locus-tag	class	description
LY388_00005	COG0513	Belongs to the DEAD box helicase family
LY388_00010	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
LY388_00015	COG0583	DNA-binding transcription factor activity
LY388_00025	COG0516	GMP reductase activity
LY388_00035	COG1226	(belongs to the monovalent cation proton antiporter 2 (CPA2) transporter (TC 2.A.37) family)
LY388_00045	COG1052	Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family
LY388_00050	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
LY388_00050	COG0063	ADP-dependent NAD(P)H-hydrate dehydratase activity
LY388_00075	COG3036	rescue of stalled ribosome
LY388_00080	COG1278	Cold shock
LY388_00085	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
LY388_00085	COG1017	nitric oxide dioxygenase activity
LY388_00090	COG3604	Transcriptional regulator
LY388_00100	COG2195	Cleaves the N-terminal amino acid of tripeptides
LY388_00105	COG1972	Belongs to the concentrative nucleoside transporter (CNT) (TC 2.A.41) family
LY388_00120	COG0840	transmembrane signaling receptor activity
LY388_00125	COG0714	Associated with various cellular activities
LY388_00145	COG2304	oxidoreductase activity
LY388_00160	COG1278	Cold shock
LY388_00165	COG5002	protein histidine kinase activity
LY388_00165	COG5001	Diguanylate cyclase
LY388_00175	COG3530	Putative quorum-sensing-regulated virulence factor
LY388_00185	COG0814	amino acid
LY388_00190	COG0589	response to stress
LY388_00200	COG2111	Na H antiporter
LY388_00200	COG1009	NADH ubiquinone oxidoreductase subunit 5 chain L Multisubunit Na H antiporter, MnhA subunit
LY388_00205	COG1006	Multisubunit Na H antiporter MnhC subunit
LY388_00210	COG0651	ATP synthesis coupled electron transport
LY388_00215	COG1863	multisubunit Na H antiporter MnhE subunit
LY388_00220	COG2212	antiporter activity
LY388_00225	COG1320	monovalent cation:proton antiporter activity
LY388_00235	COG0242	peptide deformylase activity
LY388_00245	COG0579	oxidoreductase
LY388_00280	COG2271	Major facilitator Superfamily
LY388_00285	COG0584	glycerophosphoryl diester phosphodiesterase
LY388_00295	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
LY388_00305	COG1609	Transcriptional regulator
LY388_00310	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
LY388_00315	COG1879	ABC-type sugar transport system periplasmic component
LY388_00320	COG1172	Belongs to the binding-protein-dependent transport system permease family
LY388_00325	COG1129	ABC transporter
LY388_00330	COG1869	D-ribose catabolic process
LY388_00345	COG3409	Peptidoglycan-binding domain 1 protein
LY388_00345	COG3501	Rhs element vgr protein
LY388_00370	COG3829	transcription factor binding
LY388_00435	COG0564	pseudouridine synthase activity
LY388_00445	COG0637	HAD-superfamily hydrolase subfamily IA, variant 3
LY388_00450	COG2771	luxR family
LY388_00450	COG2200	EAL domain
LY388_00460	COG0673	inositol 2-dehydrogenase activity
LY388_00465	COG1488	Catalyzes the synthesis of beta-nicotinate D- ribonucleotide from nicotinate and 5-phospho-D-ribose 1-phosphate at the expense of ATP
LY388_00495	COG1342	Belongs to the UPF0251 family
LY388_00505	COG1301	dicarboxylic acid transport
LY388_00525	COG2814	Major facilitator Superfamily
LY388_00530	COG0583	DNA-binding transcription factor activity
LY388_00535	COG3300	MHYT domain
LY388_00535	COG5001	Diguanylate cyclase
LY388_00540	COG0739	heme binding
LY388_00550	COG0659	secondary active sulfate transmembrane transporter activity
LY388_00555	COG3314	Sporulation integral membrane protein YlbJ
LY388_00575	COG1117	ATPase-coupled phosphate ion transmembrane transporter activity
LY388_00580	COG0581	inorganic phosphate transmembrane transporter activity
LY388_00585	COG0573	inorganic phosphate transmembrane transporter activity
LY388_00590	COG0226	Part of the ABC transporter complex PstSACB involved in phosphate import
LY388_00620	COG1770	oligopeptidase
LY388_00625	COG0513	Belongs to the DEAD box helicase family
LY388_00635	COG1388	LysM domain
LY388_00635	COG1376	ErfK ybiS ycfS ynhG family protein
LY388_00640	COG0415	Belongs to the DNA photolyase family
LY388_00650	COG3272	Protein of unknown function (DUF1722)
LY388_00655	COG0813	purine-nucleoside phosphorylase activity
LY388_00680	COG1566	PFAM secretion protein HlyD family protein
LY388_00700	COG0786	glutamate:sodium symporter activity
LY388_00715	COG1999	signal sequence binding
LY388_00725	COG3633	Involved in the import of serine and threonine into the cell, with the concomitant import of sodium (symport system)
LY388_00730	COG0671	phosphoesterase, PA-phosphatase related
LY388_00770	COG3110	Uncharacterized protein conserved in bacteria (DUF2057)
LY388_00775	COG0471	metal ion transport
LY388_00810	COG3501	Rhs element vgr protein
LY388_00820	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
LY388_00825	COG1640	4-alpha-glucanotransferase
LY388_00830	COG0058	SHG alpha-glucan phosphorylase activity
LY388_00835	COG2909	trisaccharide binding
LY388_00850	COG2084	Dehydrogenase
LY388_00855	COG0217	transcriptional regulatory protein
LY388_00890	COG0687	Required for the activity of the bacterial periplasmic transport system of putrescine
LY388_00895	COG1444	tRNA N-acetyltransferase activity
LY388_00930	COG0642	Histidine kinase
LY388_00935	COG2194	sulfuric ester hydrolase activity
LY388_00945	COG1173	ABC-type dipeptide oligopeptide nickel transport systems, permease components
LY388_00950	COG0601	transmembrane transport
LY388_00970	COG2198	Histidine kinase
LY388_00970	COG0643	Histidine kinase
LY388_00975	COG0835	chemotaxis
LY388_00980	COG0835	chemotaxis
LY388_00985	COG0840	transmembrane signaling receptor activity
LY388_00990	COG1352	Methylation of the membrane-bound methyl-accepting chemotaxis proteins (MCP) to form gamma-glutamyl methyl ester residues in MCP
LY388_01015	COG0745	RESPONSE REGULATOR receiver
LY388_01055	COG1262	PFAM Formylglycine-generating sulfatase enzyme
LY388_01080	COG0591	Belongs to the sodium solute symporter (SSF) (TC 2.A.21) family
LY388_01110	COG1982	Orn Lys Arg decarboxylase major
LY388_01115	COG0531	amino acid
LY388_01125	COG1901	pseudouridine methyltransferase
LY388_01140	COG4221	oxidoreductase activity
LY388_01155	COG2910	NAD(P)H-binding
LY388_01165	COG1335	isochorismatase
LY388_01180	COG0697	spore germination
LY388_01210	COG3722	fumarate hydratase activity
LY388_01215	COG0246	Mannitol dehydrogenase
LY388_01220	COG2213	PTS system mannitol-specific
LY388_01220	COG4668	phosphoenolpyruvate-dependent sugar phosphotransferase system
LY388_01225	COG1109	Catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate
LY388_01230	COG4597	amino acid ABC transporter
LY388_01235	COG0834	ABC-type amino acid transport signal transduction systems periplasmic component domain
LY388_01245	COG1126	abc transporter atp-binding protein
LY388_01250	COG0722	Stereospecific condensation of phosphoenolpyruvate (PEP) and D-erythrose-4-phosphate (E4P) giving rise to 3-deoxy-D- arabino-heptulosonate-7-phosphate (DAHP)
LY388_01260	COG0840	transmembrane signaling receptor activity
LY388_01275	COG0840	transmembrane signaling receptor activity
LY388_01290	COG4580	involved in the transport of maltose and maltodextrins
LY388_01305	COG0363	glucosamine-6-phosphate deaminase activity
LY388_01330	COG2259	Doxx family
LY388_01335	COG0122	3-methyladenine DNA glycosylase 8-oxoguanine DNA glycosylase
LY388_01340	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
LY388_01350	COG0471	metal ion transport
LY388_01360	COG4565	transcriptional regulatory protein
LY388_01365	COG1055	Involved in arsenical resistance. Thought to form the channel of an arsenite pump
LY388_01370	COG3366	ferrous iron transmembrane transporter activity
LY388_01375	COG0700	Nucleoside recognition
LY388_01385	COG0697	spore germination
LY388_01390	COG3203	Forms passive diffusion pores that allow small molecular weight hydrophilic materials across the outer membrane
LY388_01395	COG1764	response to oxidative stress
LY388_01400	COG1846	Transcriptional regulator
LY388_01420	COG2207	Transcriptional regulator
LY388_01425	COG1280	lysine exporter protein (LysE YggA)
LY388_01435	COG1902	pentaerythritol trinitrate reductase activity
LY388_01445	COG1132	(ABC) transporter
LY388_01455	COG0513	Belongs to the DEAD box helicase family
LY388_01465	COG0840	transmembrane signaling receptor activity
LY388_01475	COG1806	Bifunctional serine threonine kinase and phosphorylase involved in the regulation of the
LY388_01490	COG1620	l-lactate permease
LY388_01500	COG0583	DNA-binding transcription factor activity
LY388_01525	COG4172	Belongs to the ABC transporter superfamily
LY388_01535	COG1067	ATP-dependent peptidase activity
LY388_01540	COG0840	transmembrane signaling receptor activity
LY388_01550	COG2211	Major facilitator Superfamily
LY388_01560	COG3123	guanosine phosphorylase activity
LY388_01565	COG1741	Belongs to the pirin family
LY388_01575	COG5001	Diguanylate cyclase
LY388_01580	COG0583	DNA-binding transcription factor activity
LY388_01615	COG3706	GGDEF domain
LY388_01620	COG1846	Transcriptional regulator
LY388_01625	COG0784	Response regulator, receiver
LY388_01625	COG0835	chemotaxis
LY388_01630	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
LY388_01640	COG0393	Putative heavy-metal-binding
LY388_01655	COG1670	COG1670 acetyltransferases, including N-acetylases of ribosomal proteins
LY388_01660	COG3842	ATPase activity
LY388_01670	COG1175	transmembrane transport
LY388_01675	COG3833	ABC-type maltose transport systems, permease component
LY388_01690	COG1349	DNA-binding transcription factor activity
LY388_01695	COG2199	diguanylate cyclase activity
LY388_01720	COG1278	Cold shock
LY388_01725	COG2206	PFAM metal-dependent phosphohydrolase, HD sub domain
LY388_01730	COG2354	Protein conserved in bacteria
LY388_01735	COG2265	Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family
LY388_01745	COG3152	Membrane
LY388_01755	COG0418	dihydroorotase activity
LY388_01760	COG3217	Mosc domain protein beta barrel domain protein
LY388_01760	COG0633	Ferredoxin
LY388_01760	COG3217	Mosc domain protein beta barrel domain protein
LY388_01760	COG0633	Ferredoxin
LY388_01795	COG4559	Part of the ABC transporter complex HmuTUV involved in hemin import. Responsible for energy coupling to the transport system
LY388_01800	COG0609	Belongs to the binding-protein-dependent transport system permease family. FecCD subfamily
LY388_01805	COG4558	Periplasmic binding protein
LY388_01810	COG0848	biopolymer transport protein
LY388_01815	COG0811	peptide transport
LY388_01820	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
LY388_01830	COG3721	Heme iron utilization protein
LY388_01835	COG0748	coenzyme F420 binding
LY388_01845	COG3835	regulator
LY388_01850	COG2610	gluconate transmembrane transporter activity
LY388_01855	COG1929	Belongs to the glycerate kinase type-1 family
LY388_01880	COG0362	Catalyzes the oxidative decarboxylation of 6- phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH
LY388_01885	COG0363	glucosamine-6-phosphate deaminase activity
LY388_01890	COG0364	Catalyzes the oxidation of glucose 6-phosphate to 6- phosphogluconolactone
LY388_01895	COG2206	PFAM metal-dependent phosphohydrolase, HD sub domain
LY388_01900	COG1387	Histidinol phosphatase and related hydrolases of the PHP family
LY388_01920	COG0346	lactoylglutathione lyase activity
LY388_01945	COG1063	alcohol dehydrogenase
LY388_01960	COG0583	DNA-binding transcription factor activity
LY388_01965	COG3048	D-serine ammonia-lyase activity
LY388_01980	COG1294	oxidase, subunit
LY388_01985	COG1271	oxidase subunit
LY388_01990	COG1167	Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain MocR family and their eukaryotic orthologs
LY388_01995	COG1686	Belongs to the peptidase S11 family
LY388_02005	COG3047	cAMP biosynthetic process
LY388_02015	COG3227	Zinc metalloprotease (Elastase)
LY388_02025	COG2267	carboxylic ester hydrolase activity
LY388_02030	COG2067	long-chain fatty acid transport protein
LY388_02040	COG0366	Alpha amylase catalytic
LY388_02045	COG4989	oxidoreductase activity
LY388_02055	COG1136	(ABC) transporter
LY388_02060	COG1136	(ABC) transporter
LY388_02060	COG0577	efflux transmembrane transporter activity
LY388_02075	COG3275	phosphorelay sensor kinase activity
LY388_02080	COG3279	Response regulator of the LytR AlgR family
LY388_02095	COG0531	amino acid
LY388_02120	COG1765	OsmC-like protein
LY388_02125	COG1253	flavin adenine dinucleotide binding
LY388_02150	COG2264	protein methyltransferase activity
LY388_02165	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
LY388_02170	COG3186	Phenylalanine-4-hydroxylase
LY388_02175	COG2154	pterin-4-alpha-carbinolamine dehydratase
LY388_02185	COG0456	acetyltransferase
LY388_02190	COG0160	Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family
LY388_02195	COG0662	Cupin 2, conserved barrel domain protein
LY388_02200	COG0527	aspartate kinase activity
LY388_02210	COG0459	protein refolding
LY388_02215	COG0234	Binds to Cpn60 in the presence of Mg-ATP and suppresses the ATPase activity of the latter
LY388_02220	COG2239	Acts as a magnesium transporter
LY388_02230	COG1166	arginine decarboxylase activity
LY388_02235	COG0010	Belongs to the arginase family
LY388_02245	COG3227	Zinc metalloprotease (Elastase)
LY388_02250	COG3397	chitin binding
LY388_02255	COG3046	protein related to deoxyribodipyrimidine photolyase
LY388_02265	COG0226	Part of the ABC transporter complex PstSACB involved in phosphate import
LY388_02280	COG0513	Belongs to the DEAD box helicase family
LY388_02290	COG1368	sulfuric ester hydrolase activity
LY388_02295	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
LY388_02325	COG1196	nuclear chromosome segregation
LY388_02665	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
LY388_02690	COG0546	phosphoglycolate phosphatase activity
LY388_02705	COG0484	heat shock protein binding
LY388_02715	COG1716	ATPase activity
LY388_02715	COG5001	Diguanylate cyclase
LY388_02720	COG3007	enoyl-[acyl-carrier-protein] reductase (NADH) activity
LY388_02730	COG4181	ATPase activity
LY388_02735	COG3127	ABC-type transport system involved in lysophospholipase L1, biosynthesis, permease component
LY388_02750	COG1984	allophanate hydrolase subunit 2
LY388_02760	COG1540	5-oxoprolinase (ATP-hydrolyzing) activity
LY388_02765	COG1087	Belongs to the NAD(P)-dependent epimerase dehydratase family
LY388_02770	COG0840	transmembrane signaling receptor activity
LY388_02775	COG0814	amino acid
LY388_02780	COG3124	Converts holo-ACP to apo-ACP by hydrolytic cleavage of the phosphopantetheine prosthetic group from ACP
LY388_02785	COG0513	Belongs to the DEAD box helicase family
LY388_02790	COG1309	transcriptional regulator
LY388_02800	COG2008	Catalyzes the cleavage of L-allo-threonine and L- threonine to glycine and acetaldehyde
LY388_02805	COG0494	nUDIX hydrolase
LY388_02815	COG2425	protein containing a von Willebrand factor type A (vWA) domain
LY388_02825	COG1126	abc transporter atp-binding protein
LY388_02830	COG0834	ABC-type amino acid transport signal transduction systems periplasmic component domain
LY388_02835	COG4215	(ABC) transporter
LY388_02840	COG4160	amino acid transport
LY388_02865	COG3118	belongs to the thioredoxin family
LY388_02870	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
LY388_02875	COG0247	lactate metabolic process
LY388_02885	COG0578	Belongs to the FAD-dependent glycerol-3-phosphate dehydrogenase family
LY388_02890	COG0580	Belongs to the MIP aquaporin (TC 1.A.8) family
LY388_02895	COG0554	Key enzyme in the regulation of glycerol uptake and metabolism. Catalyzes the phosphorylation of glycerol to yield sn- glycerol 3-phosphate
LY388_02905	COG2926	Belongs to the UPF0265 family
LY388_02915	COG3132	Protein of unknown function, DUF480
LY388_02920	COG2827	Endonuclease containing a URI domain
LY388_02930	COG1879	ABC-type sugar transport system periplasmic component
LY388_02935	COG5002	protein histidine kinase activity
LY388_02935	COG0784	Response regulator, receiver
LY388_02970	COG1492	cobalamin metabolic process
LY388_02975	COG0725	ABC transporter, periplasmic molybdate-binding protein
LY388_02980	COG4149	molybdate abc transporter
LY388_02985	COG4148	Part of the ABC transporter complex ModABC involved in molybdenum import. Responsible for energy coupling to the transport system
LY388_03015	COG1289	transmembrane transporter activity
LY388_03020	COG0210	DNA helicase
LY388_03035	COG0818	Recycling of diacylglycerol produced during the turnover of membrane phospholipid
LY388_03040	COG1335	isochorismatase
LY388_03045	COG1803	Methylglyoxal synthase
LY388_03050	COG1879	ABC-type sugar transport system periplasmic component
LY388_03055	COG2198	Histidine kinase
LY388_03055	COG0784	Response regulator, receiver
LY388_03055	COG2205	protein histidine kinase activity
LY388_03060	COG0469	pyruvate kinase activity
LY388_03065	COG2271	Major facilitator Superfamily
LY388_03075	COG4191	Histidine kinase
LY388_03090	COG1979	alcohol dehydrogenase
LY388_03100	COG0448	Catalyzes the synthesis of ADP-glucose, a sugar donor used in elongation reactions on alpha-glucans
LY388_03120	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
LY388_03125	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
LY388_03135	COG0183	Belongs to the thiolase family
LY388_03145	COG3243	poly(R)-hydroxyalkanoic acid synthase
LY388_03150	COG3842	ATPase activity
LY388_03160	COG1840	ABC-type Fe3 transport system, periplasmic component
LY388_03165	COG2271	Major facilitator Superfamily
LY388_03170	COG3851	Histidine kinase
LY388_03175	COG2197	response regulator
LY388_03180	COG2206	PFAM metal-dependent phosphohydrolase, HD sub domain
LY388_03200	COG0243	molybdopterin cofactor binding
LY388_03210	COG1145	4fe-4S ferredoxin, iron-sulfur binding domain protein
LY388_03215	COG3850	Histidine kinase
LY388_03220	COG2197	response regulator
LY388_03225	COG1609	Transcriptional regulator
LY388_03245	COG1760	l-serine dehydratase
LY388_03250	COG3069	C4-dicarboxylate transmembrane transporter activity
LY388_03255	COG0840	transmembrane signaling receptor activity
LY388_03260	COG0637	HAD-superfamily hydrolase subfamily IA, variant 3
LY388_03265	COG0545	Peptidyl-prolyl cis-trans isomerase
LY388_03270	COG2885	chlorophyll binding
LY388_03280	COG0578	Belongs to the FAD-dependent glycerol-3-phosphate dehydrogenase family
LY388_03285	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
LY388_03290	COG1621	beta-fructofuranosidase activity
LY388_03295	COG1609	Transcriptional regulator
LY388_03300	COG1263	PTS System
LY388_03300	COG1264	protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
LY388_03345	COG0446	pyridine nucleotide-disulphide oxidoreductase
LY388_03385	COG1359	(4S)-4-hydroxy-5-phosphonooxypentane-2,3-dione isomerase activity
LY388_03390	COG0583	DNA-binding transcription factor activity
LY388_03415	COG0111	D-isomer specific 2-hydroxyacid dehydrogenase
LY388_03440	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
LY388_03450	COG2390	Transcriptional regulator
LY388_03460	COG2897	thiosulfate sulfurtransferase activity
LY388_03470	COG0476	Involved in molybdopterin and thiamine biosynthesis, family 2
LY388_03480	COG0302	gtp cyclohydrolase
LY388_03485	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
LY388_03485	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
LY388_03490	COG2759	Belongs to the formate--tetrahydrofolate ligase family
LY388_03495	COG1970	mechanosensitive ion channel activity
LY388_03500	COG3155	Displays glyoxalase activity, catalyzing the conversion of glyoxal to glycolate
LY388_03515	COG1011	Hydrolase
LY388_03520	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
LY388_03525	COG0637	HAD-superfamily hydrolase subfamily IA, variant 3
LY388_03530	COG0160	Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family
LY388_03535	COG0075	2-aminoethylphosphonate-pyruvate transaminase activity
LY388_03545	COG3842	ATPase activity
LY388_03610	COG0023	Translation Initiation Factor
LY388_03630	COG1042	CoA-binding domain protein
LY388_03630	COG0045	succinate-CoA ligase (ADP-forming) activity
LY388_03630	COG1670	COG1670 acetyltransferases, including N-acetylases of ribosomal proteins
LY388_03635	COG0583	DNA-binding transcription factor activity
LY388_03640	COG4771	TonB-dependent receptor
LY388_03640	COG1629	transport
LY388_03655	COG2050	protein possibly involved in aromatic compounds catabolism
LY388_03675	COG0625	glutathione transferase activity
LY388_03690	COG1207	Catalyzes the last two sequential reactions in the de novo biosynthetic pathway for UDP-N-acetylglucosamine (UDP- GlcNAc). The C-terminal domain catalyzes the transfer of acetyl group from acetyl coenzyme A to glucosamine-1-phosphate (GlcN-1-P) to produce N-acetylglucosamine-1-phosphate (GlcNAc-1-P), which is converted into UDP-GlcNAc by the transfer of uridine 5- monophosphate (from uridine 5-triphosphate), a reaction catalyzed by the N-terminal domain
LY388_03695	COG4172	Belongs to the ABC transporter superfamily
LY388_03700	COG4239	(ABC) transporter, permease
LY388_03705	COG4174	ABC transporter (Permease)
LY388_03710	COG4166	transmembrane transport
LY388_03735	COG3104	oligopeptide transport
LY388_03750	COG3140	Belongs to the UPF0181 family
LY388_03765	COG0745	RESPONSE REGULATOR receiver
LY388_03775	COG1282	The transhydrogenation between NADH and NADP is coupled to respiration and ATP hydrolysis and functions as a proton pump across the membrane
LY388_03780	COG3288	NAD(P)+ transhydrogenase (AB-specific) activity
LY388_03795	COG3706	GGDEF domain
LY388_03815	COG2199	diguanylate cyclase activity
LY388_03845	COG2824	Alkylphosphonate utilization operon protein PhnA
LY388_03860	COG0737	Belongs to the 5'-nucleotidase family
LY388_03865	COG3593	DNA synthesis involved in DNA repair
LY388_03875	COG0583	DNA-binding transcription factor activity
LY388_03880	COG2116	formate transmembrane transporter activity
LY388_03890	COG3038	cytochrome b561
LY388_03900	COG2200	EAL domain
LY388_03910	COG0586	Pfam SNARE associated Golgi protein
LY388_03915	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
LY388_03920	COG0745	RESPONSE REGULATOR receiver
LY388_03925	COG2205	protein histidine kinase activity
LY388_03930	COG0674	pyruvate-flavodoxin oxidoreductase activity
LY388_03930	COG1013	pyruvate-flavodoxin oxidoreductase activity
LY388_03930	COG1014	Oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin
LY388_03930	COG1143	NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient
LY388_03935	COG3158	transport of potassium into the cell
LY388_03945	COG0523	cobalamin synthesis protein
LY388_03960	COG0156	8-amino-7-oxononanoate synthase activity
LY388_03965	COG2205	protein histidine kinase activity
LY388_03965	COG0784	Response regulator, receiver
LY388_03970	COG0419	ATPase involved in DNA repair
LY388_03975	COG0420	3'-5' exonuclease activity
LY388_03980	COG1609	Transcriptional regulator
LY388_03985	COG4668	phosphoenolpyruvate-dependent sugar phosphotransferase system
LY388_03985	COG1925	phosphoenolpyruvate-dependent sugar phosphotransferase system
LY388_03990	COG1105	Belongs to the carbohydrate kinase PfkB family
LY388_03995	COG3925	protein-phosphocysteine-D-fructose-phosphotransferase system transporter activity
LY388_03995	COG1299	protein-N(PI)-phosphohistidine-fructose phosphotransferase system transporter activity
LY388_03995	COG1445	protein-N(PI)-phosphohistidine-fructose phosphotransferase system transporter activity
LY388_04000	COG0189	ligase activity
LY388_04000	COG4067	protein conserved in archaea
LY388_04010	COG0602	queuosine metabolic process
LY388_04015	COG1328	CTP reductase activity
LY388_04065	COG1418	mRNA catabolic process
LY388_04080	COG0494	nUDIX hydrolase
LY388_04085	COG5642	Protein of unknown function (DUF2384)
LY388_04105	COG2320	Catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A
LY388_04215	COG1670	COG1670 acetyltransferases, including N-acetylases of ribosomal proteins
LY388_04260	COG4115	mRNA cleavage
LY388_04265	COG2161	toxin-antitoxin pair type II binding
LY388_04310	COG1670	COG1670 acetyltransferases, including N-acetylases of ribosomal proteins
LY388_04330	COG2320	Catalyzes the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form coenzyme A
LY388_04370	COG1670	COG1670 acetyltransferases, including N-acetylases of ribosomal proteins
LY388_04410	COG0488	(ABC) transporter
LY388_04465	COG0454	-acetyltransferase
LY388_04565	COG2944	sequence-specific DNA binding
LY388_04570	COG4737	Cytotoxic translational repressor of toxin-antitoxin stability system
LY388_04615	COG1613	Sulfate ABC transporter periplasmic sulfate-binding protein
LY388_04640	COG3040	lipid binding
LY388_04700	COG3040	lipid binding
LY388_04765	COG4977	sequence-specific DNA binding
LY388_04805	COG0637	HAD-superfamily hydrolase subfamily IA, variant 3
LY388_04850	COG1619	proteins homologs of microcin C7 resistance protein MccF
LY388_04880	COG0384	phenazine biosynthesis protein PhzF
LY388_04895	COG1028	Short-chain dehydrogenase reductase Sdr
LY388_04950	COG1670	COG1670 acetyltransferases, including N-acetylases of ribosomal proteins
LY388_04975	COG0346	lactoylglutathione lyase activity
LY388_05030	COG4977	sequence-specific DNA binding
LY388_05160	COG0292	Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit
LY388_05165	COG0291	Belongs to the bacterial ribosomal protein bL35 family
LY388_05180	COG0404	The glycine cleavage system catalyzes the degradation of glycine
LY388_05190	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
LY388_05195	COG0509	glycine decarboxylation via glycine cleavage system
LY388_05200	COG0403	The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor
LY388_05200	COG1003	The glycine cleavage system catalyzes the degradation of glycine. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor
LY388_05220	COG1686	Belongs to the peptidase S11 family
LY388_05240	COG5000	phosphorelay sensor kinase activity
LY388_05240	COG5002	protein histidine kinase activity
LY388_05245	COG0745	RESPONSE REGULATOR receiver
LY388_05265	COG0366	Alpha amylase catalytic
LY388_05300	COG0561	phosphatase activity
LY388_05305	COG0269	3-dehydro-L-gulonate-6-phosphate decarboxylase activity
LY388_05310	COG3623	hexulose-6-phosphate isomerase
LY388_05320	COG0745	RESPONSE REGULATOR receiver
LY388_05335	COG0583	DNA-binding transcription factor activity
LY388_05350	COG0640	Transcriptional regulator
LY388_05355	COG0282	Catalyzes the formation of acetyl phosphate from acetate and ATP. Can also catalyze the reverse reaction
LY388_05370	COG2207	Transcriptional regulator
LY388_05375	COG4604	ABC transporter, ATP-binding protein
LY388_05380	COG4605	iron ion homeostasis
LY388_05385	COG4606	Belongs to the binding-protein-dependent transport system permease family. FecCD subfamily
LY388_05410	COG5380	lipid catabolic process
LY388_05415	COG1075	acetyltransferases and hydrolases with the alpha beta hydrolase fold
LY388_05420	COG0840	transmembrane signaling receptor activity
LY388_05430	COG3240	lipase activity
LY388_05435	COG3706	GGDEF domain
LY388_05445	COG2814	Major facilitator Superfamily
LY388_05450	COG1757	Na H antiporter
LY388_05460	COG0834	ABC-type amino acid transport signal transduction systems periplasmic component domain
LY388_05460	COG4191	Histidine kinase
LY388_05465	COG0784	Response regulator, receiver
LY388_05465	COG3437	response regulator, receiver
LY388_05470	COG1057	Catalyzes the reversible adenylation of nicotinate mononucleotide (NaMN) to nicotinic acid adenine dinucleotide (NaAD)
LY388_05475	COG0171	NAD+ synthase (glutamine-hydrolyzing) activity
LY388_05480	COG2704	Responsible for the transport of C4-dicarboxylates from the periplasm across the inner membrane
LY388_05485	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
LY388_05490	COG0592	DNA-directed DNA polymerase activity
LY388_05495	COG1195	it is required for DNA replication and normal SOS inducibility. RecF binds preferentially to single-stranded, linear DNA. It also seems to bind ATP
LY388_05500	COG0187	DNA topoisomerase II activity
LY388_05510	COG0071	Belongs to the small heat shock protein (HSP20) family
LY388_05515	COG3977	Valine--pyruvate aminotransferase
LY388_05520	COG0751	glycine-tRNA ligase activity
LY388_05525	COG0752	glycyl-tRNA synthetase alpha subunit
LY388_05530	COG2119	membrane
LY388_05540	COG0425	Belongs to the sulfur carrier protein TusA family
LY388_05550	COG0604	alcohol dehydrogenase
LY388_05560	COG0129	dihydroxy-acid dehydratase activity
LY388_05565	COG0115	Belongs to the class-IV pyridoxal-phosphate-dependent aminotransferase family
LY388_05580	COG0606	chelatase, subunit chli
LY388_05585	COG0204	Acyl-transferase
LY388_05590	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
LY388_05595	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
LY388_05605	COG3084	Protein conserved in bacteria
LY388_05610	COG4326	sporulation control protein
LY388_05615	COG1272	protein, Hemolysin III
LY388_05625	COG0168	Low-affinity potassium transport system. Interacts with trk system potassium uptake protein TrkA
LY388_05630	COG0569	domain protein
LY388_05635	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
LY388_05635	COG0144	Specifically methylates the cytosine at position 967 (m5C967) of 16S rRNA
LY388_05640	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
LY388_05645	COG0242	peptide deformylase activity
LY388_05650	COG1652	LysM domain
LY388_05655	COG0758	DNA mediated transformation
LY388_05660	COG2922	Belongs to the Smg family
LY388_05665	COG0551	DNA topoisomerase type I activity
LY388_05670	COG0026	Catalyzes the ATP-dependent conversion of 5- aminoimidazole ribonucleotide (AIR) and HCO(3)(-) to N5- carboxyaminoimidazole ribonucleotide (N5-CAIR)
LY388_05675	COG0041	Catalyzes the conversion of N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) to 4-carboxy-5-aminoimidazole ribonucleotide (CAIR)
LY388_05680	COG0009	L-threonylcarbamoyladenylate synthase
LY388_05685	COG0408	coproporphyrinogen oxidase activity
LY388_05690	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)
LY388_05700	COG0663	COG0663 Carbonic anhydrases acetyltransferases, isoleucine patch superfamily
LY388_05735	COG0239	Important for reducing fluoride concentration in the cell, thus reducing its toxicity
LY388_05740	COG0422	Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction
LY388_05750	COG0476	Involved in molybdopterin and thiamine biosynthesis, family 2
LY388_05755	COG2104	thiamine diphosphate biosynthetic process
LY388_05760	COG2022	thiamine diphosphate biosynthetic process
LY388_05765	COG0502	Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical- based mechanism
LY388_05770	COG0006	proline dipeptidase activity
LY388_05770	COG0006	proline dipeptidase activity
LY388_05790	COG1522	sequence-specific DNA binding
LY388_05795	COG5002	protein histidine kinase activity
LY388_05795	COG5001	Diguanylate cyclase
LY388_05815	COG0589	response to stress
LY388_05820	COG1528	Iron-storage protein
LY388_05830	COG2081	HI0933 family
LY388_05840	COG1322	Protein conserved in bacteria
LY388_05845	COG2226	methyltransferase
LY388_05860	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
LY388_05865	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
LY388_05870	COG0805	protein transport
LY388_05875	COG0534	Mate efflux family protein
LY388_05885	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
LY388_05890	COG2937	Belongs to the GPAT DAPAT family
LY388_05895	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
LY388_05900	COG3161	chorismate lyase activity
LY388_05905	COG1580	Controls the rotational direction of flagella during chemotaxis
LY388_05910	COG0840	transmembrane signaling receptor activity
LY388_05920	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
LY388_05925	COG0084	hydrolase, TatD family'
LY388_05940	COG0258	In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity
LY388_05940	COG0749	In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity
LY388_05960	COG3078	GTPase activator activity
LY388_05975	COG3071	HemY protein
LY388_05980	COG2959	enzyme of heme biosynthesis
LY388_05985	COG1587	Uroporphyrinogen-III synthase
LY388_05990	COG0181	hydroxymethylbilane synthase activity
LY388_06000	COG1965	Belongs to the frataxin family
LY388_06010	COG0019	diaminopimelate decarboxylase activity
LY388_06015	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
LY388_06025	COG4973	Belongs to the 'phage' integrase family. XerC subfamily
LY388_06030	COG1011	Hydrolase
LY388_06035	COG2199	diguanylate cyclase activity
LY388_06035	COG3287	FIST C domain
LY388_06035	COG2200	EAL domain
LY388_06050	COG0561	phosphatase activity
LY388_06055	COG2267	carboxylic ester hydrolase activity
LY388_06060	COG1280	lysine exporter protein (LysE YggA)
LY388_06065	COG3434	signal transduction protein containing EAL and modified HD-GYP domains
LY388_06070	COG0783	Belongs to the Dps family
LY388_06100	COG0742	ribosomal rna small subunit methyltransferase
LY388_06105	COG0552	protein localization to endoplasmic reticulum
LY388_06110	COG2884	Cell division ATP-binding protein ftsE
LY388_06115	COG2177	Part of the ABC transporter FtsEX involved in
LY388_06120	COG0568	sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released
LY388_06125	COG1249	Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family
LY388_06140	COG2265	Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family
LY388_06155	COG1404	Belongs to the peptidase S8 family
LY388_06160	COG0796	Provides the (R)-glutamate required for cell wall biosynthesis
LY388_06225	COG1816	Catalyzes the hydrolytic deamination of adenine to hypoxanthine. Plays an important role in the purine salvage pathway and in nitrogen catabolism
LY388_06230	COG3300	MHYT domain
LY388_06230	COG5001	Diguanylate cyclase
LY388_06240	COG3852	Histidine kinase
LY388_06250	COG0174	glutamine synthetase
LY388_06260	COG1217	gtp-binding protein TYPA
LY388_06270	COG1295	ribonuclease BN
LY388_06275	COG1490	D-aminoacyl-tRNA deacylase activity
LY388_06280	COG0456	acetyltransferase
LY388_06290	COG1866	Involved in the gluconeogenesis. Catalyzes the conversion of oxaloacetate (OAA) to phosphoenolpyruvate (PEP) through direct phosphoryl transfer between the nucleoside triphosphate and OAA
LY388_06295	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
LY388_06300	COG1188	Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit, (S4 paralog))
LY388_06305	COG3031	protein transport across the cell outer membrane
LY388_06315	COG2804	Type II secretory pathway, ATPase PulE Tfp pilus assembly pathway, ATPase PilB
LY388_06320	COG1459	type II secretion system
LY388_06325	COG2165	general secretion pathway protein
LY388_06330	COG2165	general secretion pathway protein
LY388_06335	COG2165	general secretion pathway protein
LY388_06340	COG4795	General secretion pathway protein
LY388_06345	COG3156	type II secretion system protein K
LY388_06350	COG3297	Involved in a type II secretion system (T2SS, formerly general secretion pathway, GSP) for the export of proteins
LY388_06355	COG3149	Involved in a type II secretion system (T2SS, formerly general secretion pathway, GSP) for the export of proteins
LY388_06365	COG1218	3'(2'),5'-bisphosphate nucleotidase
LY388_06370	COG0494	nUDIX hydrolase
LY388_06380	COG1040	competence protein
LY388_06390	COG0596	Alpha beta hydrolase
LY388_06400	COG2183	response to ionizing radiation
LY388_06405	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
LY388_06420	COG2233	PERMEase
LY388_06425	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)
LY388_06430	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
LY388_06435	COG1758	RNA polymerase activity
LY388_06440	COG0194	GDP metabolic process
LY388_06445	COG1738	Involved in the import of queuosine (Q) precursors, required for Q precursor salvage
LY388_06450	COG4147	Belongs to the sodium solute symporter (SSF) (TC 2.A.21) family
LY388_06470	COG4232	protein-disulfide reductase activity
LY388_06480	COG2704	Responsible for the transport of C4-dicarboxylates from the periplasm across the inner membrane
LY388_06485	COG1027	Aspartate ammonia-lyase
LY388_06490	COG3706	GGDEF domain
LY388_06495	COG3030	protein affecting phage T7 exclusion by the F plasmid
LY388_06500	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
LY388_06510	COG2205	protein histidine kinase activity
LY388_06515	COG0745	RESPONSE REGULATOR receiver
LY388_06525	COG0053	Belongs to the cation diffusion facilitator (CDF) transporter (TC 2.A.4) family
LY388_06530	COG0205	6-phosphofructokinase activity
LY388_06535	COG1494	fructose-1,6-bisphosphatase
LY388_06540	COG3074	FtsZ-dependent cytokinesis
LY388_06545	COG0685	methylenetetrahydrofolate reductase (NAD(P)H) activity
LY388_06550	COG0460	homoserine dehydrogenase
LY388_06550	COG0527	aspartate kinase activity
LY388_06555	COG0626	cystathionine gamma-synthase activity
LY388_06560	COG3060	This regulatory protein, when combined with SAM (S- adenosylmethionine) represses the expression of the methionine regulon and of enzymes involved in SAM synthesis
LY388_06565	COG0281	malic enzyme
LY388_06570	COG0254	rRNA binding
LY388_06575	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
LY388_06580	COG1609	Transcriptional regulator
LY388_06585	COG3087	Lytic transglycosylase with a strong preference for naked glycan strands that lack stem peptides
LY388_06590	COG5405	Protease subunit of a proteasome-like degradation complex believed to be a general protein degrading machinery
LY388_06595	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
LY388_06600	COG1575	Belongs to the MenA family. Type 1 subfamily
LY388_06605	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
LY388_06610	COG0534	Mate efflux family protein
LY388_06615	COG0149	triose-phosphate isomerase activity
LY388_06640	COG0234	Binds to Cpn60 in the presence of Mg-ATP and suppresses the ATPase activity of the latter
LY388_06645	COG0459	protein refolding
LY388_06655	COG1509	lysine 2,3-aminomutase activity
LY388_06660	COG0231	Involved in peptide bond synthesis. Stimulates efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase
LY388_06670	COG3029	Seems to be involved in the anchoring of the catalytic components of the fumarate reductase complex to the cytoplasmic membrane
LY388_06675	COG0479	Belongs to the succinate dehydrogenase fumarate reductase iron-sulfur protein family
LY388_06680	COG1053	succinate dehydrogenase
LY388_06685	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
LY388_06690	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
LY388_06695	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
LY388_06700	COG0240	glycerol-3-phosphate dehydrogenase [NAD(P)+] activity
LY388_06705	COG1045	serine acetyltransferase
LY388_06715	COG2352	Forms oxaloacetate, a four-carbon dicarboxylic acid source for the tricarboxylic acid cycle
LY388_06720	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
LY388_06725	COG0002	Catalyzes the NADPH-dependent reduction of N-acetyl-5- glutamyl phosphate to yield N-acetyl-L-glutamate 5-semialdehyde
LY388_06730	COG0548	Belongs to the acetylglutamate kinase family. ArgB subfamily
LY388_06735	COG0137	argininosuccinate synthase activity
LY388_06740	COG0165	Argininosuccinate lyase
LY388_06750	COG1249	Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family
LY388_06755	COG0695	Has a glutathione-disulfide oxidoreductase activity in the presence of NADPH and glutathione reductase. Reduces low molecular weight disulfides and proteins
LY388_06755	COG0678	peroxiredoxin activity
LY388_06770	COG5009	serine-type D-Ala-D-Ala carboxypeptidase activity
LY388_06800	COG0703	Catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid using ATP as a cosubstrate
LY388_06805	COG0337	Catalyzes the conversion of 3-deoxy-D-arabino- heptulosonate 7-phosphate (DAHP) to dehydroquinate (DHQ)
LY388_06815	COG0338	D12 class N6 adenine-specific DNA methyltransferase
LY388_06820	COG0036	Belongs to the ribulose-phosphate 3-epimerase family
LY388_06825	COG0546	phosphoglycolate phosphatase activity
LY388_06830	COG0180	Tryptophanyl-tRNA synthetase
LY388_06845	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
LY388_06855	COG4992	N2-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity
LY388_06880	COG3954	Phosphoribulokinase
LY388_06890	COG0429	hydrolase of the alpha beta-hydrolase fold
LY388_06900	COG0488	(ABC) transporter
LY388_06905	COG2249	NAD(P)H dehydrogenase (quinone) activity
LY388_06920	COG1047	Peptidyl-prolyl cis-trans
LY388_06930	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
LY388_06935	COG0790	COG0790 FOG TPR repeat, SEL1 subfamily
LY388_06940	COG3083	sulfuric ester hydrolase activity
LY388_06945	COG0557	exoribonuclease II activity
LY388_06950	COG0566	Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase TrmH family
LY388_06955	COG0051	transcription antitermination factor activity, RNA binding
LY388_06960	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
LY388_06965	COG0088	Forms part of the polypeptide exit tunnel
LY388_06970	COG0089	rRNA binding
LY388_06975	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
LY388_06980	COG0185	Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA
LY388_06985	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
LY388_06990	COG0092	Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation
LY388_06995	COG0197	Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs
LY388_07000	COG0255	Belongs to the universal ribosomal protein uL29 family
LY388_07005	COG0186	One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA
LY388_07010	COG0093	Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome
LY388_07015	COG0198	One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit
LY388_07020	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
LY388_07025	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
LY388_07030	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
LY388_07040	COG0256	This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance
LY388_07045	COG0098	Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body
LY388_07050	COG1841	ribosomal large subunit assembly
LY388_07060	COG0201	protein transport
LY388_07065	COG0257	Belongs to the bacterial ribosomal protein bL36 family
LY388_07070	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
LY388_07075	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
LY388_07080	COG0522	One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit
LY388_07085	COG0202	RNA polymerase activity
LY388_07090	COG0203	ribosomal protein L17
LY388_07100	COG0545	Peptidyl-prolyl cis-trans isomerase
LY388_07105	COG3061	Opacity-associated protein A
LY388_07105	COG3266	domain, Protein
LY388_07110	COG0697	spore germination
LY388_07115	COG2153	protein acetylation
LY388_07120	COG0513	Belongs to the DEAD box helicase family
LY388_07135	COG1648	precorrin-2 dehydrogenase activity
LY388_07135	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
LY388_07140	COG0175	sulfate reduction
LY388_07145	COG2895	sulfate adenylyltransferase (ATP) activity
LY388_07150	COG0529	Catalyzes the synthesis of activated sulfate
LY388_07170	COG1136	(ABC) transporter
LY388_07185	COG3054	Bacterial protein of unknown function (YtfJ_HI0045)
LY388_07190	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
LY388_07195	COG0729	surface antigen
LY388_07205	COG2105	PFAM AIG2 family protein
LY388_07210	COG0221	Catalyzes the hydrolysis of inorganic pyrophosphate (PPi) forming two phosphate ions
LY388_07220	COG0773	UDP-N-acetylmuramate-L-alanine ligase activity
LY388_07225	COG0163	prenyltransferase activity
LY388_07235	COG1178	ABC-type Fe3 transport system permease component
LY388_07240	COG3840	Part of the ABC transporter complex ThiBPQ involved in thiamine import. Responsible for energy coupling to the transport system
LY388_07245	COG3028	Belongs to the UPF0307 family
LY388_07250	COG0312	modulator of DNA gyrase
LY388_07255	COG2239	Acts as a magnesium transporter
LY388_07260	COG1925	phosphoenolpyruvate-dependent sugar phosphotransferase system
LY388_07265	COG1660	Displays ATPase and GTPase activities
LY388_07270	COG1762	phosphoenolpyruvate-dependent sugar phosphotransferase system
LY388_07275	COG1544	Required for dimerization of active 70S ribosomes into 100S ribosomes in stationary phase
LY388_07285	COG1137	ATPase activity
LY388_07290	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
LY388_07305	COG0517	IMP dehydrogenase activity
LY388_07305	COG0794	Belongs to the SIS family. GutQ KpsF subfamily
LY388_07315	COG1127	ABC transporter
LY388_07320	COG0767	ABC-type transport system involved in resistance to organic solvents, permease component
LY388_07325	COG1463	ABC-type transport system involved in resistance to organic solvents, periplasmic component
LY388_07330	COG2854	intermembrane phospholipid transfer
LY388_07340	COG5007	Belongs to the BolA IbaG family
LY388_07345	COG0766	Cell wall formation. Adds enolpyruvyl to UDP-N- acetylglucosamine
LY388_07355	COG0251	oxidation-reduction process
LY388_07365	COG0540	Belongs to the ATCase OTCase family
LY388_07375	COG1875	ATPase related to phosphate starvation-inducible protein PhoH
LY388_07385	COG0564	pseudouridine synthase activity
LY388_07390	COG1052	Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family
LY388_07395	COG0525	valine-tRNA ligase activity
LY388_07400	COG2927	DNA polymerase III (CHI subunit)
LY388_07405	COG0260	Presumably involved in the processing and regular turnover of intracellular proteins. Catalyzes the removal of unsubstituted N-terminal amino acids from various peptides
LY388_07410	COG0795	lipopolysaccharide-transporting ATPase activity
LY388_07415	COG0795	lipopolysaccharide-transporting ATPase activity
LY388_07430	COG3437	response regulator, receiver
LY388_07475	COG0066	3-isopropylmalate dehydratase activity
LY388_07480	COG0065	Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate
LY388_07485	COG0473	3-isopropylmalate dehydrogenase activity
LY388_07505	COG0583	DNA-binding transcription factor activity
LY388_07510	COG1022	Amp-dependent synthetase and ligase
LY388_07515	COG0028	Belongs to the TPP enzyme family
LY388_07520	COG0440	acetolactate synthase activity
LY388_07525	COG0111	D-isomer specific 2-hydroxyacid dehydrogenase
LY388_07530	COG0120	Catalyzes the reversible conversion of ribose-5- phosphate to ribulose 5-phosphate
LY388_07535	COG0212	Belongs to the 5-formyltetrahydrofolate cyclo-ligase family
LY388_07545	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
LY388_07550	COG3079	Belongs to the UPF0149 family
LY388_07555	COG0654	COG0654 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases
LY388_07560	COG0654	COG0654 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases
LY388_07570	COG0354	folic acid binding
LY388_07575	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
LY388_07585	COG0029	Catalyzes the oxidation of L-aspartate to iminoaspartate
LY388_07590	COG1595	DNA-templated transcription, initiation
LY388_07605	COG3086	response to oxidative stress
LY388_07610	COG0481	GTPase activity
LY388_07620	COG0571	ribonuclease III activity
LY388_07625	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
LY388_07630	COG1381	Involved in DNA repair and RecF pathway recombination
LY388_07635	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
LY388_07665	COG2265	Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family
LY388_07670	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
LY388_07675	COG3956	TIGRFAM MazG family protein
LY388_07680	COG0504	CTP synthase activity
LY388_07685	COG0148	phosphopyruvate hydratase activity
LY388_07695	COG3267	Type II secretory pathway component ExeA
LY388_07695	COG3409	Peptidoglycan-binding domain 1 protein
LY388_07705	COG4991	sh3 domain protein
LY388_07710	COG0306	phosphate transporter
LY388_07715	COG1392	Phosphate transport regulator
LY388_07720	COG3025	triphosphatase activity
LY388_07725	COG0840	transmembrane signaling receptor activity
LY388_07730	COG1391	[glutamine synthetase]-adenylyl-L-tyrosine phosphorylase
LY388_07735	COG0615	ADP-L-glycero-beta-D-manno-heptose biosynthetic process
LY388_07735	COG2870	Catalyzes the ADP transfer from ATP to D-glycero-beta-D- manno-heptose 1-phosphate, yielding ADP-D-glycero-beta-D-manno- heptose
LY388_07740	COG1538	Outer membrane efflux protein
LY388_07745	COG0494	nUDIX hydrolase
LY388_07750	COG3151	Protein conserved in bacteria
LY388_07760	COG3150	esterase
LY388_07765	COG0187	DNA topoisomerase II activity
LY388_07770	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
LY388_07780	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
LY388_07785	COG0237	dephospho-CoA kinase activity
LY388_07795	COG1459	type II secretion system
LY388_07800	COG2804	Type II secretory pathway, ATPase PulE Tfp pilus assembly pathway, ATPase PilB
LY388_07820	COG0716	FMN binding
LY388_07825	COG4974	Belongs to the 'phage' integrase family
LY388_07830	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
LY388_07835	COG0608	single-stranded DNA 5'-3' exodeoxyribonuclease activity
LY388_07840	COG0737	Belongs to the 5'-nucleotidase family
LY388_07845	COG2186	Transcriptional regulator
LY388_07850	COG2609	component of the pyruvate dehydrogenase (PDH) complex, that catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2)
LY388_07855	COG0508	dehydrogenase complex catalyzes the overall conversion of
LY388_07860	COG1249	Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family
LY388_07875	COG3116	cell division
LY388_07880	COG0768	penicillin binding
LY388_07885	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
LY388_07890	COG0770	UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase activity
LY388_07900	COG0771	Cell wall formation. Catalyzes the addition of glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-L-alanine (UMA)
LY388_07905	COG0772	Belongs to the SEDS family
LY388_07910	COG0707	Cell wall formation. Catalyzes the transfer of a GlcNAc subunit on undecaprenyl-pyrophosphoryl-MurNAc-pentapeptide (lipid intermediate I) to form undecaprenyl-pyrophosphoryl-MurNAc- (pentapeptide)GlcNAc (lipid intermediate II)
LY388_07915	COG0773	UDP-N-acetylmuramate-L-alanine ligase activity
LY388_07920	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
LY388_07925	COG0849	cell division
LY388_07930	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
LY388_07935	COG0774	UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase activity
LY388_07945	COG0653	protein targeting
LY388_07950	COG0494	nUDIX hydrolase
LY388_07955	COG0289	4-hydroxy-tetrahydrodipicolinate reductase
LY388_07965	COG0505	Belongs to the CarA family
LY388_07970	COG0458	carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity
LY388_07985	COG0730	response to heat
LY388_07990	COG0583	DNA-binding transcription factor activity
LY388_07995	COG2860	membrane
LY388_08000	COG0614	abc-type fe3 -hydroxamate transport system, periplasmic component
LY388_08010	COG0775	Catalyzes the irreversible cleavage of the glycosidic bond in both 5'-methylthioadenosine (MTA) and S- adenosylhomocysteine (SAH AdoHcy) to adenine and the corresponding thioribose, 5'-methylthioribose and S-ribosylhomocysteine, respectively
LY388_08020	COG0493	'glutamate synthase
LY388_08025	COG0067	glutamate synthase
LY388_08025	COG0070	glutamate synthase
LY388_08025	COG0069	glutamate synthase activity
LY388_08035	COG0067	glutamate synthase
LY388_08035	COG0069	glutamate synthase activity
LY388_08035	COG0070	glutamate synthase
LY388_08040	COG1242	4 iron, 4 sulfur cluster binding
LY388_08045	COG2203	Gaf domain
LY388_08045	COG3706	GGDEF domain
LY388_08045	COG4251	negative regulation of phosphorylation
LY388_08045	COG5001	Diguanylate cyclase
LY388_08050	COG5002	protein histidine kinase activity
LY388_08050	COG0784	Response regulator, receiver
LY388_08050	COG2198	Histidine kinase
LY388_08055	COG0745	RESPONSE REGULATOR receiver
LY388_08065	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
LY388_08085	COG0083	homoserine kinase activity
LY388_08090	COG0498	Catalyzes the gamma-elimination of phosphate from L- phosphohomoserine and the beta-addition of water to produce L- threonine
LY388_08095	COG3445	Acts as a radical domain for damaged PFL and possibly other radical proteins
LY388_08100	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
LY388_08105	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
LY388_08120	COG1115	amino acid carrier protein
LY388_08125	COG3022	response to hydroperoxide
LY388_08135	COG0084	hydrolase, TatD family'
LY388_08140	COG1972	Belongs to the concentrative nucleoside transporter (CNT) (TC 2.A.41) family
LY388_08150	COG0274	Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy- D-ribose 5-phosphate
LY388_08155	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
LY388_08160	COG1015	Phosphotransfer between the C1 and C5 carbon atoms of pentose
LY388_08165	COG0813	purine-nucleoside phosphorylase activity
LY388_08175	COG0560	Phosphoserine phosphatase
LY388_08185	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
LY388_08190	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
LY388_08195	COG1022	Amp-dependent synthetase and ligase
LY388_08210	COG3250	beta-galactosidase activity
LY388_08215	COG1609	Transcriptional regulator
LY388_08220	COG0073	Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation
LY388_08235	COG0189	ligase activity
LY388_08235	COG0569	domain protein
LY388_08240	COG0456	acetyltransferase
LY388_08250	COG2171	N-acyltransferase activity
LY388_08255	COG3141	response to X-ray
LY388_08270	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
LY388_08275	COG1074	ATP-dependent DNA helicase activity
LY388_08280	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
LY388_08290	COG0548	Belongs to the acetylglutamate kinase family. ArgB subfamily
LY388_08290	COG1246	Belongs to the acetyltransferase family. ArgA subfamily
LY388_08300	COG2821	murein-degrading enzyme. may play a role in recycling of muropeptides during cell elongation and or cell division
LY388_08305	COG1179	involved in molybdopterin and THIamine biosynthesis family 1
LY388_08310	COG2166	iron-sulfur cluster assembly
LY388_08315	COG0520	Catalyzes the removal of elemental sulfur and selenium atoms from L-cysteine, L-cystine, L-selenocysteine, and L- selenocystine to produce L-alanine
LY388_08320	COG0693	protein deglycase activity
LY388_08325	COG1893	Catalyzes the NADPH-dependent reduction of ketopantoate into pantoic acid
LY388_08340	COG1595	DNA-templated transcription, initiation
LY388_08350	COG2211	Major facilitator Superfamily
LY388_08355	COG0652	PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides
LY388_08365	COG2813	Specifically methylates the guanine in position
LY388_08370	COG0271	Belongs to the BolA IbaG family
LY388_08375	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
LY388_08380	COG1805	sodium ion transport
LY388_08385	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
LY388_08390	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
LY388_08395	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
LY388_08400	COG2871	sodium ion transport
LY388_08405	COG1477	protein flavinylation
LY388_08425	COG3706	GGDEF domain
LY388_08430	COG0733	neurotransmitter:sodium symporter activity
LY388_08440	COG0189	ligase activity
LY388_08445	COG4067	protein conserved in archaea
LY388_08445	COG0189	ligase activity
LY388_08450	COG2195	Cleaves the N-terminal amino acid of tripeptides
LY388_08455	COG2252	PERMEase
LY388_08460	COG2236	Acts on guanine, xanthine and to a lesser extent hypoxanthine
LY388_08465	COG1073	alpha beta
LY388_08475	COG0263	Catalyzes the transfer of a phosphate group to glutamate to form L-glutamate 5-phosphate
LY388_08480	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
LY388_08485	COG1327	Negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR- boxes
LY388_08490	COG1985	Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)- pyrimidinedione 5'-phosphate
LY388_08490	COG0117	Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)- pyrimidinedione 5'-phosphate
LY388_08505	COG0054	6,7-dimethyl-8-ribityllumazine synthase activity
LY388_08510	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
LY388_08515	COG0611	Catalyzes the ATP-dependent phosphorylation of thiamine- monophosphate (TMP) to form thiamine-pyrophosphate (TPP), the active form of vitamin B1
LY388_08520	COG1267	Lipid phosphatase which dephosphorylates phosphatidylglycerophosphate (PGP) to phosphatidylglycerol (PG)
LY388_08530	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
LY388_08535	COG0024	Methionine aminopeptidase
LY388_08540	COG0052	Belongs to the universal ribosomal protein uS2 family
LY388_08545	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
LY388_08550	COG0528	UMP kinase activity
LY388_08555	COG0233	cytoplasmic translational termination
LY388_08560	COG0020	Catalyzes the condensation of isopentenyl diphosphate (IPP) with allylic pyrophosphates generating different type of terpenoids
LY388_08565	COG0575	Belongs to the CDS family
LY388_08570	COG0743	1-deoxy-D-xylulose-5-phosphate reductoisomerase activity
LY388_08575	COG0750	zinc metalloprotease
LY388_08585	COG2825	PFAM Outer membrane chaperone Skp (OmpH)
LY388_08590	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
LY388_08595	COG0764	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity
LY388_08600	COG1043	involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell
LY388_08605	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
LY388_08610	COG0164	Endonuclease that specifically degrades the RNA of RNA- DNA hybrids
LY388_08615	COG0587	DNA-directed DNA polymerase activity
LY388_08620	COG0825	malonyl-CoA metabolic process
LY388_08625	COG0037	tRNA processing
LY388_08635	COG3479	Phenolic acid decarboxylase
LY388_08640	COG0347	Belongs to the P(II) protein family
LY388_08645	COG3021	interspecies interaction between organisms
LY388_08650	COG1388	LysM domain
LY388_08650	COG0741	lytic transglycosylase activity
LY388_08655	COG0491	Thiolesterase that catalyzes the hydrolysis of S-D- lactoyl-glutathione to form glutathione and D-lactic acid
LY388_08660	COG2226	methyltransferase
LY388_08665	COG0328	RNA-DNA hybrid ribonuclease activity
LY388_08680	COG1960	acyl-CoA dehydrogenase activity
LY388_08685	COG0279	D-glycero-D-manno-heptose 7-phosphate biosynthetic process
LY388_08690	COG0121	glutamine amidotransferase
LY388_08695	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
LY388_08700	COG0150	phosphoribosylformylglycinamidine cyclo-ligase activity
LY388_08705	COG0035	Catalyzes the conversion of uracil and 5-phospho-alpha- D-ribose 1-diphosphate (PRPP) to UMP and diphosphate
LY388_08715	COG1187	pseudouridine synthase activity
LY388_08720	COG2840	Smr protein MutS2
LY388_08750	COG2217	Heavy metal translocating P-type atpase
LY388_08750	COG2608	mercury ion transmembrane transporter activity
LY388_08755	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)
LY388_08775	COG4774	siderophore transport
LY388_08775	COG1629	transport
LY388_08780	COG2375	cellular response to nickel ion
LY388_08785	COG3433	isochorismatase activity
LY388_08785	COG2226	methyltransferase
LY388_08785	COG1020	D-alanine [D-alanyl carrier protein] ligase activity
LY388_08820	COG0835	chemotaxis
LY388_08820	COG0784	Response regulator, receiver
LY388_08825	COG1352	Methylation of the membrane-bound methyl-accepting chemotaxis proteins (MCP) to form gamma-glutamyl methyl ester residues in MCP
LY388_08830	COG1815	bacterial-type flagellum-dependent cell motility
LY388_08845	COG1749	Flagellar hook protein flgE
LY388_08850	COG4787	bacterial-type flagellum-dependent cell motility
LY388_08860	COG2063	Assembles around the rod to form the L-ring and probably protects the motor basal body from shearing forces during rotation
LY388_08865	COG1706	bacterial-type flagellum-dependent cell motility
LY388_08870	COG3951	Flagellar rod assembly protein muramidase FlgJ
LY388_08870	COG1705	Flagellar rod assembly protein muramidase FlgJ
LY388_08885	COG1344	Flagellin is the subunit protein which polymerizes to form the filaments of bacterial flagella
LY388_08890	COG1344	Flagellin is the subunit protein which polymerizes to form the filaments of bacterial flagella
LY388_08980	COG0012	GTP binding
LY388_08985	COG0193	aminoacyl-tRNA hydrolase activity
LY388_08990	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)
LY388_08995	COG1947	Catalyzes the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol
LY388_09000	COG3017	Plays a critical role in the incorporation of lipoproteins in the outer membrane after they are released by the LolA protein
LY388_09005	COG0373	Catalyzes the NADPH-dependent reduction of glutamyl- tRNA(Glu) to glutamate 1-semialdehyde (GSA)
LY388_09010	COG0216	Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA
LY388_09015	COG2890	protein-(glutamine-N5) methyltransferase activity
LY388_09025	COG2912	Transglutaminase-like superfamily
LY388_09030	COG2877	3-deoxy-8-phosphooctulonate synthase activity
LY388_09035	COG0737	Belongs to the 5'-nucleotidase family
LY388_09040	COG2606	Belongs to the prolyl-tRNA editing family. YbaK EbsC subfamily
LY388_09045	COG2233	PERMEase
LY388_09070	COG1393	Belongs to the ArsC family
LY388_09075	COG4783	chaperone-mediated protein folding
LY388_09095	COG1225	Alkyl hydroperoxide reductase Thiol specific antioxidant Mal allergen
LY388_09110	COG3317	Gram-negative-bacterium-type cell outer membrane assembly
LY388_09120	COG1876	peptidase activity
LY388_09130	COG1393	Belongs to the ArsC family
LY388_09150	COG2837	iron assimilation
LY388_09155	COG1344	Flagellin is the subunit protein which polymerizes to form the filaments of bacterial flagella
LY388_09160	COG1344	Flagellin is the subunit protein which polymerizes to form the filaments of bacterial flagella
LY388_09165	COG1344	Flagellin is the subunit protein which polymerizes to form the filaments of bacterial flagella
LY388_09170	COG1334	flagellar protein FlaG
LY388_09175	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
LY388_09185	COG1516	flagellar protein fliS
LY388_09205	COG1677	Flagellar hook-basal body complex protein FliE
LY388_09215	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
LY388_09220	COG1317	bacterial-type flagellum organization
LY388_09245	COG1580	Controls the rotational direction of flagella during chemotaxis
LY388_09270	COG1987	bacterial-type flagellum assembly
LY388_09275	COG1684	flagellar biosynthetic protein fliR
LY388_09285	COG2840	Smr protein MutS2
LY388_09290	COG2890	protein-(glutamine-N5) methyltransferase activity
LY388_09295	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
LY388_09300	COG2860	membrane
LY388_09305	COG3101	peptidyl-lysine hydroxylation
LY388_09315	COG0431	NADPH-dependent FMN reductase
LY388_09320	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
LY388_09320	COG0665	tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase activity
LY388_09325	COG0304	beta-ketoacyl-acyl-carrier-protein synthase II activity
LY388_09330	COG0111	D-isomer specific 2-hydroxyacid dehydrogenase
LY388_09335	COG0136	Catalyzes the NADPH-dependent formation of L-aspartate- semialdehyde (L-ASA) by the reductive dephosphorylation of L- aspartyl-4-phosphate
LY388_09340	COG0735	belongs to the Fur family
LY388_09350	COG0583	DNA-binding transcription factor activity
LY388_09360	COG1346	cytolysis
LY388_09375	COG0596	Alpha beta hydrolase
LY388_09380	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
LY388_09385	COG0033	Phosphoglucomutase
LY388_09395	COG0327	Belongs to the GTP cyclohydrolase I type 2 NIF3 family
LY388_09400	COG0372	Belongs to the citrate synthase family
LY388_09405	COG2009	succinate dehydrogenase
LY388_09410	COG2142	Succinate dehydrogenase hydrophobic membrane anchor
LY388_09415	COG1053	succinate dehydrogenase
LY388_09425	COG0567	Dehydrogenase, E1 component
LY388_09430	COG0508	dehydrogenase complex catalyzes the overall conversion of
LY388_09435	COG0045	succinate-CoA ligase (ADP-forming) activity
LY388_09445	COG1108	ABC-type Mn2 Zn2 transport systems permease components
LY388_09450	COG1121	(ABC) transporter
LY388_09455	COG4531	ABC-type Zn2 transport system, periplasmic component surface adhesin
LY388_09460	COG4977	sequence-specific DNA binding
LY388_09465	COG1918	ferrous iron import across plasma membrane
LY388_09485	COG0018	arginyl-trna synthetase
LY388_09495	COG1025	Belongs to the peptidase M16 family
LY388_09500	COG2062	phosphohistidine phosphatase, SixA
LY388_09530	COG3143	Plays an important role in bacterial chemotaxis signal transduction pathway by accelerating the dephosphorylation of phosphorylated CheY (CheY-P)
LY388_09535	COG0643	Histidine kinase
LY388_09535	COG0784	Response regulator, receiver
LY388_09535	COG2198	Histidine kinase
LY388_09540	COG2201	protein-glutamate methylesterase activity
LY388_09545	COG1192	Involved in chromosome partitioning
LY388_09555	COG0835	chemotaxis
LY388_09565	COG4133	protoheme IX ABC transporter activity
LY388_09570	COG2386	Required for the export of heme to the periplasm for the biogenesis of c-type cytochromes
LY388_09575	COG0755	Required for the export of heme to the periplasm for the biogenesis of c-type cytochromes
LY388_09585	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
LY388_09590	COG1138	Cytochrome C-type biogenesis protein
LY388_09595	COG0526	COG0526, thiol-disulfide isomerase and thioredoxins
LY388_09600	COG3088	subunit of a heme lyase
LY388_09600	COG4235	cytochrome complex assembly
LY388_09610	COG2853	Lipoprotein
LY388_09630	COG0278	Belongs to the glutaredoxin family. Monothiol subfamily
LY388_09635	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
LY388_09640	COG0123	including yeast histone deacetylase and acetoin utilization protein
LY388_09655	COG3083	sulfuric ester hydrolase activity
LY388_09660	COG3082	Protein of unknown function (DUF1414)
LY388_09665	COG3081	Nucleoid-associated protein
LY388_09675	COG1757	Na H antiporter
LY388_09680	COG0136	Catalyzes the NADPH-dependent formation of L-aspartate- semialdehyde (L-ASA) by the reductive dephosphorylation of L- aspartyl-4-phosphate
LY388_09685	COG2095	MarC family integral membrane protein
LY388_09690	COG1012	belongs to the aldehyde dehydrogenase family
LY388_09690	COG1454	alcohol dehydrogenase
LY388_09700	COG0659	secondary active sulfate transmembrane transporter activity
LY388_09705	COG1530	ribonuclease E activity
LY388_09710	COG0564	pseudouridine synthase activity
LY388_09715	COG0424	maF-like protein
LY388_09720	COG1399	metal-binding, possibly nucleic acid-binding protein
LY388_09725	COG0333	Belongs to the bacterial ribosomal protein bL32 family
LY388_09730	COG0416	fatty acid biosynthetic process
LY388_09735	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
LY388_09745	COG1028	Short-chain dehydrogenase reductase Sdr
LY388_09750	COG0236	Carrier of the growing fatty acid chain in fatty acid biosynthesis
LY388_09755	COG0304	beta-ketoacyl-acyl-carrier-protein synthase II activity
LY388_09760	COG0115	Belongs to the class-IV pyridoxal-phosphate-dependent aminotransferase family
LY388_09765	COG1559	Functions as a peptidoglycan terminase that cleaves nascent peptidoglycan strands endolytically to terminate their elongation
LY388_09770	COG0125	Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis
LY388_09780	COG0084	hydrolase, TatD family'
LY388_09785	COG1263	PTS System
LY388_09785	COG1264	protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
LY388_09795	COG0733	neurotransmitter:sodium symporter activity
LY388_09810	COG4667	esterase of the alpha-beta hydrolase superfamily
LY388_09820	COG1940	carbohydrate kinase activity
LY388_09825	COG0835	chemotaxis
LY388_09825	COG0784	Response regulator, receiver
LY388_09840	COG2226	methyltransferase
LY388_09850	COG0676	glucose-6-phosphate 1-epimerase activity
LY388_09855	COG0057	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
LY388_09860	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
LY388_09870	COG3139	Protein of unknown function (DUF1315)
LY388_09875	COG0252	asparaginase activity
LY388_09880	COG0616	signal peptide processing
LY388_09885	COG0446	pyridine nucleotide-disulphide oxidoreductase
LY388_09885	COG1902	pentaerythritol trinitrate reductase activity
LY388_09890	COG0788	formyltetrahydrofolate deformylase activity
LY388_09900	COG1199	ATP-dependent helicase activity
LY388_09905	COG1214	PFAM Peptidase M22, glycoprotease
LY388_09920	COG0596	Alpha beta hydrolase
LY388_09925	COG0318	PFAM AMP-dependent synthetase and ligase
LY388_09930	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
LY388_09950	COG0232	Belongs to the dGTPase family. Type 2 subfamily
LY388_09955	COG1896	Catalyzes the strictly specific dephosphorylation of 2'- deoxyribonucleoside 5'-monophosphates
LY388_09960	COG0436	Aminotransferase
LY388_09965	COG1169	isochorismate synthase
LY388_09970	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)
LY388_09975	COG0596	Alpha beta hydrolase
LY388_09995	COG3135	benzoate transporter
LY388_10000	COG1396	sequence-specific DNA binding
LY388_10005	COG0840	transmembrane signaling receptor activity
LY388_10035	COG3015	lipoprotein NlpE involved in copper resistance
LY388_10040	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
LY388_10045	COG2894	cell division
LY388_10050	COG0850	regulation of cytokinetic process
LY388_10055	COG3100	YcgL domain-containing protein
LY388_10060	COG2951	lytic endotransglycosylase activity
LY388_10070	COG1972	Belongs to the concentrative nucleoside transporter (CNT) (TC 2.A.41) family
LY388_10080	COG3005	denitrification pathway
LY388_10085	COG0243	molybdopterin cofactor binding
LY388_10100	COG0654	COG0654 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases
LY388_10110	COG0190	Catalyzes the oxidation of 5,10- methylenetetrahydrofolate to 5,10-methenyltetrahydrofolate and then the hydrolysis of 5,10-methenyltetrahydrofolate to 10- formyltetrahydrofolate
LY388_10145	COG4589	Belongs to the CDS family
LY388_10155	COG5001	Diguanylate cyclase
LY388_10155	COG3300	MHYT domain
LY388_10165	COG0397	Uncharacterized ACR, YdiU/UPF0061 family
LY388_10170	COG1638	TRAP-type C4-dicarboxylate transport system periplasmic component
LY388_10175	COG3090	Trap-type c4-dicarboxylate transport system, small permease component
LY388_10180	COG1593	TRAP-type C4-dicarboxylate transport system, large permease component
LY388_10190	COG4191	Histidine kinase
LY388_10200	COG0544	peptidyl-prolyl cis-trans isomerase activity
LY388_10210	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
LY388_10215	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
LY388_10220	COG0776	regulation of translation
LY388_10225	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
LY388_10230	COG1555	photosystem II stabilization
LY388_10235	COG0283	belongs to the cytidylate kinase family. Type 1 subfamily
LY388_10240	COG0539	negative regulation of cytoplasmic translation
LY388_10245	COG0776	regulation of translation
LY388_10250	COG3771	Involved in the assembly of lipopolysaccharide (LPS)
LY388_10255	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
LY388_10265	COG0601	transmembrane transport
LY388_10270	COG4239	(ABC) transporter, permease
LY388_10275	COG0747	negative chemotaxis
LY388_10280	COG0444	Belongs to the ABC transporter superfamily
LY388_10285	COG4608	Belongs to the ABC transporter superfamily
LY388_10310	COG0583	DNA-binding transcription factor activity
LY388_10320	COG0686	Belongs to the AlaDH PNT family
LY388_10330	COG1674	ftsk spoiiie
LY388_10335	COG1495	Required for disulfide bond formation in some periplasmic proteins. Acts by oxidizing the DsbA protein
LY388_10340	COG3067	Na( ) H( ) antiporter that extrudes sodium in exchange for external protons
LY388_10345	COG2186	Transcriptional regulator
LY388_10360	COG0537	adenosine 5'-monophosphoramidase activity
LY388_10385	COG3150	esterase
LY388_10390	COG1252	NADH dehydrogenase
LY388_10410	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
LY388_10420	COG4591	ABC-type transport system involved in lipoprotein release permease component
LY388_10425	COG1136	(ABC) transporter
LY388_10430	COG4591	ABC-type transport system involved in lipoprotein release permease component
LY388_10440	COG0658	competence protein
LY388_10440	COG2333	competence protein COMEC
LY388_10445	COG1132	(ABC) transporter
LY388_10450	COG1663	tetraacyldisaccharide 4'-kinase activity
LY388_10455	COG2835	tetraacyldisaccharide 4'-kinase activity
LY388_10460	COG1212	Activates KDO (a required 8-carbon sugar) for incorporation into bacterial lipopolysaccharide in Gram-negative bacteria
LY388_10465	COG2719	SpoVR family
LY388_10470	COG2718	Belongs to the UPF0229 family
LY388_10475	COG2766	serine protein kinase
LY388_10480	COG3013	Belongs to the UPF0304 family
LY388_10490	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
LY388_10495	COG0840	transmembrane signaling receptor activity
LY388_10505	COG1882	Formate acetyltransferase
LY388_10530	COG4160	amino acid transport
LY388_10535	COG0708	Exodeoxyribonuclease III
LY388_10540	COG0840	transmembrane signaling receptor activity
LY388_10550	COG3923	Primosomal replication protein n
LY388_10555	COG0730	response to heat
LY388_10560	COG1199	ATP-dependent helicase activity
LY388_10575	COG3012	SEC-C Motif Domain Protein
LY388_10580	COG3434	signal transduction protein containing EAL and modified HD-GYP domains
LY388_10585	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
LY388_10590	COG0652	PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides
LY388_10595	COG0215	cysteine-tRNA ligase activity
LY388_10600	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
LY388_10605	COG0632	four-way junction helicase activity
LY388_10615	COG1271	oxidase subunit
LY388_10620	COG1294	oxidase, subunit
LY388_10625	COG4890	Cyd operon protein YbgT
LY388_10630	COG3790	cyd operon protein YbgE
LY388_10635	COG0824	Thioesterase
LY388_10640	COG0811	peptide transport
LY388_10655	COG0823	Involved in the tonB-independent uptake of proteins
LY388_10660	COG2885	chlorophyll binding
LY388_10670	COG0379	Catalyzes the condensation of iminoaspartate with dihydroxyacetone phosphate to form quinolinate
LY388_10680	COG0784	Response regulator, receiver
LY388_10680	COG5002	protein histidine kinase activity
LY388_10690	COG1482	cell wall glycoprotein biosynthetic process
LY388_10695	COG1445	protein-N(PI)-phosphohistidine-fructose phosphotransferase system transporter activity
LY388_10695	COG1299	protein-N(PI)-phosphohistidine-fructose phosphotransferase system transporter activity
LY388_10695	COG1762	phosphoenolpyruvate-dependent sugar phosphotransferase system
LY388_10700	COG2207	Transcriptional regulator
LY388_10710	COG1445	protein-N(PI)-phosphohistidine-fructose phosphotransferase system transporter activity
LY388_10715	COG1299	protein-N(PI)-phosphohistidine-fructose phosphotransferase system transporter activity
LY388_10720	COG1299	protein-N(PI)-phosphohistidine-fructose phosphotransferase system transporter activity
LY388_10730	COG1012	belongs to the aldehyde dehydrogenase family
LY388_10735	COG3284	Transcriptional regulator
LY388_10740	COG4628	conserved protein (DUF2132)
LY388_10750	COG0415	Belongs to the DNA photolyase family
LY388_10800	COG2003	Belongs to the UPF0758 family
LY388_10835	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
LY388_10840	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
LY388_10860	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
LY388_10870	COG1111	helicase
LY388_10870	COG1205	dead DEAH box helicase
LY388_10905	COG0582	viral genome integration into host DNA
LY388_10920	COG0845	Belongs to the membrane fusion protein (MFP) (TC 8.A.1) family
LY388_10930	COG1463	ABC-type transport system involved in resistance to organic solvents, periplasmic component
LY388_10930	COG3008	intermembrane lipid transfer
LY388_10935	COG2995	paraquat-inducible protein a
LY388_10940	COG1309	transcriptional regulator
LY388_10945	COG1012	belongs to the aldehyde dehydrogenase family
LY388_10965	COG1960	acyl-CoA dehydrogenase activity
LY388_10970	COG3007	enoyl-[acyl-carrier-protein] reductase (NADH) activity
LY388_10975	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
LY388_10985	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
LY388_11000	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
LY388_11005	COG0448	Catalyzes the synthesis of ADP-glucose, a sugar donor used in elongation reactions on alpha-glucans
LY388_11010	COG0297	glycogen (starch) synthase activity
LY388_11030	COG3070	regulator of competence-specific genes
LY388_11035	COG1609	Transcriptional regulator
LY388_11045	COG0745	RESPONSE REGULATOR receiver
LY388_11050	COG1434	Gram-negative-bacterium-type cell wall biogenesis
LY388_11055	COG2227	3-demethylubiquinone-9 3-O-methyltransferase activity
LY388_11060	COG3006	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. Not required for mini-F plasmid partitioning. Probably acts via its interaction with MukB and MukE. Overexpression results in anucleate cells. It has a calcium binding activity
LY388_11065	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
LY388_11070	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
LY388_11075	COG1979	alcohol dehydrogenase
LY388_11080	COG2207	Transcriptional regulator
LY388_11100	COG1032	radical SAM domain protein
LY388_11105	COG5001	Diguanylate cyclase
LY388_11110	COG0612	Peptidase, M16
LY388_11125	COG0583	DNA-binding transcription factor activity
LY388_11130	COG0620	Catalyzes the transfer of a methyl group from 5- methyltetrahydrofolate to homocysteine resulting in methionine formation
LY388_11140	COG2350	Protein conserved in bacteria
LY388_11145	COG1607	acyl-coa hydrolase
LY388_11160	COG1434	Gram-negative-bacterium-type cell wall biogenesis
LY388_11165	COG0451	ADP-glyceromanno-heptose 6-epimerase activity
LY388_11175	COG2116	formate transmembrane transporter activity
LY388_11180	COG4459	periplasmic nitrate reductase
LY388_11185	COG3005	denitrification pathway
LY388_11190	COG0243	molybdopterin cofactor binding
LY388_11210	COG1227	inorganic diphosphatase activity
LY388_11225	COG4172	Belongs to the ABC transporter superfamily
LY388_11240	COG4168	peptide transport system, permease
LY388_11250	COG1221	Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain
LY388_11255	COG1842	Phage shock protein A
LY388_11270	COG0845	Belongs to the membrane fusion protein (MFP) (TC 8.A.1) family
LY388_11285	COG2818	Glycosylase
LY388_11290	COG0626	cystathionine gamma-synthase activity
LY388_11300	COG0733	neurotransmitter:sodium symporter activity
LY388_11305	COG0564	pseudouridine synthase activity
LY388_11310	COG0558	Belongs to the CDP-alcohol phosphatidyltransferase class-I family
LY388_11315	COG4136	ATPase activity
LY388_11320	COG4135	transport system, permease component
LY388_11325	COG4134	Bacterial extracellular solute-binding protein
LY388_11335	COG3313	Fe-S protein
LY388_11345	COG0842	Transport permease protein
LY388_11350	COG1131	(ABC) transporter
LY388_11355	COG0845	Belongs to the membrane fusion protein (MFP) (TC 8.A.1) family
LY388_11360	COG0814	amino acid
LY388_11370	COG2239	Acts as a magnesium transporter
LY388_11375	COG0784	Response regulator, receiver
LY388_11375	COG2205	protein histidine kinase activity
LY388_11390	COG4934	collagen metabolic process
LY388_11425	COG0840	transmembrane signaling receptor activity
LY388_11435	COG5001	Diguanylate cyclase
LY388_11435	COG4251	negative regulation of phosphorylation
LY388_11435	COG3706	GGDEF domain
LY388_11435	COG2203	Gaf domain
LY388_11440	COG1825	This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance
LY388_11460	COG1061	Type III restriction enzyme res subunit
LY388_11465	COG1187	pseudouridine synthase activity
LY388_11470	COG2814	Major facilitator Superfamily
LY388_11480	COG0702	epimerase
LY388_11485	COG0534	Mate efflux family protein
LY388_11490	COG4181	ATPase activity
LY388_11495	COG0577	efflux transmembrane transporter activity
LY388_11505	COG3004	Na( ) H( ) antiporter that extrudes sodium in exchange for external protons
LY388_11515	COG1748	Saccharopine dehydrogenase
LY388_11530	COG1538	Outer membrane efflux protein
LY388_11550	COG0583	DNA-binding transcription factor activity
LY388_11560	COG1451	nucleotide metabolic process
LY388_11575	COG3063	Type IV pilus biogenesis stability protein PilW
LY388_11580	COG1897	L-methionine biosynthetic process from homoserine via O-succinyl-L-homoserine and cystathionine
LY388_11600	COG0845	Belongs to the membrane fusion protein (MFP) (TC 8.A.1) family
LY388_11615	COG3290	protein histidine kinase activity
LY388_11620	COG4565	transcriptional regulatory protein
LY388_11630	COG0784	Response regulator, receiver
LY388_11630	COG0835	chemotaxis
LY388_11675	COG1085	galactose-1-phosphate uridylyltransferase
LY388_11680	COG0153	Catalyzes the transfer of the gamma-phosphate of ATP to D-galactose to form alpha-D-galactose-1-phosphate (Gal-1-P)
LY388_11685	COG2017	converts alpha-aldose to the beta-anomer
LY388_11695	COG2199	diguanylate cyclase activity
LY388_11695	COG2200	EAL domain
LY388_11710	COG3527	Alpha-acetolactate decarboxylase
LY388_11725	COG1009	NADH ubiquinone oxidoreductase subunit 5 chain L Multisubunit Na H antiporter, MnhA subunit
LY388_11750	COG3097	Belongs to the UPF0267 family
LY388_11775	COG1271	oxidase subunit
LY388_11780	COG1294	oxidase, subunit
LY388_11785	COG1136	(ABC) transporter
LY388_11785	COG4591	ABC-type transport system involved in lipoprotein release permease component
LY388_11790	COG0577	efflux transmembrane transporter activity
LY388_11790	COG1136	(ABC) transporter
LY388_11795	COG0577	efflux transmembrane transporter activity
LY388_11795	COG1136	(ABC) transporter
LY388_11815	COG0583	DNA-binding transcription factor activity
LY388_11825	COG2723	6-phospho-beta-galactosidase activity
LY388_11830	COG1609	Transcriptional regulator
LY388_11835	COG0251	oxidation-reduction process
LY388_11840	COG2731	YhcH YjgK YiaL family protein
LY388_11845	COG0584	glycerophosphoryl diester phosphodiesterase
LY388_11850	COG1349	DNA-binding transcription factor activity
LY388_11855	COG3842	ATPase activity
LY388_11860	COG0395	ABC-type sugar transport system, permease component
LY388_11865	COG1175	transmembrane transport
LY388_11880	COG0811	peptide transport
LY388_11885	COG0811	peptide transport
LY388_11890	COG0848	biopolymer transport protein
LY388_11895	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
LY388_11905	COG1793	dna ligase
LY388_11915	COG0534	Mate efflux family protein
LY388_11925	COG3001	Fructosamine kinase
LY388_11935	COG0791	NLP P60 protein
LY388_11940	COG0840	transmembrane signaling receptor activity
LY388_11950	COG3148	PFAM DTW domain containing protein
LY388_11955	COG1940	carbohydrate kinase activity
LY388_11965	COG0303	'Molybdopterin
LY388_11970	COG0746	molybdenum cofactor guanylyltransferase activity
LY388_11975	COG3842	ATPase activity
LY388_11980	COG4662	Binding-protein-dependent transport system inner membrane component
LY388_11990	COG2204	response regulator
LY388_11995	COG3852	Histidine kinase
LY388_12000	COG0488	(ABC) transporter
LY388_12005	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
LY388_12035	COG0243	molybdopterin cofactor binding
LY388_12035	COG3383	formate dehydrogenase (NAD+) activity
LY388_12040	COG0437	4 iron, 4 sulfur cluster binding
LY388_12055	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
LY388_12060	COG1666	GTP binding
LY388_12065	COG0722	Stereospecific condensation of phosphoenolpyruvate (PEP) and D-erythrose-4-phosphate (E4P) giving rise to 3-deoxy-D- arabino-heptulosonate-7-phosphate (DAHP)
LY388_12080	COG2996	Protein conserved in bacteria
LY388_12090	COG3008	intermembrane lipid transfer
LY388_12095	COG2995	paraquat-inducible protein a
LY388_12100	COG1132	(ABC) transporter
LY388_12105	COG1956	GAF domain-containing protein
LY388_12110	COG3109	RNA chaperone with significant RNA binding, RNA strand exchange and RNA duplexing activities
LY388_12125	COG0308	aminopeptidase N
LY388_12140	COG0167	dihydroorotate dehydrogenase activity
LY388_12150	COG1092	Specifically methylates the guanine in position 2445 (m2G2445) and the guanine in position 2069 (m7G2069) of 23S rRNA
LY388_12150	COG0116	Belongs to the methyltransferase superfamily
LY388_12160	COG0488	(ABC) transporter
LY388_12175	COG0764	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity
LY388_12180	COG1067	ATP-dependent peptidase activity
LY388_12185	COG3120	sequence-specific DNA binding
LY388_12200	COG1073	alpha beta
LY388_12200	COG2931	calcium- and calmodulin-responsive adenylate cyclase activity
LY388_12200	COG3064	Membrane
LY388_12205	COG2994	toxin metabolic process
LY388_12230	COG0784	Response regulator, receiver
LY388_12230	COG2205	protein histidine kinase activity
LY388_12245	COG3278	Belongs to the heme-copper respiratory oxidase family
LY388_12260	COG2010	Cytochrome c
LY388_12270	COG2217	Heavy metal translocating P-type atpase
LY388_12285	COG0664	- Catabolite gene activator and regulatory subunit of cAMP-dependent protein
LY388_12290	COG0589	response to stress
LY388_12295	COG0037	tRNA processing
LY388_12315	COG3842	ATPase activity
LY388_12325	COG1177	transmembrane transport
LY388_12335	COG0687	Required for the activity of the bacterial periplasmic transport system of putrescine
LY388_12350	COG1115	amino acid carrier protein
LY388_12355	COG1280	lysine exporter protein (LysE YggA)
LY388_12370	COG3675	Pfam Lipase (class 3)
LY388_12380	COG3501	Rhs element vgr protein
LY388_12390	COG2317	Broad specificity carboxypetidase that releases amino acids sequentially from the C-terminus, including neutral, aromatic, polar and basic residues
LY388_12395	COG0840	transmembrane signaling receptor activity
LY388_12400	COG2814	Major facilitator Superfamily
LY388_12405	COG1566	PFAM secretion protein HlyD family protein
LY388_12420	COG0513	Belongs to the DEAD box helicase family
LY388_12430	COG0840	transmembrane signaling receptor activity
LY388_12445	COG0415	Belongs to the DNA photolyase family
LY388_12450	COG0477	Major facilitator Superfamily
LY388_12455	COG0583	DNA-binding transcription factor activity
LY388_12465	COG0095	Lipoate-protein ligase
LY388_12470	COG0443	Heat shock 70 kDa protein
LY388_12480	COG1643	Atp-dependent helicase
LY388_12550	COG0603	Catalyzes the ATP-dependent conversion of 7-carboxy-7- deazaguanine (CDG) to 7-cyano-7-deazaguanine (preQ(0))
LY388_12555	COG0602	queuosine metabolic process
LY388_12560	COG0561	phosphatase activity
LY388_12570	COG0834	ABC-type amino acid transport signal transduction systems periplasmic component domain
LY388_12575	COG4597	amino acid ABC transporter
LY388_12580	COG0765	amino acid transport
LY388_12585	COG1126	abc transporter atp-binding protein
LY388_12590	COG0670	Belongs to the BI1 family
LY388_12595	COG2920	part of a sulfur-relay system
LY388_12600	COG1254	Belongs to the acylphosphatase family
LY388_12605	COG1092	Specifically methylates the guanine in position 2445 (m2G2445) and the guanine in position 2069 (m7G2069) of 23S rRNA
LY388_12610	COG3706	GGDEF domain
LY388_12625	COG3437	response regulator, receiver
LY388_12630	COG0625	glutathione transferase activity
LY388_12640	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
LY388_12650	COG2195	Cleaves the N-terminal amino acid of tripeptides
LY388_12680	COG0372	Belongs to the citrate synthase family
LY388_12685	COG2513	Catalyzes the thermodynamically favored C-C bond cleavage of (2R,3S)-2-methylisocitrate to yield pyruvate and succinate
LY388_12725	COG1566	PFAM secretion protein HlyD family protein
LY388_12745	COG1129	ABC transporter
LY388_12770	COG0745	RESPONSE REGULATOR receiver
LY388_12775	COG2205	protein histidine kinase activity
LY388_12780	COG3713	MltA-interacting MipA family protein
LY388_12785	COG2990	Protein conserved in bacteria
LY388_12795	COG4191	Histidine kinase
LY388_12795	COG0834	ABC-type amino acid transport signal transduction systems periplasmic component domain
LY388_12800	COG0471	metal ion transport
LY388_12810	COG0787	Catalyzes the interconversion of L-alanine and D- alanine. May also act on other amino acids
LY388_12825	COG1670	COG1670 acetyltransferases, including N-acetylases of ribosomal proteins
LY388_12835	COG3768	UPF0283 membrane protein
LY388_12840	COG3106	COG3106 Predicted ATPase
LY388_12855	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
LY388_12860	COG0494	nUDIX hydrolase
LY388_12865	COG0814	amino acid
LY388_12870	COG1760	l-serine dehydratase
LY388_12875	COG0720	synthase
LY388_12880	COG0840	transmembrane signaling receptor activity
LY388_12885	COG0017	Asparaginyl-tRNA synthetase
LY388_12890	COG0351	phosphomethylpyrimidine kinase
LY388_12890	COG0352	thiamine-phosphate diphosphorylase activity
LY388_12895	COG3437	response regulator, receiver
LY388_12895	COG2770	Histidine kinase
LY388_12900	COG1448	Aminotransferase
LY388_12915	COG0840	transmembrane signaling receptor activity
LY388_12920	COG3131	Involved in the biosynthesis of osmoregulated periplasmic glucans (OPGs)
LY388_12925	COG2943	transferase activity, transferring hexosyl groups
LY388_12930	COG1609	Transcriptional regulator
LY388_12935	COG3394	polysaccharide catabolic process
LY388_12940	COG1486	melibiose metabolic process
LY388_12945	COG1447	Phosphotransferase system cellobiose-specific component IIA
LY388_12955	COG1440	protein-N(PI)-phosphohistidine-lactose phosphotransferase system transporter activity
LY388_12960	COG0726	polysaccharide deacetylase
LY388_12965	COG1292	Belongs to the BCCT transporter (TC 2.A.15) family
LY388_12970	COG1846	Transcriptional regulator
LY388_12995	COG4663	Part of the tripartite ATP-independent periplasmic (TRAP) transport system
LY388_13010	COG0491	Thiolesterase that catalyzes the hydrolysis of S-D- lactoyl-glutathione to form glutathione and D-lactic acid
LY388_13015	COG3108	Peptidase M15
LY388_13050	COG0807	Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate
LY388_13060	COG2814	Major facilitator Superfamily
LY388_13070	COG1054	Belongs to the UPF0176 family
LY388_13080	COG2227	3-demethylubiquinone-9 3-O-methyltransferase activity
LY388_13085	COG0209	Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides
LY388_13090	COG0208	Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides
LY388_13135	COG4138	Part of the ABC transporter complex BtuCDF involved in vitamin B12 import. Responsible for energy coupling to the transport system
LY388_13140	COG4139	cobalamin transport
LY388_13145	COG2988	succinylglutamate desuccinylase activity
LY388_13160	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
LY388_13165	COG2038	nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity
LY388_13170	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
LY388_13175	COG1823	symporter activity
LY388_13180	COG2925	Exonuclease
LY388_13185	COG1380	Effector of murein hydrolase LrgA
LY388_13190	COG1346	cytolysis
LY388_13220	COG0776	regulation of translation
LY388_13225	COG0072	phenylalanine-tRNA ligase activity
LY388_13225	COG0073	Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation
LY388_13230	COG0016	Belongs to the class-II aminoacyl-tRNA synthetase family. Phe-tRNA synthetase alpha subunit type 1 subfamily
LY388_13270	COG0322	excinuclease ABC activity
LY388_13275	COG2197	response regulator
LY388_13280	COG0417	DNA replication proofreading
LY388_13285	COG5001	Diguanylate cyclase
LY388_13295	COG0231	Involved in peptide bond synthesis. Stimulates efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. Probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase
LY388_13300	COG3099	Belongs to the UPF0263 family
LY388_13315	COG1228	amidohydrolase
LY388_13320	COG0010	Belongs to the arginase family
LY388_13325	COG2987	Catalyzes the conversion of urocanate to 4-imidazolone- 5-propionate
LY388_13330	COG2986	histidine ammonia-lyase
LY388_13350	COG0247	lactate metabolic process
LY388_13350	COG0277	FAD linked oxidase domain protein
LY388_13365	COG2885	chlorophyll binding
LY388_13385	COG0152	phosphoribosylaminoimidazolesuccinocarboxamide synthase activity
LY388_13395	COG0281	malic enzyme
LY388_13405	COG2949	membrane
LY388_13410	COG3706	GGDEF domain
LY388_13425	COG0492	ferredoxin-NADP+ reductase activity
LY388_13430	COG4988	ABC transporter
LY388_13435	COG4987	ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease ATP-binding protein CydC
LY388_13440	COG1187	pseudouridine synthase activity
LY388_13445	COG0009	L-threonylcarbamoyladenylate synthase
LY388_13450	COG0613	PHP domain protein
LY388_13460	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
LY388_13465	COG0512	Glutamine amidotransferase of anthranilate synthase
LY388_13470	COG0547	Catalyzes the transfer of the phosphoribosyl group of 5- phosphorylribose-1-pyrophosphate (PRPP) to anthranilate to yield N-(5'-phosphoribosyl)-anthranilate (PRA)
LY388_13475	COG0134	indole-3-glycerol-phosphate synthase activity
LY388_13475	COG0135	phosphoribosylanthranilate isomerase activity
LY388_13480	COG0133	tryptophan synthase activity
LY388_13485	COG0159	tryptophan synthase activity
LY388_13495	COG1435	thymidine kinase activity
LY388_13500	COG0173	Aspartyl-tRNA synthetase with relaxed tRNA specificity since it is able to aspartylate not only its cognate tRNA(Asp) but also tRNA(Asn). Reaction proceeds in two steps L-aspartate is first activated by ATP to form Asp-AMP and then transferred to the acceptor end of tRNA(Asp Asn)
LY388_13505	COG1801	Protein of unknown function DUF72
LY388_13510	COG4106	trans-aconitate 2-methyltransferase activity
LY388_13515	COG0500	methyltransferase
LY388_13520	COG0189	ligase activity
LY388_13520	COG4067	protein conserved in archaea
LY388_13535	COG1932	Catalyzes the reversible conversion of 3- phosphohydroxypyruvate to phosphoserine and of 3-hydroxy-2-oxo-4- phosphonooxybutanoate to phosphohydroxythreonine
LY388_13545	COG3852	Histidine kinase
LY388_13560	COG3070	regulator of competence-specific genes
LY388_13570	COG2431	L-lysine efflux transmembrane transporter activity
LY388_13580	COG0076	glutamate decarboxylase activity
LY388_13585	COG1737	Transcriptional regulator
LY388_13590	COG1012	belongs to the aldehyde dehydrogenase family
LY388_13590	COG1454	alcohol dehydrogenase
LY388_13595	COG0695	Has a glutathione-disulfide oxidoreductase activity in the presence of NADPH and glutathione reductase. Reduces low molecular weight disulfides and proteins
LY388_13600	COG2985	domain, Protein
LY388_13600	COG3273	potassium ion transport
LY388_13605	COG0542	response to heat
LY388_13610	COG2127	Involved in the modulation of the specificity of the ClpAP-mediated ATP-dependent protein degradation
LY388_13615	COG1278	Cold shock
LY388_13625	COG1187	pseudouridine synthase activity
LY388_13630	COG0139	Catalyzes the hydrolysis of the adenine ring of phosphoribosyl-AMP
LY388_13630	COG0140	phosphoribosyl-ATP diphosphatase activity
LY388_13635	COG0107	imidazoleglycerol-phosphate synthase activity
LY388_13640	COG0106	1-(5-phosphoribosyl)-5- 5-phosphoribosylamino)methylideneamino imidazole-4-carboxamide isomerase
LY388_13645	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
LY388_13650	COG0131	Imidazoleglycerol-phosphate dehydratase
LY388_13650	COG0241	D,D-heptose 1,7-bisphosphate phosphatase
LY388_13655	COG0079	Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. Histidinol-phosphate aminotransferase subfamily
LY388_13660	COG0141	Catalyzes the sequential NAD-dependent oxidations of L- histidinol to L-histidinaldehyde and then to L-histidine
LY388_13665	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
LY388_13670	COG1757	Na H antiporter
LY388_13675	COG2916	Histone family protein nucleoid-structuring protein H-NS
LY388_13680	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
LY388_13685	COG0482	sulfurtransferase activity
LY388_13690	COG2915	High frequency lysogenization protein hflD homolog
LY388_13695	COG0015	Belongs to the lyase 1 family. Adenylosuccinate lyase subfamily
LY388_13705	COG2268	Band 7 protein
LY388_13715	COG2230	cyclopropane-fatty-acyl-phospholipid synthase
LY388_13730	COG0300	oxidoreductase activity
LY388_13740	COG0501	Belongs to the peptidase M48B family
LY388_13750	COG2932	Transcriptional regulator
LY388_13755	COG3423	Transcriptional regulator
LY388_13760	COG2801	Transposase and inactivated derivatives
LY388_13765	COG2842	Transposition protein
LY388_13875	COG0640	Transcriptional regulator
LY388_13890	COG4373	Mu-like prophage FluMu protein gp28
LY388_13895	COG4383	Mu-like prophage protein gp29
LY388_13930	COG4397	Mu-like prophage major head subunit gpT
LY388_13940	COG4387	Mu-like prophage protein GP36
LY388_13965	COG4386	tail sheath protein
LY388_13975	COG4518	Phage tail assembly chaperone proteins, E, or 41 or 14
LY388_13995	COG4384	Bacteriophage Mu Gp45 protein
LY388_14005	COG3299	homolog of phage Mu protein gp47
LY388_14010	COG3778	Protein conserved in bacteria
LY388_14025	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
LY388_14030	COG2226	methyltransferase
LY388_14035	COG0156	8-amino-7-oxononanoate synthase activity
LY388_14040	COG0502	Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical- based mechanism
LY388_14045	COG0161	adenosylmethionine-8-amino-7-oxononanoate transaminase activity
LY388_14050	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)
LY388_14055	COG2256	atpase related to the helicase subunit of the holliday junction resolvase
LY388_14060	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)
LY388_14070	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
LY388_14075	COG2199	diguanylate cyclase activity
LY388_14075	COG2203	Gaf domain
LY388_14085	COG4120	Belongs to the binding-protein-dependent transport system permease family
LY388_14095	COG4628	conserved protein (DUF2132)
LY388_14100	COG3092	negative regulation of chromosome organization
LY388_14105	COG0282	Catalyzes the formation of acetyl phosphate from acetate and ATP. Can also catalyze the reverse reaction
LY388_14110	COG0280	phosphate acetyltransferase
LY388_14110	COG0857	belongs to the CobB CobQ family
LY388_14115	COG0435	Glutathione S-transferase
LY388_14120	COG4608	Belongs to the ABC transporter superfamily
LY388_14125	COG0444	Belongs to the ABC transporter superfamily
LY388_14130	COG1173	ABC-type dipeptide oligopeptide nickel transport systems, permease components
LY388_14135	COG0601	transmembrane transport
LY388_14155	COG2204	response regulator
LY388_14160	COG5001	Diguanylate cyclase
LY388_14160	COG3300	MHYT domain
LY388_14165	COG4191	Histidine kinase
LY388_14170	COG5002	protein histidine kinase activity
LY388_14180	COG2201	protein-glutamate methylesterase activity
LY388_14195	COG0009	L-threonylcarbamoyladenylate synthase
LY388_14210	COG1881	PFAM PEBP family protein
LY388_14235	COG0057	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
LY388_14240	COG0640	Transcriptional regulator
LY388_14250	COG3706	GGDEF domain
LY388_14270	COG1946	Acyl-CoA thioesterase
LY388_14275	COG1522	sequence-specific DNA binding
LY388_14285	COG0616	signal peptide processing
LY388_14290	COG1028	Short-chain dehydrogenase reductase Sdr
LY388_14295	COG2983	Belongs to the UPF0260 family
LY388_14305	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
LY388_14310	COG0718	Binds to DNA and alters its conformation. May be involved in regulation of gene expression, nucleoid organization and DNA protection
LY388_14320	COG0503	Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis
LY388_14325	COG2832	Protein of unknown function (DUF454)
LY388_14330	COG0745	RESPONSE REGULATOR receiver
LY388_14335	COG0583	DNA-binding transcription factor activity
LY388_14340	COG0778	Nitroreductase
LY388_14345	COG1024	Enoyl-CoA hydratase
LY388_14345	COG1250	3-hydroxyacyl-CoA dehydrogenase
LY388_14350	COG0183	Belongs to the thiolase family
LY388_14365	COG2067	long-chain fatty acid transport protein
LY388_14375	COG0394	Belongs to the low molecular weight phosphotyrosine protein phosphatase family
LY388_14380	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
LY388_14385	COG2982	Protein involved in outer membrane biogenesis
LY388_14390	COG0572	uridine kinase
LY388_14395	COG0489	protein tyrosine kinase activity
LY388_14400	COG0143	Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation
LY388_14400	COG0073	Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation
LY388_14410	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
LY388_14420	COG0617	tRNA 3'-terminal CCA addition
LY388_14420	COG0517	IMP dehydrogenase activity
LY388_14420	COG0618	3'(2'),5'-bisphosphate nucleotidase activity
LY388_14425	COG2199	diguanylate cyclase activity
LY388_14430	COG0314	molybdopterin synthase activity
LY388_14435	COG1977	Involved in sulfur transfer in the conversion of molybdopterin precursor Z to molybdopterin
LY388_14440	COG0315	cyclic pyranopterin monophosphate synthase activity
LY388_14445	COG0521	Mo-molybdopterin cofactor biosynthetic process
LY388_14450	COG2896	Catalyzes the cyclization of GTP to (8S)-3',8-cyclo-7,8- dihydroguanosine 5'-triphosphate
LY388_14455	COG0391	Required for morphogenesis under gluconeogenic growth conditions
LY388_14460	COG2198	Histidine kinase
LY388_14465	COG2204	response regulator
LY388_14470	COG0556	nucleotide-excision repair
LY388_14480	COG4657	Part of a membrane complex involved in electron transport
LY388_14485	COG2878	Part of a membrane complex involved in electron transport
LY388_14490	COG4656	Part of a membrane complex involved in electron transport
LY388_14505	COG4660	Part of a membrane complex involved in electron transport
LY388_14510	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
LY388_14515	COG0346	lactoylglutathione lyase activity
LY388_14530	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
LY388_14535	COG2056	Na+-H+ antiporter family
LY388_14540	COG0034	Catalyzes the formation of phosphoribosylamine from phosphoribosylpyrophosphate (PRPP) and glutamine
LY388_14545	COG1286	toxin biosynthetic process
LY388_14550	COG3147	Non-essential cell division protein that could be required for efficient cell constriction
LY388_14555	COG0285	dihydrofolate synthase activity
LY388_14560	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
LY388_14565	COG0101	tRNA pseudouridine synthase activity
LY388_14585	COG2190	(PTS) system
LY388_14585	COG1263	PTS System
LY388_14585	COG1264	protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
LY388_14590	COG1820	Belongs to the metallo-dependent hydrolases superfamily. NagA family
LY388_14595	COG1846	Transcriptional regulator
LY388_14595	COG1940	carbohydrate kinase activity
LY388_14600	COG1226	(belongs to the monovalent cation proton antiporter 2 (CPA2) transporter (TC 2.A.37) family)
LY388_14600	COG4651	solute:proton antiporter activity
LY388_14605	COG0367	asparagine synthase
LY388_14620	COG0276	Catalyzes the ferrous insertion into protoporphyrin IX
LY388_14625	COG0563	adenylate kinase activity
LY388_14630	COG0326	Molecular chaperone. Has ATPase activity
LY388_14635	COG3710	Transcriptional regulator
LY388_14650	COG0622	Phosphoesterase
LY388_14655	COG1090	epimerase
LY388_14660	COG0300	oxidoreductase activity
LY388_14665	COG3118	belongs to the thioredoxin family
LY388_14670	COG0330	HflC and HflK could
LY388_14675	COG1585	Membrane protein implicated in regulation of membrane protease activity
LY388_14680	COG0789	Transcriptional regulator
LY388_14695	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
LY388_14700	COG3115	cell septum assembly
LY388_14705	COG2981	High affinity, high specificity proton-dependent sulfate transporter, which mediates sulfate uptake. Provides the sulfur source for the cysteine synthesis pathway
LY388_14710	COG0031	Belongs to the cysteine synthase cystathionine beta- synthase family
LY388_14715	COG1925	phosphoenolpyruvate-dependent sugar phosphotransferase system
LY388_14725	COG2190	(PTS) system
LY388_14730	COG0654	COG0654 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases
LY388_14735	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
LY388_14740	COG1702	phosphate starvation-inducible protein PhoH
LY388_14745	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
LY388_14750	COG4535	Mg2 and Co2 transporter CorC
LY388_14755	COG0815	Transfers the fatty acyl group on membrane lipoproteins
LY388_14760	COG2888	peptidyl-tyrosine sulfation
LY388_14765	COG0495	leucyl-tRNA aminoacylation
LY388_14770	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
LY388_14775	COG1466	dna polymerase III delta subunit
LY388_14780	COG0799	negative regulation of ribosome biogenesis
LY388_14785	COG1576	Specifically methylates the pseudouridine at position 1915 (m3Psi1915) in 23S rRNA
LY388_14790	COG0768	penicillin binding
LY388_14795	COG0772	Belongs to the SEDS family
LY388_14800	COG0797	Lytic transglycosylase with a strong preference for naked glycan strands that lack stem peptides
LY388_14805	COG1686	Belongs to the peptidase S11 family
LY388_14810	COG2921	Belongs to the UPF0250 family
LY388_14815	COG0321	lipoyl(octanoyl) transferase activity
LY388_14820	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
LY388_14830	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
LY388_14855	COG1596	polysaccharide export
LY388_14865	COG2148	undecaprenyl-phosphate glucose phosphotransferase activity
LY388_14895	COG1922	lipopolysaccharide N-acetylmannosaminouronosyltransferase activity
LY388_14905	COG0438	transferase activity, transferring glycosyl groups
LY388_14915	COG1045	serine acetyltransferase
LY388_14935	COG0110	maltose O-acetyltransferase activity
LY388_14940	COG0677	UDP-N-acetyl-D-mannosamine dehydrogenase activity
LY388_14945	COG0381	UDP-N-acetylglucosamine 2-epimerase activity
LY388_14950	COG0394	Belongs to the low molecular weight phosphotyrosine protein phosphatase family
LY388_14955	COG0841	Belongs to the resistance-nodulation-cell division (RND) (TC 2.A.6) family
LY388_14985	COG0366	Alpha amylase catalytic
LY388_14990	COG1264	protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
LY388_14990	COG1263	PTS System
LY388_14995	COG1609	Transcriptional regulator
LY388_15000	COG0241	D,D-heptose 1,7-bisphosphate phosphatase
LY388_15005	COG1135	Part of the ABC transporter complex MetNIQ involved in methionine import. Responsible for energy coupling to the transport system
LY388_15010	COG2011	ABC-type metal ion transport system permease component
LY388_15015	COG1464	Belongs to the NlpA lipoprotein family
LY388_15020	COG5595	Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310)
LY388_15030	COG2904	Catalyzes the NADPH-dependent reduction of 7-cyano-7- deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1)
LY388_15030	COG0780	Catalyzes the NADPH-dependent reduction of 7-cyano-7- deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1)
LY388_15045	COG1611	Belongs to the LOG family
LY388_15050	COG0258	In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity
LY388_15055	COG2363	Small membrane protein
LY388_15060	COG0583	DNA-binding transcription factor activity
LY388_15065	COG0301	tRNA thio-modification
LY388_15065	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
LY388_15075	COG1291	archaeal or bacterial-type flagellum-dependent cell motility
LY388_15085	COG1722	exodeoxyribonuclease VII activity
LY388_15090	COG0142	geranyltranstransferase activity
LY388_15095	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)
LY388_15100	COG0564	pseudouridine synthase activity
LY388_15105	COG3098	single-species biofilm formation
LY388_15120	COG1670	COG1670 acetyltransferases, including N-acetylases of ribosomal proteins
LY388_15130	COG1671	Belongs to the UPF0178 family
LY388_15135	COG2978	secondary active p-aminobenzoyl-glutamate transmembrane transporter activity
LY388_15140	COG0257	Belongs to the bacterial ribosomal protein bL36 family
LY388_15145	COG0254	rRNA binding
LY388_15150	COG1720	tRNA m6t6A37 methyltransferase activity
LY388_15155	COG0442	prolyl-tRNA aminoacylation
LY388_15175	COG0047	phosphoribosylformylglycinamidine synthase activity
LY388_15175	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
LY388_15185	COG4623	carbon-oxygen lyase activity, acting on polysaccharides
LY388_15195	COG2978	secondary active p-aminobenzoyl-glutamate transmembrane transporter activity
LY388_15225	COG0484	heat shock protein binding
LY388_15230	COG0443	Heat shock 70 kDa protein
LY388_15240	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
LY388_15245	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
LY388_15250	COG0497	DNA recombination
LY388_15255	COG2913	Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane
LY388_15260	COG2914	Belongs to the UPF0125 (RnfH) family
LY388_15265	COG2867	negative regulation of translational initiation
LY388_15270	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
LY388_15320	COG2509	5-formyltetrahydrofolate cyclo-ligase activity
LY388_15325	COG1146	Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions
LY388_15330	COG0566	Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase TrmH family
LY388_15350	COG3051	citrate lyase alpha subunit
LY388_15355	COG2301	Belongs to the HpcH HpaI aldolase family
LY388_15365	COG3053	Acetylation of prosthetic group (2-(5''-phosphoribosyl)- 3'-dephosphocoenzyme-A) of the gamma subunit of citrate lyase
LY388_15380	COG0511	ligase activity, forming carbon-carbon bonds
LY388_15380	COG5016	pyruvate
LY388_15385	COG1883	Na -transporting methylmalonyl-CoA oxaloacetate decarboxylase, beta subunit
LY388_15395	COG4565	transcriptional regulatory protein
LY388_15410	COG0583	DNA-binding transcription factor activity
LY388_15420	COG1115	amino acid carrier protein
LY388_15425	COG2015	COG2015, Alkyl sulfatase and related hydrolases
LY388_15430	COG0583	DNA-binding transcription factor activity
LY388_15440	COG1120	ATPase activity
LY388_15445	COG4779	Belongs to the binding-protein-dependent transport system permease family. FecCD subfamily
LY388_15450	COG0609	Belongs to the binding-protein-dependent transport system permease family. FecCD subfamily
LY388_15455	COG4592	Periplasmic binding protein
LY388_15465	COG1028	Short-chain dehydrogenase reductase Sdr
LY388_15470	COG1169	isochorismate synthase
LY388_15475	COG1021	2,3-dihydroxybenzoate-AMP ligase
LY388_15480	COG1535	isochorismatase
LY388_15480	COG3433	isochorismatase activity
LY388_15485	COG1584	GPR1 FUN34 yaaH family protein
LY388_15495	COG0518	GMP synthase (glutamine-hydrolyzing) activity
LY388_15495	COG0519	Catalyzes the synthesis of GMP from XMP
LY388_15500	COG0516	GMP reductase activity
LY388_15500	COG0517	IMP dehydrogenase activity
LY388_15505	COG1570	exodeoxyribonuclease VII activity
LY388_15520	COG1160	GTP binding
LY388_15525	COG1520	Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane
LY388_15530	COG2976	Protein conserved in bacteria
LY388_15535	COG0124	histidyl-tRNA synthetase
LY388_15540	COG0821	Converts 2C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-2,4cPP) into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate
LY388_15545	COG1426	Protein conserved in bacteria
LY388_15555	COG0105	UTP biosynthetic process
LY388_15560	COG0260	Presumably involved in the processing and regular turnover of intracellular proteins. Catalyzes the removal of unsubstituted N-terminal amino acids from various peptides
LY388_15565	COG2975	iron-sulfur cluster assembly
LY388_15570	COG0633	Ferredoxin
LY388_15590	COG0822	iron-sulfur transferase activity
LY388_15600	COG1959	2 iron, 2 sulfur cluster binding
LY388_15610	COG0483	inositol monophosphate 1-phosphatase activity
LY388_15615	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
LY388_15620	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
LY388_15625	COG1862	Preprotein translocase
LY388_15635	COG0809	Transfers and isomerizes the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to give epoxyqueuosine (oQ-tRNA)
LY388_15640	COG0517	IMP dehydrogenase activity
LY388_15650	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
LY388_15655	COG0583	DNA-binding transcription factor activity
LY388_15660	COG0450	alkyl hydroperoxide reductase
LY388_15665	COG3142	Participates in the control of copper homeostasis
LY388_15680	COG1117	ATPase-coupled phosphate ion transmembrane transporter activity
LY388_15685	COG0581	inorganic phosphate transmembrane transporter activity
LY388_15695	COG0855	Catalyzes the reversible transfer of the terminal phosphate of ATP to form a long-chain polyphosphate (polyP)
LY388_15700	COG0248	Ppx GppA phosphatase
LY388_15710	COG5002	protein histidine kinase activity
LY388_15715	COG0745	RESPONSE REGULATOR receiver
LY388_15725	COG0826	peptidase U32
LY388_15730	COG1145	4fe-4S ferredoxin, iron-sulfur binding domain protein
LY388_15775	COG0542	response to heat
LY388_15785	COG0564	pseudouridine synthase activity
LY388_15790	COG4105	Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane
LY388_15795	COG1544	Required for dimerization of active 70S ribosomes into 100S ribosomes in stationary phase
LY388_15800	COG0077	Prephenate dehydratase
LY388_15800	COG1605	Chorismate mutase
LY388_15805	COG0687	Required for the activity of the bacterial periplasmic transport system of putrescine
LY388_15810	COG5001	Diguanylate cyclase
LY388_15820	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
LY388_15830	COG0488	(ABC) transporter
LY388_15840	COG0287	Prephenate dehydrogenase
LY388_15840	COG1605	Chorismate mutase
LY388_15845	COG0722	Stereospecific condensation of phosphoenolpyruvate (PEP) and D-erythrose-4-phosphate (E4P) giving rise to 3-deoxy-D- arabino-heptulosonate-7-phosphate (DAHP)
LY388_15850	COG3275	phosphorelay sensor kinase activity
LY388_15855	COG3279	Response regulator of the LytR AlgR family
LY388_15865	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
LY388_15870	COG2103	Specifically catalyzes the cleavage of the D-lactyl ether substituent of MurNAc 6-phosphate, producing GlcNAc 6- phosphate and D-lactate
LY388_15885	COG1966	Carbon starvation protein
LY388_15890	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
LY388_15895	COG1047	Peptidyl-prolyl cis-trans
LY388_15900	COG0597	This protein specifically catalyzes the removal of signal peptides from prolipoproteins
LY388_15910	COG0196	riboflavin kinase activity
LY388_15915	COG0728	peptidoglycan biosynthetic process
LY388_15920	COG0268	Binds directly to 16S ribosomal RNA
LY388_15925	COG0640	Transcriptional regulator
LY388_15930	COG0583	DNA-binding transcription factor activity
LY388_15935	COG1283	sodium-dependent phosphate transmembrane transporter activity
LY388_15945	COG0682	Transfers the N-acyl diglyceride group on what will become the N-terminal cysteine of membrane lipoproteins
LY388_15950	COG0730	response to heat
LY388_15955	COG3605	phosphoenolpyruvate-protein phosphotransferase activity
LY388_15960	COG0494	nUDIX hydrolase
LY388_15970	COG0667	Aldo Keto reductase
LY388_15980	COG2204	response regulator
LY388_15985	COG1190	Belongs to the class-II aminoacyl-tRNA synthetase family
LY388_16005	COG0513	Belongs to the DEAD box helicase family
LY388_16115	COG2003	Belongs to the UPF0758 family
LY388_16140	COG0714	Associated with various cellular activities
LY388_16160	COG0629	single-stranded DNA binding
LY388_16175	COG0464	growth
LY388_16180	COG1404	Belongs to the peptidase S8 family
LY388_16190	COG1074	ATP-dependent DNA helicase activity
LY388_16210	COG0681	Belongs to the peptidase S26 family
LY388_16230	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
LY388_16235	COG5001	Diguanylate cyclase
LY388_16245	COG0659	secondary active sulfate transmembrane transporter activity
LY388_16315	COG1196	nuclear chromosome segregation
LY388_16370	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
LY388_16435	COG1357	PFAM Pentapeptide repeats (8 copies)
LY388_16480	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
LY388_16500	COG3153	acetyltransferase
LY388_16505	COG3154	lipid carrier protein
LY388_16515	COG0826	peptidase U32
LY388_16520	COG0826	peptidase U32
LY388_16545	COG0184	Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome
LY388_16555	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
LY388_16560	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
LY388_16565	COG0195	Participates in both transcription termination and antitermination
LY388_16570	COG0779	Required for maturation of 30S ribosomal subunits
LY388_16585	COG1314	P-P-bond-hydrolysis-driven protein transmembrane transporter activity
LY388_16595	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
LY388_16600	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
LY388_16605	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
LY388_16610	COG1534	Rna-binding protein
LY388_16615	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
LY388_16620	COG3203	Forms passive diffusion pores that allow small molecular weight hydrophilic materials across the outer membrane
LY388_16625	COG2027	D-alanyl-D-alanine carboxypeptidase
LY388_16630	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)
LY388_16635	COG0739	heme binding
LY388_16650	COG0316	Belongs to the HesB IscA family
LY388_16655	COG0001	glutamate-1-semialdehyde 2,1-aminomutase activity
LY388_16660	COG0628	permease
LY388_16665	COG2813	Specifically methylates the guanine in position
LY388_16670	COG2205	protein histidine kinase activity
LY388_16670	COG0784	Response regulator, receiver
LY388_16675	COG0747	negative chemotaxis
LY388_16680	COG0601	transmembrane transport
LY388_16685	COG1173	ABC-type dipeptide oligopeptide nickel transport systems, permease components
LY388_16690	COG0444	Belongs to the ABC transporter superfamily
LY388_16695	COG4608	Belongs to the ABC transporter superfamily
LY388_16705	COG2971	BadF BadG BcrA BcrD
LY388_16720	COG1109	Catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate
LY388_16725	COG3842	ATPase activity
LY388_16735	COG1840	ABC-type Fe3 transport system, periplasmic component
LY388_16740	COG0004	ammonium transporteR
LY388_16745	COG0347	Belongs to the P(II) protein family
LY388_16750	COG3112	Uncharacterised protein family (UPF0231)
LY388_16755	COG1049	propionate catabolic process, 2-methylcitrate cycle
LY388_16760	COG1752	Esterase of the alpha-beta hydrolase superfamily
LY388_16765	COG0744	Peptidoglycan polymerase that catalyzes glycan chain elongation from lipid-linked precursors
LY388_16770	COG1643	Atp-dependent helicase
LY388_16780	COG1489	DNA binding
LY388_16790	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)
LY388_16800	COG0801	2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
LY388_16805	COG0413	3-methyl-2-oxobutanoate hydroxymethyltransferase activity
LY388_16810	COG0414	Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate
LY388_16815	COG0842	Transport permease protein
LY388_16820	COG1131	(ABC) transporter
LY388_16825	COG0659	secondary active sulfate transmembrane transporter activity
LY388_16830	COG0288	reversible hydration of carbon dioxide
LY388_16845	COG0313	Catalyzes the 2'-O-methylation of the ribose of cytidine 1402 (C1402) in 16S rRNA
LY388_16850	COG3107	peptidoglycan biosynthetic process
LY388_16855	COG0792	nuclease activity
LY388_16860	COG0279	D-glycero-D-manno-heptose 7-phosphate biosynthetic process
LY388_16865	COG2823	Periplasmic or secreted lipoprotein
LY388_16870	COG2969	positive regulation of protein catabolic process
LY388_16875	COG0625	glutathione transferase activity
LY388_16880	COG2857	Cytochrome c1
LY388_16885	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
LY388_16890	COG0723	plastoquinol--plastocyanin reductase activity
LY388_16895	COG0103	maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
LY388_16900	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
LY388_16905	COG1485	Reduces the stability of FtsZ polymers in the presence of ATP
LY388_16915	COG0265	Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain
LY388_16920	COG0265	Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain
LY388_16925	COG0335	large ribosomal subunit rRNA binding
LY388_16930	COG0336	Belongs to the RNA methyltransferase TrmD family
LY388_16935	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
LY388_16940	COG0228	four-way junction DNA binding
LY388_16945	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
LY388_16950	COG4137	Cytochrome C assembly protein
LY388_16955	COG4536	flavin adenine dinucleotide binding
LY388_16960	COG1854	S-ribosylhomocysteine lyase activity
LY388_16965	COG2918	glutathione biosynthetic process
LY388_16970	COG0612	Peptidase, M16
LY388_16975	COG1238	metal cluster binding
LY388_16985	COG1883	Na -transporting methylmalonyl-CoA oxaloacetate decarboxylase, beta subunit
LY388_16990	COG5016	pyruvate
LY388_16990	COG0511	ligase activity, forming carbon-carbon bonds
LY388_16995	COG3630	sodium ion export across plasma membrane
LY388_17040	COG1551	Could accelerate the degradation of some genes transcripts potentially through selective RNA binding
LY388_17045	COG0527	aspartate kinase activity
LY388_17050	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
LY388_17055	COG2137	regulation of response to DNA damage stimulus
LY388_17060	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
LY388_17070	COG1118	Part of the ABC transporter complex CysAWTP involved in sulfate thiosulfate import. Responsible for energy coupling to the transport system
LY388_17075	COG4208	sulfate ABC transporter
LY388_17095	COG0249	that it carries out the mismatch recognition step. This protein has a weak ATPase activity
LY388_17100	COG0568	sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released
LY388_17110	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
LY388_17115	COG0496	Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates
LY388_17120	COG0585	pseudouridine synthase activity
LY388_17125	COG0245	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity
LY388_17130	COG1211	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity
LY388_17135	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
LY388_17140	COG1968	undecaprenyl-diphosphatase activity
LY388_17145	COG0801	2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
LY388_17150	COG1539	Catalyzes the conversion of 7,8-dihydroneopterin to 6- hydroxymethyl-7,8-dihydropterin
LY388_17155	COG0344	acyl-phosphate glycerol-3-phosphate acyltransferase activity
LY388_17165	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
LY388_17170	COG0828	Belongs to the bacterial ribosomal protein bS21 family
LY388_17175	COG1610	YqeY-like protein
LY388_17180	COG0358	DNA primase activity
LY388_17200	COG4663	Part of the tripartite ATP-independent periplasmic (TRAP) transport system
LY388_17205	COG0449	glutamine-fructose-6-phosphate transaminase (isomerizing) activity
LY388_17210	COG1349	DNA-binding transcription factor activity
LY388_17230	COG1279	arginine transmembrane transporter activity
LY388_17235	COG0668	transmembrane transport
LY388_17240	COG0191	fructose-bisphosphate aldolase activity
LY388_17245	COG0126	phosphoglycerate kinase activity
LY388_17250	COG0057	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
LY388_17255	COG4771	TonB-dependent receptor
LY388_17260	COG0583	DNA-binding transcription factor activity
LY388_17265	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
LY388_17270	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
LY388_17280	COG2356	endonuclease I
LY388_17285	COG1385	rRNA (uridine-N3-)-methyltransferase activity
LY388_17290	COG0189	ligase activity
LY388_17295	COG1678	Uncharacterized ACR, COG1678
LY388_17300	COG0816	Could be a nuclease involved in processing of the 5'-end of pre-16S rRNA
LY388_17305	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)
LY388_17325	COG0325	Pyridoxal 5'-phosphate (PLP)-binding protein, which is involved in PLP homeostasis
LY388_17330	COG0345	Catalyzes the reduction of 1-pyrroline-5-carboxylate (PCA) to L-proline
LY388_17335	COG0762	integral membrane protein
LY388_17350	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
LY388_17355	COG0635	Involved in the biosynthesis of porphyrin-containing compound
LY388_17360	COG2066	Belongs to the glutaminase family
LY388_17365	COG0220	tRNA (guanine-N7-)-methyltransferase activity
LY388_17370	COG1194	a g-specific adenine glycosylase
LY388_17375	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
LY388_17380	COG0741	lytic transglycosylase activity
LY388_17435	COG1076	Co-chaperone involved in the maturation of iron-sulfur cluster-containing proteins. Seems to help targeting proteins to be folded toward HscA
LY388_17440	COG1452	involved in the assembly of lipopolysaccharide (LPS) at the surface of the outer membrane
LY388_17445	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
LY388_17450	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)
LY388_17455	COG0030	16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity
LY388_17460	COG2967	ApaG domain
LY388_17465	COG0639	Hydrolyzes diadenosine 5',5'''-P1,P4-tetraphosphate to yield ADP
LY388_17475	COG3610	response to peptide
LY388_17480	COG2966	Psort location CytoplasmicMembrane, score
LY388_17485	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
LY388_17490	COG0211	Belongs to the bacterial ribosomal protein bL27 family
LY388_17495	COG0261	This protein binds to 23S rRNA in the presence of protein L20
LY388_17500	COG0142	geranyltranstransferase activity
LY388_17505	COG0531	amino acid
LY388_17510	COG0039	L-malate dehydrogenase activity
LY388_17515	COG1438	arginine binding
LY388_17520	COG2358	TRAP transporter, solute receptor (TAXI family
LY388_17530	COG0589	response to stress
LY388_17550	COG2235	arginine
LY388_17555	COG0312	modulator of DNA gyrase
LY388_17560	COG0388	Catalyzes the ATP-dependent amidation of deamido-NAD to form NAD. Uses L-glutamine as a nitrogen source
LY388_17565	COG3164	Protein of unknown function
LY388_17575	COG0424	maF-like protein
LY388_17580	COG2891	Involved in formation of the rod shape of the cell. May also contribute to regulation of formation of penicillin-binding proteins
LY388_17585	COG1792	Involved in formation and maintenance of cell shape
LY388_17590	COG1077	Cell shape determining protein MreB Mrl
LY388_17620	COG2165	general secretion pathway protein
LY388_17625	COG2165	general secretion pathway protein
LY388_17635	COG1459	type II secretion system
LY388_17640	COG2804	Type II secretory pathway, ATPase PulE Tfp pilus assembly pathway, ATPase PilB
LY388_17650	COG3409	Peptidoglycan-binding domain 1 protein
LY388_17650	COG3267	Type II secretory pathway component ExeA
LY388_17675	COG2200	EAL domain
LY388_17675	COG2199	diguanylate cyclase activity
LY388_17680	COG0629	single-stranded DNA binding
LY388_17695	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
LY388_17705	COG0075	2-aminoethylphosphonate-pyruvate transaminase activity
LY388_17710	COG0527	aspartate kinase activity
LY388_17715	COG1410	methionine synthase
LY388_17715	COG0646	methionine synthase
LY388_17755	COG0175	sulfate reduction
LY388_17765	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
LY388_17790	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
LY388_17905	COG0840	transmembrane signaling receptor activity
LY388_17910	COG4772	TonB-dependent receptor
LY388_17930	COG0840	transmembrane signaling receptor activity
LY388_17950	COG0735	belongs to the Fur family
LY388_17965	COG0166	Belongs to the GPI family
LY388_17970	COG0432	Pfam Uncharacterised protein family UPF0047
LY388_17975	COG0787	Catalyzes the interconversion of L-alanine and D- alanine. May also act on other amino acids
LY388_17990	COG0359	binds to the 23S rRNA
LY388_17995	COG0238	Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit
LY388_18000	COG2965	DNA replication, synthesis of RNA primer
LY388_18005	COG0360	Binds together with S18 to 16S ribosomal RNA
LY388_18015	COG2906	2 iron, 2 sulfur cluster binding
LY388_18020	COG0050	This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis
LY388_18025	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
LY388_18030	COG0049	tRNA binding
LY388_18045	COG2923	Belongs to the DsrF TusC family
LY388_18050	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
LY388_18055	COG2964	Protein conserved in bacteria
LY388_18060	COG0545	Peptidyl-prolyl cis-trans isomerase
LY388_18070	COG2900	Belongs to the SlyX family
LY388_18075	COG3242	Uncharacterized protein conserved in bacteria (DUF2065)
LY388_18080	COG0330	HflC and HflK could
LY388_18085	COG0330	HflC and HflK could
LY388_18090	COG2262	GTPase that associates with the 50S ribosomal subunit and may have a role during protein synthesis or ribosome biogenesis
LY388_18095	COG1923	regulation of RNA biosynthetic process
LY388_18100	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)
LY388_18105	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
LY388_18115	COG0802	atpase or kinase
LY388_18120	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)
LY388_18165	COG1949	3'-to-5' exoribonuclease specific for small oligoribonucleotides
LY388_18170	COG1162	GTPase activity
LY388_18175	COG0688	phosphatidylethanolamine metabolic process
LY388_18180	COG0471	metal ion transport
LY388_18190	COG0696	Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate
LY388_18195	COG4942	peptidase
LY388_18210	COG0407	Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III
LY388_18215	COG2816	NAD+ diphosphatase activity
LY388_18220	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
LY388_18230	COG0086	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates
LY388_18235	COG0085	RNA polymerase activity
LY388_18240	COG0222	ribosome binding
LY388_18245	COG0244	Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors
LY388_18255	COG0080	Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors
LY388_18260	COG0250	Participates in transcription elongation, termination and antitermination
LY388_18265	COG0690	P-P-bond-hydrolysis-driven protein transmembrane transporter activity
LY388_18270	COG0050	This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis
LY388_18295	COG1072	(Pantothenic acid kinase))
LY388_18305	COG0812	UDP-N-acetylmuramate dehydrogenase activity
LY388_18315	COG1502	Catalyzes the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) (diphosphatidylglycerol) and glycerol
LY388_18395	COG0043	3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity
LY388_18410	COG3118	belongs to the thioredoxin family
LY388_18415	COG0513	Belongs to the DEAD box helicase family
LY388_18420	COG0248	Ppx GppA phosphatase
LY388_18425	COG2205	protein histidine kinase activity
LY388_18425	COG0784	Response regulator, receiver
LY388_18430	COG2814	Major facilitator Superfamily
LY388_18445	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
LY388_18450	COG0757	Catalyzes a trans-dehydration via an enolate intermediate
LY388_18455	COG0511	ligase activity, forming carbon-carbon bonds
LY388_18460	COG0439	Biotin carboxylase
LY388_18465	COG2264	protein methyltransferase activity
LY388_18470	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
LY388_18475	COG2901	Activates ribosomal RNA transcription. Plays a direct role in upstream activation of rRNA promoters
LY388_18485	COG1609	Transcriptional regulator
LY388_18490	COG0129	dihydroxy-acid dehydratase activity
LY388_18495	COG3265	gluconokinase activity
LY388_18500	COG2610	gluconate transmembrane transporter activity
LY388_18505	COG0800	Aldolase
LY388_18525	COG0840	transmembrane signaling receptor activity
LY388_18530	COG1982	Orn Lys Arg decarboxylase major
LY388_18535	COG0531	amino acid
LY388_18540	COG3710	Transcriptional regulator
LY388_18545	COG0789	Transcriptional regulator
LY388_18560	COG0151	Belongs to the GarS family
LY388_18570	COG0776	regulation of translation
LY388_18575	COG1253	flavin adenine dinucleotide binding
LY388_18580	COG3068	Protein conserved in bacteria
LY388_18590	COG1573	uracil-dna glycosylase
LY388_18595	COG0668	transmembrane transport
LY388_18610	COG1236	Exonuclease of the beta-lactamase fold involved in RNA processing
LY388_18620	COG0472	First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
LY388_18630	COG1216	Glycosyl transferase, family 2
LY388_18655	COG0381	UDP-N-acetylglucosamine 2-epimerase activity
LY388_18670	COG1596	polysaccharide export
LY388_18690	COG4775	Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane
LY388_18710	COG2030	dehydratase
LY388_18720	COG2148	undecaprenyl-phosphate glucose phosphotransferase activity
LY388_18730	COG2746	aminoglycoside 3-N-acetyltransferase activity
LY388_18775	COG0677	UDP-N-acetyl-D-mannosamine dehydrogenase activity
LY388_18790	COG0451	ADP-glyceromanno-heptose 6-epimerase activity
LY388_18815	COG0859	PFAM glycosyl transferase family 9
LY388_18825	COG1519	Transferase
LY388_18855	COG3642	lipopolysaccharide core region biosynthetic process
LY388_18860	COG0859	PFAM glycosyl transferase family 9
LY388_18865	COG0463	Glycosyl transferase, family 2
LY388_18870	COG0859	PFAM glycosyl transferase family 9
LY388_18875	COG0669	Reversibly transfers an adenylyl group from ATP to 4'- phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate
LY388_18880	COG0266	class I DNA-(apurinic or apyrimidinic site) endonuclease activity
LY388_18890	COG0267	Belongs to the bacterial ribosomal protein bL33 family
LY388_18895	COG0227	Belongs to the bacterial ribosomal protein bL28 family
LY388_18900	COG2003	Belongs to the UPF0758 family
LY388_18910	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
LY388_18920	COG1309	transcriptional regulator
LY388_18925	COG1560	Kdo2-lipid A biosynthetic process
LY388_18930	COG1560	Kdo2-lipid A biosynthetic process
LY388_18935	COG0461	Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP)
LY388_18940	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
LY388_18945	COG1561	YicC-like family, N-terminal region
LY388_18950	COG2862	Uncharacterized protein family, UPF0114
LY388_18955	COG1264	protein-N(PI)-phosphohistidine-sugar phosphotransferase activity
LY388_18955	COG1263	PTS System
LY388_18960	COG2103	Specifically catalyzes the cleavage of the D-lactyl ether substituent of MurNAc 6-phosphate, producing GlcNAc 6- phosphate and D-lactate
LY388_18980	COG1120	ATPase activity
LY388_18985	COG4774	siderophore transport
LY388_18990	COG1132	(ABC) transporter
LY388_19005	COG0514	ATP-dependent DNA helicase (RecQ)
LY388_19010	COG2962	Rard protein
LY388_19015	COG0405	Gamma-glutamyltransferase
LY388_19020	COG2207	Transcriptional regulator
LY388_19025	COG1280	lysine exporter protein (LysE YggA)
LY388_19030	COG0210	DNA helicase
LY388_19040	COG2961	Specifically methylates the adenine in position 2030 of 23S rRNA
LY388_19045	COG1249	Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family
LY388_19055	COG1173	ABC-type dipeptide oligopeptide nickel transport systems, permease components
LY388_19060	COG0601	transmembrane transport
LY388_19065	COG0747	negative chemotaxis
LY388_19115	COG1309	transcriptional regulator
LY388_19120	COG0845	Belongs to the membrane fusion protein (MFP) (TC 8.A.1) family
LY388_19125	COG0841	Belongs to the resistance-nodulation-cell division (RND) (TC 2.A.6) family
LY388_19130	COG2960	long-chain fatty acid transporting porin activity
LY388_19135	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
LY388_19140	COG0583	DNA-binding transcription factor activity
LY388_19210	COG4635	menaquinone-dependent protoporphyrinogen oxidase activity
LY388_19215	COG0168	Low-affinity potassium transport system. Interacts with trk system potassium uptake protein TrkA
LY388_19220	COG1739	Uncharacterized protein family UPF0029
LY388_19225	COG1024	Enoyl-CoA hydratase
LY388_19225	COG1250	3-hydroxyacyl-CoA dehydrogenase
LY388_19230	COG0183	Belongs to the thiolase family
LY388_19235	COG0583	DNA-binding transcription factor activity
LY388_19240	COG2814	Major facilitator Superfamily
LY388_19250	COG0355	proton-transporting ATP synthase activity, rotational mechanism
LY388_19255	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
LY388_19260	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
LY388_19265	COG0056	Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit
LY388_19270	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
LY388_19275	COG0711	Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0)
LY388_19285	COG0356	it plays a direct role in the translocation of protons across the membrane
LY388_19290	COG3312	ion transport
LY388_19295	COG1475	DNA binding
LY388_19300	COG1192	Involved in chromosome partitioning
LY388_19305	COG0357	Ribosomal RNA small subunit methyltransferase G
LY388_19310	COG0445	tRNA wobble uridine modification
LY388_19315	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
LY388_19345	COG0286	site-specific DNA-methyltransferase (adenine-specific) activity
LY388_19395	COG4974	Belongs to the 'phage' integrase family
LY388_19400	COG0486	Exhibits a very high intrinsic GTPase hydrolysis rate. Involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA- cmnm(5)s(2)U34
LY388_19405	COG0706	membrane insertase activity
LY388_19415	COG0594	ribonuclease P activity
LY388_19420	COG0230	Belongs to the bacterial ribosomal protein bL34 family
LY388_19425	COG1126	abc transporter atp-binding protein
LY388_19520	COG1598	PFAM Uncharacterised protein family UPF0150
LY388_19595	COG0741	lytic transglycosylase activity
LY388_19680	COG3504	Conjugal transfer protein
LY388_19700	COG3451	type IV secretory pathway VirB4
LY388_19720	COG1396	sequence-specific DNA binding