetic process
D3M96_06830	COG1562	ergosterol biosynthetic process
D3M96_06835	COG0787	Catalyzes the interconversion of L-alanine and D- alanine. May also act on other amino acids
D3M96_06840	COG1028	Short-chain dehydrogenase reductase Sdr
D3M96_06865	COG3842	ATPase activity
D3M96_06870	COG1176	ABC-type spermidine putrescine transport system, permease component I
D3M96_06875	COG1177	transmembrane transport
D3M96_06880	COG1393	Belongs to the ArsC family
D3M96_06885	COG0120	Catalyzes the reversible conversion of ribose-5- phosphate to ribulose 5-phosphate
D3M96_06890	COG0704	Plays a role in the regulation of phosphate uptake
D3M96_06895	COG3706	GGDEF domain
D3M96_06895	COG5001	Diguanylate cyclase
D3M96_06895	COG2203	Gaf domain
D3M96_06895	COG4251	negative regulation of phosphorylation
D3M96_06900	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
D3M96_06905	COG1246	Belongs to the acetyltransferase family. ArgA subfamily
D3M96_06905	COG0548	Belongs to the acetylglutamate kinase family. ArgB subfamily
D3M96_06910	COG1643	Atp-dependent helicase
D3M96_06920	COG0438	transferase activity, transferring glycosyl groups
D3M96_06925	COG0726	polysaccharide deacetylase
D3M96_06940	COG0297	glycogen (starch) synthase activity
D3M96_06965	COG1132	(ABC) transporter
D3M96_06980	COG1530	ribonuclease E activity
D3M96_06985	COG3328	transposase activity
D3M96_07030	COG2186	Transcriptional regulator
D3M96_07035	COG0277	FAD linked oxidase domain protein
D3M96_07040	COG0277	FAD linked oxidase domain protein
D3M96_07045	COG0247	lactate metabolic process
D3M96_07075	COG2159	amidohydrolase
D3M96_07090	COG0583	DNA-binding transcription factor activity
D3M96_07095	COG0477	Major facilitator Superfamily
D3M96_07150	COG1283	sodium-dependent phosphate transmembrane transporter activity
D3M96_07165	COG3203	Forms passive diffusion pores that allow small molecular weight hydrophilic materials across the outer membrane
D3M96_07175	COG0697	spore germination
D3M96_07195	COG3094	Invasion gene expression up-regulator, SirB
D3M96_07205	COG0640	Transcriptional regulator
D3M96_07230	COG0659	secondary active sulfate transmembrane transporter activity
D3M96_07240	COG2314	TM2 domain
D3M96_07245	COG0554	Key enzyme in the regulation of glycerol uptake and metabolism. Catalyzes the phosphorylation of glycerol to yield sn- glycerol 3-phosphate
D3M96_07250	COG0578	Belongs to the FAD-dependent glycerol-3-phosphate dehydrogenase family
D3M96_07255	COG0791	NLP P60 protein
D3M96_07255	COG1388	LysM domain
D3M96_07275	COG1360	Flagellar Motor Protein
D3M96_07285	COG0835	chemotaxis
D3M96_07290	COG0840	transmembrane signaling receptor activity
D3M96_07295	COG1352	Methylation of the membrane-bound methyl-accepting chemotaxis proteins (MCP) to form gamma-glutamyl methyl ester residues in MCP
D3M96_07305	COG0745	RESPONSE REGULATOR receiver
D3M96_07310	COG3143	Plays an important role in bacterial chemotaxis signal transduction pathway by accelerating the dephosphorylation of phosphorylated CheY (CheY-P)
D3M96_07315	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
D3M96_07320	COG1298	Required for formation of the rod structure of the flagellar apparatus. Together with FliI and FliH, may constitute the export apparatus of flagellin
D3M96_07330	COG3550	peptidyl-serine autophosphorylation
D3M96_07345	COG2747	anti-sigma28 factor FlgM
D3M96_07355	COG1815	bacterial-type flagellum-dependent cell motility
D3M96_07360	COG1558	bacterial-type flagellum-dependent cell motility
D3M96_07365	COG1843	Required for flagellar hook formation. May act as a scaffolding protein
D3M96_07370	COG1749	Flagellar hook protein flgE
D3M96_07380	COG4786	Flagellar basal body rod
D3M96_07390	COG1706	bacterial-type flagellum-dependent cell motility
D3M96_07400	COG1256	bacterial-type flagellum assembly
D3M96_07405	COG1344	Flagellin is the subunit protein which polymerizes to form the filaments of bacterial flagella
D3M96_07420	COG0840	transmembrane signaling receptor activity
D3M96_07440	COG1987	bacterial-type flagellum assembly
D3M96_07455	COG1886	FliN is one of three proteins (FliG, FliN, FliM) that form 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
D3M96_07475	COG2882	bacterial-type flagellum organization
D3M96_07480	COG1157	protein secretion by the type III secretion system
D3M96_07490	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
D3M96_07495	COG1766	The M ring may be actively involved in energy transduction
D3M96_07500	COG1677	Flagellar hook-basal body complex protein FliE
D3M96_07505	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
D3M96_07530	COG1334	flagellar protein FlaG
D3M96_07535	COG1191	sigma factor activity
D3M96_07590	COG1262	PFAM Formylglycine-generating sulfatase enzyme
D3M96_07610	COG2733	membrane
D3M96_07615	COG0840	transmembrane signaling receptor activity
D3M96_07620	COG0840	transmembrane signaling receptor activity
D3M96_07645	COG2610	gluconate transmembrane transporter activity
D3M96_07665	COG4974	Belongs to the 'phage' integrase family
D3M96_07695	COG1028	Short-chain dehydrogenase reductase Sdr
D3M96_07730	COG2824	Alkylphosphonate utilization operon protein PhnA
D3M96_07745	COG4771	TonB-dependent receptor
D3M96_07750	COG1858	cytochrome C peroxidase
D3M96_07755	COG1454	alcohol dehydrogenase
D3M96_07775	COG0668	transmembrane transport
D3M96_07780	COG1113	amino acid transport
D3M96_07785	COG0580	Belongs to the MIP aquaporin (TC 1.A.8) family
D3M96_07835	COG3846	protein secretion by the type IV secretion system
D3M96_07850	COG3451	type IV secretory pathway VirB4
D3M96_07860	COG3838	Conjugal transfer protein Trbc
D3M96_07865	COG4962	Type ii secretion system protein e
D3M96_07885	COG0583	DNA-binding transcription factor activity
D3M96_07900	COG0667	Aldo Keto reductase
D3M96_07920	COG4959	Type IV secretory pathway protease TraF
D3M96_07935	COG1192	Involved in chromosome partitioning
D3M96_07965	COG1396	sequence-specific DNA binding
D3M96_08005	COG0515	serine threonine protein kinase
D3M96_08010	COG2815	serine threonine protein kinase
D3M96_08010	COG0515	serine threonine protein kinase
D3M96_08015	COG2003	Belongs to the UPF0758 family
D3M96_08030	COG4804	nuclease activity
D3M96_08065	COG0446	pyridine nucleotide-disulphide oxidoreductase
D3M96_08090	COG1278	Cold shock
D3M96_08095	COG0642	Histidine kinase
D3M96_08100	COG0745	RESPONSE REGULATOR receiver
D3M96_08105	COG3278	Belongs to the heme-copper respiratory oxidase family
D3M96_08115	COG2863	cytochrome
D3M96_08120	COG3258	Cytochrome c
D3M96_08125	COG3328	transposase activity
D3M96_08130	COG0639	Hydrolyzes diadenosine 5',5'''-P1,P4-tetraphosphate to yield ADP
D3M96_08135	COG4774	siderophore transport
D3M96_08170	COG0025	NhaP-type Na H and K H
D3M96_08185	COG1289	transmembrane transporter activity
D3M96_08190	COG2252	PERMEase
D3M96_08195	COG0560	Phosphoserine phosphatase
D3M96_08210	COG1999	signal sequence binding
D3M96_08220	COG0069	glutamate synthase activity
D3M96_08230	COG1846	Transcriptional regulator
D3M96_08235	COG1546	Belongs to the CinA family
D3M96_08235	COG1058	Belongs to the CinA family
D3M96_08240	COG1048	Catalyzes the isomerization of citrate to isocitrate via cis-aconitate
D3M96_08280	COG1028	Short-chain dehydrogenase reductase Sdr
D3M96_08290	COG1012	belongs to the aldehyde dehydrogenase family
D3M96_08305	COG2128	Antioxidant protein with alkyl hydroperoxidase activity. Required for the reduction of the AhpC active site cysteine residues and for the regeneration of the AhpC enzyme activity
D3M96_08315	COG3264	Mechanosensitive ion channel
D3M96_08315	COG1511	domain protein
D3M96_08320	COG1511	domain protein
D3M96_08320	COG3264	Mechanosensitive ion channel
D3M96_08325	COG0477	Major facilitator Superfamily
D3M96_08340	COG1396	sequence-specific DNA binding
D3M96_08345	COG3437	response regulator, receiver
D3M96_08355	COG2239	Acts as a magnesium transporter
D3M96_08365	COG3004	Na( ) H( ) antiporter that extrudes sodium in exchange for external protons
D3M96_08370	COG1490	D-aminoacyl-tRNA deacylase activity
D3M96_08385	COG0456	acetyltransferase
D3M96_08390	COG3012	SEC-C Motif Domain Protein
D3M96_08395	COG0501	Belongs to the peptidase M48B family
D3M96_08465	COG3706	GGDEF domain
D3M96_08480	COG1522	sequence-specific DNA binding
D3M96_08485	COG0626	cystathionine gamma-synthase activity
D3M96_08495	COG0494	nUDIX hydrolase
D3M96_08500	COG2832	Protein of unknown function (DUF454)
D3M96_08510	COG0137	argininosuccinate synthase activity
D3M96_08520	COG1409	Hydrolyzes cAMP to 5'-AMP. Plays an important regulatory role in modulating the intracellular concentration of cAMP, thereby influencing cAMP-dependent processes
D3M96_08545	COG1609	Transcriptional regulator
D3M96_08550	COG0518	GMP synthase (glutamine-hydrolyzing) activity
D3M96_08550	COG0519	Catalyzes the synthesis of GMP from XMP
D3M96_08560	COG2060	Part of the high-affinity ATP-driven potassium transport (or Kdp) system, which catalyzes the hydrolysis of ATP coupled with the electrogenic transport of potassium into the cytoplasm. This subunit binds and transports the potassium across the cytoplasmic membrane
D3M96_08570	COG2216	Part of the high-affinity ATP-driven potassium transport (or Kdp) system, which catalyzes the hydrolysis of ATP coupled with the electrogenic transport of potassium into the cytoplasm. This subunit is responsible for energy coupling to the transport system
D3M96_08575	COG2205	protein histidine kinase activity
D3M96_08580	COG0745	RESPONSE REGULATOR receiver
D3M96_08585	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
D3M96_08595	COG1052	Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family
D3M96_08600	COG0268	Binds directly to 16S ribosomal RNA
D3M96_08605	COG0728	peptidoglycan biosynthetic process
D3M96_08615	COG0563	adenylate kinase activity
D3M96_08620	COG1212	Activates KDO (a required 8-carbon sugar) for incorporation into bacterial lipopolysaccharide in Gram-negative bacteria
D3M96_08625	COG2835	tetraacyldisaccharide 4'-kinase activity
D3M96_08630	COG1663	tetraacyldisaccharide 4'-kinase activity
D3M96_08635	COG0848	biopolymer transport protein
D3M96_08640	COG0811	peptide transport
D3M96_08645	COG1570	exodeoxyribonuclease VII activity
D3M96_08650	COG0605	Destroys radicals which are normally produced within the cells and which are toxic to biological systems
D3M96_08660	COG0183	Belongs to the thiolase family
D3M96_08670	COG1278	Cold shock
D3M96_08675	COG2127	Involved in the modulation of the specificity of the ClpAP-mediated ATP-dependent protein degradation
D3M96_08680	COG0542	response to heat
D3M96_08685	COG2995	paraquat-inducible protein a
D3M96_08690	COG1463	ABC-type transport system involved in resistance to organic solvents, periplasmic component
D3M96_08690	COG3008	intermembrane lipid transfer
D3M96_08720	COG0411	ABC transporter
D3M96_08760	COG3129	Specifically methylates the adenine in position 1618 of 23S rRNA
D3M96_08765	COG0756	dUTP diphosphatase activity
D3M96_08775	COG0597	This protein specifically catalyzes the removal of signal peptides from prolipoproteins
D3M96_08780	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)
D3M96_08785	COG0196	riboflavin kinase activity
D3M96_08790	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
D3M96_08795	COG0144	Specifically methylates the cytosine at position 967 (m5C967) of 16S rRNA
D3M96_08795	COG0781	Involved in transcription antitermination. Required for transcription of ribosomal RNA (rRNA) genes. Binds specifically to the boxA antiterminator sequence of the ribosomal RNA (rrn) operons
D3M96_08805	COG0210	DNA helicase
D3M96_08830	COG0488	(ABC) transporter
D3M96_08835	COG2890	protein-(glutamine-N5) methyltransferase activity
D3M96_08840	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
D3M96_08845	COG2171	N-acyltransferase activity
D3M96_08855	COG2207	Transcriptional regulator
D3M96_08865	COG0471	metal ion transport
D3M96_08865	COG3273	potassium ion transport
D3M96_08910	COG0789	Transcriptional regulator
D3M96_08925	COG1804	L-carnitine dehydratase bile acid-inducible protein F
D3M96_08930	COG0544	peptidyl-prolyl cis-trans isomerase activity
D3M96_08935	COG0740	serine-type endopeptidase activity
D3M96_08940	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
D3M96_08945	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
D3M96_08955	COG1670	COG1670 acetyltransferases, including N-acetylases of ribosomal proteins
D3M96_08965	COG0556	nucleotide-excision repair
D3M96_08970	COG0394	Belongs to the low molecular weight phosphotyrosine protein phosphatase family
D3M96_08975	COG1959	2 iron, 2 sulfur cluster binding
D3M96_08980	COG1104	cysteine desulfurase activity
D3M96_08990	COG0316	Belongs to the HesB IscA family
D3M96_09005	COG1190	Belongs to the class-II aminoacyl-tRNA synthetase family
D3M96_09010	COG4221	oxidoreductase activity
D3M96_09020	COG0840	transmembrane signaling receptor activity
D3M96_09025	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
D3M96_09030	COG0697	spore germination
D3M96_09035	COG0385	Bile acid
D3M96_09045	COG0608	single-stranded DNA 5'-3' exodeoxyribonuclease activity
D3M96_09060	COG1136	(ABC) transporter
D3M96_09065	COG0084	hydrolase, TatD family'
D3M96_09075	COG0596	Alpha beta hydrolase
D3M96_09080	COG0613	PHP domain protein
D3M96_09090	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
D3M96_09090	COG0047	phosphoribosylformylglycinamidine synthase activity
D3M96_09105	COG0519	Catalyzes the synthesis of GMP from XMP
D3M96_09105	COG0518	GMP synthase (glutamine-hydrolyzing) activity
D3M96_09120	COG1002	Type II restriction enzyme, methylase subunits
D3M96_09130	COG1061	Type III restriction enzyme res subunit
D3M96_09135	COG0226	Part of the ABC transporter complex PstSACB involved in phosphate import
D3M96_09155	COG0583	DNA-binding transcription factor activity
D3M96_09170	COG0620	Catalyzes the transfer of a methyl group from 5- methyltetrahydrofolate to homocysteine resulting in methionine formation
D3M96_09180	COG1960	acyl-CoA dehydrogenase activity
D3M96_09195	COG2378	regulation of single-species biofilm formation
D3M96_09200	COG0523	cobalamin synthesis protein
D3M96_09205	COG1469	GTP cyclohydrolase I activity
D3M96_09210	COG0759	Could be involved in insertion of integral membrane proteins into the membrane
D3M96_09220	COG0044	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides
D3M96_09225	COG0735	belongs to the Fur family
D3M96_09230	COG0139	Catalyzes the hydrolysis of the adenine ring of phosphoribosyl-AMP
D3M96_09245	COG1942	4-Oxalocrotonate Tautomerase
D3M96_09260	COG2070	2-Nitropropane dioxygenase
D3M96_09265	COG0583	DNA-binding transcription factor activity
D3M96_09290	COG0625	glutathione transferase activity
D3M96_09295	COG0583	DNA-binding transcription factor activity
D3M96_09315	COG0494	nUDIX hydrolase
D3M96_09320	COG0625	glutathione transferase activity
D3M96_09325	COG0740	serine-type endopeptidase activity
D3M96_09375	COG1804	L-carnitine dehydratase bile acid-inducible protein F
D3M96_09385	COG1960	acyl-CoA dehydrogenase activity
D3M96_09405	COG0599	Antioxidant protein with alkyl hydroperoxidase activity. Required for the reduction of the AhpC active site cysteine residues and for the regeneration of the AhpC enzyme activity
D3M96_09410	COG0640	Transcriptional regulator
D3M96_09435	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)
D3M96_09460	COG3485	protocatechuate 3,4-dioxygenase
D3M96_09470	COG2057	Acyl CoA acetate 3-ketoacid CoA transferase beta subunit
D3M96_09475	COG2021	Transfers an acetyl group from acetyl-CoA to L- homoserine, forming acetyl-L-homoserine
D3M96_09485	COG3135	benzoate transporter
D3M96_09490	COG1159	An essential GTPase that binds both GDP and GTP, with rapid nucleotide exchange. Plays a role in 16S rRNA processing and 30S ribosomal subunit biogenesis and possibly also in cell cycle regulation and energy metabolism
D3M96_09495	COG0699	ATPase. Has a role at an early stage in the morphogenesis of the spore coat
D3M96_09505	COG4555	ABC transporter
D3M96_09515	COG2197	response regulator
D3M96_09550	COG1846	Transcriptional regulator
D3M96_09555	COG0654	COG0654 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases
D3M96_09560	COG2271	Major facilitator Superfamily
D3M96_09570	COG0325	Pyridoxal 5'-phosphate (PLP)-binding protein, which is involved in PLP homeostasis
D3M96_09580	COG0697	spore germination
D3M96_09610	COG0379	Catalyzes the condensation of iminoaspartate with dihydroxyacetone phosphate to form quinolinate
D3M96_09615	COG0667	Aldo Keto reductase
D3M96_09645	COG0456	acetyltransferase
D3M96_09650	COG1272	protein, Hemolysin III
D3M96_09655	COG3422	double-strand break repair
D3M96_09665	COG0477	Major facilitator Superfamily
D3M96_09670	COG0154	amidase activity
D3M96_09705	COG0765	amino acid transport
D3M96_09710	COG1126	abc transporter atp-binding protein
D3M96_09760	COG2871	sodium ion transport
D3M96_09800	COG2814	Major facilitator Superfamily
D3M96_09810	COG1280	lysine exporter protein (LysE YggA)
D3M96_09820	COG1609	Transcriptional regulator
D3M96_09830	COG0402	S-adenosylhomocysteine deaminase activity
D3M96_09850	COG0330	HflC and HflK could
D3M96_09855	COG1585	Membrane protein implicated in regulation of membrane protease activity
D3M96_09860	COG2226	methyltransferase
D3M96_09870	COG3042	response to heat
D3M96_09880	COG0524	Catalyzes the phosphorylation of ribose at O-5 in a reaction requiring ATP and magnesium. The resulting D-ribose-5- phosphate can then be used either for sythesis of nucleotides, histidine, and tryptophan, or as a component of the pentose phosphate pathway
D3M96_09890	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)
D3M96_09895	COG0290	IF-3 binds to the 30S ribosomal subunit and shifts the equilibrum between 70S ribosomes and their 50S and 30S subunits in favor of the free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins
D3M96_09900	COG0189	ligase activity
D3M96_09910	COG1925	phosphoenolpyruvate-dependent sugar phosphotransferase system
D3M96_09915	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)
D3M96_09950	COG0291	Belongs to the bacterial ribosomal protein bL35 family
D3M96_09955	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
D3M96_09960	COG0016	Belongs to the class-II aminoacyl-tRNA synthetase family. Phe-tRNA synthetase alpha subunit type 1 subfamily
D3M96_09965	COG0073	Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation
D3M96_09965	COG0072	phenylalanine-tRNA ligase activity
D3M96_09970	COG0776	regulation of translation
D3M96_09980	COG2833	Protein of unknown function (DUF455)
D3M96_09990	COG5265	(ABC) transporter
D3M96_09995	COG1959	2 iron, 2 sulfur cluster binding
D3M96_10000	COG0719	Fe-S assembly protein
D3M96_10005	COG0396	ATPase activity
D3M96_10010	COG0719	Fe-S assembly protein
D3M96_10020	COG0822	iron-sulfur transferase activity
D3M96_10025	COG2151	metal-sulfur cluster biosynthetic enzyme
D3M96_10040	COG1462	curli production assembly transport component CsgG
D3M96_10060	COG1215	transferase activity, transferring glycosyl groups
D3M96_10065	COG1649	PFAM Uncharacterised BCR, COG1649
D3M96_10065	COG0726	polysaccharide deacetylase
D3M96_10070	COG0457	Tetratricopeptide repeat
D3M96_10085	COG1278	Cold shock
D3M96_10100	COG4372	Transposase
D3M96_10150	COG0747	negative chemotaxis
D3M96_10155	COG0601	transmembrane transport
D3M96_10160	COG1173	ABC-type dipeptide oligopeptide nickel transport systems, permease components
D3M96_10165	COG4172	Belongs to the ABC transporter superfamily
D3M96_10175	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
D3M96_10235	COG3949	Membrane
D3M96_10245	COG1262	PFAM Formylglycine-generating sulfatase enzyme
D3M96_10260	COG0168	Low-affinity potassium transport system. Interacts with trk system potassium uptake protein TrkA
D3M96_10265	COG0569	domain protein
D3M96_10270	COG1902	pentaerythritol trinitrate reductase activity
D3M96_10280	COG1610	YqeY-like protein
D3M96_10285	COG0587	DNA-directed DNA polymerase activity
D3M96_10320	COG3181	Tripartite tricarboxylate transporter family receptor
D3M96_10325	COG0583	DNA-binding transcription factor activity
D3M96_10330	COG1686	Belongs to the peptidase S11 family
D3M96_10355	COG1028	Short-chain dehydrogenase reductase Sdr
D3M96_10365	COG4221	oxidoreductase activity
D3M96_10370	COG0307	riboflavin synthase, alpha
D3M96_10385	COG1301	dicarboxylic acid transport
D3M96_10390	COG4191	Histidine kinase
D3M96_10400	COG0583	DNA-binding transcription factor activity
D3M96_10405	COG1053	succinate dehydrogenase
D3M96_10455	COG2233	PERMEase
D3M96_10460	COG0071	Belongs to the small heat shock protein (HSP20) family
D3M96_10475	COG2814	Major facilitator Superfamily
D3M96_10505	COG2816	NAD+ diphosphatase activity
D3M96_10510	COG1561	YicC-like family, N-terminal region
D3M96_10525	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
D3M96_10530	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
D3M96_10535	COG0635	Involved in the biosynthesis of porphyrin-containing compound
D3M96_10545	COG2153	protein acetylation
D3M96_10555	COG3842	ATPase activity
D3M96_10560	COG0555	PFAM binding-protein-dependent transport systems inner membrane component
D3M96_10565	COG1840	ABC-type Fe3 transport system, periplasmic component
D3M96_10580	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)
D3M96_10590	COG0783	Belongs to the Dps family
D3M96_10600	COG3842	ATPase activity
D3M96_10605	COG0395	ABC-type sugar transport system, permease component
D3M96_10610	COG1175	transmembrane transport
D3M96_10615	COG1653	transport
D3M96_10630	COG0559	Belongs to the binding-protein-dependent transport system permease family
D3M96_10640	COG0411	ABC transporter
D3M96_10655	COG0625	glutathione transferase activity
D3M96_10665	COG1052	Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family
D3M96_10670	COG1028	Short-chain dehydrogenase reductase Sdr
D3M96_10675	COG0057	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
D3M96_10680	COG0114	fumarate hydratase activity
D3M96_10685	COG2133	pyrroloquinoline quinone binding
D3M96_10690	COG0589	response to stress
D3M96_10700	COG2807	transmembrane transport
D3M96_10710	COG0583	DNA-binding transcription factor activity
D3M96_10740	COG0583	DNA-binding transcription factor activity
D3M96_10745	COG4974	Belongs to the 'phage' integrase family
D3M96_10755	COG2132	Multicopper oxidase
D3M96_10820	COG3501	Rhs element vgr protein
D3M96_10865	COG1028	Short-chain dehydrogenase reductase Sdr
D3M96_10890	COG3038	cytochrome b561
D3M96_10905	COG1393	Belongs to the ArsC family
D3M96_10910	COG0625	glutathione transferase activity
D3M96_10935	COG0084	hydrolase, TatD family'
D3M96_10940	COG0470	DNA polymerase III
D3M96_10950	COG1559	Functions as a peptidoglycan terminase that cleaves nascent peptidoglycan strands endolytically to terminate their elongation
D3M96_10955	COG0354	folic acid binding
D3M96_10970	COG1960	acyl-CoA dehydrogenase activity
D3M96_10975	COG2914	Belongs to the UPF0125 (RnfH) family
D3M96_10980	COG2867	negative regulation of translational initiation
D3M96_10985	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
D3M96_10990	COG1252	NADH dehydrogenase
D3M96_11005	COG1806	Bifunctional serine threonine kinase and phosphorylase involved in the regulation of the
D3M96_11015	COG0566	Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase TrmH family
D3M96_11020	COG0164	Endonuclease that specifically degrades the RNA of RNA- DNA hybrids
D3M96_11025	COG0763	Condensation of UDP-2,3-diacylglucosamine and 2,3- diacylglucosamine-1-phosphate to form lipid A disaccharide, a precursor of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell
D3M96_11035	COG0764	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity
D3M96_11040	COG1044	Catalyzes the N-acylation of UDP-3-O-acylglucosamine using 3-hydroxyacyl-ACP as the acyl donor. Is involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell
D3M96_11050	COG4775	Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane
D3M96_11060	COG0743	1-deoxy-D-xylulose-5-phosphate reductoisomerase activity
D3M96_11065	COG0575	Belongs to the CDS family
D3M96_11070	COG0020	Catalyzes the condensation of isopentenyl diphosphate (IPP) with allylic pyrophosphates generating different type of terpenoids
D3M96_11075	COG0233	cytoplasmic translational termination
D3M96_11080	COG0528	UMP kinase activity
D3M96_11085	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
D3M96_11090	COG0052	Belongs to the universal ribosomal protein uS2 family
D3M96_11095	COG0024	Methionine aminopeptidase
D3M96_11100	COG2844	Modifies, by uridylylation and deuridylylation, the PII regulatory proteins (GlnB and homologs), in response to the nitrogen status of the cell that GlnD senses through the glutamine level. Under low glutamine levels, catalyzes the conversion of the PII proteins and UTP to PII-UMP and PPi, while under higher glutamine levels, GlnD hydrolyzes PII-UMP to PII and UMP (deuridylylation). Thus, controls uridylylation state and activity of the PII proteins, and plays an important role in the regulation of nitrogen
D3M96_11125	COG1286	toxin biosynthetic process
D3M96_11135	COG0285	dihydrofolate synthase activity
D3M96_11140	COG1249	Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family
D3M96_11145	COG0508	dehydrogenase complex catalyzes the overall conversion of
D3M96_11150	COG2609	component of the pyruvate dehydrogenase (PDH) complex, that catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2)
D3M96_11165	COG0190	Catalyzes the oxidation of 5,10- methylenetetrahydrofolate to 5,10-methenyltetrahydrofolate and then the hydrolysis of 5,10-methenyltetrahydrofolate to 10- formyltetrahydrofolate
D3M96_11175	COG1999	signal sequence binding
D3M96_11180	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
D3M96_11190	COG0640	Transcriptional regulator
D3M96_11210	COG0854	Catalyzes the complicated ring closure reaction between the two acyclic compounds 1-deoxy-D-xylulose-5-phosphate (DXP) and 3-amino-2-oxopropyl phosphate (1-amino-acetone-3-phosphate or AAP) to form pyridoxine 5'-phosphate (PNP) and inorganic phosphate
D3M96_11215	COG1538	Outer membrane efflux protein
D3M96_11220	COG0841	Belongs to the resistance-nodulation-cell division (RND) (TC 2.A.6) family
D3M96_11225	COG0845	Belongs to the membrane fusion protein (MFP) (TC 8.A.1) family
D3M96_11230	COG3638	Part of the ABC transporter complex PhnCDE involved in phosphonates import. Responsible for energy coupling to the transport system
D3M96_11250	COG0183	Belongs to the thiolase family
D3M96_11255	COG0183	Belongs to the thiolase family
D3M96_11265	COG2513	Catalyzes the thermodynamically favored C-C bond cleavage of (2R,3S)-2-methylisocitrate to yield pyruvate and succinate
D3M96_11270	COG0583	DNA-binding transcription factor activity
D3M96_11275	COG1982	Orn Lys Arg decarboxylase major
D3M96_11295	COG0194	GDP metabolic process
D3M96_11300	COG1758	RNA polymerase activity
D3M96_11305	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
D3M96_11315	COG1296	Branched-chain amino acid permease (Azaleucine resistance)
D3M96_11320	COG0739	heme binding
D3M96_11325	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
D3M96_11330	COG0584	glycerophosphoryl diester phosphodiesterase
D3M96_11335	COG2961	Specifically methylates the adenine in position 2030 of 23S rRNA
D3M96_11340	COG1187	pseudouridine synthase activity
D3M96_11345	COG3161	chorismate lyase activity
D3M96_11350	COG2814	Major facilitator Superfamily
D3M96_11355	COG0656	L-ascorbic acid biosynthetic process
D3M96_11365	COG0668	transmembrane transport
D3M96_11370	COG0165	Argininosuccinate lyase
D3M96_11385	COG0665	tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase activity
D3M96_11395	COG2265	Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family
D3M96_11405	COG2518	Catalyzes the methyl esterification of L-isoaspartyl residues in peptides and proteins that result from spontaneous decomposition of normal L-aspartyl and L-asparaginyl residues. It plays a role in the repair and or degradation of damaged proteins
D3M96_11410	COG0496	Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates
D3M96_11415	COG0344	acyl-phosphate glycerol-3-phosphate acyltransferase activity
D3M96_11420	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
D3M96_11425	COG2252	PERMEase
D3M96_11430	COG0526	COG0526, thiol-disulfide isomerase and thioredoxins
D3M96_11450	COG0488	(ABC) transporter
D3M96_11455	COG1619	proteins homologs of microcin C7 resistance protein MccF
D3M96_11460	COG0590	tRNA wobble adenosine to inosine editing
D3M96_11465	COG1131	(ABC) transporter
D3M96_11470	COG0842	Transport permease protein
D3M96_11475	COG0840	transmembrane signaling receptor activity
D3M96_11485	COG3090	Trap-type c4-dicarboxylate transport system, small permease component
D3M96_11490	COG1638	TRAP-type C4-dicarboxylate transport system periplasmic component
D3M96_11495	COG0665	tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase activity
D3M96_11505	COG2022	thiamine diphosphate biosynthetic process
D3M96_11525	COG1414	Transcriptional regulator
D3M96_11535	COG0730	response to heat
D3M96_11545	COG1666	GTP binding
D3M96_11550	COG0318	PFAM AMP-dependent synthetase and ligase
D3M96_11555	COG0239	Important for reducing fluoride concentration in the cell, thus reducing its toxicity
D3M96_11560	COG0518	GMP synthase (glutamine-hydrolyzing) activity
D3M96_11560	COG0519	Catalyzes the synthesis of GMP from XMP
D3M96_11565	COG2207	Transcriptional regulator
D3M96_11580	COG0526	COG0526, thiol-disulfide isomerase and thioredoxins
D3M96_11585	COG0135	phosphoribosylanthranilate isomerase activity
D3M96_11590	COG1593	TRAP-type C4-dicarboxylate transport system, large permease component
D3M96_11600	COG0101	tRNA pseudouridine synthase activity
D3M96_11610	COG0136	Catalyzes the NADPH-dependent formation of L-aspartate- semialdehyde (L-ASA) by the reductive dephosphorylation of L- aspartyl-4-phosphate
D3M96_11615	COG0473	3-isopropylmalate dehydrogenase activity
D3M96_11620	COG0066	3-isopropylmalate dehydratase activity
D3M96_11625	COG0065	Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate
D3M96_11630	COG2128	Antioxidant protein with alkyl hydroperoxidase activity. Required for the reduction of the AhpC active site cysteine residues and for the regeneration of the AhpC enzyme activity
D3M96_11640	COG4566	intracellular signal transduction
D3M96_11655	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
D3M96_11660	COG0397	Uncharacterized ACR, YdiU/UPF0061 family
D3M96_11670	COG1295	ribonuclease BN
D3M96_11680	COG0042	Catalyzes the synthesis of 5,6-dihydrouridine (D), a modified base found in the D-loop of most tRNAs, via the reduction of the C5-C6 double bond in target uridines
D3M96_11715	COG4964	Belongs to the GSP D family
D3M96_11755	COG3712	iron ion homeostasis
D3M96_11760	COG1595	DNA-templated transcription, initiation
D3M96_11770	COG0221	Catalyzes the hydrolysis of inorganic pyrophosphate (PPi) forming two phosphate ions
D3M96_11780	COG2959	enzyme of heme biosynthesis
D3M96_11790	COG0181	hydroxymethylbilane synthase activity
D3M96_11795	COG0861	Integral membrane protein TerC family
D3M96_11800	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
D3M96_11805	COG0045	succinate-CoA ligase (ADP-forming) activity
D3M96_11815	COG0620	Catalyzes the transfer of a methyl group from 5- methyltetrahydrofolate to homocysteine resulting in methionine formation
D3M96_11820	COG0583	DNA-binding transcription factor activity
D3M96_11825	COG2137	regulation of response to DNA damage stimulus
D3M96_11845	COG0477	Major facilitator Superfamily
D3M96_11860	COG0318	PFAM AMP-dependent synthetase and ligase
D3M96_11865	COG1024	Enoyl-CoA hydratase
D3M96_11870	COG3162	membrane
D3M96_11885	COG0540	Belongs to the ATCase OTCase family
D3M96_11900	COG0744	Peptidoglycan polymerase that catalyzes glycan chain elongation from lipid-linked precursors
D3M96_11915	COG2070	2-Nitropropane dioxygenase
D3M96_11920	COG0635	Involved in the biosynthesis of porphyrin-containing compound
D3M96_11925	COG1009	NADH ubiquinone oxidoreductase subunit 5 chain L Multisubunit Na H antiporter, MnhA subunit
D3M96_11925	COG2111	Na H antiporter
D3M96_11930	COG1006	Multisubunit Na H antiporter MnhC subunit
D3M96_11935	COG0651	ATP synthesis coupled electron transport
D3M96_11945	COG2212	antiporter activity
D3M96_11960	COG3158	transport of potassium into the cell
D3M96_11965	COG0642	Histidine kinase
D3M96_11990	COG1118	Part of the ABC transporter complex CysAWTP involved in sulfate thiosulfate import. Responsible for energy coupling to the transport system
D3M96_11995	COG4208	sulfate ABC transporter
D3M96_12000	COG0555	PFAM binding-protein-dependent transport systems inner membrane component
D3M96_12005	COG1613	Sulfate ABC transporter periplasmic sulfate-binding protein
D3M96_12025	COG1278	Cold shock
D3M96_12050	COG0776	regulation of translation
D3M96_12055	COG0007	Multifunctional enzyme that catalyzes the SAM-dependent methylations of uroporphyrinogen III at position C-2 and C-7 to form precorrin-2 via precorrin-1. Then it catalyzes the NAD- dependent ring dehydrogenation of precorrin-2 to yield sirohydrochlorin. Finally, it catalyzes the ferrochelation of sirohydrochlorin to yield siroheme
D3M96_12055	COG1648	precorrin-2 dehydrogenase activity
D3M96_12060	COG2010	Cytochrome c
D3M96_12085	COG2896	Catalyzes the cyclization of GTP to (8S)-3',8-cyclo-7,8- dihydroguanosine 5'-triphosphate
D3M96_12090	COG1648	precorrin-2 dehydrogenase activity
D3M96_12090	COG0007	Multifunctional enzyme that catalyzes the SAM-dependent methylations of uroporphyrinogen III at position C-2 and C-7 to form precorrin-2 via precorrin-1. Then it catalyzes the NAD- dependent ring dehydrogenation of precorrin-2 to yield sirohydrochlorin. Finally, it catalyzes the ferrochelation of sirohydrochlorin to yield siroheme
D3M96_12100	COG2010	Cytochrome c
D3M96_12105	COG1167	Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain MocR family and their eukaryotic orthologs
D3M96_12110	COG0626	cystathionine gamma-synthase activity
D3M96_12115	COG0566	Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase TrmH family
D3M96_12120	COG0557	exoribonuclease II activity
D3M96_12135	COG0076	glutamate decarboxylase activity
D3M96_12140	COG0531	amino acid
D3M96_12170	COG2375	cellular response to nickel ion
D3M96_12200	COG0583	DNA-binding transcription factor activity
D3M96_12205	COG3842	ATPase activity
D3M96_12215	COG0637	HAD-superfamily hydrolase subfamily IA, variant 3
D3M96_12220	COG1840	ABC-type Fe3 transport system, periplasmic component
D3M96_12245	COG3530	Putative quorum-sensing-regulated virulence factor
D3M96_12250	COG0625	glutathione transferase activity
D3M96_12260	COG1741	Belongs to the pirin family
D3M96_12270	COG0388	Catalyzes the ATP-dependent amidation of deamido-NAD to form NAD. Uses L-glutamine as a nitrogen source
D3M96_12275	COG2814	Major facilitator Superfamily
D3M96_12280	COG2807	transmembrane transport
D3M96_12285	COG2207	Transcriptional regulator
D3M96_12290	COG3135	benzoate transporter
D3M96_12300	COG1540	5-oxoprolinase (ATP-hydrolyzing) activity
D3M96_12315	COG1529	Aldehyde oxidase and xanthine dehydrogenase
D3M96_12325	COG0402	S-adenosylhomocysteine deaminase activity
D3M96_12335	COG0745	RESPONSE REGULATOR receiver
D3M96_12340	COG2205	protein histidine kinase activity
D3M96_12345	COG0568	sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released
D3M96_12355	COG0828	Belongs to the bacterial ribosomal protein bS21 family
D3M96_12360	COG2236	Acts on guanine, xanthine and to a lesser extent hypoxanthine
D3M96_12365	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
D3M96_12370	COG3705	Required for the first step of histidine biosynthesis. May allow the feedback regulation of ATP phosphoribosyltransferase activity by histidine
D3M96_12375	COG0330	HflC and HflK could
D3M96_12380	COG0330	HflC and HflK could
D3M96_12385	COG2262	GTPase that associates with the 50S ribosomal subunit and may have a role during protein synthesis or ribosome biogenesis
D3M96_12390	COG1923	regulation of RNA biosynthetic process
D3M96_12400	COG1160	GTP binding
D3M96_12405	COG1520	Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane
D3M96_12410	COG2976	Protein conserved in bacteria
D3M96_12415	COG0124	histidyl-tRNA synthetase
D3M96_12420	COG0821	Converts 2C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-2,4cPP) into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate
D3M96_12430	COG0820	rRNA (adenine-C2-)-methyltransferase activity
D3M96_12435	COG0105	UTP biosynthetic process
D3M96_12445	COG0336	Belongs to the RNA methyltransferase TrmD family
D3M96_12450	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
D3M96_12455	COG0228	four-way junction DNA binding
D3M96_12460	COG0425	Belongs to the sulfur carrier protein TusA family
D3M96_12465	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
D3M96_12480	COG2351	hydroxyisourate hydrolase activity
D3M96_12510	COG1653	transport
D3M96_12515	COG0665	tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase activity
D3M96_12530	COG0187	DNA topoisomerase II activity
D3M96_12540	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
D3M96_12545	COG0334	Belongs to the Glu Leu Phe Val dehydrogenases family
D3M96_12560	COG1391	[glutamine synthetase]-adenylyl-L-tyrosine phosphorylase
D3M96_12565	COG1636	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)
D3M96_12570	COG0542	response to heat
D3M96_12575	COG0664	- Catabolite gene activator and regulatory subunit of cAMP-dependent protein
D3M96_12610	COG3278	Belongs to the heme-copper respiratory oxidase family
D3M96_12620	COG2217	Heavy metal translocating P-type atpase
D3M96_12630	COG2224	Isocitrate lyase
D3M96_12635	COG0780	Catalyzes the NADPH-dependent reduction of 7-cyano-7- deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1)
D3M96_12635	COG2904	Catalyzes the NADPH-dependent reduction of 7-cyano-7- deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1)
D3M96_12655	COG0322	excinuclease ABC activity
D3M96_12660	COG1472	Belongs to the glycosyl hydrolase 3 family
D3M96_12665	COG0736	holo-[acyl-carrier-protein] synthase activity
D3M96_12675	COG2050	protein possibly involved in aromatic compounds catabolism
D3M96_12680	COG1024	Enoyl-CoA hydratase
D3M96_12685	COG1012	belongs to the aldehyde dehydrogenase family
D3M96_12690	COG1018	Is involved in NO detoxification in an aerobic process, termed nitric oxide dioxygenase (NOD) reaction that utilizes O(2) and NAD(P)H to convert NO to nitrate, which protects the bacterium from various noxious nitrogen compounds. Therefore, plays a central role in the inducible response to nitrosative stress
D3M96_12695	COG2151	metal-sulfur cluster biosynthetic enzyme
D3M96_12700	COG3396	Phenylacetate-CoA oxygenase
D3M96_12705	COG3460	Phenylacetate-CoA oxygenase
D3M96_12710	COG3396	Phenylacetate-CoA oxygenase
D3M96_12715	COG1949	3'-to-5' exoribonuclease specific for small oligoribonucleotides
D3M96_12720	COG0501	Belongs to the peptidase M48B family
D3M96_12725	COG1162	GTPase activity
D3M96_12735	COG0335	large ribosomal subunit rRNA binding
D3M96_12750	COG0450	alkyl hydroperoxide reductase
D3M96_12755	COG1960	acyl-CoA dehydrogenase activity
D3M96_12775	COG2951	lytic endotransglycosylase activity
D3M96_12790	COG0451	ADP-glyceromanno-heptose 6-epimerase activity
D3M96_12795	COG2870	Catalyzes the ADP transfer from ATP to D-glycero-beta-D- manno-heptose 1-phosphate, yielding ADP-D-glycero-beta-D-manno- heptose
D3M96_12800	COG2956	Modulates cellular lipopolysaccharide (LPS) levels by regulating LpxC, which is involved in lipid A biosynthesis. May act by modulating the proteolytic activity of FtsH towards LpxC. May also coordinate assembly of proteins involved in LPS synthesis at the plasma membrane
D3M96_12820	COG0283	belongs to the cytidylate kinase family. Type 1 subfamily
D3M96_12825	COG0128	3-phosphoshikimate 1-carboxyvinyltransferase activity
D3M96_12830	COG0287	Prephenate dehydrogenase
D3M96_12840	COG1932	Catalyzes the reversible conversion of 3- phosphohydroxypyruvate to phosphoserine and of 3-hydroxy-2-oxo-4- phosphonooxybutanoate to phosphohydroxythreonine
D3M96_12855	COG2227	3-demethylubiquinone-9 3-O-methyltransferase activity
D3M96_12875	COG1146	Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions
D3M96_12885	COG4771	TonB-dependent receptor
D3M96_12900	COG0753	catalase activity
D3M96_12910	COG4335	DNA alkylation repair
D3M96_12915	COG1846	Transcriptional regulator
D3M96_12920	COG0436	Aminotransferase
D3M96_12925	COG1309	transcriptional regulator
D3M96_12960	COG0625	glutathione transferase activity
D3M96_12970	COG3633	Involved in the import of serine and threonine into the cell, with the concomitant import of sodium (symport system)
D3M96_12975	COG1280	lysine exporter protein (LysE YggA)
D3M96_12995	COG4147	Belongs to the sodium solute symporter (SSF) (TC 2.A.21) family
D3M96_13005	COG2205	protein histidine kinase activity
D3M96_13005	COG2198	Histidine kinase
D3M96_13005	COG0784	Response regulator, receiver
D3M96_13015	COG2046	Belongs to the sulfate adenylyltransferase family
D3M96_13030	COG0583	DNA-binding transcription factor activity
D3M96_13035	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
D3M96_13050	COG0840	transmembrane signaling receptor activity
D3M96_13055	COG2119	membrane
D3M96_13070	COG1182	Catalyzes the reductive cleavage of azo bond in aromatic azo compounds to the corresponding amines. Requires NADH, but not NADPH, as an electron donor for its activity
D3M96_13080	COG0807	Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate
D3M96_13095	COG0661	Is probably a protein kinase regulator of UbiI activity which is involved in aerobic coenzyme Q (ubiquinone) biosynthesis
D3M96_13100	COG2321	neutral zinc metallopeptidase
D3M96_13110	COG0347	Belongs to the P(II) protein family
D3M96_13115	COG0004	ammonium transporteR
D3M96_13120	COG3909	cytochrome
D3M96_13130	COG0625	glutathione transferase activity
D3M96_13140	COG0657	acetylesterase activity
D3M96_13145	COG0730	response to heat
D3M96_13150	COG0482	sulfurtransferase activity
D3M96_13155	COG0277	FAD linked oxidase domain protein
D3M96_13160	COG0722	Stereospecific condensation of phosphoenolpyruvate (PEP) and D-erythrose-4-phosphate (E4P) giving rise to 3-deoxy-D- arabino-heptulosonate-7-phosphate (DAHP)
D3M96_13165	COG2879	small protein
D3M96_13170	COG1966	Carbon starvation protein
D3M96_13175	COG0834	ABC-type amino acid transport signal transduction systems periplasmic component domain
D3M96_13180	COG0765	amino acid transport
D3M96_13185	COG0765	amino acid transport
D3M96_13190	COG1126	abc transporter atp-binding protein
D3M96_13195	COG0028	Belongs to the TPP enzyme family
D3M96_13205	COG1712	Catalyzes the reversible NADPH-dependent reductive amination of L-2-amino-6-oxopimelate, the acyclic form of L- tetrahydrodipicolinate, to generate the meso compound, D,L-2,6- diaminopimelate
D3M96_13210	COG1028	Short-chain dehydrogenase reductase Sdr
D3M96_13220	COG0600	ABC-type nitrate sulfonate bicarbonate transport system permease component
D3M96_13225	COG1116	anion transmembrane transporter activity
D3M96_13240	COG3203	Forms passive diffusion pores that allow small molecular weight hydrophilic materials across the outer membrane
D3M96_13245	COG1414	Transcriptional regulator
D3M96_13255	COG5285	phytanoyl-CoA dioxygenase
D3M96_13260	COG0662	Cupin 2, conserved barrel domain protein
D3M96_13265	COG0160	Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family
D3M96_13270	COG0456	acetyltransferase
D3M96_13275	COG1846	Transcriptional regulator
D3M96_13285	COG0312	modulator of DNA gyrase
D3M96_13300	COG0308	aminopeptidase N
D3M96_13305	COG0158	D-fructose-1,6-bisphosphate 1-phosphohydrolase class 1
D3M96_13320	COG0473	3-isopropylmalate dehydrogenase activity
D3M96_13330	COG0433	COG0433 Predicted ATPase
D3M96_13335	COG0217	transcriptional regulatory protein
D3M96_13340	COG0151	Belongs to the GarS family
D3M96_13345	COG0408	coproporphyrinogen oxidase activity
D3M96_13350	COG1057	Catalyzes the reversible adenylation of nicotinate mononucleotide (NaMN) to nicotinic acid adenine dinucleotide (NaAD)
D3M96_13355	COG0799	negative regulation of ribosome biogenesis
D3M96_13360	COG1576	Specifically methylates the pseudouridine at position 1915 (m3Psi1915) in 23S rRNA
D3M96_13365	COG0424	maF-like protein
D3M96_13385	COG0023	Translation Initiation Factor
D3M96_13395	COG2084	Dehydrogenase
D3M96_13400	COG0625	glutathione transferase activity
D3M96_13405	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
D3M96_13410	COG1047	Peptidyl-prolyl cis-trans
D3M96_13415	COG2003	Belongs to the UPF0758 family
D3M96_13420	COG0254	rRNA binding
D3M96_13430	COG0534	Mate efflux family protein
D3M96_13435	COG4175	Glycine betaine
D3M96_13440	COG4176	ABC-type proline glycine betaine transport system permease component
D3M96_13450	COG2230	cyclopropane-fatty-acyl-phospholipid synthase
D3M96_13455	COG2814	Major facilitator Superfamily
D3M96_13460	COG0227	Belongs to the bacterial ribosomal protein bL28 family
D3M96_13465	COG0267	Belongs to the bacterial ribosomal protein bL33 family
D3M96_13470	COG0495	leucyl-tRNA aminoacylation
D3M96_13485	COG0014	Catalyzes the NADPH-dependent reduction of L-glutamate 5-phosphate into L-glutamate 5-semialdehyde and phosphate. The product spontaneously undergoes cyclization to form 1-pyrroline-5- carboxylate
D3M96_13505	COG1281	Redox regulated molecular chaperone. Protects both thermally unfolding and oxidatively damaged proteins from irreversible aggregation. Plays an important role in the bacterial defense system toward oxidative stress
D3M96_13515	COG2919	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
D3M96_13520	COG0148	phosphopyruvate hydratase activity
D3M96_13530	COG2814	Major facilitator Superfamily
D3M96_13550	COG0504	CTP synthase activity
D3M96_13585	COG0697	spore germination
D3M96_13590	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
D3M96_13600	COG0791	NLP P60 protein
D3M96_13610	COG0583	DNA-binding transcription factor activity
D3M96_13620	COG0583	DNA-binding transcription factor activity
D3M96_13625	COG4774	siderophore transport
D3M96_13635	COG0609	Belongs to the binding-protein-dependent transport system permease family. FecCD subfamily
D3M96_13640	COG4559	Part of the ABC transporter complex HmuTUV involved in hemin import. Responsible for energy coupling to the transport system
D3M96_13650	COG1309	transcriptional regulator
D3M96_13660	COG0260	Presumably involved in the processing and regular turnover of intracellular proteins. Catalyzes the removal of unsubstituted N-terminal amino acids from various peptides
D3M96_13680	COG1045	serine acetyltransferase
D3M96_13695	COG1381	Involved in DNA repair and RecF pathway recombination
D3M96_13700	COG1159	An essential GTPase that binds both GDP and GTP, with rapid nucleotide exchange. Plays a role in 16S rRNA processing and 30S ribosomal subunit biogenesis and possibly also in cell cycle regulation and energy metabolism
D3M96_13705	COG0571	ribonuclease III activity
D3M96_13715	COG0481	GTPase activity
D3M96_13720	COG0265	Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain
D3M96_13745	COG0304	beta-ketoacyl-acyl-carrier-protein synthase II activity
D3M96_13755	COG1028	Short-chain dehydrogenase reductase Sdr
D3M96_13760	COG0331	[acyl-carrier-protein] S-malonyltransferase activity
D3M96_13765	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
D3M96_13770	COG0416	fatty acid biosynthetic process
D3M96_13775	COG0333	Belongs to the bacterial ribosomal protein bL32 family
D3M96_13780	COG1399	metal-binding, possibly nucleic acid-binding protein
D3M96_13785	COG0424	maF-like protein
D3M96_13795	COG3023	N-Acetylmuramoyl-L-alanine amidase
D3M96_13800	COG2717	Part of the MsrPQ system that repairs oxidized periplasmic proteins containing methionine sulfoxide residues (Met-O), using respiratory chain electrons. Thus protects these proteins from oxidative-stress damage caused by reactive species of oxygen and chlorine generated by the host defense mechanisms. MsrPQ is essential for the maintenance of envelope integrity under bleach stress, rescuing a wide series of structurally unrelated periplasmic proteins from methionine oxidation. MsrQ provides electrons for reduction to the reductase catalytic subunit MsrP, using the quinone pool of the respiratory chain
D3M96_13805	COG2041	Part of the MsrPQ system that repairs oxidized periplasmic proteins containing methionine sulfoxide residues (Met-O), using respiratory chain electrons. Thus protects these proteins from oxidative-stress damage caused by reactive species of oxygen and chlorine generated by the host defense mechanisms. MsrPQ is essential for the maintenance of envelope integrity under bleach stress, rescuing a wide series of structurally unrelated periplasmic proteins from methionine oxidation. The catalytic subunit MsrP is non-stereospecific, being able to reduce both (R-) and (S-) diastereoisomers of methionine sulfoxide
D3M96_13810	COG0546	phosphoglycolate phosphatase activity
D3M96_13815	COG0564	pseudouridine synthase activity
D3M96_13820	COG1530	ribonuclease E activity
D3M96_13825	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
D3M96_13830	COG0159	tryptophan synthase activity
D3M96_13835	COG0133	tryptophan synthase activity
D3M96_13840	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
D3M96_13850	COG1488	Catalyzes the synthesis of beta-nicotinate D- ribonucleotide from nicotinate and 5-phospho-D-ribose 1-phosphate at the expense of ATP
D3M96_13855	COG1146	Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions
D3M96_13865	COG2878	Part of a membrane complex involved in electron transport
D3M96_13870	COG0177	DNA repair enzyme that has both DNA N-glycosylase activity and AP-lyase activity. The DNA N-glycosylase activity releases various damaged pyrimidines from DNA by cleaving the N- glycosidic bond, leaving an AP (apurinic apyrimidinic) site. The AP-lyase activity cleaves the phosphodiester bond 3' to the AP site by a beta-elimination, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate
D3M96_13875	COG1129	ABC transporter
D3M96_13880	COG3047	cAMP biosynthetic process
D3M96_13890	COG0411	ABC transporter
D3M96_13905	COG0229	Has an important function as a repair enzyme for proteins that have been inactivated by oxidation. Catalyzes the reversible oxidation-reduction of methionine sulfoxide in proteins to methionine
D3M96_13910	COG2917	probably involved in intracellular septation
D3M96_13920	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
D3M96_13925	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
D3M96_13935	COG1196	nuclear chromosome segregation
D3M96_13940	COG0477	Major facilitator Superfamily
D3M96_13945	COG1573	uracil-dna glycosylase
D3M96_13950	COG1214	PFAM Peptidase M22, glycoprotease
D3M96_13955	COG0745	RESPONSE REGULATOR receiver
D3M96_13960	COG2205	protein histidine kinase activity
D3M96_13975	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
D3M96_13980	COG0560	Phosphoserine phosphatase
D3M96_13995	COG1007	ATP synthesis coupled electron transport
D3M96_14010	COG0713	ATP synthesis coupled electron transport
D3M96_14020	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
D3M96_14025	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
D3M96_14030	COG1034	ATP synthesis coupled electron transport
D3M96_14045	COG0649	NAD binding
D3M96_14050	COG0852	NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient
D3M96_14055	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
D3M96_14060	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
D3M96_14070	COG3203	Forms passive diffusion pores that allow small molecular weight hydrophilic materials across the outer membrane
D3M96_14085	COG0149	triose-phosphate isomerase activity
D3M96_14090	COG0604	alcohol dehydrogenase
D3M96_14110	COG0184	Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome
D3M96_14115	COG1183	phosphatidylcholine synthase activity
D3M96_14120	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
D3M96_14125	COG0440	acetolactate synthase activity
D3M96_14130	COG0028	Belongs to the TPP enzyme family
D3M96_14135	COG1289	transmembrane transporter activity
D3M96_14140	COG3022	response to hydroperoxide
D3M96_14145	COG1028	Short-chain dehydrogenase reductase Sdr
D3M96_14185	COG0582	viral genome integration into host DNA
D3M96_14205	COG3299	homolog of phage Mu protein gp47
D3M96_14250	COG4386	tail sheath protein
D3M96_14290	COG0616	signal peptide processing
D3M96_14300	COG4626	Terminase
D3M96_14300	COG1802	Transcriptional regulator
D3M96_14325	COG4570	Endonuclease that resolves Holliday junction intermediates made during homologous genetic recombination and DNA repair. Exhibits sequence and structure-selective cleavage of four-way DNA junctions, where it introduces symmetrical nicks in two strands of the same polarity at the 5' side of dinucleotides. Corrects the defects in genetic recombination and DNA repair associated with inactivation of ruvAB or ruvC
D3M96_14465	COG0582	viral genome integration into host DNA
D3M96_14490	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)
D3M96_14495	COG2256	atpase related to the helicase subunit of the holliday junction resolvase
D3M96_14500	COG2834	Participates in the translocation of lipoproteins from the inner membrane to the outer membrane. Only forms a complex with a lipoprotein if the residue after the N-terminal Cys is not an aspartate (The Asp acts as a targeting signal to indicate that the lipoprotein should stay in the inner membrane)
D3M96_14505	COG1674	ftsk spoiiie
D3M96_14510	COG0492	ferredoxin-NADP+ reductase activity
D3M96_14530	COG0477	Major facilitator Superfamily
D3M96_14550	COG2272	Belongs to the type-B carboxylesterase lipase family
D3M96_14555	COG1960	acyl-CoA dehydrogenase activity
D3M96_14580	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
D3M96_14605	COG0612	Peptidase, M16
D3M96_14610	COG0484	heat shock protein binding
D3M96_14615	COG0443	Heat shock 70 kDa protein
D3M96_14620	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
D3M96_14625	COG0276	Catalyzes the ferrous insertion into protoporphyrin IX
D3M96_14630	COG1420	regulation of RNA biosynthetic process
D3M96_14635	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
D3M96_14640	COG0497	DNA recombination
D3M96_14645	COG0735	belongs to the Fur family
D3M96_14650	COG2913	Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane
D3M96_14655	COG0289	4-hydroxy-tetrahydrodipicolinate reductase
D3M96_14665	COG0812	UDP-N-acetylmuramate dehydrogenase activity
D3M96_14685	COG3300	MHYT domain
D3M96_14685	COG5001	Diguanylate cyclase
D3M96_14700	COG2814	Major facilitator Superfamily
D3M96_14715	COG2819	hydrolase of the alpha beta superfamily
D3M96_14730	COG0506	proline dehydrogenase activity
D3M96_14730	COG3905	.,Oxidizes proline to glutamate for use as a carbon and nitrogen source
D3M96_14730	COG4230	.,Oxidizes proline to glutamate for use as a carbon and nitrogen source
D3M96_14735	COG1522	sequence-specific DNA binding
D3M96_14745	COG2423	ornithine cyclodeaminase activity
D3M96_14750	COG0477	Major facilitator Superfamily
D3M96_14755	COG0513	Belongs to the DEAD box helicase family
D3M96_14760	COG3657	addiction module killer protein
D3M96_14765	COG3636	A helicase nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair. Binds to DSBs and unwinds DNA via a highly rapid and processive ATP-dependent bidirectional helicase activity. Unwinds dsDNA until it encounters a Chi (crossover hotspot instigator) sequence from the 3' direction. Cuts ssDNA a few nucleotides 3' to the Chi site. The properties and activities of the enzyme are changed at Chi. The Chi-altered holoenzyme produces a long 3'-ssDNA overhang and facilitates RecA-binding to the ssDNA for homologous DNA recombination and repair. Holoenzyme degrades any linearized DNA that is unable to undergo homologous recombination. In the holoenzyme this subunit has ssDNA-dependent ATPase and 5'-3' helicase activity. When added to pre-assembled RecBC greatly stimulates nuclease activity and augments holoenzyme processivity. Negatively regulates the RecA-loading ability of RecBCD
D3M96_14770	COG0583	DNA-binding transcription factor activity
D3M96_14775	COG4638	Rieske (2fe-2S)
D3M96_14795	COG0446	pyridine nucleotide-disulphide oxidoreductase
D3M96_14815	COG4569	acetaldehyde dehydrogenase (acetylating) activity
D3M96_14820	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)
D3M96_14825	COG2814	Major facilitator Superfamily
D3M96_14830	COG0166	Belongs to the GPI family
D3M96_14850	COG1167	Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain MocR family and their eukaryotic orthologs
D3M96_14855	COG2814	Major facilitator Superfamily
D3M96_14885	COG1028	Short-chain dehydrogenase reductase Sdr
D3M96_14895	COG0842	Transport permease protein
D3M96_14900	COG0842	Transport permease protein
D3M96_14900	COG1129	ABC transporter
D3M96_14905	COG0845	Belongs to the membrane fusion protein (MFP) (TC 8.A.1) family
D3M96_14910	COG1538	Outer membrane efflux protein
D3M96_14915	COG3243	poly(R)-hydroxyalkanoic acid synthase
D3M96_14920	COG1309	transcriptional regulator
D3M96_14925	COG1738	Involved in the import of queuosine (Q) precursors, required for Q precursor salvage
D3M96_14930	COG0603	Catalyzes the ATP-dependent conversion of 7-carboxy-7- deazaguanine (CDG) to 7-cyano-7-deazaguanine (preQ(0))
D3M96_14935	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
D3M96_14950	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
D3M96_14965	COG0505	Belongs to the CarA family
D3M96_14970	COG2240	Pyridoxal kinase involved in the salvage pathway of pyridoxal 5'-phosphate (PLP). Catalyzes the phosphorylation of pyridoxal to PLP
D3M96_14980	COG0789	Transcriptional regulator
D3M96_14995	COG0841	Belongs to the resistance-nodulation-cell division (RND) (TC 2.A.6) family
D3M96_15040	COG3278	Belongs to the heme-copper respiratory oxidase family
D3M96_15045	COG1167	Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain MocR family and their eukaryotic orthologs
D3M96_15065	COG0796	Provides the (R)-glutamate required for cell wall biosynthesis
D3M96_15165	COG0516	GMP reductase activity
D3M96_15165	COG0517	IMP dehydrogenase activity
D3M96_15180	COG1027	Aspartate ammonia-lyase
D3M96_15185	COG1846	Transcriptional regulator
D3M96_15195	COG0494	nUDIX hydrolase
D3M96_15200	COG2360	Functions in the N-end rule pathway of protein degradation where it conjugates Leu, Phe and, less efficiently, Met from aminoacyl-tRNAs to the N-termini of proteins containing an N-terminal arginine or lysine
D3M96_15205	COG2935	proteasome-mediated ubiquitin-dependent protein catabolic process
D3M96_15220	COG1414	Transcriptional regulator
D3M96_15240	COG0513	Belongs to the DEAD box helicase family
D3M96_15260	COG0429	hydrolase of the alpha beta-hydrolase fold
D3M96_15265	COG4783	chaperone-mediated protein folding
D3M96_15285	COG0654	COG0654 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases
D3M96_15295	COG2901	Activates ribosomal RNA transcription. Plays a direct role in upstream activation of rRNA promoters
D3M96_15305	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
D3M96_15310	COG0632	four-way junction helicase activity
D3M96_15320	COG2255	four-way junction helicase activity
D3M96_15330	COG0418	dihydroorotase activity
D3M96_15340	COG0415	Belongs to the DNA photolyase family
D3M96_15360	COG4372	Transposase
D3M96_15370	COG3328	transposase activity
D3M96_15445	COG0225	Has an important function as a repair enzyme for proteins that have been inactivated by oxidation. Catalyzes the reversible oxidation-reduction of methionine sulfoxide in proteins to methionine
D3M96_15490	COG1177	transmembrane transport
D3M96_15495	COG3842	ATPase activity
D3M96_15500	COG1840	ABC-type Fe3 transport system, periplasmic component
D3M96_15505	COG2084	Dehydrogenase
D3M96_15520	COG0494	nUDIX hydrolase
D3M96_15525	COG0442	prolyl-tRNA aminoacylation
D3M96_15530	COG0824	Thioesterase
D3M96_15535	COG0811	peptide transport
D3M96_15550	COG0823	Involved in the tonB-independent uptake of proteins
D3M96_15580	COG0534	Mate efflux family protein
D3M96_15600	COG1129	ABC transporter
D3M96_15620	COG0427	acetyl-CoA hydrolase
D3M96_15625	COG0583	DNA-binding transcription factor activity
D3M96_15650	COG3634	alkyl hydroperoxide reductase activity
D3M96_15665	COG0697	spore germination
D3M96_15670	COG0175	sulfate reduction
D3M96_15680	COG2895	sulfate adenylyltransferase (ATP) activity
D3M96_15690	COG1012	belongs to the aldehyde dehydrogenase family
D3M96_15695	COG0665	tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase activity
D3M96_15700	COG5383	Protein conserved in bacteria
D3M96_15710	COG0282	Catalyzes the formation of acetyl phosphate from acetate and ATP. Can also catalyze the reverse reaction
D3M96_15725	COG0583	DNA-binding transcription factor activity
D3M96_15730	COG1741	Belongs to the pirin family
D3M96_15735	COG3706	GGDEF domain
D3M96_15740	COG0154	amidase activity
D3M96_15750	COG0234	Binds to Cpn60 in the presence of Mg-ATP and suppresses the ATPase activity of the latter
D3M96_15755	COG0459	protein refolding
D3M96_15765	COG0284	orotidine-5'-phosphate decarboxylase activity
D3M96_15785	COG1414	Transcriptional regulator
D3M96_15790	COG1546	Belongs to the CinA family
D3M96_15795	COG1267	Lipid phosphatase which dephosphorylates phosphatidylglycerophosphate (PGP) to phosphatidylglycerol (PG)
D3M96_15805	COG0781	Involved in transcription antitermination. Required for transcription of ribosomal RNA (rRNA) genes. Binds specifically to the boxA antiterminator sequence of the ribosomal RNA (rrn) operons
D3M96_15810	COG0054	6,7-dimethyl-8-ribityllumazine synthase activity
D3M96_15835	COG0742	ribosomal rna small subunit methyltransferase
D3M96_15840	COG0669	Reversibly transfers an adenylyl group from ATP to 4'- phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate
D3M96_15845	COG1145	4fe-4S ferredoxin, iron-sulfur binding domain protein
D3M96_15875	COG5581	Acts as a flagellar brake, regulating swimming and swarming in a bis-(3'-5') cyclic diguanylic acid (c-di-GMP)- dependent manner. Binds 1 c-di-GMP dimer per subunit. Increasing levels of c-di-GMP lead to decreased motility
D3M96_15890	COG1335	isochorismatase
D3M96_15895	COG2309	aminopeptidase activity
D3M96_15900	COG0596	Alpha beta hydrolase
D3M96_15905	COG1529	Aldehyde oxidase and xanthine dehydrogenase
D3M96_15905	COG2010	Cytochrome c
D3M96_15910	COG2080	2 iron, 2 sulfur cluster binding
D3M96_15915	COG1529	Aldehyde oxidase and xanthine dehydrogenase
D3M96_15915	COG2010	Cytochrome c
D3M96_15925	COG0410	ABC transporter
D3M96_15930	COG0411	ABC transporter
D3M96_15940	COG0683	leucine binding
D3M96_15950	COG3706	GGDEF domain
D3M96_15965	COG3181	Tripartite tricarboxylate transporter family receptor
D3M96_15970	COG3328	transposase activity
D3M96_15980	COG1234	tRNA 3'-trailer cleavage
D3M96_15995	COG1502	Catalyzes the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) (diphosphatidylglycerol) and glycerol
D3M96_16010	COG1975	Xanthine and CO dehydrogenases maturation factor, XdhC CoxF family
D3M96_16010	COG3608	succinylglutamate desuccinylase aspartoacylase
D3M96_16015	COG1593	TRAP-type C4-dicarboxylate transport system, large permease component
D3M96_16040	COG4663	Part of the tripartite ATP-independent periplasmic (TRAP) transport system
D3M96_16070	COG1335	isochorismatase
D3M96_16075	COG2309	aminopeptidase activity
D3M96_16080	COG0596	Alpha beta hydrolase
D3M96_16095	COG1120	ATPase activity
D3M96_16115	COG2031	fatty acid transporter
D3M96_16130	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
D3M96_16135	COG0841	Belongs to the resistance-nodulation-cell division (RND) (TC 2.A.6) family
D3M96_16140	COG0845	Belongs to the membrane fusion protein (MFP) (TC 8.A.1) family
D3M96_16145	COG0328	RNA-DNA hybrid ribonuclease activity
D3M96_16150	COG2226	methyltransferase
D3M96_16155	COG0491	Thiolesterase that catalyzes the hydrolysis of S-D- lactoyl-glutathione to form glutathione and D-lactic acid
D3M96_16160	COG1388	LysM domain
D3M96_16160	COG0741	lytic transglycosylase activity
D3M96_16170	COG2204	response regulator
D3M96_16175	COG4191	Histidine kinase
D3M96_16180	COG1301	dicarboxylic acid transport
D3M96_16210	COG2606	Belongs to the prolyl-tRNA editing family. YbaK EbsC subfamily
D3M96_16235	COG0604	alcohol dehydrogenase
D3M96_16245	COG1024	Enoyl-CoA hydratase
D3M96_16265	COG2015	COG2015, Alkyl sulfatase and related hydrolases
D3M96_16315	COG1393	Belongs to the ArsC family
D3M96_16320	COG0431	NADPH-dependent FMN reductase
D3M96_16325	COG0745	RESPONSE REGULATOR receiver
D3M96_16330	COG0642	Histidine kinase
D3M96_16415	COG2948	multi-organism process
D3M96_16450	COG0433	COG0433 Predicted ATPase
D3M96_16515	COG4974	Belongs to the 'phage' integrase family
D3M96_16520	COG3344	reverse transcriptase
D3M96_16560	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
D3M96_16565	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
D3M96_16585	COG0582	viral genome integration into host DNA
D3M96_16595	COG0117	Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)- pyrimidinedione 5'-phosphate
D3M96_16595	COG1985	Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)- pyrimidinedione 5'-phosphate
D3M96_16600	COG1327	Negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR- boxes
D3M96_16605	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
D3M96_16610	COG1881	PFAM PEBP family protein
D3M96_16615	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)
D3M96_16620	COG0739	heme binding
D3M96_16625	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
D3M96_16630	COG0316	Belongs to the HesB IscA family
D3M96_16640	COG0002	Catalyzes the NADPH-dependent reduction of N-acetyl-5- glutamyl phosphate to yield N-acetyl-L-glutamate 5-semialdehyde
D3M96_16645	COG0103	maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
D3M96_16650	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
D3M96_16655	COG4663	Part of the tripartite ATP-independent periplasmic (TRAP) transport system
D3M96_16660	COG0312	modulator of DNA gyrase
D3M96_16665	COG3028	Belongs to the UPF0307 family
D3M96_16695	COG0745	RESPONSE REGULATOR receiver
D3M96_16695	COG2205	protein histidine kinase activity
D3M96_16695	COG4191	Histidine kinase
D3M96_16715	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)
D3M96_16720	COG4681	YaeQ
D3M96_16745	COG0762	integral membrane protein
D3M96_16750	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
D3M96_16750	COG2169	Transcriptional regulator
D3M96_16755	COG3133	Outer membrane lipoprotein
D3M96_16770	COG2264	protein methyltransferase activity
D3M96_16775	COG0439	Biotin carboxylase
D3M96_16780	COG0511	ligase activity, forming carbon-carbon bonds
D3M96_16785	COG0757	Catalyzes a trans-dehydration via an enolate intermediate
D3M96_16790	COG0526	COG0526, thiol-disulfide isomerase and thioredoxins
D3M96_16795	COG0773	UDP-N-acetylmuramate-L-alanine ligase activity
D3M96_16800	COG3150	esterase
D3M96_16815	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)
D3M96_16820	COG0744	Peptidoglycan polymerase that catalyzes glycan chain elongation from lipid-linked precursors
D3M96_16830	COG0639	Hydrolyzes diadenosine 5',5'''-P1,P4-tetraphosphate to yield ADP
D3M96_16840	COG0816	Could be a nuclease involved in processing of the 5'-end of pre-16S rRNA
D3M96_16845	COG1678	Uncharacterized ACR, COG1678
D3M96_16860	COG0352	thiamine-phosphate diphosphorylase activity
D3M96_16865	COG0001	glutamate-1-semialdehyde 2,1-aminomutase activity
D3M96_16880	COG1364	Catalyzes two activities which are involved in the cyclic version of arginine biosynthesis the synthesis of N- acetylglutamate from glutamate and acetyl-CoA as the acetyl donor, and of ornithine by transacetylation between N(2)-acetylornithine and glutamate
D3M96_16890	COG3237	CsbD-like
D3M96_16895	COG0261	This protein binds to 23S rRNA in the presence of protein L20
D3M96_16900	COG0211	Belongs to the bacterial ribosomal protein bL27 family
D3M96_16905	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
D3M96_16910	COG0263	Catalyzes the transfer of a phosphate group to glutamate to form L-glutamate 5-phosphate
D3M96_16935	COG0422	Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction
D3M96_16940	COG3328	transposase activity
D3M96_16960	COG1126	abc transporter atp-binding protein
D3M96_16965	COG0765	amino acid transport
D3M96_16970	COG4597	amino acid ABC transporter
D3M96_16975	COG0834	ABC-type amino acid transport signal transduction systems periplasmic component domain
D3M96_16980	COG2884	Cell division ATP-binding protein ftsE
D3M96_16985	COG2177	Part of the ABC transporter FtsEX involved in
D3M96_16995	COG0772	Belongs to the SEDS family
D3M96_17000	COG0768	penicillin binding
D3M96_17010	COG1792	Involved in formation and maintenance of cell shape
D3M96_17015	COG1077	Cell shape determining protein MreB Mrl
D3M96_17020	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)
D3M96_17025	COG0154	amidase activity
D3M96_17030	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)
D3M96_17040	COG0583	DNA-binding transcription factor activity
D3M96_17045	COG2259	Doxx family
D3M96_17050	COG3384	dioxygenase
D3M96_17060	COG3245	cytochrome
D3M96_17070	COG1846	Transcriptional regulator
D3M96_17075	COG1960	acyl-CoA dehydrogenase activity
D3M96_17080	COG2814	Major facilitator Superfamily
D3M96_17090	COG1024	Enoyl-CoA hydratase
D3M96_17100	COG3604	Transcriptional regulator
D3M96_17120	COG1309	transcriptional regulator
D3M96_17135	COG2230	cyclopropane-fatty-acyl-phospholipid synthase
D3M96_17160	COG1090	epimerase
D3M96_17165	COG0786	glutamate:sodium symporter activity
D3M96_17170	COG0142	geranyltranstransferase activity
D3M96_17180	COG0494	nUDIX hydrolase
D3M96_17185	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
D3M96_17190	COG1538	Outer membrane efflux protein
D3M96_17210	COG4582	Cell division factor that enhances FtsZ-ring assembly. Directly interacts with FtsZ and promotes bundling of FtsZ protofilaments, with a reduction in FtsZ GTPase activity
D3M96_17215	COG0237	dephospho-CoA kinase activity
D3M96_17225	COG2197	response regulator
D3M96_17230	COG0414	Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate
D3M96_17235	COG1354	Participates in chromosomal partition during cell division. May act via the formation of a condensin-like complex containing Smc and ScpB that pull DNA away from mid-cell into both cell halves
D3M96_17245	COG0477	Major facilitator Superfamily
D3M96_17275	COG4206	TonB-dependent receptor
D3M96_17280	COG0614	abc-type fe3 -hydroxamate transport system, periplasmic component
D3M96_17295	COG1595	DNA-templated transcription, initiation
D3M96_17310	COG2022	thiamine diphosphate biosynthetic process
D3M96_17315	COG0351	phosphomethylpyrimidine kinase
D3M96_17320	COG0775	Catalyzes the irreversible cleavage of the glycosidic bond in both 5'-methylthioadenosine (MTA) and S- adenosylhomocysteine (SAH AdoHcy) to adenine and the corresponding thioribose, 5'-methylthioribose and S-ribosylhomocysteine, respectively
D3M96_17325	COG2518	Catalyzes the methyl esterification of L-isoaspartyl residues in peptides and proteins that result from spontaneous decomposition of normal L-aspartyl and L-asparaginyl residues. It plays a role in the repair and or degradation of damaged proteins
D3M96_17330	COG1538	Outer membrane efflux protein
D3M96_17335	COG0615	ADP-L-glycero-beta-D-manno-heptose biosynthetic process
D3M96_17345	COG0661	Is probably a protein kinase regulator of UbiI activity which is involved in aerobic coenzyme Q (ubiquinone) biosynthesis
D3M96_17360	COG2226	methyltransferase
D3M96_17365	COG0745	RESPONSE REGULATOR receiver
D3M96_17370	COG5002	protein histidine kinase activity
D3M96_17380	COG2049	5-oxoprolinase (ATP-hydrolyzing) activity
D3M96_17385	COG1984	allophanate hydrolase subunit 2
D3M96_17390	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
D3M96_17395	COG1238	metal cluster binding
D3M96_17420	COG0503	Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis
D3M96_17425	COG4987	ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease ATP-binding protein CydC
D3M96_17430	COG4988	ABC transporter
D3M96_17440	COG1294	oxidase, subunit
D3M96_17445	COG1271	oxidase subunit
D3M96_17460	COG1778	Involved in the biosynthesis of lipopolysaccharides (LPSs). Catalyzes the hydrolysis of 3-deoxy-D-manno-octulosonate 8-phosphate (KDO 8-P) to 3-deoxy-D-manno-octulosonate (KDO) and inorganic phosphate
D3M96_17475	COG1137	ATPase activity
D3M96_17485	COG1762	phosphoenolpyruvate-dependent sugar phosphotransferase system
D3M96_17490	COG1493	Catalyzes the ATP- as well as the pyrophosphate- dependent phosphorylation of a specific serine residue in HPr, a phosphocarrier protein of the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS). HprK P also catalyzes the pyrophosphate-producing, inorganic phosphate-dependent dephosphorylation (phosphorolysis) of seryl-phosphorylated HPr (P- Ser-HPr). The two antagonistic activities of HprK P are regulated by several intracellular metabolites, which change their concentration in response to the absence or presence of rapidly metabolisable carbon sources (glucose, fructose, etc.) in the growth medium. Therefore, by controlling the phosphorylation state of HPr, HPrK P is a sensor enzyme that plays a major role in the regulation of carbon metabolism and sugar transport it mediates carbon catabolite repression (CCR), and regulates PTS-catalyzed carbohydrate uptake and inducer exclusion
D3M96_17495	COG1660	Displays ATPase and GTPase activities
D3M96_17505	COG0313	Catalyzes the 2'-O-methylation of the ribose of cytidine 1402 (C1402) in 16S rRNA
D3M96_17510	COG0792	nuclease activity
D3M96_17515	COG0279	D-glycero-D-manno-heptose 7-phosphate biosynthetic process
D3M96_17530	COG0548	Belongs to the acetylglutamate kinase family. ArgB subfamily
D3M96_17540	COG0476	Involved in molybdopterin and thiamine biosynthesis, family 2
D3M96_17545	COG0793	Belongs to the peptidase S41A family
D3M96_17550	COG4942	peptidase
D3M96_17555	COG0588	phosphoglycerate mutase activity
D3M96_17560	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
D3M96_17570	COG1952	One of the proteins required for the normal export of preproteins out of the cell cytoplasm. It is a molecular chaperone that binds to a subset of precursor proteins, maintaining them in a translocation-competent state. It also specifically binds to its receptor SecA
D3M96_17575	COG0240	glycerol-3-phosphate dehydrogenase [NAD(P)+] activity
D3M96_17580	COG3181	Tripartite tricarboxylate transporter family receptor
D3M96_17585	COG0219	Methylates the ribose at the nucleotide 34 wobble position in the two leucyl isoacceptors tRNA(Leu)(CmAA) and tRNA(Leu)(cmnm5UmAA). Catalyzes the methyl transfer from S- adenosyl-L-methionine to the 2'-OH of the wobble nucleotide
D3M96_17590	COG1040	competence protein
D3M96_17595	COG2226	methyltransferase
D3M96_17605	COG2204	response regulator
D3M96_17635	COG1087	Belongs to the NAD(P)-dependent epimerase dehydratase family
D3M96_17640	COG3473	Maleate cis-trans isomerase
D3M96_17660	COG3971	2-oxopent-4-enoate hydratase activity
D3M96_17670	COG4525	Part of the ABC transporter complex TauABC involved in taurine import. Responsible for energy coupling to the transport system
D3M96_17700	COG1086	Polysaccharide biosynthesis protein
D3M96_17725	COG0472	First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
D3M96_17740	COG3307	-O-antigen
D3M96_17755	COG1898	dTDP-4-dehydrorhamnose 3,5-epimerase activity
D3M96_17765	COG0355	proton-transporting ATP synthase activity, rotational mechanism
D3M96_17770	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
D3M96_17775	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
D3M96_17780	COG0056	Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit
D3M96_17785	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
D3M96_17790	COG0711	Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0)
D3M96_17800	COG0356	it plays a direct role in the translocation of protons across the membrane
D3M96_17810	COG1024	Enoyl-CoA hydratase
D3M96_17825	COG0037	tRNA processing
D3M96_17830	COG0163	prenyltransferase activity
D3M96_17835	COG0278	Belongs to the glutaredoxin family. Monothiol subfamily
D3M96_17840	COG2890	protein-(glutamine-N5) methyltransferase activity
D3M96_17850	COG0373	Catalyzes the NADPH-dependent reduction of glutamyl- tRNA(Glu) to glutamate 1-semialdehyde (GSA)
D3M96_17860	COG0582	viral genome integration into host DNA
D3M96_17890	COG0582	viral genome integration into host DNA
D3M96_17900	COG0210	DNA helicase
D3M96_17935	COG3706	GGDEF domain
D3M96_17940	COG0030	16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity
D3M96_17945	COG2264	protein methyltransferase activity
D3M96_17960	COG3180	Ammonia monooxygenase
D3M96_17980	COG5002	protein histidine kinase activity
D3M96_17995	COG0477	Major facilitator Superfamily
D3M96_18000	COG0388	Catalyzes the ATP-dependent amidation of deamido-NAD to form NAD. Uses L-glutamine as a nitrogen source
D3M96_18020	COG4525	Part of the ABC transporter complex TauABC involved in taurine import. Responsible for energy coupling to the transport system
D3M96_18045	COG0243	molybdopterin cofactor binding
D3M96_18045	COG3383	formate dehydrogenase (NAD+) activity
D3M96_18050	COG3383	formate dehydrogenase (NAD+) activity
D3M96_18050	COG0243	molybdopterin cofactor binding
D3M96_18055	COG0437	4 iron, 4 sulfur cluster binding
D3M96_18060	COG2864	formate dehydrogenase
D3M96_18070	COG1921	L-seryl-tRNASec selenium transferase activity
D3M96_18075	COG3276	selenocysteine insertion sequence binding
D3M96_18085	COG1476	TRANSCRIPTIONal
D3M96_18090	COG0235	Class ii aldolase
D3M96_18100	COG3181	Tripartite tricarboxylate transporter family receptor
D3M96_18115	COG0709	Synthesizes selenophosphate from selenide and ATP
D3M96_18120	COG2603	Catalyzes the transfer of selenium from selenophosphate for conversion of 2-thiouridine to 2-selenouridine at the wobble position in tRNA
D3M96_18125	COG0348	domain, Protein
D3M96_18125	COG3901	Regulator of nitric oxide reductase transcription
D3M96_18130	COG4263	nitrous-oxide reductase activity
D3M96_18145	COG1277	ABC-type transport system involved in multi-copper enzyme maturation permease component
D3M96_18160	COG0166	Belongs to the GPI family
D3M96_18190	COG2233	PERMEase
D3M96_18195	COG0697	spore germination
D3M96_18200	COG1167	Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain MocR family and their eukaryotic orthologs
D3M96_18205	COG0697	spore germination
D3M96_18230	COG2885	chlorophyll binding
D3M96_18315	COG3501	Rhs element vgr protein
D3M96_18325	COG0183	Belongs to the thiolase family
D3M96_18330	COG1024	Enoyl-CoA hydratase
D3M96_18330	COG1250	3-hydroxyacyl-CoA dehydrogenase
D3M96_18345	COG1127	ABC transporter
D3M96_18350	COG0767	ABC-type transport system involved in resistance to organic solvents, permease component
D3M96_18355	COG1463	ABC-type transport system involved in resistance to organic solvents, periplasmic component
D3M96_18370	COG1131	(ABC) transporter
D3M96_18375	COG0842	Transport permease protein
D3M96_18385	COG0766	Cell wall formation. Adds enolpyruvyl to UDP-N- acetylglucosamine
D3M96_18390	COG0040	Catalyzes the condensation of ATP and 5-phosphoribose 1- diphosphate to form N'-(5'-phosphoribosyl)-ATP (PR-ATP). Has a crucial role in the pathway because the rate of histidine biosynthesis seems to be controlled primarily by regulation of hisG enzymatic activity
D3M96_18395	COG0141	Catalyzes the sequential NAD-dependent oxidations of L- histidinol to L-histidinaldehyde and then to L-histidine
D3M96_18400	COG0131	Imidazoleglycerol-phosphate dehydratase
D3M96_18405	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
D3M96_18410	COG0106	1-(5-phosphoribosyl)-5- 5-phosphoribosylamino)methylideneamino imidazole-4-carboxamide isomerase
D3M96_18415	COG0107	imidazoleglycerol-phosphate synthase activity
D3M96_18420	COG0139	Catalyzes the hydrolysis of the adenine ring of phosphoribosyl-AMP
D3M96_18425	COG0140	phosphoribosyl-ATP diphosphatase activity
D3M96_18430	COG0537	adenosine 5'-monophosphoramidase activity
D3M96_18435	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
D3M96_18440	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
D3M96_18450	COG0265	Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain
D3M96_18460	COG1970	mechanosensitive ion channel activity
D3M96_18465	COG0723	plastoquinol--plastocyanin reductase activity
D3M96_18470	COG1290	Component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex), which is a respiratory chain that generates an electrochemical potential coupled to ATP synthesis
D3M96_18475	COG2857	Cytochrome c1
D3M96_18480	COG0625	glutathione transferase activity
D3M96_18485	COG2969	positive regulation of protein catabolic process
D3M96_18490	COG4208	sulfate ABC transporter
D3M96_18495	COG0555	PFAM binding-protein-dependent transport systems inner membrane component
D3M96_18500	COG4150	thiosulfate binding
D3M96_18520	COG1052	Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family
D3M96_18540	COG4663	Part of the tripartite ATP-independent periplasmic (TRAP) transport system
D3M96_18545	COG0451	ADP-glyceromanno-heptose 6-epimerase activity
D3M96_18550	COG3622	Belongs to the hyi family
D3M96_18560	COG0129	dihydroxy-acid dehydratase activity
D3M96_18565	COG1802	Transcriptional regulator
D3M96_18570	COG1522	sequence-specific DNA binding
D3M96_18575	COG3483	tryptophan 2,3-dioxygenase activity
D3M96_18595	COG0413	3-methyl-2-oxobutanoate hydroxymethyltransferase activity
D3M96_18600	COG0656	L-ascorbic acid biosynthetic process
D3M96_18610	COG1048	Catalyzes the isomerization of citrate to isocitrate via cis-aconitate
D3M96_18615	COG3706	GGDEF domain
D3M96_18620	COG2226	methyltransferase
D3M96_18630	COG0388	Catalyzes the ATP-dependent amidation of deamido-NAD to form NAD. Uses L-glutamine as a nitrogen source
D3M96_18645	COG3653	N-Acyl-D-aspartate D-glutamate deacylase
D3M96_18650	COG0583	DNA-binding transcription factor activity
D3M96_18655	COG1028	Short-chain dehydrogenase reductase Sdr
D3M96_18660	COG1335	isochorismatase
D3M96_18680	COG2823	Periplasmic or secreted lipoprotein
D3M96_18690	COG3284	Transcriptional regulator
D3M96_18695	COG0637	HAD-superfamily hydrolase subfamily IA, variant 3
D3M96_18715	COG4172	Belongs to the ABC transporter superfamily
D3M96_18725	COG1173	ABC-type dipeptide oligopeptide nickel transport systems, permease components
D3M96_18765	COG3712	iron ion homeostasis
D3M96_18770	COG1595	DNA-templated transcription, initiation
D3M96_18780	COG0449	glutamine-fructose-6-phosphate transaminase (isomerizing) activity
D3M96_18785	COG1522	sequence-specific DNA binding
D3M96_18795	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
D3M96_18815	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
D3M96_18850	COG0109	protoheme IX farnesyltransferase activity
D3M96_18855	COG4753	response regulator
D3M96_18855	COG2207	Transcriptional regulator
D3M96_18900	COG3568	Endonuclease Exonuclease Phosphatase
D3M96_18905	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)
D3M96_18930	COG1167	Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain MocR family and their eukaryotic orthologs
D3M96_18940	COG1228	amidohydrolase
D3M96_18960	COG2986	histidine ammonia-lyase
D3M96_18965	COG2987	Catalyzes the conversion of urocanate to 4-imidazolone- 5-propionate
D3M96_18990	COG0789	Transcriptional regulator
D3M96_19010	COG0625	glutathione transferase activity
D3M96_19040	COG2365	Tyrosine phosphatase family
D3M96_19045	COG1236	Exonuclease of the beta-lactamase fold involved in RNA processing
D3M96_19065	COG2423	ornithine cyclodeaminase activity
D3M96_19115	COG3069	C4-dicarboxylate transmembrane transporter activity
D3M96_19125	COG1802	Transcriptional regulator
D3M96_19130	COG1309	transcriptional regulator
D3M96_19135	COG2814	Major facilitator Superfamily
D3M96_19150	COG2814	Major facilitator Superfamily
D3M96_19155	COG3344	reverse transcriptase
D3M96_19160	COG0629	single-stranded DNA binding
D3M96_19165	COG2814	Major facilitator Superfamily
D3M96_19175	COG0232	Belongs to the dGTPase family. Type 2 subfamily
D3M96_19180	COG0337	Catalyzes the conversion of 3-deoxy-D-arabino- heptulosonate 7-phosphate (DAHP) to dehydroquinate (DHQ)
D3M96_19185	COG0703	Catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid using ATP as a cosubstrate
D3M96_19205	COG5001	Diguanylate cyclase
D3M96_19205	COG5002	protein histidine kinase activity
D3M96_19215	COG1333	cytochrome c biogenesis protein
D3M96_19225	COG0218	Necessary for normal cell division and for the maintenance of normal septation
D3M96_19235	COG4232	protein-disulfide reductase activity
D3M96_19255	COG2141	COG2141 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases
D3M96_19260	COG0203	ribosomal protein L17
D3M96_19265	COG0202	RNA polymerase activity
D3M96_19270	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
D3M96_19275	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
D3M96_19280	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
D3M96_19285	COG0257	Belongs to the bacterial ribosomal protein bL36 family
D3M96_19295	COG0201	protein transport
D3M96_19300	COG0200	Binds to the 23S rRNA
D3M96_19305	COG1841	ribosomal large subunit assembly
D3M96_19310	COG0098	Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body
D3M96_19315	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
D3M96_19320	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
D3M96_19325	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
D3M96_19330	COG0199	Binds 16S rRNA, required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site
D3M96_19335	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
D3M96_19340	COG0198	One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit
D3M96_19345	COG0093	Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome
D3M96_19400	COG1960	acyl-CoA dehydrogenase activity
D3M96_19405	COG0183	Belongs to the thiolase family
D3M96_19430	COG0318	PFAM AMP-dependent synthetase and ligase
D3M96_19435	COG0369	Component of the sulfite reductase complex that catalyzes the 6-electron reduction of sulfite to sulfide. This is one of several activities required for the biosynthesis of L- cysteine from sulfate. The flavoprotein component catalyzes the electron flow from NADPH - FAD - FMN to the hemoprotein component
D3M96_19440	COG0155	Belongs to the nitrite and sulfite reductase 4Fe-4S domain family
D3M96_19445	COG0007	Multifunctional enzyme that catalyzes the SAM-dependent methylations of uroporphyrinogen III at position C-2 and C-7 to form precorrin-2 via precorrin-1. Then it catalyzes the NAD- dependent ring dehydrogenation of precorrin-2 to yield sirohydrochlorin. Finally, it catalyzes the ferrochelation of sirohydrochlorin to yield siroheme
D3M96_19445	COG1648	precorrin-2 dehydrogenase activity
D3M96_19460	COG1960	acyl-CoA dehydrogenase activity
D3M96_19475	COG0186	One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA
D3M96_19480	COG0255	Belongs to the universal ribosomal protein uL29 family
D3M96_19485	COG0197	Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs
D3M96_19490	COG0092	Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation
D3M96_19495	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
D3M96_19500	COG0185	Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA
D3M96_19505	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
D3M96_19510	COG0089	rRNA binding
D3M96_19515	COG0088	Forms part of the polypeptide exit tunnel
D3M96_19520	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
D3M96_19525	COG4175	Glycine betaine
D3M96_19530	COG4176	ABC-type proline glycine betaine transport system permease component
D3M96_19535	COG0051	transcription antitermination factor activity, RNA binding
D3M96_19540	COG0050	This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis
D3M96_19545	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
D3M96_19550	COG0049	tRNA binding
D3M96_19555	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
D3M96_19570	COG2205	protein histidine kinase activity
D3M96_19585	COG3241	Transfers electrons from cytochrome c551 to cytochrome oxidase
D3M96_19590	COG0086	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates
D3M96_19595	COG0085	RNA polymerase activity
D3M96_19600	COG0222	ribosome binding
D3M96_19605	COG0244	Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors
D3M96_19610	COG0081	regulation of translation
D3M96_19615	COG0080	Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors
D3M96_19635	COG0050	This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis
D3M96_19655	COG1475	DNA binding
D3M96_19660	COG1192	Involved in chromosome partitioning
D3M96_19670	COG0445	tRNA wobble uridine modification
D3M96_19675	COG0436	Aminotransferase
D3M96_19685	COG0639	Hydrolyzes diadenosine 5',5'''-P1,P4-tetraphosphate to yield ADP
D3M96_19690	COG3706	GGDEF domain
D3M96_19695	COG0688	phosphatidylethanolamine metabolic process
D3M96_19705	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
D3M96_19750	COG0486	Exhibits a very high intrinsic GTPase hydrolysis rate. Involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA- cmnm(5)s(2)U34
D3M96_19795	COG0753	catalase activity
D3M96_19800	COG0706	membrane insertase activity
D3M96_19805	COG0759	Could be involved in insertion of integral membrane proteins into the membrane
D3M96_19810	COG0594	ribonuclease P activity
D3M96_19815	COG0230	Belongs to the bacterial ribosomal protein bL34 family