locus-tag	class	description
VagYM4_00010	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
VagYM4_00020	COG0592	DNA-directed DNA polymerase activity
VagYM4_00040	COG0187	DNA topoisomerase II activity
VagYM4_00070	COG0071	Belongs to the small heat shock protein (HSP20) family
VagYM4_00080	COG3977	Valine--pyruvate aminotransferase
VagYM4_00090	COG0366	Alpha amylase catalytic
VagYM4_00100	COG0751	glycine-tRNA ligase activity
VagYM4_00120	COG2119	membrane
VagYM4_00140	COG0425	Belongs to the sulfur carrier protein TusA family
VagYM4_00170	COG0604	alcohol dehydrogenase
VagYM4_00180	COG0183	Belongs to the thiolase family
VagYM4_00200	COG1739	Uncharacterized protein family UPF0029
VagYM4_00210	COG0168	Low-affinity potassium transport system. Interacts with trk system potassium uptake protein TrkA
VagYM4_00230	COG0583	DNA-binding transcription factor activity
VagYM4_00240	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
VagYM4_00250	COG2960	long-chain fatty acid transporting porin activity
VagYM4_00260	COG0841	Belongs to the resistance-nodulation-cell division (RND) (TC 2.A.6) family
VagYM4_00270	COG0845	Belongs to the membrane fusion protein (MFP) (TC 8.A.1) family
VagYM4_00330	COG4166	transmembrane transport
VagYM4_00350	COG1173	ABC-type dipeptide oligopeptide nickel transport systems, permease components
VagYM4_00420	COG1609	Transcriptional regulator
VagYM4_00430	COG0583	DNA-binding transcription factor activity
VagYM4_00460	COG0129	dihydroxy-acid dehydratase activity
VagYM4_00470	COG3265	gluconokinase activity
VagYM4_00480	COG2610	gluconate transmembrane transporter activity
VagYM4_00490	COG0800	Aldolase
VagYM4_00500	COG0005	The purine nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the beta- (deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate
VagYM4_00510	COG0583	DNA-binding transcription factor activity
VagYM4_00520	COG1249	Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family
VagYM4_00530	COG2961	Specifically methylates the adenine in position 2030 of 23S rRNA
VagYM4_00550	COG1522	sequence-specific DNA binding
VagYM4_00560	COG5002	protein histidine kinase activity
VagYM4_00560	COG5001	Diguanylate cyclase
VagYM4_00570	COG0742	ribosomal rna small subunit methyltransferase
VagYM4_00600	COG0589	response to stress
VagYM4_00610	COG1528	Iron-storage protein
VagYM4_00630	COG2081	HI0933 family
VagYM4_00640	COG2204	response regulator
VagYM4_00690	COG1597	lipid kinase activity
VagYM4_00750	COG0628	permease
VagYM4_00780	COG1322	Protein conserved in bacteria
VagYM4_00790	COG2226	methyltransferase
VagYM4_00800	COG3165	ubiquinone biosynthetic process from chorismate
VagYM4_00810	COG0661	Is probably a protein kinase regulator of UbiI activity which is involved in aerobic coenzyme Q (ubiquinone) biosynthesis
VagYM4_00830	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
VagYM4_00840	COG0805	protein transport
VagYM4_00850	COG0084	hydrolase, TatD family'
VagYM4_00870	COG0456	acetyltransferase
VagYM4_00880	COG0258	In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity
VagYM4_00880	COG0749	In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity
VagYM4_00890	COG0218	Necessary for normal cell division and for the maintenance of normal septation
VagYM4_00950	COG1816	Catalyzes the hydrolytic deamination of adenine to hypoxanthine. Plays an important role in the purine salvage pathway and in nitrogen catabolism
VagYM4_00970	COG2204	response regulator
VagYM4_00980	COG3852	Histidine kinase
VagYM4_01000	COG0174	glutamine synthetase
VagYM4_01040	COG1295	ribonuclease BN
VagYM4_01050	COG1490	D-aminoacyl-tRNA deacylase activity
VagYM4_01060	COG0456	acetyltransferase
VagYM4_01080	COG1866	Involved in the gluconeogenesis. Catalyzes the conversion of oxaloacetate (OAA) to phosphoenolpyruvate (PEP) through direct phosphoryl transfer between the nucleoside triphosphate and OAA
VagYM4_01090	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
VagYM4_01100	COG1188	Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit, (S4 paralog))
VagYM4_01110	COG3031	protein transport across the cell outer membrane
VagYM4_01130	COG2804	Type II secretory pathway, ATPase PulE Tfp pilus assembly pathway, ATPase PilB
VagYM4_01140	COG1459	type II secretion system
VagYM4_01150	COG2165	general secretion pathway protein
VagYM4_01160	COG2165	general secretion pathway protein
VagYM4_01170	COG2165	general secretion pathway protein
VagYM4_01180	COG4795	General secretion pathway protein
VagYM4_01190	COG3156	type II secretion system protein K
VagYM4_01200	COG3297	Involved in a type II secretion system (T2SS, formerly general secretion pathway, GSP) for the export of proteins
VagYM4_01210	COG3149	Involved in a type II secretion system (T2SS, formerly general secretion pathway, GSP) for the export of proteins
VagYM4_01230	COG1218	3'(2'),5'-bisphosphate nucleotidase
VagYM4_01240	COG0494	nUDIX hydrolase
VagYM4_01250	COG0316	Belongs to the HesB IscA family
VagYM4_01250	COG0694	Involved in iron-sulfur cluster biogenesis. Binds a 4Fe- 4S cluster, can transfer this cluster to apoproteins, and thereby intervenes in the maturation of Fe S proteins. Could also act as a scaffold chaperone for damaged Fe S proteins
VagYM4_01260	COG1040	competence protein
VagYM4_01270	COG0596	Alpha beta hydrolase
VagYM4_01290	COG2183	response to ionizing radiation
VagYM4_01310	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
VagYM4_01330	COG0745	RESPONSE REGULATOR receiver
VagYM4_01340	COG2205	protein histidine kinase activity
VagYM4_01350	COG2233	PERMEase
VagYM4_01360	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)
VagYM4_01370	COG0566	Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase TrmH family
VagYM4_01380	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
VagYM4_01390	COG1758	RNA polymerase activity
VagYM4_01400	COG0194	GDP metabolic process
VagYM4_01430	COG0848	biopolymer transport protein
VagYM4_01440	COG0811	peptide transport
VagYM4_01480	COG4174	ABC transporter (Permease)
VagYM4_01490	COG4239	(ABC) transporter, permease
VagYM4_01500	COG0747	negative chemotaxis
VagYM4_01510	COG0444	Belongs to the ABC transporter superfamily
VagYM4_01520	COG4608	Belongs to the ABC transporter superfamily
VagYM4_01540	COG1561	YicC-like family, N-terminal region
VagYM4_01550	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
VagYM4_01570	COG1560	Kdo2-lipid A biosynthetic process
VagYM4_01580	COG1309	transcriptional regulator
VagYM4_01590	COG0452	Catalyzes two steps in the biosynthesis of coenzyme A. In the first step cysteine is conjugated to 4'-phosphopantothenate to form 4-phosphopantothenoylcysteine, in the latter compound is decarboxylated to form 4'-phosphopantotheine
VagYM4_01610	COG2003	Belongs to the UPF0758 family
VagYM4_01700	COG0463	Glycosyl transferase, family 2
VagYM4_01710	COG0859	PFAM glycosyl transferase family 9
VagYM4_01720	COG0818	Recycling of diacylglycerol produced during the turnover of membrane phospholipid
VagYM4_01730	COG3642	lipopolysaccharide core region biosynthetic process
VagYM4_01770	COG0399	UDP-4-amino-4-deoxy-L-arabinose aminotransferase
VagYM4_01790	COG1086	Polysaccharide biosynthesis protein
VagYM4_01800	COG0399	UDP-4-amino-4-deoxy-L-arabinose aminotransferase
VagYM4_01810	COG0381	UDP-N-acetylglucosamine 2-epimerase activity
VagYM4_01820	COG2089	acid synthase
VagYM4_01840	COG1208	COG1208 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis translation initiation factor 2B, gamma epsilon subunits eIF-2Bgamma eIF-2Bepsilon
VagYM4_01850	COG1083	cytidylyl-transferase
VagYM4_01870	COG1519	Transferase
VagYM4_01880	COG0859	PFAM glycosyl transferase family 9
VagYM4_01890	COG1560	Kdo2-lipid A biosynthetic process
VagYM4_01910	COG4775	Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane
VagYM4_02070	COG0472	First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
VagYM4_02080	COG1236	Exonuclease of the beta-lactamase fold involved in RNA processing
VagYM4_02090	COG0677	UDP-N-acetyl-D-mannosamine dehydrogenase activity
VagYM4_02140	COG1045	serine acetyltransferase
VagYM4_02170	COG0438	transferase activity, transferring glycosyl groups
VagYM4_02180	COG2148	undecaprenyl-phosphate glucose phosphotransferase activity
VagYM4_02200	COG0399	UDP-4-amino-4-deoxy-L-arabinose aminotransferase
VagYM4_02240	COG0149	triose-phosphate isomerase activity
VagYM4_02290	COG1494	fructose-1,6-bisphosphatase
VagYM4_02310	COG0684	Catalyzes the aldol cleavage of 4-hydroxy-4-methyl-2- oxoglutarate (HMG) into 2 molecules of pyruvate. Also contains a secondary oxaloacetate (OAA) decarboxylase activity due to the common pyruvate enolate transition state formed following C-C bond cleavage in the retro-aldol and decarboxylation reactions
VagYM4_02320	COG1575	Belongs to the MenA family. Type 1 subfamily
VagYM4_02330	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
VagYM4_02340	COG5405	Protease subunit of a proteasome-like degradation complex believed to be a general protein degrading machinery
VagYM4_02370	COG1609	Transcriptional regulator
VagYM4_02380	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
VagYM4_02390	COG0254	rRNA binding
VagYM4_02410	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
VagYM4_02420	COG0088	Forms part of the polypeptide exit tunnel
VagYM4_02440	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
VagYM4_02450	COG0185	Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA
VagYM4_02460	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
VagYM4_02470	COG0092	Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation
VagYM4_02490	COG0255	Belongs to the universal ribosomal protein uL29 family
VagYM4_02500	COG0186	One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA
VagYM4_02520	COG0198	One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit
VagYM4_02530	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
VagYM4_02540	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
VagYM4_02550	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
VagYM4_02560	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
VagYM4_02590	COG1841	ribosomal large subunit assembly
VagYM4_02610	COG0201	protein transport
VagYM4_02620	COG0257	Belongs to the bacterial ribosomal protein bL36 family
VagYM4_02630	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
VagYM4_02640	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
VagYM4_02660	COG0202	RNA polymerase activity
VagYM4_02670	COG0203	ribosomal protein L17
VagYM4_02690	COG0545	Peptidyl-prolyl cis-trans isomerase
VagYM4_02710	COG2153	protein acetylation
VagYM4_02720	COG0513	Belongs to the DEAD box helicase family
VagYM4_02740	COG0737	Belongs to the 5'-nucleotidase family
VagYM4_02750	COG1648	precorrin-2 dehydrogenase activity
VagYM4_02750	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
VagYM4_02760	COG0175	sulfate reduction
VagYM4_02770	COG2895	sulfate adenylyltransferase (ATP) activity
VagYM4_02780	COG3273	potassium ion transport
VagYM4_02780	COG0471	metal ion transport
VagYM4_02790	COG0529	Catalyzes the synthesis of activated sulfate
VagYM4_02840	COG4181	ATPase activity
VagYM4_02870	COG3054	Bacterial protein of unknown function (YtfJ_HI0045)
VagYM4_02890	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
VagYM4_02900	COG0729	surface antigen
VagYM4_02910	COG2911	Protein conserved in bacteria
VagYM4_02920	COG2105	PFAM AIG2 family protein
VagYM4_02940	COG0221	Catalyzes the hydrolysis of inorganic pyrophosphate (PPi) forming two phosphate ions
VagYM4_02950	COG0158	D-fructose-1,6-bisphosphate 1-phosphohydrolase class 1
VagYM4_02960	COG0773	UDP-N-acetylmuramate-L-alanine ligase activity
VagYM4_02970	COG0163	prenyltransferase activity
VagYM4_02980	COG4143	(ABC) transporter
VagYM4_02990	COG1178	ABC-type Fe3 transport system permease component
VagYM4_03000	COG3840	Part of the ABC transporter complex ThiBPQ involved in thiamine import. Responsible for energy coupling to the transport system
VagYM4_03010	COG0583	DNA-binding transcription factor activity
VagYM4_03020	COG1902	pentaerythritol trinitrate reductase activity
VagYM4_03050	COG2358	TRAP transporter, solute receptor (TAXI family
VagYM4_03090	COG0142	geranyltranstransferase activity
VagYM4_03100	COG0261	This protein binds to 23S rRNA in the presence of protein L20
VagYM4_03120	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
VagYM4_03130	COG2966	Psort location CytoplasmicMembrane, score
VagYM4_03160	COG0639	Hydrolyzes diadenosine 5',5'''-P1,P4-tetraphosphate to yield ADP
VagYM4_03170	COG2967	ApaG domain
VagYM4_03180	COG0030	16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity
VagYM4_03190	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)
VagYM4_03200	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
VagYM4_03210	COG1452	involved in the assembly of lipopolysaccharide (LPS) at the surface of the outer membrane
VagYM4_03220	COG1076	Co-chaperone involved in the maturation of iron-sulfur cluster-containing proteins. Seems to help targeting proteins to be folded toward HscA
VagYM4_03260	COG0473	3-isopropylmalate dehydrogenase activity
VagYM4_03270	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)
VagYM4_03310	COG0583	DNA-binding transcription factor activity
VagYM4_03320	COG1022	Amp-dependent synthetase and ligase
VagYM4_03330	COG0028	Belongs to the TPP enzyme family
VagYM4_03350	COG3706	GGDEF domain
VagYM4_03370	COG0469	pyruvate kinase activity
VagYM4_03380	COG1349	DNA-binding transcription factor activity
VagYM4_03390	COG0449	glutamine-fructose-6-phosphate transaminase (isomerizing) activity
VagYM4_03420	COG5002	protein histidine kinase activity
VagYM4_03440	COG2376	Dihydroxyacetone kinase
VagYM4_03450	COG1461	Dihydroxyacetone kinase
VagYM4_03480	COG3722	fumarate hydratase activity
VagYM4_03490	COG0246	Mannitol dehydrogenase
VagYM4_03500	COG2213	PTS system mannitol-specific
VagYM4_03500	COG4668	phosphoenolpyruvate-dependent sugar phosphotransferase system
VagYM4_03560	COG1464	Belongs to the NlpA lipoprotein family
VagYM4_03580	COG0358	DNA primase activity
VagYM4_03590	COG1610	YqeY-like protein
VagYM4_03600	COG0828	Belongs to the bacterial ribosomal protein bS21 family
VagYM4_03610	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
VagYM4_03620	COG2021	Transfers an acetyl group from acetyl-CoA to L- homoserine, forming acetyl-L-homoserine
VagYM4_03630	COG0344	acyl-phosphate glycerol-3-phosphate acyltransferase activity
VagYM4_03640	COG1539	Catalyzes the conversion of 7,8-dihydroneopterin to 6- hydroxymethyl-7,8-dihydropterin
VagYM4_03650	COG0801	2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
VagYM4_03660	COG1968	undecaprenyl-diphosphatase activity
VagYM4_03670	COG0617	tRNA 3'-terminal CCA addition
VagYM4_03680	COG3409	Peptidoglycan-binding domain 1 protein
VagYM4_03680	COG3267	Type II secretory pathway component ExeA
VagYM4_03700	COG0405	Gamma-glutamyltransferase
VagYM4_03710	COG4991	sh3 domain protein
VagYM4_03720	COG0306	phosphate transporter
VagYM4_03730	COG1392	Phosphate transport regulator
VagYM4_03740	COG3025	triphosphatase activity
VagYM4_03770	COG1391	[glutamine synthetase]-adenylyl-L-tyrosine phosphorylase
VagYM4_03780	COG0615	ADP-L-glycero-beta-D-manno-heptose biosynthetic process
VagYM4_03780	COG2870	Catalyzes the ADP transfer from ATP to D-glycero-beta-D- manno-heptose 1-phosphate, yielding ADP-D-glycero-beta-D-manno- heptose
VagYM4_03790	COG1538	Outer membrane efflux protein
VagYM4_03800	COG0494	nUDIX hydrolase
VagYM4_03810	COG3151	Protein conserved in bacteria
VagYM4_03830	COG3150	esterase
VagYM4_03850	COG0188	A type II topoisomerase that negatively supercoils closed circular double-stranded (ds) DNA in an ATP-dependent manner to modulate DNA topology and maintain chromosomes in an underwound state. Negative supercoiling favors strand separation, and DNA replication, transcription, recombination and repair, all of which involve strand separation. Also able to catalyze the interconversion of other topological isomers of dsDNA rings, including catenanes and knotted rings. Type II topoisomerases break and join 2 DNA strands simultaneously in an ATP-dependent manner
VagYM4_03860	COG0265	Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain
VagYM4_03880	COG3105	Protein conserved in bacteria
VagYM4_03890	COG1485	Reduces the stability of FtsZ polymers in the presence of ATP
VagYM4_03900	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
VagYM4_03910	COG0103	maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
VagYM4_03920	COG0723	plastoquinol--plastocyanin reductase activity
VagYM4_03930	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
VagYM4_03940	COG2857	Cytochrome c1
VagYM4_03950	COG0625	glutathione transferase activity
VagYM4_03960	COG2969	positive regulation of protein catabolic process
VagYM4_03970	COG2823	Periplasmic or secreted lipoprotein
VagYM4_03980	COG0279	D-glycero-D-manno-heptose 7-phosphate biosynthetic process
VagYM4_04010	COG0313	Catalyzes the 2'-O-methylation of the ribose of cytidine 1402 (C1402) in 16S rRNA
VagYM4_04030	COG3116	cell division
VagYM4_04040	COG0768	penicillin binding
VagYM4_04050	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
VagYM4_04060	COG0770	UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase activity
VagYM4_04070	COG0472	First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
VagYM4_04080	COG0771	Cell wall formation. Catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA)
VagYM4_04090	COG0772	Belongs to the SEDS family
VagYM4_04110	COG0773	UDP-N-acetylmuramate-L-alanine ligase activity
VagYM4_04120	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
VagYM4_04130	COG0849	cell division
VagYM4_04140	COG0206	Essential cell division protein that forms a contractile ring structure (Z ring) at the future cell division site. The regulation of the ring assembly controls the timing and the location of cell division. One of the functions of the FtsZ ring is to recruit other cell division proteins to the septum to produce a new cell wall between the dividing cells. Binds GTP and shows GTPase activity
VagYM4_04150	COG0774	UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase activity
VagYM4_04170	COG0653	protein targeting
VagYM4_04180	COG0494	nUDIX hydrolase
VagYM4_04210	COG0505	Belongs to the CarA family
VagYM4_04220	COG0458	carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity
VagYM4_04250	COG0730	response to heat
VagYM4_04260	COG0583	DNA-binding transcription factor activity
VagYM4_04270	COG2860	membrane
VagYM4_04320	COG0493	'glutamate synthase
VagYM4_04330	COG0069	glutamate synthase activity
VagYM4_04330	COG0070	glutamate synthase
VagYM4_04330	COG0067	glutamate synthase
VagYM4_04350	COG0070	glutamate synthase
VagYM4_04350	COG0069	glutamate synthase activity
VagYM4_04350	COG0067	glutamate synthase
VagYM4_04360	COG1242	4 iron, 4 sulfur cluster binding
VagYM4_04370	COG5001	Diguanylate cyclase
VagYM4_04370	COG2203	Gaf domain
VagYM4_04370	COG3706	GGDEF domain
VagYM4_04370	COG4251	negative regulation of phosphorylation
VagYM4_04380	COG0784	Response regulator, receiver
VagYM4_04380	COG2198	Histidine kinase
VagYM4_04380	COG5002	protein histidine kinase activity
VagYM4_04400	COG0745	RESPONSE REGULATOR receiver
VagYM4_04420	COG0684	Catalyzes the aldol cleavage of 4-hydroxy-4-methyl-2- oxoglutarate (HMG) into 2 molecules of pyruvate. Also contains a secondary oxaloacetate (OAA) decarboxylase activity due to the common pyruvate enolate transition state formed following C-C bond cleavage in the retro-aldol and decarboxylation reactions
VagYM4_04450	COG0083	homoserine kinase activity
VagYM4_04460	COG0498	Catalyzes the gamma-elimination of phosphate from L- phosphohomoserine and the beta-addition of water to produce L- threonine
VagYM4_04480	COG3445	Acts as a radical domain for damaged PFL and possibly other radical proteins
VagYM4_04490	COG0648	Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic sites (AP sites) to produce new 5'-ends that are base-free deoxyribose 5-phosphate residues. It preferentially attacks modified AP sites created by bleomycin and neocarzinostatin
VagYM4_04500	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
VagYM4_04530	COG1115	amino acid carrier protein
VagYM4_04540	COG3022	response to hydroperoxide
VagYM4_04550	COG0513	Belongs to the DEAD box helicase family
VagYM4_04560	COG4123	Specifically methylates the adenine in position 37 of tRNA(1)(Val) (anticodon cmo5UAC)
VagYM4_04580	COG0716	FMN binding
VagYM4_04590	COG4974	Belongs to the 'phage' integrase family
VagYM4_04600	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
VagYM4_04610	COG0608	single-stranded DNA 5'-3' exodeoxyribonuclease activity
VagYM4_04620	COG1186	Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA
VagYM4_04630	COG1190	Belongs to the class-II aminoacyl-tRNA synthetase family
VagYM4_04640	COG2204	response regulator
VagYM4_04670	COG0667	Aldo Keto reductase
VagYM4_04720	COG0730	response to heat
VagYM4_04740	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
VagYM4_04760	COG1283	sodium-dependent phosphate transmembrane transporter activity
VagYM4_04770	COG0583	DNA-binding transcription factor activity
VagYM4_04780	COG0640	Transcriptional regulator
VagYM4_04790	COG0268	Binds directly to 16S ribosomal RNA
VagYM4_04800	COG0728	peptidoglycan biosynthetic process
VagYM4_04810	COG0196	riboflavin kinase activity
VagYM4_04830	COG0597	This protein specifically catalyzes the removal of signal peptides from prolipoproteins
VagYM4_04840	COG1047	Peptidyl-prolyl cis-trans
VagYM4_04850	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
VagYM4_04890	COG3279	Response regulator of the LytR AlgR family
VagYM4_04900	COG3275	phosphorelay sensor kinase activity
VagYM4_04910	COG1966	Carbon starvation protein
VagYM4_04950	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
VagYM4_04960	COG1472	Belongs to the glycosyl hydrolase 3 family
VagYM4_04970	COG0722	Stereospecific condensation of phosphoenolpyruvate (PEP) and D-erythrose-4-phosphate (E4P) giving rise to 3-deoxy-D- arabino-heptulosonate-7-phosphate (DAHP)
VagYM4_04980	COG0287	Prephenate dehydrogenase
VagYM4_04980	COG1605	Chorismate mutase
VagYM4_04990	COG0739	heme binding
VagYM4_04990	COG0741	lytic transglycosylase activity
VagYM4_04990	COG1196	nuclear chromosome segregation
VagYM4_05010	COG0488	(ABC) transporter
VagYM4_05030	COG2973	This protein is an aporepressor. When complexed with L- tryptophan it binds the operator region of the trp operon (5'- ACTAGT-'3') and prevents the initiation of transcription. The complex also regulates trp repressor biosynthesis by binding to its regulatory region
VagYM4_05040	COG1986	Phosphatase that hydrolyzes non-canonical purine nucleotides such as XTP and ITP to their respective diphosphate derivatives. Probably excludes non-canonical purines from DNA precursor pool, thus preventing their incorporation into DNA and avoiding chromosomal lesions
VagYM4_05050	COG1605	Chorismate mutase
VagYM4_05050	COG0077	Prephenate dehydratase
VagYM4_05060	COG1544	Required for dimerization of active 70S ribosomes into 100S ribosomes in stationary phase
VagYM4_05070	COG4623	carbon-oxygen lyase activity, acting on polysaccharides
VagYM4_05080	COG4105	Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane
VagYM4_05090	COG0564	pseudouridine synthase activity
VagYM4_05110	COG0542	response to heat
VagYM4_05150	COG1145	4fe-4S ferredoxin, iron-sulfur binding domain protein
VagYM4_05170	COG2974	May be involved in recombination
VagYM4_05180	COG0745	RESPONSE REGULATOR receiver
VagYM4_05190	COG5002	protein histidine kinase activity
VagYM4_05210	COG0248	Ppx GppA phosphatase
VagYM4_05220	COG0855	Catalyzes the reversible transfer of the terminal phosphate of ATP to form a long-chain polyphosphate (polyP)
VagYM4_05230	COG0573	inorganic phosphate transmembrane transporter activity
VagYM4_05240	COG0581	inorganic phosphate transmembrane transporter activity
VagYM4_05250	COG1117	ATPase-coupled phosphate ion transmembrane transporter activity
VagYM4_05260	COG0704	Plays a role in the regulation of phosphate uptake
VagYM4_05280	COG3142	Participates in the control of copper homeostasis
VagYM4_05290	COG0450	alkyl hydroperoxide reductase
VagYM4_05300	COG0583	DNA-binding transcription factor activity
VagYM4_05310	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
VagYM4_05330	COG0517	IMP dehydrogenase activity
VagYM4_05350	COG0809	Transfers and isomerizes the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to give epoxyqueuosine (oQ-tRNA)
VagYM4_05370	COG1862	Preprotein translocase
VagYM4_05380	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
VagYM4_05390	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
VagYM4_05400	COG0483	inositol monophosphate 1-phosphatase activity
VagYM4_05410	COG0565	Catalyzes the formation of 2'O-methylated cytidine (Cm32) or 2'O-methylated uridine (Um32) at position 32 in tRNA
VagYM4_05430	COG1104	cysteine desulfurase activity
VagYM4_05440	COG0822	iron-sulfur transferase activity
VagYM4_05470	COG0443	Heat shock 70 kDa protein
VagYM4_05480	COG0633	Ferredoxin
VagYM4_05490	COG2975	iron-sulfur cluster assembly
VagYM4_05510	COG0105	UTP biosynthetic process
VagYM4_05540	COG0821	Converts 2C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-2,4cPP) into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate
VagYM4_05550	COG0124	histidyl-tRNA synthetase
VagYM4_05560	COG2976	Protein conserved in bacteria
VagYM4_05570	COG1520	Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane
VagYM4_05580	COG1160	GTP binding
VagYM4_05620	COG0517	IMP dehydrogenase activity
VagYM4_05620	COG0516	GMP reductase activity
VagYM4_05630	COG0518	GMP synthase (glutamine-hydrolyzing) activity
VagYM4_05630	COG0519	Catalyzes the synthesis of GMP from XMP
VagYM4_05640	COG0582	viral genome integration into host DNA
VagYM4_05810	COG1757	Na H antiporter
VagYM4_05830	COG1584	GPR1 FUN34 yaaH family protein
VagYM4_05840	COG1115	amino acid carrier protein
VagYM4_05880	COG2873	o-acetylhomoserine
VagYM4_05890	COG0161	adenosylmethionine-8-amino-7-oxononanoate transaminase activity
VagYM4_05930	COG0388	Catalyzes the ATP-dependent amidation of deamido-NAD to form NAD. Uses L-glutamine as a nitrogen source
VagYM4_05930	COG3153	acetyltransferase
VagYM4_05940	COG0583	DNA-binding transcription factor activity
VagYM4_05960	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
VagYM4_05970	COG2867	negative regulation of translational initiation
VagYM4_05980	COG2914	Belongs to the UPF0125 (RnfH) family
VagYM4_05990	COG2913	Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane
VagYM4_06000	COG0497	DNA recombination
VagYM4_06020	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
VagYM4_06030	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
VagYM4_06040	COG1301	dicarboxylic acid transport
VagYM4_06060	COG0484	heat shock protein binding
VagYM4_06120	COG2978	secondary active p-aminobenzoyl-glutamate transmembrane transporter activity
VagYM4_06140	COG4623	carbon-oxygen lyase activity, acting on polysaccharides
VagYM4_06150	COG0047	phosphoribosylformylglycinamidine synthase activity
VagYM4_06150	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
VagYM4_06180	COG1629	transport
VagYM4_06210	COG2195	Cleaves the N-terminal amino acid of tripeptides
VagYM4_06220	COG2252	PERMEase
VagYM4_06230	COG2236	Acts on guanine, xanthine and to a lesser extent hypoxanthine
VagYM4_06270	COG0263	Catalyzes the transfer of a phosphate group to glutamate to form L-glutamate 5-phosphate
VagYM4_06280	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
VagYM4_06290	COG1327	Negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR- boxes
VagYM4_06300	COG0117	Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)- pyrimidinedione 5'-phosphate
VagYM4_06300	COG1985	Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)- pyrimidinedione 5'-phosphate
VagYM4_06330	COG0054	6,7-dimethyl-8-ribityllumazine synthase activity
VagYM4_06350	COG0611	Catalyzes the ATP-dependent phosphorylation of thiamine- monophosphate (TMP) to form thiamine-pyrophosphate (TPP), the active form of vitamin B1
VagYM4_06360	COG1267	Lipid phosphatase which dephosphorylates phosphatidylglycerophosphate (PGP) to phosphatidylglycerol (PG)
VagYM4_06370	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)
VagYM4_06380	COG0142	geranyltranstransferase activity
VagYM4_06390	COG1722	exodeoxyribonuclease VII activity
VagYM4_06400	COG1291	archaeal or bacterial-type flagellum-dependent cell motility
VagYM4_06420	COG0301	tRNA thio-modification
VagYM4_06420	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
VagYM4_06440	COG0583	DNA-binding transcription factor activity
VagYM4_06460	COG2363	Small membrane protein
VagYM4_06480	COG0258	In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity
VagYM4_06490	COG1611	Belongs to the LOG family
VagYM4_06520	COG2904	Catalyzes the NADPH-dependent reduction of 7-cyano-7- deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1)
VagYM4_06520	COG0780	Catalyzes the NADPH-dependent reduction of 7-cyano-7- deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1)
VagYM4_06540	COG5595	Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310)
VagYM4_06550	COG1464	Belongs to the NlpA lipoprotein family
VagYM4_06560	COG2011	ABC-type metal ion transport system permease component
VagYM4_06570	COG1135	Part of the ABC transporter complex MetNIQ involved in methionine import. Responsible for energy coupling to the transport system
VagYM4_06580	COG0241	D,D-heptose 1,7-bisphosphate phosphatase
VagYM4_06600	COG1264	protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
VagYM4_06600	COG1263	PTS System
VagYM4_06610	COG0366	Alpha amylase catalytic
VagYM4_06650	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
VagYM4_06660	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
VagYM4_06670	COG0321	lipoyl(octanoyl) transferase activity
VagYM4_06690	COG1686	Belongs to the peptidase S11 family
VagYM4_06700	COG0797	Lytic transglycosylase with a strong preference for naked glycan strands that lack stem peptides
VagYM4_06710	COG0772	Belongs to the SEDS family
VagYM4_06720	COG0768	penicillin binding
VagYM4_06730	COG1576	Specifically methylates the pseudouridine at position 1915 (m3Psi1915) in 23S rRNA
VagYM4_06740	COG0799	negative regulation of ribosome biogenesis
VagYM4_06750	COG1466	dna polymerase III delta subunit
VagYM4_06760	COG2980	Together with LptD, is involved in the assembly of lipopolysaccharide (LPS) at the surface of the outer membrane. Required for the proper assembly of LptD. Binds LPS and may serve as the LPS recognition site at the outer membrane
VagYM4_06770	COG0495	leucyl-tRNA aminoacylation
VagYM4_06780	COG2888	peptidyl-tyrosine sulfation
VagYM4_06790	COG0815	Transfers the fatty acyl group on membrane lipoproteins
VagYM4_06800	COG4535	Mg2 and Co2 transporter CorC
VagYM4_06810	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
VagYM4_06820	COG1702	phosphate starvation-inducible protein PhoH
VagYM4_06830	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
VagYM4_06840	COG0654	COG0654 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases
VagYM4_06850	COG0012	GTP binding
VagYM4_06860	COG0193	aminoacyl-tRNA hydrolase activity
VagYM4_06870	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)
VagYM4_06880	COG1947	Catalyzes the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol
VagYM4_06890	COG3017	Plays a critical role in the incorporation of lipoproteins in the outer membrane after they are released by the LolA protein
VagYM4_06900	COG0373	Catalyzes the NADPH-dependent reduction of glutamyl- tRNA(Glu) to glutamate 1-semialdehyde (GSA)
VagYM4_06920	COG2890	protein-(glutamine-N5) methyltransferase activity
VagYM4_06930	COG3094	Invasion gene expression up-regulator, SirB
VagYM4_06940	COG2912	Transglutaminase-like superfamily
VagYM4_06950	COG2877	3-deoxy-8-phosphooctulonate synthase activity
VagYM4_06960	COG0737	Belongs to the 5'-nucleotidase family
VagYM4_06980	COG1187	pseudouridine synthase activity
VagYM4_06990	COG2840	Smr protein MutS2
VagYM4_07060	COG2608	mercury ion transmembrane transporter activity
VagYM4_07060	COG2217	Heavy metal translocating P-type atpase
VagYM4_07080	COG3110	Uncharacterized protein conserved in bacteria (DUF2057)
VagYM4_07180	COG0784	Response regulator, receiver
VagYM4_07180	COG0835	chemotaxis
VagYM4_07190	COG1352	Methylation of the membrane-bound methyl-accepting chemotaxis proteins (MCP) to form gamma-glutamyl methyl ester residues in MCP
VagYM4_07200	COG1815	bacterial-type flagellum-dependent cell motility
VagYM4_07210	COG1558	bacterial-type flagellum-dependent cell motility
VagYM4_07230	COG1749	Flagellar hook protein flgE
VagYM4_07240	COG4787	bacterial-type flagellum-dependent cell motility
VagYM4_07260	COG2063	Assembles around the rod to form the L-ring and probably protects the motor basal body from shearing forces during rotation
VagYM4_07270	COG1706	bacterial-type flagellum-dependent cell motility
VagYM4_07280	COG1705	Flagellar rod assembly protein muramidase FlgJ
VagYM4_07280	COG3951	Flagellar rod assembly protein muramidase FlgJ
VagYM4_07300	COG1344	Flagellin is the subunit protein which polymerizes to form the filaments of bacterial flagella
VagYM4_07320	COG1344	Flagellin is the subunit protein which polymerizes to form the filaments of bacterial flagella
VagYM4_07330	COG1344	Flagellin is the subunit protein which polymerizes to form the filaments of bacterial flagella
VagYM4_07340	COG1344	Flagellin is the subunit protein which polymerizes to form the filaments of bacterial flagella
VagYM4_07350	COG2190	(PTS) system
VagYM4_07360	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)
VagYM4_07380	COG1925	phosphoenolpyruvate-dependent sugar phosphotransferase system
VagYM4_07390	COG0031	Belongs to the cysteine synthase cystathionine beta- synthase family
VagYM4_07400	COG2981	High affinity, high specificity proton-dependent sulfate transporter, which mediates sulfate uptake. Provides the sulfur source for the cysteine synthesis pathway
VagYM4_07410	COG3115	cell septum assembly
VagYM4_07420	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
VagYM4_07470	COG0330	HflC and HflK could
VagYM4_07480	COG3118	belongs to the thioredoxin family
VagYM4_07490	COG0300	oxidoreductase activity
VagYM4_07500	COG1090	epimerase
VagYM4_07560	COG0622	Phosphoesterase
VagYM4_07600	COG3710	Transcriptional regulator
VagYM4_07610	COG0326	Molecular chaperone. Has ATPase activity
VagYM4_07630	COG0276	Catalyzes the ferrous insertion into protoporphyrin IX
VagYM4_07650	COG3104	oligopeptide transport
VagYM4_07660	COG0250	Participates in transcription elongation, termination and antitermination
VagYM4_07670	COG0367	asparagine synthase
VagYM4_07680	COG4651	solute:proton antiporter activity
VagYM4_07680	COG1226	(belongs to the monovalent cation proton antiporter 2 (CPA2) transporter (TC 2.A.37) family)
VagYM4_07690	COG1940	carbohydrate kinase activity
VagYM4_07690	COG1846	Transcriptional regulator
VagYM4_07700	COG1820	Belongs to the metallo-dependent hydrolases superfamily. NagA family
VagYM4_07710	COG1263	PTS System
VagYM4_07710	COG1264	protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
VagYM4_07710	COG2190	(PTS) system
VagYM4_07720	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)
VagYM4_07730	COG0735	belongs to the Fur family
VagYM4_07750	COG0716	FMN binding
VagYM4_07770	COG0596	Alpha beta hydrolase
VagYM4_07780	COG3057	Negative regulator of replication initiation, which contributes to regulation of DNA replication and ensures that replication initiation occurs exactly once per chromosome per cell cycle. Binds to pairs of hemimethylated GATC sequences in the oriC region, thus preventing assembly of replication proteins and re- initiation at newly replicated origins. Repression is relieved when the region becomes fully methylated
VagYM4_07790	COG0033	Phosphoglucomutase
VagYM4_07810	COG0327	Belongs to the GTP cyclohydrolase I type 2 NIF3 family
VagYM4_07840	COG2142	Succinate dehydrogenase hydrophobic membrane anchor
VagYM4_07850	COG1053	succinate dehydrogenase
VagYM4_07860	COG0479	Belongs to the succinate dehydrogenase fumarate reductase iron-sulfur protein family
VagYM4_07870	COG0567	Dehydrogenase, E1 component
VagYM4_07880	COG0508	dehydrogenase complex catalyzes the overall conversion of
VagYM4_07910	COG1108	ABC-type Mn2 Zn2 transport systems permease components
VagYM4_07920	COG1121	(ABC) transporter
VagYM4_07930	COG4531	ABC-type Zn2 transport system, periplasmic component surface adhesin
VagYM4_07940	COG4977	sequence-specific DNA binding
VagYM4_07950	COG1918	ferrous iron import across plasma membrane
VagYM4_07990	COG0018	arginyl-trna synthetase
VagYM4_08000	COG3102	Protein conserved in bacteria
VagYM4_08030	COG0788	formyltetrahydrofolate deformylase activity
VagYM4_08040	COG1199	ATP-dependent helicase activity
VagYM4_08050	COG1214	PFAM Peptidase M22, glycoprotease
VagYM4_08070	COG3065	identical protein binding
VagYM4_08080	COG2267	carboxylic ester hydrolase activity
VagYM4_08090	COG0318	PFAM AMP-dependent synthetase and ligase
VagYM4_08100	COG0349	Exonuclease involved in the 3' processing of various precursor tRNAs. Initiates hydrolysis at the 3'-terminus of an RNA molecule and releases 5'-mononucleotides
VagYM4_08110	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
VagYM4_08120	COG2894	cell division
VagYM4_08130	COG0850	regulation of cytokinetic process
VagYM4_08140	COG3100	YcgL domain-containing protein
VagYM4_08150	COG2951	lytic endotransglycosylase activity
VagYM4_08170	COG1972	Belongs to the concentrative nucleoside transporter (CNT) (TC 2.A.41) family
VagYM4_08180	COG0190	Catalyzes the oxidation of 5,10- methylenetetrahydrofolate to 5,10-methenyltetrahydrofolate and then the hydrolysis of 5,10-methenyltetrahydrofolate to 10- formyltetrahydrofolate
VagYM4_08190	COG2226	methyltransferase
VagYM4_08200	COG0304	beta-ketoacyl-acyl-carrier-protein synthase II activity
VagYM4_08210	COG1028	Short-chain dehydrogenase reductase Sdr
VagYM4_08230	COG0304	beta-ketoacyl-acyl-carrier-protein synthase II activity
VagYM4_08280	COG2986	histidine ammonia-lyase
VagYM4_08290	COG1216	Glycosyl transferase, family 2
VagYM4_08300	COG0764	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity
VagYM4_08330	COG0236	Carrier of the growing fatty acid chain in fatty acid biosynthesis
VagYM4_08340	COG0236	Carrier of the growing fatty acid chain in fatty acid biosynthesis
VagYM4_08410	COG1253	flavin adenine dinucleotide binding
VagYM4_08420	COG0513	Belongs to the DEAD box helicase family
VagYM4_08430	COG0569	domain protein
VagYM4_08440	COG0168	Low-affinity potassium transport system. Interacts with trk system potassium uptake protein TrkA
VagYM4_08470	COG0397	Uncharacterized ACR, YdiU/UPF0061 family
VagYM4_08480	COG1638	TRAP-type C4-dicarboxylate transport system periplasmic component
VagYM4_08490	COG3090	Trap-type c4-dicarboxylate transport system, small permease component
VagYM4_08500	COG1593	TRAP-type C4-dicarboxylate transport system, large permease component
VagYM4_08530	COG0544	peptidyl-prolyl cis-trans isomerase activity
VagYM4_08550	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
VagYM4_08560	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
VagYM4_08570	COG0776	regulation of translation
VagYM4_08580	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
VagYM4_08590	COG1555	photosystem II stabilization
VagYM4_08620	COG0232	Belongs to the dGTPase family. Type 2 subfamily
VagYM4_08630	COG1896	Catalyzes the strictly specific dephosphorylation of 2'- deoxyribonucleoside 5'-monophosphates
VagYM4_08640	COG0436	Aminotransferase
VagYM4_08650	COG1169	isochorismate synthase
VagYM4_08660	COG1165	Catalyzes the thiamine diphosphate-dependent decarboxylation of 2-oxoglutarate and the subsequent addition of the resulting succinic semialdehyde-thiamine pyrophosphate anion to isochorismate to yield 2-succinyl-5-enolpyruvyl-6-hydroxy-3- cyclohexene-1-carboxylate (SEPHCHC)
VagYM4_08670	COG0596	Alpha beta hydrolase
VagYM4_08680	COG0447	Converts o-succinylbenzoyl-CoA (OSB-CoA) to 1,4- dihydroxy-2-naphthoyl-CoA (DHNA-CoA)
VagYM4_08720	COG2855	membrane
VagYM4_08730	COG0477	Major facilitator Superfamily
VagYM4_08760	COG0845	Belongs to the membrane fusion protein (MFP) (TC 8.A.1) family
VagYM4_08770	COG0841	Belongs to the resistance-nodulation-cell division (RND) (TC 2.A.6) family
VagYM4_08810	COG0031	Belongs to the cysteine synthase cystathionine beta- synthase family
VagYM4_08820	COG1522	sequence-specific DNA binding
VagYM4_08840	COG1946	Acyl-CoA thioesterase
VagYM4_08850	COG3126	Type III secretion system lipoprotein chaperone (YscW)
VagYM4_08990	COG0583	DNA-binding transcription factor activity
VagYM4_09000	COG2220	Zn-dependent hydrolases of the beta-lactamase fold
VagYM4_09010	COG2207	Transcriptional regulator
VagYM4_09020	COG0566	Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase TrmH family
VagYM4_09030	COG0516	GMP reductase activity
VagYM4_09030	COG0517	IMP dehydrogenase activity
VagYM4_09080	COG0537	adenosine 5'-monophosphoramidase activity
VagYM4_09130	COG3150	esterase
VagYM4_09140	COG1252	NADH dehydrogenase
VagYM4_09170	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
VagYM4_09190	COG4591	ABC-type transport system involved in lipoprotein release permease component
VagYM4_09200	COG1136	(ABC) transporter
VagYM4_09210	COG4591	ABC-type transport system involved in lipoprotein release permease component
VagYM4_09230	COG2333	competence protein COMEC
VagYM4_09230	COG0658	competence protein
VagYM4_09240	COG1132	(ABC) transporter
VagYM4_09250	COG1663	tetraacyldisaccharide 4'-kinase activity
VagYM4_09280	COG2719	SpoVR family
VagYM4_09290	COG2718	Belongs to the UPF0229 family
VagYM4_09300	COG2766	serine protein kinase
VagYM4_09310	COG3013	Belongs to the UPF0304 family
VagYM4_09330	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
VagYM4_09350	COG1882	Formate acetyltransferase
VagYM4_09430	COG0708	Exodeoxyribonuclease III
VagYM4_09450	COG3923	Primosomal replication protein n
VagYM4_09460	COG0730	response to heat
VagYM4_09470	COG1199	ATP-dependent helicase activity
VagYM4_09480	COG3203	Forms passive diffusion pores that allow small molecular weight hydrophilic materials across the outer membrane
VagYM4_09490	COG3110	Uncharacterized protein conserved in bacteria (DUF2057)
VagYM4_09500	COG1187	pseudouridine synthase activity
VagYM4_09520	COG1278	Cold shock
VagYM4_09530	COG2127	Involved in the modulation of the specificity of the ClpAP-mediated ATP-dependent protein degradation
VagYM4_09540	COG0542	response to heat
VagYM4_09550	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
VagYM4_09560	COG2935	proteasome-mediated ubiquitin-dependent protein catabolic process
VagYM4_09570	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
VagYM4_09610	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
VagYM4_09620	COG0448	Catalyzes the synthesis of ADP-glucose, a sugar donor used in elongation reactions on alpha-glucans
VagYM4_09630	COG0297	glycogen (starch) synthase activity
VagYM4_09670	COG3070	regulator of competence-specific genes
VagYM4_09680	COG1609	Transcriptional regulator
VagYM4_09690	COG3381	protein complex oligomerization
VagYM4_09700	COG0745	RESPONSE REGULATOR receiver
VagYM4_09710	COG1434	Gram-negative-bacterium-type cell wall biogenesis
VagYM4_09720	COG2227	3-demethylubiquinone-9 3-O-methyltransferase activity
VagYM4_09740	COG3095	Involved in chromosome condensation, segregation and cell cycle progression. May participate in facilitating chromosome segregation by condensation DNA from both sides of a centrally located replisome during cell division. Probably acts via its interaction with MukB and MukF
VagYM4_09750	COG3096	Plays a central role in chromosome condensation, segregation and cell cycle progression. Functions as a homodimer, which is essential for chromosome partition. Involved in negative DNA supercoiling in vivo, and by this means organize and compact chromosomes. May achieve or facilitate chromosome segregation by condensation DNA from both sides of a centrally located replisome during cell division
VagYM4_09790	COG4067	protein conserved in archaea
VagYM4_09790	COG0189	ligase activity
VagYM4_09800	COG0500	methyltransferase
VagYM4_09820	COG1801	Protein of unknown function DUF72
VagYM4_09840	COG0217	transcriptional regulatory protein
VagYM4_09850	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
VagYM4_09860	COG0632	four-way junction helicase activity
VagYM4_09870	COG2255	four-way junction helicase activity
VagYM4_09880	COG1271	oxidase subunit
VagYM4_09890	COG1294	oxidase, subunit
VagYM4_09900	COG4890	Cyd operon protein YbgT
VagYM4_09920	COG0824	Thioesterase
VagYM4_09930	COG0811	peptide transport
VagYM4_09960	COG0823	Involved in the tonB-independent uptake of proteins
VagYM4_09970	COG2885	chlorophyll binding
VagYM4_09980	COG1729	Mediates coordination of peptidoglycan synthesis and outer membrane constriction during cell division
VagYM4_09990	COG0379	Catalyzes the condensation of iminoaspartate with dihydroxyacetone phosphate to form quinolinate
VagYM4_10010	COG3766	membrane
VagYM4_10030	COG0754	glutathionylspermidine amidase activity
VagYM4_10050	COG0784	Response regulator, receiver
VagYM4_10050	COG5002	protein histidine kinase activity
VagYM4_10070	COG0840	transmembrane signaling receptor activity
VagYM4_10080	COG0845	Belongs to the membrane fusion protein (MFP) (TC 8.A.1) family
VagYM4_10090	COG0841	Belongs to the resistance-nodulation-cell division (RND) (TC 2.A.6) family
VagYM4_10140	COG3568	Endonuclease Exonuclease Phosphatase
VagYM4_10160	COG0840	transmembrane signaling receptor activity
VagYM4_10190	COG0583	DNA-binding transcription factor activity
VagYM4_10210	COG0686	Belongs to the AlaDH PNT family
VagYM4_10230	COG1674	ftsk spoiiie
VagYM4_10240	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)
VagYM4_10250	COG2256	atpase related to the helicase subunit of the holliday junction resolvase
VagYM4_10260	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)
VagYM4_10320	COG1073	alpha beta
VagYM4_10320	COG2226	methyltransferase
VagYM4_10330	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
VagYM4_10380	COG0300	oxidoreductase activity
VagYM4_10410	COG2230	cyclopropane-fatty-acyl-phospholipid synthase
VagYM4_10430	COG2268	Band 7 protein
VagYM4_10450	COG0015	Belongs to the lyase 1 family. Adenylosuccinate lyase subfamily
VagYM4_10460	COG2915	High frequency lysogenization protein hflD homolog
VagYM4_10470	COG0482	sulfurtransferase activity
VagYM4_10490	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
VagYM4_10510	COG1757	Na H antiporter
VagYM4_10530	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
VagYM4_10540	COG0141	Catalyzes the sequential NAD-dependent oxidations of L- histidinol to L-histidinaldehyde and then to L-histidine
VagYM4_10550	COG0079	Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. Histidinol-phosphate aminotransferase subfamily
VagYM4_10560	COG0241	D,D-heptose 1,7-bisphosphate phosphatase
VagYM4_10560	COG0131	Imidazoleglycerol-phosphate dehydratase
VagYM4_10570	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
VagYM4_10580	COG0106	1-(5-phosphoribosyl)-5- 5-phosphoribosylamino)methylideneamino imidazole-4-carboxamide isomerase
VagYM4_10600	COG0139	Catalyzes the hydrolysis of the adenine ring of phosphoribosyl-AMP
VagYM4_10600	COG0140	phosphoribosyl-ATP diphosphatase activity
VagYM4_10680	COG3850	Histidine kinase
VagYM4_10680	COG5002	protein histidine kinase activity
VagYM4_10690	COG0745	RESPONSE REGULATOR receiver
VagYM4_10700	COG0840	transmembrane signaling receptor activity
VagYM4_10730	COG1032	radical SAM domain protein
VagYM4_10740	COG5001	Diguanylate cyclase
VagYM4_10770	COG0583	DNA-binding transcription factor activity
VagYM4_10780	COG0620	Catalyzes the transfer of a methyl group from 5- methyltetrahydrofolate to homocysteine resulting in methionine formation
VagYM4_10800	COG2350	Protein conserved in bacteria
VagYM4_10820	COG2917	probably involved in intracellular septation
VagYM4_10860	COG1301	dicarboxylic acid transport
VagYM4_10870	COG0318	PFAM AMP-dependent synthetase and ligase
VagYM4_10880	COG0664	- Catabolite gene activator and regulatory subunit of cAMP-dependent protein
VagYM4_10890	COG0159	tryptophan synthase activity
VagYM4_10910	COG0134	indole-3-glycerol-phosphate synthase activity
VagYM4_10910	COG0135	phosphoribosylanthranilate isomerase activity
VagYM4_10930	COG0512	Glutamine amidotransferase of anthranilate synthase
VagYM4_10940	COG0147	Part of a heterotetrameric complex that catalyzes the two-step biosynthesis of anthranilate, an intermediate in the biosynthesis of L-tryptophan. In the first step, the glutamine- binding beta subunit (TrpG) of anthranilate synthase (AS) provides the glutamine amidotransferase activity which generates ammonia as a substrate that, along with chorismate, is used in the second step, catalyzed by the large alpha subunit of AS (TrpE) to produce anthranilate. In the absence of TrpG, TrpE can synthesize anthranilate directly from chorismate and high concentrations of ammonia
VagYM4_10960	COG0613	PHP domain protein
VagYM4_10970	COG0009	L-threonylcarbamoyladenylate synthase
VagYM4_11000	COG1187	pseudouridine synthase activity
VagYM4_11040	COG0417	DNA replication proofreading
VagYM4_11050	COG2197	response regulator
VagYM4_11060	COG0322	excinuclease ABC activity
VagYM4_11100	COG0019	diaminopimelate decarboxylase activity
VagYM4_11160	COG0209	Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides
VagYM4_11170	COG2227	3-demethylubiquinone-9 3-O-methyltransferase activity
VagYM4_11220	COG3303	Catalyzes the reduction of nitrite to ammonia, consuming six electrons in the process
VagYM4_11240	COG0437	4 iron, 4 sulfur cluster binding
VagYM4_11250	COG3301	Polysulphide reductase, NrfD
VagYM4_11260	COG1138	Cytochrome C-type biogenesis protein
VagYM4_11280	COG3088	subunit of a heme lyase
VagYM4_11280	COG4235	cytochrome complex assembly
VagYM4_11300	COG0807	Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate
VagYM4_11350	COG2989	Protein conserved in bacteria
VagYM4_11360	COG3108	Peptidase M15
VagYM4_11370	COG0491	Thiolesterase that catalyzes the hydrolysis of S-D- lactoyl-glutathione to form glutathione and D-lactic acid
VagYM4_11400	COG4663	Part of the tripartite ATP-independent periplasmic (TRAP) transport system
VagYM4_11460	COG1292	Belongs to the BCCT transporter (TC 2.A.15) family
VagYM4_11470	COG0840	transmembrane signaling receptor activity
VagYM4_11510	COG1448	Aminotransferase
VagYM4_11540	COG1167	Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain MocR family and their eukaryotic orthologs
VagYM4_11560	COG0017	Asparaginyl-tRNA synthetase
VagYM4_11570	COG0840	transmembrane signaling receptor activity
VagYM4_11590	COG0720	synthase
VagYM4_11610	COG2200	EAL domain
VagYM4_11620	COG1760	l-serine dehydratase
VagYM4_11630	COG0814	amino acid
VagYM4_11640	COG0494	nUDIX hydrolase
VagYM4_11660	COG2205	protein histidine kinase activity
VagYM4_11660	COG0784	Response regulator, receiver
VagYM4_11670	COG0147	Part of a heterotetrameric complex that catalyzes the two-step biosynthesis of anthranilate, an intermediate in the biosynthesis of L-tryptophan. In the first step, the glutamine- binding beta subunit (TrpG) of anthranilate synthase (AS) provides the glutamine amidotransferase activity which generates ammonia as a substrate that, along with chorismate, is used in the second step, catalyzed by the large alpha subunit of AS (TrpE) to produce anthranilate. In the absence of TrpG, TrpE can synthesize anthranilate directly from chorismate and high concentrations of ammonia
VagYM4_11700	COG3106	COG3106 Predicted ATPase
VagYM4_11710	COG3768	UPF0283 membrane protein
VagYM4_11730	COG1670	COG1670 acetyltransferases, including N-acetylases of ribosomal proteins
VagYM4_12180	COG0729	surface antigen
VagYM4_12190	COG1502	Catalyzes the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) (diphosphatidylglycerol) and glycerol
VagYM4_12200	COG2272	Belongs to the type-B carboxylesterase lipase family
VagYM4_12270	COG2985	domain, Protein
VagYM4_12290	COG2240	Pyridoxal kinase involved in the salvage pathway of pyridoxal 5'-phosphate (PLP). Catalyzes the phosphorylation of pyridoxal to PLP
VagYM4_12320	COG0583	DNA-binding transcription factor activity
VagYM4_12380	COG0210	DNA helicase
VagYM4_12410	COG4735	regulation of single-species biofilm formation
VagYM4_12480	COG4737	Cytotoxic translational repressor of toxin-antitoxin stability system
VagYM4_12490	COG2944	sequence-specific DNA binding
VagYM4_12560	COG1566	PFAM secretion protein HlyD family protein
VagYM4_12590	COG0845	Belongs to the membrane fusion protein (MFP) (TC 8.A.1) family
VagYM4_12620	COG3290	protein histidine kinase activity
VagYM4_12630	COG4565	transcriptional regulatory protein
VagYM4_12640	COG4774	siderophore transport
VagYM4_12660	COG0364	Catalyzes the oxidation of glucose 6-phosphate to 6- phosphogluconolactone
VagYM4_12670	COG0363	glucosamine-6-phosphate deaminase activity
VagYM4_12680	COG0362	Catalyzes the oxidative decarboxylation of 6- phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH
VagYM4_12710	COG3284	Transcriptional regulator
VagYM4_12720	COG1012	belongs to the aldehyde dehydrogenase family
VagYM4_12860	COG4669	(LipO)protein
VagYM4_12900	COG3177	Filamentation induced by cAMP protein fic
VagYM4_12960	COG1028	Short-chain dehydrogenase reductase Sdr
VagYM4_13010	COG4792	protein secretion
VagYM4_13020	COG4791	protein targeting
VagYM4_13030	COG4794	Type iii secretion
VagYM4_13040	COG4790	Type iii secretion
VagYM4_13180	COG0457	Tetratricopeptide repeat
VagYM4_13220	COG2358	TRAP transporter, solute receptor (TAXI family
VagYM4_13230	COG0730	response to heat
VagYM4_13300	COG2513	Catalyzes the thermodynamically favored C-C bond cleavage of (2R,3S)-2-methylisocitrate to yield pyruvate and succinate
VagYM4_13310	COG0372	Belongs to the citrate synthase family
VagYM4_13330	COG2828	Protein conserved in bacteria
VagYM4_13380	COG0561	phosphatase activity
VagYM4_13390	COG0602	queuosine metabolic process
VagYM4_13400	COG0603	Catalyzes the ATP-dependent conversion of 7-carboxy-7- deazaguanine (CDG) to 7-cyano-7-deazaguanine (preQ(0))
VagYM4_13410	COG3706	GGDEF domain
VagYM4_13510	COG1254	Belongs to the acylphosphatase family
VagYM4_13520	COG2920	part of a sulfur-relay system
VagYM4_13540	COG0670	Belongs to the BI1 family
VagYM4_13550	COG1126	abc transporter atp-binding protein
VagYM4_13560	COG0765	amino acid transport
VagYM4_13570	COG4597	amino acid ABC transporter
VagYM4_13580	COG0834	ABC-type amino acid transport signal transduction systems periplasmic component domain
VagYM4_13600	COG1666	GTP binding
VagYM4_13610	COG0722	Stereospecific condensation of phosphoenolpyruvate (PEP) and D-erythrose-4-phosphate (E4P) giving rise to 3-deoxy-D- arabino-heptulosonate-7-phosphate (DAHP)
VagYM4_13660	COG3008	intermembrane lipid transfer
VagYM4_13670	COG2995	paraquat-inducible protein a
VagYM4_13680	COG1132	(ABC) transporter
VagYM4_13690	COG1956	GAF domain-containing protein
VagYM4_13700	COG3109	RNA chaperone with significant RNA binding, RNA strand exchange and RNA duplexing activities
VagYM4_13730	COG0308	aminopeptidase N
VagYM4_13750	COG2902	Dehydrogenase
VagYM4_13760	COG0167	dihydroorotate dehydrogenase activity
VagYM4_13780	COG1092	Specifically methylates the guanine in position 2445 (m2G2445) and the guanine in position 2069 (m7G2069) of 23S rRNA
VagYM4_13780	COG0116	Belongs to the methyltransferase superfamily
VagYM4_13830	COG0764	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity
VagYM4_13840	COG1067	ATP-dependent peptidase activity
VagYM4_13850	COG3120	sequence-specific DNA binding
VagYM4_14120	COG0784	Response regulator, receiver
VagYM4_14120	COG2205	protein histidine kinase activity
VagYM4_14150	COG3278	Belongs to the heme-copper respiratory oxidase family
VagYM4_14180	COG2010	Cytochrome c
VagYM4_14200	COG2217	Heavy metal translocating P-type atpase
VagYM4_14230	COG0664	- Catabolite gene activator and regulatory subunit of cAMP-dependent protein
VagYM4_14240	COG0589	response to stress
VagYM4_14290	COG3842	ATPase activity
VagYM4_14310	COG1177	transmembrane transport
VagYM4_14330	COG0687	Required for the activity of the bacterial periplasmic transport system of putrescine
VagYM4_14340	COG0846	NAD-dependent lysine deacetylase and desuccinylase that specifically removes acetyl and succinyl groups on target proteins. Modulates the activities of several proteins which are inactive in their acylated form
VagYM4_14360	COG0004	ammonium transporteR
VagYM4_14410	COG0437	4 iron, 4 sulfur cluster binding
VagYM4_14420	COG3383	formate dehydrogenase (NAD+) activity
VagYM4_14420	COG0243	molybdopterin cofactor binding
VagYM4_14440	COG3381	protein complex oligomerization
VagYM4_14480	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
VagYM4_14500	COG0488	(ABC) transporter
VagYM4_14510	COG4191	Histidine kinase
VagYM4_14520	COG2204	response regulator
VagYM4_14550	COG3842	ATPase activity
VagYM4_14560	COG0746	molybdenum cofactor guanylyltransferase activity
VagYM4_14590	COG1940	carbohydrate kinase activity
VagYM4_14660	COG0791	NLP P60 protein
VagYM4_14680	COG3706	GGDEF domain
VagYM4_14700	COG3001	Fructosamine kinase
VagYM4_14720	COG0307	riboflavin synthase, alpha
VagYM4_14730	COG0534	Mate efflux family protein
VagYM4_14750	COG1793	dna ligase
VagYM4_14810	COG2204	response regulator
VagYM4_14830	COG0438	transferase activity, transferring glycosyl groups
VagYM4_14890	COG0438	transferase activity, transferring glycosyl groups
VagYM4_14900	COG1215	transferase activity, transferring glycosyl groups
VagYM4_14910	COG2148	undecaprenyl-phosphate glucose phosphotransferase activity
VagYM4_14930	COG1292	Belongs to the BCCT transporter (TC 2.A.15) family
VagYM4_14960	COG1643	Atp-dependent helicase
VagYM4_14970	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
VagYM4_15060	COG0443	Heat shock 70 kDa protein
VagYM4_15070	COG0443	Heat shock 70 kDa protein
VagYM4_15110	COG4968	Prepilin-type N-terminal cleavage methylation domain
VagYM4_15120	COG1132	(ABC) transporter
VagYM4_15130	COG1132	(ABC) transporter
VagYM4_15150	COG4774	siderophore transport
VagYM4_15160	COG4774	siderophore transport
VagYM4_15180	COG0614	abc-type fe3 -hydroxamate transport system, periplasmic component
VagYM4_15190	COG1120	ATPase activity
VagYM4_15220	COG0814	amino acid
VagYM4_15240	COG2206	PFAM metal-dependent phosphohydrolase, HD sub domain
VagYM4_15260	COG0861	Integral membrane protein TerC family
VagYM4_15280	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
VagYM4_15290	COG1328	CTP reductase activity
VagYM4_15320	COG3300	MHYT domain
VagYM4_15320	COG5001	Diguanylate cyclase
VagYM4_15340	COG4191	Histidine kinase
VagYM4_15350	COG0471	metal ion transport
VagYM4_15400	COG4702	Belongs to the UPF0303 family
VagYM4_15410	COG0673	inositol 2-dehydrogenase activity
VagYM4_15450	COG0641	radical SAM
VagYM4_15490	COG3119	arylsulfatase activity
VagYM4_15500	COG0527	aspartate kinase activity
VagYM4_15510	COG0662	Cupin 2, conserved barrel domain protein
VagYM4_15520	COG0160	Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family
VagYM4_15530	COG0456	acetyltransferase
VagYM4_15540	COG1292	Belongs to the BCCT transporter (TC 2.A.15) family
VagYM4_15580	COG4176	ABC-type proline glycine betaine transport system permease component
VagYM4_15590	COG2113	Glycine betaine
VagYM4_15630	COG1028	Short-chain dehydrogenase reductase Sdr
VagYM4_15650	COG0745	RESPONSE REGULATOR receiver
VagYM4_15660	COG0642	Histidine kinase
VagYM4_15670	COG1368	sulfuric ester hydrolase activity
VagYM4_15750	COG1115	amino acid carrier protein
VagYM4_15770	COG1280	lysine exporter protein (LysE YggA)
VagYM4_15780	COG2317	Broad specificity carboxypetidase that releases amino acids sequentially from the C-terminus, including neutral, aromatic, polar and basic residues
VagYM4_15850	COG1162	GTPase activity
VagYM4_15880	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
VagYM4_15890	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
VagYM4_15900	COG1160	GTP binding
VagYM4_15910	COG0699	ATPase. Has a role at an early stage in the morphogenesis of the spore coat
VagYM4_15930	COG1160	GTP binding
VagYM4_16000	COG1570	exodeoxyribonuclease VII activity
VagYM4_16100	COG0553	Transcription regulator that activates transcription by stimulating RNA polymerase (RNAP) recycling in case of stress conditions such as supercoiled DNA or high salt concentrations. Probably acts by releasing the RNAP, when it is trapped or immobilized on tightly supercoiled DNA. Does not activate transcription on linear DNA. Probably not involved in DNA repair
VagYM4_16120	COG0125	Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis
VagYM4_16190	COG1961	COG1961 Site-specific recombinases, DNA invertase Pin homologs
VagYM4_16200	COG2317	Broad specificity carboxypetidase that releases amino acids sequentially from the C-terminus, including neutral, aromatic, polar and basic residues
VagYM4_16210	COG1560	Kdo2-lipid A biosynthetic process
VagYM4_16230	COG0531	amino acid
VagYM4_16260	COG1897	L-methionine biosynthetic process from homoserine via O-succinyl-L-homoserine and cystathionine
VagYM4_16270	COG3063	Type IV pilus biogenesis stability protein PilW
VagYM4_16330	COG0110	maltose O-acetyltransferase activity
VagYM4_16360	COG2315	Protein conserved in bacteria
VagYM4_16370	COG1846	Transcriptional regulator
VagYM4_16390	COG2200	EAL domain
VagYM4_16440	COG0625	glutathione transferase activity
VagYM4_16460	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
VagYM4_16480	COG2195	Cleaves the N-terminal amino acid of tripeptides
VagYM4_16500	COG0601	transmembrane transport
VagYM4_16510	COG1173	ABC-type dipeptide oligopeptide nickel transport systems, permease components
VagYM4_16550	COG3291	Pkd domain containing protein
VagYM4_16580	COG1177	transmembrane transport
VagYM4_16590	COG1176	ABC-type spermidine putrescine transport system, permease component I
VagYM4_16600	COG3842	ATPase activity
VagYM4_16610	COG0329	Catalyzes the condensation of (S)-aspartate-beta- semialdehyde (S)-ASA and pyruvate to 4-hydroxy- tetrahydrodipicolinate (HTPA)
VagYM4_16620	COG2423	ornithine cyclodeaminase activity
VagYM4_16650	COG3938	Belongs to the proline racemase family
VagYM4_16710	COG3129	Specifically methylates the adenine in position 1618 of 23S rRNA
VagYM4_16720	COG1451	nucleotide metabolic process
VagYM4_16740	COG0583	DNA-binding transcription factor activity
VagYM4_16780	COG4138	Part of the ABC transporter complex BtuCDF involved in vitamin B12 import. Responsible for energy coupling to the transport system
VagYM4_16790	COG4139	cobalamin transport
VagYM4_16800	COG2988	succinylglutamate desuccinylase activity
VagYM4_16840	COG0368	Joins adenosylcobinamide-GDP and alpha-ribazole to generate adenosylcobalamin (Ado-cobalamin). Also synthesizes adenosylcobalamin 5'-phosphate from adenosylcobinamide-GDP and alpha-ribazole 5'-phosphate
VagYM4_16850	COG2038	nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity
VagYM4_16860	COG0702	epimerase
VagYM4_16880	COG2925	Exonuclease
VagYM4_16890	COG1380	Effector of murein hydrolase LrgA
VagYM4_16900	COG1346	cytolysis
VagYM4_16910	COG0295	cytidine deaminase activity
VagYM4_16920	COG0027	Involved in the de novo purine biosynthesis. Catalyzes the transfer of formate to 5-phospho-ribosyl-glycinamide (GAR), producing 5-phospho-ribosyl-N-formylglycinamide (FGAR). Formate is provided by PurU via hydrolysis of 10-formyl-tetrahydrofolate
VagYM4_16930	COG0500	methyltransferase
VagYM4_16950	COG0776	regulation of translation
VagYM4_16970	COG0072	phenylalanine-tRNA ligase activity
VagYM4_16970	COG0073	Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation
VagYM4_16980	COG0016	Belongs to the class-II aminoacyl-tRNA synthetase family. Phe-tRNA synthetase alpha subunit type 1 subfamily
VagYM4_17040	COG0393	Putative heavy-metal-binding
VagYM4_17060	COG0291	Belongs to the bacterial ribosomal protein bL35 family
VagYM4_17080	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)
VagYM4_17110	COG2188	Transcriptional regulator
VagYM4_17120	COG1228	amidohydrolase
VagYM4_17130	COG0010	Belongs to the arginase family
VagYM4_17140	COG2987	Catalyzes the conversion of urocanate to 4-imidazolone- 5-propionate
VagYM4_17150	COG2986	histidine ammonia-lyase
VagYM4_17180	COG0277	FAD linked oxidase domain protein
VagYM4_17180	COG0247	lactate metabolic process
VagYM4_17250	COG0152	phosphoribosylaminoimidazolesuccinocarboxamide synthase activity
VagYM4_17280	COG1643	Atp-dependent helicase
VagYM4_17290	COG0281	malic enzyme
VagYM4_17300	COG2949	membrane
VagYM4_17310	COG0471	metal ion transport
VagYM4_17320	COG0471	metal ion transport
VagYM4_17380	COG0492	ferredoxin-NADP+ reductase activity
VagYM4_17390	COG4988	ABC transporter
VagYM4_17400	COG4987	ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease ATP-binding protein CydC
VagYM4_17420	COG2885	chlorophyll binding
VagYM4_17460	COG3121	Chaperone
VagYM4_17480	COG1932	Catalyzes the reversible conversion of 3- phosphohydroxypyruvate to phosphoserine and of 3-hydroxy-2-oxo-4- phosphonooxybutanoate to phosphohydroxythreonine
VagYM4_17500	COG0834	ABC-type amino acid transport signal transduction systems periplasmic component domain
VagYM4_17500	COG4191	Histidine kinase
VagYM4_17540	COG3070	regulator of competence-specific genes
VagYM4_17560	COG2431	L-lysine efflux transmembrane transporter activity
VagYM4_17580	COG0076	glutamate decarboxylase activity
VagYM4_17590	COG1737	Transcriptional regulator
VagYM4_17610	COG0695	Has a glutathione-disulfide oxidoreductase activity in the presence of NADPH and glutathione reductase. Reduces low molecular weight disulfides and proteins
VagYM4_17620	COG3273	potassium ion transport
VagYM4_17620	COG2985	domain, Protein
VagYM4_17630	COG3007	enoyl-[acyl-carrier-protein] reductase (NADH) activity
VagYM4_17640	COG1960	acyl-CoA dehydrogenase activity
VagYM4_17660	COG3004	Na( ) H( ) antiporter that extrudes sodium in exchange for external protons
VagYM4_17700	COG0534	Mate efflux family protein
VagYM4_17710	COG0702	epimerase
VagYM4_17720	COG3005	denitrification pathway
VagYM4_17780	COG2814	Major facilitator Superfamily
VagYM4_17790	COG1187	pseudouridine synthase activity
VagYM4_17800	COG1061	Type III restriction enzyme res subunit
VagYM4_17820	COG0745	RESPONSE REGULATOR receiver
VagYM4_17830	COG2205	protein histidine kinase activity
VagYM4_17840	COG1825	This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance
VagYM4_17890	COG4134	Bacterial extracellular solute-binding protein
VagYM4_17900	COG4135	transport system, permease component
VagYM4_17910	COG4136	ATPase activity
VagYM4_17920	COG0558	Belongs to the CDP-alcohol phosphatidyltransferase class-I family
VagYM4_17940	COG3604	Transcriptional regulator
VagYM4_17950	COG1151	hydroxylamine reductase activity
VagYM4_17960	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
VagYM4_17980	COG0564	pseudouridine synthase activity
VagYM4_17990	COG0733	neurotransmitter:sodium symporter activity
VagYM4_18000	COG0733	neurotransmitter:sodium symporter activity
VagYM4_18020	COG0626	cystathionine gamma-synthase activity
VagYM4_18030	COG1075	acetyltransferases and hydrolases with the alpha beta hydrolase fold
VagYM4_18040	COG5380	lipid catabolic process
VagYM4_18050	COG2818	Glycosylase
VagYM4_18090	COG1983	PspC domain protein
VagYM4_18110	COG1842	Phage shock protein A
VagYM4_18120	COG1221	Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain
VagYM4_18150	COG4171	peptide transport system, permease
VagYM4_18170	COG4172	Belongs to the ABC transporter superfamily
VagYM4_18190	COG1227	inorganic diphosphatase activity
VagYM4_18220	COG0243	molybdopterin cofactor binding
VagYM4_18230	COG3005	denitrification pathway
VagYM4_18240	COG4459	periplasmic nitrate reductase
VagYM4_18250	COG0390	transport system, permease component
VagYM4_18270	COG2116	formate transmembrane transporter activity
VagYM4_18320	COG1434	Gram-negative-bacterium-type cell wall biogenesis
VagYM4_18330	COG1435	thymidine kinase activity
VagYM4_18340	COG0215	cysteine-tRNA ligase activity
VagYM4_18350	COG0652	PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides
VagYM4_18360	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
VagYM4_18370	COG3434	signal transduction protein containing EAL and modified HD-GYP domains
VagYM4_18380	COG3012	SEC-C Motif Domain Protein
VagYM4_18440	COG1136	(ABC) transporter
VagYM4_18440	COG0577	efflux transmembrane transporter activity
VagYM4_18460	COG0577	efflux transmembrane transporter activity
VagYM4_18460	COG1136	(ABC) transporter
VagYM4_18480	COG0845	Belongs to the membrane fusion protein (MFP) (TC 8.A.1) family
VagYM4_18530	COG3118	belongs to the thioredoxin family
VagYM4_18540	COG4232	protein-disulfide reductase activity
VagYM4_18610	COG2863	cytochrome
VagYM4_18620	COG3258	Cytochrome c
VagYM4_18630	COG2995	paraquat-inducible protein a
VagYM4_18640	COG1463	ABC-type transport system involved in resistance to organic solvents, periplasmic component
VagYM4_18640	COG3008	intermembrane lipid transfer
VagYM4_18670	COG4166	transmembrane transport
VagYM4_18690	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
VagYM4_18700	COG3771	Involved in the assembly of lipopolysaccharide (LPS)
VagYM4_18720	COG0539	negative regulation of cytoplasmic translation
VagYM4_18730	COG0283	belongs to the cytidylate kinase family. Type 1 subfamily
VagYM4_18740	COG0616	signal peptide processing
VagYM4_18750	COG1028	Short-chain dehydrogenase reductase Sdr
VagYM4_18780	COG0587	DNA-directed DNA polymerase activity
VagYM4_18790	COG0784	Response regulator, receiver
VagYM4_18790	COG0835	chemotaxis
VagYM4_18800	COG1940	carbohydrate kinase activity
VagYM4_18810	COG0469	pyruvate kinase activity
VagYM4_18820	COG4667	esterase of the alpha-beta hydrolase superfamily
VagYM4_18850	COG0733	neurotransmitter:sodium symporter activity
VagYM4_18880	COG1264	protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
VagYM4_18880	COG1263	PTS System
VagYM4_18890	COG0084	hydrolase, TatD family'
VagYM4_18900	COG0470	DNA polymerase III
VagYM4_18910	COG0125	Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis
VagYM4_18920	COG1559	Functions as a peptidoglycan terminase that cleaves nascent peptidoglycan strands endolytically to terminate their elongation
VagYM4_18980	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
VagYM4_18990	COG0416	fatty acid biosynthetic process
VagYM4_19010	COG1399	metal-binding, possibly nucleic acid-binding protein
VagYM4_19020	COG0424	maF-like protein
VagYM4_19030	COG0564	pseudouridine synthase activity
VagYM4_19040	COG1530	ribonuclease E activity
VagYM4_19050	COG0659	secondary active sulfate transmembrane transporter activity
VagYM4_19060	COG0394	Belongs to the low molecular weight phosphotyrosine protein phosphatase family
VagYM4_19070	COG2109	Required for both de novo synthesis of the corrin ring for the assimilation of exogenous corrinoids. Participates in the adenosylation of a variety of incomplete and complete corrinoids
VagYM4_19090	COG0572	uridine kinase
VagYM4_19140	COG2186	Transcriptional regulator
VagYM4_19150	COG3067	Na( ) H( ) antiporter that extrudes sodium in exchange for external protons
VagYM4_19160	COG1495	Required for disulfide bond formation in some periplasmic proteins. Acts by oxidizing the DsbA protein
VagYM4_19170	COG0653	protein targeting
VagYM4_19180	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
VagYM4_19190	COG3706	GGDEF domain
VagYM4_19200	COG0366	Alpha amylase catalytic
VagYM4_19210	COG1122	ATPase activity
VagYM4_19220	COG4120	Belongs to the binding-protein-dependent transport system permease family
VagYM4_19240	COG3092	negative regulation of chromosome organization
VagYM4_19250	COG0282	Catalyzes the formation of acetyl phosphate from acetate and ATP. Can also catalyze the reverse reaction
VagYM4_19260	COG0280	phosphate acetyltransferase
VagYM4_19260	COG0857	belongs to the CobB CobQ family
VagYM4_19270	COG3174	membrane
VagYM4_19290	COG0435	Glutathione S-transferase
VagYM4_19310	COG0444	Belongs to the ABC transporter superfamily
VagYM4_19320	COG1173	ABC-type dipeptide oligopeptide nickel transport systems, permease components
VagYM4_19330	COG0601	transmembrane transport
VagYM4_19350	COG0314	molybdopterin synthase activity
VagYM4_19360	COG1977	Involved in sulfur transfer in the conversion of molybdopterin precursor Z to molybdopterin
VagYM4_19370	COG0315	cyclic pyranopterin monophosphate synthase activity
VagYM4_19380	COG0521	Mo-molybdopterin cofactor biosynthetic process
VagYM4_19390	COG2896	Catalyzes the cyclization of GTP to (8S)-3',8-cyclo-7,8- dihydroguanosine 5'-triphosphate
VagYM4_19400	COG0391	Required for morphogenesis under gluconeogenic growth conditions
VagYM4_19410	COG2198	Histidine kinase
VagYM4_19420	COG2204	response regulator
VagYM4_19430	COG0556	nucleotide-excision repair
VagYM4_19440	COG4657	Part of a membrane complex involved in electron transport
VagYM4_19450	COG2878	Part of a membrane complex involved in electron transport
VagYM4_19460	COG4656	Part of a membrane complex involved in electron transport
VagYM4_19470	COG4658	electron transport chain
VagYM4_19480	COG4659	FMN binding
VagYM4_19490	COG4660	Part of a membrane complex involved in electron transport
VagYM4_19500	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
VagYM4_19510	COG0346	lactoylglutathione lyase activity
VagYM4_19530	COG2885	chlorophyll binding
VagYM4_19550	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
VagYM4_19560	COG2056	Na+-H+ antiporter family
VagYM4_19580	COG0278	Belongs to the glutaredoxin family. Monothiol subfamily
VagYM4_19620	COG1012	belongs to the aldehyde dehydrogenase family
VagYM4_19620	COG1454	alcohol dehydrogenase
VagYM4_19630	COG2095	MarC family integral membrane protein
VagYM4_19640	COG0664	- Catabolite gene activator and regulatory subunit of cAMP-dependent protein
VagYM4_19650	COG0136	Catalyzes the NADPH-dependent formation of L-aspartate- semialdehyde (L-ASA) by the reductive dephosphorylation of L- aspartyl-4-phosphate
VagYM4_19660	COG1757	Na H antiporter
VagYM4_19690	COG3081	Nucleoid-associated protein
VagYM4_19700	COG3082	Protein of unknown function (DUF1414)
VagYM4_19720	COG0123	including yeast histone deacetylase and acetoin utilization protein
VagYM4_19750	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
VagYM4_19760	COG0778	Nitroreductase
VagYM4_19780	COG1902	pentaerythritol trinitrate reductase activity
VagYM4_19780	COG0446	pyridine nucleotide-disulphide oxidoreductase
VagYM4_19790	COG0616	signal peptide processing
VagYM4_19800	COG0252	asparaginase activity
VagYM4_19810	COG3139	Protein of unknown function (DUF1315)
VagYM4_19830	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
VagYM4_19840	COG0057	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
VagYM4_19870	COG2226	methyltransferase
VagYM4_19900	COG1785	Belongs to the alkaline phosphatase family
VagYM4_19920	COG0346	lactoylglutathione lyase activity
VagYM4_19930	COG1359	(4S)-4-hydroxy-5-phosphonooxypentane-2,3-dione isomerase activity
VagYM4_19940	COG0668	transmembrane transport
VagYM4_19950	COG2983	Belongs to the UPF0260 family
VagYM4_19960	COG2261	transglycosylase associated protein
VagYM4_19990	COG3681	Belongs to the UPF0597 family
VagYM4_20000	COG0251	oxidation-reduction process
VagYM4_20010	COG0814	amino acid
VagYM4_20020	COG0580	Belongs to the MIP aquaporin (TC 1.A.8) family
VagYM4_20030	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
VagYM4_20060	COG0503	Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis
VagYM4_20070	COG2832	Protein of unknown function (DUF454)
VagYM4_20090	COG0745	RESPONSE REGULATOR receiver
VagYM4_20100	COG0583	DNA-binding transcription factor activity
VagYM4_20110	COG0034	Catalyzes the formation of phosphoribosylamine from phosphoribosylpyrophosphate (PRPP) and glutamine
VagYM4_20120	COG1286	toxin biosynthetic process
VagYM4_20130	COG3147	Non-essential cell division protein that could be required for efficient cell constriction
VagYM4_20140	COG0285	dihydrofolate synthase activity
VagYM4_20150	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
VagYM4_20160	COG0101	tRNA pseudouridine synthase activity
VagYM4_20180	COG0136	Catalyzes the NADPH-dependent formation of L-aspartate- semialdehyde (L-ASA) by the reductive dephosphorylation of L- aspartyl-4-phosphate
VagYM4_20190	COG0111	D-isomer specific 2-hydroxyacid dehydrogenase
VagYM4_20200	COG0304	beta-ketoacyl-acyl-carrier-protein synthase II activity
VagYM4_20210	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
VagYM4_20210	COG0665	tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase activity
VagYM4_20220	COG0431	NADPH-dependent FMN reductase
VagYM4_20240	COG3101	peptidyl-lysine hydroxylation
VagYM4_20250	COG2860	membrane
VagYM4_20260	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
VagYM4_20270	COG2890	protein-(glutamine-N5) methyltransferase activity
VagYM4_20280	COG2840	Smr protein MutS2
VagYM4_20290	COG2062	phosphohistidine phosphatase, SixA
VagYM4_20320	COG1024	Enoyl-CoA hydratase
VagYM4_20320	COG1250	3-hydroxyacyl-CoA dehydrogenase
VagYM4_20330	COG0183	Belongs to the thiolase family
VagYM4_20370	COG2067	long-chain fatty acid transport protein
VagYM4_20390	COG3088	subunit of a heme lyase
VagYM4_20390	COG4235	cytochrome complex assembly
VagYM4_20410	COG0526	COG0526, thiol-disulfide isomerase and thioredoxins
VagYM4_20420	COG1138	Cytochrome C-type biogenesis protein
VagYM4_20430	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
VagYM4_20440	COG3114	Required for the export of heme to the periplasm for the biogenesis of c-type cytochromes
VagYM4_20450	COG0755	Required for the export of heme to the periplasm for the biogenesis of c-type cytochromes
VagYM4_20460	COG2386	Required for the export of heme to the periplasm for the biogenesis of c-type cytochromes
VagYM4_20470	COG4133	protoheme IX ABC transporter activity
VagYM4_20490	COG0835	chemotaxis
VagYM4_20510	COG1192	Involved in chromosome partitioning
VagYM4_20520	COG2201	protein-glutamate methylesterase activity
VagYM4_20530	COG0643	Histidine kinase
VagYM4_20530	COG2198	Histidine kinase
VagYM4_20530	COG0784	Response regulator, receiver
VagYM4_20540	COG3143	Plays an important role in bacterial chemotaxis signal transduction pathway by accelerating the dephosphorylation of phosphorylated CheY (CheY-P)
VagYM4_20620	COG1987	bacterial-type flagellum assembly
VagYM4_20720	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
VagYM4_20740	COG1677	Flagellar hook-basal body complex protein FliE
VagYM4_20760	COG4191	Histidine kinase
VagYM4_20780	COG1516	flagellar protein fliS
VagYM4_20800	COG1345	Required for morphogenesis and for the elongation of the flagellar filament by facilitating polymerization of the flagellin monomers at the tip of growing filament. Forms a capping structure, which prevents flagellin subunits (transported through the central channel of the flagellum) from leaking out without polymerization at the distal end
VagYM4_20810	COG1334	flagellar protein FlaG
VagYM4_20820	COG1344	Flagellin is the subunit protein which polymerizes to form the filaments of bacterial flagella
VagYM4_20830	COG1344	Flagellin is the subunit protein which polymerizes to form the filaments of bacterial flagella
VagYM4_20840	COG1344	Flagellin is the subunit protein which polymerizes to form the filaments of bacterial flagella
VagYM4_20850	COG2837	iron assimilation
VagYM4_20900	COG1393	Belongs to the ArsC family
VagYM4_20910	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
VagYM4_20950	COG0329	Catalyzes the condensation of (S)-aspartate-beta- semialdehyde (S)-ASA and pyruvate to 4-hydroxy- tetrahydrodipicolinate (HTPA)
VagYM4_20970	COG1225	Alkyl hydroperoxide reductase Thiol specific antioxidant Mal allergen
VagYM4_21000	COG4783	chaperone-mediated protein folding
VagYM4_21010	COG1393	Belongs to the ArsC family
VagYM4_21050	COG2233	PERMEase
VagYM4_21060	COG0035	Catalyzes the conversion of uracil and 5-phospho-alpha- D-ribose 1-diphosphate (PRPP) to UMP and diphosphate
VagYM4_21070	COG0150	phosphoribosylformylglycinamidine cyclo-ligase activity
VagYM4_21080	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
VagYM4_21090	COG0121	glutamine amidotransferase
VagYM4_21100	COG0279	D-glycero-D-manno-heptose 7-phosphate biosynthetic process
VagYM4_21110	COG1960	acyl-CoA dehydrogenase activity
VagYM4_21180	COG0328	RNA-DNA hybrid ribonuclease activity
VagYM4_21190	COG2226	methyltransferase
VagYM4_21200	COG0491	Thiolesterase that catalyzes the hydrolysis of S-D- lactoyl-glutathione to form glutathione and D-lactic acid
VagYM4_21210	COG1388	LysM domain
VagYM4_21210	COG0741	lytic transglycosylase activity
VagYM4_21230	COG3021	interspecies interaction between organisms
VagYM4_21240	COG0347	Belongs to the P(II) protein family
VagYM4_21270	COG0825	malonyl-CoA metabolic process
VagYM4_21280	COG0587	DNA-directed DNA polymerase activity
VagYM4_21300	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
VagYM4_21310	COG1043	involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell
VagYM4_21330	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
VagYM4_21340	COG2825	PFAM Outer membrane chaperone Skp (OmpH)
VagYM4_21360	COG0750	zinc metalloprotease
VagYM4_21370	COG0743	1-deoxy-D-xylulose-5-phosphate reductoisomerase activity
VagYM4_21380	COG0575	Belongs to the CDS family
VagYM4_21390	COG0020	Catalyzes the condensation of isopentenyl diphosphate (IPP) with allylic pyrophosphates generating different type of terpenoids
VagYM4_21400	COG0233	cytoplasmic translational termination
VagYM4_21410	COG0528	UMP kinase activity
VagYM4_21420	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
VagYM4_21430	COG0052	Belongs to the universal ribosomal protein uS2 family
VagYM4_21440	COG0024	Methionine aminopeptidase
VagYM4_21450	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
VagYM4_21470	COG0564	pseudouridine synthase activity
VagYM4_21540	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
VagYM4_21550	COG0451	ADP-glyceromanno-heptose 6-epimerase activity
VagYM4_21600	COG2978	secondary active p-aminobenzoyl-glutamate transmembrane transporter activity
VagYM4_21610	COG0254	rRNA binding
VagYM4_21620	COG1720	tRNA m6t6A37 methyltransferase activity
VagYM4_21630	COG0442	prolyl-tRNA aminoacylation
VagYM4_21670	COG0733	neurotransmitter:sodium symporter activity
VagYM4_21700	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
VagYM4_21710	COG0514	ATP-dependent DNA helicase (RecQ)
VagYM4_21720	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
VagYM4_21750	COG1477	protein flavinylation
VagYM4_21760	COG2871	sodium ion transport
VagYM4_21770	COG2209	NQR complex catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na( ) ions from the cytoplasm to the periplasm. NqrA to NqrE are probably involved in the second step, the conversion of ubisemiquinone to ubiquinol
VagYM4_21780	COG1347	NQR complex catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na( ) ions from the cytoplasm to the periplasm. NqrA to NqrE are probably involved in the second step, the conversion of ubisemiquinone to ubiquinol
VagYM4_21790	COG2869	NQR complex catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na( ) ions from the cytoplasm to the periplasm. NqrA to NqrE are probably involved in the second step, the conversion of ubisemiquinone to ubiquinol
VagYM4_21800	COG1805	sodium ion transport
VagYM4_21810	COG1726	NQR complex catalyzes the reduction of ubiquinone-1 to ubiquinol by two successive reactions, coupled with the transport of Na( ) ions from the cytoplasm to the periplasm. NqrA to NqrE are probably involved in the second step, the conversion of ubisemiquinone to ubiquinol
VagYM4_21820	COG0271	Belongs to the BolA IbaG family
VagYM4_21830	COG2813	Specifically methylates the guanine in position
VagYM4_21840	COG3056	Lipoprotein
VagYM4_21880	COG1595	DNA-templated transcription, initiation
VagYM4_21920	COG1893	Catalyzes the NADPH-dependent reduction of ketopantoate into pantoic acid
VagYM4_21930	COG0693	protein deglycase activity
VagYM4_21940	COG0520	Catalyzes the removal of elemental sulfur and selenium atoms from L-cysteine, L-cystine, L-selenocysteine, and L- selenocystine to produce L-alanine
VagYM4_21950	COG3706	GGDEF domain
VagYM4_21970	COG2166	iron-sulfur cluster assembly
VagYM4_21980	COG1179	involved in molybdopterin and THIamine biosynthesis family 1
VagYM4_21990	COG2821	murein-degrading enzyme. may play a role in recycling of muropeptides during cell elongation and or cell division
VagYM4_22010	COG0548	Belongs to the acetylglutamate kinase family. ArgB subfamily
VagYM4_22010	COG1246	Belongs to the acetyltransferase family. ArgA subfamily
VagYM4_22050	COG0507	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
VagYM4_22060	COG1074	ATP-dependent DNA helicase activity
VagYM4_22070	COG1330	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 recognizes the wild- type Chi sequence, and when added to isolated RecB increases its ATP-dependent helicase processivity
VagYM4_22110	COG3141	response to X-ray
VagYM4_22120	COG2171	N-acyltransferase activity
VagYM4_22130	COG0584	glycerophosphoryl diester phosphodiesterase
VagYM4_22140	COG2271	Major facilitator Superfamily
VagYM4_22150	COG0580	Belongs to the MIP aquaporin (TC 1.A.8) family
VagYM4_22160	COG0554	Key enzyme in the regulation of glycerol uptake and metabolism. Catalyzes the phosphorylation of glycerol to yield sn- glycerol 3-phosphate
VagYM4_22170	COG1349	DNA-binding transcription factor activity
VagYM4_22180	COG0578	Belongs to the FAD-dependent glycerol-3-phosphate dehydrogenase family
VagYM4_22220	COG0073	Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation
VagYM4_22230	COG1609	Transcriptional regulator
VagYM4_22240	COG2211	Major facilitator Superfamily
VagYM4_22270	COG2017	converts alpha-aldose to the beta-anomer
VagYM4_22280	COG0153	Catalyzes the transfer of the gamma-phosphate of ATP to D-galactose to form alpha-D-galactose-1-phosphate (Gal-1-P)
VagYM4_22300	COG1087	Belongs to the NAD(P)-dependent epimerase dehydratase family
VagYM4_22310	COG1609	Transcriptional regulator
VagYM4_22320	COG3250	beta-galactosidase activity
VagYM4_22330	COG2731	YhcH YjgK YiaL family protein
VagYM4_22340	COG0531	amino acid
VagYM4_22350	COG0583	DNA-binding transcription factor activity
VagYM4_22470	COG4964	Belongs to the GSP D family
VagYM4_22520	COG2169	Transcriptional regulator
VagYM4_22530	COG1022	Amp-dependent synthetase and ligase
VagYM4_22550	COG0583	DNA-binding transcription factor activity
VagYM4_22560	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
VagYM4_22570	COG1066	DNA-dependent ATPase involved in processing of recombination intermediates, plays a role in repairing DNA breaks. Stimulates the branch migration of RecA-mediated strand transfer reactions, allowing the 3' invading strand to extend heteroduplex DNA faster. Binds ssDNA in the presence of ADP but not other nucleotides, has ATPase activity that is stimulated by ssDNA and various branched DNA structures, but inhibited by SSB. Does not have RecA's homology-searching function
VagYM4_22590	COG0560	Phosphoserine phosphatase
VagYM4_22610	COG0813	purine-nucleoside phosphorylase activity
VagYM4_22620	COG1015	Phosphotransfer between the C1 and C5 carbon atoms of pentose
VagYM4_22630	COG0213	The enzymes which catalyze the reversible phosphorolysis of pyrimidine nucleosides are involved in the degradation of these compounds and in their utilization as carbon and energy sources, or in the rescue of pyrimidine bases for nucleotide synthesis
VagYM4_22650	COG1972	Belongs to the concentrative nucleoside transporter (CNT) (TC 2.A.41) family
VagYM4_22660	COG0084	hydrolase, TatD family'
VagYM4_22680	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
VagYM4_22830	COG0191	fructose-bisphosphate aldolase activity
VagYM4_22880	COG0501	Belongs to the peptidase M48B family
VagYM4_22910	COG0542	response to heat
VagYM4_22940	COG0443	Heat shock 70 kDa protein
VagYM4_22950	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
VagYM4_22980	COG0071	Belongs to the small heat shock protein (HSP20) family
VagYM4_22990	COG0071	Belongs to the small heat shock protein (HSP20) family
VagYM4_23110	COG2003	Belongs to the UPF0758 family
VagYM4_23160	COG0714	Associated with various cellular activities
VagYM4_23200	COG0629	single-stranded DNA binding
VagYM4_23240	COG3385	transposase activity
VagYM4_23260	COG3344	reverse transcriptase
VagYM4_23290	COG0668	transmembrane transport
VagYM4_23300	COG1292	Belongs to the BCCT transporter (TC 2.A.15) family
VagYM4_23390	COG0681	Belongs to the peptidase S26 family
VagYM4_23420	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
VagYM4_23660	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
VagYM4_23780	COG3153	acetyltransferase
VagYM4_23790	COG3154	lipid carrier protein
VagYM4_23810	COG0826	peptidase U32
VagYM4_23820	COG0826	peptidase U32
VagYM4_23830	COG0534	Mate efflux family protein
VagYM4_23860	COG1185	polyribonucleotide nucleotidyltransferase activity
VagYM4_23870	COG0184	Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome
VagYM4_23880	COG0130	Responsible for synthesis of pseudouridine from uracil- 55 in the psi GC loop of transfer RNAs
VagYM4_23890	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
VagYM4_23900	COG0532	One of the essential components for the initiation of protein synthesis. Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex
VagYM4_23910	COG0195	Participates in both transcription termination and antitermination
VagYM4_23920	COG0779	Required for maturation of 30S ribosomal subunits
VagYM4_23930	COG1314	P-P-bond-hydrolysis-driven protein transmembrane transporter activity
VagYM4_23940	COG1109	Catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate
VagYM4_23950	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
VagYM4_23960	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
VagYM4_23970	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
VagYM4_23980	COG1534	Rna-binding protein
VagYM4_23990	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
VagYM4_24000	COG3203	Forms passive diffusion pores that allow small molecular weight hydrophilic materials across the outer membrane
VagYM4_24010	COG2027	D-alanyl-D-alanine carboxypeptidase
VagYM4_24030	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)
VagYM4_24040	COG0739	heme binding
VagYM4_24080	COG0001	glutamate-1-semialdehyde 2,1-aminomutase activity
VagYM4_24090	COG0628	permease
VagYM4_24110	COG0784	Response regulator, receiver
VagYM4_24110	COG2205	protein histidine kinase activity
VagYM4_24120	COG0747	negative chemotaxis
VagYM4_24150	COG0444	Belongs to the ABC transporter superfamily
VagYM4_24160	COG4608	Belongs to the ABC transporter superfamily
VagYM4_24180	COG2971	BadF BadG BcrA BcrD
VagYM4_24210	COG1109	Catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate
VagYM4_24220	COG3842	ATPase activity
VagYM4_24240	COG1840	ABC-type Fe3 transport system, periplasmic component
VagYM4_24250	COG0004	ammonium transporteR
VagYM4_24260	COG0347	Belongs to the P(II) protein family
VagYM4_24270	COG3112	Uncharacterised protein family (UPF0231)
VagYM4_24280	COG1049	propionate catabolic process, 2-methylcitrate cycle
VagYM4_24290	COG1752	Esterase of the alpha-beta hydrolase superfamily
VagYM4_24300	COG0744	Peptidoglycan polymerase that catalyzes glycan chain elongation from lipid-linked precursors
VagYM4_24310	COG1643	Atp-dependent helicase
VagYM4_24320	COG1489	DNA binding
VagYM4_24340	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)
VagYM4_24360	COG0801	2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
VagYM4_24370	COG0413	3-methyl-2-oxobutanoate hydroxymethyltransferase activity
VagYM4_24380	COG0414	Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate
VagYM4_24390	COG1560	Kdo2-lipid A biosynthetic process
VagYM4_24400	COG0842	Transport permease protein
VagYM4_24410	COG1131	(ABC) transporter
VagYM4_24420	COG0659	secondary active sulfate transmembrane transporter activity
VagYM4_24430	COG0288	reversible hydration of carbon dioxide
VagYM4_24460	COG1249	Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family
VagYM4_24470	COG0508	dehydrogenase complex catalyzes the overall conversion of
VagYM4_24480	COG2609	component of the pyruvate dehydrogenase (PDH) complex, that catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2)
VagYM4_24490	COG2186	Transcriptional regulator
VagYM4_24510	COG0157	Belongs to the NadC ModD family
VagYM4_24530	COG2804	Type II secretory pathway, ATPase PulE Tfp pilus assembly pathway, ATPase PilB
VagYM4_24540	COG1459	type II secretion system
VagYM4_24560	COG0237	dephospho-CoA kinase activity
VagYM4_24570	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
VagYM4_24580	COG3024	Inhibits all the catalytic activities of DNA gyrase by preventing its interaction with DNA. Acts by binding directly to the C-terminal domain of GyrB, which probably disrupts DNA binding by the gyrase
VagYM4_24610	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
VagYM4_24620	COG0228	four-way junction DNA binding
VagYM4_24630	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
VagYM4_24640	COG4137	Cytochrome C assembly protein
VagYM4_24650	COG4536	flavin adenine dinucleotide binding
VagYM4_24660	COG1854	S-ribosylhomocysteine lyase activity
VagYM4_24690	COG0612	Peptidase, M16
VagYM4_24700	COG1238	metal cluster binding
VagYM4_24720	COG1883	Na -transporting methylmalonyl-CoA oxaloacetate decarboxylase, beta subunit
VagYM4_24730	COG0511	ligase activity, forming carbon-carbon bonds
VagYM4_24730	COG5016	pyruvate
VagYM4_24740	COG3630	sodium ion export across plasma membrane
VagYM4_24760	COG0527	aspartate kinase activity
VagYM4_24770	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
VagYM4_24780	COG2137	regulation of response to DNA damage stimulus
VagYM4_24790	COG0468	Can catalyze the hydrolysis of ATP in the presence of single-stranded DNA, the ATP-dependent uptake of single-stranded DNA by duplex DNA, and the ATP-dependent hybridization of homologous single-stranded DNAs. It interacts with LexA causing its activation and leading to its autocatalytic cleavage
VagYM4_24800	COG1546	Belongs to the CinA family
VagYM4_24810	COG0249	that it carries out the mismatch recognition step. This protein has a weak ATPase activity
VagYM4_24820	COG0568	sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released
VagYM4_24840	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
VagYM4_24850	COG0496	Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates
VagYM4_24870	COG0245	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity
VagYM4_24880	COG1211	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity
VagYM4_24890	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
VagYM4_24900	COG0148	phosphopyruvate hydratase activity
VagYM4_24910	COG0504	CTP synthase activity
VagYM4_24920	COG3956	TIGRFAM MazG family protein
VagYM4_24930	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
VagYM4_24940	COG2265	Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family
VagYM4_24960	COG0736	holo-[acyl-carrier-protein] synthase activity
VagYM4_24970	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
VagYM4_24980	COG1381	Involved in DNA repair and RecF pathway recombination
VagYM4_24990	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
VagYM4_25010	COG0681	Belongs to the peptidase S26 family
VagYM4_25020	COG0481	GTPase activity
VagYM4_25030	COG3086	response to oxidative stress
VagYM4_25060	COG1595	DNA-templated transcription, initiation
VagYM4_25070	COG0029	Catalyzes the oxidation of L-aspartate to iminoaspartate
VagYM4_25090	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
VagYM4_25100	COG0354	folic acid binding
VagYM4_25130	COG0654	COG0654 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases
VagYM4_25140	COG0654	COG0654 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases
VagYM4_25150	COG3079	Belongs to the UPF0149 family
VagYM4_25160	COG3027	Activator of cell division through the inhibition of FtsZ GTPase activity, therefore promoting FtsZ assembly into bundles of protofilaments necessary for the formation of the division Z ring. It is recruited early at mid-cell but it is not essential for cell division
VagYM4_25170	COG0212	Belongs to the 5-formyltetrahydrofolate cyclo-ligase family
VagYM4_25180	COG0120	Catalyzes the reversible conversion of ribose-5- phosphate to ribulose 5-phosphate
VagYM4_25190	COG0111	D-isomer specific 2-hydroxyacid dehydrogenase
VagYM4_25210	COG0583	DNA-binding transcription factor activity
VagYM4_25240	COG0668	transmembrane transport
VagYM4_25250	COG0191	fructose-bisphosphate aldolase activity
VagYM4_25260	COG0126	phosphoglycerate kinase activity
VagYM4_25270	COG0057	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
VagYM4_25280	COG4771	TonB-dependent receptor
VagYM4_25290	COG0583	DNA-binding transcription factor activity
VagYM4_25300	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
VagYM4_25310	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
VagYM4_25340	COG2356	endonuclease I
VagYM4_25350	COG1385	rRNA (uridine-N3-)-methyltransferase activity
VagYM4_25360	COG0189	ligase activity
VagYM4_25370	COG1678	Uncharacterized ACR, COG1678
VagYM4_25380	COG0816	Could be a nuclease involved in processing of the 5'-end of pre-16S rRNA
VagYM4_25410	COG0325	Pyridoxal 5'-phosphate (PLP)-binding protein, which is involved in PLP homeostasis
VagYM4_25420	COG0345	Catalyzes the reduction of 1-pyrroline-5-carboxylate (PCA) to L-proline
VagYM4_25430	COG0762	integral membrane protein
VagYM4_25440	COG1872	DUF167
VagYM4_25460	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
VagYM4_25470	COG0635	Involved in the biosynthesis of porphyrin-containing compound
VagYM4_25480	COG2066	Belongs to the glutaminase family
VagYM4_25500	COG0220	tRNA (guanine-N7-)-methyltransferase activity
VagYM4_25520	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
VagYM4_25560	COG2206	PFAM metal-dependent phosphohydrolase, HD sub domain
VagYM4_25580	COG3394	polysaccharide catabolic process
VagYM4_25590	COG1486	melibiose metabolic process
VagYM4_25600	COG1447	Phosphotransferase system cellobiose-specific component IIA
VagYM4_25610	COG1455	protein-N(PI)-phosphohistidine-lactose phosphotransferase system transporter activity
VagYM4_25620	COG1440	protein-N(PI)-phosphohistidine-lactose phosphotransferase system transporter activity
VagYM4_25630	COG0726	polysaccharide deacetylase
VagYM4_25640	COG3706	GGDEF domain
VagYM4_25650	COG3547	Transposase (IS116 IS110 IS902 family)
VagYM4_25660	COG3547	Transposase (IS116 IS110 IS902 family)
VagYM4_25940	COG1028	Short-chain dehydrogenase reductase Sdr
VagYM4_25970	COG0795	lipopolysaccharide-transporting ATPase activity
VagYM4_25980	COG0795	lipopolysaccharide-transporting ATPase activity
VagYM4_26000	COG2927	DNA polymerase III (CHI subunit)
VagYM4_26010	COG0525	valine-tRNA ligase activity
VagYM4_26090	COG0540	Belongs to the ATCase OTCase family
VagYM4_26100	COG1781	'de novo' pyrimidine nucleobase biosynthetic process
VagYM4_26110	COG0251	oxidation-reduction process
VagYM4_26120	COG0204	Acyl-transferase
VagYM4_26140	COG5007	Belongs to the BolA IbaG family
VagYM4_26160	COG2854	intermembrane phospholipid transfer
VagYM4_26170	COG1463	ABC-type transport system involved in resistance to organic solvents, periplasmic component
VagYM4_26180	COG0767	ABC-type transport system involved in resistance to organic solvents, permease component
VagYM4_26190	COG1127	ABC transporter
VagYM4_26210	COG0517	IMP dehydrogenase activity
VagYM4_26210	COG0794	Belongs to the SIS family. GutQ KpsF subfamily
VagYM4_26230	COG1934	Involved in the assembly of lipopolysaccharide (LPS). Required for the translocation of LPS from the inner membrane to the outer membrane. May form a bridge between the inner membrane and the outer membrane, via interactions with LptC and LptD, thereby facilitating LPS transfer across the periplasm
VagYM4_26240	COG1137	ATPase activity
VagYM4_26260	COG1544	Required for dimerization of active 70S ribosomes into 100S ribosomes in stationary phase
VagYM4_26270	COG1762	phosphoenolpyruvate-dependent sugar phosphotransferase system
VagYM4_26280	COG1660	Displays ATPase and GTPase activities
VagYM4_26290	COG1925	phosphoenolpyruvate-dependent sugar phosphotransferase system
VagYM4_26300	COG2239	Acts as a magnesium transporter
VagYM4_26310	COG0312	modulator of DNA gyrase
VagYM4_26320	COG3028	Belongs to the UPF0307 family
VagYM4_26330	COG1052	Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family
VagYM4_26340	COG0564	pseudouridine synthase activity
VagYM4_26360	COG0553	Transcription regulator that activates transcription by stimulating RNA polymerase (RNAP) recycling in case of stress conditions such as supercoiled DNA or high salt concentrations. Probably acts by releasing the RNAP, when it is trapped or immobilized on tightly supercoiled DNA. Does not activate transcription on linear DNA. Probably not involved in DNA repair
VagYM4_26370	COG1875	ATPase related to phosphate starvation-inducible protein PhoH
VagYM4_26380	COG0312	modulator of DNA gyrase
VagYM4_26390	COG0388	Catalyzes the ATP-dependent amidation of deamido-NAD to form NAD. Uses L-glutamine as a nitrogen source
VagYM4_26400	COG3164	Protein of unknown function
VagYM4_26410	COG1530	ribonuclease E activity
VagYM4_26420	COG0424	maF-like protein
VagYM4_26430	COG2891	Involved in formation of the rod shape of the cell. May also contribute to regulation of formation of penicillin-binding proteins
VagYM4_26440	COG1792	Involved in formation and maintenance of cell shape
VagYM4_26450	COG1077	Cell shape determining protein MreB Mrl
VagYM4_26540	COG1459	type II secretion system
VagYM4_26550	COG2804	Type II secretory pathway, ATPase PulE Tfp pilus assembly pathway, ATPase PilB
VagYM4_26570	COG3409	Peptidoglycan-binding domain 1 protein
VagYM4_26570	COG3267	Type II secretory pathway component ExeA
VagYM4_26580	COG1450	Type ii and iii secretion system protein
VagYM4_26620	COG2199	diguanylate cyclase activity
VagYM4_26620	COG2200	EAL domain
VagYM4_26640	COG0629	single-stranded DNA binding
VagYM4_26670	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
VagYM4_26690	COG0075	2-aminoethylphosphonate-pyruvate transaminase activity
VagYM4_26700	COG0527	aspartate kinase activity
VagYM4_26710	COG0646	methionine synthase
VagYM4_26710	COG1410	methionine synthase
VagYM4_26750	COG0175	sulfate reduction
VagYM4_26760	COG0155	Belongs to the nitrite and sulfite reductase 4Fe-4S domain family
VagYM4_26770	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
VagYM4_26810	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
VagYM4_26860	COG0247	lactate metabolic process
VagYM4_26870	COG3075	Conversion of glycerol 3-phosphate to dihydroxyacetone. Uses fumarate or nitrate as electron acceptor
VagYM4_26880	COG0578	Belongs to the FAD-dependent glycerol-3-phosphate dehydrogenase family
VagYM4_27020	COG0735	belongs to the Fur family
VagYM4_27040	COG0166	Belongs to the GPI family
VagYM4_27060	COG0432	Pfam Uncharacterised protein family UPF0047
VagYM4_27070	COG0787	Catalyzes the interconversion of L-alanine and D- alanine. May also act on other amino acids
VagYM4_27120	COG2965	DNA replication, synthesis of RNA primer
VagYM4_27130	COG0360	Binds together with S18 to 16S ribosomal RNA
VagYM4_27140	COG0036	Belongs to the ribulose-phosphate 3-epimerase family
VagYM4_27150	COG0338	D12 class N6 adenine-specific DNA methyltransferase
VagYM4_27170	COG0337	Catalyzes the conversion of 3-deoxy-D-arabino- heptulosonate 7-phosphate (DAHP) to dehydroquinate (DHQ)
VagYM4_27180	COG0703	Catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid using ATP as a cosubstrate
VagYM4_27240	COG5009	serine-type D-Ala-D-Ala carboxypeptidase activity
VagYM4_27260	COG0695	Has a glutathione-disulfide oxidoreductase activity in the presence of NADPH and glutathione reductase. Reduces low molecular weight disulfides and proteins
VagYM4_27260	COG0678	peroxiredoxin activity
VagYM4_27270	COG1249	Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family
VagYM4_27300	COG1246	Belongs to the acetyltransferase family. ArgA subfamily
VagYM4_27300	COG0165	Argininosuccinate lyase
VagYM4_27310	COG0137	argininosuccinate synthase activity
VagYM4_27330	COG0002	Catalyzes the NADPH-dependent reduction of N-acetyl-5- glutamyl phosphate to yield N-acetyl-L-glutamate 5-semialdehyde
VagYM4_27350	COG2352	Forms oxaloacetate, a four-carbon dicarboxylic acid source for the tricarboxylic acid cycle
VagYM4_27370	COG0685	methylenetetrahydrofolate reductase (NAD(P)H) activity
VagYM4_27380	COG0527	aspartate kinase activity
VagYM4_27380	COG0460	homoserine dehydrogenase
VagYM4_27390	COG0626	cystathionine gamma-synthase activity
VagYM4_27410	COG0281	malic enzyme
VagYM4_27430	COG2906	2 iron, 2 sulfur cluster binding
VagYM4_27440	COG0050	This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis
VagYM4_27450	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
VagYM4_27490	COG2923	Belongs to the DsrF TusC family
VagYM4_27500	COG1553	Part of a sulfur-relay system required for 2-thiolation of 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at tRNA wobble positions. Accepts sulfur from TusA and transfers it in turn to TusE
VagYM4_27510	COG2964	Protein conserved in bacteria
VagYM4_27520	COG0545	Peptidyl-prolyl cis-trans isomerase
VagYM4_27550	COG1446	asparaginase
VagYM4_27560	COG1047	Peptidyl-prolyl cis-trans
VagYM4_27590	COG2249	NAD(P)H dehydrogenase (quinone) activity
VagYM4_27600	COG0488	(ABC) transporter
VagYM4_27620	COG0429	hydrolase of the alpha beta-hydrolase fold
VagYM4_27630	COG3089	Belongs to the UPF0270 family
VagYM4_27640	COG3954	Phosphoribulokinase
VagYM4_27650	COG0664	- Catabolite gene activator and regulatory subunit of cAMP-dependent protein
VagYM4_27690	COG4992	N2-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity
VagYM4_27700	COG0512	Glutamine amidotransferase of anthranilate synthase
VagYM4_27730	COG0180	Tryptophanyl-tRNA synthetase
VagYM4_27740	COG0546	phosphoglycolate phosphatase activity
VagYM4_27750	COG0566	Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase TrmH family
VagYM4_27760	COG0557	exoribonuclease II activity
VagYM4_27770	COG1959	2 iron, 2 sulfur cluster binding
VagYM4_27780	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
VagYM4_27780	COG1017	nitric oxide dioxygenase activity
VagYM4_27790	COG0790	COG0790 FOG TPR repeat, SEL1 subfamily
VagYM4_27800	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
VagYM4_27810	COG3242	Uncharacterized protein conserved in bacteria (DUF2065)
VagYM4_27820	COG0330	HflC and HflK could
VagYM4_27830	COG0330	HflC and HflK could
VagYM4_27840	COG2262	GTPase that associates with the 50S ribosomal subunit and may have a role during protein synthesis or ribosome biogenesis
VagYM4_27860	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)
VagYM4_27870	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
VagYM4_27890	COG0802	atpase or kinase
VagYM4_27900	COG1600	Catalyzes the conversion of epoxyqueuosine (oQ) to queuosine (Q), which is a hypermodified base found in the wobble positions of tRNA(Asp), tRNA(Asn), tRNA(His) and tRNA(Tyr)
VagYM4_27910	COG1949	3'-to-5' exoribonuclease specific for small oligoribonucleotides
VagYM4_27920	COG1162	GTPase activity
VagYM4_27930	COG0688	phosphatidylethanolamine metabolic process
VagYM4_27940	COG3273	potassium ion transport
VagYM4_27940	COG0471	metal ion transport
VagYM4_27960	COG0696	Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate
VagYM4_27970	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
VagYM4_27980	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
VagYM4_27990	COG0240	glycerol-3-phosphate dehydrogenase [NAD(P)+] activity
VagYM4_28000	COG1045	serine acetyltransferase
VagYM4_28010	COG4942	peptidase
VagYM4_28050	COG2269	With EpmB is involved in the beta-lysylation step of the post-translational modification of translation elongation factor P (EF-P). Catalyzes the ATP-dependent activation of (R)-beta-lysine produced by EpmB, forming a lysyl-adenylate, from which the beta- lysyl moiety is then transferred to the epsilon-amino group of a conserved specific lysine residue in EF-P
VagYM4_28060	COG1053	succinate dehydrogenase
VagYM4_28070	COG0479	Belongs to the succinate dehydrogenase fumarate reductase iron-sulfur protein family
VagYM4_28080	COG3029	Seems to be involved in the anchoring of the catalytic components of the fumarate reductase complex to the cytoplasmic membrane
VagYM4_28120	COG1509	lysine 2,3-aminomutase activity
VagYM4_28130	COG1285	pathogenesis
VagYM4_28150	COG0459	protein refolding
VagYM4_28170	COG0534	Mate efflux family protein
VagYM4_28180	COG0205	6-phosphofructokinase activity
VagYM4_28190	COG0053	Belongs to the cation diffusion facilitator (CDF) transporter (TC 2.A.4) family
VagYM4_28210	COG0745	RESPONSE REGULATOR receiver
VagYM4_28220	COG2205	protein histidine kinase activity
VagYM4_28240	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
VagYM4_28250	COG3030	protein affecting phage T7 exclusion by the F plasmid
VagYM4_28260	COG1027	Aspartate ammonia-lyase
VagYM4_28270	COG2704	Responsible for the transport of C4-dicarboxylates from the periplasm across the inner membrane
VagYM4_28280	COG4232	protein-disulfide reductase activity
VagYM4_28300	COG3263	regulation of cellular component size
VagYM4_28320	COG4147	Belongs to the sodium solute symporter (SSF) (TC 2.A.21) family
VagYM4_28370	COG2814	Major facilitator Superfamily
VagYM4_28400	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
VagYM4_28410	COG0757	Catalyzes a trans-dehydration via an enolate intermediate
VagYM4_28420	COG0511	ligase activity, forming carbon-carbon bonds
VagYM4_28430	COG0439	Biotin carboxylase
VagYM4_28440	COG2264	protein methyltransferase activity
VagYM4_28450	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
VagYM4_28460	COG2901	Activates ribosomal RNA transcription. Plays a direct role in upstream activation of rRNA promoters
VagYM4_28480	COG0488	(ABC) transporter
VagYM4_28490	COG1982	Orn Lys Arg decarboxylase major
VagYM4_28500	COG0531	amino acid
VagYM4_28520	COG3710	Transcriptional regulator
VagYM4_28530	COG0789	Transcriptional regulator
VagYM4_28540	COG0138	bifunctional purine biosynthesis protein purh
VagYM4_28550	COG0151	Belongs to the GarS family
VagYM4_28580	COG1253	flavin adenine dinucleotide binding
VagYM4_28590	COG3068	Protein conserved in bacteria
VagYM4_28610	COG1573	uracil-dna glycosylase
VagYM4_28620	COG0407	Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III
VagYM4_28630	COG2816	NAD+ diphosphatase activity
VagYM4_28640	COG3160	Binds RpoD and negatively regulates RpoD-mediated transcription activation by preventing the interaction between the primary sigma factor RpoD with the catalytic core of the RNA polymerase and with promoter DNA. May be involved in replacement of the RNA polymerase sigma subunit from RpoD to RpoS during the transition from exponential growth to the stationary phase
VagYM4_28650	COG0086	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates
VagYM4_28660	COG0085	RNA polymerase activity
VagYM4_28670	COG0222	ribosome binding
VagYM4_28680	COG0244	Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors
VagYM4_28710	COG0250	Participates in transcription elongation, termination and antitermination
VagYM4_28720	COG0690	P-P-bond-hydrolysis-driven protein transmembrane transporter activity
VagYM4_28730	COG0050	This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis
VagYM4_28750	COG0340	biotin-[acetyl-CoA-carboxylase] ligase activity
VagYM4_28750	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
VagYM4_28760	COG0812	UDP-N-acetylmuramate dehydrogenase activity
VagYM4_28780	COG1502	Catalyzes the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) (diphosphatidylglycerol) and glycerol
VagYM4_28820	COG4206	TonB-dependent receptor
VagYM4_28860	COG1249	Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family
VagYM4_28870	COG0534	Mate efflux family protein
VagYM4_28880	COG3315	Exhibits S-adenosyl-L-methionine-dependent methyltransferase activity
VagYM4_28890	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
VagYM4_28900	COG2937	Belongs to the GPAT DAPAT family
VagYM4_28910	COG0382	Catalyzes the prenylation of para-hydroxybenzoate (PHB) with an all-trans polyprenyl group. Mediates the second step in the final reaction sequence of ubiquinone-8 (UQ-8) biosynthesis, which is the condensation of the polyisoprenoid side chain with PHB, generating the first membrane-bound Q intermediate 3- octaprenyl-4-hydroxybenzoate
VagYM4_28920	COG3161	chorismate lyase activity
VagYM4_28930	COG1580	Controls the rotational direction of flagella during chemotaxis
VagYM4_28940	COG0705	Rhomboid family
VagYM4_28950	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
VagYM4_28970	COG2177	Part of the ABC transporter FtsEX involved in
VagYM4_28980	COG2884	Cell division ATP-binding protein ftsE
VagYM4_28990	COG0552	protein localization to endoplasmic reticulum
VagYM4_29000	COG0742	ribosomal rna small subunit methyltransferase
VagYM4_29020	COG2095	MarC family integral membrane protein
VagYM4_29110	COG0057	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
VagYM4_29120	COG0640	Transcriptional regulator
VagYM4_29130	COG3434	signal transduction protein containing EAL and modified HD-GYP domains
VagYM4_29140	COG1280	lysine exporter protein (LysE YggA)
VagYM4_29150	COG2267	carboxylic ester hydrolase activity
VagYM4_29160	COG0561	phosphatase activity
VagYM4_29200	COG2199	diguanylate cyclase activity
VagYM4_29200	COG3287	FIST C domain
VagYM4_29200	COG2200	EAL domain
VagYM4_29210	COG1011	Hydrolase
VagYM4_29220	COG4973	Belongs to the 'phage' integrase family. XerC subfamily
VagYM4_29240	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
VagYM4_29250	COG0019	diaminopimelate decarboxylase activity
VagYM4_29260	COG1965	Belongs to the frataxin family
VagYM4_29280	COG3072	Adenylate cyclase
VagYM4_29290	COG0181	hydroxymethylbilane synthase activity
VagYM4_29300	COG1587	Uroporphyrinogen-III synthase
VagYM4_29310	COG2959	enzyme of heme biosynthesis
VagYM4_29320	COG3071	HemY protein
VagYM4_29340	COG0633	Ferredoxin
VagYM4_29350	COG0043	3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity
VagYM4_29380	COG3118	belongs to the thioredoxin family
VagYM4_29390	COG0513	Belongs to the DEAD box helicase family
VagYM4_29400	COG0248	Ppx GppA phosphatase
VagYM4_29410	COG1738	Involved in the import of queuosine (Q) precursors, required for Q precursor salvage
VagYM4_29430	COG0514	ATP-dependent DNA helicase (RecQ)
VagYM4_29440	COG2962	Rard protein
VagYM4_29460	COG1280	lysine exporter protein (LysE YggA)
VagYM4_29470	COG0405	Gamma-glutamyltransferase
VagYM4_29490	COG0210	DNA helicase
VagYM4_29510	COG3220	belongs to the UPF0276 family
VagYM4_29570	COG0006	proline dipeptidase activity
VagYM4_29570	COG0006	proline dipeptidase activity
VagYM4_29610	COG0476	Involved in molybdopterin and thiamine biosynthesis, family 2
VagYM4_29640	COG0239	Important for reducing fluoride concentration in the cell, thus reducing its toxicity
VagYM4_29650	COG2132	Multicopper oxidase
VagYM4_29660	COG0663	COG0663 Carbonic anhydrases acetyltransferases, isoleucine patch superfamily
VagYM4_29680	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)
VagYM4_29690	COG0408	coproporphyrinogen oxidase activity
VagYM4_29700	COG0009	L-threonylcarbamoyladenylate synthase
VagYM4_29710	COG0041	Catalyzes the conversion of N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) to 4-carboxy-5-aminoimidazole ribonucleotide (CAIR)
VagYM4_29720	COG0026	Catalyzes the ATP-dependent conversion of 5- aminoimidazole ribonucleotide (AIR) and HCO(3)(-) to N5- carboxyaminoimidazole ribonucleotide (N5-CAIR)
VagYM4_29730	COG0551	DNA topoisomerase type I activity
VagYM4_29740	COG2922	Belongs to the Smg family
VagYM4_29750	COG0758	DNA mediated transformation
VagYM4_29770	COG0242	peptide deformylase activity
VagYM4_29780	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
VagYM4_29790	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
VagYM4_29790	COG0144	Specifically methylates the cytosine at position 967 (m5C967) of 16S rRNA
VagYM4_29800	COG0144	Specifically methylates the cytosine at position 967 (m5C967) of 16S rRNA
VagYM4_29800	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
VagYM4_29810	COG0569	domain protein
VagYM4_29820	COG0168	Low-affinity potassium transport system. Interacts with trk system potassium uptake protein TrkA
VagYM4_29840	COG1272	protein, Hemolysin III
VagYM4_29850	COG4326	sporulation control protein
VagYM4_29870	COG3084	Protein conserved in bacteria
VagYM4_29890	COG2334	A protein kinase that phosphorylates Ser and Thr residues. Probably acts to suppress the effects of stress linked to accumulation of reactive oxygen species. Probably involved in the extracytoplasmic stress response
VagYM4_29900	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
VagYM4_29910	COG0204	Acyl-transferase
VagYM4_29930	COG0606	chelatase, subunit chli
VagYM4_29950	COG3978	acetolactate synthase activity
VagYM4_29960	COG0115	Belongs to the class-IV pyridoxal-phosphate-dependent aminotransferase family
VagYM4_29970	COG0129	dihydroxy-acid dehydratase activity
VagYM4_29990	COG0583	DNA-binding transcription factor activity
VagYM4_30000	COG2814	Major facilitator Superfamily
VagYM4_30020	COG0765	amino acid transport
VagYM4_30040	COG0355	proton-transporting ATP synthase activity, rotational mechanism
VagYM4_30050	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
VagYM4_30060	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
VagYM4_30070	COG0056	Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit
VagYM4_30080	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
VagYM4_30090	COG0711	Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0)
VagYM4_30110	COG0356	it plays a direct role in the translocation of protons across the membrane
VagYM4_30120	COG3312	ion transport
VagYM4_30130	COG1475	DNA binding
VagYM4_30140	COG1192	Involved in chromosome partitioning
VagYM4_30150	COG0357	Ribosomal RNA small subunit methyltransferase G
VagYM4_30160	COG0445	tRNA wobble uridine modification
VagYM4_30170	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
VagYM4_30190	COG3706	GGDEF domain
VagYM4_30220	COG1087	Belongs to the NAD(P)-dependent epimerase dehydratase family
VagYM4_30230	COG4146	Belongs to the sodium solute symporter (SSF) (TC 2.A.21) family
VagYM4_30250	COG1609	Transcriptional regulator
VagYM4_30460	COG4974	Belongs to the 'phage' integrase family
VagYM4_30480	COG0706	membrane insertase activity
VagYM4_30490	COG0594	ribonuclease P activity
VagYM4_30510	COG1126	abc transporter atp-binding protein
VagYM4_30560	COG4608	Belongs to the ABC transporter superfamily
VagYM4_30570	COG0444	Belongs to the ABC transporter superfamily
VagYM4_30590	COG3236	hydrolase activity, hydrolyzing N-glycosyl compounds
VagYM4_30590	COG0807	Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate
VagYM4_30640	COG0772	Belongs to the SEDS family
VagYM4_30660	COG1136	(ABC) transporter
VagYM4_30700	COG3275	phosphorelay sensor kinase activity
VagYM4_30710	COG3279	Response regulator of the LytR AlgR family
VagYM4_30730	COG0652	PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides
VagYM4_30770	COG0786	glutamate:sodium symporter activity
VagYM4_30790	COG1131	(ABC) transporter
VagYM4_30800	COG1167	Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain MocR family and their eukaryotic orthologs
VagYM4_30810	COG0786	glutamate:sodium symporter activity
VagYM4_30830	COG0363	glucosamine-6-phosphate deaminase activity
VagYM4_30870	COG1741	Belongs to the pirin family
VagYM4_30880	COG2259	Doxx family
VagYM4_30900	COG0122	3-methyladenine DNA glycosylase 8-oxoguanine DNA glycosylase
VagYM4_30910	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
VagYM4_30930	COG1284	Uncharacterised 5xTM membrane BCR, YitT family COG1284
VagYM4_30990	COG0596	Alpha beta hydrolase
VagYM4_31020	COG3123	guanosine phosphorylase activity
VagYM4_31050	COG0534	Mate efflux family protein
VagYM4_31060	COG0564	pseudouridine synthase activity
VagYM4_31090	COG0583	DNA-binding transcription factor activity
VagYM4_31100	COG0561	phosphatase activity
VagYM4_31120	COG2199	diguanylate cyclase activity
VagYM4_31150	COG1062	S-(hydroxymethyl)glutathione dehydrogenase activity
VagYM4_31160	COG2162	N-hydroxyarylamine O-acetyltransferase activity
VagYM4_31170	COG0583	DNA-binding transcription factor activity
VagYM4_31250	COG1357	PFAM Pentapeptide repeats (8 copies)
VagYM4_31260	COG3047	cAMP biosynthetic process
VagYM4_31320	COG1626	Provides the cells with the ability to utilize trehalose at high osmolarity by splitting it into glucose molecules that can subsequently be taken up by the phosphotransferase-mediated uptake system
VagYM4_31320	COG3408	Glycogen debranching enzyme
VagYM4_31330	COG2110	phosphatase homologous to the C-terminal domain of histone macroH2A1
VagYM4_31370	COG0583	DNA-binding transcription factor activity
VagYM4_31400	COG0546	phosphoglycolate phosphatase activity
VagYM4_31450	COG3835	regulator
VagYM4_31460	COG2610	gluconate transmembrane transporter activity
VagYM4_31470	COG1929	Belongs to the glycerate kinase type-1 family
VagYM4_31480	COG1167	Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain MocR family and their eukaryotic orthologs
VagYM4_31520	COG0456	acetyltransferase
VagYM4_31550	COG1028	Short-chain dehydrogenase reductase Sdr
VagYM4_31560	COG1670	COG1670 acetyltransferases, including N-acetylases of ribosomal proteins
VagYM4_31570	COG3005	denitrification pathway
VagYM4_31580	COG0243	molybdopterin cofactor binding
VagYM4_31600	COG0352	thiamine-phosphate diphosphorylase activity
VagYM4_31610	COG2145	Catalyzes the phosphorylation of the hydroxyl group of 4-methyl-5-beta-hydroxyethylthiazole (THZ)
VagYM4_31620	COG0819	Catalyzes an amino-pyrimidine hydrolysis reaction at the C5' of the pyrimidine moiety of thiamine compounds, a reaction that is part of a thiamine salvage pathway
VagYM4_31630	COG0715	COG0715 ABC-type nitrate sulfonate bicarbonate transport systems periplasmic components
VagYM4_31640	COG0600	ABC-type nitrate sulfonate bicarbonate transport system permease component
VagYM4_31650	COG1116	anion transmembrane transporter activity
VagYM4_31660	COG0351	phosphomethylpyrimidine kinase
VagYM4_31670	COG0312	modulator of DNA gyrase
VagYM4_31680	COG0312	modulator of DNA gyrase
VagYM4_31690	COG1901	pseudouridine methyltransferase
VagYM4_31740	COG1052	Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family
VagYM4_31760	COG0584	glycerophosphoryl diester phosphodiesterase
VagYM4_31770	COG0039	L-malate dehydrogenase activity
VagYM4_31780	COG0745	RESPONSE REGULATOR receiver
VagYM4_31820	COG0811	peptide transport
VagYM4_31830	COG0811	peptide transport
VagYM4_31840	COG0848	biopolymer transport protein
VagYM4_31930	COG0803	Belongs to the bacterial solute-binding protein 9 family
VagYM4_31940	COG1121	(ABC) transporter
VagYM4_31950	COG1108	ABC-type Mn2 Zn2 transport systems permease components
VagYM4_31980	COG1770	oligopeptidase
VagYM4_31990	COG2814	Major facilitator Superfamily
VagYM4_32000	COG0010	Belongs to the arginase family
VagYM4_32010	COG1166	arginine decarboxylase activity
VagYM4_32030	COG0189	ligase activity
VagYM4_32030	COG4067	protein conserved in archaea
VagYM4_32040	COG0189	ligase activity
VagYM4_32050	COG0583	DNA-binding transcription factor activity
VagYM4_32120	COG4191	Histidine kinase
VagYM4_32130	COG2204	response regulator
VagYM4_32140	COG3706	GGDEF domain
VagYM4_32180	COG0579	oxidoreductase
VagYM4_32200	COG1294	oxidase, subunit
VagYM4_32210	COG1271	oxidase subunit
VagYM4_32230	COG3033	Beta-eliminating lyase
VagYM4_32250	COG1972	Belongs to the concentrative nucleoside transporter (CNT) (TC 2.A.41) family
VagYM4_32280	COG3706	GGDEF domain
VagYM4_32310	COG3706	GGDEF domain
VagYM4_32320	COG0415	Belongs to the DNA photolyase family
VagYM4_32330	COG3046	protein related to deoxyribodipyrimidine photolyase
VagYM4_32350	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
VagYM4_32350	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
VagYM4_32360	COG1765	OsmC-like protein
VagYM4_32370	COG0110	maltose O-acetyltransferase activity
VagYM4_32450	COG1011	Hydrolase
VagYM4_32480	COG3054	Bacterial protein of unknown function (YtfJ_HI0045)
VagYM4_32490	COG3338	carbonate dehydratase activity
VagYM4_32500	COG2067	long-chain fatty acid transport protein
VagYM4_32510	COG3240	lipase activity
VagYM4_32570	COG1609	Transcriptional regulator
VagYM4_32580	COG0637	HAD-superfamily hydrolase subfamily IA, variant 3
VagYM4_32610	COG1840	ABC-type Fe3 transport system, periplasmic component
VagYM4_32620	COG3842	ATPase activity
VagYM4_32670	COG2990	Protein conserved in bacteria
VagYM4_32690	COG0665	tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase activity
VagYM4_32700	COG2866	Carboxypeptidase
VagYM4_32720	COG0583	DNA-binding transcription factor activity
VagYM4_32760	COG3104	oligopeptide transport
VagYM4_32770	COG1760	l-serine dehydratase
VagYM4_32810	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)
VagYM4_32820	COG0741	lytic transglycosylase activity
VagYM4_32860	COG1815	bacterial-type flagellum-dependent cell motility
VagYM4_32870	COG1558	bacterial-type flagellum-dependent cell motility
VagYM4_32880	COG1843	Required for flagellar hook formation. May act as a scaffolding protein
VagYM4_32890	COG1749	Flagellar hook protein flgE
VagYM4_32900	COG4787	bacterial-type flagellum-dependent cell motility
VagYM4_32910	COG4786	Flagellar basal body rod
VagYM4_32920	COG2063	Assembles around the rod to form the L-ring and probably protects the motor basal body from shearing forces during rotation
VagYM4_32930	COG1706	bacterial-type flagellum-dependent cell motility
VagYM4_32950	COG4786	Flagellar basal body rod
VagYM4_32950	COG1256	bacterial-type flagellum assembly
VagYM4_32960	COG1344	Flagellin is the subunit protein which polymerizes to form the filaments of bacterial flagella
VagYM4_33000	COG1304	FMN binding
VagYM4_33030	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
VagYM4_33040	COG0234	Binds to Cpn60 in the presence of Mg-ATP and suppresses the ATPase activity of the latter
VagYM4_33050	COG0459	protein refolding
VagYM4_33080	COG1280	lysine exporter protein (LysE YggA)
VagYM4_33120	COG1309	transcriptional regulator
VagYM4_33140	COG4303	Ethanolamine ammonia lyase large subunit
VagYM4_33150	COG4302	ethanolamine ammonia-lyase activity
VagYM4_33160	COG0531	amino acid
VagYM4_33170	COG2070	2-Nitropropane dioxygenase
VagYM4_33180	COG3537	Alpha-1,2-mannosidase
VagYM4_33190	COG3537	Alpha-1,2-mannosidase
VagYM4_33210	COG3537	Alpha-1,2-mannosidase
VagYM4_33220	COG3537	Alpha-1,2-mannosidase
VagYM4_33230	COG1299	protein-N(PI)-phosphohistidine-fructose phosphotransferase system transporter activity
VagYM4_33250	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
VagYM4_33250	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
VagYM4_33260	COG0346	lactoylglutathione lyase activity
VagYM4_33270	COG1349	DNA-binding transcription factor activity
VagYM4_33290	COG1335	isochorismatase
VagYM4_33310	COG1488	Catalyzes the synthesis of beta-nicotinate D- ribonucleotide from nicotinate and 5-phospho-D-ribose 1-phosphate at the expense of ATP
VagYM4_33360	COG0583	DNA-binding transcription factor activity
VagYM4_33390	COG3713	MltA-interacting MipA family protein
VagYM4_33400	COG3015	lipoprotein NlpE involved in copper resistance
VagYM4_33410	COG3448	diguanylate cyclase activity
VagYM4_33410	COG4175	Glycine betaine
VagYM4_33420	COG4176	ABC-type proline glycine betaine transport system permease component
VagYM4_33430	COG1342	Belongs to the UPF0251 family
VagYM4_33490	COG4948	Mandelate Racemase Muconate Lactonizing
VagYM4_33510	COG0583	DNA-binding transcription factor activity
VagYM4_33580	COG1502	Catalyzes the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) (diphosphatidylglycerol) and glycerol
VagYM4_33650	COG3842	ATPase activity
VagYM4_33710	COG1292	Belongs to the BCCT transporter (TC 2.A.15) family
VagYM4_33770	COG0845	Belongs to the membrane fusion protein (MFP) (TC 8.A.1) family
VagYM4_33800	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)
VagYM4_33810	COG2197	response regulator
VagYM4_33840	COG1806	Bifunctional serine threonine kinase and phosphorylase involved in the regulation of the
VagYM4_33850	COG0252	asparaginase activity
VagYM4_33870	COG0583	DNA-binding transcription factor activity
VagYM4_33890	COG1280	lysine exporter protein (LysE YggA)
VagYM4_33900	COG3122	Protein conserved in bacteria
VagYM4_33920	COG2423	ornithine cyclodeaminase activity
VagYM4_33930	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
VagYM4_33940	COG0161	adenosylmethionine-8-amino-7-oxononanoate transaminase activity
VagYM4_33950	COG1012	belongs to the aldehyde dehydrogenase family
VagYM4_33960	COG1522	sequence-specific DNA binding
VagYM4_33970	COG1638	TRAP-type C4-dicarboxylate transport system periplasmic component
VagYM4_33980	COG1638	TRAP-type C4-dicarboxylate transport system periplasmic component
VagYM4_33990	COG3608	succinylglutamate desuccinylase aspartoacylase
VagYM4_34000	COG0006	proline dipeptidase activity
VagYM4_34010	COG1167	Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain MocR family and their eukaryotic orthologs
VagYM4_34020	COG3090	Trap-type c4-dicarboxylate transport system, small permease component
VagYM4_34030	COG1593	TRAP-type C4-dicarboxylate transport system, large permease component
VagYM4_34040	COG2207	Transcriptional regulator
VagYM4_34050	COG1028	Short-chain dehydrogenase reductase Sdr
VagYM4_34070	COG1063	alcohol dehydrogenase
VagYM4_34080	COG1902	pentaerythritol trinitrate reductase activity
VagYM4_34110	COG0583	DNA-binding transcription factor activity
VagYM4_34130	COG0513	Belongs to the DEAD box helicase family
VagYM4_34170	COG1167	Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain MocR family and their eukaryotic orthologs
VagYM4_34180	COG2207	Transcriptional regulator
VagYM4_34180	COG0614	abc-type fe3 -hydroxamate transport system, periplasmic component
VagYM4_34230	COG3746	phosphate-selective porin O and P
VagYM4_34260	COG1028	Short-chain dehydrogenase reductase Sdr
VagYM4_34320	COG1263	PTS System
VagYM4_34320	COG1264	protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
VagYM4_34330	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
VagYM4_34340	COG1621	beta-fructofuranosidase activity
VagYM4_34350	COG0625	glutathione transferase activity
VagYM4_34370	COG1686	Belongs to the peptidase S11 family
VagYM4_34400	COG0678	peroxiredoxin activity
VagYM4_34400	COG0695	Has a glutathione-disulfide oxidoreductase activity in the presence of NADPH and glutathione reductase. Reduces low molecular weight disulfides and proteins
VagYM4_34410	COG1816	Catalyzes the hydrolytic deamination of adenine to hypoxanthine. Plays an important role in the purine salvage pathway and in nitrogen catabolism
VagYM4_34420	COG1816	Catalyzes the hydrolytic deamination of adenine to hypoxanthine. Plays an important role in the purine salvage pathway and in nitrogen catabolism
VagYM4_34450	COG1278	Cold shock
VagYM4_34460	COG1741	Belongs to the pirin family
VagYM4_34470	COG4667	esterase of the alpha-beta hydrolase superfamily
VagYM4_34520	COG2194	sulfuric ester hydrolase activity
VagYM4_34530	COG0818	Recycling of diacylglycerol produced during the turnover of membrane phospholipid
VagYM4_34550	COG2205	protein histidine kinase activity
VagYM4_34560	COG0745	RESPONSE REGULATOR receiver
VagYM4_34590	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
VagYM4_34630	COG0108	Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate
VagYM4_34650	COG2814	Major facilitator Superfamily
VagYM4_34670	COG1418	mRNA catabolic process
VagYM4_34680	COG0402	S-adenosylhomocysteine deaminase activity
VagYM4_34690	COG1457	Belongs to the purine-cytosine permease (2.A.39) family
VagYM4_34700	COG2239	Acts as a magnesium transporter
VagYM4_34710	COG0661	Is probably a protein kinase regulator of UbiI activity which is involved in aerobic coenzyme Q (ubiquinone) biosynthesis
VagYM4_34720	COG1566	PFAM secretion protein HlyD family protein
VagYM4_34770	COG0745	RESPONSE REGULATOR receiver
VagYM4_34780	COG2205	protein histidine kinase activity
VagYM4_34810	COG0531	amino acid
VagYM4_34830	COG0583	DNA-binding transcription factor activity
VagYM4_34880	COG5002	protein histidine kinase activity
VagYM4_34880	COG2205	protein histidine kinase activity
VagYM4_34880	COG0784	Response regulator, receiver
VagYM4_34890	COG0534	Mate efflux family protein
VagYM4_34920	COG3132	Protein of unknown function, DUF480
VagYM4_34930	COG2827	Endonuclease containing a URI domain
VagYM4_34940	COG1879	ABC-type sugar transport system periplasmic component
VagYM4_34950	COG0784	Response regulator, receiver
VagYM4_34950	COG2205	protein histidine kinase activity
VagYM4_35060	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
VagYM4_35070	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
VagYM4_35090	COG1280	lysine exporter protein (LysE YggA)
VagYM4_35110	COG0183	Belongs to the thiolase family
VagYM4_35130	COG3243	poly(R)-hydroxyalkanoic acid synthase
VagYM4_35150	COG3005	denitrification pathway
VagYM4_35170	COG0243	molybdopterin cofactor binding
VagYM4_35190	COG1145	4fe-4S ferredoxin, iron-sulfur binding domain protein
VagYM4_35200	COG3850	Histidine kinase
VagYM4_35210	COG2197	response regulator
VagYM4_35240	COG2195	Cleaves the N-terminal amino acid of tripeptides
VagYM4_35280	COG0840	transmembrane signaling receptor activity
VagYM4_35300	COG0637	HAD-superfamily hydrolase subfamily IA, variant 3
VagYM4_35320	COG0722	Stereospecific condensation of phosphoenolpyruvate (PEP) and D-erythrose-4-phosphate (E4P) giving rise to 3-deoxy-D- arabino-heptulosonate-7-phosphate (DAHP)
VagYM4_35330	COG2814	Major facilitator Superfamily
VagYM4_35340	COG0840	transmembrane signaling receptor activity
VagYM4_35350	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
VagYM4_35360	COG0176	Transaldolase is important for the balance of metabolites in the pentose-phosphate pathway
VagYM4_35400	COG2897	thiosulfate sulfurtransferase activity
VagYM4_35440	COG0476	Involved in molybdopterin and thiamine biosynthesis, family 2
VagYM4_35470	COG1914	H( )-stimulated, divalent metal cation uptake system
VagYM4_35490	COG0038	chloride channel
VagYM4_35520	COG4989	oxidoreductase activity
VagYM4_35550	COG0063	ADP-dependent NAD(P)H-hydrate dehydratase activity
VagYM4_35550	COG0062	Bifunctional enzyme that catalyzes the epimerization of the S- and R-forms of NAD(P)HX and the dehydration of the S-form of NAD(P)HX at the expense of ADP, which is converted to AMP. This allows the repair of both epimers of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or heat-dependent hydration
VagYM4_35570	COG1013	pyruvate-flavodoxin oxidoreductase activity
VagYM4_35580	COG0674	pyruvate-flavodoxin oxidoreductase activity
VagYM4_35580	COG1014	Oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin
VagYM4_35600	COG0739	heme binding
VagYM4_35690	COG3501	Rhs element vgr protein
VagYM4_35740	COG0515	serine threonine protein kinase
VagYM4_35810	COG1522	sequence-specific DNA binding
VagYM4_35950	COG2814	Major facilitator Superfamily
VagYM4_35970	COG0583	DNA-binding transcription factor activity
VagYM4_35980	COG4221	oxidoreductase activity
VagYM4_35990	COG0589	response to stress
VagYM4_36010	COG1009	NADH ubiquinone oxidoreductase subunit 5 chain L Multisubunit Na H antiporter, MnhA subunit
VagYM4_36010	COG2111	Na H antiporter
VagYM4_36050	COG2212	antiporter activity
VagYM4_36060	COG1320	monovalent cation:proton antiporter activity
VagYM4_36070	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
VagYM4_36200	COG1292	Belongs to the BCCT transporter (TC 2.A.15) family
VagYM4_36230	COG3527	Alpha-acetolactate decarboxylase
VagYM4_36290	COG0384	phenazine biosynthesis protein PhzF
VagYM4_36310	COG1294	oxidase, subunit
VagYM4_36320	COG1271	oxidase subunit
VagYM4_36330	COG1167	Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain MocR family and their eukaryotic orthologs
VagYM4_36370	COG4999	Histidine kinase
VagYM4_36370	COG3850	Histidine kinase
VagYM4_36370	COG3437	response regulator, receiver
VagYM4_36370	COG2205	protein histidine kinase activity
VagYM4_36390	COG4770	biotin carboxylase activity
VagYM4_36410	COG4799	Acetyl-CoA carboxylase, carboxyltransferase component subunits alpha and beta
VagYM4_36420	COG1960	acyl-CoA dehydrogenase activity
VagYM4_36440	COG0183	Belongs to the thiolase family
VagYM4_36460	COG1960	acyl-CoA dehydrogenase activity
VagYM4_36470	COG1024	Enoyl-CoA hydratase
VagYM4_36500	COG1028	Short-chain dehydrogenase reductase Sdr
VagYM4_36520	COG1309	transcriptional regulator
VagYM4_36530	COG1012	belongs to the aldehyde dehydrogenase family
VagYM4_36560	COG4176	ABC-type proline glycine betaine transport system permease component
VagYM4_36570	COG0517	IMP dehydrogenase activity
VagYM4_36570	COG4175	Glycine betaine
VagYM4_36600	COG0330	HflC and HflK could
VagYM4_36630	COG5001	Diguanylate cyclase
VagYM4_36630	COG3300	MHYT domain
VagYM4_36660	COG0784	Response regulator, receiver
VagYM4_36660	COG2205	protein histidine kinase activity
VagYM4_36680	COG0334	Belongs to the Glu Leu Phe Val dehydrogenases family
VagYM4_36770	COG5001	Diguanylate cyclase
VagYM4_36780	COG1869	D-ribose catabolic process
VagYM4_36790	COG1129	ABC transporter
VagYM4_36800	COG1172	Belongs to the binding-protein-dependent transport system permease family
VagYM4_36810	COG1879	ABC-type sugar transport system periplasmic component
VagYM4_36820	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
VagYM4_36830	COG1609	Transcriptional regulator
VagYM4_36860	COG2820	Catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1- phosphate. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis
VagYM4_36880	COG4607	ABC-type enterochelin transport system periplasmic component
VagYM4_36890	COG4606	Belongs to the binding-protein-dependent transport system permease family. FecCD subfamily
VagYM4_36900	COG4605	iron ion homeostasis
VagYM4_36910	COG4604	ABC transporter, ATP-binding protein
VagYM4_36920	COG0789	Transcriptional regulator
VagYM4_36930	COG2207	Transcriptional regulator
VagYM4_36940	COG1629	transport
VagYM4_36940	COG4771	TonB-dependent receptor
VagYM4_37000	COG1289	transmembrane transporter activity
VagYM4_37010	COG0210	DNA helicase
VagYM4_37020	COG1803	Methylglyoxal synthase
VagYM4_37030	COG1879	ABC-type sugar transport system periplasmic component
VagYM4_37040	COG2205	protein histidine kinase activity
VagYM4_37040	COG0784	Response regulator, receiver
VagYM4_37040	COG2198	Histidine kinase
VagYM4_37080	COG3119	arylsulfatase activity
VagYM4_37100	COG3119	arylsulfatase activity
VagYM4_37110	COG0641	radical SAM
VagYM4_37120	COG0714	Associated with various cellular activities
VagYM4_37180	COG0117	Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)- pyrimidinedione 5'-phosphate
VagYM4_37180	COG1985	Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)- pyrimidinedione 5'-phosphate
VagYM4_37190	COG0583	DNA-binding transcription factor activity
VagYM4_37200	COG1597	lipid kinase activity
VagYM4_37210	COG3111	PFAM Bacterial OB fold (BOF) protein
VagYM4_37270	COG0501	Belongs to the peptidase M48B family
VagYM4_37280	COG1704	LemA family
VagYM4_37290	COG3069	C4-dicarboxylate transmembrane transporter activity
VagYM4_37310	COG1214	PFAM Peptidase M22, glycoprotease
VagYM4_37310	COG0456	acetyltransferase
VagYM4_37350	COG1161	Required for a late step of 50S ribosomal subunit assembly. Has GTPase activity
VagYM4_37370	COG3706	GGDEF domain
VagYM4_37390	COG2197	response regulator
VagYM4_37400	COG0784	Response regulator, receiver
VagYM4_37400	COG0835	chemotaxis
VagYM4_37430	COG2962	Rard protein
VagYM4_37530	COG0471	metal ion transport
VagYM4_37540	COG3290	protein histidine kinase activity
VagYM4_37550	COG4565	transcriptional regulatory protein
VagYM4_37580	COG0376	Bifunctional enzyme with both catalase and broad- spectrum peroxidase activity
VagYM4_37590	COG5642	Protein of unknown function (DUF2384)
VagYM4_37610	COG1835	transferase activity, transferring acyl groups other than amino-acyl groups
VagYM4_37610	COG2755	lipolytic protein G-D-S-L family
VagYM4_37630	COG1902	pentaerythritol trinitrate reductase activity
VagYM4_37640	COG0346	lactoylglutathione lyase activity
VagYM4_37680	COG2239	Acts as a magnesium transporter
VagYM4_37720	COG0242	peptide deformylase activity
VagYM4_37800	COG2176	DNA-directed DNA polymerase activity
VagYM4_37860	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
VagYM4_37870	COG0346	lactoylglutathione lyase activity
VagYM4_37940	COG1979	alcohol dehydrogenase
VagYM4_37950	COG2207	Transcriptional regulator
VagYM4_37970	COG0448	Catalyzes the synthesis of ADP-glucose, a sugar donor used in elongation reactions on alpha-glucans
VagYM4_37980	COG2759	Belongs to the formate--tetrahydrofolate ligase family
VagYM4_37990	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
VagYM4_38030	COG0546	phosphoglycolate phosphatase activity
VagYM4_38040	COG0840	transmembrane signaling receptor activity
VagYM4_38070	COG0513	Belongs to the DEAD box helicase family
VagYM4_38080	COG4943	cyclic-guanylate-specific phosphodiesterase activity
VagYM4_38110	COG3038	cytochrome b561
VagYM4_38120	COG2353	YceI-like domain
VagYM4_38130	COG2116	formate transmembrane transporter activity
VagYM4_38140	COG0583	DNA-binding transcription factor activity
VagYM4_38160	COG3593	DNA synthesis involved in DNA repair
VagYM4_38170	COG0737	Belongs to the 5'-nucleotidase family
VagYM4_38230	COG2267	carboxylic ester hydrolase activity
VagYM4_38240	COG2067	long-chain fatty acid transport protein
VagYM4_38270	COG2050	protein possibly involved in aromatic compounds catabolism
VagYM4_38290	COG4533	DNA binding
VagYM4_38360	COG1716	ATPase activity
VagYM4_38360	COG5001	Diguanylate cyclase
VagYM4_38370	COG3007	enoyl-[acyl-carrier-protein] reductase (NADH) activity
VagYM4_38390	COG4181	ATPase activity
VagYM4_38400	COG3127	ABC-type transport system involved in lysophospholipase L1, biosynthesis, permease component
VagYM4_38420	COG1984	allophanate hydrolase subunit 2
VagYM4_38430	COG2049	5-oxoprolinase (ATP-hydrolyzing) activity
VagYM4_38440	COG1540	5-oxoprolinase (ATP-hydrolyzing) activity
VagYM4_38450	COG5002	protein histidine kinase activity
VagYM4_38450	COG5001	Diguanylate cyclase
VagYM4_38450	COG3447	MASE1 domain protein
VagYM4_38460	COG1087	Belongs to the NAD(P)-dependent epimerase dehydratase family
VagYM4_38480	COG0583	DNA-binding transcription factor activity
VagYM4_38490	COG1042	CoA-binding domain protein
VagYM4_38490	COG0045	succinate-CoA ligase (ADP-forming) activity
VagYM4_38490	COG1670	COG1670 acetyltransferases, including N-acetylases of ribosomal proteins
VagYM4_38510	COG1181	Belongs to the D-alanine--D-alanine ligase family
VagYM4_38530	COG0023	Translation Initiation Factor
VagYM4_38550	COG4128	Pfam Zonular occludens toxin
VagYM4_38650	COG4128	Pfam Zonular occludens toxin
VagYM4_38770	COG0583	DNA-binding transcription factor activity
VagYM4_38790	COG0589	response to stress
VagYM4_38800	COG3140	Belongs to the UPF0181 family
VagYM4_38850	COG1282	The transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane
VagYM4_38860	COG3288	NAD(P)+ transhydrogenase (AB-specific) activity
VagYM4_38910	COG4251	negative regulation of phosphorylation
VagYM4_38910	COG2203	Gaf domain
VagYM4_38910	COG3706	GGDEF domain
VagYM4_38910	COG5001	Diguanylate cyclase
VagYM4_38930	COG4148	Part of the ABC transporter complex ModABC involved in molybdenum import. Responsible for energy coupling to the transport system
VagYM4_38940	COG4149	molybdate abc transporter
VagYM4_38950	COG0725	ABC transporter, periplasmic molybdate-binding protein
VagYM4_38990	COG0189	ligase activity
VagYM4_38990	COG4067	protein conserved in archaea
VagYM4_39010	COG2207	Transcriptional regulator
VagYM4_39020	COG0534	Mate efflux family protein
VagYM4_39030	COG0602	queuosine metabolic process
VagYM4_39040	COG1328	CTP reductase activity
VagYM4_39070	COG0841	Belongs to the resistance-nodulation-cell division (RND) (TC 2.A.6) family
VagYM4_39130	COG1794	racemase activity, acting on amino acids and derivatives
VagYM4_39140	COG0384	phenazine biosynthesis protein PhzF
VagYM4_39160	COG0243	molybdopterin cofactor binding
VagYM4_39170	COG0583	DNA-binding transcription factor activity
VagYM4_39180	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
VagYM4_39200	COG2197	response regulator
VagYM4_39210	COG3851	Histidine kinase
VagYM4_39220	COG2271	Major facilitator Superfamily
VagYM4_39270	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
VagYM4_39280	COG3118	belongs to the thioredoxin family
VagYM4_39350	COG2704	Responsible for the transport of C4-dicarboxylates from the periplasm across the inner membrane
VagYM4_39390	COG2116	formate transmembrane transporter activity
VagYM4_39410	COG1251	Belongs to the nitrite and sulfite reductase 4Fe-4S domain family
VagYM4_39420	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
VagYM4_39430	COG5001	Diguanylate cyclase
VagYM4_39530	COG0787	Catalyzes the interconversion of L-alanine and D- alanine. May also act on other amino acids
VagYM4_39600	COG0277	FAD linked oxidase domain protein
VagYM4_39610	COG0583	DNA-binding transcription factor activity
VagYM4_39620	COG2425	protein containing a von Willebrand factor type A (vWA) domain
VagYM4_39650	COG2008	Catalyzes the cleavage of L-allo-threonine and L- threonine to glycine and acetaldehyde
VagYM4_39670	COG1288	antiporter activity
VagYM4_39690	COG3040	lipid binding
VagYM4_39710	COG0419	ATPase involved in DNA repair
VagYM4_39720	COG0420	3'-5' exonuclease activity
VagYM4_39750	COG3501	Rhs element vgr protein
VagYM4_39860	COG0631	protein serine/threonine phosphatase activity
VagYM4_39930	COG2815	serine threonine protein kinase
VagYM4_39930	COG0515	serine threonine protein kinase
VagYM4_39970	COG0745	RESPONSE REGULATOR receiver
VagYM4_39990	COG0625	glutathione transferase activity
VagYM4_40030	COG2146	nitrite reductase [NAD(P)H] activity
VagYM4_40030	COG1251	Belongs to the nitrite and sulfite reductase 4Fe-4S domain family
VagYM4_40040	COG1116	anion transmembrane transporter activity
VagYM4_40050	COG0600	ABC-type nitrate sulfonate bicarbonate transport system permease component
VagYM4_40060	COG0715	COG0715 ABC-type nitrate sulfonate bicarbonate transport systems periplasmic components
VagYM4_40060	COG1116	anion transmembrane transporter activity
VagYM4_40110	COG0243	molybdopterin cofactor binding
VagYM4_40130	COG0814	amino acid
VagYM4_40150	COG3706	GGDEF domain
VagYM4_40250	COG2847	Copper chaperone PCu(A)C
VagYM4_40260	COG0443	Heat shock 70 kDa protein
VagYM4_40390	COG4160	amino acid transport
VagYM4_40400	COG4215	(ABC) transporter
VagYM4_40410	COG0834	ABC-type amino acid transport signal transduction systems periplasmic component domain
VagYM4_40420	COG1126	abc transporter atp-binding protein
VagYM4_40480	COG1292	Belongs to the BCCT transporter (TC 2.A.15) family
VagYM4_40500	COG1012	belongs to the aldehyde dehydrogenase family
VagYM4_40540	COG0446	pyridine nucleotide-disulphide oxidoreductase
VagYM4_40540	COG1902	pentaerythritol trinitrate reductase activity
VagYM4_40560	COG0109	protoheme IX farnesyltransferase activity
VagYM4_40570	COG3125	oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor
VagYM4_40580	COG1845	cytochrome c oxidase, subunit III
VagYM4_40590	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
VagYM4_40600	COG1622	oxidoreductase activity, acting on a heme group of donors, oxygen as acceptor
VagYM4_40610	COG1028	Short-chain dehydrogenase reductase Sdr
VagYM4_40630	COG1024	Enoyl-CoA hydratase
VagYM4_40640	COG1024	Enoyl-CoA hydratase
VagYM4_40670	COG0183	Belongs to the thiolase family
VagYM4_40690	COG1960	acyl-CoA dehydrogenase activity
VagYM4_40700	COG4799	Acetyl-CoA carboxylase, carboxyltransferase component subunits alpha and beta
VagYM4_40710	COG1024	Enoyl-CoA hydratase
VagYM4_40730	COG5413	integral membrane protein
VagYM4_40750	COG0247	lactate metabolic process
VagYM4_40750	COG0277	FAD linked oxidase domain protein
VagYM4_40860	COG0282	Catalyzes the formation of acetyl phosphate from acetate and ATP. Can also catalyze the reverse reaction
VagYM4_40880	COG0513	Belongs to the DEAD box helicase family
VagYM4_40890	COG4776	Involved in mRNA degradation. Hydrolyzes single-stranded polyribonucleotides processively in the 3' to 5' direction
VagYM4_40940	COG0840	transmembrane signaling receptor activity
VagYM4_40950	COG1119	ATPase activity
VagYM4_40960	COG2200	EAL domain
VagYM4_41010	COG0513	Belongs to the DEAD box helicase family
VagYM4_41020	COG0523	cobalamin synthesis protein
VagYM4_41040	COG2039	Removes 5-oxoproline from various penultimate amino acid residues except L-proline
VagYM4_41060	COG1278	Cold shock
VagYM4_41070	COG0557	exoribonuclease II activity
VagYM4_41080	COG0133	tryptophan synthase activity
VagYM4_41100	COG4628	conserved protein (DUF2132)
VagYM4_41110	COG0513	Belongs to the DEAD box helicase family
VagYM4_41130	COG0730	response to heat
VagYM4_41160	COG0697	spore germination
VagYM4_41170	COG1982	Orn Lys Arg decarboxylase major
VagYM4_41180	COG1335	isochorismatase
VagYM4_41200	COG1404	Belongs to the peptidase S8 family
VagYM4_41230	COG3530	Putative quorum-sensing-regulated virulence factor
VagYM4_41280	COG3186	Phenylalanine-4-hydroxylase
VagYM4_41290	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
VagYM4_41300	COG2227	3-demethylubiquinone-9 3-O-methyltransferase activity
VagYM4_41350	COG3155	Displays glyoxalase activity, catalyzing the conversion of glyoxal to glycolate
VagYM4_41360	COG1454	alcohol dehydrogenase
VagYM4_41370	COG2133	pyrroloquinoline quinone binding
VagYM4_41390	COG0783	Belongs to the Dps family
VagYM4_41400	COG0840	transmembrane signaling receptor activity
VagYM4_41420	COG0577	efflux transmembrane transporter activity
VagYM4_41420	COG1136	(ABC) transporter
VagYM4_41460	COG2199	diguanylate cyclase activity
VagYM4_41470	COG3036	rescue of stalled ribosome
VagYM4_41480	COG1278	Cold shock
VagYM4_41520	COG2885	chlorophyll binding
VagYM4_41540	COG0545	Peptidyl-prolyl cis-trans isomerase
VagYM4_41550	COG0109	protoheme IX farnesyltransferase activity
VagYM4_41560	COG1612	heme a metabolic process
VagYM4_41600	COG3175	Exerts its effect at some terminal stage of cytochrome c oxidase synthesis, probably by being involved in the insertion of the copper B into subunit I
VagYM4_41610	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
VagYM4_41620	COG1622	oxidoreductase activity, acting on a heme group of donors, oxygen as acceptor
VagYM4_41630	COG1109	Catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate
VagYM4_41650	COG1280	lysine exporter protein (LysE YggA)
VagYM4_41660	COG2207	Transcriptional regulator
VagYM4_41690	COG0179	Fumarylacetoacetate (FAA) hydrolase
VagYM4_41730	COG0697	spore germination
VagYM4_41770	COG2814	Major facilitator Superfamily
VagYM4_41780	COG0583	DNA-binding transcription factor activity
VagYM4_41790	COG5001	Diguanylate cyclase
VagYM4_41800	COG0739	heme binding
VagYM4_41860	COG0840	transmembrane signaling receptor activity
VagYM4_41880	COG0814	amino acid
VagYM4_41910	COG1387	Histidinol phosphatase and related hydrolases of the PHP family
VagYM4_41920	COG1072	(Pantothenic acid kinase))
VagYM4_41940	COG1063	alcohol dehydrogenase
VagYM4_41950	COG2213	PTS system mannitol-specific
VagYM4_41960	COG1762	phosphoenolpyruvate-dependent sugar phosphotransferase system
VagYM4_41990	COG0798	PFAM Bile acid sodium symporter
VagYM4_42010	COG1881	PFAM PEBP family protein
VagYM4_42030	COG2706	6-phosphogluconolactonase activity
VagYM4_42050	COG1131	(ABC) transporter
VagYM4_42060	COG0842	Transport permease protein
VagYM4_42090	COG3383	formate dehydrogenase (NAD+) activity
VagYM4_42130	COG3696	Belongs to the resistance-nodulation-cell division (RND) (TC 2.A.6) family
VagYM4_42190	COG1670	COG1670 acetyltransferases, including N-acetylases of ribosomal proteins
VagYM4_42210	COG2067	long-chain fatty acid transport protein
VagYM4_42230	COG0845	Belongs to the membrane fusion protein (MFP) (TC 8.A.1) family
VagYM4_42260	COG1505	serine-type exopeptidase activity
VagYM4_42270	COG0488	(ABC) transporter
VagYM4_42280	COG0589	response to stress
VagYM4_42290	COG2249	NAD(P)H dehydrogenase (quinone) activity
VagYM4_42330	COG0366	Alpha amylase catalytic
VagYM4_42340	COG0789	Transcriptional regulator
VagYM4_42370	COG4934	collagen metabolic process
VagYM4_42390	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
VagYM4_42400	COG0583	DNA-binding transcription factor activity
VagYM4_42470	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
VagYM4_42480	COG0784	Response regulator, receiver
VagYM4_42480	COG0835	chemotaxis
VagYM4_42500	COG0748	coenzyme F420 binding
VagYM4_42510	COG3721	Heme iron utilization protein
VagYM4_42530	COG0810	Interacts with outer membrane receptor proteins that carry out high-affinity binding and energy dependent uptake into the periplasmic space of specific substrates. It could act to transduce energy from the cytoplasmic membrane to specific energy- requiring processes in the outer membrane, resulting in the release into the periplasm of ligands bound by these outer membrane proteins
VagYM4_42540	COG0811	peptide transport
VagYM4_42550	COG0848	biopolymer transport protein
VagYM4_42570	COG0609	Belongs to the binding-protein-dependent transport system permease family. FecCD subfamily
VagYM4_42580	COG4559	Part of the ABC transporter complex HmuTUV involved in hemin import. Responsible for energy coupling to the transport system
VagYM4_42670	COG1057	Catalyzes the reversible adenylation of nicotinate mononucleotide (NaMN) to nicotinic acid adenine dinucleotide (NaAD)
VagYM4_42680	COG0171	NAD+ synthase (glutamine-hydrolyzing) activity
VagYM4_42690	COG3217	Mosc domain protein beta barrel domain protein
VagYM4_42690	COG0633	Ferredoxin
VagYM4_42690	COG3217	Mosc domain protein beta barrel domain protein
VagYM4_42690	COG0633	Ferredoxin
VagYM4_42700	COG0401	homolog of Blt101
VagYM4_42710	COG0418	dihydroorotase activity
VagYM4_42720	COG2354	Protein conserved in bacteria
VagYM4_42780	COG3833	ABC-type maltose transport systems, permease component
VagYM4_42790	COG1175	transmembrane transport
VagYM4_42810	COG3842	ATPase activity
VagYM4_42820	COG2148	undecaprenyl-phosphate glucose phosphotransferase activity
VagYM4_42940	COG1309	transcriptional regulator
VagYM4_42950	COG2130	NADP-dependent
VagYM4_42970	COG0753	catalase activity
VagYM4_42980	COG2084	Dehydrogenase
VagYM4_42990	COG1299	protein-N(PI)-phosphohistidine-fructose phosphotransferase system transporter activity
VagYM4_43000	COG1445	protein-N(PI)-phosphohistidine-fructose phosphotransferase system transporter activity
VagYM4_43020	COG2207	Transcriptional regulator
VagYM4_43030	COG1762	phosphoenolpyruvate-dependent sugar phosphotransferase system
VagYM4_43030	COG1445	protein-N(PI)-phosphohistidine-fructose phosphotransferase system transporter activity
VagYM4_43030	COG1299	protein-N(PI)-phosphohistidine-fructose phosphotransferase system transporter activity
VagYM4_43060	COG0637	HAD-superfamily hydrolase subfamily IA, variant 3
VagYM4_43070	COG3241	Transfers electrons from cytochrome c551 to cytochrome oxidase
VagYM4_43080	COG1455	protein-N(PI)-phosphohistidine-lactose phosphotransferase system transporter activity
VagYM4_43100	COG0665	tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase activity
VagYM4_43110	COG1251	Belongs to the nitrite and sulfite reductase 4Fe-4S domain family
VagYM4_43120	COG1012	belongs to the aldehyde dehydrogenase family
VagYM4_43150	COG0583	DNA-binding transcription factor activity
VagYM4_43160	COG0168	Low-affinity potassium transport system. Interacts with trk system potassium uptake protein TrkA
VagYM4_43170	COG0569	domain protein
VagYM4_43190	COG2205	protein histidine kinase activity
VagYM4_43190	COG2205	protein histidine kinase activity
VagYM4_43200	COG1132	(ABC) transporter
VagYM4_43210	COG4774	siderophore transport
VagYM4_43220	COG1120	ATPase activity
VagYM4_43230	COG4594	ABC-type Fe3 -citrate transport system, periplasmic component
VagYM4_43300	COG2197	response regulator
VagYM4_43320	COG0840	transmembrane signaling receptor activity
VagYM4_43330	COG0714	Associated with various cellular activities
VagYM4_43360	COG2304	oxidoreductase activity
VagYM4_43370	COG2304	oxidoreductase activity
VagYM4_43400	COG1117	ATPase-coupled phosphate ion transmembrane transporter activity
VagYM4_43410	COG0581	inorganic phosphate transmembrane transporter activity
VagYM4_43420	COG0573	inorganic phosphate transmembrane transporter activity
VagYM4_43480	COG4771	TonB-dependent receptor
VagYM4_43490	COG1770	oligopeptidase
VagYM4_43500	COG0513	Belongs to the DEAD box helicase family
VagYM4_43520	COG1376	ErfK ybiS ycfS ynhG family protein
VagYM4_43520	COG1388	LysM domain
VagYM4_43530	COG0415	Belongs to the DNA photolyase family
VagYM4_43540	COG0789	Transcriptional regulator
VagYM4_43550	COG3272	Protein of unknown function (DUF1722)
VagYM4_43560	COG0813	purine-nucleoside phosphorylase activity
VagYM4_43590	COG3706	GGDEF domain
VagYM4_43610	COG1566	PFAM secretion protein HlyD family protein
VagYM4_43620	COG4720	Psort location CytoplasmicMembrane, score
VagYM4_43630	COG1122	ATPase activity
VagYM4_43670	COG0348	domain, Protein
VagYM4_43680	COG0437	4 iron, 4 sulfur cluster binding
VagYM4_43690	COG1247	-acetyltransferase
VagYM4_43730	COG3203	Forms passive diffusion pores that allow small molecular weight hydrophilic materials across the outer membrane
VagYM4_43740	COG0840	transmembrane signaling receptor activity
VagYM4_43750	COG1067	ATP-dependent peptidase activity
VagYM4_43770	COG4172	Belongs to the ABC transporter superfamily
VagYM4_43780	COG1505	serine-type exopeptidase activity
VagYM4_43790	COG0583	DNA-binding transcription factor activity
VagYM4_43800	COG1620	l-lactate permease
VagYM4_43810	COG1304	FMN binding
VagYM4_43830	COG0668	transmembrane transport
VagYM4_43850	COG1063	alcohol dehydrogenase
VagYM4_43860	COG0156	8-amino-7-oxononanoate synthase activity
VagYM4_43870	COG5001	Diguanylate cyclase
VagYM4_43870	COG3300	MHYT domain
VagYM4_43880	COG0834	ABC-type amino acid transport signal transduction systems periplasmic component domain
VagYM4_43920	COG0745	RESPONSE REGULATOR receiver
VagYM4_43970	COG0346	lactoylglutathione lyase activity
VagYM4_44080	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
VagYM4_44160	COG1987	bacterial-type flagellum assembly
VagYM4_44180	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
VagYM4_44210	COG1344	Flagellin is the subunit protein which polymerizes to form the filaments of bacterial flagella
VagYM4_44250	COG1345	Required for morphogenesis and for the elongation of the flagellar filament by facilitating polymerization of the flagellin monomers at the tip of growing filament. Forms a capping structure, which prevents flagellin subunits (transported through the central channel of the flagellum) from leaking out without polymerization at the distal end
VagYM4_44260	COG1516	flagellar protein fliS
VagYM4_44290	COG1580	Controls the rotational direction of flagella during chemotaxis
VagYM4_44300	COG1191	sigma factor activity
VagYM4_44310	COG1291	archaeal or bacterial-type flagellum-dependent cell motility
VagYM4_44320	COG1360	Flagellar Motor Protein
VagYM4_44420	COG1882	Formate acetyltransferase
VagYM4_44430	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
VagYM4_44440	COG0176	Transaldolase is important for the balance of metabolites in the pentose-phosphate pathway
VagYM4_44460	COG0454	-acetyltransferase
VagYM4_44480	COG2814	Major facilitator Superfamily
VagYM4_44560	COG0628	permease
VagYM4_44570	COG3110	Uncharacterized protein conserved in bacteria (DUF2057)
VagYM4_44580	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
VagYM4_44600	COG4628	conserved protein (DUF2132)
VagYM4_44610	COG0583	DNA-binding transcription factor activity
VagYM4_44660	COG1686	Belongs to the peptidase S11 family
VagYM4_44710	COG0415	Belongs to the DNA photolyase family
VagYM4_44720	COG2335	COG2335, Secreted and surface protein containing fasciclin-like repeats
VagYM4_44730	COG3397	chitin binding
VagYM4_44740	COG4667	esterase of the alpha-beta hydrolase superfamily
VagYM4_44750	COG2095	MarC family integral membrane protein
VagYM4_44780	COG1596	polysaccharide export
VagYM4_44820	COG1301	dicarboxylic acid transport
VagYM4_44830	COG3339	Conserved Protein
VagYM4_44850	COG0700	Nucleoside recognition
VagYM4_44860	COG3366	ferrous iron transmembrane transporter activity
VagYM4_44880	COG0366	Alpha amylase catalytic
VagYM4_44890	COG0744	Peptidoglycan polymerase that catalyzes glycan chain elongation from lipid-linked precursors
VagYM4_44900	COG0296	Catalyzes the formation of the alpha-1,6-glucosidic linkages in glycogen by scission of a 1,4-alpha-linked oligosaccharide from growing alpha-1,4-glucan chains and the subsequent attachment of the oligosaccharide to the alpha-1,6 position
VagYM4_44910	COG1640	4-alpha-glucanotransferase
VagYM4_44920	COG0058	SHG alpha-glucan phosphorylase activity
VagYM4_44930	COG2909	trisaccharide binding
VagYM4_44960	COG1999	signal sequence binding
VagYM4_44970	COG1264	protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
VagYM4_44970	COG1263	PTS System
VagYM4_44980	COG1162	GTPase activity
VagYM4_44990	COG3633	Involved in the import of serine and threonine into the cell, with the concomitant import of sodium (symport system)
VagYM4_45000	COG2240	Pyridoxal kinase involved in the salvage pathway of pyridoxal 5'-phosphate (PLP). Catalyzes the phosphorylation of pyridoxal to PLP
VagYM4_45020	COG0531	amino acid
VagYM4_45030	COG1982	Orn Lys Arg decarboxylase major
VagYM4_45070	COG2356	endonuclease I
VagYM4_45110	COG4580	involved in the transport of maltose and maltodextrins
VagYM4_45190	COG0739	heme binding
VagYM4_45200	COG0612	Peptidase, M16
VagYM4_45210	COG0840	transmembrane signaling receptor activity
VagYM4_45220	COG1120	ATPase activity
VagYM4_45230	COG0609	Belongs to the binding-protein-dependent transport system permease family. FecCD subfamily
VagYM4_45240	COG0609	Belongs to the binding-protein-dependent transport system permease family. FecCD subfamily
VagYM4_45250	COG4594	ABC-type Fe3 -citrate transport system, periplasmic component
VagYM4_45260	COG4772	TonB-dependent receptor
VagYM4_45310	COG4264	IucA IucC family
VagYM4_45320	COG0019	diaminopimelate decarboxylase activity
VagYM4_45330	COG1653	transport
VagYM4_45350	COG0745	RESPONSE REGULATOR receiver
VagYM4_45420	COG0463	Glycosyl transferase, family 2
VagYM4_45450	COG1136	(ABC) transporter
VagYM4_45490	COG1764	response to oxidative stress
VagYM4_45500	COG1846	Transcriptional regulator
VagYM4_45520	COG3634	alkyl hydroperoxide reductase activity
VagYM4_45570	COG1595	DNA-templated transcription, initiation
VagYM4_45610	COG2258	MOSC domain
VagYM4_45660	COG2207	Transcriptional regulator
VagYM4_45680	COG1132	(ABC) transporter
VagYM4_45770	COG0591	Belongs to the sodium solute symporter (SSF) (TC 2.A.21) family
VagYM4_45820	COG0259	pyridoxamine-phosphate oxidase activity
VagYM4_45920	COG4166	transmembrane transport
VagYM4_45950	COG2103	Specifically catalyzes the cleavage of the D-lactyl ether substituent of MurNAc 6-phosphate, producing GlcNAc 6- phosphate and D-lactate
VagYM4_45960	COG1264	protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
VagYM4_45960	COG1263	PTS System
VagYM4_45970	COG3203	Forms passive diffusion pores that allow small molecular weight hydrophilic materials across the outer membrane
VagYM4_46010	COG1444	tRNA N-acetyltransferase activity