locus-tag	class	description
APE_0002	COG1695	Transcriptional regulator
APE_0009.1	COG2608	mercury ion transmembrane transporter activity
APE_0010.1	COG0531	amino acid
APE_0012	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
APE_0013.1	COG0129	dihydroxy-acid dehydratase activity
APE_0017.1	COG1070	Carbohydrate kinase
APE_0026	COG3848	Pyruvate phosphate dikinase
APE_0026	COG0574	Belongs to the PEP-utilizing enzyme family
APE_0028	COG0574	Belongs to the PEP-utilizing enzyme family
APE_0028	COG3848	Pyruvate phosphate dikinase
APE_0033.1	COG1866	Involved in the gluconeogenesis. Catalyzes the conversion of oxaloacetate (OAA) to phosphoenolpyruvate (PEP) through direct phosphoryl transfer between the nucleoside triphosphate and OAA
APE_0035.1	COG1653	transport
APE_0038.1	COG1175	transmembrane transport
APE_0040.1	COG0395	ABC-type sugar transport system, permease component
APE_0043.1	COG3842	ATPase activity
APE_0048	COG0581	inorganic phosphate transmembrane transporter activity
APE_0050	COG1117	ATPase-coupled phosphate ion transmembrane transporter activity
APE_0051	COG0704	Plays a role in the regulation of phosphate uptake
APE_0056.1	COG1024	Enoyl-CoA hydratase
APE_0060.1	COG0503	Catalyzes a salvage reaction resulting in the formation of AMP, that is energically less costly than de novo synthesis
APE_0063	COG1129	ABC transporter
APE_0067.1	COG1079	Belongs to the binding-protein-dependent transport system permease family
APE_0071.1	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
APE_0072	COG0755	Required for the export of heme to the periplasm for the biogenesis of c-type cytochromes
APE_0077	COG0315	cyclic pyranopterin monophosphate synthase activity
APE_0077	COG0521	Mo-molybdopterin cofactor biosynthetic process
APE_0079	COG1586	Catalyzes the decarboxylation of S-adenosylmethionine to S-adenosylmethioninamine (dcAdoMet), the propylamine donor required for the synthesis of the polyamines spermine and spermidine from the diamine putrescine
APE_0084.1	COG0778	Nitroreductase
APE_0086	COG1225	Alkyl hydroperoxide reductase Thiol specific antioxidant Mal allergen
APE_0089.1	COG0312	modulator of DNA gyrase
APE_0092.1	COG0123	including yeast histone deacetylase and acetoin utilization protein
APE_0099	COG0417	DNA replication proofreading
APE_0101.1	COG2181	nitrate reductase activity
APE_0101.1	COG0247	lactate metabolic process
APE_0105	COG1161	Required for a late step of 50S ribosomal subunit assembly. Has GTPase activity
APE_0110	COG0419	ATPase involved in DNA repair
APE_0110	COG0419	ATPase involved in DNA repair
APE_0117.1	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)
APE_0127	COG0714	Associated with various cellular activities
APE_0134.1	COG2086	electron transfer activity
APE_0135	COG2025	fatty acid beta-oxidation using acyl-CoA dehydrogenase
APE_0137	COG0405	Gamma-glutamyltransferase
APE_0146.1	COG0345	Catalyzes the reduction of 1-pyrroline-5-carboxylate (PCA) to L-proline
APE_0163.1	COG1012	belongs to the aldehyde dehydrogenase family
APE_0169.1	COG1167	Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain MocR family and their eukaryotic orthologs
APE_0171.1	COG0057	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
APE_0173.1	COG0126	phosphoglycerate kinase activity
APE_0179	COG0746	molybdenum cofactor guanylyltransferase activity
APE_0181	COG1236	Exonuclease of the beta-lactamase fold involved in RNA processing
APE_0182.1	COG1872	DUF167
APE_0191.1	COG4581	dead DEAH box helicase
APE_0193.1	COG0451	ADP-glyceromanno-heptose 6-epimerase activity
APE_0204.1	COG1859	Removes the 2'-phosphate from RNA via an intermediate in which the phosphate is ADP-ribosylated by NAD followed by a presumed transesterification to release the RNA and generate ADP- ribose 1''-2''-cyclic phosphate (APPR P). May function as an ADP- ribosylase
APE_0212.1	COG0612	Peptidase, M16
APE_0218	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
APE_0222.1	COG2513	Catalyzes the thermodynamically favored C-C bond cleavage of (2R,3S)-2-methylisocitrate to yield pyruvate and succinate
APE_0227	COG0087	One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit
APE_0228a.1	COG0089	rRNA binding
APE_0230.1	COG0489	protein tyrosine kinase activity
APE_0231	COG4109	DRTGG domain
APE_0236.1	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
APE_0236.1	COG1648	precorrin-2 dehydrogenase activity
APE_0244.1	COG0311	Catalyzes the hydrolysis of glutamine to glutamate and ammonia as part of the biosynthesis of pyridoxal 5'-phosphate. The resulting ammonia molecule is channeled to the active site of PdxS
APE_0246.1	COG0214	Catalyzes the formation of pyridoxal 5'-phosphate from ribose 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia. The ammonia is provided by the PdxT subunit. Can also use ribulose 5-phosphate and dihydroxyacetone phosphate as substrates, resulting from enzyme-catalyzed isomerization of RBP and G3P, respectively
APE_0248.1	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)
APE_0249.1	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
APE_0252	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
APE_0255.1	COG1208	COG1208 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis translation initiation factor 2B, gamma epsilon subunits eIF-2Bgamma eIF-2Bepsilon
APE_0258.1	COG1139	Iron-sulfur cluster binding protein
APE_0260.1	COG0167	dihydroorotate dehydrogenase activity
APE_0262	COG0584	glycerophosphoryl diester phosphodiesterase
APE_0267	COG0517	IMP dehydrogenase activity
APE_0272.1	COG0725	ABC transporter, periplasmic molybdate-binding protein
APE_0288	COG1846	Transcriptional regulator
APE_0291	COG1225	Alkyl hydroperoxide reductase Thiol specific antioxidant Mal allergen
APE_0300.1	COG4608	Belongs to the ABC transporter superfamily
APE_0301.1	COG0444	Belongs to the ABC transporter superfamily
APE_0302.1	COG1173	ABC-type dipeptide oligopeptide nickel transport systems, permease components
APE_0303	COG0601	transmembrane transport
APE_0304.1	COG0747	negative chemotaxis
APE_0306.1	COG0554	Key enzyme in the regulation of glycerol uptake and metabolism. Catalyzes the phosphorylation of glycerol to yield sn- glycerol 3-phosphate
APE_0308.1	COG0277	FAD linked oxidase domain protein
APE_0317.1	COG1109	Catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate
APE_0319	COG0693	protein deglycase activity
APE_0326.1	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
APE_0333.1	COG0717	Belongs to the dCTP deaminase family
APE_0336.1	COG2366	antibiotic biosynthetic process
APE_0338.1	COG1680	COG1680 Beta-lactamase class C and other penicillin binding
APE_0342.1	COG1607	acyl-coa hydrolase
APE_0350	COG0097	This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7 L12 stalk, and near the tRNA binding site of the peptidyltransferase center
APE_0352.1	COG0096	One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit
APE_0354.1	COG0094	This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits
APE_0356.1	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
APE_0358	COG0198	One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit
APE_0359	COG0093	Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome
APE_0362a	COG0255	Belongs to the universal ribosomal protein uL29 family
APE_0365	COG0091	The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome
APE_0367.1	COG0185	Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA
APE_0374	COG0060	amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile)
APE_0382	COG0491	Thiolesterase that catalyzes the hydrolysis of S-D- lactoyl-glutathione to form glutathione and D-lactic acid
APE_0383.1	COG0517	IMP dehydrogenase activity
APE_0383.1	COG0794	Belongs to the SIS family. GutQ KpsF subfamily
APE_0385.1	COG1960	acyl-CoA dehydrogenase activity
APE_0396.1	COG0318	PFAM AMP-dependent synthetase and ligase
APE_0401.1	COG0528	UMP kinase activity
APE_0404.1	COG1156	Produces ATP from ADP in the presence of a proton gradient across the membrane. The V-type beta chain is a regulatory subunit
APE_0405.1	COG1155	Produces ATP from ADP in the presence of a proton gradient across the membrane. The V-type alpha chain is a catalytic subunit
APE_0412	COG0076	glutamate decarboxylase activity
APE_0413	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
APE_0423.1	COG0084	hydrolase, TatD family'
APE_0426.1	COG0463	Glycosyl transferase, family 2
APE_0427.1	COG1573	uracil-dna glycosylase
APE_0436.1	COG1185	polyribonucleotide nucleotidyltransferase activity
APE_0445	COG1098	S1 RNA binding domain
APE_0449	COG0197	Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs
APE_0454	COG1489	DNA binding
APE_0457	COG0160	Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family
APE_0471.1	COG1131	(ABC) transporter
APE_0475.1	COG2895	sulfate adenylyltransferase (ATP) activity
APE_0475.1	COG0529	Catalyzes the synthesis of activated sulfate
APE_0487	COG0277	FAD linked oxidase domain protein
APE_0496.1	COG0164	Endonuclease that specifically degrades the RNA of RNA- DNA hybrids
APE_0510.1	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
APE_0511.1	COG0430	RNA-3'-phosphate cyclase activity
APE_0514	COG3270	Specifically methylates the cytosine at position 1407 (m5C1407) of 16S rRNA
APE_0514	COG0144	Specifically methylates the cytosine at position 967 (m5C967) of 16S rRNA
APE_0519.1	COG0371	Dehydrogenase
APE_0521.1	COG0638	Catalyzes the covalent attachment of the prokaryotic ubiquitin-like protein modifier Pup to the proteasomal substrate proteins, thereby targeting them for proteasomal degradation. This tagging system is termed pupylation. The ligation reaction involves the side-chain carboxylate of the C-terminal glutamate of Pup and the side-chain amino group of a substrate lysine
APE_0522.1	COG1236	Exonuclease of the beta-lactamase fold involved in RNA processing
APE_0526.1	COG0006	proline dipeptidase activity
APE_0545.1	COG0035	Catalyzes the conversion of uracil and 5-phospho-alpha- D-ribose 1-diphosphate (PRPP) to UMP and diphosphate
APE_0553	COG0030	16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity
APE_0555.1	COG0565	Catalyzes the formation of 2'O-methylated cytidine (Cm32) or 2'O-methylated uridine (Um32) at position 32 in tRNA
APE_0557	COG0116	Belongs to the methyltransferase superfamily
APE_0564	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
APE_0569	COG0128	3-phosphoshikimate 1-carboxyvinyltransferase activity
APE_0574.1	COG0169	Involved in the biosynthesis of the chorismate, which leads to the biosynthesis of aromatic amino acids. Catalyzes the reversible NADPH linked reduction of 3-dehydroshikimate (DHSA) to yield shikimate (SA)
APE_0579	COG0337	Catalyzes the conversion of 3-deoxy-D-arabino- heptulosonate 7-phosphate (DAHP) to dehydroquinate (DHQ)
APE_0581.1	COG1605	Chorismate mutase
APE_0581.1	COG2876	3-deoxy-7-phosphoheptulonate synthase activity
APE_0583	COG3958	Transketolase
APE_0586.1	COG3959	Transketolase, thiamine diphosphate binding domain
APE_0591.1	COG1024	Enoyl-CoA hydratase
APE_0595.1	COG1252	NADH dehydrogenase
APE_0607	COG1404	Belongs to the peptidase S8 family
APE_0621.1	COG1646	35 carbon atoms) to the C3 hydroxyl of sn-glycerol-1-phosphate (G1P), producing heptaprenylglyceryl phosphate (HepGP). This reaction is an ether-bond-formation step in the biosynthesis of archaea-type G1P-based membrane lipids found in Bacillales
APE_0624.1	COG0499	May play a key role in the regulation of the intracellular concentration of adenosylhomocysteine
APE_0632.1	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
APE_0639.1	COG1586	Catalyzes the decarboxylation of S-adenosylmethionine to S-adenosylmethioninamine (dcAdoMet), the propylamine donor required for the synthesis of the polyamines spermine and spermidine from the diamine putrescine
APE_0641	COG3118	belongs to the thioredoxin family
APE_0650.1	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)
APE_0650.1	COG0574	Belongs to the PEP-utilizing enzyme family
APE_0662.1	COG0124	histidyl-tRNA synthetase
APE_0665	COG0120	Catalyzes the reversible conversion of ribose-5- phosphate to ribulose 5-phosphate
APE_0669.1	COG0819	Catalyzes an amino-pyrimidine hydrolysis reaction at the C5' of the pyrimidine moiety of thiamine compounds, a reaction that is part of a thiamine salvage pathway
APE_0672.1	COG0039	L-malate dehydrogenase activity
APE_0674.1	COG0436	Aminotransferase
APE_0675.1	COG0143	Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation
APE_0675.1	COG0073	Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation
APE_0676	COG0413	3-methyl-2-oxobutanoate hydroxymethyltransferase activity
APE_0677.1	COG1893	Catalyzes the NADPH-dependent reduction of ketopantoate into pantoic acid
APE_0686	COG0182	Catalyzes the interconversion of methylthioribose-1- phosphate (MTR-1-P) into methylthioribulose-1-phosphate (MTRu-1- P)
APE_0688	COG0346	lactoylglutathione lyase activity
APE_0689.1	COG0538	isocitrate dehydrogenase activity
APE_0695.1	COG0630	type IV secretory pathway, VirB11 components, and related ATPases involved in Archaeal flagella biosynthesis
APE_0712.1	COG4948	Mandelate Racemase Muconate Lactonizing
APE_0739	COG1960	acyl-CoA dehydrogenase activity
APE_0745.1	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
APE_0767.1	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
APE_0782.1	COG1867	N(2),N(2)-dimethylguanosine tRNA methyltransferase
APE_0785.1	COG2239	Acts as a magnesium transporter
APE_0793.1	COG1845	cytochrome c oxidase, subunit III
APE_0793.1	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
APE_0801.1	COG0496	Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates
APE_0807.1	COG1012	belongs to the aldehyde dehydrogenase family
APE_0809.1	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)
APE_0815.1	COG2264	protein methyltransferase activity
APE_0892.1	COG3842	ATPase activity
APE_0903.1	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
APE_0907.1	COG0459	protein refolding
APE_0912	COG1028	Short-chain dehydrogenase reductase Sdr
APE_0929.1	COG0183	Belongs to the thiolase family
APE_0935	COG0493	'glutamate synthase
APE_0941	COG1177	transmembrane transport
APE_0943	COG1176	ABC-type spermidine putrescine transport system, permease component I
APE_0944.1	COG3842	ATPase activity
APE_0945.1	COG0687	Required for the activity of the bacterial periplasmic transport system of putrescine
APE_0946	COG0479	Belongs to the succinate dehydrogenase fumarate reductase iron-sulfur protein family
APE_0948.1	COG2009	succinate dehydrogenase
APE_0950.1	COG1053	succinate dehydrogenase
APE_0951.1	COG0509	glycine decarboxylation via glycine cleavage system
APE_0955	COG0664	- Catabolite gene activator and regulatory subunit of cAMP-dependent protein
APE_0959	COG0350	Involved in the cellular defense against the biological effects of O6-methylguanine (O6-MeG) and O4-methylthymine (O4-MeT) in DNA. Repairs the methylated nucleobase in DNA by stoichiometrically transferring the methyl group to a cysteine residue in the enzyme. This is a suicide reaction the enzyme is irreversibly inactivated
APE_0959	COG2169	Transcriptional regulator
APE_0960	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
APE_0972.1	COG0591	Belongs to the sodium solute symporter (SSF) (TC 2.A.21) family
APE_0978.1	COG0563	adenylate kinase activity
APE_0979.1	COG0154	amidase activity
APE_0986.1	COG0108	Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate
APE_0993.1	COG0813	purine-nucleoside phosphorylase activity
APE_0996.1	COG2379	hydroxypyruvate reductase
APE_1011.1	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
APE_1015	COG0495	leucyl-tRNA aminoacylation
APE_1026.1	COG4133	protoheme IX ABC transporter activity
APE_1038.1	COG0295	cytidine deaminase activity
APE_1043.1	COG1252	NADH dehydrogenase
APE_1044	COG0778	Nitroreductase
APE_1045.1	COG0501	Belongs to the peptidase M48B family
APE_1049.1	COG0614	abc-type fe3 -hydroxamate transport system, periplasmic component
APE_1053.1	COG0609	Belongs to the binding-protein-dependent transport system permease family. FecCD subfamily
APE_1055.1	COG1121	(ABC) transporter
APE_1056.1	COG2078	PFAM AMMECR1 domain protein
APE_1061.1	COG0492	ferredoxin-NADP+ reductase activity
APE_1072.1	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
APE_1073	COG1061	Type III restriction enzyme res subunit
APE_1081.1	COG0552	protein localization to endoplasmic reticulum
APE_1094.1	COG1793	dna ligase
APE_1098	COG0144	Specifically methylates the cytosine at position 967 (m5C967) of 16S rRNA
APE_1098	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
APE_1104.1	COG0061	Involved in the regulation of the intracellular balance of NAD and NADP, and is a key enzyme in the biosynthesis of NADP. Catalyzes specifically the phosphorylation on 2'-hydroxyl of the adenosine moiety of NAD to yield NADP
APE_1106.1	COG2265	Belongs to the class I-like SAM-binding methyltransferase superfamily. RNA M5U methyltransferase family
APE_1109.1	COG1980	fructose-bisphosphate aldolase activity
APE_1117	COG2220	Zn-dependent hydrolases of the beta-lactamase fold
APE_1119.1	COG1129	ABC transporter
APE_1129	COG0143	Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation
APE_1138.1	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
APE_1139	COG0184	Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome
APE_1140.1	COG0527	aspartate kinase activity
APE_1144.1	COG0460	homoserine dehydrogenase
APE_1156.1	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
APE_1156.1	COG0301	tRNA thio-modification
APE_1158.1	COG0621	Catalyzes the methylthiolation of N6- (dimethylallyl)adenosine (i(6)A), leading to the formation of 2- methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine
APE_1164	COG0012	GTP binding
APE_1178	COG1898	dTDP-4-dehydrorhamnose 3,5-epimerase activity
APE_1180	COG1088	dTDP-glucose 4,6-dehydratase activity
APE_1183	COG2226	methyltransferase
APE_1189.1	COG1215	transferase activity, transferring glycosyl groups
APE_1191	COG0438	transferase activity, transferring glycosyl groups
APE_1195.1	COG0529	Catalyzes the synthesis of activated sulfate
APE_1197.1	COG2046	Belongs to the sulfate adenylyltransferase family
APE_1205.1	COG0449	glutamine-fructose-6-phosphate transaminase (isomerizing) activity
APE_1209f	COG1960	acyl-CoA dehydrogenase activity
APE_1226	COG0626	cystathionine gamma-synthase activity
APE_1245.1	COG1063	alcohol dehydrogenase
APE_1253	COG1136	(ABC) transporter
APE_1255.1	COG1131	(ABC) transporter
APE_1260	COG0491	Thiolesterase that catalyzes the hydrolysis of S-D- lactoyl-glutathione to form glutathione and D-lactic acid
APE_1275	COG3033	Beta-eliminating lyase
APE_1285.1	COG0123	including yeast histone deacetylase and acetoin utilization protein
APE_1288.1	COG5013	Belongs to the prokaryotic molybdopterin-containing oxidoreductase family
APE_1294.1	COG1140	nitrate reductase beta subunit
APE_1300.1	COG2180	nitrate reductase molybdenum cofactor assembly chaperone
APE_1307	COG1022	Amp-dependent synthetase and ligase
APE_1317	COG0714	Associated with various cellular activities
APE_1335.1	COG1363	Peptidase, m42
APE_1340.1	COG1110	DNA topoisomerase II activity
APE_1346.1	COG0365	Catalyzes the conversion of acetate into acetyl-CoA (AcCoA), an essential intermediate at the junction of anabolic and catabolic pathways. AcsA undergoes a two-step reaction. In the first half reaction, AcsA combines acetate with ATP to form acetyl-adenylate (AcAMP) intermediate. In the second half reaction, it can then transfer the acetyl group from AcAMP to the sulfhydryl group of CoA, forming the product AcCoA
APE_1350.1	COG0315	cyclic pyranopterin monophosphate synthase activity
APE_1367	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
APE_1376.1	COG1110	DNA topoisomerase II activity
APE_1380.1	COG1131	(ABC) transporter
APE_1385	COG0020	Catalyzes the condensation of isopentenyl diphosphate (IPP) with allylic pyrophosphates generating different type of terpenoids
APE_1386.1	COG0334	Belongs to the Glu Leu Phe Val dehydrogenases family
APE_1390.1	COG0747	negative chemotaxis
APE_1395.1	COG0601	transmembrane transport
APE_1396	COG1173	ABC-type dipeptide oligopeptide nickel transport systems, permease components
APE_1399	COG0444	Belongs to the ABC transporter superfamily
APE_1402.1	COG4608	Belongs to the ABC transporter superfamily
APE_1404.1	COG0128	3-phosphoshikimate 1-carboxyvinyltransferase activity
APE_1410.1	COG1007	ATP synthesis coupled electron transport
APE_1411.1	COG1009	NADH ubiquinone oxidoreductase subunit 5 chain L Multisubunit Na H antiporter, MnhA subunit
APE_1415	COG1008	NDH-1 shuttles electrons from NAD(P)H, 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 plastoquinone. 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
APE_1421.1	COG1005	NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient. This subunit may bind ubiquinone
APE_1422	COG0649	NAD binding
APE_1426	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
APE_1428.1	COG0377	NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain. The immediate electron acceptor for the enzyme in this species is believed to be ubiquinone. Couples the redox reaction to proton translocation (for every two electrons transferred, four hydrogen ions are translocated across the cytoplasmic membrane), and thus conserves the redox energy in a proton gradient
APE_1432	COG0480	Catalyzes the GTP-dependent ribosomal translocation step during translation elongation. During this step, the ribosome changes from the pre-translocational (PRE) to the post- translocational (POST) state as the newly formed A-site-bound peptidyl-tRNA and P-site-bound deacylated tRNA move to the P and E sites, respectively. Catalyzes the coordinated movement of the two tRNA molecules, the mRNA and conformational changes in the ribosome
APE_1436.1	COG1623	Has also diadenylate cyclase activity, catalyzing the condensation of 2 ATP molecules into cyclic di-AMP (c-di-AMP). c- di-AMP acts as a signaling molecule that couples DNA integrity with progression of sporulation. The rise in c-di-AMP level generated by DisA while scanning the chromosome, operates as a positive signal that advances sporulation
APE_1445	COG1185	polyribonucleotide nucleotidyltransferase activity
APE_1447	COG1185	polyribonucleotide nucleotidyltransferase activity
APE_1454.1	COG2217	Heavy metal translocating P-type atpase
APE_1458	COG1249	Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family
APE_1461.1	COG0548	Belongs to the acetylglutamate kinase family. ArgB subfamily
APE_1462	COG0002	Catalyzes the NADPH-dependent reduction of N-acetyl-5- glutamyl phosphate to yield N-acetyl-L-glutamate 5-semialdehyde
APE_1463	COG0189	ligase activity
APE_1464	COG4992	N2-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity
APE_1467.1	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
APE_1470.1	COG0603	Catalyzes the ATP-dependent conversion of 7-carboxy-7- deazaguanine (CDG) to 7-cyano-7-deazaguanine (preQ(0))
APE_1471.1	COG0780	Catalyzes the NADPH-dependent reduction of 7-cyano-7- deazaguanine (preQ0) to 7-aminomethyl-7-deazaguanine (preQ1)
APE_1472	COG1013	pyruvate-flavodoxin oxidoreductase activity
APE_1473.1	COG0674	pyruvate-flavodoxin oxidoreductase activity
APE_1473.1	COG1014	Oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin
APE_1484.1	COG1024	Enoyl-CoA hydratase
APE_1488.1	COG0498	Catalyzes the gamma-elimination of phosphate from L- phosphohomoserine and the beta-addition of water to produce L- threonine
APE_1491.1	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
APE_1491.1	COG1648	precorrin-2 dehydrogenase activity
APE_1495a	COG0864	Transcriptional regulator
APE_1498.1	COG1171	Catalyzes the anaerobic formation of alpha-ketobutyrate and ammonia from threonine in a two-step reaction. The first step involved a dehydration of threonine and a production of enamine intermediates (aminocrotonate), which tautomerizes to its imine form (iminobutyrate). Both intermediates are unstable and short- lived. The second step is the nonenzymatic hydrolysis of the enamine imine intermediates to form 2-ketobutyrate and free ammonia. In the low water environment of the cell, the second step is accelerated by RidA
APE_1501.1	COG0251	oxidation-reduction process
APE_1505.1	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
APE_1516.1	COG1213	nucleotidyl transferase
APE_1516.1	COG0558	Belongs to the CDP-alcohol phosphatidyltransferase class-I family
APE_1520.1	COG0432	Pfam Uncharacterised protein family UPF0047
APE_1522.1	COG2255	four-way junction helicase activity
APE_1530.1	COG0621	Catalyzes the methylthiolation of N6- (dimethylallyl)adenosine (i(6)A), leading to the formation of 2- methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine
APE_1538.1	COG2022	thiamine diphosphate biosynthetic process
APE_1543	COG1444	tRNA N-acetyltransferase activity
APE_1547.1	COG1506	peptidase
APE_1547.1	COG0823	Involved in the tonB-independent uptake of proteins
APE_1555.1	COG0038	chloride channel
APE_1564.1	COG1458	PINc domain ribonuclease
APE_1571.1	COG0043	3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity
APE_1576	COG4608	Belongs to the ABC transporter superfamily
APE_1578	COG0444	Belongs to the ABC transporter superfamily
APE_1581.1	COG1173	ABC-type dipeptide oligopeptide nickel transport systems, permease components
APE_1582	COG0601	transmembrane transport
APE_1586a	COG1960	acyl-CoA dehydrogenase activity
APE_1588a	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)
APE_1588a	COG0574	Belongs to the PEP-utilizing enzyme family
APE_1588b	COG3848	Pyruvate phosphate dikinase
APE_1588b	COG0574	Belongs to the PEP-utilizing enzyme family
APE_1591.1	COG1254	Belongs to the acylphosphatase family
APE_1596	COG1812	S-adenosylmethionine synthetase (AdoMet synthetase)
APE_1604	COG0504	CTP synthase activity
APE_1616.1	COG3635	2,3-bisphosphoglycerate-independent phosphoglycerate mutase activity
APE_1618.1	COG1048	Catalyzes the isomerization of citrate to isocitrate via cis-aconitate
APE_1622.1	COG0654	COG0654 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases
APE_1623	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
APE_1635.1	COG3842	ATPase activity
APE_1637.1	COG0010	Belongs to the arginase family
APE_1639	COG0423	glycine-tRNA ligase activity
APE_1647	COG0163	prenyltransferase activity
APE_1648.1	COG2110	phosphatase homologous to the C-terminal domain of histone macroH2A1
APE_1652	COG2896	Catalyzes the cyclization of GTP to (8S)-3',8-cyclo-7,8- dihydroguanosine 5'-triphosphate
APE_1655	COG0535	radical SAM domain protein
APE_1659	COG0667	Aldo Keto reductase
APE_1662.1	COG1781	'de novo' pyrimidine nucleobase biosynthetic process
APE_1663.1	COG0540	Belongs to the ATCase OTCase family
APE_1668	COG1324	tolerance protein
APE_1669.1	COG1249	Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family
APE_1674	COG0022	dehydrogenase e1 component
APE_1681.1	COG1960	acyl-CoA dehydrogenase activity
APE_1687	COG2185	Catalyzes the reversible interconversion of isobutyryl- CoA and n-butyryl-CoA, using radical chemistry. Also exhibits GTPase activity, associated with its G-protein domain (MeaI) that functions as a chaperone that assists cofactor delivery and proper holo-enzyme assembly
APE_1687	COG1884	Catalyzes the reversible interconversion of isobutyryl- CoA and n-butyryl-CoA, using radical chemistry. Also exhibits GTPase activity, associated with its G-protein domain (MeaI) that functions as a chaperone that assists cofactor delivery and proper holo-enzyme assembly
APE_1694.1	COG1612	heme a metabolic process
APE_1695.1	COG0404	The glycine cleavage system catalyzes the degradation of glycine
APE_1702	COG0396	ATPase activity
APE_1713	COG0372	Belongs to the citrate synthase family
APE_1717.1	COG0154	amidase activity
APE_1718	COG0064	Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp- tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln)
APE_1720	COG1622	oxidoreductase activity, acting on a heme group of donors, oxygen as acceptor
APE_1722	COG3118	belongs to the thioredoxin family
APE_1723.1	COG4122	O-methyltransferase activity
APE_1725	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
APE_1730.1	COG1177	transmembrane transport
APE_1732	COG3842	ATPase activity
APE_1735	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
APE_1737.1	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
APE_1739.1	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
APE_1742.1	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
APE_1747	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
APE_1749	COG0103	maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
APE_1765.1	COG1304	FMN binding
APE_1771	COG1355	regulation of microtubule-based process
APE_1773.1	COG0534	Mate efflux family protein
APE_1775.1	COG2317	Broad specificity carboxypetidase that releases amino acids sequentially from the C-terminus, including neutral, aromatic, polar and basic residues
APE_1782.1	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
APE_1786.1	COG1012	belongs to the aldehyde dehydrogenase family
APE_1792	COG1514	Hydrolyzes RNA 2',3'-cyclic phosphodiester to an RNA 2'- phosphomonoester
APE_1794	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
APE_1798.1	COG0483	inositol monophosphate 1-phosphatase activity
APE_1805.1	COG0525	valine-tRNA ligase activity
APE_1829	COG1131	(ABC) transporter
APE_1831.1	COG1052	Belongs to the D-isomer specific 2-hydroxyacid dehydrogenase family
APE_1832	COG4946	Tricorn protease homolog
APE_1832	COG0823	Involved in the tonB-independent uptake of proteins
APE_1832	COG1506	peptidase
APE_1834.1	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)
APE_1836.1	COG1234	tRNA 3'-trailer cleavage
APE_1838.1	COG0516	GMP reductase activity
APE_1838.1	COG0517	IMP dehydrogenase activity
APE_1842	COG0051	transcription antitermination factor activity, RNA binding
APE_1844	COG0050	This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis
APE_1846.1	COG0049	tRNA binding
APE_1856	COG0085	RNA polymerase activity
APE_1873.1	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
APE_1874.1	COG2896	Catalyzes the cyclization of GTP to (8S)-3',8-cyclo-7,8- dihydroguanosine 5'-triphosphate
APE_1877.1	COG0705	Rhomboid family
APE_1878	COG0109	protoheme IX farnesyltransferase activity
APE_1885	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
APE_1892	COG0765	amino acid transport
APE_1893.1	COG4623	carbon-oxygen lyase activity, acting on polysaccharides
APE_1911.1	COG1135	Part of the ABC transporter complex MetNIQ involved in methionine import. Responsible for energy coupling to the transport system
APE_1917	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
APE_1932.1	COG1668	transmembrane transport
APE_1940.1	COG0794	Belongs to the SIS family. GutQ KpsF subfamily
APE_1950.1	COG0071	Belongs to the small heat shock protein (HSP20) family
APE_1958.1	COG0171	NAD+ synthase (glutamine-hydrolyzing) activity
APE_1961	COG0656	L-ascorbic acid biosynthetic process
APE_1968	COG0549	Belongs to the carbamate kinase family
APE_1976.1	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)
APE_1979.1	COG2151	metal-sulfur cluster biosynthetic enzyme
APE_1980.1	COG1058	Belongs to the CinA family
APE_1980.1	COG1546	Belongs to the CinA family
APE_1992.1	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
APE_2007	COG2262	GTPase that associates with the 50S ribosomal subunit and may have a role during protein synthesis or ribosome biogenesis
APE_2012	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
APE_2017	COG0343	queuine tRNA-ribosyltransferase activity
APE_2021.1	COG0735	belongs to the Fur family
APE_2023	COG0520	Catalyzes the removal of elemental sulfur and selenium atoms from L-cysteine, L-cystine, L-selenocysteine, and L- selenocystine to produce L-alanine
APE_2029.1	COG2038	nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase activity
APE_2035.1	COG0079	Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. Histidinol-phosphate aminotransferase subfamily
APE_2037.1	COG0368	Joins adenosylcobinamide-GDP and alpha-ribazole to generate adenosylcobalamin (Ado-cobalamin). Also synthesizes adenosylcobalamin 5'-phosphate from adenosylcobinamide-GDP and alpha-ribazole 5'-phosphate
APE_2044.1	COG0309	Hydrogenase expression formation protein (HypE)
APE_2048	COG0620	Catalyzes the transfer of a methyl group from 5- methyltetrahydrofolate to homocysteine resulting in methionine formation
APE_2050.1	COG0620	Catalyzes the transfer of a methyl group from 5- methyltetrahydrofolate to homocysteine resulting in methionine formation
APE_2052.1	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
APE_2060.1	COG3842	ATPase activity
APE_2062.1	COG0209	Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides
APE_2066.1	COG0438	transferase activity, transferring glycosyl groups
APE_2067.1	COG0083	homoserine kinase activity
APE_2068	COG0626	cystathionine gamma-synthase activity
APE_2072.1	COG0459	protein refolding
APE_2074.1	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)
APE_2078	COG0043	3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity
APE_2081.1	COG2309	aminopeptidase activity
APE_2085.1	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
APE_2086	COG0037	tRNA processing
APE_2090	COG0125	Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis
APE_2094.1	COG0703	Catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid using ATP as a cosubstrate
APE_2104.1	COG0648	Endonuclease IV plays a role in DNA repair. It cleaves phosphodiester bonds at apurinic or apyrimidinic sites (AP sites) to produce new 5'-ends that are base-free deoxyribose 5-phosphate residues. It preferentially attacks modified AP sites created by bleomycin and neocarzinostatin
APE_2105.1	COG2820	Catalyzes the reversible phosphorylytic cleavage of uridine and deoxyuridine to uracil and ribose- or deoxyribose-1- phosphate. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis
APE_2106.1	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
APE_2108	COG0183	Belongs to the thiolase family
APE_2109	COG0621	Catalyzes the methylthiolation of N6- (dimethylallyl)adenosine (i(6)A), leading to the formation of 2- methylthio-N6-(dimethylallyl)adenosine (ms(2)i(6)A) at position 37 in tRNAs that read codons beginning with uridine
APE_2121.1	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
APE_2124.1	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
APE_2125.1	COG1225	Alkyl hydroperoxide reductase Thiol specific antioxidant Mal allergen
APE_2126.1	COG1014	Oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin
APE_2126.1	COG0674	pyruvate-flavodoxin oxidoreductase activity
APE_2128	COG1013	pyruvate-flavodoxin oxidoreductase activity
APE_2130.1	COG0001	glutamate-1-semialdehyde 2,1-aminomutase activity
APE_2136.1	COG2358	TRAP transporter, solute receptor (TAXI family
APE_2139a	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
APE_2144.1	COG1201	RNA secondary structure unwinding
APE_2149.1	COG1635	Involved in the biosynthesis of the thiazole moiety of thiamine. Catalyzes the conversion of NAD and glycine to adenosine diphosphate 5-(2-hydroxyethyl)-4-methylthiazole-2-carboxylate (ADT), an adenylated thiazole intermediate, using free sulfide as a source of sulfur
APE_2153.1	COG0330	HflC and HflK could
APE_2154.1	COG0805	protein transport
APE_2154a	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
APE_2154b	COG0444	Belongs to the ABC transporter superfamily
APE_2158.1	COG1960	acyl-CoA dehydrogenase activity
APE_2162.1	COG1966	Carbon starvation protein
APE_2164.1	COG0003	Pfam Anion-transporting ATPase
APE_2165	COG0003	Pfam Anion-transporting ATPase
APE_2166	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
APE_2173.1	COG0081	regulation of translation
APE_2174	COG0080	Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors
APE_2188.1	COG1201	RNA secondary structure unwinding
APE_2192.1	COG0017	Asparaginyl-tRNA synthetase
APE_2200	COG0252	asparaginase activity
APE_2202	COG0064	Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp- tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln)
APE_2220.1	COG2255	four-way junction helicase activity
APE_2227	COG1975	Xanthine and CO dehydrogenases maturation factor, XdhC CoxF family
APE_2227	COG3608	succinylglutamate desuccinylase aspartoacylase
APE_2242.1	COG2151	metal-sulfur cluster biosynthetic enzyme
APE_2242.1	COG0489	protein tyrosine kinase activity
APE_2247	COG2094	Belongs to the DNA glycosylase MPG family
APE_2248.1	COG0436	Aminotransferase
APE_2252.1	COG3833	ABC-type maltose transport systems, permease component
APE_2258	COG0601	transmembrane transport
APE_2260	COG1173	ABC-type dipeptide oligopeptide nickel transport systems, permease components
APE_2263.1	COG4608	Belongs to the ABC transporter superfamily
APE_2272.1	COG3638	Part of the ABC transporter complex PhnCDE involved in phosphonates import. Responsible for energy coupling to the transport system
APE_2273.1	COG3118	belongs to the thioredoxin family
APE_2278	COG0450	alkyl hydroperoxide reductase
APE_2279.1	COG0466	ATP-dependent serine protease that mediates the selective degradation of mutant and abnormal proteins as well as certain short-lived regulatory proteins. Required for cellular homeostasis and for survival from DNA damage and developmental changes induced by stress. Degrades polypeptides processively to yield small peptide fragments that are 5 to 10 amino acids long. Binds to DNA in a double-stranded, site-specific manner
APE_2281.1	COG2870	Catalyzes the ADP transfer from ATP to D-glycero-beta-D- manno-heptose 1-phosphate, yielding ADP-D-glycero-beta-D-manno- heptose
APE_2281.1	COG0615	ADP-L-glycero-beta-D-manno-heptose biosynthetic process
APE_2284.1	COG0318	PFAM AMP-dependent synthetase and ligase
APE_2286	COG0498	Catalyzes the gamma-elimination of phosphate from L- phosphohomoserine and the beta-addition of water to produce L- threonine
APE_2290.1	COG1506	peptidase
APE_2290.1	COG4946	Tricorn protease homolog
APE_2290.1	COG0823	Involved in the tonB-independent uptake of proteins
APE_2291	COG1208	COG1208 Nucleoside-diphosphate-sugar pyrophosphorylase involved in lipopolysaccharide biosynthesis translation initiation factor 2B, gamma epsilon subunits eIF-2Bgamma eIF-2Bepsilon
APE_2298.1	COG0181	hydroxymethylbilane synthase activity
APE_2299.1	COG0001	glutamate-1-semialdehyde 2,1-aminomutase activity
APE_2300.1	COG0113	porphobilinogen synthase activity
APE_2305	COG0072	phenylalanine-tRNA ligase activity
APE_2308	COG1469	GTP cyclohydrolase I activity
APE_2316	COG1350	The beta subunit is responsible for the synthesis of L- tryptophan from indole and L-serine
APE_2317.1	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)
APE_2328	COG0442	prolyl-tRNA aminoacylation
APE_2341	COG0095	Lipoate-protein ligase
APE_2342.1	COG0095	Lipoate-protein ligase
APE_2344.1	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
APE_2348	COG0284	orotidine-5'-phosphate decarboxylase activity
APE_2349.1	COG0461	Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP)
APE_2350.1	COG1335	isochorismatase
APE_2354	COG1960	acyl-CoA dehydrogenase activity
APE_2362.1	COG0063	ADP-dependent NAD(P)H-hydrate dehydratase activity
APE_2362.1	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
APE_2374	COG0532	One of the essential components for the initiation of protein synthesis. Protects formylmethionyl-tRNA from spontaneous hydrolysis and promotes its binding to the 30S ribosomal subunits. Also involved in the hydrolysis of GTP during the formation of the 70S ribosomal complex
APE_2377	COG0105	UTP biosynthetic process
APE_2381.1	COG2031	fatty acid transporter
APE_2392.1	COG1444	tRNA N-acetyltransferase activity
APE_2397	COG0009	L-threonylcarbamoyladenylate synthase
APE_2400.1	COG0351	phosphomethylpyrimidine kinase
APE_2406.1	COG1122	ATPase activity
APE_2408.1	COG1129	ABC transporter
APE_2414.1	COG0534	Mate efflux family protein
APE_2418.1	COG2086	electron transfer activity
APE_2419	COG2025	fatty acid beta-oxidation using acyl-CoA dehydrogenase
APE_2421	COG0644	oxidoreductase
APE_2423	COG0075	2-aminoethylphosphonate-pyruvate transaminase activity
APE_2433.1	COG1109	Catalyzes the conversion of glucosamine-6-phosphate to glucosamine-1-phosphate
APE_2437.1	COG0274	Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy- D-ribose 5-phosphate
APE_2439	COG0153	Catalyzes the transfer of the gamma-phosphate of ATP to D-galactose to form alpha-D-galactose-1-phosphate (Gal-1-P)
APE_2441.1	COG4946	Tricorn protease homolog
APE_2441.1	COG0823	Involved in the tonB-independent uptake of proteins
APE_2441.1	COG1506	peptidase
APE_2446	COG2848	UPF0210 protein
APE_2450.1	COG0260	Presumably involved in the processing and regular turnover of intracellular proteins. Catalyzes the removal of unsubstituted N-terminal amino acids from various peptides
APE_2452	COG0518	GMP synthase (glutamine-hydrolyzing) activity
APE_2452	COG0519	Catalyzes the synthesis of GMP from XMP
APE_2458	COG0148	phosphopyruvate hydratase activity
APE_2464.1	COG1875	ATPase related to phosphate starvation-inducible protein PhoH
APE_2465.1	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
APE_2465.1	COG0144	Specifically methylates the cytosine at position 967 (m5C967) of 16S rRNA
APE_2474.1	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
APE_2489.1	COG0794	Belongs to the SIS family. GutQ KpsF subfamily
APE_2489.1	COG0517	IMP dehydrogenase activity
APE_2495.1	COG0537	adenosine 5'-monophosphoramidase activity
APE_2497	COG2095	MarC family integral membrane protein
APE_2503.1	COG1028	Short-chain dehydrogenase reductase Sdr
APE_2507.1	COG0111	D-isomer specific 2-hydroxyacid dehydrogenase
APE_2522.1	COG0559	Belongs to the binding-protein-dependent transport system permease family
APE_2533.1	COG1331	Highly conserved protein containing a thioredoxin domain
APE_2538	COG1757	Na H antiporter
APE_2540.1	COG0442	prolyl-tRNA aminoacylation
APE_2546	COG0134	indole-3-glycerol-phosphate synthase activity
APE_2548	COG1350	The beta subunit is responsible for the synthesis of L- tryptophan from indole and L-serine
APE_2550	COG0159	tryptophan synthase activity
APE_2553.1	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
APE_2555	COG0547	Catalyzes the transfer of the phosphoribosyl group of 5- phosphorylribose-1-pyrophosphate (PRPP) to anthranilate to yield N-(5'-phosphoribosyl)-anthranilate (PRA)
APE_2555	COG0512	Glutamine amidotransferase of anthranilate synthase
APE_2556.1	COG0243	molybdopterin cofactor binding
APE_2575	COG0079	Belongs to the class-II pyridoxal-phosphate-dependent aminotransferase family. Histidinol-phosphate aminotransferase subfamily
APE_2580	COG0426	domain, Protein
APE_2580	COG1853	conserved protein domain typically associated with flavoprotein oxygenases, DIM6 NTAB family
APE_2581	COG0095	Lipoate-protein ligase
APE_2583.1	COG1301	dicarboxylic acid transport
APE_2586.1	COG1079	Belongs to the binding-protein-dependent transport system permease family
APE_2587.1	COG4603	Belongs to the binding-protein-dependent transport system permease family
APE_2588	COG1129	ABC transporter
APE_2595.1	COG2897	thiosulfate sulfurtransferase activity
APE_2598	COG2896	Catalyzes the cyclization of GTP to (8S)-3',8-cyclo-7,8- dihydroguanosine 5'-triphosphate
APE_2601.1	COG2235	arginine
APE_2604	COG0365	Catalyzes the conversion of acetate into acetyl-CoA (AcCoA), an essential intermediate at the junction of anabolic and catabolic pathways. AcsA undergoes a two-step reaction. In the first half reaction, AcsA combines acetate with ATP to form acetyl-adenylate (AcAMP) intermediate. In the second half reaction, it can then transfer the acetyl group from AcAMP to the sulfhydryl group of CoA, forming the product AcCoA
APE_2604a.1	COG0365	Catalyzes the conversion of acetate into acetyl-CoA (AcCoA), an essential intermediate at the junction of anabolic and catabolic pathways. AcsA undergoes a two-step reaction. In the first half reaction, AcsA combines acetate with ATP to form acetyl-adenylate (AcAMP) intermediate. In the second half reaction, it can then transfer the acetyl group from AcAMP to the sulfhydryl group of CoA, forming the product AcCoA