Transporter Classification Database: Difference between revisions

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{{Short description|Classification of membrane proteins including ion channels}}

The '''Transporter Classification Database''' (or '''TCDB''') is an [[International Union of Biochemistry and Molecular Biology]] (IUBMB)-approved classification system for [[membrane transport protein]]s, including [[ion channel]]s.<ref>{{cite journal|last1=Saier|first1=Milton H.|last2=Reddy|first2=Vamsee S.|last3=Tamang|first3=Dorjee G.|last4=Västermark|first4=Åke|title=The Transporter Classification Database|journal=Nucleic Acids Research|date=January 2014|volume=42|issue=D1|pages=D251–D258|doi=10.1093/nar/gkt1097|pmid=24225317|url=http://nar.oxfordjournals.org/content/42/D1/D251 |accessdatepmc=1 March 20163964967}}</ref><ref>{{cite journal|last1=Saier|first1=M. H.|last2=Yen|first2=M. R.|last3=Noto|first3=K.|last4=Tamang|first4=D. G.|last5=Elkan|first5=C.|title=The Transporter Classification Database: recent advances|journal=Nucleic Acids Research|date=1 January 2009|volume=37|issue=Database|pages=D274–D278|doi=10.1093/nar/gkn862|url=http://nar.oxfordjournals.org/content/37/suppl_1/D274|accessdate=1 March 2016|pmid=19022853|pmc=2686586}}</ref><ref>{{cite journal|last1=Saier|first1=M. H.|last2=Tran|first2=C. V.|last3=Barabote|first3=R. D.|title=TCDB: the Transporter Classification Database for membrane transport protein analyses and information|journal=Nucleic Acids Research|date=1 January 2006|volume=34|issue=90001|pages=D181–D186|doi=10.1093/nar/gkj001|url=http://nar.oxfordjournals.org/content/34/suppl_1/D181|accessdate=1 March 2016|pmid=16381841|pmc=1334385}}</ref>

==Classification==

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====1.A α-type channels====

* 1.A.1 [[Voltage-gated ion channel|Voltage-gated ion channel superfamily]]

* 1.A.2 I[[inward-rectifier K+ channel|nwardInward-rectifier K⁺ channel family]]

* 1.A.3 [[Ryanodine-inositol-1,4,5-trisphosphate receptor Ca2+ channel|Ryanodine-inositol-1,4,5-trisphosphate receptor Ca²⁺ channel family]]

* 1.A.4 [[Transient receptor potential Ca2+ channel|Transient receptor potential Ca²⁺ channel family]]

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*1.A.55 The Synaptic Vesicle-Associated Ca²⁺ Channel, Flower (Flower) Family

*1.A.56 The Copper Transporter (Ctr) Family

*1.A.57 The Human SARS CaronavirusCoronavirus Viroporin (SARS-VP)

*1.A.58 The Type B Influenza Virus Matrix Protein 2 (BM2-C) Family

*1.A.59 The Bursal Disease Virus Pore-Forming Peptide, Pep46 (Pep46) Family

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*1.A.86 The Human Papilloma Virus type 16 (HPV16) L2 Viroporin (L2 Viroporin) Family

*1.A.87 The Mechanosensitive Calcium Channel (MCA) Family

*1.A.88 The Fungal Potassium Channel (F-Kch) Family

*1.A.89 The Human Coronavirus 229E Viroporin (229E Viroporin) Family

*1.A.90 The Human Metapneumovirus (HMPV) Viroporin (HMPV-Viroporin) Family

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====1.B. [[Porin (protein)|β-Barrel porins]] and other outer membrane proteins====

* 1.B.1 [[General bacterial porin family]]

* 1.B.2 [[Chlamydia (genusbacterium)|Chlamydial]] porin (CP) family

* 1.B.3 [[Maltoporin|Sugar porin]] (SP) family

* 1.B.4 [[Brucella-Rhizobium porin]] (BRP) family

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* 1.B.25 [[Outer membrane porin D|Outer membrane porin (Opr) family]]

* 1.B.26 Cyclodextrin porin (CDP) family

* 1.B.31 [[Campylobacter jejuni]] major outer membrane oorinporin (MomP) family

* 1.B.32 Fusobacterial outer membrane porin (FomP) family

* 1.B.33 Outer membrane protein insertion porin (Bam complex) (OmpIP) family

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* 1.B.44 Probable protein translocating porphyromonas gingivalis porin (PorT) family

* 1.B.49 Anaplasma P44 (A-P44) porin family

* 1.B.48 Curli-like transporters

* 1.B.48 Curli-like transporters<ref>{{cite web|url=http://opm.phar.umich.edu/families.php?superfamily=503|title=Superfamily » 1.3.029. Curli-like transporters (n=36) (1 family) 1.B.48 (TCDB) PF03783, PDBsum - Orientations of Proteins in Membranes (OPM) database|first=Mikhail|last=Lomize|website=opm.phar.umich.edu}}</ref>

* 1.B.54 [[Intimin]]/Invasin (Int/Inv) or [[Autotransporter ___domain|Autotransporter-3]] family

* 1.B.55 Poly-acetyl-D-glucosamine porin (PgaA) family

* 1.B.55 Poly-acetyl-D-glucosamine porin (PgaA) family<ref>{{cite web|url=http://opm.phar.umich.edu/families.php?superfamily=545|title=Superfamily » 1.3.031. Poly acetyl glucosamine porin (n=16,S=18) (1 family) 1.B.55 (TCDB) - Orientations of Proteins in Membranes (OPM) database|first=Mikhail|last=Lomize|website=opm.phar.umich.edu}}</ref>

* 1.B.57 Legionella major-outer membrane protein (LM-OMP) family

* 1.B.60 Omp50 porin (Omp50 Porin) family

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* 1.B.71 Proteobacterial/verrucomicrobial porin (PVP) family

* 1.B.72 Protochlamydial outer membrane porin (PomS/T) family

* 1.B.73 Capsule biogenesis/assembly (CBA) family

* 1.B.73 Capsule biogenesis/assembly (CBA) family<ref>{{cite web|url=http://opm.phar.umich.edu/families.php?superfamily=476|title=Superfamily » 1.3.027. Capsule assembly protein (n=18,S=20) (1 family) 1.B.73 (TCDB) PF14052, PDBsum - Orientations of Proteins in Membranes (OPM) database|first=Mikhail|last=Lomize|website=opm.phar.umich.edu}}</ref>

* 1.B.78 DUF3374 electron transport-associated porin (ETPorin) family

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* 1.C.56 [[HrpZ Family|''Pseudomonas syringae'' HrpZ cation channel family]]

* 1.C.57 [[Clostridial Cytotoxin family|Clostridial cytotoxin family]]

*1.C.58 [[Microcin|The Microcin E492/C24 (Microcin E492) Family]]

* 1.C.74 [[Snake venom|Snake cytotoxin]] (SCT) family

* 1.C.97 [[Pleurotolysin|Pleurotolysin pore-forming family]]

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* 1.D.58 The Anion Transporting Prodigiosene (Prodigiosene) Family

* 1.D.59 The Anion Transporting Perenosin (Perenosin) Family

* 1.D.60 The Alpha,Gamma-CycicCyclic Peptide (AGCP) Family

* 1.D.61 The Anionophoric {{Chem name|2,6-Bis(Benzimidazol-2-yl)Pyridine}} (ABBP) Family

* 1.D.62 The Bis-Triazolyl DiGuanosine Derivative Channel-forming (TDG) Family

* 1.D.63 The Peptide-based Nanopore (PepNP) Family

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*2.A.3 [[APC superfamily|The Amino Acid-Polyamine-Organocation (APC) Family]]

*2.A.4 [[Cation diffusion facilitator]] (CDF) Family

*2.A.5 [[Ferroportin|Zinc (Zn²⁺)-Iron (Fe²⁺) Permease]] Family<ref>{{cite web|url=http://opm.phar.umich.edu/families.php?family=873|title=Family » 1.1.25.09. Ferroportin 2.A.100 (TCDB) PF06963, PDBsum - Orientations of Proteins in Membranes (OPM) database|first=Mikhail|last=Lomize|website=opm.phar.umich.edu}}</ref>

*2.A.6 [[Resistance-nodulation-cell division superfamily|Resistance-Nodulation-Cell Division Superfamily]], see also [[SecDF protein-export membrane protein]]

*2.A.7 The [[Small multidrug resistance protein|Drug/Metabolite Transporter]] (DMT) Superfamily

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*2.A.29 [[Mitochondrial carrier]] Family

*2.A.30 [[Chloride potassium symporter|Cation-Chloride Cotransporter]] (CCC) Family

*2.A.31 [[Anion exchanger family|Anion Exchanger]] Family]]

*2.A.32 The Silicon Transporter (Sit) Family

*2.A.33 [[Sodium-proton antiporter|NhaA Na⁺:H⁺ Antiporter]] (NhaA) Family

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*2.A.35 The NhaC Na⁺:H⁺ Antiporter (NhaC) Family

*2.A.36 [[Monovalent cation:proton antiporter-1|Monovalent Cation:Proton Antiporter-1]] (CPA1) Family

*2.A.37 [[Monovalent cation:proton antiporter-32|Monovalent Cation:Proton Antiporter-2]] (CPA2) Family

*2.A.38 [[Potassium transporter family|K⁺ Transporter (Trk)]] Family

*2.A.39 [[Nucleobase cation symporter-1|Nucleobase:Cation Symporter-1]] (NCS1) Family

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*2.A.61 The C4-dicarboxylate Uptake C (DcuC) Family

*2.A.62 The NhaD Na⁺:H⁺ Antiporter (NhaD) Family

*2.A.63 [[Monovalent cation:proton antiporter-3|The Monovalent Cation (K⁺ or Na⁺):Proton Antiporter-3]] (CPA3) Family

*2.A.64 [[Twin-arginine translocation pathway|Twin Arginine Targeting (Tat) Family]]

*2.A.65 The Bilirubin Transporter (BRT) Family

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*2.B.22 The Imidazolium-functionalized Anion Transporter (IAT) Family

*2.B.23 The Homotetrameric Transmembrane Zn²⁺/Co²⁺:Proton Synthetic Antiporter, Rocker (Rocker) Family

*2.B.24 The {{Chem name|2,6-Bis(benzimidazol-2-yl)pyridine}} Anion Carrier (BBP-AC) Family

*2.B.25 The Peptide-mediated Lipid Flip-Flop (PLFF) Family

*2.B.26 The {{Not a typo|Bis(imidazolyl)-functionalized}} {{Not a typo|Bis(Choloyl)}} Conjugate (BIBCC) Family

*2.B.27 The Tris-Urea Anion Transporter Family

*2.B.29 The Anionophoric Marine Alkaloid [[Tambjamine]] Family

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*4.A.4 The PTS Glucitol (Gut) Family

*4.A.5 The PTS Galactitol (Gat) Family

*4.A.6 [[PTS Mannose-Fructose-Sorbose Family|The PTS Mannose-Fructose-Sorbose (Man) Family]]

*4.A.7 The PTS L-Ascorbate (L-Asc) Family

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====5.B Transmembrane 1-electron transfer carriers====

*5.B.1 The Phagocyte ([[gp91phox]]) [[NADPH oxidase|NADPH Oxidase]] Family

*5.B.2 The Eukaryotic [[Cytochrome b561]] (Cytb561) Family

*5.B.3 The Geobacter Nanowire Electron Transfer (G-NET) Family

*5.B.4 The Plant Photosystem I Supercomplex (PSI) Family

*5.B.5 The Extracellular Metal Oxido-Reductase (EMOR) Family

*5.B.6 The [[STEAP3|Transmembrane Epithelial Antigen Protein-3]] Ferric Reductase (STEAP) Family

*5.B.7 The [[YedZ family|YedZ (YedZ) Family]]

*5.B.8 The Trans-Outer Membrane Electron Transfer Porin/Cytochrome Complex (ET-PCC) Family

*5.B.9 The Porin-Cytochrome c (Cyc2) Family

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* [http://www.tcdb.org/ Transporter Classification Database]

* [http://www.chem.qmul.ac.uk/iubmb/mtp/ List] at qmul.ac.uk

* {{cite journal |vauthors=Saier MH, Tran CV, Barabote RD |title=TCDB: the Transporter Classification Database for membrane transport protein analyses and information |journal=Nucleic Acids Res. |volume=34 |issue=Database issue |pages=D181–6 |date=January 2006 |pmid=16381841 |pmc=1334385 |doi=10.1093/nar/gkj001 |url=http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=16381841}}

* {{cite journal |vauthors=Busch W, Saier MH |title=The transporter classification (TC) system, 2002 |journal=Crit. Rev. Biochem. Mol. Biol. |volume=37 |issue=5 |pages=287–337 |year=2002 |pmid=12449427 |doi= 10.1080/10409230290771528|urls2cid=10558982 }}

* [http://www.guidetopharmacology.org/GRAC/ReceptorFamiliesForward?type=TRANSPORTER Classification of human transporters in pharmacology]

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{{Oxidoreduction-driven transporters}}

[[Category:BiologicalBiochemistry databases]]

[[Category:Transport proteins]]

[[Category:Transmembrane proteins]]

[[Category:ClassificationProtein systemsclassification]]

[[Category:Biological databases]]