locus-tag	class	description
BER93_00025	COG0187	DNA topoisomerase II activity
BER93_00035	COG0501	Belongs to the peptidase M48B family
BER93_00075	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
BER93_00115	COG0111	D-isomer specific 2-hydroxyacid dehydrogenase
BER93_00120	COG0793	Belongs to the peptidase S41A family
BER93_00125	COG4942	peptidase
BER93_00130	COG2234	aminopeptidase activity
BER93_00145	COG0277	FAD linked oxidase domain protein
BER93_00165	COG1028	Short-chain dehydrogenase reductase Sdr
BER93_00175	COG0616	signal peptide processing
BER93_00180	COG0534	Mate efflux family protein
BER93_00200	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
BER93_00215	COG0568	sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released
BER93_00220	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
BER93_00225	COG2201	protein-glutamate methylesterase activity
BER93_00230	COG2177	Part of the ABC transporter FtsEX involved in
BER93_00235	COG2884	Cell division ATP-binding protein ftsE
BER93_00240	COG0513	Belongs to the DEAD box helicase family
BER93_00245	COG3118	belongs to the thioredoxin family
BER93_00250	COG1158	Facilitates transcription termination by a mechanism that involves Rho binding to the nascent RNA, activation of Rho's RNA-dependent ATPase activity, and release of the mRNA from the DNA template
BER93_00280	COG1652	LysM domain
BER93_00295	COG0845	Belongs to the membrane fusion protein (MFP) (TC 8.A.1) family
BER93_00300	COG0841	Belongs to the resistance-nodulation-cell division (RND) (TC 2.A.6) family
BER93_00320	COG5383	Protein conserved in bacteria
BER93_00335	COG3131	Involved in the biosynthesis of osmoregulated periplasmic glucans (OPGs)
BER93_00340	COG1435	thymidine kinase activity
BER93_00345	COG0210	DNA helicase
BER93_00375	COG3132	Protein of unknown function, DUF480
BER93_00400	COG2937	Belongs to the GPAT DAPAT family
BER93_00460	COG2963	transposase activity
BER93_00510	COG0513	Belongs to the DEAD box helicase family
BER93_00515	COG0508	dehydrogenase complex catalyzes the overall conversion of
BER93_00530	COG1071	oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
BER93_00535	COG3483	tryptophan 2,3-dioxygenase activity
BER93_00540	COG3104	oligopeptide transport
BER93_00565	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
BER93_00590	COG1893	Catalyzes the NADPH-dependent reduction of ketopantoate into pantoic acid
BER93_00600	COG0842	Transport permease protein
BER93_00605	COG1131	(ABC) transporter
BER93_00610	COG0633	Ferredoxin
BER93_00610	COG0543	2 iron, 2 sulfur cluster binding
BER93_00625	COG4555	ABC transporter
BER93_00635	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
BER93_00650	COG0625	glutathione transferase activity
BER93_00740	COG3501	Rhs element vgr protein
BER93_00760	COG4695	Portal protein
BER93_00915	COG0568	sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released
BER93_00930	COG1247	-acetyltransferase
BER93_00935	COG0807	Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate
BER93_00965	COG1807	4-amino-4-deoxy-L-arabinose transferase and related glycosyltransferases of PMT family
BER93_00970	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
BER93_00970	COG0144	Specifically methylates the cytosine at position 967 (m5C967) of 16S rRNA
BER93_00975	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
BER93_00980	COG0242	peptide deformylase activity
BER93_00985	COG1652	LysM domain
BER93_00990	COG0758	DNA mediated transformation
BER93_01010	COG1754	DNA topoisomerase type I activity
BER93_01010	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
BER93_01015	COG0009	L-threonylcarbamoyladenylate synthase
BER93_01040	COG4771	TonB-dependent receptor
BER93_01045	COG0729	surface antigen
BER93_01050	COG2911	Protein conserved in bacteria
BER93_01065	COG1520	Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane
BER93_01070	COG3265	gluconokinase activity
BER93_01075	COG2211	Major facilitator Superfamily
BER93_01085	COG2205	protein histidine kinase activity
BER93_01090	COG1971	Probably functions as a manganese efflux pump
BER93_01095	COG1414	Transcriptional regulator
BER93_01100	COG0738	Major facilitator superfamily
BER93_01105	COG3254	rhamnose metabolic process
BER93_01110	COG4948	Mandelate Racemase Muconate Lactonizing
BER93_01120	COG1028	Short-chain dehydrogenase reductase Sdr
BER93_01150	COG3162	membrane
BER93_01155	COG4147	Belongs to the sodium solute symporter (SSF) (TC 2.A.21) family
BER93_01160	COG0708	Exodeoxyribonuclease III
BER93_01175	COG2091	lysine biosynthetic process via aminoadipic acid
BER93_01200	COG0227	Belongs to the bacterial ribosomal protein bL28 family
BER93_01205	COG0267	Belongs to the bacterial ribosomal protein bL33 family
BER93_01210	COG1502	Catalyzes the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) (diphosphatidylglycerol) and glycerol
BER93_01220	COG0210	DNA helicase
BER93_01250	COG0340	biotin-[acetyl-CoA-carboxylase] ligase activity
BER93_01250	COG1654	Acts both as a biotin-- acetyl-CoA-carboxylase ligase and a biotin-operon repressor. In the presence of ATP, BirA activates biotin to form the BirA-biotinyl-5'-adenylate (BirA-bio- 5'-AMP or holoBirA) complex. HoloBirA can either transfer the biotinyl moiety to the biotin carboxyl carrier protein (BCCP) subunit of acetyl-CoA carboxylase, or bind to the biotin operator site and inhibit transcription of the operon
BER93_01255	COG1521	Catalyzes the phosphorylation of pantothenate (Pan), the first step in CoA biosynthesis
BER93_01280	COG2963	transposase activity
BER93_01325	COG0180	Tryptophanyl-tRNA synthetase
BER93_01365	COG0125	Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis
BER93_01385	COG0260	Presumably involved in the processing and regular turnover of intracellular proteins. Catalyzes the removal of unsubstituted N-terminal amino acids from various peptides
BER93_01390	COG0637	HAD-superfamily hydrolase subfamily IA, variant 3
BER93_01415	COG0265	Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain
BER93_01435	COG0642	Histidine kinase
BER93_01440	COG0745	RESPONSE REGULATOR receiver
BER93_01475	COG1090	epimerase
BER93_01530	COG1690	Belongs to the RtcB family
BER93_01550	COG4943	cyclic-guanylate-specific phosphodiesterase activity
BER93_01565	COG0606	chelatase, subunit chli
BER93_01580	COG3291	Pkd domain containing protein
BER93_01580	COG3525	Glycosyl hydrolase, family 20, catalytic domain
BER93_01600	COG0421	Catalyzes the irreversible transfer of a propylamine group from the amino donor S-adenosylmethioninamine (decarboxy- AdoMet) to putrescine (1,4-diaminobutane) to yield spermidine
BER93_01605	COG1166	arginine decarboxylase activity
BER93_01610	COG3039	Transposase
BER93_01675	COG0236	Carrier of the growing fatty acid chain in fatty acid biosynthesis
BER93_01690	COG0764	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity
BER93_01720	COG1028	Short-chain dehydrogenase reductase Sdr
BER93_01730	COG0463	Glycosyl transferase, family 2
BER93_01740	COG0304	beta-ketoacyl-acyl-carrier-protein synthase II activity
BER93_01745	COG3100	YcgL domain-containing protein
BER93_01760	COG3387	PFAM Glycoside hydrolase 15-related
BER93_01765	COG0364	Catalyzes the oxidation of glucose 6-phosphate to 6- phosphogluconolactone
BER93_01770	COG1226	(belongs to the monovalent cation proton antiporter 2 (CPA2) transporter (TC 2.A.37) family)
BER93_01770	COG0475	glutathione-regulated potassium exporter activity
BER93_01775	COG3338	carbonate dehydratase activity
BER93_01780	COG2239	Acts as a magnesium transporter
BER93_01785	COG0045	succinate-CoA ligase (ADP-forming) activity
BER93_01785	COG1670	COG1670 acetyltransferases, including N-acetylases of ribosomal proteins
BER93_01785	COG1042	CoA-binding domain protein
BER93_01795	COG0209	Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides
BER93_01800	COG0208	Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides
BER93_01820	COG1272	protein, Hemolysin III
BER93_01825	COG1205	dead DEAH box helicase
BER93_01825	COG1111	helicase
BER93_01865	COG0841	Belongs to the resistance-nodulation-cell division (RND) (TC 2.A.6) family
BER93_01925	COG2801	Transposase and inactivated derivatives
BER93_01930	COG2801	Transposase and inactivated derivatives
BER93_01935	COG2963	transposase activity
BER93_01940	COG3007	enoyl-[acyl-carrier-protein] reductase (NADH) activity
BER93_01960	COG1304	FMN binding
BER93_02010	COG2816	NAD+ diphosphatase activity
BER93_02050	COG0183	Belongs to the thiolase family
BER93_02080	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
BER93_02090	COG0240	glycerol-3-phosphate dehydrogenase [NAD(P)+] activity
BER93_02100	COG0028	Belongs to the TPP enzyme family
BER93_02110	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
BER93_02120	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
BER93_02130	COG2963	transposase activity
BER93_02135	COG2801	Transposase and inactivated derivatives
BER93_02150	COG0566	Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase TrmH family
BER93_02160	COG3200	phospho-2-dehydro-3-deoxyheptonate aldolase
BER93_02185	COG0652	PPIases accelerate the folding of proteins. It catalyzes the cis-trans isomerization of proline imidic peptide bonds in oligopeptides
BER93_02215	COG3039	Transposase
BER93_02225	COG0446	pyridine nucleotide-disulphide oxidoreductase
BER93_02225	COG1902	pentaerythritol trinitrate reductase activity
BER93_02230	COG0604	alcohol dehydrogenase
BER93_02260	COG1613	Sulfate ABC transporter periplasmic sulfate-binding protein
BER93_02265	COG0555	PFAM binding-protein-dependent transport systems inner membrane component
BER93_02270	COG4208	sulfate ABC transporter
BER93_02275	COG1118	Part of the ABC transporter complex CysAWTP involved in sulfate thiosulfate import. Responsible for energy coupling to the transport system
BER93_02285	COG1063	alcohol dehydrogenase
BER93_02300	COG0406	alpha-ribazole phosphatase activity
BER93_02335	COG0189	ligase activity
BER93_02345	COG0745	RESPONSE REGULATOR receiver
BER93_02380	COG0054	6,7-dimethyl-8-ribityllumazine synthase activity
BER93_02385	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
BER93_02390	COG0611	Catalyzes the ATP-dependent phosphorylation of thiamine- monophosphate (TMP) to form thiamine-pyrophosphate (TPP), the active form of vitamin B1
BER93_02445	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
BER93_02515	COG1113	amino acid transport
BER93_02525	COG0598	Magnesium transport protein CorA
BER93_02585	COG2730	Belongs to the glycosyl hydrolase 5 (cellulase A) family
BER93_02585	COG5297	Belongs to the glycosyl hydrolase family 6
BER93_02590	COG0659	secondary active sulfate transmembrane transporter activity
BER93_02600	COG2943	transferase activity, transferring hexosyl groups
BER93_02620	COG0181	hydroxymethylbilane synthase activity
BER93_02645	COG1505	serine-type exopeptidase activity
BER93_02670	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
BER93_02680	COG4973	Belongs to the 'phage' integrase family. XerC subfamily
BER93_02685	COG5405	Protease subunit of a proteasome-like degradation complex believed to be a general protein degrading machinery
BER93_02690	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
BER93_02715	COG2226	methyltransferase
BER93_02720	COG5001	Diguanylate cyclase
BER93_02720	COG3300	MHYT domain
BER93_02745	COG1077	Cell shape determining protein MreB Mrl
BER93_02750	COG1792	Involved in formation and maintenance of cell shape
BER93_02765	COG0772	Belongs to the SEDS family
BER93_02775	COG2951	lytic endotransglycosylase activity
BER93_02780	COG0797	Lytic transglycosylase with a strong preference for naked glycan strands that lack stem peptides
BER93_02785	COG1686	Belongs to the peptidase S11 family
BER93_02805	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
BER93_02875	COG1023	phosphogluconate dehydrogenase (decarboxylating) activity
BER93_02880	COG0673	inositol 2-dehydrogenase activity
BER93_02885	COG2823	Periplasmic or secreted lipoprotein
BER93_02890	COG4251	negative regulation of phosphorylation
BER93_02895	COG0784	Response regulator, receiver
BER93_02900	COG4191	Histidine kinase
BER93_02905	COG0801	2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
BER93_02910	COG1028	Short-chain dehydrogenase reductase Sdr
BER93_02935	COG2801	Transposase and inactivated derivatives
BER93_02940	COG2963	transposase activity
BER93_02965	COG1609	Transcriptional regulator
BER93_02970	COG0449	glutamine-fructose-6-phosphate transaminase (isomerizing) activity
BER93_02975	COG1820	Belongs to the metallo-dependent hydrolases superfamily. NagA family
BER93_02990	COG1062	S-(hydroxymethyl)glutathione dehydrogenase activity
BER93_02995	COG3791	Glutathione-dependent formaldehyde-activating
BER93_03025	COG3964	amidohydrolase
BER93_03070	COG2963	transposase activity
BER93_03080	COG0278	Belongs to the glutaredoxin family. Monothiol subfamily
BER93_03120	COG2931	calcium- and calmodulin-responsive adenylate cyclase activity
BER93_03150	COG2211	Major facilitator Superfamily
BER93_03160	COG1028	Short-chain dehydrogenase reductase Sdr
BER93_03165	COG2851	Citrate transporter
BER93_03180	COG0642	Histidine kinase
BER93_03185	COG1840	ABC-type Fe3 transport system, periplasmic component
BER93_03190	COG2197	response regulator
BER93_03200	COG2963	transposase activity
BER93_03215	COG2963	transposase activity
BER93_03240	COG0281	malic enzyme
BER93_03240	COG0280	phosphate acetyltransferase
BER93_03265	COG1560	Kdo2-lipid A biosynthetic process
BER93_03270	COG1519	Transferase
BER93_03275	COG1538	Outer membrane efflux protein
BER93_03280	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
BER93_03305	COG0473	3-isopropylmalate dehydrogenase activity
BER93_03310	COG4771	TonB-dependent receptor
BER93_03320	COG0119	Catalyzes the condensation of the acetyl group of acetyl-CoA with 3-methyl-2-oxobutanoate (2-oxoisovalerate) to form 3-carboxy-3-hydroxy-4-methylpentanoate (2-isopropylmalate)
BER93_03370	COG3039	Transposase
BER93_03390	COG0221	Catalyzes the hydrolysis of inorganic pyrophosphate (PPi) forming two phosphate ions
BER93_03425	COG0563	adenylate kinase activity
BER93_03430	COG0773	UDP-N-acetylmuramate-L-alanine ligase activity
BER93_03445	COG0671	phosphoesterase, PA-phosphatase related
BER93_03455	COG1028	Short-chain dehydrogenase reductase Sdr
BER93_03465	COG3039	Transposase
BER93_03475	COG4992	N2-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity
BER93_03480	COG0001	glutamate-1-semialdehyde 2,1-aminomutase activity
BER93_03485	COG0352	thiamine-phosphate diphosphorylase activity
BER93_03490	COG1773	rubredoxin
BER93_03495	COG2912	Transglutaminase-like superfamily
BER93_03515	COG0212	Belongs to the 5-formyltetrahydrofolate cyclo-ligase family
BER93_03540	COG0006	proline dipeptidase activity
BER93_03545	COG0006	proline dipeptidase activity
BER93_03560	COG0635	Involved in the biosynthesis of porphyrin-containing compound
BER93_03565	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
BER93_03570	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
BER93_03575	COG1561	YicC-like family, N-terminal region
BER93_03585	COG1758	RNA polymerase activity
BER93_03590	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
BER93_03600	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)
BER93_03615	COG0254	rRNA binding
BER93_03630	COG5009	serine-type D-Ala-D-Ala carboxypeptidase activity
BER93_03660	COG3039	Transposase
BER93_03690	COG3039	Transposase
BER93_03745	COG3116	cell division
BER93_03755	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
BER93_03760	COG0770	UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase activity
BER93_03765	COG0472	First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
BER93_03780	COG0773	UDP-N-acetylmuramate-L-alanine ligase activity
BER93_03785	COG1181	Belongs to the D-alanine--D-alanine ligase family
BER93_03790	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
BER93_03815	COG0739	heme binding
BER93_03820	COG0653	protein targeting
BER93_03830	COG0494	nUDIX hydrolase
BER93_03840	COG0685	methylenetetrahydrofolate reductase (NAD(P)H) activity
BER93_03850	COG0604	alcohol dehydrogenase
BER93_03850	COG1028	Short-chain dehydrogenase reductase Sdr
BER93_03850	COG3321	synthase
BER93_03875	COG2963	transposase activity
BER93_03885	COG0237	dephospho-CoA kinase activity
BER93_03890	COG1989	Cleaves type-4 fimbrial leader sequence and methylates the N-terminal (generally Phe) residue
BER93_03895	COG1459	type II secretion system
BER93_03935	COG0045	succinate-CoA ligase (ADP-forming) activity
BER93_03940	COG0074	Succinyl-CoA synthetase functions in the citric acid cycle (TCA), coupling the hydrolysis of succinyl-CoA to the synthesis of either ATP or GTP and thus represents the only step of substrate-level phosphorylation in the TCA. The alpha subunit of the enzyme binds the substrates coenzyme A and phosphate, while succinate binding and nucleotide specificity is provided by the beta subunit
BER93_03945	COG0171	NAD+ synthase (glutamine-hydrolyzing) activity
BER93_03945	COG0388	Catalyzes the ATP-dependent amidation of deamido-NAD to form NAD. Uses L-glutamine as a nitrogen source
BER93_03950	COG4105	Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane
BER93_03955	COG0564	pseudouridine synthase activity
BER93_03990	COG3387	PFAM Glycoside hydrolase 15-related
BER93_03995	COG1877	trehalose-phosphatase activity
BER93_04040	COG2963	transposase activity
BER93_04055	COG0603	Catalyzes the ATP-dependent conversion of 7-carboxy-7- deazaguanine (CDG) to 7-cyano-7-deazaguanine (preQ(0))
BER93_04090	COG0783	Belongs to the Dps family
BER93_04095	COG1643	Atp-dependent helicase
BER93_04100	COG0535	radical SAM domain protein
BER93_04115	COG1235	May be involved in the transport of PQQ or its precursor to the periplasm
BER93_04120	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
BER93_04135	COG0744	Peptidoglycan polymerase that catalyzes glycan chain elongation from lipid-linked precursors
BER93_04145	COG1199	ATP-dependent helicase activity
BER93_04160	COG0189	ligase activity
BER93_04175	COG0835	chemotaxis
BER93_04180	COG0840	transmembrane signaling receptor activity
BER93_04215	COG3142	Participates in the control of copper homeostasis
BER93_04245	COG3501	Rhs element vgr protein
BER93_04280	COG2963	transposase activity
BER93_04285	COG2801	Transposase and inactivated derivatives
BER93_04290	COG0525	valine-tRNA ligase activity
BER93_04300	COG0260	Presumably involved in the processing and regular turnover of intracellular proteins. Catalyzes the removal of unsubstituted N-terminal amino acids from various peptides
BER93_04310	COG0795	lipopolysaccharide-transporting ATPase activity
BER93_04325	COG4974	Belongs to the 'phage' integrase family
BER93_04330	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
BER93_04335	COG0047	phosphoribosylformylglycinamidine synthase activity
BER93_04335	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
BER93_04350	COG1404	Belongs to the peptidase S8 family
BER93_04355	COG2804	Type II secretory pathway, ATPase PulE Tfp pilus assembly pathway, ATPase PilB
BER93_04360	COG1459	type II secretion system
BER93_04365	COG2165	general secretion pathway protein
BER93_04370	COG4970	Tfp pilus assembly protein FimT
BER93_04375	COG2165	general secretion pathway protein
BER93_04380	COG4795	General secretion pathway protein
BER93_04385	COG3156	type II secretion system protein K
BER93_04390	COG3166	PFAM Fimbrial assembly family protein
BER93_04405	COG1450	Type ii and iii secretion system protein
BER93_04415	COG2188	Transcriptional regulator
BER93_04465	COG0242	peptide deformylase activity
BER93_04470	COG0488	(ABC) transporter
BER93_04480	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
BER93_04495	COG0117	Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)- pyrimidinedione 5'-phosphate
BER93_04495	COG1985	Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)- pyrimidinedione 5'-phosphate
BER93_04515	COG3039	Transposase
BER93_04565	COG2352	Forms oxaloacetate, a four-carbon dicarboxylic acid source for the tricarboxylic acid cycle
BER93_04585	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
BER93_04595	COG4106	trans-aconitate 2-methyltransferase activity
BER93_04600	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
BER93_04615	COG0818	Recycling of diacylglycerol produced during the turnover of membrane phospholipid
BER93_04625	COG0642	Histidine kinase
BER93_04640	COG4181	ATPase activity
BER93_04680	COG0667	Aldo Keto reductase
BER93_04685	COG1972	Belongs to the concentrative nucleoside transporter (CNT) (TC 2.A.41) family
BER93_04705	COG0682	Transfers the N-acyl diglyceride group on what will become the N-terminal cysteine of membrane lipoproteins
BER93_04725	COG0639	Hydrolyzes diadenosine 5',5'''-P1,P4-tetraphosphate to yield ADP
BER93_04730	COG2967	ApaG domain
BER93_04735	COG0030	16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity
BER93_04740	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)
BER93_04755	COG0123	including yeast histone deacetylase and acetoin utilization protein
BER93_04760	COG2096	Adenosyltransferase
BER93_04770	COG0654	COG0654 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases
BER93_04775	COG0654	COG0654 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases
BER93_04790	COG0583	DNA-binding transcription factor activity
BER93_04800	COG1024	Enoyl-CoA hydratase
BER93_04810	COG3386	PFAM SMP-30 Gluconolaconase
BER93_04815	COG0673	inositol 2-dehydrogenase activity
BER93_04835	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)
BER93_04855	COG2197	response regulator
BER93_04860	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
BER93_04865	COG0176	Transaldolase is important for the balance of metabolites in the pentose-phosphate pathway
BER93_04870	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
BER93_04875	COG0583	DNA-binding transcription factor activity
BER93_04880	COG3634	alkyl hydroperoxide reductase activity
BER93_04890	COG2890	protein-(glutamine-N5) methyltransferase activity
BER93_04915	COG0749	In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity
BER93_04915	COG0258	In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity
BER93_04955	COG0115	Belongs to the class-IV pyridoxal-phosphate-dependent aminotransferase family
BER93_04970	COG1404	Belongs to the peptidase S8 family
BER93_04995	COG1295	ribonuclease BN
BER93_05000	COG0526	COG0526, thiol-disulfide isomerase and thioredoxins
BER93_05015	COG0521	Mo-molybdopterin cofactor biosynthetic process
BER93_05040	COG3017	Plays a critical role in the incorporation of lipoproteins in the outer membrane after they are released by the LolA protein
BER93_05045	COG1947	Catalyzes the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol
BER93_05055	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)
BER93_05060	COG1825	This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance
BER93_05065	COG0193	aminoacyl-tRNA hydrolase activity
BER93_05070	COG0012	GTP binding
BER93_05090	COG0050	This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis
BER93_05100	COG0690	P-P-bond-hydrolysis-driven protein transmembrane transporter activity
BER93_05105	COG0250	Participates in transcription elongation, termination and antitermination
BER93_05115	COG0081	regulation of translation
BER93_05120	COG0244	Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors
BER93_05125	COG0222	ribosome binding
BER93_05135	COG0086	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates
BER93_05140	COG0048	Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit
BER93_05155	COG0050	This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis
BER93_05160	COG0051	transcription antitermination factor activity, RNA binding
BER93_05180	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
BER93_05205	COG0255	Belongs to the universal ribosomal protein uL29 family
BER93_05210	COG0186	One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA
BER93_05215	COG0093	Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome
BER93_05220	COG0198	One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit
BER93_05230	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
BER93_05250	COG0098	Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body
BER93_05255	COG1841	ribosomal large subunit assembly
BER93_05260	COG0200	Binds to the 23S rRNA
BER93_05265	COG0201	protein transport
BER93_05270	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
BER93_05275	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
BER93_05280	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
BER93_05285	COG0202	RNA polymerase activity
BER93_05290	COG0203	ribosomal protein L17
BER93_05295	COG1495	Required for disulfide bond formation in some periplasmic proteins. Acts by oxidizing the DsbA protein
BER93_05340	COG1970	mechanosensitive ion channel activity
BER93_05355	COG3273	potassium ion transport
BER93_05355	COG0471	metal ion transport
BER93_05360	COG0220	tRNA (guanine-N7-)-methyltransferase activity
BER93_05385	COG0582	viral genome integration into host DNA
BER93_05410	COG1396	sequence-specific DNA binding
BER93_05430	COG2801	Transposase and inactivated derivatives
BER93_05435	COG2963	transposase activity
BER93_05445	COG5001	Diguanylate cyclase
BER93_05585	COG2963	transposase activity
BER93_05615	COG1309	transcriptional regulator
BER93_05620	COG0406	alpha-ribazole phosphatase activity
BER93_05620	COG0328	RNA-DNA hybrid ribonuclease activity
BER93_05625	COG0063	ADP-dependent NAD(P)H-hydrate dehydratase activity
BER93_05645	COG1028	Short-chain dehydrogenase reductase Sdr
BER93_05675	COG1385	rRNA (uridine-N3-)-methyltransferase activity
BER93_05685	COG0494	nUDIX hydrolase
BER93_05690	COG1218	3'(2'),5'-bisphosphate nucleotidase
BER93_05695	COG3956	TIGRFAM MazG family protein
BER93_05700	COG0404	The glycine cleavage system catalyzes the degradation of glycine
BER93_05730	COG1960	acyl-CoA dehydrogenase activity
BER93_05740	COG1309	transcriptional regulator
BER93_05775	COG2963	transposase activity
BER93_05785	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
BER93_05790	COG0744	Peptidoglycan polymerase that catalyzes glycan chain elongation from lipid-linked precursors
BER93_05795	COG0463	Glycosyl transferase, family 2
BER93_05800	COG0516	GMP reductase activity
BER93_05800	COG0517	IMP dehydrogenase activity
BER93_05805	COG2982	Protein involved in outer membrane biogenesis
BER93_05810	COG1272	protein, Hemolysin III
BER93_05815	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
BER93_05830	COG2021	Transfers an acetyl group from acetyl-CoA to L- homoserine, forming acetyl-L-homoserine
BER93_05835	COG0626	cystathionine gamma-synthase activity
BER93_05840	COG0460	homoserine dehydrogenase
BER93_05840	COG0527	aspartate kinase activity
BER93_05855	COG0626	cystathionine gamma-synthase activity
BER93_05880	COG2353	YceI-like domain
BER93_05905	COG0755	Required for the export of heme to the periplasm for the biogenesis of c-type cytochromes
BER93_05910	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
BER93_05940	COG0336	Belongs to the RNA methyltransferase TrmD family
BER93_05950	COG0534	Mate efflux family protein
BER93_05985	COG3706	GGDEF domain
BER93_06000	COG0441	Catalyzes the attachment of threonine to tRNA(Thr) in a two-step reaction L-threonine is first activated by ATP to form Thr-AMP and then transferred to the acceptor end of tRNA(Thr)
BER93_06005	COG0290	IF-3 binds to the 30S ribosomal subunit and shifts the equilibrum between 70S ribosomes and their 50S and 30S subunits in favor of the free subunits, thus enhancing the availability of 30S subunits on which protein synthesis initiation begins
BER93_06010	COG0291	Belongs to the bacterial ribosomal protein bL35 family
BER93_06020	COG0016	Belongs to the class-II aminoacyl-tRNA synthetase family. Phe-tRNA synthetase alpha subunit type 1 subfamily
BER93_06030	COG0776	regulation of translation
BER93_06075	COG0438	transferase activity, transferring glycosyl groups
BER93_06080	COG0438	transferase activity, transferring glycosyl groups
BER93_06095	COG2327	Polysaccharide pyruvyl transferase
BER93_06110	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)
BER93_06125	COG1960	acyl-CoA dehydrogenase activity
BER93_06135	COG3040	lipid binding
BER93_06200	COG0552	protein localization to endoplasmic reticulum
BER93_06210	COG3938	Belongs to the proline racemase family
BER93_06215	COG0665	tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase activity
BER93_06230	COG0329	Catalyzes the condensation of (S)-aspartate-beta- semialdehyde (S)-ASA and pyruvate to 4-hydroxy- tetrahydrodipicolinate (HTPA)
BER93_06240	COG0006	proline dipeptidase activity
BER93_06255	COG0531	amino acid
BER93_06280	COG3039	Transposase
BER93_06300	COG4206	TonB-dependent receptor
BER93_06345	COG2963	transposase activity
BER93_06365	COG0825	malonyl-CoA metabolic process
BER93_06380	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
BER93_06385	COG1043	involved in the biosynthesis of lipid A, a phosphorylated glycolipid that anchors the lipopolysaccharide to the outer membrane of the cell
BER93_06395	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
BER93_06410	COG0750	zinc metalloprotease
BER93_06415	COG0743	1-deoxy-D-xylulose-5-phosphate reductoisomerase activity
BER93_06420	COG0575	Belongs to the CDS family
BER93_06425	COG0020	Catalyzes the condensation of isopentenyl diphosphate (IPP) with allylic pyrophosphates generating different type of terpenoids
BER93_06435	COG0528	UMP kinase activity
BER93_06445	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
BER93_06485	COG0024	Methionine aminopeptidase
BER93_06500	COG1393	Belongs to the ArsC family
BER93_06505	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
BER93_06510	COG0367	asparagine synthase
BER93_06520	COG4774	siderophore transport
BER93_06540	COG2265	Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family
BER93_06560	COG1566	PFAM secretion protein HlyD family protein
BER93_06565	COG2814	Major facilitator Superfamily
BER93_06615	COG0386	Belongs to the glutathione peroxidase family
BER93_06675	COG1179	involved in molybdopterin and THIamine biosynthesis family 1
BER93_06680	COG0084	hydrolase, TatD family'
BER93_06705	COG0367	asparagine synthase
BER93_06715	COG0305	Participates in initiation and elongation during chromosome replication
BER93_06720	COG0415	Belongs to the DNA photolyase family
BER93_06740	COG2963	transposase activity
BER93_06770	COG1960	acyl-CoA dehydrogenase activity
BER93_06775	COG1024	Enoyl-CoA hydratase
BER93_06810	COG0265	Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain
BER93_06820	COG3039	Transposase
BER93_06830	COG2963	transposase activity
BER93_06835	COG2801	Transposase and inactivated derivatives
BER93_06855	COG4535	Mg2 and Co2 transporter CorC
BER93_06865	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
BER93_06870	COG1702	phosphate starvation-inducible protein PhoH
BER93_06885	COG0741	lytic transglycosylase activity
BER93_06890	COG0723	plastoquinol--plastocyanin reductase activity
BER93_06895	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
BER93_06900	COG2857	Cytochrome c1
BER93_06905	COG0625	glutathione transferase activity
BER93_06910	COG2969	positive regulation of protein catabolic process
BER93_06920	COG1201	RNA secondary structure unwinding
BER93_06925	COG2094	Belongs to the DNA glycosylase MPG family
BER93_06960	COG1262	PFAM Formylglycine-generating sulfatase enzyme
BER93_06975	COG0481	GTPase activity
BER93_06990	COG0571	ribonuclease III activity
BER93_07020	COG3380	Catalyzes the oxidation of the 1,2-dihydro- and 1,6- dihydro- isomeric forms of beta-NAD(P) back to beta-NAD(P) . May serve to protect primary metabolism dehydrogenases from inhibition by the 1,2-dihydro- and 1,6-dihydro-beta-NAD(P) isomers
BER93_07025	COG3046	protein related to deoxyribodipyrimidine photolyase
BER93_07030	COG1472	Belongs to the glycosyl hydrolase 3 family
BER93_07040	COG0005	The purine nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the beta- (deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate
BER93_07045	COG1278	Cold shock
BER93_07055	COG1201	RNA secondary structure unwinding
BER93_07060	COG1793	dna ligase
BER93_07070	COG1236	Exonuclease of the beta-lactamase fold involved in RNA processing
BER93_07070	COG1793	dna ligase
BER93_07100	COG0183	Belongs to the thiolase family
BER93_07105	COG3039	Transposase
BER93_07120	COG1451	nucleotide metabolic process
BER93_07130	COG5487	UPF0391 membrane protein
BER93_07140	COG0433	COG0433 Predicted ATPase
BER93_07165	COG0135	phosphoribosylanthranilate isomerase activity
BER93_07180	COG3039	Transposase
BER93_07195	COG0133	tryptophan synthase activity
BER93_07210	COG1109	Catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate
BER93_07240	COG4221	oxidoreductase activity
BER93_07260	COG0838	NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient
BER93_07270	COG0852	NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient
BER93_07275	COG0649	NAD binding
BER93_07280	COG1905	PFAM NADH dehydrogenase (ubiquinone) 24 kDa subunit
BER93_07285	COG1894	NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain
BER93_07290	COG1034	ATP synthesis coupled electron transport
BER93_07300	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
BER93_07310	COG0713	ATP synthesis coupled electron transport
BER93_07325	COG1007	ATP synthesis coupled electron transport
BER93_07335	COG0779	Required for maturation of 30S ribosomal subunits
BER93_07340	COG0195	Participates in both transcription termination and antitermination
BER93_07350	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
BER93_07355	COG0130	Responsible for synthesis of pseudouridine from uracil- 55 in the psi GC loop of transfer RNAs
BER93_07360	COG0184	Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome
BER93_07410	COG0278	Belongs to the glutaredoxin family. Monothiol subfamily
BER93_07420	COG2095	MarC family integral membrane protein
BER93_07430	COG1611	Belongs to the LOG family
BER93_07440	COG3275	phosphorelay sensor kinase activity
BER93_07465	COG5002	protein histidine kinase activity
BER93_07465	COG2205	protein histidine kinase activity
BER93_07465	COG0784	Response regulator, receiver
BER93_07470	COG2733	membrane
BER93_07475	COG1121	(ABC) transporter
BER93_07490	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
BER93_07495	COG0243	molybdopterin cofactor binding
BER93_07510	COG2963	transposase activity
BER93_07515	COG2801	Transposase and inactivated derivatives
BER93_07525	COG0665	tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase activity
BER93_07530	COG0174	glutamine synthetase
BER93_07560	COG3842	ATPase activity
BER93_07565	COG1176	ABC-type spermidine putrescine transport system, permease component I
BER93_07570	COG1177	transmembrane transport
BER93_07575	COG1012	belongs to the aldehyde dehydrogenase family
BER93_07585	COG3920	Histidine kinase
BER93_07595	COG0841	Belongs to the resistance-nodulation-cell division (RND) (TC 2.A.6) family
BER93_07600	COG0845	Belongs to the membrane fusion protein (MFP) (TC 8.A.1) family
BER93_07610	COG2902	Dehydrogenase
BER93_07655	COG3609	addiction module antidote protein, CC2985 family
BER93_07680	COG1271	oxidase subunit
BER93_07690	COG3039	Transposase
BER93_07695	COG2963	transposase activity
BER93_07700	COG2801	Transposase and inactivated derivatives
BER93_07705	COG2801	Transposase and inactivated derivatives
BER93_07715	COG0556	nucleotide-excision repair
BER93_07745	COG2948	multi-organism process
BER93_07875	COG3039	Transposase
BER93_07960	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
BER93_07970	COG2914	Belongs to the UPF0125 (RnfH) family
BER93_07975	COG2913	Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane
BER93_07985	COG0497	DNA recombination
BER93_07990	COG1420	regulation of RNA biosynthetic process
BER93_07995	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
BER93_08005	COG0484	heat shock protein binding
BER93_08010	COG2240	Pyridoxal kinase involved in the salvage pathway of pyridoxal 5'-phosphate (PLP). Catalyzes the phosphorylation of pyridoxal to PLP
BER93_08015	COG1605	Chorismate mutase
BER93_08015	COG0287	Prephenate dehydrogenase
BER93_08035	COG2274	protein secretion by the type I secretion system
BER93_08050	COG1132	(ABC) transporter
BER93_08085	COG2850	peptidyl-arginine hydroxylation
BER93_08105	COG2963	transposase activity
BER93_08110	COG2801	Transposase and inactivated derivatives
BER93_08115	COG2801	Transposase and inactivated derivatives
BER93_08120	COG3039	Transposase
BER93_08145	COG1131	(ABC) transporter
BER93_08150	COG1725	Transcriptional regulator
BER93_08160	COG0386	Belongs to the glutathione peroxidase family
BER93_08190	COG1609	Transcriptional regulator
BER93_08200	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
BER93_08210	COG0646	methionine synthase
BER93_08210	COG1410	methionine synthase
BER93_08215	COG0646	methionine synthase
BER93_08215	COG1410	methionine synthase
BER93_08225	COG1960	acyl-CoA dehydrogenase activity
BER93_08240	COG0557	exoribonuclease II activity
BER93_08245	COG0566	Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase TrmH family
BER93_08255	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
BER93_08260	COG0704	Plays a role in the regulation of phosphate uptake
BER93_08265	COG1117	ATPase-coupled phosphate ion transmembrane transporter activity
BER93_08270	COG0581	inorganic phosphate transmembrane transporter activity
BER93_08275	COG0573	inorganic phosphate transmembrane transporter activity
BER93_08280	COG0226	Part of the ABC transporter complex PstSACB involved in phosphate import
BER93_08315	COG0659	secondary active sulfate transmembrane transporter activity
BER93_08320	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
BER93_08340	COG0494	nUDIX hydrolase
BER93_08395	COG3039	Transposase
BER93_08410	COG2925	Exonuclease
BER93_08415	COG0654	COG0654 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases
BER93_08420	COG3844	kynureninase activity
BER93_08435	COG0288	reversible hydration of carbon dioxide
BER93_08460	COG0017	Asparaginyl-tRNA synthetase
BER93_08465	COG0316	Belongs to the HesB IscA family
BER93_08475	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
BER93_08495	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
BER93_08500	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
BER93_08515	COG0182	Catalyzes the interconversion of methylthioribose-1- phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1- P)
BER93_08535	COG2987	Catalyzes the conversion of urocanate to 4-imidazolone- 5-propionate
BER93_08545	COG2986	histidine ammonia-lyase
BER93_08580	COG2717	Part of the MsrPQ system that repairs oxidized periplasmic proteins containing methionine sulfoxide residues (Met-O), using respiratory chain electrons. Thus protects these proteins from oxidative-stress damage caused by reactive species of oxygen and chlorine generated by the host defense mechanisms. MsrPQ is essential for the maintenance of envelope integrity under bleach stress, rescuing a wide series of structurally unrelated periplasmic proteins from methionine oxidation. MsrQ provides electrons for reduction to the reductase catalytic subunit MsrP, using the quinone pool of the respiratory chain
BER93_08595	COG2890	protein-(glutamine-N5) methyltransferase activity
BER93_08605	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
BER93_08610	COG1052	Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family
BER93_08615	COG0136	Catalyzes the NADPH-dependent formation of L-aspartate- semialdehyde (L-ASA) by the reductive dephosphorylation of L- aspartyl-4-phosphate
BER93_08625	COG0840	transmembrane signaling receptor activity
BER93_08630	COG0467	Core component of the KaiABC clock protein complex, which constitutes the main circadian regulator in cyanobacteria. Binds to DNA. The KaiABC complex may act as a promoter-nonspecific transcription regulator that represses transcription, possibly by acting on the state of chromosome compaction
BER93_08640	COG2963	transposase activity
BER93_08660	COG3088	subunit of a heme lyase
BER93_08715	COG2141	COG2141 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and related flavin-dependent oxidoreductases
BER93_08725	COG1253	flavin adenine dinucleotide binding
BER93_08740	COG1434	Gram-negative-bacterium-type cell wall biogenesis
BER93_08760	COG0504	CTP synthase activity
BER93_08765	COG2877	3-deoxy-8-phosphooctulonate synthase activity
BER93_08770	COG0148	phosphopyruvate hydratase activity
BER93_08780	COG1211	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity
BER93_08795	COG2840	Smr protein MutS2
BER93_08800	COG0496	Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates
BER93_08805	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
BER93_08810	COG1238	metal cluster binding
BER93_08855	COG2021	Transfers an acetyl group from acetyl-CoA to L- homoserine, forming acetyl-L-homoserine
BER93_08885	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
BER93_08905	COG4133	protoheme IX ABC transporter activity
BER93_08910	COG0436	Aminotransferase
BER93_08930	COG1187	pseudouridine synthase activity
BER93_08935	COG1386	Participates in chromosomal partition during cell division. May act via the formation of a condensin-like complex containing Smc and ScpA that pull DNA away from mid-cell into both cell halves
BER93_08940	COG1354	Participates in chromosomal partition during cell division. May act via the formation of a condensin-like complex containing Smc and ScpB that pull DNA away from mid-cell into both cell halves
BER93_08945	COG2350	Protein conserved in bacteria
BER93_08975	COG1175	transmembrane transport
BER93_08980	COG0395	ABC-type sugar transport system, permease component
BER93_09010	COG0388	Catalyzes the ATP-dependent amidation of deamido-NAD to form NAD. Uses L-glutamine as a nitrogen source
BER93_09015	COG2957	Belongs to the agmatine deiminase family
BER93_09030	COG0539	negative regulation of cytoplasmic translation
BER93_09045	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
BER93_09050	COG0472	First step of the lipid cycle reactions in the biosynthesis of the cell wall peptidoglycan
BER93_09070	COG2963	transposase activity
BER93_09100	COG0190	Catalyzes the oxidation of 5,10- methylenetetrahydrofolate to 5,10-methenyltetrahydrofolate and then the hydrolysis of 5,10-methenyltetrahydrofolate to 10- formyltetrahydrofolate
BER93_09115	COG0582	viral genome integration into host DNA
BER93_09155	COG4691	Plasmid stability protein
BER93_09160	COG1487	ribonuclease activity
BER93_09170	COG2963	transposase activity
BER93_09180	COG2801	Transposase and inactivated derivatives
BER93_09210	COG0124	histidyl-tRNA synthetase
BER93_09220	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
BER93_09225	COG0141	Catalyzes the sequential NAD-dependent oxidations of L- histidinol to L-histidinaldehyde and then to L-histidine
BER93_09230	COG0079	Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. Histidinol-phosphate aminotransferase subfamily
BER93_09245	COG0106	1-(5-phosphoribosyl)-5- 5-phosphoribosylamino)methylideneamino imidazole-4-carboxamide isomerase
BER93_09250	COG0107	imidazoleglycerol-phosphate synthase activity
BER93_09255	COG0140	phosphoribosyl-ATP diphosphatase activity
BER93_09255	COG0139	Catalyzes the hydrolysis of the adenine ring of phosphoribosyl-AMP
BER93_09280	COG4229	Bifunctional enzyme that catalyzes the enolization of 2,3-diketo-5-methylthiopentyl-1-phosphate (DK-MTP-1-P) into the intermediate 2-hydroxy-3-keto-5-methylthiopentenyl-1-phosphate (HK-MTPenyl-1-P), which is then dephosphorylated to form the acireductone 1,2-dihydroxy-3-keto-5-methylthiopentene (DHK- MTPene)
BER93_09285	COG1791	Catalyzes 2 different reactions between oxygene and the acireductone 1,2-dihydroxy-3-keto-5-methylthiopentene (DHK-MTPene) depending upon the metal bound in the active site. Fe-containing acireductone dioxygenase (Fe-ARD) produces formate and 2-keto-4- methylthiobutyrate (KMTB), the alpha-ketoacid precursor of methionine in the methionine recycle pathway. Ni-containing acireductone dioxygenase (Ni-ARD) produces methylthiopropionate, carbon monoxide and formate, and does not lie on the methionine recycle pathway
BER93_09290	COG0235	Class ii aldolase
BER93_09295	COG0531	amino acid
BER93_09300	COG0531	amino acid
BER93_09310	COG0111	D-isomer specific 2-hydroxyacid dehydrogenase
BER93_09315	COG0277	FAD linked oxidase domain protein
BER93_09330	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
BER93_09345	COG1024	Enoyl-CoA hydratase
BER93_09375	COG0505	Belongs to the CarA family
BER93_09390	COG0458	carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity
BER93_09395	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
BER93_09405	COG0608	single-stranded DNA 5'-3' exodeoxyribonuclease activity
BER93_09410	COG1186	Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA
BER93_09415	COG1190	Belongs to the class-II aminoacyl-tRNA synthetase family
BER93_09430	COG2198	Histidine kinase
BER93_09430	COG0784	Response regulator, receiver
BER93_09430	COG2205	protein histidine kinase activity
BER93_09435	COG1024	Enoyl-CoA hydratase
BER93_09440	COG0318	PFAM AMP-dependent synthetase and ligase
BER93_09470	COG2021	Transfers an acetyl group from acetyl-CoA to L- homoserine, forming acetyl-L-homoserine
BER93_09480	COG2201	protein-glutamate methylesterase activity
BER93_09500	COG0835	chemotaxis
BER93_09510	COG0840	transmembrane signaling receptor activity
BER93_09520	COG0840	transmembrane signaling receptor activity
BER93_09525	COG0840	transmembrane signaling receptor activity
BER93_09535	COG0840	transmembrane signaling receptor activity
BER93_09560	COG2198	Histidine kinase
BER93_09560	COG0643	Histidine kinase
BER93_09565	COG0745	RESPONSE REGULATOR receiver
BER93_09575	COG0835	chemotaxis
BER93_09580	COG1192	Involved in chromosome partitioning
BER93_09585	COG1360	Flagellar Motor Protein
BER93_09590	COG1291	archaeal or bacterial-type flagellum-dependent cell motility
BER93_09710	COG2154	pterin-4-alpha-carbinolamine dehydratase
BER93_09720	COG2963	transposase activity
BER93_09725	COG2801	Transposase and inactivated derivatives
BER93_09750	COG0564	pseudouridine synthase activity
BER93_09755	COG1530	ribonuclease E activity
BER93_09785	COG0677	UDP-N-acetyl-D-mannosamine dehydrogenase activity
BER93_09795	COG3039	Transposase
BER93_09805	COG2963	transposase activity
BER93_09810	COG2801	Transposase and inactivated derivatives
BER93_09815	COG2801	Transposase and inactivated derivatives
BER93_09845	COG3501	Rhs element vgr protein
BER93_09910	COG3501	Rhs element vgr protein
BER93_09935	COG3501	Rhs element vgr protein
BER93_09975	COG3501	Rhs element vgr protein
BER93_09980	COG2963	transposase activity
BER93_10015	COG3685	Protein conserved in bacteria
BER93_10030	COG3039	Transposase
BER93_10040	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
BER93_10040	COG1648	precorrin-2 dehydrogenase activity
BER93_10050	COG0746	molybdenum cofactor guanylyltransferase activity
BER93_10075	COG0476	Involved in molybdopterin and thiamine biosynthesis, family 2
BER93_10080	COG0303	'Molybdopterin
BER93_10085	COG1160	GTP binding
BER93_10090	COG1520	Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane
BER93_10110	COG0820	rRNA (adenine-C2-)-methyltransferase activity
BER93_10115	COG0105	UTP biosynthetic process
BER93_10125	COG1250	3-hydroxyacyl-CoA dehydrogenase
BER93_10125	COG1024	Enoyl-CoA hydratase
BER93_10130	COG0183	Belongs to the thiolase family
BER93_10135	COG0038	chloride channel
BER93_10145	COG2256	atpase related to the helicase subunit of the holliday junction resolvase
BER93_10160	COG1674	ftsk spoiiie
BER93_10165	COG0492	ferredoxin-NADP+ reductase activity
BER93_10175	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
BER93_10180	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
BER93_10185	COG0542	response to heat
BER93_10190	COG2127	Involved in the modulation of the specificity of the ClpAP-mediated ATP-dependent protein degradation
BER93_10200	COG0482	sulfurtransferase activity
BER93_10205	COG2915	High frequency lysogenization protein hflD homolog
BER93_10230	COG4585	Histidine kinase
BER93_10240	COG5002	protein histidine kinase activity
BER93_10260	COG0784	Response regulator, receiver
BER93_10260	COG0835	chemotaxis
BER93_10265	COG1815	bacterial-type flagellum-dependent cell motility
BER93_10270	COG1558	bacterial-type flagellum-dependent cell motility
BER93_10275	COG1843	Required for flagellar hook formation. May act as a scaffolding protein
BER93_10280	COG1749	Flagellar hook protein flgE
BER93_10290	COG4786	Flagellar basal body rod
BER93_10300	COG1706	bacterial-type flagellum-dependent cell motility
BER93_10315	COG1344	Flagellin is the subunit protein which polymerizes to form the filaments of bacterial flagella
BER93_10325	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
BER93_10345	COG2197	response regulator
BER93_10355	COG2201	protein-glutamate methylesterase activity
BER93_10360	COG2204	response regulator
BER93_10380	COG1677	Flagellar hook-basal body complex protein FliE
BER93_10430	COG3190	flagellar
BER93_10440	COG1987	bacterial-type flagellum assembly
BER93_10445	COG1684	flagellar biosynthetic protein fliR
BER93_10455	COG5001	Diguanylate cyclase
BER93_10455	COG3300	MHYT domain
BER93_10460	COG5001	Diguanylate cyclase
BER93_10460	COG3300	MHYT domain
BER93_10470	COG1298	Required for formation of the rod structure of the flagellar apparatus. Together with FliI and FliH, may constitute the export apparatus of flagellin
BER93_10480	COG0455	bacterial-type flagellum organization
BER93_10500	COG2198	Histidine kinase
BER93_10500	COG0643	Histidine kinase
BER93_10580	COG2963	transposase activity
BER93_10640	COG2963	transposase activity
BER93_10650	COG3039	Transposase
BER93_10680	COG1112	Superfamily I DNA and RNA helicases and helicase subunits
BER93_10685	COG2801	Transposase and inactivated derivatives
BER93_10690	COG2963	transposase activity
BER93_10695	COG1012	belongs to the aldehyde dehydrogenase family
BER93_10710	COG0167	dihydroorotate dehydrogenase activity
BER93_10715	COG0812	UDP-N-acetylmuramate dehydrogenase activity
BER93_10725	COG0671	phosphoesterase, PA-phosphatase related
BER93_10730	COG0821	Converts 2C-methyl-D-erythritol 2,4-cyclodiphosphate (ME-2,4cPP) into 1-hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate
BER93_10750	COG3706	GGDEF domain
BER93_10750	COG4251	negative regulation of phosphorylation
BER93_10750	COG5001	Diguanylate cyclase
BER93_10750	COG2203	Gaf domain
BER93_10770	COG3039	Transposase
BER93_10840	COG0166	Belongs to the GPI family
BER93_10845	COG0853	Catalyzes the pyruvoyl-dependent decarboxylation of aspartate to produce beta-alanine
BER93_10850	COG0414	Catalyzes the condensation of pantoate with beta-alanine in an ATP-dependent reaction via a pantoyl-adenylate intermediate
BER93_10855	COG0413	3-methyl-2-oxobutanoate hydroxymethyltransferase activity
BER93_10880	COG0477	Major facilitator Superfamily
BER93_10890	COG1070	Carbohydrate kinase
BER93_10900	COG1501	Belongs to the glycosyl hydrolase 31 family
BER93_10950	COG0800	Aldolase
BER93_10965	COG3734	2-keto-3-deoxy-galactonokinase
BER93_10970	COG1146	Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions
BER93_10980	COG0329	Catalyzes the condensation of (S)-aspartate-beta- semialdehyde (S)-ASA and pyruvate to 4-hydroxy- tetrahydrodipicolinate (HTPA)
BER93_10995	COG1225	Alkyl hydroperoxide reductase Thiol specific antioxidant Mal allergen
BER93_11000	COG1875	ATPase related to phosphate starvation-inducible protein PhoH
BER93_11010	COG0351	phosphomethylpyrimidine kinase
BER93_11010	COG0352	thiamine-phosphate diphosphorylase activity
BER93_11025	COG0583	DNA-binding transcription factor activity
BER93_11030	COG1741	Belongs to the pirin family
BER93_11050	COG1551	Could accelerate the degradation of some genes transcripts potentially through selective RNA binding
BER93_11055	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
BER93_11060	COG2137	regulation of response to DNA damage stimulus
BER93_11065	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
BER93_11070	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
BER93_11125	COG2963	transposase activity
BER93_11130	COG2801	Transposase and inactivated derivatives
BER93_11175	COG4771	TonB-dependent receptor
BER93_11180	COG1546	Belongs to the CinA family
BER93_11190	COG2262	GTPase that associates with the 50S ribosomal subunit and may have a role during protein synthesis or ribosome biogenesis
BER93_11195	COG1923	regulation of RNA biosynthetic process
BER93_11200	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)
BER93_11205	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
BER93_11210	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
BER93_11215	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
BER93_11220	COG1534	Rna-binding protein
BER93_11225	COG3737	Protein of unknown function (DUF498/DUF598)
BER93_11245	COG2963	transposase activity
BER93_11330	COG3501	Rhs element vgr protein
BER93_11335	COG1262	PFAM Formylglycine-generating sulfatase enzyme
BER93_11345	COG3501	Rhs element vgr protein
BER93_11445	COG3501	Rhs element vgr protein
BER93_11460	COG3039	Transposase
BER93_11500	COG0558	Belongs to the CDP-alcohol phosphatidyltransferase class-I family
BER93_11520	COG1212	Activates KDO (a required 8-carbon sugar) for incorporation into bacterial lipopolysaccharide in Gram-negative bacteria
BER93_11525	COG1663	tetraacyldisaccharide 4'-kinase activity
BER93_11530	COG1132	(ABC) transporter
BER93_11535	COG0848	biopolymer transport protein
BER93_11540	COG0811	peptide transport
BER93_11555	COG1136	(ABC) transporter
BER93_11560	COG4591	ABC-type transport system involved in lipoprotein release permease component
BER93_11570	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
BER93_11575	COG0479	Belongs to the succinate dehydrogenase fumarate reductase iron-sulfur protein family
BER93_11590	COG2142	Succinate dehydrogenase hydrophobic membrane anchor
BER93_11610	COG0364	Catalyzes the oxidation of glucose 6-phosphate to 6- phosphogluconolactone
BER93_11615	COG0837	glucose binding
BER93_11625	COG0129	dihydroxy-acid dehydratase activity
BER93_11630	COG0800	Aldolase
BER93_11685	COG2198	Histidine kinase
BER93_11685	COG0784	Response regulator, receiver
BER93_11685	COG2205	protein histidine kinase activity
BER93_11690	COG2183	response to ionizing radiation
BER93_11715	COG3243	poly(R)-hydroxyalkanoic acid synthase
BER93_11725	COG1183	phosphatidylcholine synthase activity
BER93_11750	COG0668	transmembrane transport
BER93_11760	COG0590	tRNA wobble adenosine to inosine editing
BER93_11765	COG1321	iron dependent repressor
BER93_11770	COG1914	H( )-stimulated, divalent metal cation uptake system
BER93_11820	COG2963	transposase activity
BER93_11840	COG2801	Transposase and inactivated derivatives
BER93_11845	COG2963	transposase activity
BER93_11890	COG0002	Catalyzes the NADPH-dependent reduction of N-acetyl-5- glutamyl phosphate to yield N-acetyl-L-glutamate 5-semialdehyde
BER93_11900	COG0548	Belongs to the acetylglutamate kinase family. ArgB subfamily
BER93_11910	COG0137	argininosuccinate synthase activity
BER93_11915	COG0078	Reversibly catalyzes the transfer of the carbamoyl group from carbamoyl phosphate (CP) to the N(epsilon) atom of ornithine (ORN) to produce L-citrulline
BER93_11930	COG2166	iron-sulfur cluster assembly
BER93_11940	COG1734	Transcription factor that acts by binding directly to the RNA polymerase (RNAP). Required for negative regulation of rRNA expression and positive regulation of several amino acid biosynthesis promoters
BER93_11950	COG0044	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides
BER93_11960	COG3039	Transposase
BER93_12000	COG2227	3-demethylubiquinone-9 3-O-methyltransferase activity
BER93_12005	COG0402	S-adenosylhomocysteine deaminase activity
BER93_12020	COG1509	lysine 2,3-aminomutase activity
BER93_12030	COG0483	inositol monophosphate 1-phosphatase activity
BER93_12055	COG0513	Belongs to the DEAD box helicase family
BER93_12060	COG0503	Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis
BER93_12065	COG0397	Uncharacterized ACR, YdiU/UPF0061 family
BER93_12075	COG0625	glutathione transferase activity
BER93_12090	COG4681	YaeQ
BER93_12095	COG2081	HI0933 family
BER93_12105	COG0501	Belongs to the peptidase M48B family
BER93_12110	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)
BER93_12115	COG1028	Short-chain dehydrogenase reductase Sdr
BER93_12135	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
BER93_12140	COG0860	N-Acetylmuramoyl-L-alanine amidase
BER93_12150	COG0063	ADP-dependent NAD(P)H-hydrate dehydratase activity
BER93_12150	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
BER93_12155	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)
BER93_12180	COG1738	Involved in the import of queuosine (Q) precursors, required for Q precursor salvage
BER93_12200	COG2040	homocysteine
BER93_12205	COG0833	amino acid
BER93_12215	COG0073	Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation
BER93_12215	COG0143	Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation
BER93_12225	COG2878	Part of a membrane complex involved in electron transport
BER93_12240	COG1595	DNA-templated transcription, initiation
BER93_12265	COG2230	cyclopropane-fatty-acyl-phospholipid synthase
BER93_12280	COG2230	cyclopropane-fatty-acyl-phospholipid synthase
BER93_12285	COG0251	oxidation-reduction process
BER93_12295	COG2898	Catalyzes the transfer of a lysyl group from L-lysyl- tRNA(Lys) to membrane-bound phosphatidylglycerol (PG), which produces lysylphosphatidylglycerol (LPG), a major component of the bacterial membrane with a positive net charge. LPG synthesis contributes to bacterial virulence as it is involved in the resistance mechanism against cationic antimicrobial peptides (CAMP) produces by the host's immune system (defensins, cathelicidins) and by the competing microorganisms
BER93_12295	COG0392	lysyltransferase activity
BER93_12330	COG2814	Major facilitator Superfamily
BER93_12335	COG1902	pentaerythritol trinitrate reductase activity
BER93_12340	COG2824	Alkylphosphonate utilization operon protein PhnA
BER93_12375	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
BER93_12415	COG0717	Belongs to the dCTP deaminase family
BER93_12420	COG0489	protein tyrosine kinase activity
BER93_12435	COG3590	peptidase
BER93_12460	COG0665	tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase activity
BER93_12465	COG2311	Membrane
BER93_12470	COG1047	Peptidyl-prolyl cis-trans
BER93_12475	COG0791	NLP P60 protein
BER93_12480	COG0791	NLP P60 protein
BER93_12490	COG2963	transposase activity
BER93_12495	COG2801	Transposase and inactivated derivatives
BER93_12505	COG3039	Transposase
BER93_12530	COG0583	DNA-binding transcription factor activity
BER93_12535	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)
BER93_12550	COG0128	3-phosphoshikimate 1-carboxyvinyltransferase activity
BER93_12555	COG1605	Chorismate mutase
BER93_12555	COG0077	Prephenate dehydratase
BER93_12560	COG1932	Catalyzes the reversible conversion of 3- phosphohydroxypyruvate to phosphoserine and of 3-hydroxy-2-oxo-4- phosphonooxybutanoate to phosphohydroxythreonine
BER93_12565	COG2041	Part of the MsrPQ system that repairs oxidized periplasmic proteins containing methionine sulfoxide residues (Met-O), using respiratory chain electrons. Thus protects these proteins from oxidative-stress damage caused by reactive species of oxygen and chlorine generated by the host defense mechanisms. MsrPQ is essential for the maintenance of envelope integrity under bleach stress, rescuing a wide series of structurally unrelated periplasmic proteins from methionine oxidation. The catalytic subunit MsrP is non-stereospecific, being able to reduce both (R-) and (S-) diastereoisomers of methionine sulfoxide
BER93_12570	COG1609	Transcriptional regulator
BER93_12575	COG4668	phosphoenolpyruvate-dependent sugar phosphotransferase system
BER93_12575	COG1080	General (non sugar-specific) component of the phosphoenolpyruvate-dependent sugar phosphotransferase system (sugar PTS). This major carbohydrate active-transport system catalyzes the phosphorylation of incoming sugar substrates concomitantly with their translocation across the cell membrane. Enzyme I transfers the phosphoryl group from phosphoenolpyruvate (PEP) to the phosphoryl carrier protein (HPr)
BER93_12580	COG1105	Belongs to the carbohydrate kinase PfkB family
BER93_12585	COG1299	protein-N(PI)-phosphohistidine-fructose phosphotransferase system transporter activity
BER93_12585	COG1445	protein-N(PI)-phosphohistidine-fructose phosphotransferase system transporter activity
BER93_12600	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
BER93_12605	COG1862	Preprotein translocase
BER93_12610	COG0343	queuine tRNA-ribosyltransferase activity
BER93_12615	COG0809	Transfers and isomerizes the ribose moiety from AdoMet to the 7-aminomethyl group of 7-deazaguanine (preQ1-tRNA) to give epoxyqueuosine (oQ-tRNA)
BER93_12655	COG3291	Pkd domain containing protein
BER93_12665	COG1145	4fe-4S ferredoxin, iron-sulfur binding domain protein
BER93_12675	COG0669	Reversibly transfers an adenylyl group from ATP to 4'- phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate
BER93_12680	COG0742	ribosomal rna small subunit methyltransferase
BER93_12685	COG0326	Molecular chaperone. Has ATPase activity
BER93_12710	COG3039	Transposase
BER93_12725	COG1301	dicarboxylic acid transport
BER93_12730	COG1785	Belongs to the alkaline phosphatase family
BER93_12735	COG0037	tRNA processing
BER93_12740	COG1722	exodeoxyribonuclease VII activity
BER93_12745	COG0142	geranyltranstransferase activity
BER93_12760	COG0312	modulator of DNA gyrase
BER93_12765	COG3028	Belongs to the UPF0307 family
BER93_12770	COG0312	modulator of DNA gyrase
BER93_12785	COG1530	ribonuclease E activity
BER93_12790	COG0424	maF-like protein
BER93_12795	COG2968	Membrane
BER93_12805	COG2963	transposase activity
BER93_12830	COG1057	Catalyzes the reversible adenylation of nicotinate mononucleotide (NaMN) to nicotinic acid adenine dinucleotide (NaAD)
BER93_12845	COG0495	leucyl-tRNA aminoacylation
BER93_12855	COG3118	belongs to the thioredoxin family
BER93_12935	COG1377	Required for formation of the rod structure in the basal body of the flagellar apparatus. Together with FliI and FliH, may constitute the export apparatus of flagellin
BER93_12990	COG5297	Belongs to the glycosyl hydrolase family 6
BER93_13015	COG2155	Conserved Protein
BER93_13050	COG1132	(ABC) transporter
BER93_13060	COG0475	glutathione-regulated potassium exporter activity
BER93_13085	COG1187	pseudouridine synthase activity
BER93_13095	COG5002	protein histidine kinase activity
BER93_13095	COG5001	Diguanylate cyclase
BER93_13170	COG3383	formate dehydrogenase (NAD+) activity
BER93_13180	COG1404	Belongs to the peptidase S8 family
BER93_13205	COG2730	Belongs to the glycosyl hydrolase 5 (cellulase A) family
BER93_13215	COG0735	belongs to the Fur family
BER93_13220	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)
BER93_13250	COG2961	Specifically methylates the adenine in position 2030 of 23S rRNA
BER93_13260	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
BER93_13265	COG0249	that it carries out the mismatch recognition step. This protein has a weak ATPase activity
BER93_13270	COG0376	Bifunctional enzyme with both catalase and broad- spectrum peroxidase activity
BER93_13285	COG2963	transposase activity
BER93_13305	COG0588	phosphoglycerate mutase activity
BER93_13340	COG1966	Carbon starvation protein
BER93_13345	COG2879	small protein
BER93_13350	COG0637	HAD-superfamily hydrolase subfamily IA, variant 3
BER93_13375	COG1529	Aldehyde oxidase and xanthine dehydrogenase
BER93_13375	COG1529	Aldehyde oxidase and xanthine dehydrogenase
BER93_13380	COG3706	GGDEF domain
BER93_13380	COG4251	negative regulation of phosphorylation
BER93_13380	COG2203	Gaf domain
BER93_13380	COG5001	Diguanylate cyclase
BER93_13385	COG0629	single-stranded DNA binding
BER93_13395	COG0142	geranyltranstransferase activity
BER93_13420	COG0527	aspartate kinase activity
BER93_13430	COG0384	phenazine biosynthesis protein PhzF
BER93_13440	COG1764	response to oxidative stress
BER93_13450	COG0816	Could be a nuclease involved in processing of the 5'-end of pre-16S rRNA
BER93_13455	COG1678	Uncharacterized ACR, COG1678
BER93_13490	COG0325	Pyridoxal 5'-phosphate (PLP)-binding protein, which is involved in PLP homeostasis
BER93_13525	COG1959	2 iron, 2 sulfur cluster binding
BER93_13530	COG0719	Fe-S assembly protein
BER93_13535	COG0396	ATPase activity
BER93_13540	COG0719	Fe-S assembly protein
BER93_13545	COG0520	Catalyzes the removal of elemental sulfur and selenium atoms from L-cysteine, L-cystine, L-selenocysteine, and L- selenocystine to produce L-alanine
BER93_13560	COG4774	siderophore transport
BER93_13565	COG3128	pkhd-type hydroxylase
BER93_13575	COG2963	transposase activity
BER93_13595	COG1555	photosystem II stabilization
BER93_13600	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
BER93_13610	COG3178	'Phosphotransferase
BER93_13615	COG1208	COG1208 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis translation initiation factor 2B, gamma epsilon subunits eIF-2Bgamma eIF-2Bepsilon
BER93_13630	COG0628	permease
BER93_13645	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
BER93_13670	COG0766	Cell wall formation. Adds enolpyruvyl to UDP-N- acetylglucosamine
BER93_13675	COG0271	Belongs to the BolA IbaG family
BER93_13685	COG1778	Involved in the biosynthesis of lipopolysaccharides (LPSs). Catalyzes the hydrolysis of 3-deoxy-D-manno-octulosonate 8-phosphate (KDO 8-P) to 3-deoxy-D-manno-octulosonate (KDO) and inorganic phosphate
BER93_13695	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
BER93_13700	COG1137	ATPase activity
BER93_13715	COG1762	phosphoenolpyruvate-dependent sugar phosphotransferase system
BER93_13735	COG1925	phosphoenolpyruvate-dependent sugar phosphotransferase system
BER93_13740	COG1080	General (non sugar-specific) component of the phosphoenolpyruvate-dependent sugar phosphotransferase system (sugar PTS). This major carbohydrate active-transport system catalyzes the phosphorylation of incoming sugar substrates concomitantly with their translocation across the cell membrane. Enzyme I transfers the phosphoryl group from phosphoenolpyruvate (PEP) to the phosphoryl carrier protein (HPr)
BER93_13745	COG2239	Acts as a magnesium transporter
BER93_13750	COG2963	transposase activity
BER93_13780	COG0837	glucose binding
BER93_13795	COG3858	chitin binding
BER93_13795	COG1388	LysM domain
BER93_13800	COG3525	Glycosyl hydrolase, family 20, catalytic domain
BER93_13810	COG1472	Belongs to the glycosyl hydrolase 3 family
BER93_13820	COG2963	transposase activity
BER93_13840	COG3039	Transposase
BER93_13850	COG2801	Transposase and inactivated derivatives
BER93_13855	COG2963	transposase activity
BER93_13875	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
BER93_13885	COG0330	HflC and HflK could
BER93_13890	COG0330	HflC and HflK could
BER93_13910	COG0678	peroxiredoxin activity
BER93_13980	COG3829	transcription factor binding
BER93_13995	COG3039	Transposase
BER93_14020	COG1559	Functions as a peptidoglycan terminase that cleaves nascent peptidoglycan strands endolytically to terminate their elongation
BER93_14025	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
BER93_14035	COG0236	Carrier of the growing fatty acid chain in fatty acid biosynthesis
BER93_14040	COG1028	Short-chain dehydrogenase reductase Sdr
BER93_14045	COG0331	[acyl-carrier-protein] S-malonyltransferase activity
BER93_14050	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
BER93_14055	COG0333	Belongs to the bacterial ribosomal protein bL32 family
BER93_14060	COG1399	metal-binding, possibly nucleic acid-binding protein
BER93_14065	COG0424	maF-like protein
BER93_14085	COG0714	Associated with various cellular activities
BER93_14105	COG0537	adenosine 5'-monophosphoramidase activity
BER93_14115	COG0718	Binds to DNA and alters its conformation. May be involved in regulation of gene expression, nucleoid organization and DNA protection
BER93_14135	COG0314	molybdopterin synthase activity
BER93_14145	COG0315	cyclic pyranopterin monophosphate synthase activity
BER93_14150	COG2896	Catalyzes the cyclization of GTP to (8S)-3',8-cyclo-7,8- dihydroguanosine 5'-triphosphate
BER93_14155	COG1234	tRNA 3'-trailer cleavage
BER93_14165	COG0859	PFAM glycosyl transferase family 9
BER93_14180	COG0631	protein serine/threonine phosphatase activity
BER93_14185	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
BER93_14200	COG0491	Thiolesterase that catalyzes the hydrolysis of S-D- lactoyl-glutathione to form glutathione and D-lactic acid
BER93_14205	COG3942	CHAP domain
BER93_14205	COG1388	LysM domain
BER93_14215	COG0266	class I DNA-(apurinic or apyrimidinic site) endonuclease activity
BER93_14220	COG0823	Involved in the tonB-independent uptake of proteins
BER93_14220	COG1506	peptidase
BER93_14225	COG1297	OPT oligopeptide transporter protein
BER93_14255	COG0587	DNA-directed DNA polymerase activity
BER93_14305	COG2080	2 iron, 2 sulfur cluster binding
BER93_14310	COG1319	Aerobic-type carbon monoxide dehydrogenase, middle subunit CoxM
BER93_14315	COG1529	Aldehyde oxidase and xanthine dehydrogenase
BER93_14320	COG1028	Short-chain dehydrogenase reductase Sdr
BER93_14365	COG3039	Transposase
BER93_14390	COG0544	peptidyl-prolyl cis-trans isomerase activity
BER93_14395	COG0740	serine-type endopeptidase activity
BER93_14400	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
BER93_14430	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
BER93_14455	COG0602	queuosine metabolic process
BER93_14465	COG2885	chlorophyll binding
BER93_14470	COG0823	Involved in the tonB-independent uptake of proteins
BER93_14480	COG0848	biopolymer transport protein
BER93_14490	COG0824	Thioesterase
BER93_14530	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)
BER93_14545	COG2951	lytic endotransglycosylase activity
BER93_14550	COG0488	(ABC) transporter
BER93_14580	COG4651	solute:proton antiporter activity
BER93_14580	COG1226	(belongs to the monovalent cation proton antiporter 2 (CPA2) transporter (TC 2.A.37) family)
BER93_14610	COG1113	amino acid transport
BER93_14620	COG0840	transmembrane signaling receptor activity
BER93_14635	COG2197	response regulator
BER93_14640	COG0531	amino acid
BER93_14670	COG0754	glutathionylspermidine amidase activity
BER93_14695	COG1842	Phage shock protein A
BER93_14715	COG0703	Catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid using ATP as a cosubstrate
BER93_14730	COG0407	Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III
BER93_14735	COG2814	Major facilitator Superfamily
BER93_14740	COG3039	Transposase
BER93_14750	COG5002	protein histidine kinase activity
BER93_14750	COG0784	Response regulator, receiver
BER93_14775	COG4191	Histidine kinase
BER93_14775	COG0784	Response regulator, receiver
BER93_14805	COG2207	Transcriptional regulator
BER93_14815	COG3152	Membrane
BER93_14830	COG3125	oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor
BER93_14835	COG1845	cytochrome c oxidase, subunit III
BER93_14840	COG0843	Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Subunits 1- 3 form the functional core of the enzyme complex. CO I is the catalytic subunit of the enzyme. Electrons originating in cytochrome c are transferred via the copper A center of subunit 2 and heme A of subunit 1 to the bimetallic center formed by heme A3 and copper B
BER93_14845	COG1622	oxidoreductase activity, acting on a heme group of donors, oxygen as acceptor
BER93_14855	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
BER93_14860	COG0597	This protein specifically catalyzes the removal of signal peptides from prolipoproteins
BER93_14870	COG0196	riboflavin kinase activity
BER93_14885	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
BER93_14900	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
BER93_14905	COG0824	Thioesterase
BER93_14920	COG1946	Acyl-CoA thioesterase
BER93_14935	COG1595	DNA-templated transcription, initiation
BER93_14945	COG2935	proteasome-mediated ubiquitin-dependent protein catabolic process
BER93_14970	COG2963	transposase activity
BER93_15005	COG0122	3-methyladenine DNA glycosylase 8-oxoguanine DNA glycosylase
BER93_15020	COG2197	response regulator
BER93_15025	COG4585	Histidine kinase
BER93_15040	COG2894	cell division
BER93_15045	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
BER93_15055	COG0642	Histidine kinase
BER93_15075	COG2194	sulfuric ester hydrolase activity
BER93_15095	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
BER93_15095	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
BER93_15100	COG0753	catalase activity
BER93_15110	COG2207	Transcriptional regulator
BER93_15110	COG1917	Cupin 2, conserved barrel domain protein
BER93_15155	COG4772	TonB-dependent receptor
BER93_15165	COG4264	IucA IucC family
BER93_15175	COG4264	IucA IucC family
BER93_15180	COG0019	diaminopimelate decarboxylase activity
BER93_15195	COG0542	response to heat
BER93_15250	COG3501	Rhs element vgr protein
BER93_15255	COG2801	Transposase and inactivated derivatives
BER93_15260	COG2963	transposase activity
BER93_15320	COG0473	3-isopropylmalate dehydrogenase activity
BER93_15340	COG4783	chaperone-mediated protein folding
BER93_15355	COG0855	Catalyzes the reversible transfer of the terminal phosphate of ATP to form a long-chain polyphosphate (polyP)
BER93_15370	COG0671	phosphoesterase, PA-phosphatase related
BER93_15375	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
BER93_15385	COG3291	Pkd domain containing protein
BER93_15395	COG2833	Protein of unknown function (DUF455)
BER93_15415	COG0285	dihydrofolate synthase activity
BER93_15445	COG3537	Alpha-1,2-mannosidase
BER93_15500	COG3645	SOS response
BER93_15515	COG0610	Subunit R is required for both nuclease and ATPase activities, but not for modification
BER93_15535	COG2963	transposase activity
BER93_15555	COG1183	phosphatidylcholine synthase activity
BER93_15580	COG0767	ABC-type transport system involved in resistance to organic solvents, permease component
BER93_15585	COG1127	ABC transporter
BER93_15590	COG3218	ABC-type transport auxiliary lipoprotein component
BER93_15590	COG1463	ABC-type transport system involved in resistance to organic solvents, periplasmic component
BER93_15620	COG1788	Acyl CoA acetate 3-ketoacid CoA transferase, alpha subunit
BER93_15625	COG1109	Catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate
BER93_15655	COG2086	electron transfer activity
BER93_15690	COG0451	ADP-glyceromanno-heptose 6-epimerase activity
BER93_15695	COG1089	Catalyzes the conversion of GDP-D-mannose to GDP-4- dehydro-6-deoxy-D-mannose
BER93_15735	COG0626	cystathionine gamma-synthase activity
BER93_15770	COG0625	glutathione transferase activity
BER93_15780	COG0513	Belongs to the DEAD box helicase family
BER93_15785	COG0720	synthase
BER93_15795	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
BER93_15800	COG1956	GAF domain-containing protein
BER93_15815	COG3039	Transposase
BER93_15825	COG0546	phosphoglycolate phosphatase activity
BER93_15830	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
BER93_15840	COG0764	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity
BER93_15855	COG0339	signal peptide processing
BER93_15870	COG2132	Multicopper oxidase
BER93_15890	COG0449	glutamine-fructose-6-phosphate transaminase (isomerizing) activity
BER93_15905	COG3852	Histidine kinase
BER93_15915	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
BER93_15930	COG0355	proton-transporting ATP synthase activity, rotational mechanism
BER93_15940	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
BER93_15950	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
BER93_15965	COG0356	it plays a direct role in the translocation of protons across the membrane
BER93_15980	COG1249	Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family
BER93_16020	COG2011	ABC-type metal ion transport system permease component
BER93_16025	COG1135	Part of the ABC transporter complex MetNIQ involved in methionine import. Responsible for energy coupling to the transport system
BER93_16030	COG1666	GTP binding
BER93_16075	COG1187	pseudouridine synthase activity
BER93_16080	COG2813	Specifically methylates the guanine in position
BER93_16100	COG2202	Pas domain
BER93_16100	COG2205	protein histidine kinase activity
BER93_16120	COG0787	Catalyzes the interconversion of L-alanine and D- alanine. May also act on other amino acids
BER93_16125	COG0665	tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase activity
BER93_16250	COG2801	Transposase and inactivated derivatives
BER93_16305	COG0757	Catalyzes a trans-dehydration via an enolate intermediate
BER93_16310	COG0511	ligase activity, forming carbon-carbon bonds
BER93_16320	COG0439	Biotin carboxylase
BER93_16325	COG2264	protein methyltransferase activity
BER93_16345	COG2901	Activates ribosomal RNA transcription. Plays a direct role in upstream activation of rRNA promoters
BER93_16355	COG0138	bifunctional purine biosynthesis protein purh
BER93_16360	COG0151	Belongs to the GarS family
BER93_16365	COG1289	transmembrane transporter activity
BER93_16370	COG2814	Major facilitator Superfamily
BER93_16385	COG2814	Major facilitator Superfamily
BER93_16400	COG1270	Converts cobyric acid to cobinamide by the addition of aminopropanol on the F carboxylic group
BER93_16405	COG2816	NAD+ diphosphatase activity
BER93_16415	COG3039	Transposase
BER93_16425	COG2963	transposase activity
BER93_16430	COG2801	Transposase and inactivated derivatives
BER93_16475	COG1733	regulation of RNA biosynthetic process
BER93_16480	COG0129	dihydroxy-acid dehydratase activity
BER93_16485	COG0663	COG0663 Carbonic anhydrases acetyltransferases, isoleucine patch superfamily
BER93_16500	COG2963	transposase activity
BER93_16515	COG3039	Transposase
BER93_16520	COG0841	Belongs to the resistance-nodulation-cell division (RND) (TC 2.A.6) family
BER93_16525	COG0841	Belongs to the resistance-nodulation-cell division (RND) (TC 2.A.6) family
BER93_16540	COG1902	pentaerythritol trinitrate reductase activity
BER93_16545	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
BER93_16555	COG2814	Major facilitator Superfamily
BER93_16560	COG0084	hydrolase, TatD family'
BER93_16565	COG4807	Protein conserved in bacteria
BER93_16575	COG1643	Atp-dependent helicase
BER93_16595	COG1187	pseudouridine synthase activity
BER93_16610	COG2130	NADP-dependent
BER93_16615	COG0656	L-ascorbic acid biosynthetic process
BER93_16625	COG1764	response to oxidative stress
BER93_16635	COG1485	Reduces the stability of FtsZ polymers in the presence of ATP
BER93_16685	COG1960	acyl-CoA dehydrogenase activity
BER93_16690	COG4799	Acetyl-CoA carboxylase, carboxyltransferase component subunits alpha and beta
BER93_16735	COG2801	Transposase and inactivated derivatives
BER93_16740	COG2801	Transposase and inactivated derivatives
BER93_16745	COG2963	transposase activity
BER93_16755	COG0841	Belongs to the resistance-nodulation-cell division (RND) (TC 2.A.6) family
BER93_16765	COG2895	sulfate adenylyltransferase (ATP) activity
BER93_16765	COG0529	Catalyzes the synthesis of activated sulfate
BER93_16775	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
BER93_16780	COG0155	Belongs to the nitrite and sulfite reductase 4Fe-4S domain family
BER93_16805	COG2205	protein histidine kinase activity
BER93_16805	COG2198	Histidine kinase
BER93_16805	COG0784	Response regulator, receiver
BER93_16835	COG3588	fructose-bisphosphate aldolase
BER93_16840	COG0469	pyruvate kinase activity
BER93_16875	COG2205	protein histidine kinase activity
BER93_16880	COG1104	cysteine desulfurase activity
BER93_16915	COG2963	transposase activity
BER93_16920	COG2801	Transposase and inactivated derivatives
BER93_16930	COG3039	Transposase
BER93_16945	COG0057	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
BER93_16960	COG3453	Protein conserved in bacteria
BER93_16960	COG0491	Thiolesterase that catalyzes the hydrolysis of S-D- lactoyl-glutathione to form glutathione and D-lactic acid
BER93_16965	COG0725	ABC transporter, periplasmic molybdate-binding protein
BER93_16970	COG4149	molybdate abc transporter
BER93_16975	COG4148	Part of the ABC transporter complex ModABC involved in molybdenum import. Responsible for energy coupling to the transport system
BER93_17000	COG1376	ErfK ybiS ycfS ynhG family protein
BER93_17005	COG0739	heme binding
BER93_17005	COG0741	lytic transglycosylase activity
BER93_17005	COG1196	nuclear chromosome segregation
BER93_17010	COG4773	Receptor
BER93_17020	COG1301	dicarboxylic acid transport
BER93_17050	COG0714	Associated with various cellular activities
BER93_17075	COG3039	Transposase
BER93_17090	COG0025	NhaP-type Na H and K H
BER93_17115	COG2335	COG2335, Secreted and surface protein containing fasciclin-like repeats
BER93_17120	COG1573	uracil-dna glycosylase
BER93_17130	COG0667	Aldo Keto reductase
BER93_17140	COG3590	peptidase
BER93_17155	COG0531	amino acid
BER93_17170	COG3685	Protein conserved in bacteria
BER93_17175	COG3546	catalase activity
BER93_17205	COG2204	response regulator
BER93_17230	COG1028	Short-chain dehydrogenase reductase Sdr
BER93_17235	COG1087	Belongs to the NAD(P)-dependent epimerase dehydratase family
BER93_17255	COG1132	(ABC) transporter
BER93_17270	COG1063	alcohol dehydrogenase
BER93_17355	COG0659	secondary active sulfate transmembrane transporter activity
BER93_17380	COG2963	transposase activity
BER93_17470	COG3052	prosthetic group binding
BER93_17485	COG3385	transposase activity
BER93_17490	COG2353	YceI-like domain
BER93_17495	COG0778	Nitroreductase
BER93_17505	COG1738	Involved in the import of queuosine (Q) precursors, required for Q precursor salvage
BER93_17510	COG1391	[glutamine synthetase]-adenylyl-L-tyrosine phosphorylase
BER93_17520	COG3386	PFAM SMP-30 Gluconolaconase
BER93_17540	COG0722	Stereospecific condensation of phosphoenolpyruvate (PEP) and D-erythrose-4-phosphate (E4P) giving rise to 3-deoxy-D- arabino-heptulosonate-7-phosphate (DAHP)
BER93_17555	COG3385	transposase activity
BER93_17560	COG0459	protein refolding
BER93_17565	COG0234	Binds to Cpn60 in the presence of Mg-ATP and suppresses the ATPase activity of the latter
BER93_17580	COG1324	tolerance protein
BER93_17585	COG4232	protein-disulfide reductase activity
BER93_17615	COG2801	Transposase and inactivated derivatives
BER93_17620	COG2963	transposase activity
BER93_17625	COG0702	epimerase
BER93_17650	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
BER93_17655	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
BER93_17660	COG0297	glycogen (starch) synthase activity
BER93_17675	COG2354	Protein conserved in bacteria
BER93_17680	COG0661	Is probably a protein kinase regulator of UbiI activity which is involved in aerobic coenzyme Q (ubiquinone) biosynthesis
BER93_17685	COG1511	domain protein
BER93_17685	COG3264	Mechanosensitive ion channel
BER93_17705	COG1040	competence protein
BER93_17710	COG0502	Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical- based mechanism
BER93_17805	COG0580	Belongs to the MIP aquaporin (TC 1.A.8) family
BER93_17820	COG2963	transposase activity
BER93_17835	COG0339	signal peptide processing
BER93_17900	COG0451	ADP-glyceromanno-heptose 6-epimerase activity
BER93_17905	COG0318	PFAM AMP-dependent synthetase and ligase
BER93_17915	COG0596	Alpha beta hydrolase
BER93_17935	COG0316	Belongs to the HesB IscA family
BER93_17990	COG0103	maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
BER93_17995	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
BER93_18015	COG0664	- Catabolite gene activator and regulatory subunit of cAMP-dependent protein
BER93_18025	COG0134	indole-3-glycerol-phosphate synthase activity
BER93_18030	COG0547	Catalyzes the transfer of the phosphoribosyl group of 5- phosphorylribose-1-pyrophosphate (PRPP) to anthranilate to yield N-(5'-phosphoribosyl)-anthranilate (PRA)
BER93_18100	COG1597	lipid kinase activity
BER93_18105	COG0456	acetyltransferase
BER93_18120	COG1076	Co-chaperone involved in the maturation of iron-sulfur cluster-containing proteins. Seems to help targeting proteins to be folded toward HscA
BER93_18160	COG1009	NADH ubiquinone oxidoreductase subunit 5 chain L Multisubunit Na H antiporter, MnhA subunit
BER93_18160	COG2111	Na H antiporter
BER93_18165	COG1006	Multisubunit Na H antiporter MnhC subunit
BER93_18170	COG0651	ATP synthesis coupled electron transport
BER93_18180	COG2212	antiporter activity
BER93_18185	COG1320	monovalent cation:proton antiporter activity
BER93_18190	COG3039	Transposase
BER93_18225	COG3023	N-Acetylmuramoyl-L-alanine amidase
BER93_18235	COG4948	Mandelate Racemase Muconate Lactonizing
BER93_18245	COG0531	amino acid
BER93_18265	COG2133	pyrroloquinoline quinone binding
BER93_18275	COG1539	Catalyzes the conversion of 7,8-dihydroneopterin to 6- hydroxymethyl-7,8-dihydropterin
BER93_18280	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
BER93_18285	COG0828	Belongs to the bacterial ribosomal protein bS21 family
BER93_18295	COG1295	ribonuclease BN
BER93_18300	COG0358	DNA primase activity
BER93_18315	COG0109	protoheme IX farnesyltransferase activity
BER93_18345	COG3175	Exerts its effect at some terminal stage of cytochrome c oxidase synthesis, probably by being involved in the insertion of the copper B into subunit I
BER93_18355	COG1622	oxidoreductase activity, acting on a heme group of donors, oxygen as acceptor
BER93_18370	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)
BER93_18375	COG0739	heme binding
BER93_18380	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
BER93_18390	COG2211	Major facilitator Superfamily
BER93_18400	COG0708	Exodeoxyribonuclease III
BER93_18415	COG1192	Involved in chromosome partitioning
BER93_18420	COG1475	DNA binding
BER93_18440	COG0463	Glycosyl transferase, family 2
BER93_18465	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
BER93_18470	COG2003	Belongs to the UPF0758 family
BER93_18475	COG0018	arginyl-trna synthetase
BER93_18485	COG4221	oxidoreductase activity
BER93_18515	COG1819	glycosyl
BER93_18520	COG1020	D-alanine [D-alanyl carrier protein] ligase activity
BER93_18530	COG2205	protein histidine kinase activity
BER93_18535	COG0745	RESPONSE REGULATOR receiver
BER93_18545	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
BER93_18570	COG1199	ATP-dependent helicase activity
BER93_18640	COG0174	glutamine synthetase
BER93_18645	COG0347	Belongs to the P(II) protein family
BER93_18650	COG0004	ammonium transporteR
BER93_18655	COG3852	Histidine kinase
BER93_18660	COG2204	response regulator
BER93_18665	COG2032	superoxide dismutase activity
BER93_18670	COG2032	superoxide dismutase activity
BER93_18710	COG1502	Catalyzes the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) (diphosphatidylglycerol) and glycerol
BER93_18720	COG2062	phosphohistidine phosphatase, SixA
BER93_18725	COG0489	protein tyrosine kinase activity
BER93_18760	COG1262	PFAM Formylglycine-generating sulfatase enzyme
BER93_18775	COG1125	glycine betaine transport
BER93_18785	COG1119	ATPase activity
BER93_18790	COG1522	sequence-specific DNA binding
BER93_18795	COG3186	Phenylalanine-4-hydroxylase
BER93_18800	COG1028	Short-chain dehydrogenase reductase Sdr
BER93_18805	COG3717	Catalyzes the isomerization of 5-dehydro-4-deoxy-D- glucuronate to 3-deoxy-D-glycero-2,5-hexodiulosonate
BER93_18815	COG1609	Transcriptional regulator
BER93_18840	COG0657	acetylesterase activity
BER93_18840	COG2755	lipolytic protein G-D-S-L family
BER93_18860	COG0366	Alpha amylase catalytic
BER93_18865	COG0366	Alpha amylase catalytic
BER93_18935	COG2730	Belongs to the glycosyl hydrolase 5 (cellulase A) family
BER93_18945	COG2730	Belongs to the glycosyl hydrolase 5 (cellulase A) family
BER93_18950	COG1064	alcohol dehydrogenase
BER93_18955	COG0493	'glutamate synthase
BER93_18960	COG0069	glutamate synthase activity
BER93_18960	COG0067	glutamate synthase
BER93_18960	COG0070	glutamate synthase
BER93_18985	COG2804	Type II secretory pathway, ATPase PulE Tfp pilus assembly pathway, ATPase PilB
BER93_18990	COG0519	Catalyzes the synthesis of GMP from XMP
BER93_18990	COG0518	GMP synthase (glutamine-hydrolyzing) activity
BER93_19000	COG0805	protein transport
BER93_19005	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
BER93_19020	COG0276	Catalyzes the ferrous insertion into protoporphyrin IX
BER93_19035	COG2974	May be involved in recombination
BER93_19040	COG0037	tRNA processing
BER93_19045	COG2115	Belongs to the xylose isomerase family
BER93_19055	COG3661	Belongs to the glycosyl hydrolase 67 family
BER93_19080	COG2801	Transposase and inactivated derivatives
BER93_19085	COG2963	transposase activity
BER93_19125	COG0676	glucose-6-phosphate 1-epimerase activity
BER93_19135	COG3012	SEC-C Motif Domain Protein
BER93_19140	COG0730	response to heat
BER93_19180	COG0302	gtp cyclohydrolase
BER93_19185	COG0477	Major facilitator Superfamily
BER93_19215	COG3039	Transposase
BER93_19235	COG3549	Plasmid maintenance system killer
BER93_19245	COG1074	ATP-dependent DNA helicase activity
BER93_19250	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
BER93_19255	COG1127	ABC transporter
BER93_19260	COG0767	ABC-type transport system involved in resistance to organic solvents, permease component
BER93_19265	COG1463	ABC-type transport system involved in resistance to organic solvents, periplasmic component
BER93_19280	COG2853	Lipoprotein
BER93_19290	COG0386	Belongs to the glutathione peroxidase family
BER93_19300	COG1322	Protein conserved in bacteria
BER93_19310	COG0531	amino acid
BER93_19320	COG2203	Gaf domain
BER93_19320	COG2199	diguanylate cyclase activity
BER93_19325	COG1929	Belongs to the glycerate kinase type-1 family
BER93_19340	COG1092	Specifically methylates the guanine in position 2445 (m2G2445) and the guanine in position 2069 (m7G2069) of 23S rRNA
BER93_19345	COG0861	Integral membrane protein TerC family
BER93_19355	COG2963	transposase activity
BER93_19370	COG0706	membrane insertase activity
BER93_19375	COG0594	ribonuclease P activity
BER93_19380	COG0230	Belongs to the bacterial ribosomal protein bL34 family
BER93_19405	COG1192	Involved in chromosome partitioning
BER93_19450	COG3451	type IV secretory pathway VirB4
BER93_19485	COG0630	type IV secretory pathway, VirB11 components, and related ATPases involved in Archaeal flagella biosynthesis
BER93_19500	COG0741	lytic transglycosylase activity
BER93_19510	COG1961	COG1961 Site-specific recombinases, DNA invertase Pin homologs
BER93_19520	COG3077	Addiction module antitoxin, RelB DinJ family
BER93_19640	COG3077	Addiction module antitoxin, RelB DinJ family
BER93_19650	COG1961	COG1961 Site-specific recombinases, DNA invertase Pin homologs
BER93_19700	COG1961	COG1961 Site-specific recombinases, DNA invertase Pin homologs