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Gene categories
0 unknown function
  0.1 conserved hypothetical product
1 metabolism
  1.1 carbon utilization
    1.1.1 carbon compounds
    1.1.2 fatty acids
    1.1.3 amino acids
    1.1.4 amines
    1.1.5 other compounds
  1.2 macromolecule degradation
    1.2.1 RNA
    1.2.2 DNA
    1.2.3 proteins/peptides/glycopeptides
    1.2.4 polysaccharides
  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 glutamate glutamine arginine proline aspartate asparagine lysine, diaminopimelate threonine methionine glycine serine cysteine phenylalanine tyrosine tryptophan histidine alanine isoleucine/valine leucine chorismate homoserine
    1.5.2 nucleotide purine biosynthesis pyrimidine biosynthesis purine ribonucleotide biosynthesis pyrimidine ribonucleotide biosynthesis
    1.5.3 cofactor, small molecule carrier biotin folic acid lipoate molybdenum Coenzyme A pyridoxine (vitamin B6) nicotinamide adenine dinucleotide thiamin riboflavin (Vitamin B2), FAD, FMN glutathione menaquinone, ubiquinone heme, porphyrine cobalamin (Vitamin B12) enterochelin (enterobactin) chrysobactin achromobactin
    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 O antigen core region 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 cytoplasmic polysaccharides
    1.6.10 lipoprotein
    1.6.11 glycoprotein
    1.6.12 flagella
    1.6.13 fimbria, pili
	 	  1.6.14. phage strutures phage head-capsid phage tail phage fiber phage internal virion protein
    1.6.15 large molecule carriers cytochromes thioredoxin, glutaredoxin biotin carboxyl carrier protein acyl carrier protein
  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 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 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 oxidation
    1.7.29 acetate catabolism
    1.7.30 threonine 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
  1.8 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 DNA bending, supercoiling, inversion methylation
    3.1.2 transcriptional level sigma factors, anti-sigmafactors activator repressor complex regulation more than one signal needed regulons or multilayer component regulatory systems two component regulatory systems (external signal) quorum sensing action unknown
    3.1.3 posttranscriptional translation attenuation and efficiency covalent modification, demodification, maturation inhibition / activation of enzymes proteases, cleavage of compounds multilayer regulatory system antisense RNA
    3.1.4 regulation level unknown
  3.3 genetic unit regulated
    3.3.1 operon
    3.3.2 regulon
    3.3.3 stimulon
    3.3.4 global
  3.4 trigger
  3.5 trigger modulation
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.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.35 The CorA Metal Ion Transporter (MIT) 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.17 The Outer Membrane Factor (OMF) 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 L-Rhamnose Transporter (RhaT) 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.24 The Citrate:Cation Symporter (CCS) 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.A.80 The Tricarboxylate Transporter (TTT) 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 ABC superfamily ATP binding cytoplasmic component
        4.3.A.1.am ABC superfamily, ATP binding and membrane component
        4.3.A.1.m ABC superfamily, membrane component
        4.3.A.1.p ABC superfamily, periplasmic binding 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 or VirB) Secretory Pathway
    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
  4.5 Transport Electron Carriers
    4.5.A Transmembrane 2-Electron Transfer Carriers
      4.5.A.1 The Disulfide Bond Oxidoreductase D (DsbD) Family
      4.5.A.2 The Disulfide Bond Oxidoreductase B (DsbB) Family
      4.5.A.3 The Prokaryotic Molybdopterin-containing Oxidoreductase (PMO) Family
  4.8 Accessory Factors Involved in Transport
    4.8.A Auxiliary transport proteins
      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 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
      4.9.B.37 The HlyC/CorC (HCC) Family
  4.S substrate
    4.S.1 (D)-glucarate/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.7 alklphosphonate
    4.S.8 alkylphosphonate
    4.S.9 allantoin/ion
    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/ornitine
    4.S.19 arsenite
    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.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.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.55 ferric dicitrate
    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.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.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.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.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
    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 mellobiose
    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-inositor
    4.S.130 Na+
    4.S.131 Na+/ alanine/glycine
    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.149 oligopeptides
    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.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.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.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.190 xylose/H+
    4.S.191 Zn
    4.S.192 chrysobactin
    4.S.193 achromobactin
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 (mechanical, nutritional, oxidative stress)
    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/survivial
  5.11 DNA uptake
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 MGE related
  8.1 phage life cycle
  8.2 extrachromosomal maintenance 
  8.3 integration-excision

9 DNA sites
10 cryptic genes