MaGe

Gene History: BRADO0001

» CURRENT ANNOTATION

MaGe curated annotation

Type	Begin	End	Length	Frame	Mutation	Gene	Synonyms	Status
			1431 (476aa)	+3
Product	Chromosomal replication initiator protein dnaA
Product Type
EC number
Reaction	_
Localization
BioProcess	16.9 : Replicate
Roles	2.1.1 : DNA replication2.3.7 : Nucleoproteins, basic proteins3.1.2.5 : Action unknown3.3.2 : Regulon (a network of operons encoding related functions)7.1 : Cytoplasm
PubMedId
Note
Additional Data	Selection is empty.
DBxref	Selection is empty.
Class

» PRIMARY ANNOTATION

MicroScope pipeline

Type	Begin	End	Length	Frame	Mutation	Gene	Synonyms	Status
			1431 (476aa)	+3
Product	Chromosomal replication initiator protein DnaA
Product Type
EC number
Reaction	_
Localization
BioProcess	Selection is empty.
Roles	Selection is empty.
PubMedId
Note
Additional Data	Selection is empty.
DBxref	Selection is empty.
Class

1 : Amino acid biosynthesis
1.1 : Aromatic amino acid family
1.2 : Aspartate family
1.3 : Glutamate family
1.4 : Pyruvate family
1.5 : Serine family
1.6 : Histidine family
2 : Purines, pyrimidines, nucleosides, and nucleotides
2.1 : 2'-Deoxyribonucleotide metabolism
2.2 : Nucleotide and nucleoside interconversions
2.3 : Purine ribonucleotide biosynthesis
2.4 : Pyrimidine ribonucleotide biosynthesis
2.5 : Salvage of nucleosides and nucleotides
2.6 : Sugar-nucleotide biosynthesis and conversions
3 : Fatty acid and phospholipid metabolism
3.1 : Biosynthesis
3.2 : Degradation
4 : Biosynthesis of cofactors, prosthetic groups, and carriers
4.1 : Biotin
4.2 : Folic acid
4.3 : Heme, porphyrin, and cobalamin
4.4 : Lipoate
4.5 : Menaquinone and ubiquinone
4.6 : Molybdopterin
4.7 : Pantothenate and coenzyme A
4.8 : Pyridoxine
4.9 : Riboflavin, FMN, and FAD
4.10 : Glutathione and analogs
4.11 : Thiamine
4.12 : Pyridine nucleotides
4.13 : Chlorophyll and bacteriochlorphyll
4.14 : Siderophores
5 : Central intermediary metabolism
5.1 : Amino sugars
5.2 : One-carbon metabolism
5.3 : Phosphorus compounds
5.4 : Polyamine biosynthesis
5.5 : Sulfur metabolism
5.6 : Nitrogen fixation
5.7 : Nitrogen metabolism
5.8 : Electron carrier regeneration
6 : Energy metabolism
6.1 : Aerobic
6.2 : Amino acids and amines
6.3 : Anaerobic
6.4 : ATP-proton motive force interconversion
6.5 : Electron transport
6.6 : Entner-Doudoroff
6.7 : Fermentation
6.8 : Glycolysis/gluconeogenesis
6.9 : Pentose phosphate pathway
6.10 : Pyruvate dehydrogenase
6.11 : Sugars
6.12 : TCA cycle
6.13 : Methanogenesis
6.14 : Biosynthesis and degradation of polysaccharides
6.15 : Photosynthesis
6.16 : Chemoautotrophy
7 : Transport and binding proteins
7.1 : Amino acids, peptides and amines
7.2 : Anions
7.3 : Carbohydrates, organic alcohols, and acids
7.4 : Cations and iron carrying compounds
7.5 : Nucleosides, purines and pyrimidines
7.6 : Porins
7.7 : Unknown substrate
8 : DNA metabolism
8.1 : DNA replication, recombination, and repair
8.2 : Restriction/modification
8.3 : Degradation of DNA
8.4 : Chromosome-associated proteins
9 : Transcription
9.1 : Degradation of RNA
9.2 : DNA-dependent RNA polymerase
9.3 : Transcription factors
9.4 : RNA processing
10 : Protein synthesis
10.1 : tRNA aminoacylation
10.2 : Ribosomal proteins: synthesis and modification
10.3 : tRNA and rRNA base modification
10.4 : Translation factors
11 : Protein fate
11.1 : Protein and peptide secretion and trafficking
11.2 : Protein modification and repair
11.3 : Protein folding and stabilization
11.4 : Degradation of proteins, peptides, and glycopeptides
12 : Regulatory functions
12.1 : DNA interactions
12.2 : RNA interactions
12.3 : Protein interactions
12.4 : Small molecule interactions
13 : Signal transduction
13.1 : Two-component systems
13.2 : PTS
14 : Cell envelope
14.1 : Surface structures
14.2 : Biosynthesis and degradation of murein sacculus and peptidoglycan
14.3 : Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides
15 : Cellular processes
15.1 : Cell division
15.2 : Chemotaxis and motility
15.3 : Cell adhesion
15.4 : Conjugation
15.5 : Detoxification
15.6 : DNA transformation
15.7 : Sporulation and germination
15.8 : Toxin production and resistance
15.9 : Pathogenesis
15.10 : Adaptations to atypical conditions
15.11 : Biosynthesis of natural products
15.12 : Bioluminescence
16 : Biological processes
16.1 : Circulate
16.2 : Construct biomass (Anabolism)
16.3 : Control
16.4 : Excrete
16.5 : Explore
16.6 : Maintain
16.7 : Manage energy
16.8 : Protect
16.9 : Replicate
16.10 : Respire
16.11 : Scavenge (Catabolism)
16.12 : Sense
16.13 : Shape
16.14 : Store
16.15 : Symbiosis
17 : Mobile and extrachromosomal element functions
17.1 : Plasmid functions
17.2 : Prophage functions
17.3 : Transposon functions
18 : Unknown function
18.1 : Enzymes of unknown specificity
19 : Unclassified

1 : Metabolism
1.1 : Carbon compound utilization
1.1.1 : Carbohydrates/Carbon compounds
1.1.1.1 : D-allose catabolism
1.1.1.2 : 2,5-ketogluconate metabolism
1.1.1.3 : D-arabinose catabolism
1.1.1.4 : D-galactarate catabolism
1.1.1.5 : D-galacturonate catabolism
1.1.1.6 : D-glucarate catabolism
1.1.1.7 : D-glucuronate catabolism
1.1.1.8 : L-arabinose catabolism
1.1.1.9 : L-idonate catabolism
1.1.1.10 : L-lyxose metabolism
1.1.1.11 : Fucose catabolism
1.1.1.12 : Galactitol catabolism
1.1.1.13 : Galactonate catabolism
1.1.1.14 : Lactose degradation
1.1.1.15 : Mannose catabolism
1.1.1.16 : Rhamnose catabolism
1.1.1.17 : Sorbitol degradation
1.1.1.18 : Trehalose degradation, low osmolarity+
1.1.1.19 : Xylose catabolism
1.1.1.20 : Glycol degradation
1.1.1.21 : Mannitol degradation
1.1.1.22 : Ribose degradation
1.1.1.23 : Galactose degradation
1.1.1.24 : Sorbose degradation
1.1.1.25 : L-ascorbate degradation
1.1.2 : Fatty acids (fatty acid oxidation)
1.1.2.1 : Degradation of short-chain fatty acids
1.1.2.2 : 3-phenylpropionate and 3-(3-hydroxyphenyl)propionate degradation
1.1.2.3 : Propionate degradation
1.1.3 : Amino acids
1.1.3.1 : L-alanine degradation
1.1.3.2 : L-serine degradation
1.1.3.3 : Arginine catabolism
1.1.3.4 : Glutamate degradation
1.1.3.5 : Glycine cleavage
1.1.3.6 : Proline utilization
1.1.3.7 : Threonine catabolism
1.1.3.8 : Tryptophan utilization
1.1.3.9 : L-cysteine catabolism
1.1.3.10 : Lysine cleavage
1.1.3.11 : Histidine degradation
1.1.3.12 : Leucine degradation
1.1.3.13 : Methionine degradation
1.1.3.14 : Valine degradation
1.1.3.15 : Phenylalanine, tyrosine degradation
1.1.4 : Amines
1.1.4.1 : Phenylethylamine degradation
1.1.4.2 : Carnitine degradation
1.1.4.3 : Ornithine degradation
1.1.5 : Others
1.1.5.1 : Phenylacetic acid degradation
1.1.5.2 : Ethanol degradation
1.1.5.3 : Eugenol catabolism
1.1.5.4 : Beta-ketoadipate pathway
1.1.5.5 : Mandelate catabolism
1.2 : Macromolecule degradation
1.2.1 : RNA
1.2.2 : DNA
1.2.3 : Proteins/peptides/glycopeptides
1.2.4 : Polysaccharides
1.2.4.1 : Glycogen catabolism
1.2.4.2 : Chitin catabolism
1.3 : Energy metabolism (carbon)
1.3.1 : Glycolysis
1.3.2 : Pentose phosphate shunt, oxidative branch
1.3.3 : Pyruvate dehydrogenase
1.3.4 : Tricarboxylic acid cycle
1.3.5 : Fermentation
1.3.6 : Aerobic respiration
1.3.7 : Anaerobic respiration
1.3.8 : ATP proton motive force interconversion
1.3.9 : Entner-Doudoroff pathway
1.4 : Energy production/transport
1.4.1 : Electron donor
1.4.2 : Electron acceptor
1.4.3 : Electron carrier
1.5 : Building block biosynthesis
1.5.1 : Amino acids
1.5.1.1 : Glutamate
1.5.1.2 : Glutamine
1.5.1.3 : Arginine
1.5.1.4 : Proline
1.5.1.5 : Aspartate
1.5.1.6 : Asparagine
1.5.1.7 : Lysine, diaminopimelate
1.5.1.8 : Threonine
1.5.1.9 : Methionine
1.5.1.10 : Glycine
1.5.1.11 : Serine
1.5.1.12 : Cysteine
1.5.1.13 : Phenylalanine
1.5.1.14 : Tyrosine
1.5.1.15 : Tryptophan
1.5.1.16 : Histidine
1.5.1.17 : Alanine
1.5.1.18 : Isoleucine/valine
1.5.1.19 : Leucine
1.5.1.20 : Chorismate
1.5.1.21 : Homoserine
1.5.2 : Nucleotide
1.5.2.1 : Purine biosynthesis
1.5.2.2 : Pyrimidine biosynthesis
1.5.2.3 : Purine ribonucleotide biosynthesis
1.5.2.4 : Pyrimidine ribonucleotide/ribonucleoside biosynthesis
1.5.3 : Cofactor, small molecule carrier
1.5.3.1 : Biotin
1.5.3.2 : Folic acid
1.5.3.3 : Lipoate
1.5.3.4 : Molybdenum (molybdopterin)
1.5.3.5 : Coenzyme A
1.5.3.6 : Pyridoxine (vitamin B6)
1.5.3.7 : Nicotinamide adenine dinucleotide (NAD)
1.5.3.8 : Thiamine (Vitamin B1)
1.5.3.9 : Riboflavin (Vitamin B2), FAD, FMN
1.5.3.10 : Glutathione
1.5.3.11 : Menaquinone (MK), ubiquinone (Q)
1.5.3.12 : Heme, porphyrin
1.5.3.13 : Cobalamin (Vitamin B12)
1.5.3.14 : Enterochelin (enterobactin)
1.5.3.15 : Chrysobactin
1.5.3.16 : Achromobactin
1.5.3.19 : Isoprenoid biosynthesis
1.5.3.20 : Tetrahydrobiopterin biosynthesis
1.5.3.21 : Pyochelin biosynthesis
1.5.4 : Fatty acid and phosphatidic acid
1.6 : Macromolecules (cellular constituent) biosynthesis
1.6.1 : Phospholipid
1.6.2 : Colanic acid (M antigen)
1.6.3 : Lipopolysaccharide
1.6.3.1 : O antigen
1.6.3.2 : Core region
1.6.3.3 : Lipid A
1.6.4 : Enterobacterial common antigen (surface glycolipid)
1.6.5 : K antigen
1.6.6 : Osmoregulated periplasmic glucan
1.6.7 : Peptidoglycan (murein)
1.6.9 : Polysaccharides, cytoplasmic
1.6.10 : Lipoprotein
1.6.11 : Glycoprotein
1.6.12 : Flagella
1.6.13 : Fimbria, pili, curli
1.6.15 : Large molecule carriers
1.6.15.1 : Cytochromes
1.6.15.2 : Thioredoxin, glutaredoxin
1.6.15.3 : Biotin carboxyl carrier protein
1.6.15.4 : Acyl carrier protein
1.6.16 : Cellulose biosynthesis
1.7 : Central intermediary metabolism
1.7.1 : Unassigned reversible reactions
1.7.2 : Glyoxylate bypass
1.7.3 : Pentose phosphate shunt, non-oxidative branch
1.7.6 : Glycerol metabolism
1.7.7 : Galactose metabolism
1.7.8 : Gluconeogenesis
1.7.9 : Misc. glucose metabolism
1.7.10 : Sugar nucleotide biosynthesis, conversions
1.7.12 : Amino sugar conversions
1.7.13 : Amino acid conversion
1.7.14 : Polyamine biosynthesis
1.7.15 : 2'-deoxyribonucleotide/ribonucleoside metabolism
1.7.17 : Formyl-tetrahydrofolate biosynthesis
1.7.18 : Betaine biosynthesis
1.7.19 : Incorporation of metal ions
1.7.20 : S-adenosyl methionine biosynthesis
1.7.21 : Glyoxylate degradation
1.7.22 : Carnitine metabolism
1.7.23 : Methylglyoxal metabolism
1.7.24 : Cyanate catabolism
1.7.25 : Glycolate metabolism
1.7.26 : Allantoin assimilation
1.7.27 : Pyridoxal 5'-phosphate salvage
1.7.28 : Pyruvate catabolism
1.7.29 : Acetate catabolism
1.7.31 : Aminobutyrate catabolism
1.7.32 : Putrescine catabolism
1.7.33 : Nucleotide and nucleoside conversions
1.7.34 : Peptidoglycan (murein) turnover, recycling
1.7.35 : Lactate oxidation
1.7.36 : Trehalose biosynthesis
1.7.37 : C1 assimilation, serine pathway
1.7.38 : Methionine salvage pathway
1.8 : Metabolism of other compounds
1.8.1 : Phosphorous metabolism
1.8.2 : Sulfur metabolism
1.8.3 : Nitrogen metabolism
2 : Information transfer
2.1 : DNA related
2.1.1 : DNA replication
2.1.2 : DNA restriction/modification
2.1.3 : DNA recombination
2.1.4 : DNA repair
2.1.5 : DNA degradation
2.2 : RNA related
2.2.2 : Transcription related
2.2.3 : RNA modification
2.2.4 : RNA degradation
2.2.5 : tRNA
2.2.6 : rRNA, stable RNA
2.2.7 : Antisense RNA
2.3 : Protein related
2.3.1 : Amino acid-activation
2.3.2 : Translation
2.3.3 : Posttranslational modification
2.3.4 : Chaperoning, folding
2.3.5 : Export, signal peptide cleavage
2.3.6 : Turnover, degradation
2.3.7 : Nucleoproteins, basic proteins
2.3.8 : Ribosomal proteins
2.3.9 : Non-ribosomal peptide synthetase
3 : Regulation
3.1. : Type of regulation
3.1.1 : DNA structure level
3.1.1.1 : DNA bending, supercoiling, inversion
3.1.1.2 : Methylation
3.1.2 : Transcriptional level
3.1.2.1 : Sigma factors, anti-sigmafactors
3.1.2.2 : Activator
3.1.2.3 : Repressor
3.1.2.4 : Complex regulation
3.1.2.4.1 : More than one signal needed
3.1.2.4.2 : Regulons or multilayer component regulatory systems
3.1.2.4.3 : Two-component regulatory systems (external signal)
3.1.2.4.4 : Quorum sensing
3.1.2.5 : Action unknown
3.1.3 : Posttranscriptional
3.1.3.1 : Translation attenuation and efficiency
3.1.3.2 : Covalent modification, demodification, maturation
3.1.3.3 : Inhibition / activation of enzymes
3.1.3.4 : Proteases, cleavage of compounds
3.1.3.5 : Multilayer regulatory systems
3.1.3.6 : Antisense RNA
3.1.4 : Regulation level unknown
3.3 : Genetic unit regulated
3.3.1 : Operon (regulation of one operon)
3.3.2 : Regulon (a network of operons encoding related functions)
3.3.3 : Stimulon (ie. environmental stimulus)
3.3.4 : Global
3.4 : Trigger (some information added)
3.5 : Trigger modulation (some information added)
4 : Transport
4.1 : Channel-type Transporters
4.1.A. : alpha-type channels
4.1.A.1. : The Voltage-gated Ion Channel (VIC) Superfamily
4.1.A.8. : The Major Intrinsic Protein (MIP) Family
4.1.A.11 : The Chloride Channel (ClC) Family
4.1.B.17 : The Outer Membrane Factor (OMF) Family
4.1.A.22 : The Large Conductance Mechanosensitive Ion Channel (MscL) Family
4.1.A.23 : The Small Conductance Mechanosensitive Ion Channel (MscS) Family
4.1.A.46 : The H+- or Na+-translocating Bacterial Flagellar Motor (Mot) Family
4.1.B : Beta barrel porins (The Outer Membrane Porin (OMP) Functional Superfamily)
4.1.B.1 : The General Bacterial Porin (GBP) Family
4.1.B.3 : The Sugar Porin (SP) Family
4.1.B.9 : The FadL Outer Membrane Protein (FadL) Family
4.1.B.10 : The Nucleoside-specific Channel-forming Outer Membrane Porin (Tsx) Family
4.1.B.14 : The Outer Membrane Receptor (OMR) Family
4.1.B.21 : The OmpG Porin (OmpG) Family
4.2 : Electrochemical potential driven transporters
4.2.A. : Porters (Uni-, Sym- and Antiporters)
4.2.A.1 : The Major Facilitator Superfamily (MFS)
4.2.A.2 : The Glycoside-Pentoside-Hexuronide (GPH):Cation Symporter Family
4.2.A.3 : The Amino Acid-Polyamine-Choline (APC) Family
4.2.A.4 : The Cation Diffusion Facilitator (CDF) Family
4.2.A.6 : The Resistance-Nodulation-Cell Division (RND) Superfamily
4.2.A.7 : The Drug/Metabolite Transporter (DMT) Superfamily
4.2.A.8 : The Gluconate:H+ Symporter (GntP) Family
4.2.A.9 : The Cytochrome oxidase biogenesis (Oxa1) Family
4.2.A.10 : The 2-Keto-3-Deoxygluconate Transporter (KDGT) Family
4.2.A.13 : The C4-Dicarboxylate Uptake (Dcu) Family
4.2.A.14 : The Lactate Permease (LctP) Family
4.2.A.15 : The Betaine/Carnitine/Choline Transporter (BCCT) Family
4.2.A.16 : The Telurite-resistance/Dicarboxylate Transporter (TDT) Family
4.2.A.17 : The Proton-dependent Oligopeptide Transporter (POT) Family
4.2.A.19 : The Ca2+:Cation Antiporter (CaCA) Family
4.2.A.20 : The Inorganic Phosphate Transporter (PiT) Family
4.2.A.21 : The Solute:Sodium Symporter (SSS) Family
4.2.A.23 : The Dicarboxylate/Amino Acid:Cation (Na+ or H+) Symporter (DAACS) Family
4.2.A.25 : The Alanine/Glycine:Cation symporter (AGCS) Family
4.2.A.26 : The Branched Chain Amino Acid:Cation Symporter (LIVCS) Family
4.2.A.27 : The Glutamate:Na+ Symporter (GltS) Family
4.2.A.33 : The NhaA Na+:H+ Antiporter (NhaA) Family
4.2.A.34 : The NhaB Na+:H+ Antiporter (NhaB) Family
4.2.A.36 : The Monovalent Cation:Proton Antiporter-1 (CPA1) Family
4.2.A.37 : The Monovalent Cation:Proton Antiporter-2 (CPA2) Family
4.2.A.38 : The K+ Transporter (Trk) Family
4.2.A.39 : The Nucleobase:Cation Symporter-1 (NCS1) Family
4.2.A.40 : The Nucleobase:Cation Symporter-2 (NCS2) Family
4.2.A.41 : The Concentrative Nucleoside Transporter (CNT) Family
4.2.A.42 : The Hydroxy/Aromatic Amino Acid Permease (HAAAP) Family
4.2.A.44 : The Formate-Nitrite Transporter (FNT) Family
4.2.A.45 : The Metal Ion Transporter (MIT) Family
4.2.A.47 : The Divalent Anion:Na+ Symporter (DASS) Family
4.2.A.49 : The Ammonium Transporter (Amt) Family
4.2.A.53 : The Sulfate Permease (SulP) Family
4.2.A.55 : The Manganese (Nramp) Fam.
4.2.A.58 : The Phosphate:Na+ Symporter (PNaS) Family
4.2.A.61 : The C4-dicarboxylate Uptake C (DcuC) Family
4.2.A.64 : The Type V Secretory Pathway or Twin Arginine Targeting (Tat) Family
4.2.A.66 : The Multi Antimicrobial Extrusion (MATE) Family
4.2.A.68 : The p-Aminobenzoyl-glutamate Transporter (AbgT) Family
4.2.A.69 : The Auxin Efflux Carrier (AEC) Family
4.2.A.72 : The K+ uptake permease (KUP) family
4.2.A.75 : The L-lysine exporter (LysE) family
4.2.A.76 : The Resistance to Homoserine/Threonine (RhtB) Family
4.2.C : Ion-gradient driven energizers
4.2.C.1 : TonB Family of Auxiliary Proteins for Energization of OMR-mediated Transport
4.3 : Primary Active Transporters
4.3.A. : Pyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active Transporters
4.3.A.1 : The ATP-binding Cassette (ABC) Superfamily + ABC-type Uptake Permeases
4.3.A.1.a : ATP binding component
4.3.A.1.m : membrane component
4.3.A.1.p : periplasmic binding component
4.3.A.1.am : ATP binding and membrane component
4.3.A.2 : The H+/Na+-translocating F-, V- and A-type ATPase (F-ATPase) Superfamily
4.3.A.3 : The P-type ATPase (P-ATPase) Superfamily
4.3.A.4 : The Arsenite-Antimonite (Ars) Efflux Family
4.3.A.5 : The Type II (General) Secretory Pathway (IISP) Family
4.3.A.6 : The Type III (Virulence-related) Secretory Pathway (IIISP) Family
4.3.A.7 : The Type IV (Conjugal DNA-Protein Transfer) Secretory Pathway (IVSP) Family
4.3.D. : Oxidoreduction-driven Active Transporters
4.3.D.1 : The Proton- or sodium ion-translocating NADH Dehydrogenase (NDH) Family
4.3.D.4 : The Proton-translocating Cytochrome Oxidase (COX) Superfamily
4.4 : Group Translocators
4.4.A : Phosphotransferase Systems (PEP-dependent PTS)
4.4.A.1 : The PTS Glucose-Glucoside (Glc) Family
4.4.A.2 : The PTS Fructose-Mannitol (Fru) Family
4.4.A.3 : The PTS Lactose-N,N'-Diacetylchitobiose-betaucoside (Lac) Family
4.4.A.4 : The PTS Glucitol (Gut) Family
4.4.A.5 : The PTS Galactitol (Gat) Family
4.4.A.6 : The PTS Mannose-Fructose-Sorbose (Man) Family
4.8.A : Accessory Factors Involved in Transport
4.8.A.1 : The Membrane Fusion Protein (MFP) Family
4.8.A.2 : The Secretin Auxiliary Lipoprotein (SAL) Family
4.8.A.3 : MPA1 Family auxillary transport protein
4.8.A.7 : The Phosphotransferase System Enzyme I (EI) Family
4.8.A.8 : The Phosphotransferase System HPr (HPr) Family
4.9.A : Transporters of Unknown Classification
4.9.A.1 : The Polysaccharide Transporter (PST) Family
4.9.A.4 : The Nicotinamide Mononucleotide (NMN) Uptake Permease (PnuC) Family
4.9.A.8 : The Ferrous Iron Uptake (FeoB) Family
4.9.A.13 : The Short Chain Fatty Acid Transporter (scFAT) Family
4.9.A.16 : The Septal DNA Translocator (SDT) Family
4.9.A.17 : The Metal Ion Transporter (MIT) Family
4.9.B : Putative uncharacterized transport protein
4.9.B.3 : The Putative Bacterial Murein Precursor Exporter (MPE) Family
4.9.B.4 : The Putative Efflux Transporter (PET) Family
4.9.B.6 : The Toxic Hok/Gef Protein (Hok/Gef) Family
4.9.B.10 : The 6TMS Putative MarC Transporter (MarC) Family
4.9.B.18 : The SecDF-associated Single Transmembrane Protein (SSTP) Family
4.9.B.21 : The Frataxin (Frataxin) Family
4.9.B.22 : The Putative Permease (PerM) Family
4.9.B.24 : The Testis-Enhanced Gene Transfer (TEGT) Family
4.9.B.25 : The YbbM (YbbM) Family
4.9.B.27 : The YdjX-Z (YdjX-Z) Family
4.9.B.28 : The YqaE (YqaE) Family
4.9.B.29 : The YebN (YebN) Family
4.9.B.31 : The YqiH (YqiH) Family
4.9.B.32 : The Putative Vectorial Glycosyl Polymerization (VGP) Family
4.S : substrate
4.S.1 : (D)-glucarate/galactarate
4.S.10 : allose/ribose
4.S.100 : L-arabinose
4.S.101 : L-arabinose /H+
4.S.102 : L-arabinose/ isopropyl-beta-D-thiogalactopyranoside
4.S.103 : L-asparagine
4.S.104 : lipooligosaccharides
4.S.105 : lipopolysaccharide
4.S.106 : lipoprotein
4.S.107 : L-lactate
4.S.108 : L-leucine/L-valine/L-iso-leucine
4.S.109 : L-rhamnose/H+
4.S.11 : alpha-ketoglutarate
4.S.110 : L-threonine/L-serine
4.S.111 : lysine
4.S.112 : lysine/arginine/ornithine
4.S.113 : maltose
4.S.114 : maltose/maltodextrin
4.S.115 : mannitol
4.S.116 : mannose
4.S.117 : mellobiose
4.S.118 : methionine
4.S.119 : methylgalactoside/galactose
4.S.12 : amino acid
4.S.120 : Mg++
4.S.121 : Mg2+/Ni2+/Co2+
4.S.122 : microcin B17
4.S.123 : Mn+/H+
4.S.124 : molybdate
4.S.125 : molybdenum
4.S.126 : multidrug
4.S.127 : multidrug/bicyclomycin
4.S.128 : muropeptide
4.S.129 : myo-inositor
4.S.13 : amino acid/amide
4.S.130 : Na+
4.S.131 : Na+/ alanine/glycine
4.S.132 : Na+/ H+
4.S.133 : Na+/Ca+
4.S.134 : Na+/dicarboxylate
4.S.135 : Na+/glutamate/aspartate
4.S.136 : Na+/H+
4.S.137 : Na+/leucine/valine/iso-leucine
4.S.138 : Na+/pantothenate
4.S.139 : Na+/proline
4.S.14 : ammonium
4.S.140 : Na+/serine/threonine
4.S.141 : N-acetylgalactosamine
4.S.142 : N-acetylglucosamine
4.S.143 : Ni++
4.S.144 : nicotinamide mononucleotide
4.S.145 : nitrite
4.S.146 : nucleoside
4.S.147 : nucleoside/H+
4.S.148 : oligopeptide
4.S.149 : oligopeptides
4.S.15 : antibiotic
4.S.150 : p-aminobenzoyl-glutamate
4.S.151 : Pb/Cd/Zn/Hg
4.S.152 : peptide
4.S.153 : phenylalanine
4.S.154 : phenylalanine/ tyrosine
4.S.155 : phosphate
4.S.156 : polymyxin
4.S.157 : potassium
4.S.158 : proline
4.S.159 : proline/betaine
4.S.16 : arabinose polymer
4.S.160 : protein
4.S.161 : protein/DNA
4.S.162 : purine/xanthine
4.S.163 : putrescine
4.S.164 : putrescine/ornithine
4.S.165 : putrescine/ornitine
4.S.166 : putrescine/spermidine
4.S.167 : serine
4.S.168 : shikimate/dehydroshikimate
4.S.169 : sialic acid
4.S.17 : arginine
4.S.170 : S-methylmethionine
4.S.171 : spermidine/putrescine
4.S.172 : sucrose
4.S.173 : sugar
4.S.174 : sulfate
4.S.175 : taurine
4.S.176 : tellurite
4.S.177 : thiamine
4.S.178 : thiosulfate
4.S.179 : thiosulfate/sulfate
4.S.18 : arginine/ornitine
4.S.180 : threonine
4.S.181 : trehalose
4.S.182 : tripeptide
4.S.183 : tryptophan
4.S.184 : tyrosine
4.S.185 : uracil
4.S.186 : urasil
4.S.187 : vitamin B12
4.S.188 : water
4.S.189 : xanthosine
4.S.19 : arsenite
4.S.190 : xylose/H+
4.S.191 : Zn
4.S.192 : chrysobactin
4.S.193 : achromobactin
4.S.2 : 2-keto-3-deoxy-D-gluconate
4.S.20 : benzoate
4.S.21 : beta-galactosidase/lactose and glucose
4.S.22 : beta-glucoside
4.S.23 : betaine/choline/glycine
4.S.24 : betaine/choline/glycine transport protein
4.S.25 : Ca+/ H+
4.S.26 : cadaverine/lysine
4.S.27 : carnitine
4.S.28 : cation
4.S.29 : cellobiose/arbutin/salicin
4.S.3 : 3-hydroxyphenylpropionic acid
4.S.30 : cellobiose/salicin/arbutin
4.S.31 : chloramphenicol
4.S.32 : chloride
4.S.33 : choline
4.S.34 : citrate/succinate
4.S.35 : colicin4
4.S.36 : Cu
4.S.37 : curli subunit
4.S.38 : cyanate
4.S.39 : cysteine
4.S.4 : 3-phenylpropionic acid
4.S.40 : cysteine/O-acetyl-L-serine/cysteine metabolites
4.S.41 : cytosine
4.S.42 : D-alanine/D-serine/glycine
4.S.43 : D-galactonate
4.S.44 : D-glucarate
4.S.45 : D-glucose/trehalose
4.S.46 : dicarboxylate
4.S.47 : dipeptide
4.S.48 : D-ribose
4.S.49 : drug
4.S.5 : alkanesulfonate
4.S.50 : D-xylose
4.S.51 : enterochelin
4.S.52 : fatty acid
4.S.53 : Fe
4.S.54 : Fe++
4.S.55 : ferric dicitrate
4.S.56 : ferric enterobactin
4.S.57 : ferric hydroxamate
4.S.58 : ferrichrome
4.S.59 : formate
4.S.6 : alkanesulphonate
4.S.60 : formate/oxalate
4.S.61 : fosfidomycin/H+
4.S.62 : frucose
4.S.63 : fructose
4.S.64 : fucose
4.S.65 : galactitol
4.S.66 : galactose/H+
4.S.67 : gamma-aminobutyrate
4.S.68 : glucitol/sorbitol
4.S.69 : gluconate
4.S.7 : alklphosphonate
4.S.70 : gluconate/L-idonate
4.S.71 : glucose
4.S.72 : glucose/maltose
4.S.73 : glucuronide
4.S.74 : glutamate/aminobutyric acid
4.S.75 : glutamate/aspartate
4.S.76 : glutamine
4.S.77 : glycerol
4.S.78 : glycerol-3-P
4.S.79 : glycine betaine choline transport
4.S.8 : alkylphosphonate
4.S.80 : glycine/betaine/proline
4.S.81 : group A colicins
4.S.82 : H+
4.S.83 : H+/acridine
4.S.84 : H+/lactose/glucose
4.S.85 : heme
4.S.86 : hexose phosphate
4.S.87 : hexuronate
4.S.88 : histidine
4.S.89 : histidine/lysine/arginine/ornithine
4.S.9 : allantoin/ion
4.S.90 : homoserine/lactone
4.S.91 : hydrophilic molecule
4.S.92 : hydrophilic molecules
4.S.93 : ion
4.S.94 : ions
4.S.95 : iron dicitrate
4.S.96 : K+
4.S.97 : K+/H+
4.S.98 : lactate
4.S.99 : lactose
5 : Cell processes
5.1 : Cell division
5.2 : Cell cycle physiology
5.3 : Motility (incl. chemotaxis, energytaxis, aerotaxis, redoxtaxis)
5.4 : Genetic exchange, recombination
5.5 : Adaptation to stress
5.5.1 : Osmotic pressure
5.5.2 : Temperature extremes
5.5.3 : Starvation response
5.5.4 : pH response
5.5.5 : Dessication
5.5.6 : Other stresses (mechanical, nutritional, oxidative)
5.5.7 : Fe aquisition
5.6 : Protection
5.6.1 : Radiation
5.6.2 : Detoxification (xenobiotic metabolism)
5.6.3 : Cell killing
5.6.4 : Drug resistance/sensitivity
5.8 : SOS response
5.10 : Defense/survival
5.11 : DNA uptake
5.12 : Biofilm production
5.13 : Virulence associated
6 : Cell structure
6.1 : Membrane
6.2 : Peptidoglycan (murein)
6.3 : Surface antigens (ECA, O antigen of LPS)
6.4 : Flagellum
6.5 : Pilus
6.6 : Ribosome
6.7 : Capsule (M and K antigens)
7 : Location of gene products
7.1 : Cytoplasm
7.2 : Periplasmic space
7.3 : Inner membrane
7.4 : Outer membrane
7.5 : Extracellular
8 : extrachromosomal
8.1 : Prophage genes and phage related functions
8.1.1 : DNA packaging, phage assembly
8.1.2 : Replication
8.1.3 : Regulation
8.1.4 : Integration, recombination
8.1.5 : Lysis
8.1.6 : Structural component
8.2 : Plasmid related
8.2.1 : replication and maintenance
8.2.2 : plasmid transfer
8.3 : Transposon related
8.3.1 : transposases
8.3.2 : regulation of mobility
8.4 : Colicin related
9 : DNA sites
10 : cryptic genes

1 : Amino acid biosynthesis
1.1 : Aromatic amino acid family
1.2 : Aspartate family
1.3 : Glutamate family
1.4 : Pyruvate family
1.5 : Serine family
1.6 : Histidine family
2 : Purines, pyrimidines, nucleosides, and nucleotides
2.1 : 2'-Deoxyribonucleotide metabolism
2.2 : Nucleotide and nucleoside interconversions
2.3 : Purine ribonucleotide biosynthesis
2.4 : Pyrimidine ribonucleotide biosynthesis
2.5 : Salvage of nucleosides and nucleotides
2.6 : Sugar-nucleotide biosynthesis and conversions
3 : Fatty acid and phospholipid metabolism
3.1 : Biosynthesis
3.2 : Degradation
4 : Biosynthesis of cofactors, prosthetic groups, and carriers
4.1 : Biotin
4.2 : Folic acid
4.3 : Heme, porphyrin, and cobalamin
4.4 : Lipoate
4.5 : Menaquinone and ubiquinone
4.6 : Molybdopterin
4.7 : Pantothenate and coenzyme A
4.8 : Pyridoxine
4.9 : Riboflavin, FMN, and FAD
4.10 : Glutathione and analogs
4.11 : Thiamine
4.12 : Pyridine nucleotides
4.13 : Chlorophyll and bacteriochlorphyll
4.14 : Siderophores
5 : Central intermediary metabolism
5.1 : Amino sugars
5.2 : One-carbon metabolism
5.3 : Phosphorus compounds
5.4 : Polyamine biosynthesis
5.5 : Sulfur metabolism
5.6 : Nitrogen fixation
5.7 : Nitrogen metabolism
5.8 : Electron carrier regeneration
6 : Energy metabolism
6.1 : Aerobic
6.2 : Amino acids and amines
6.3 : Anaerobic
6.4 : ATP-proton motive force interconversion
6.5 : Electron transport
6.6 : Entner-Doudoroff
6.7 : Fermentation
6.8 : Glycolysis/gluconeogenesis
6.9 : Pentose phosphate pathway
6.10 : Pyruvate dehydrogenase
6.11 : Sugars
6.12 : TCA cycle
6.13 : Methanogenesis
6.14 : Biosynthesis and degradation of polysaccharides
6.15 : Photosynthesis
6.16 : Chemoautotrophy
7 : Transport and binding proteins
7.1 : Amino acids, peptides and amines
7.2 : Anions
7.3 : Carbohydrates, organic alcohols, and acids
7.4 : Cations and iron carrying compounds
7.5 : Nucleosides, purines and pyrimidines
7.6 : Porins
7.7 : Unknown substrate
8 : DNA metabolism
8.1 : DNA replication, recombination, and repair
8.2 : Restriction/modification
8.3 : Degradation of DNA
8.4 : Chromosome-associated proteins
9 : Transcription
9.1 : Degradation of RNA
9.2 : DNA-dependent RNA polymerase
9.3 : Transcription factors
9.4 : RNA processing
10 : Protein synthesis
10.1 : tRNA aminoacylation
10.2 : Ribosomal proteins: synthesis and modification
10.3 : tRNA and rRNA base modification
10.4 : Translation factors
11 : Protein fate
11.1 : Protein and peptide secretion and trafficking
11.2 : Protein modification and repair
11.3 : Protein folding and stabilization
11.4 : Degradation of proteins, peptides, and glycopeptides
12 : Regulatory functions
12.1 : DNA interactions
12.2 : RNA interactions
12.3 : Protein interactions
12.4 : Small molecule interactions
13 : Signal transduction
13.1 : Two-component systems
13.2 : PTS
14 : Cell envelope
14.1 : Surface structures
14.2 : Biosynthesis and degradation of murein sacculus and peptidoglycan
14.3 : Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides
15 : Cellular processes
15.1 : Cell division
15.2 : Chemotaxis and motility
15.3 : Cell adhesion
15.4 : Conjugation
15.5 : Detoxification
15.6 : DNA transformation
15.7 : Sporulation and germination
15.8 : Toxin production and resistance
15.9 : Pathogenesis
15.10 : Adaptations to atypical conditions
15.11 : Biosynthesis of natural products
15.12 : Bioluminescence
16 : Biological processes
16.1 : Circulate
16.2 : Construct biomass (Anabolism)
16.3 : Control
16.4 : Excrete
16.5 : Explore
16.6 : Maintain
16.7 : Manage energy
16.8 : Protect
16.9 : Replicate
16.10 : Respire
16.11 : Scavenge (Catabolism)
16.12 : Sense
16.13 : Shape
16.14 : Store
16.15 : Symbiosis
17 : Mobile and extrachromosomal element functions
17.1 : Plasmid functions
17.2 : Prophage functions
17.3 : Transposon functions
18 : Unknown function
18.1 : Enzymes of unknown specificity
19 : Unclassified

1 : Metabolism
1.1 : Carbon compound utilization
1.1.1 : Carbohydrates/Carbon compounds
1.1.1.1 : D-allose catabolism
1.1.1.2 : 2,5-ketogluconate metabolism
1.1.1.3 : D-arabinose catabolism
1.1.1.4 : D-galactarate catabolism
1.1.1.5 : D-galacturonate catabolism
1.1.1.6 : D-glucarate catabolism
1.1.1.7 : D-glucuronate catabolism
1.1.1.8 : L-arabinose catabolism
1.1.1.9 : L-idonate catabolism
1.1.1.10 : L-lyxose metabolism
1.1.1.11 : Fucose catabolism
1.1.1.12 : Galactitol catabolism
1.1.1.13 : Galactonate catabolism
1.1.1.14 : Lactose degradation
1.1.1.15 : Mannose catabolism
1.1.1.16 : Rhamnose catabolism
1.1.1.17 : Sorbitol degradation
1.1.1.18 : Trehalose degradation, low osmolarity+
1.1.1.19 : Xylose catabolism
1.1.1.20 : Glycol degradation
1.1.1.21 : Mannitol degradation
1.1.1.22 : Ribose degradation
1.1.1.23 : Galactose degradation
1.1.1.24 : Sorbose degradation
1.1.1.25 : L-ascorbate degradation
1.1.2 : Fatty acids (fatty acid oxidation)
1.1.2.1 : Degradation of short-chain fatty acids
1.1.2.2 : 3-phenylpropionate and 3-(3-hydroxyphenyl)propionate degradation
1.1.2.3 : Propionate degradation
1.1.3 : Amino acids
1.1.3.1 : L-alanine degradation
1.1.3.2 : L-serine degradation
1.1.3.3 : Arginine catabolism
1.1.3.4 : Glutamate degradation
1.1.3.5 : Glycine cleavage
1.1.3.6 : Proline utilization
1.1.3.7 : Threonine catabolism
1.1.3.8 : Tryptophan utilization
1.1.3.9 : L-cysteine catabolism
1.1.3.10 : Lysine cleavage
1.1.3.11 : Histidine degradation
1.1.3.12 : Leucine degradation
1.1.3.13 : Methionine degradation
1.1.3.14 : Valine degradation
1.1.3.15 : Phenylalanine, tyrosine degradation
1.1.4 : Amines
1.1.4.1 : Phenylethylamine degradation
1.1.4.2 : Carnitine degradation
1.1.4.3 : Ornithine degradation
1.1.5 : Others
1.1.5.1 : Phenylacetic acid degradation
1.1.5.2 : Ethanol degradation
1.1.5.3 : Eugenol catabolism
1.1.5.4 : Beta-ketoadipate pathway
1.1.5.5 : Mandelate catabolism
1.2 : Macromolecule degradation
1.2.1 : RNA
1.2.2 : DNA
1.2.3 : Proteins/peptides/glycopeptides
1.2.4 : Polysaccharides
1.2.4.1 : Glycogen catabolism
1.2.4.2 : Chitin catabolism
1.3 : Energy metabolism (carbon)
1.3.1 : Glycolysis
1.3.2 : Pentose phosphate shunt, oxidative branch
1.3.3 : Pyruvate dehydrogenase
1.3.4 : Tricarboxylic acid cycle
1.3.5 : Fermentation
1.3.6 : Aerobic respiration
1.3.7 : Anaerobic respiration
1.3.8 : ATP proton motive force interconversion
1.3.9 : Entner-Doudoroff pathway
1.4 : Energy production/transport
1.4.1 : Electron donor
1.4.2 : Electron acceptor
1.4.3 : Electron carrier
1.5 : Building block biosynthesis
1.5.1 : Amino acids
1.5.1.1 : Glutamate
1.5.1.2 : Glutamine
1.5.1.3 : Arginine
1.5.1.4 : Proline
1.5.1.5 : Aspartate
1.5.1.6 : Asparagine
1.5.1.7 : Lysine, diaminopimelate
1.5.1.8 : Threonine
1.5.1.9 : Methionine
1.5.1.10 : Glycine
1.5.1.11 : Serine
1.5.1.12 : Cysteine
1.5.1.13 : Phenylalanine
1.5.1.14 : Tyrosine
1.5.1.15 : Tryptophan
1.5.1.16 : Histidine
1.5.1.17 : Alanine
1.5.1.18 : Isoleucine/valine
1.5.1.19 : Leucine
1.5.1.20 : Chorismate
1.5.1.21 : Homoserine
1.5.2 : Nucleotide
1.5.2.1 : Purine biosynthesis
1.5.2.2 : Pyrimidine biosynthesis
1.5.2.3 : Purine ribonucleotide biosynthesis
1.5.2.4 : Pyrimidine ribonucleotide/ribonucleoside biosynthesis
1.5.3 : Cofactor, small molecule carrier
1.5.3.1 : Biotin
1.5.3.2 : Folic acid
1.5.3.3 : Lipoate
1.5.3.4 : Molybdenum (molybdopterin)
1.5.3.5 : Coenzyme A
1.5.3.6 : Pyridoxine (vitamin B6)
1.5.3.7 : Nicotinamide adenine dinucleotide (NAD)
1.5.3.8 : Thiamine (Vitamin B1)
1.5.3.9 : Riboflavin (Vitamin B2), FAD, FMN
1.5.3.10 : Glutathione
1.5.3.11 : Menaquinone (MK), ubiquinone (Q)
1.5.3.12 : Heme, porphyrin
1.5.3.13 : Cobalamin (Vitamin B12)
1.5.3.14 : Enterochelin (enterobactin)
1.5.3.15 : Chrysobactin
1.5.3.16 : Achromobactin
1.5.3.19 : Isoprenoid biosynthesis
1.5.3.20 : Tetrahydrobiopterin biosynthesis
1.5.3.21 : Pyochelin biosynthesis
1.5.4 : Fatty acid and phosphatidic acid
1.6 : Macromolecules (cellular constituent) biosynthesis
1.6.1 : Phospholipid
1.6.2 : Colanic acid (M antigen)
1.6.3 : Lipopolysaccharide
1.6.3.1 : O antigen
1.6.3.2 : Core region
1.6.3.3 : Lipid A
1.6.4 : Enterobacterial common antigen (surface glycolipid)
1.6.5 : K antigen
1.6.6 : Osmoregulated periplasmic glucan
1.6.7 : Peptidoglycan (murein)
1.6.9 : Polysaccharides, cytoplasmic
1.6.10 : Lipoprotein
1.6.11 : Glycoprotein
1.6.12 : Flagella
1.6.13 : Fimbria, pili, curli
1.6.15 : Large molecule carriers
1.6.15.1 : Cytochromes
1.6.15.2 : Thioredoxin, glutaredoxin
1.6.15.3 : Biotin carboxyl carrier protein
1.6.15.4 : Acyl carrier protein
1.6.16 : Cellulose biosynthesis
1.7 : Central intermediary metabolism
1.7.1 : Unassigned reversible reactions
1.7.2 : Glyoxylate bypass
1.7.3 : Pentose phosphate shunt, non-oxidative branch
1.7.6 : Glycerol metabolism
1.7.7 : Galactose metabolism
1.7.8 : Gluconeogenesis
1.7.9 : Misc. glucose metabolism
1.7.10 : Sugar nucleotide biosynthesis, conversions
1.7.12 : Amino sugar conversions
1.7.13 : Amino acid conversion
1.7.14 : Polyamine biosynthesis
1.7.15 : 2'-deoxyribonucleotide/ribonucleoside metabolism
1.7.17 : Formyl-tetrahydrofolate biosynthesis
1.7.18 : Betaine biosynthesis
1.7.19 : Incorporation of metal ions
1.7.20 : S-adenosyl methionine biosynthesis
1.7.21 : Glyoxylate degradation
1.7.22 : Carnitine metabolism
1.7.23 : Methylglyoxal metabolism
1.7.24 : Cyanate catabolism
1.7.25 : Glycolate metabolism
1.7.26 : Allantoin assimilation
1.7.27 : Pyridoxal 5'-phosphate salvage
1.7.28 : Pyruvate catabolism
1.7.29 : Acetate catabolism
1.7.31 : Aminobutyrate catabolism
1.7.32 : Putrescine catabolism
1.7.33 : Nucleotide and nucleoside conversions
1.7.34 : Peptidoglycan (murein) turnover, recycling
1.7.35 : Lactate oxidation
1.7.36 : Trehalose biosynthesis
1.7.37 : C1 assimilation, serine pathway
1.7.38 : Methionine salvage pathway
1.8 : Metabolism of other compounds
1.8.1 : Phosphorous metabolism
1.8.2 : Sulfur metabolism
1.8.3 : Nitrogen metabolism
2 : Information transfer
2.1 : DNA related
2.1.1 : DNA replication
2.1.2 : DNA restriction/modification
2.1.3 : DNA recombination
2.1.4 : DNA repair
2.1.5 : DNA degradation
2.2 : RNA related
2.2.2 : Transcription related
2.2.3 : RNA modification
2.2.4 : RNA degradation
2.2.5 : tRNA
2.2.6 : rRNA, stable RNA
2.2.7 : Antisense RNA
2.3 : Protein related
2.3.1 : Amino acid-activation
2.3.2 : Translation
2.3.3 : Posttranslational modification
2.3.4 : Chaperoning, folding
2.3.5 : Export, signal peptide cleavage
2.3.6 : Turnover, degradation
2.3.7 : Nucleoproteins, basic proteins
2.3.8 : Ribosomal proteins
2.3.9 : Non-ribosomal peptide synthetase
3 : Regulation
3.1. : Type of regulation
3.1.1 : DNA structure level
3.1.1.1 : DNA bending, supercoiling, inversion
3.1.1.2 : Methylation
3.1.2 : Transcriptional level
3.1.2.1 : Sigma factors, anti-sigmafactors
3.1.2.2 : Activator
3.1.2.3 : Repressor
3.1.2.4 : Complex regulation
3.1.2.4.1 : More than one signal needed
3.1.2.4.2 : Regulons or multilayer component regulatory systems
3.1.2.4.3 : Two-component regulatory systems (external signal)
3.1.2.4.4 : Quorum sensing
3.1.2.5 : Action unknown
3.1.3 : Posttranscriptional
3.1.3.1 : Translation attenuation and efficiency
3.1.3.2 : Covalent modification, demodification, maturation
3.1.3.3 : Inhibition / activation of enzymes
3.1.3.4 : Proteases, cleavage of compounds
3.1.3.5 : Multilayer regulatory systems
3.1.3.6 : Antisense RNA
3.1.4 : Regulation level unknown
3.3 : Genetic unit regulated
3.3.1 : Operon (regulation of one operon)
3.3.2 : Regulon (a network of operons encoding related functions)
3.3.3 : Stimulon (ie. environmental stimulus)
3.3.4 : Global
3.4 : Trigger (some information added)
3.5 : Trigger modulation (some information added)
4 : Transport
4.1 : Channel-type Transporters
4.1.A. : alpha-type channels
4.1.A.1. : The Voltage-gated Ion Channel (VIC) Superfamily
4.1.A.8. : The Major Intrinsic Protein (MIP) Family
4.1.A.11 : The Chloride Channel (ClC) Family
4.1.B.17 : The Outer Membrane Factor (OMF) Family
4.1.A.22 : The Large Conductance Mechanosensitive Ion Channel (MscL) Family
4.1.A.23 : The Small Conductance Mechanosensitive Ion Channel (MscS) Family
4.1.A.46 : The H+- or Na+-translocating Bacterial Flagellar Motor (Mot) Family
4.1.B : Beta barrel porins (The Outer Membrane Porin (OMP) Functional Superfamily)
4.1.B.1 : The General Bacterial Porin (GBP) Family
4.1.B.3 : The Sugar Porin (SP) Family
4.1.B.9 : The FadL Outer Membrane Protein (FadL) Family
4.1.B.10 : The Nucleoside-specific Channel-forming Outer Membrane Porin (Tsx) Family
4.1.B.14 : The Outer Membrane Receptor (OMR) Family
4.1.B.21 : The OmpG Porin (OmpG) Family
4.2 : Electrochemical potential driven transporters
4.2.A. : Porters (Uni-, Sym- and Antiporters)
4.2.A.1 : The Major Facilitator Superfamily (MFS)
4.2.A.2 : The Glycoside-Pentoside-Hexuronide (GPH):Cation Symporter Family
4.2.A.3 : The Amino Acid-Polyamine-Choline (APC) Family
4.2.A.4 : The Cation Diffusion Facilitator (CDF) Family
4.2.A.6 : The Resistance-Nodulation-Cell Division (RND) Superfamily
4.2.A.7 : The Drug/Metabolite Transporter (DMT) Superfamily
4.2.A.8 : The Gluconate:H+ Symporter (GntP) Family
4.2.A.9 : The Cytochrome oxidase biogenesis (Oxa1) Family
4.2.A.10 : The 2-Keto-3-Deoxygluconate Transporter (KDGT) Family
4.2.A.13 : The C4-Dicarboxylate Uptake (Dcu) Family
4.2.A.14 : The Lactate Permease (LctP) Family
4.2.A.15 : The Betaine/Carnitine/Choline Transporter (BCCT) Family
4.2.A.16 : The Telurite-resistance/Dicarboxylate Transporter (TDT) Family
4.2.A.17 : The Proton-dependent Oligopeptide Transporter (POT) Family
4.2.A.19 : The Ca2+:Cation Antiporter (CaCA) Family
4.2.A.20 : The Inorganic Phosphate Transporter (PiT) Family
4.2.A.21 : The Solute:Sodium Symporter (SSS) Family
4.2.A.23 : The Dicarboxylate/Amino Acid:Cation (Na+ or H+) Symporter (DAACS) Family
4.2.A.25 : The Alanine/Glycine:Cation symporter (AGCS) Family
4.2.A.26 : The Branched Chain Amino Acid:Cation Symporter (LIVCS) Family
4.2.A.27 : The Glutamate:Na+ Symporter (GltS) Family
4.2.A.33 : The NhaA Na+:H+ Antiporter (NhaA) Family
4.2.A.34 : The NhaB Na+:H+ Antiporter (NhaB) Family
4.2.A.36 : The Monovalent Cation:Proton Antiporter-1 (CPA1) Family
4.2.A.37 : The Monovalent Cation:Proton Antiporter-2 (CPA2) Family
4.2.A.38 : The K+ Transporter (Trk) Family
4.2.A.39 : The Nucleobase:Cation Symporter-1 (NCS1) Family
4.2.A.40 : The Nucleobase:Cation Symporter-2 (NCS2) Family
4.2.A.41 : The Concentrative Nucleoside Transporter (CNT) Family
4.2.A.42 : The Hydroxy/Aromatic Amino Acid Permease (HAAAP) Family
4.2.A.44 : The Formate-Nitrite Transporter (FNT) Family
4.2.A.45 : The Metal Ion Transporter (MIT) Family
4.2.A.47 : The Divalent Anion:Na+ Symporter (DASS) Family
4.2.A.49 : The Ammonium Transporter (Amt) Family
4.2.A.53 : The Sulfate Permease (SulP) Family
4.2.A.55 : The Manganese (Nramp) Fam.
4.2.A.58 : The Phosphate:Na+ Symporter (PNaS) Family
4.2.A.61 : The C4-dicarboxylate Uptake C (DcuC) Family
4.2.A.64 : The Type V Secretory Pathway or Twin Arginine Targeting (Tat) Family
4.2.A.66 : The Multi Antimicrobial Extrusion (MATE) Family
4.2.A.68 : The p-Aminobenzoyl-glutamate Transporter (AbgT) Family
4.2.A.69 : The Auxin Efflux Carrier (AEC) Family
4.2.A.72 : The K+ uptake permease (KUP) family
4.2.A.75 : The L-lysine exporter (LysE) family
4.2.A.76 : The Resistance to Homoserine/Threonine (RhtB) Family
4.2.C : Ion-gradient driven energizers
4.2.C.1 : TonB Family of Auxiliary Proteins for Energization of OMR-mediated Transport
4.3 : Primary Active Transporters
4.3.A. : Pyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active Transporters
4.3.A.1 : The ATP-binding Cassette (ABC) Superfamily + ABC-type Uptake Permeases
4.3.A.1.a : ATP binding component
4.3.A.1.m : membrane component
4.3.A.1.p : periplasmic binding component
4.3.A.1.am : ATP binding and membrane component
4.3.A.2 : The H+/Na+-translocating F-, V- and A-type ATPase (F-ATPase) Superfamily
4.3.A.3 : The P-type ATPase (P-ATPase) Superfamily
4.3.A.4 : The Arsenite-Antimonite (Ars) Efflux Family
4.3.A.5 : The Type II (General) Secretory Pathway (IISP) Family
4.3.A.6 : The Type III (Virulence-related) Secretory Pathway (IIISP) Family
4.3.A.7 : The Type IV (Conjugal DNA-Protein Transfer) Secretory Pathway (IVSP) Family
4.3.D. : Oxidoreduction-driven Active Transporters
4.3.D.1 : The Proton- or sodium ion-translocating NADH Dehydrogenase (NDH) Family
4.3.D.4 : The Proton-translocating Cytochrome Oxidase (COX) Superfamily
4.4 : Group Translocators
4.4.A : Phosphotransferase Systems (PEP-dependent PTS)
4.4.A.1 : The PTS Glucose-Glucoside (Glc) Family
4.4.A.2 : The PTS Fructose-Mannitol (Fru) Family
4.4.A.3 : The PTS Lactose-N,N'-Diacetylchitobiose-betaucoside (Lac) Family
4.4.A.4 : The PTS Glucitol (Gut) Family
4.4.A.5 : The PTS Galactitol (Gat) Family
4.4.A.6 : The PTS Mannose-Fructose-Sorbose (Man) Family
4.8.A : Accessory Factors Involved in Transport
4.8.A.1 : The Membrane Fusion Protein (MFP) Family
4.8.A.2 : The Secretin Auxiliary Lipoprotein (SAL) Family
4.8.A.3 : MPA1 Family auxillary transport protein
4.8.A.7 : The Phosphotransferase System Enzyme I (EI) Family
4.8.A.8 : The Phosphotransferase System HPr (HPr) Family
4.9.A : Transporters of Unknown Classification
4.9.A.1 : The Polysaccharide Transporter (PST) Family
4.9.A.4 : The Nicotinamide Mononucleotide (NMN) Uptake Permease (PnuC) Family
4.9.A.8 : The Ferrous Iron Uptake (FeoB) Family
4.9.A.13 : The Short Chain Fatty Acid Transporter (scFAT) Family
4.9.A.16 : The Septal DNA Translocator (SDT) Family
4.9.A.17 : The Metal Ion Transporter (MIT) Family
4.9.B : Putative uncharacterized transport protein
4.9.B.3 : The Putative Bacterial Murein Precursor Exporter (MPE) Family
4.9.B.4 : The Putative Efflux Transporter (PET) Family
4.9.B.6 : The Toxic Hok/Gef Protein (Hok/Gef) Family
4.9.B.10 : The 6TMS Putative MarC Transporter (MarC) Family
4.9.B.18 : The SecDF-associated Single Transmembrane Protein (SSTP) Family
4.9.B.21 : The Frataxin (Frataxin) Family
4.9.B.22 : The Putative Permease (PerM) Family
4.9.B.24 : The Testis-Enhanced Gene Transfer (TEGT) Family
4.9.B.25 : The YbbM (YbbM) Family
4.9.B.27 : The YdjX-Z (YdjX-Z) Family
4.9.B.28 : The YqaE (YqaE) Family
4.9.B.29 : The YebN (YebN) Family
4.9.B.31 : The YqiH (YqiH) Family
4.9.B.32 : The Putative Vectorial Glycosyl Polymerization (VGP) Family
4.S : substrate
4.S.1 : (D)-glucarate/galactarate
4.S.10 : allose/ribose
4.S.100 : L-arabinose
4.S.101 : L-arabinose /H+
4.S.102 : L-arabinose/ isopropyl-beta-D-thiogalactopyranoside
4.S.103 : L-asparagine
4.S.104 : lipooligosaccharides
4.S.105 : lipopolysaccharide
4.S.106 : lipoprotein
4.S.107 : L-lactate
4.S.108 : L-leucine/L-valine/L-iso-leucine
4.S.109 : L-rhamnose/H+
4.S.11 : alpha-ketoglutarate
4.S.110 : L-threonine/L-serine
4.S.111 : lysine
4.S.112 : lysine/arginine/ornithine
4.S.113 : maltose
4.S.114 : maltose/maltodextrin
4.S.115 : mannitol
4.S.116 : mannose
4.S.117 : mellobiose
4.S.118 : methionine
4.S.119 : methylgalactoside/galactose
4.S.12 : amino acid
4.S.120 : Mg++
4.S.121 : Mg2+/Ni2+/Co2+
4.S.122 : microcin B17
4.S.123 : Mn+/H+
4.S.124 : molybdate
4.S.125 : molybdenum
4.S.126 : multidrug
4.S.127 : multidrug/bicyclomycin
4.S.128 : muropeptide
4.S.129 : myo-inositor
4.S.13 : amino acid/amide
4.S.130 : Na+
4.S.131 : Na+/ alanine/glycine
4.S.132 : Na+/ H+
4.S.133 : Na+/Ca+
4.S.134 : Na+/dicarboxylate
4.S.135 : Na+/glutamate/aspartate
4.S.136 : Na+/H+
4.S.137 : Na+/leucine/valine/iso-leucine
4.S.138 : Na+/pantothenate
4.S.139 : Na+/proline
4.S.14 : ammonium
4.S.140 : Na+/serine/threonine
4.S.141 : N-acetylgalactosamine
4.S.142 : N-acetylglucosamine
4.S.143 : Ni++
4.S.144 : nicotinamide mononucleotide
4.S.145 : nitrite
4.S.146 : nucleoside
4.S.147 : nucleoside/H+
4.S.148 : oligopeptide
4.S.149 : oligopeptides
4.S.15 : antibiotic
4.S.150 : p-aminobenzoyl-glutamate
4.S.151 : Pb/Cd/Zn/Hg
4.S.152 : peptide
4.S.153 : phenylalanine
4.S.154 : phenylalanine/ tyrosine
4.S.155 : phosphate
4.S.156 : polymyxin
4.S.157 : potassium
4.S.158 : proline
4.S.159 : proline/betaine
4.S.16 : arabinose polymer
4.S.160 : protein
4.S.161 : protein/DNA
4.S.162 : purine/xanthine
4.S.163 : putrescine
4.S.164 : putrescine/ornithine
4.S.165 : putrescine/ornitine
4.S.166 : putrescine/spermidine
4.S.167 : serine
4.S.168 : shikimate/dehydroshikimate
4.S.169 : sialic acid
4.S.17 : arginine
4.S.170 : S-methylmethionine
4.S.171 : spermidine/putrescine
4.S.172 : sucrose
4.S.173 : sugar
4.S.174 : sulfate
4.S.175 : taurine
4.S.176 : tellurite
4.S.177 : thiamine
4.S.178 : thiosulfate
4.S.179 : thiosulfate/sulfate
4.S.18 : arginine/ornitine
4.S.180 : threonine
4.S.181 : trehalose
4.S.182 : tripeptide
4.S.183 : tryptophan
4.S.184 : tyrosine
4.S.185 : uracil
4.S.186 : urasil
4.S.187 : vitamin B12
4.S.188 : water
4.S.189 : xanthosine
4.S.19 : arsenite
4.S.190 : xylose/H+
4.S.191 : Zn
4.S.192 : chrysobactin
4.S.193 : achromobactin
4.S.2 : 2-keto-3-deoxy-D-gluconate
4.S.20 : benzoate
4.S.21 : beta-galactosidase/lactose and glucose
4.S.22 : beta-glucoside
4.S.23 : betaine/choline/glycine
4.S.24 : betaine/choline/glycine transport protein
4.S.25 : Ca+/ H+
4.S.26 : cadaverine/lysine
4.S.27 : carnitine
4.S.28 : cation
4.S.29 : cellobiose/arbutin/salicin
4.S.3 : 3-hydroxyphenylpropionic acid
4.S.30 : cellobiose/salicin/arbutin
4.S.31 : chloramphenicol
4.S.32 : chloride
4.S.33 : choline
4.S.34 : citrate/succinate
4.S.35 : colicin4
4.S.36 : Cu
4.S.37 : curli subunit
4.S.38 : cyanate
4.S.39 : cysteine
4.S.4 : 3-phenylpropionic acid
4.S.40 : cysteine/O-acetyl-L-serine/cysteine metabolites
4.S.41 : cytosine
4.S.42 : D-alanine/D-serine/glycine
4.S.43 : D-galactonate
4.S.44 : D-glucarate
4.S.45 : D-glucose/trehalose
4.S.46 : dicarboxylate
4.S.47 : dipeptide
4.S.48 : D-ribose
4.S.49 : drug
4.S.5 : alkanesulfonate
4.S.50 : D-xylose
4.S.51 : enterochelin
4.S.52 : fatty acid
4.S.53 : Fe
4.S.54 : Fe++
4.S.55 : ferric dicitrate
4.S.56 : ferric enterobactin
4.S.57 : ferric hydroxamate
4.S.58 : ferrichrome
4.S.59 : formate
4.S.6 : alkanesulphonate
4.S.60 : formate/oxalate
4.S.61 : fosfidomycin/H+
4.S.62 : frucose
4.S.63 : fructose
4.S.64 : fucose
4.S.65 : galactitol
4.S.66 : galactose/H+
4.S.67 : gamma-aminobutyrate
4.S.68 : glucitol/sorbitol
4.S.69 : gluconate
4.S.7 : alklphosphonate
4.S.70 : gluconate/L-idonate
4.S.71 : glucose
4.S.72 : glucose/maltose
4.S.73 : glucuronide
4.S.74 : glutamate/aminobutyric acid
4.S.75 : glutamate/aspartate
4.S.76 : glutamine
4.S.77 : glycerol
4.S.78 : glycerol-3-P
4.S.79 : glycine betaine choline transport
4.S.8 : alkylphosphonate
4.S.80 : glycine/betaine/proline
4.S.81 : group A colicins
4.S.82 : H+
4.S.83 : H+/acridine
4.S.84 : H+/lactose/glucose
4.S.85 : heme
4.S.86 : hexose phosphate
4.S.87 : hexuronate
4.S.88 : histidine
4.S.89 : histidine/lysine/arginine/ornithine
4.S.9 : allantoin/ion
4.S.90 : homoserine/lactone
4.S.91 : hydrophilic molecule
4.S.92 : hydrophilic molecules
4.S.93 : ion
4.S.94 : ions
4.S.95 : iron dicitrate
4.S.96 : K+
4.S.97 : K+/H+
4.S.98 : lactate
4.S.99 : lactose
5 : Cell processes
5.1 : Cell division
5.2 : Cell cycle physiology
5.3 : Motility (incl. chemotaxis, energytaxis, aerotaxis, redoxtaxis)
5.4 : Genetic exchange, recombination
5.5 : Adaptation to stress
5.5.1 : Osmotic pressure
5.5.2 : Temperature extremes
5.5.3 : Starvation response
5.5.4 : pH response
5.5.5 : Dessication
5.5.6 : Other stresses (mechanical, nutritional, oxidative)
5.5.7 : Fe aquisition
5.6 : Protection
5.6.1 : Radiation
5.6.2 : Detoxification (xenobiotic metabolism)
5.6.3 : Cell killing
5.6.4 : Drug resistance/sensitivity
5.8 : SOS response
5.10 : Defense/survival
5.11 : DNA uptake
5.12 : Biofilm production
5.13 : Virulence associated
6 : Cell structure
6.1 : Membrane
6.2 : Peptidoglycan (murein)
6.3 : Surface antigens (ECA, O antigen of LPS)
6.4 : Flagellum
6.5 : Pilus
6.6 : Ribosome
6.7 : Capsule (M and K antigens)
7 : Location of gene products
7.1 : Cytoplasm
7.2 : Periplasmic space
7.3 : Inner membrane
7.4 : Outer membrane
7.5 : Extracellular
8 : extrachromosomal
8.1 : Prophage genes and phage related functions
8.1.1 : DNA packaging, phage assembly
8.1.2 : Replication
8.1.3 : Regulation
8.1.4 : Integration, recombination
8.1.5 : Lysis
8.1.6 : Structural component
8.2 : Plasmid related
8.2.1 : replication and maintenance
8.2.2 : plasmid transfer
8.3 : Transposon related
8.3.1 : transposases
8.3.2 : regulation of mobility
8.4 : Colicin related
9 : DNA sites
10 : cryptic genes