MultiFun, a cellfunction assignment schema.

Gretta Serres and Monica Riley, March 2007

Some categories have been assigned by Nicole Perna et al. at ASAP (http://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm).

See download section for text file of MultiFun.

 

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 D-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

                  1.1.1.26 2-O-alpha-mannosyl-D-glycerate degradation

                  1.1.1.27 Trehalose degradation, high osmolarity

                  1.1.1.28 L-galactonate catabolism

                  1.1.1.29 Malate utilization

            1.1.2 Fatty acids (fatty acid oxidation)

                  1.1.2.2 3-phenylpropionate and 3-(3-hydroxyphenyl)propionate degradation

                  1.1.2.3 Propionate degradation

                  1.1.2.4 Anaerobic fatty acid oxidation pathway

                  1.1.2.5 Propionyl-CoA (methylmalonyl pathway)

                  1.1.2.6 Aerobic fatty acid oxidation pathway

                  1.1.2.7 Acetoacetate 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 degradation II

                  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

                  1.1.3.16 Glutamine

                  1.1.3.17 Taurine

                  1.1.3.18 Arginine degradation III (agmatinase pathway)

                  1.1.3.19 Aspartate degradation

                  1.1.3.20 Isoleucine 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

                  1.1.5.6 (deoxy)ribose phosphate degradation

                  1.1.5.7 Formaldehyde degradation

      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

            1.3.10 Formate oxidation

            1.3.11 Acyclic isoprenoid degradation

      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 biosynthesis III

                  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 biosynthesis I

                  1.5.1.18 Leucine/valine

                  1.5.1.19 Isoleucine

                  1.5.1.20 Chorismate

                  1.5.1.21 Homoserine

                  1.5.1.22 Ornithine

                  1.5.1.23 Selenocysteine

                  1.5.1.24 Glutamate biosynthesis I

                  1.5.1.25 Alanine biosynthesis III

            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 (tetrahydrofolate)

                  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

                  1.5.3.22 Glutathione redox reactions

                  1.5.3.23 Pantothenate biosynthesis I

                  1.5.3.24 Folate polyglutamylation

            1.5.4 Fatty acid and phosphatidic acid

                  1.5.4.1 Fatty acid  elongation - unsaturated

                  1.5.4.2 Fatty acid  elongation - saturated

                  1.5.4.3 Fatty acid biosynthesis -- initial steps

      1.6 Macromolecules (cellular constituent)  biosynthesis

            1.6.1 Phospholipid

                  1.6.1.1 Cyclopropane fatty acid (CFA) biosynthesis

                  1.6.1.2 Phospholipid biosynthesis I

            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

            1.6.17 GDP-mannose metabolism

            1.6.18 Siderophore

      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

                  1.7.6.1 Glycerol degradation I

                  1.7.6.2Glycerol degradation II

            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

                  1.7.14.1 Putrescine biosynthesis I

                  1.7.14.2 Putrescine biosynthesis III

                  1.7.14.3 Spermidine 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

                  1.7.32.1 Putrescine degradation I

                  1.7.32.2 Putrescine degradation II

            1.7.33 Nucleotide and nucleoside conversions

                  1.7.33.1 Salvage pathways of adenine, hypoxanthine, and their nucleosides

                  1.7.33.2 Salvage pathways of guanine, xanthine, and their nucleosides

                  1.7.33.3 Salvage pathways of pyrimidine deoxyribonucleotides

                  1.7.33.4 Salvage pathways of pyrimidine ribonucleotides

            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

            1.7.39 Conversion of succinate to propionate

            1.7.40 Fructoselysine and psicoselysine degradation

            1.7.41 PRPP biosynthesis I

            1.7.42 PRPP biosynthesis II

            1.7.43 ppGpp biosynthesis

            1.7.44 NAD phosphorylation and dephosphorylation

            1.7.45 Pyridine nucleotide cycling

            1.7.46 Pyridine nucleotide synthesis

      1.8 Metabolism of other compounds

            1.8.1 Phosphorous metabolism

            1.8.2 Sulfur metabolism

                  1.8.2.1 Sulfate assimilation

            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

                  3.1.3.7 binding, sequestering

            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 Recognized transporters of unknown biochemical mechanism

                  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)-galactarate

                  4.S.2 2-keto-3-deoxy-D-gluconate

                  4.S.3 3-hydroxyphenylpropionic acid

                  4.S.4 3-phenylpropionic acid

                  4.S.5 alkanesulfonate

                  4.S.6 alkanesulphonate

                  4.S.8 alkylphosphonate

                  4.S.9 allantoin

                  4.S.10 allose/ribose

                  4.S.11 alpha-ketoglutarate

                  4.S.12 amino acid

                  4.S.13 amino acid/amide

                  4.S.14 ammonium

                  4.S.15 antibiotic

                  4.S.16 arabinose polymer

                  4.S.17 arginine

                  4.S.18 arginine/ornithine

                  4.S.19 arsenite

                  4.S.20 benzoate

                  4.S.21 lactose/glucose

                  4.S.22 beta-glucoside

                  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.31 chloramphenicol

                  4.S.32 chloride

                  4.S.33 choline

                  4.S.34 citrate/succinate

                  4.S.35 colicin

                  4.S.36 Cu+

                  4.S.37 curli subunit

                  4.S.38 cyanate

                  4.S.39 cysteine

                  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.50 D-xylose

                  4.S.51 enterochelin

                  4.S.52 fatty acid

                  4.S.53 Fe

                  4.S.54 Fe++

                  4.S.56 ferric enterobactin

                  4.S.57 ferric hydroxamate

                  4.S.58 ferrichrome

                  4.S.59 formate

                  4.S.60 formate/oxalate

                  4.S.61 fosfidomycin/H+

                  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.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

                  4.S.80 glycine betaine/proline

                  4.S.81 group A colicin

                  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.90 homoserine/lactone

                  4.S.91 hydrophilic molecule

                  4.S.92 hydrophilic molecules

                  4.S.93 ion

                  4.S.95 iron dicitrate

                  4.S.96 K+

                  4.S.97 K+/H+

                  4.S.98 lactate

                  4.S.99 lactose

                  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.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 melibiose

                  4.S.118 methionine

                  4.S.119 methylgalactoside/galactose

                  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-inositol

                  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.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.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.158 proline

                  4.S.159 proline/betaine

                  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.166 putrescine/spermidine

                  4.S.167 serine

                  4.S.168 shikimate/dehydroshikimate

                  4.S.169 sialic acid

                  4.S.170 S-methylmethionine

                  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.180 threonine

                  4.S.181 trehalose

                  4.S.182 tripeptide

                  4.S.183 tryptophan

                  4.S.184 tyrosine

                  4.S.185 uracil

                  4.S.187 vitamin B12

                  4.S.188 water

                  4.S.189 xanthosine

                  4.S.190 xylose/H+

                  4.S.191 Zn

                  4.S.192 chrysobactin

                  4.S.193 achromobactin

                  4.S.194 acetate

                  4.S.195 2-O-alpha-mannosyl-D-glycerate

                  4.S.196 Zn(2+)

                  4.S.197 N-acetylmuramic acid (MurNAc)

 

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

      5.14 Cell-cell communication

 

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