MaGe

Gene History: ACIAD3159

» CURRENT ANNOTATION

MaGe curated annotation

Type	Begin	End	Length	Frame	Mutation	Gene	Synonyms	Status
			1083 (360aa)	+1
Product	phosphate starvation-inducible protein (PhoH-like)
Product Type
EC number
Reaction	_
Localization
BioProcess	Selection is empty.
Roles	1.8.1 : phosphorous metabolism3.1.2.4.3 : two component regulatory systems (external signal)
PubMedId
Note
Additional Data	Selection is empty.
DBxref	Selection is empty.
Class

» PREVIOUS ANNOTATION

MaGe curated annotation

Type	Begin	End	Length	Frame	Mutation	Gene	Synonyms	Status
			1083 (360aa)	+1
Product	PhoH-like protein
Product Type
EC number
Reaction	_
Localization
BioProcess	Selection is empty.
Roles	1.8.1 : phosphorous metabolism3.1.2.4.3 : two component regulatory systems (external signal)
PubMedId
Note	similar to Hypothetical protein PA3981 from Pseudomonas aeruginosa, swall : Q9HX38 (340 aa), Evalue = 1.95397e-104, %identity = 64.17, on 307 aa ; and similar to PhoH-like protein from Escherichia coli, and Escherichia coli O157:H7, swall : PHOL_ECOLI (359 aa), Evalue = 1.60216e-98, %identity = 55.72, on 337 aa ; and similar to YbeZ protein (Putative phosphate starvation-inducible protein, ATP-binding) (PhoH-like ATP-binding protein) from Salmonella typhimurium, and Salmonella typhi, swall : Q9RCI1 (361 aa), Evalue = 4.66157e-98, %identity = 56.51, on 333 aa
Additional Data	Selection is empty.
DBxref	Selection is empty.
Class

» PREVIOUS ANNOTATION

MaGe curated annotation

Type	Begin	End	Length	Frame	Mutation	Gene	Synonyms	Status
			1083 (360aa)	+1
Product	PhoH-like protein,phosphate starvation-inducible protein, ATP-binding
Product Type
EC number
Reaction	_
Localization
BioProcess	Selection is empty.
Roles	1.8.1 : phosphorous metabolism3.1.2.4.3 : two component regulatory systems (external signal)
PubMedId
Note	similar to Hypothetical protein PA3981 from Pseudomonas aeruginosa, swall : Q9HX38 (340 aa), Evalue = 1.95397e-104, %identity = 64.17, on 307 aa ; and similar to PhoH-like protein from Escherichia coli, and Escherichia coli O157:H7, swall : PHOL_ECOLI (359 aa), Evalue = 1.60216e-98, %identity = 55.72, on 337 aa ; and similar to YbeZ protein (Putative phosphate starvation-inducible protein, ATP-binding) (PhoH-like ATP-binding protein) from Salmonella typhimurium, and Salmonella typhi, swall : Q9RCI1 (361 aa), Evalue = 4.66157e-98, %identity = 56.51, on 333 aaACIAD3158 to 3160,are syntenic to three genes from V.cholerae(chr1),X.campestris,Ps.aeruginosa, X.fastidiosa,E.coli and R.solanacearum.ACIAD 3159 and 3160 are syntenic to two genes fromP.multocida and Ps.putida.
Additional Data	Selection is empty.
DBxref	Selection is empty.
Class

» PREVIOUS ANNOTATION

MaGe curated annotation

Type	Begin	End	Length	Frame	Mutation	Gene	Synonyms	Status
			1083 (360aa)	+1
Product	PhoH-like protein,phosphate starvation-inducible protein, ATP-binding
Product Type
EC number
Reaction	_
Localization
BioProcess	Selection is empty.
Roles	1.8.1 : phosphorous metabolism3.1.2.4.3 : two component regulatory systems (external signal)
PubMedId
Note	similar to Hypothetical protein PA3981 from Pseudomonas aeruginosa, swall : Q9HX38 (340 aa), Evalue = 1.95397e-104, %identity = 64.17, on 307 aa ; and similar to PhoH-like protein from Escherichia coli, and Escherichia coli O157:H7, swall : PHOL_ECOLI (359 aa), Evalue = 1.60216e-98, %identity = 55.72, on 337 aa ; and similar to YbeZ protein (Putative phosphate starvation-inducible protein, ATP-binding) (PhoH-like ATP-binding protein) from Salmonella typhimurium, and Salmonella typhi, swall : Q9RCI1 (361 aa), Evalue = 4.66157e-98, %identity = 56.51, on 333 aaACIAD3158 to 3160,are syntenic to three genes from V.cholerae(chr1),X.campestris,Ps.aeruginosa, X.fastidiosa,E.coli and R.solanacearum.ACIAD 3159 and 3160 are syntenic to two genes fromP.multocida and Ps.putida.
Additional Data	Selection is empty.
DBxref	Selection is empty.
Class

» PREVIOUS ANNOTATION

MaGe curated annotation

Type	Begin	End	Length	Frame	Mutation	Gene	Synonyms	Status
			1083 (360aa)	+1
Product	PhoH-like protein,phosphate starvation-inducible protein, ATP-binding
Product Type
EC number
Reaction	_
Localization
BioProcess	Selection is empty.
Roles	1.8.1 : phosphorous metabolism
PubMedId
Note	similar to Hypothetical protein PA3981 from Pseudomonas aeruginosa, swall : Q9HX38 (340 aa), Evalue = 1.95397e-104, %identity = 64.17, on 307 aa ; and similar to PhoH-like protein from Escherichia coli, and Escherichia coli O157:H7, swall : PHOL_ECOLI (359 aa), Evalue = 1.60216e-98, %identity = 55.72, on 337 aa ; and similar to YbeZ protein (Putative phosphate starvation-inducible protein, ATP-binding) (PhoH-like ATP-binding protein) from Salmonella typhimurium, and Salmonella typhi, swall : Q9RCI1 (361 aa), Evalue = 4.66157e-98, %identity = 56.51, on 333 aaACIAD3158 to 3160,are syntenic to three genes from V.cholerae(chr1),X.campestris,Ps.aeruginosa, X.fastidiosa,E.coli and R.solanacearum.ACIAD 3159 and 3160 are syntenic to two genes from.
Additional Data	Selection is empty.
DBxref	Selection is empty.
Class

» PREVIOUS ANNOTATION

MaGe curated annotation

Type	Begin	End	Length	Frame	Mutation	Gene	Synonyms	Status
			1083 (360aa)	+1
Product	conserved hypothetical protein
Product Type
EC number
Reaction	_
Localization
BioProcess	Selection is empty.
Roles	Selection is empty.
PubMedId
Note	similar to Hypothetical protein PA3981 from Pseudomonas aeruginosa, swall : Q9HX38 (340 aa), Evalue = 1.95397e-104, %identity = 64.17, on 307 aa ; and similar to PhoH-like protein from Escherichia coli, and Escherichia coli O157:H7, swall : PHOL_ECOLI (359 aa), Evalue = 1.60216e-98, %identity = 55.72, on 337 aa ; and similar to YbeZ protein (Putative phosphate starvation-inducible protein, ATP-binding) (PhoH-like ATP-binding protein) from Salmonella typhimurium, and Salmonella typhi, swall : Q9RCI1 (361 aa), Evalue = 4.66157e-98, %identity = 56.51, on 333 aa.
Additional Data	Selection is empty.
DBxref	Selection is empty.
Class

» PRIMARY ANNOTATION

MicroScope pipeline

Type	Begin	End	Length	Frame	Mutation	Gene	Synonyms	Status
			1083 (360aa)	+1
Product	PhoH-like protein
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

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

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

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