locus-tag	class	description
APH_0001	COG0258	In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity
APH_0001	COG0749	In addition to polymerase activity, this DNA polymerase exhibits 5'-3' exonuclease activity
APH_0002	COG0036	Belongs to the ribulose-phosphate 3-epimerase family
APH_0003	COG0767	ABC-type transport system involved in resistance to organic solvents, permease component
APH_0004	COG1127	ABC transporter
APH_0006	COG3155	Displays glyoxalase activity, catalyzing the conversion of glyoxal to glycolate
APH_0007	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
APH_0009	COG0654	COG0654 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases
APH_0013	COG0752	glycyl-tRNA synthetase alpha subunit
APH_0015	COG0484	heat shock protein binding
APH_0017	COG0344	acyl-phosphate glycerol-3-phosphate acyltransferase activity
APH_0018	COG0817	Nuclease that resolves Holliday junction intermediates in genetic recombination. Cleaves the cruciform structure in supercoiled DNA by nicking to strands with the same polarity at sites symmetrically opposed at the junction in the homologous arms and leaves a 5'-terminal phosphate and a 3'-terminal hydroxyl group
APH_0019	COG1845	cytochrome c oxidase, subunit III
APH_0020	COG0407	Catalyzes the decarboxylation of four acetate groups of uroporphyrinogen-III to yield coproporphyrinogen-III
APH_0021	COG1253	flavin adenine dinucleotide binding
APH_0023	COG4695	Portal protein
APH_0026	COG0379	Catalyzes the condensation of iminoaspartate with dihydroxyacetone phosphate to form quinolinate
APH_0035	COG0180	Tryptophanyl-tRNA synthetase
APH_0036	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
APH_0037	COG1985	Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)- pyrimidinedione 5'-phosphate
APH_0037	COG0117	Converts 2,5-diamino-6-(ribosylamino)-4(3h)-pyrimidinone 5'-phosphate into 5-amino-6-(ribosylamino)-2,4(1h,3h)- pyrimidinedione 5'-phosphate
APH_0038	COG0504	CTP synthase activity
APH_0040	COG4974	Belongs to the 'phage' integrase family
APH_0042	COG0281	malic enzyme
APH_0042	COG0280	phosphate acetyltransferase
APH_0044	COG0651	ATP synthesis coupled electron transport
APH_0045	COG1463	ABC-type transport system involved in resistance to organic solvents, periplasmic component
APH_0047	COG1327	Negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR- boxes
APH_0051	COG1840	ABC-type Fe3 transport system, periplasmic component
APH_0052	COG2835	tetraacyldisaccharide 4'-kinase activity
APH_0054	COG0228	four-way junction DNA binding
APH_0058	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
APH_0060	COG0292	Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit
APH_0061	COG0291	Belongs to the bacterial ribosomal protein bL35 family
APH_0064	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
APH_0065	COG1249	Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family
APH_0066	COG0484	heat shock protein binding
APH_0067	COG0694	Involved in iron-sulfur cluster biogenesis. Binds a 4Fe- 4S cluster, can transfer this cluster to apoproteins, and thereby intervenes in the maturation of Fe S proteins. Could also act as a scaffold chaperone for damaged Fe S proteins
APH_0072	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)
APH_0072	COG1384	Belongs to the class-I aminoacyl-tRNA synthetase family
APH_0079	COG1722	exodeoxyribonuclease VII activity
APH_0080	COG3118	belongs to the thioredoxin family
APH_0082	COG1071	oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
APH_0083	COG2267	carboxylic ester hydrolase activity
APH_0087	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
APH_0088	COG0516	GMP reductase activity
APH_0088	COG0517	IMP dehydrogenase activity
APH_0089	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
APH_0091	COG4695	Portal protein
APH_0092	COG0331	[acyl-carrier-protein] S-malonyltransferase activity
APH_0093	COG0125	Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis
APH_0097	COG1952	One of the proteins required for the normal export of preproteins out of the cell cytoplasm. It is a molecular chaperone that binds to a subset of precursor proteins, maintaining them in a translocation-competent state. It also specifically binds to its receptor SecA
APH_0098	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
APH_0101	COG0612	Peptidase, M16
APH_0104	COG0528	UMP kinase activity
APH_0106	COG0307	riboflavin synthase, alpha
APH_0111	COG0528	UMP kinase activity
APH_0112	COG0233	cytoplasmic translational termination
APH_0113	COG4589	Belongs to the CDS family
APH_0119	COG0152	phosphoribosylaminoimidazolesuccinocarboxamide synthase activity
APH_0120	COG0124	histidyl-tRNA synthetase
APH_0123	COG1612	heme a metabolic process
APH_0130	COG0717	Belongs to the dCTP deaminase family
APH_0135	COG1278	Cold shock
APH_0136	COG5000	phosphorelay sensor kinase activity
APH_0137	COG0349	Exonuclease involved in the 3' processing of various precursor tRNAs. Initiates hydrolysis at the 3'-terminus of an RNA molecule and releases 5'-mononucleotides
APH_0138	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
APH_0147	COG0194	GDP metabolic process
APH_0151	COG0360	Binds together with S18 to 16S ribosomal RNA
APH_0152	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
APH_0153	COG0359	binds to the 23S rRNA
APH_0154	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
APH_0157	COG1132	(ABC) transporter
APH_0164	COG2814	Major facilitator Superfamily
APH_0165	COG0752	glycyl-tRNA synthetase alpha subunit
APH_0166	COG2255	four-way junction helicase activity
APH_0167	COG0632	four-way junction helicase activity
APH_0168	COG0755	Required for the export of heme to the periplasm for the biogenesis of c-type cytochromes
APH_0170	COG0194	GDP metabolic process
APH_0175	COG0190	Catalyzes the oxidation of 5,10- methylenetetrahydrofolate to 5,10-methenyltetrahydrofolate and then the hydrolysis of 5,10-methenyltetrahydrofolate to 10- formyltetrahydrofolate
APH_0180	COG3474	cytochrome
APH_0181	COG0651	ATP synthesis coupled electron transport
APH_0185	COG0574	Belongs to the PEP-utilizing enzyme family
APH_0185	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)
APH_0187	COG0546	phosphoglycolate phosphatase activity
APH_0190	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)
APH_0195	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
APH_0196	COG2204	response regulator
APH_0198	COG0240	glycerol-3-phosphate dehydrogenase [NAD(P)+] activity
APH_0200	COG4974	Belongs to the 'phage' integrase family
APH_0202	COG0150	phosphoribosylformylglycinamidine cyclo-ligase activity
APH_0210	COG0150	phosphoribosylformylglycinamidine cyclo-ligase activity
APH_0212	COG0801	2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
APH_0213	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
APH_0218	COG0502	Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical- based mechanism
APH_0221	COG4942	peptidase
APH_0222	COG1494	fructose-1,6-bisphosphatase
APH_0224	COG0445	tRNA wobble uridine modification
APH_0225	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
APH_0225	COG0047	phosphoribosylformylglycinamidine synthase activity
APH_0230	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
APH_0232	COG3485	protocatechuate 3,4-dioxygenase
APH_0235	COG0542	response to heat
APH_0241	COG0234	Binds to Cpn60 in the presence of Mg-ATP and suppresses the ATPase activity of the latter
APH_0242	COG2003	Belongs to the UPF0758 family
APH_0243	COG0321	lipoyl(octanoyl) transferase activity
APH_0245	COG0044	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides
APH_0246	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
APH_0247	COG0114	fumarate hydratase activity
APH_0254	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
APH_0258	COG1074	ATP-dependent DNA helicase activity
APH_0268	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
APH_0271	COG0776	regulation of translation
APH_0272	COG0616	signal peptide processing
APH_0273	COG0539	negative regulation of cytoplasmic translation
APH_0274	COG0283	belongs to the cytidylate kinase family. Type 1 subfamily
APH_0275	COG0566	Belongs to the class IV-like SAM-binding methyltransferase superfamily. RNA methyltransferase TrmH family
APH_0278	COG0050	This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis
APH_0279	COG0051	transcription antitermination factor activity, RNA binding
APH_0280	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
APH_0281	COG0088	Forms part of the polypeptide exit tunnel
APH_0282	COG0089	rRNA binding
APH_0283	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
APH_0284	COG0185	Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA
APH_0285	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
APH_0286	COG0092	Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation
APH_0287	COG0197	Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs
APH_0288	COG0255	Belongs to the universal ribosomal protein uL29 family
APH_0289	COG0186	One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA
APH_0290	COG0093	Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome
APH_0291	COG0198	One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit
APH_0292	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
APH_0293	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
APH_0294	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
APH_0295	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
APH_0296	COG0256	This is one of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance
APH_0297	COG0098	Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body
APH_0299	COG0201	protein transport
APH_0301	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
APH_0302	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
APH_0303	COG0202	RNA polymerase activity
APH_0304	COG0203	ribosomal protein L17
APH_0306	COG2333	competence protein COMEC
APH_0306	COG0658	competence protein
APH_0309	COG0230	Belongs to the bacterial ribosomal protein bL34 family
APH_0311	COG1853	conserved protein domain typically associated with flavoprotein oxygenases, DIM6 NTAB family
APH_0314	COG0343	queuine tRNA-ribosyltransferase activity
APH_0315	COG0333	Belongs to the bacterial ribosomal protein bL32 family
APH_0316	COG0416	fatty acid biosynthetic process
APH_0321	COG0590	tRNA wobble adenosine to inosine editing
APH_0329	COG0142	geranyltranstransferase activity
APH_0331	COG0209	Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides
APH_0332	COG0816	Could be a nuclease involved in processing of the 5'-end of pre-16S rRNA
APH_0337	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
APH_0345	COG1530	ribonuclease E activity
APH_0348	COG1007	ATP synthesis coupled electron transport
APH_0349	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
APH_0350	COG1159	An essential GTPase that binds both GDP and GTP, with rapid nucleotide exchange. Plays a role in 16S rRNA processing and 30S ribosomal subunit biogenesis and possibly also in cell cycle regulation and energy metabolism
APH_0352	COG3577	Aspartyl protease
APH_0359	COG0227	Belongs to the bacterial ribosomal protein bL28 family
APH_0362	COG0564	pseudouridine synthase activity
APH_0364	COG0439	Biotin carboxylase
APH_0367	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
APH_0370	COG0581	inorganic phosphate transmembrane transporter activity
APH_0373	COG3451	type IV secretory pathway VirB4
APH_0375	COG3704	protein secretion by the type IV secretion system
APH_0376	COG3704	protein secretion by the type IV secretion system
APH_0377	COG3704	protein secretion by the type IV secretion system
APH_0377	COG0419	ATPase involved in DNA repair
APH_0379	COG0756	dUTP diphosphatase activity
APH_0381	COG0505	Belongs to the CarA family
APH_0389	COG0696	Catalyzes the interconversion of 2-phosphoglycerate and 3-phosphoglycerate
APH_0390	COG1160	GTP binding
APH_0393	COG1249	Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family
APH_0395	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
APH_0396	COG0424	maF-like protein
APH_0397	COG0052	Belongs to the universal ribosomal protein uS2 family
APH_0398	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
APH_0399	COG1108	ABC-type Mn2 Zn2 transport systems permease components
APH_0401	COG0723	plastoquinol--plastocyanin reductase activity
APH_0402	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
APH_0408	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)
APH_0412	COG0445	tRNA wobble uridine modification
APH_0415	COG4799	Acetyl-CoA carboxylase, carboxyltransferase component subunits alpha and beta
APH_0419	COG3451	type IV secretory pathway VirB4
APH_0420	COG0216	Peptide chain release factor 1 directs the termination of translation in response to the peptide chain termination codons UAG and UAA
APH_0421	COG0218	Necessary for normal cell division and for the maintenance of normal septation
APH_0427	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)
APH_0431	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)
APH_0434	COG1894	NDH-1 shuttles electrons from NADH, via FMN and iron- sulfur (Fe-S) centers, to quinones in the respiratory chain
APH_0436	COG0713	ATP synthesis coupled electron transport
APH_0437	COG1009	NADH ubiquinone oxidoreductase subunit 5 chain L Multisubunit Na H antiporter, MnhA subunit
APH_0439	COG1007	ATP synthesis coupled electron transport
APH_0440	COG0743	1-deoxy-D-xylulose-5-phosphate reductoisomerase activity
APH_0443	COG0805	protein transport
APH_0445	COG0195	Participates in both transcription termination and antitermination
APH_0445	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
APH_0446	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
APH_0448	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
APH_0449	COG1253	flavin adenine dinucleotide binding
APH_0462	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)
APH_0463	COG1186	Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA
APH_0465	COG0629	single-stranded DNA binding
APH_0468	COG1186	Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA
APH_0470	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)
APH_0473	COG0623	enoyl-[acyl-carrier-protein] reductase (NADH) activity
APH_0478	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)
APH_0480	COG0217	transcriptional regulatory protein
APH_0482	COG0502	Catalyzes the conversion of dethiobiotin (DTB) to biotin by the insertion of a sulfur atom into dethiobiotin via a radical- based mechanism
APH_0482	COG0161	adenosylmethionine-8-amino-7-oxononanoate transaminase activity
APH_0492	COG0176	Transaldolase is important for the balance of metabolites in the pentose-phosphate pathway
APH_0494	COG0055	Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits
APH_0502	COG0101	tRNA pseudouridine synthase activity
APH_0503	COG0540	Belongs to the ATCase OTCase family
APH_0504	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
APH_0508	COG0257	Belongs to the bacterial ribosomal protein bL36 family
APH_0511	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
APH_0514	COG1758	RNA polymerase activity
APH_0519	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
APH_0520	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
APH_0521	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
APH_0524	COG0496	Nucleotidase that shows phosphatase activity on nucleoside 5'-monophosphates
APH_0526	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
APH_0528	COG0084	hydrolase, TatD family'
APH_0539	COG0054	6,7-dimethyl-8-ribityllumazine synthase activity
APH_0540	COG0706	membrane insertase activity
APH_0541	COG0706	membrane insertase activity
APH_0542	COG1034	ATP synthesis coupled electron transport
APH_0543	COG1183	phosphatidylcholine synthase activity
APH_0544	COG0688	phosphatidylethanolamine metabolic process
APH_0545	COG0493	'glutamate synthase
APH_0545	COG0543	2 iron, 2 sulfur cluster binding
APH_0547	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
APH_0548	COG0483	inositol monophosphate 1-phosphatase activity
APH_0549	COG0564	pseudouridine synthase activity
APH_0551	COG0745	RESPONSE REGULATOR receiver
APH_0551	COG3706	GGDEF domain
APH_0554	COG3932	Exopolysaccharide synthesis, ExoD
APH_0555	COG0215	cysteine-tRNA ligase activity
APH_0560	COG0208	Provides the precursors necessary for DNA synthesis. Catalyzes the biosynthesis of deoxyribonucleotides from the corresponding ribonucleotides
APH_0564	COG0018	arginyl-trna synthetase
APH_0571	COG0358	DNA primase activity
APH_0572	COG0249	that it carries out the mismatch recognition step. This protein has a weak ATPase activity
APH_0574	COG1947	Catalyzes the phosphorylation of the position 2 hydroxy group of 4-diphosphocytidyl-2C-methyl-D-erythritol
APH_0575	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
APH_0576	COG0568	sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released
APH_0581	COG1324	tolerance protein
APH_0586	COG0422	Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction
APH_0588	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
APH_0588	COG0063	ADP-dependent NAD(P)H-hydrate dehydratase activity
APH_0597	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
APH_0600	COG0422	Catalyzes the synthesis of the hydroxymethylpyrimidine phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) in a radical S-adenosyl-L-methionine (SAM)-dependent reaction
APH_0606	COG2227	3-demethylubiquinone-9 3-O-methyltransferase activity
APH_0607	COG1384	Belongs to the class-I aminoacyl-tRNA synthetase family
APH_0610	COG1214	PFAM Peptidase M22, glycoprotease
APH_0622	COG0030	16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity
APH_0624	COG0149	triose-phosphate isomerase activity
APH_0626	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
APH_0629	COG0039	L-malate dehydrogenase activity
APH_0642	COG0698	ribose 5-phosphate isomerase
APH_0646	COG0736	holo-[acyl-carrier-protein] synthase activity
APH_0647	COG0442	prolyl-tRNA aminoacylation
APH_0650	COG0669	Reversibly transfers an adenylyl group from ATP to 4'- phosphopantetheine, yielding dephospho-CoA (dPCoA) and pyrophosphate
APH_0658	COG0492	ferredoxin-NADP+ reductase activity
APH_0659	COG0450	alkyl hydroperoxide reductase
APH_0669	COG0506	proline dehydrogenase activity
APH_0669	COG3905	.,Oxidizes proline to glutamate for use as a carbon and nitrogen source
APH_0669	COG4230	.,Oxidizes proline to glutamate for use as a carbon and nitrogen source
APH_0671	COG2945	thiolester hydrolase activity
APH_0674	COG1104	cysteine desulfurase activity
APH_0675	COG0822	iron-sulfur transferase activity
APH_0676	COG0316	Belongs to the HesB IscA family
APH_0678	COG0443	Heat shock 70 kDa protein
APH_0690	COG0275	rRNA processing
APH_0694	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
APH_0695	COG0148	phosphopyruvate hydratase activity
APH_0697	COG0261	This protein binds to 23S rRNA in the presence of protein L20
APH_0698	COG0211	Belongs to the bacterial ribosomal protein bL27 family
APH_0700	COG0018	arginyl-trna synthetase
APH_0701	COG0018	arginyl-trna synthetase
APH_0705	COG0312	modulator of DNA gyrase
APH_0706	COG0302	gtp cyclohydrolase
APH_0707	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
APH_0711	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
APH_0712	COG1034	ATP synthesis coupled electron transport
APH_0716	COG0187	DNA topoisomerase II activity
APH_0730	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
APH_0731	COG1905	PFAM NADH dehydrogenase (ubiquinone) 24 kDa subunit
APH_0732	COG0649	NAD binding
APH_0734	COG0492	ferredoxin-NADP+ reductase activity
APH_0735	COG0611	Catalyzes the ATP-dependent phosphorylation of thiamine- monophosphate (TMP) to form thiamine-pyrophosphate (TPP), the active form of vitamin B1
APH_0736	COG1381	Involved in DNA repair and RecF pathway recombination
APH_0745	COG0812	UDP-N-acetylmuramate dehydrogenase activity
APH_0746	COG0181	hydroxymethylbilane synthase activity
APH_0747	COG0285	dihydrofolate synthase activity
APH_0748	COG0154	amidase activity
APH_0754	COG0606	chelatase, subunit chli
APH_0759	COG0568	sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released
APH_0765	COG0481	GTPase activity
APH_0767	COG1185	polyribonucleotide nucleotidyltransferase activity
APH_0768	COG0184	Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome
APH_0769	COG0130	Responsible for synthesis of pseudouridine from uracil- 55 in the psi GC loop of transfer RNAs
APH_0782	COG0009	L-threonylcarbamoyladenylate synthase
APH_0783	COG0470	DNA polymerase III
APH_0790	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
APH_0791	COG1057	Catalyzes the reversible adenylation of nicotinate mononucleotide (NaMN) to nicotinic acid adenine dinucleotide (NaAD)
APH_0794	COG1385	rRNA (uridine-N3-)-methyltransferase activity
APH_0795	COG1225	Alkyl hydroperoxide reductase Thiol specific antioxidant Mal allergen
APH_0801	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
APH_0802	COG0681	Belongs to the peptidase S26 family
APH_0803	COG0316	Belongs to the HesB IscA family
APH_0814	COG0302	gtp cyclohydrolase
APH_0830	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
APH_0851	COG0113	porphobilinogen synthase activity
APH_0852	COG0388	Catalyzes the ATP-dependent amidation of deamido-NAD to form NAD. Uses L-glutamine as a nitrogen source
APH_0852	COG0171	NAD+ synthase (glutamine-hydrolyzing) activity
APH_0857	COG0249	that it carries out the mismatch recognition step. This protein has a weak ATPase activity
APH_0863	COG0567	Dehydrogenase, E1 component
APH_0867	COG0015	Belongs to the lyase 1 family. Adenylosuccinate lyase subfamily
APH_0876	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
APH_0876	COG0340	biotin-[acetyl-CoA-carboxylase] ligase activity
APH_0880	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
APH_0883	COG0249	that it carries out the mismatch recognition step. This protein has a weak ATPase activity
APH_0884	COG0322	excinuclease ABC activity
APH_0893	COG0326	Molecular chaperone. Has ATPase activity
APH_0897	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
APH_0903	COG0210	DNA helicase
APH_0910	COG0482	sulfurtransferase activity
APH_0923	COG1495	Required for disulfide bond formation in some periplasmic proteins. Acts by oxidizing the DsbA protein
APH_0925	COG0267	Belongs to the bacterial ribosomal protein bL33 family
APH_0929	COG0236	Carrier of the growing fatty acid chain in fatty acid biosynthesis
APH_0930	COG0304	beta-ketoacyl-acyl-carrier-protein synthase II activity
APH_0933	COG0758	DNA mediated transformation
APH_0939	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
APH_0944	COG2202	Pas domain
APH_0944	COG2205	protein histidine kinase activity
APH_0945	COG4992	N2-acetyl-L-ornithine:2-oxoglutarate 5-aminotransferase activity
APH_0955	COG1674	ftsk spoiiie
APH_0957	COG4536	flavin adenine dinucleotide binding
APH_0960	COG0352	thiamine-phosphate diphosphorylase activity
APH_0961	COG1806	Bifunctional serine threonine kinase and phosphorylase involved in the regulation of the
APH_0965	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
APH_0968	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
APH_0969	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
APH_0970	COG0740	serine-type endopeptidase activity
APH_0971	COG0544	peptidyl-prolyl cis-trans isomerase activity
APH_0979	COG0156	8-amino-7-oxononanoate synthase activity
APH_0983	COG1121	(ABC) transporter
APH_0984	COG0661	Is probably a protein kinase regulator of UbiI activity which is involved in aerobic coenzyme Q (ubiquinone) biosynthesis
APH_0986	COG3842	ATPase activity
APH_0987	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
APH_0988	COG0353	May play a role in DNA repair. It seems to be involved in an RecBC-independent recombinational process of DNA repair. It may act with RecF and RecO
APH_0989	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
APH_0993	COG0351	phosphomethylpyrimidine kinase
APH_0993	COG0352	thiamine-phosphate diphosphorylase activity
APH_0995	COG0628	permease
APH_0998	COG2142	Succinate dehydrogenase hydrophobic membrane anchor
APH_0999	COG2009	succinate dehydrogenase
APH_1001	COG0128	3-phosphoshikimate 1-carboxyvinyltransferase activity
APH_1003	COG0587	DNA-directed DNA polymerase activity
APH_1008	COG0259	pyridoxamine-phosphate oxidase activity
APH_1010	COG0400	carboxylic ester hydrolase activity
APH_1012	COG0242	peptide deformylase activity
APH_1013	COG0167	dihydroorotate dehydrogenase activity
APH_1014	COG1521	Catalyzes the phosphorylation of pantothenate (Pan), the first step in CoA biosynthesis
APH_1016	COG0156	8-amino-7-oxononanoate synthase activity
APH_1022	COG0164	Endonuclease that specifically degrades the RNA of RNA- DNA hybrids
APH_1023	COG0086	DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates
APH_1024	COG0085	RNA polymerase activity
APH_1025	COG0222	ribosome binding
APH_1026	COG0244	Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors
APH_1027	COG0081	regulation of translation
APH_1028	COG0080	Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors
APH_1029	COG0250	Participates in transcription elongation, termination and antitermination
APH_1032	COG0050	This protein promotes the GTP-dependent binding of aminoacyl-tRNA to the A-site of ribosomes during protein biosynthesis
APH_1033	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
APH_1034	COG0049	tRNA binding
APH_1035	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
APH_1045	COG1178	ABC-type Fe3 transport system permease component
APH_1049	COG1999	signal sequence binding
APH_1051	COG0828	Belongs to the bacterial ribosomal protein bS21 family
APH_1052	COG0045	succinate-CoA ligase (ADP-forming) activity
APH_1053	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
APH_1058	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
APH_1059	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
APH_1060	COG0573	inorganic phosphate transmembrane transporter activity
APH_1070	COG1249	Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family
APH_1071	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
APH_1073	COG5405	Protease subunit of a proteasome-like degradation complex believed to be a general protein degrading machinery
APH_1074	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
APH_1075	COG2226	methyltransferase
APH_1079	COG0143	Is required not only for elongation of protein synthesis but also for the initiation of all mRNA translation through initiator tRNA(fMet) aminoacylation
APH_1085	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
APH_1086	COG0109	protoheme IX farnesyltransferase activity
APH_1087	COG4105	Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane
APH_1090	COG1862	Preprotein translocase
APH_1095	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
APH_1096	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
APH_1097	COG0592	DNA-directed DNA polymerase activity
APH_1099	COG0745	RESPONSE REGULATOR receiver
APH_1101	COG0221	Catalyzes the hydrolysis of inorganic pyrophosphate (PPi) forming two phosphate ions
APH_1107	COG0103	maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
APH_1108	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
APH_1111	COG0489	protein tyrosine kinase activity
APH_1113	COG0721	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)
APH_1119	COG0026	Catalyzes the ATP-dependent conversion of 5- aminoimidazole ribonucleotide (AIR) and HCO(3)(-) to N5- carboxyaminoimidazole ribonucleotide (N5-CAIR)
APH_1120	COG2967	ApaG domain
APH_1146	COG0330	HflC and HflK could
APH_1147	COG0330	HflC and HflK could
APH_1148	COG0265	Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain
APH_1149	COG0571	ribonuclease III activity
APH_1150	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
APH_1159	COG0612	Peptidase, M16
APH_1160	COG0597	This protein specifically catalyzes the removal of signal peptides from prolipoproteins
APH_1161	COG0196	riboflavin kinase activity
APH_1162	COG0695	Has a glutathione-disulfide oxidoreductase activity in the presence of NADPH and glutathione reductase. Reduces low molecular weight disulfides and proteins
APH_1165	COG4199	Single-strand DNA-specific exonuclease, C terminal domain
APH_1165	COG0608	single-stranded DNA 5'-3' exodeoxyribonuclease activity
APH_1166	COG0473	3-isopropylmalate dehydrogenase activity
APH_1171	COG3346	SURF1 family
APH_1173	COG0461	Catalyzes the transfer of a ribosyl phosphate group from 5-phosphoribose 1-diphosphate to orotate, leading to the formation of orotidine monophosphate (OMP)
APH_1174	COG0476	Involved in molybdopterin and thiamine biosynthesis, family 2
APH_1175	COG0695	Has a glutathione-disulfide oxidoreductase activity in the presence of NADPH and glutathione reductase. Reduces low molecular weight disulfides and proteins
APH_1178	COG0653	protein targeting
APH_1179	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
APH_1182	COG0168	Low-affinity potassium transport system. Interacts with trk system potassium uptake protein TrkA
APH_1191	COG0636	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
APH_1192	COG0356	it plays a direct role in the translocation of protons across the membrane
APH_1198	COG0508	dehydrogenase complex catalyzes the overall conversion of
APH_1199	COG0024	Methionine aminopeptidase
APH_1200	COG2890	protein-(glutamine-N5) methyltransferase activity
APH_1204	COG1138	Cytochrome C-type biogenesis protein
APH_1205	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
APH_1206	COG0558	Belongs to the CDP-alcohol phosphatidyltransferase class-I family
APH_1207	COG0138	bifunctional purine biosynthesis protein purh
APH_1208	COG0764	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity
APH_1210	COG4775	Part of the outer membrane protein assembly complex, which is involved in assembly and insertion of beta-barrel proteins into the outer membrane
APH_1211	COG0750	zinc metalloprotease
APH_1214	COG1686	Belongs to the peptidase S11 family
APH_1216	COG0617	tRNA 3'-terminal CCA addition
APH_1217	COG0105	UTP biosynthetic process
APH_1218	COG1396	sequence-specific DNA binding
APH_1223	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
APH_1227	COG0552	protein localization to endoplasmic reticulum
APH_1228	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
APH_1232	COG0372	Belongs to the citrate synthase family
APH_1233	COG0519	Catalyzes the synthesis of GMP from XMP
APH_1243	COG0156	8-amino-7-oxononanoate synthase activity
APH_1244	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)
APH_1246	COG0174	glutamine synthetase
APH_1247	COG0142	geranyltranstransferase activity
APH_1257	COG0508	dehydrogenase complex catalyzes the overall conversion of
APH_1258	COG1830	Aldolase
APH_1263	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
APH_1265	COG1546	Belongs to the CinA family
APH_1265	COG1058	Belongs to the CinA family
APH_1267	COG0336	Belongs to the RNA methyltransferase TrmD family
APH_1268	COG0806	An accessory protein needed during the final step in the assembly of 30S ribosomal subunit, possibly for assembly of the head region. Probably interacts with S19. Essential for efficient processing of 16S rRNA. May be needed both before and after RbfA during the maturation of 16S rRNA. It has affinity for free ribosomal 30S subunits but not for 70S ribosomes
APH_1271	COG1138	Cytochrome C-type biogenesis protein
APH_1276	COG0245	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity
APH_1277	COG0245	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity
APH_1277	COG1211	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity
APH_1279	COG0041	Catalyzes the conversion of N5-carboxyaminoimidazole ribonucleotide (N5-CAIR) to 4-carboxy-5-aminoimidazole ribonucleotide (CAIR)
APH_1281	COG0776	regulation of translation
APH_1285	COG0012	GTP binding
APH_1288	COG0486	Exhibits a very high intrinsic GTPase hydrolysis rate. Involved in the addition of a carboxymethylaminomethyl (cmnm) group at the wobble position (U34) of certain tRNAs, forming tRNA- cmnm(5)s(2)U34
APH_1290	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
APH_1294	COG0817	Nuclease that resolves Holliday junction intermediates in genetic recombination. Cleaves the cruciform structure in supercoiled DNA by nicking to strands with the same polarity at sites symmetrically opposed at the junction in the homologous arms and leaves a 5'-terminal phosphate and a 3'-terminal hydroxyl group
APH_1297	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
APH_1298	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)
APH_1299	COG0451	ADP-glyceromanno-heptose 6-epimerase activity
APH_1300	COG0034	Catalyzes the formation of phosphoribosylamine from phosphoribosylpyrophosphate (PRPP) and glutamine
APH_1301	COG0193	aminoacyl-tRNA hydrolase activity
APH_1302	COG1825	This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance
APH_1303	COG1040	competence protein
APH_1308	COG0022	dehydrogenase e1 component
APH_1310	COG0312	modulator of DNA gyrase
APH_1316	COG0500	methyltransferase
APH_1322	COG1570	exodeoxyribonuclease VII activity
APH_1331	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
APH_1332	COG0108	Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate
APH_1332	COG0807	Catalyzes the conversion of D-ribulose 5-phosphate to formate and 3,4-dihydroxy-2-butanone 4-phosphate
APH_1333	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
APH_1334	COG0056	Produces ATP from ADP in the presence of a proton gradient across the membrane. The alpha chain is a regulatory subunit
APH_1335	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
APH_1341	COG4591	ABC-type transport system involved in lipoprotein release permease component
APH_1344	COG0802	atpase or kinase
APH_1345	COG0670	Belongs to the BI1 family
APH_1346	COG0136	Catalyzes the NADPH-dependent formation of L-aspartate- semialdehyde (L-ASA) by the reductive dephosphorylation of L- aspartyl-4-phosphate
APH_1348	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
APH_1349	COG0057	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
APH_1354	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
APH_1360	COG0043	3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity
APH_1366	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
APH_1367	COG0556	nucleotide-excision repair
APH_1372	COG0242	peptide deformylase activity
APH_1373	COG0204	Acyl-transferase
APH_1374	COG0268	Binds directly to 16S ribosomal RNA
APH_1375	COG0242	peptide deformylase activity
APH_1376	COG0682	Transfers the N-acyl diglyceride group on what will become the N-terminal cysteine of membrane lipoproteins
APH_1377	COG0728	peptidoglycan biosynthetic process
APH_1395	COG1230	cation diffusion facilitator family transporter
APH_1398	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
APH_1402	COG3505	Type IV secretory pathway VirD4
APH_1403	COG0630	type IV secretory pathway, VirB11 components, and related ATPases involved in Archaeal flagella biosynthesis
APH_1404	COG2948	multi-organism process
APH_1409	COG1195	it is required for DNA replication and normal SOS inducibility. RecF binds preferentially to single-stranded, linear DNA. It also seems to bind ATP