locus-tag	class	description
L3404_RS00055	COG1560	Kdo2-lipid A biosynthetic process
L3404_RS00065	COG1624	Catalyzes the condensation of 2 ATP molecules into cyclic di-AMP (c-di-AMP), a second messenger used to regulate differing processes in different bacteria
L3404_RS00070	COG1271	oxidase subunit
L3404_RS00075	COG1294	oxidase, subunit
L3404_RS00080	COG1875	ATPase related to phosphate starvation-inducible protein PhoH
L3404_RS00105	COG0681	Belongs to the peptidase S26 family
L3404_RS00105	COG0681	Belongs to the peptidase S26 family
L3404_RS00130	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
L3404_RS00170	COG0507	A helicase nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair. Binds to DSBs and unwinds DNA via a highly rapid and processive ATP-dependent bidirectional helicase activity. Unwinds dsDNA until it encounters a Chi (crossover hotspot instigator) sequence from the 3' direction. Cuts ssDNA a few nucleotides 3' to the Chi site. The properties and activities of the enzyme are changed at Chi. The Chi-altered holoenzyme produces a long 3'-ssDNA overhang and facilitates RecA-binding to the ssDNA for homologous DNA recombination and repair. Holoenzyme degrades any linearized DNA that is unable to undergo homologous recombination. In the holoenzyme this subunit has ssDNA-dependent ATPase and 5'-3' helicase activity. When added to pre-assembled RecBC greatly stimulates nuclease activity and augments holoenzyme processivity. Negatively regulates the RecA-loading ability of RecBCD
L3404_RS00255	COG0313	Catalyzes the 2'-O-methylation of the ribose of cytidine 1402 (C1402) in 16S rRNA
L3404_RS00275	COG0635	Involved in the biosynthesis of porphyrin-containing compound
L3404_RS00290	COG0508	dehydrogenase complex catalyzes the overall conversion of
L3404_RS00310	COG0633	Ferredoxin
L3404_RS00320	COG1298	Required for formation of the rod structure of the flagellar apparatus. Together with FliI and FliH, may constitute the export apparatus of flagellin
L3404_RS00325	COG1191	sigma factor activity
L3404_RS00470	COG4789	Type iii secretion
L3404_RS00475	COG4792	protein secretion
L3404_RS00480	COG0012	GTP binding
L3404_RS00485	COG0196	riboflavin kinase activity
L3404_RS00505	COG0195	Participates in both transcription termination and antitermination
L3404_RS00540	COG0623	enoyl-[acyl-carrier-protein] reductase (NADH) activity
L3404_RS00550	COG0564	pseudouridine synthase activity
L3404_RS00580	COG1164	Oligoendopeptidase f
L3404_RS00640	COG0439	Biotin carboxylase
L3404_RS00650	COG0103	maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
L3404_RS00665	COG0765	amino acid transport
L3404_RS00670	COG1126	abc transporter atp-binding protein
L3404_RS00715	COG4166	transmembrane transport
L3404_RS00725	COG3318	Belongs to the UPF0149 family
L3404_RS00725	COG3012	SEC-C Motif Domain Protein
L3404_RS00770	COG0654	COG0654 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases
L3404_RS00790	COG1136	(ABC) transporter
L3404_RS00890	COG4166	transmembrane transport
L3404_RS00915	COG1116	anion transmembrane transporter activity
L3404_RS00950	COG0364	Catalyzes the oxidation of glucose 6-phosphate to 6- phosphogluconolactone
L3404_RS00960	COG2812	DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity
L3404_RS00995	COG2239	Acts as a magnesium transporter
L3404_RS01015	COG4166	transmembrane transport
L3404_RS01020	COG0601	transmembrane transport
L3404_RS01025	COG1173	ABC-type dipeptide oligopeptide nickel transport systems, permease components
L3404_RS01030	COG0444	Belongs to the ABC transporter superfamily
L3404_RS01035	COG4608	Belongs to the ABC transporter superfamily
L3404_RS01045	COG0471	metal ion transport
L3404_RS01050	COG0205	6-phosphofructokinase activity
L3404_RS01115	COG0531	amino acid
L3404_RS01120	COG0037	tRNA processing
L3404_RS01130	COG0382	Catalyzes the prenylation of para-hydroxybenzoate (PHB) with an all-trans polyprenyl group. Mediates the second step in the final reaction sequence of ubiquinone-8 (UQ-8) biosynthesis, which is the condensation of the polyisoprenoid side chain with PHB, generating the first membrane-bound Q intermediate 3- octaprenyl-4-hydroxybenzoate
L3404_RS01140	COG1284	Uncharacterised 5xTM membrane BCR, YitT family COG1284
L3404_RS01205	COG0733	neurotransmitter:sodium symporter activity
L3404_RS01240	COG0331	[acyl-carrier-protein] S-malonyltransferase activity
L3404_RS01255	COG4775	Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane
L3404_RS01275	COG1071	oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
L3404_RS01280	COG0022	dehydrogenase e1 component
L3404_RS01280	COG0508	dehydrogenase complex catalyzes the overall conversion of
L3404_RS01285	COG0508	dehydrogenase complex catalyzes the overall conversion of
L3404_RS01320	COG1266	CAAX protease self-immunity
L3404_RS01330	COG4536	flavin adenine dinucleotide binding
L3404_RS01340	COG1104	cysteine desulfurase activity
L3404_RS01345	COG0631	protein serine/threonine phosphatase activity
L3404_RS01355	COG2176	DNA-directed DNA polymerase activity
L3404_RS01360	COG2107	Catalyzes the conversion of cyclic dehypoxanthine futalosine (cyclic DHFL) into 1,4-dihydroxy-6-naphthoate, a step in the biosynthesis of menaquinone (MK, vitamin K2)
L3404_RS01370	COG1132	(ABC) transporter
L3404_RS01390	COG0860	N-Acetylmuramoyl-L-alanine amidase
L3404_RS01400	COG0768	penicillin binding
L3404_RS01470	COG1502	Catalyzes the reversible phosphatidyl group transfer from one phosphatidylglycerol molecule to another to form cardiolipin (CL) (diphosphatidylglycerol) and glycerol
L3404_RS01505	COG1762	phosphoenolpyruvate-dependent sugar phosphotransferase system
L3404_RS01515	COG0777	Component of the acetyl coenzyme A carboxylase (ACC) complex. Biotin carboxylase (BC) catalyzes the carboxylation of biotin on its carrier protein (BCCP) and then the CO(2) group is transferred by the transcarboxylase to acetyl-CoA to form malonyl- CoA
L3404_RS01525	COG1109	Catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate
L3404_RS01685	COG2166	iron-sulfur cluster assembly
L3404_RS01750	COG2812	DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria. This DNA polymerase also exhibits 3' to 5' exonuclease activity
L3404_RS01785	COG0022	dehydrogenase e1 component
L3404_RS01825	COG0488	(ABC) transporter
L3404_RS01865	COG1331	Highly conserved protein containing a thioredoxin domain
L3404_RS01990	COG2262	GTPase that associates with the 50S ribosomal subunit and may have a role during protein synthesis or ribosome biogenesis
L3404_RS01995	COG0321	lipoyl(octanoyl) transferase activity
L3404_RS01995	COG1235	May be involved in the transport of PQQ or its precursor to the periplasm
L3404_RS02005	COG2876	3-deoxy-7-phosphoheptulonate synthase activity
L3404_RS02005	COG1605	Chorismate mutase
L3404_RS02100	COG0508	dehydrogenase complex catalyzes the overall conversion of
L3404_RS02105	COG1301	dicarboxylic acid transport
L3404_RS02115	COG0566	Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase TrmH family
L3404_RS02135	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
L3404_RS02145	COG1115	amino acid carrier protein
L3404_RS02150	COG0617	tRNA 3'-terminal CCA addition
L3404_RS02240	COG1366	Belongs to the anti-sigma-factor antagonist family
L3404_RS02250	COG1060	Radical SAM enzyme that catalyzes the addition of the adenosyl radical to the double bond of 3- (1- carboxyvinyl)oxy benzoate, leading to aminodeoxyfutalosine (AFL), a key intermediate in the formation of menaquinone (MK, vitamin K2) from chorismate
L3404_RS02295	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
L3404_RS02325	COG0793	Belongs to the peptidase S41A family
L3404_RS02360	COG0608	single-stranded DNA 5'-3' exodeoxyribonuclease activity
L3404_RS02365	COG0341	Part of the Sec protein translocase complex. Interacts with the SecYEG preprotein conducting channel. SecDF uses the proton motive force (PMF) to complete protein translocation after the ATP-dependent function of SecA
L3404_RS02365	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
L3404_RS02395	COG0204	Acyl-transferase
L3404_RS02395	COG0318	PFAM AMP-dependent synthetase and ligase
L3404_RS02420	COG1247	-acetyltransferase
L3404_RS02450	COG0637	HAD-superfamily hydrolase subfamily IA, variant 3
L3404_RS02540	COG1173	ABC-type dipeptide oligopeptide nickel transport systems, permease components
L3404_RS02545	COG0601	transmembrane transport
L3404_RS02590	COG0742	ribosomal rna small subunit methyltransferase
L3404_RS02600	COG0448	Catalyzes the synthesis of ADP-glucose, a sugar donor used in elongation reactions on alpha-glucans
L3404_RS02610	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
L3404_RS02620	COG0749	In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity
L3404_RS02620	COG0258	In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity
L3404_RS02625	COG0616	signal peptide processing
L3404_RS02635	COG0558	Belongs to the CDP-alcohol phosphatidyltransferase class-I family
L3404_RS02650	COG0305	Participates in initiation and elongation during chromosome replication
L3404_RS02850	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
L3404_RS02875	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
L3404_RS02930	COG1686	Belongs to the peptidase S11 family
L3404_RS02970	COG4669	(LipO)protein
L3404_RS02995	COG4794	Type iii secretion
L3404_RS03000	COG4791	protein targeting
L3404_RS03030	COG1459	type II secretion system
L3404_RS03140	COG0479	Belongs to the succinate dehydrogenase fumarate reductase iron-sulfur protein family
L3404_RS03145	COG1053	succinate dehydrogenase
L3404_RS03160	COG0084	hydrolase, TatD family'
L3404_RS03170	COG0811	peptide transport
L3404_RS03190	COG2885	chlorophyll binding
L3404_RS03195	COG1388	LysM domain
L3404_RS03195	COG4641	Protein conserved in bacteria
L3404_RS03205	COG0450	alkyl hydroperoxide reductase
L3404_RS03215	COG0459	protein refolding
L3404_RS03220	COG3876	Protein conserved in bacteria
L3404_RS03240	COG0210	DNA helicase
L3404_RS03245	COG1508	bacterial-type RNA polymerase transcriptional activator activity, sequence-specific DNA binding
L3404_RS03350	COG0142	geranyltranstransferase activity
L3404_RS03355	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
L3404_RS03435	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
L3404_RS03440	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
L3404_RS03465	COG0212	Belongs to the 5-formyltetrahydrofolate cyclo-ligase family
L3404_RS03480	COG0507	A helicase nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair. Binds to DSBs and unwinds DNA via a highly rapid and processive ATP-dependent bidirectional helicase activity. Unwinds dsDNA until it encounters a Chi (crossover hotspot instigator) sequence from the 3' direction. Cuts ssDNA a few nucleotides 3' to the Chi site. The properties and activities of the enzyme are changed at Chi. The Chi-altered holoenzyme produces a long 3'-ssDNA overhang and facilitates RecA-binding to the ssDNA for homologous DNA recombination and repair. Holoenzyme degrades any linearized DNA that is unable to undergo homologous recombination. In the holoenzyme this subunit has ssDNA-dependent ATPase and 5'-3' helicase activity. When added to pre-assembled RecBC greatly stimulates nuclease activity and augments holoenzyme processivity. Negatively regulates the RecA-loading ability of RecBCD
L3404_RS03520	COG0564	pseudouridine synthase activity
L3404_RS03595	COG0515	serine threonine protein kinase
L3404_RS03595	COG2815	serine threonine protein kinase
L3404_RS03660	COG0768	penicillin binding
L3404_RS03670	COG0719	Fe-S assembly protein
L3404_RS03675	COG0396	ATPase activity
L3404_RS03680	COG0719	Fe-S assembly protein
L3404_RS03695	COG4608	Belongs to the ABC transporter superfamily
L3404_RS03700	COG0444	Belongs to the ABC transporter superfamily
L3404_RS03735	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
L3404_RS03800	COG0553	Transcription regulator that activates transcription by stimulating RNA polymerase (RNAP) recycling in case of stress conditions such as supercoiled DNA or high salt concentrations. Probably acts by releasing the RNAP, when it is trapped or immobilized on tightly supercoiled DNA. Does not activate transcription on linear DNA. Probably not involved in DNA repair
L3404_RS03805	COG1077	Cell shape determining protein MreB Mrl
L3404_RS03835	COG4284	Utp--glucose-1-phosphate uridylyltransferase
L3404_RS03875	COG1187	pseudouridine synthase activity
L3404_RS03885	COG0340	biotin-[acetyl-CoA-carboxylase] ligase activity
L3404_RS03885	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
L3404_RS03890	COG0772	Belongs to the SEDS family
L3404_RS03935	COG1115	amino acid carrier protein
L3404_RS03950	COG1235	May be involved in the transport of PQQ or its precursor to the periplasm
L3404_RS04010	COG1232	Catalyzes the 6-electron oxidation of protoporphyrinogen-IX to form protoporphyrin-IX
L3404_RS04015	COG0635	Involved in the biosynthesis of porphyrin-containing compound
L3404_RS04025	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
L3404_RS04055	COG0021	Catalyzes the transfer of a two-carbon ketol group from a ketose donor to an aldose acceptor, via a covalent intermediate with the cofactor thiamine pyrophosphate
L3404_RS04090	COG0770	UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase activity
L3404_RS04110	COG0772	Belongs to the SEDS family
L3404_RS04125	COG1837	Belongs to the UPF0109 family
L3404_RS04135	COG1366	Belongs to the anti-sigma-factor antagonist family
L3404_RS04145	COG1060	Radical SAM enzyme that catalyzes the addition of the adenosyl radical to the double bond of 3- (1- carboxyvinyl)oxy benzoate, leading to aminodeoxyfutalosine (AFL), a key intermediate in the formation of menaquinone (MK, vitamin K2) from chorismate
L3404_RS04155	COG0799	negative regulation of ribosome biogenesis
L3404_RS04160	COG0304	beta-ketoacyl-acyl-carrier-protein synthase II activity
L3404_RS04180	COG1218	3'(2'),5'-bisphosphate nucleotidase
L3404_RS04195	COG0156	8-amino-7-oxononanoate synthase activity
L3404_RS04210	COG0526	COG0526, thiol-disulfide isomerase and thioredoxins
L3404_RS04225	COG0526	COG0526, thiol-disulfide isomerase and thioredoxins
L3404_RS04355	COG1025	Belongs to the peptidase M16 family
L3404_RS04420	COG0814	amino acid
L3404_RS04425	COG0814	amino acid
L3404_RS04435	COG0552	protein localization to endoplasmic reticulum
L3404_RS04445	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
L3404_RS04485	COG2519	Catalyzes the S-adenosyl-L-methionine-dependent formation of N(1)-methyladenine at position 58 (m1A58) in tRNA
L3404_RS04500	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
L3404_RS04615	COG0600	ABC-type nitrate sulfonate bicarbonate transport system permease component
L3404_RS04625	COG0659	secondary active sulfate transmembrane transporter activity