Database

TMFunction

noimage
NameTMFunction
AliasesNone
DescriptionTMFunction is a database of functional residues in alpha-helical and beta-barrel membrane proteins (cited from the original site).
TypeDB
Main Institutes of managementComputational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST)
Country of the InstituteJapan
URL of the sitehttps://dbarchive.biosciencedbc.jp/jp/tmfunction/desc.html
InterfaceGUI
Input exampleClick "Search" munu, then Push the "Search" button.
Keywordfunctional residues | UniProt ID | PDB code | PMID
Amount of the all data for download(Mbyte) | Method to obtain the all data.0|None
External resources (databases) in building the product.PDB | PDB-REPRDB | Protein Data Bank of Transmembrane proteins | Membrane protein structures | MPtopo | PDBsum | UniProt | Transport Classification Database | OCA | Prosite | Pfam | Ion channels database | The mitochondria database | Orientations of proteins in membranes database | GPCRDB | SEVENS | GENIUS II | GRIFFIN | ARAMEMNON | TMBETA-GENOME | HMMTOP | TMPro | PONGO | TMHMM | SOSUI | TMBETA-DISC | TMBETA-SVM | TMBETA-RBF | TMBETA-NET | ProfTMB | Transfold | TMB-Hunt | PRED-TMBB | TBB-Pred | PUBMED
Data typeProtein-structure , functional residues
Biological species in the main concernHomo sapiens | Escherichia coli | xenopus | Bacillus halodurans [Taxonomy_id: 86665] | Bacteriophage M13 [Taxonomy_id: 10870] | Bordetella pertussis [Taxonomy_id: 520] | Bos taurus [Taxonomy_id: 9913, cattle] | Carassius auratus [Taxonomy_id: 7957, goldfish] | Clostridium botulinum [Taxonomy_id: 1491] | Corynebacterium diphtheriae [Taxonomy_id: 1717] | Cricetulus griseus [Taxonomy_id: 10029, Chinese hamster] | Danio rerio [Taxonomy_id: 7955, zebrafish] | Emericella nidulans [Taxonomy_id: 162425] | Escherichia coli [Taxonomy_id: 562] | Escherichia coli O157 [Taxonomy_id: 1045010] | Escherichia coli UTI89 [Taxonomy_id: 364106] | Gallus gallus [Taxonomy_id: 9031, chicken] | Helicobacter pylori [Taxonomy_id: 210] | Homo sapiens [Taxonomy_id: 9606, human] | Human herpesvirus 8 [Taxonomy_id: 37296] | Leishmania donovani [Taxonomy_id: 5661] | Manduca sexta [Taxonomy_id: 7130, tobacco hornworm] | Mus musculus [Taxonomy_id: 10090, house mouse] | Oryctolagus cuniculus [Taxonomy_id: 9986, rabbit] | Pongo pygmaeus [Taxonomy_id: 9600, Bornean orangutan] | Pseudomonas aeruginosa [Taxonomy_id: 287] | Rattus norvegicus [Taxonomy_id: 10116, Norway rat] | Rhodobacter sphaeroides [Taxonomy_id: 1063] | Rhodopseudomonas blastica [Taxonomy_id: 1075] | Saccharomyces cerevisiae [Taxonomy_id: 4932, baker's yeast] | Saimiri boliviensis [Taxonomy_id: 27679, Bolivian squirrel monkey] | Salmonella enterica subsp. enterica serovar Typhimurium [Taxonomy_id: 90371] | Shigella dysenteriae [Taxonomy_id: 622] | Staphylococcus aureus [Taxonomy_id: 1280] | Vibrio parahaemolyticus [Taxonomy_id: 670] | Xenopus [Taxonomy_id: 8353] | Xenopus laevis [Taxonomy_id: 8355, African clawed frog]
Conditions of useCC BY-SA 2.1 JP
Frequency of updates (in last two years)1 time / year
Last date of updates (date of confirmation)2008/09/00 (2019/07/02)
Main IDs used in the productsN/A
How to make a link to get access to each IDs.None
external databases to which this database/tool have linksPDB (http://www.rcsb.org/) | PDB-REPRDB | Protein Data Bank of Transmembrane proteins (http://pdbtm.enzim.hu) | Membrane protein structures | MPtopo (MPtopo) | PDBsum (http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/) | UniProt (http://www.uniprot.org/) | Transport Classification Database (http://www.tcdb.org) | OCA | Prosite (http://prosite.expasy.org/) | Pfam (http://pfam.xfam.org/) | Ion channels database (http://scifeeds.com/category/life-science/ion-channels/) | The mitochondria database (http://www.mitochondrial.net/database.php#geneinfo) | Orientations of proteins in membranes database (http://opm.phar.umich.edu/) | GPCRDB (http://www.gpcr.org/7tm/) | SEVENS (http://sevens.cbrc.jp/) | GENIUS II | GRIFFIN | ARAMEMNON (http://aramemnon.botanik.uni-koeln.de/) | TMBETA-GENOME | HMMTOP (http://www.enzim.hu/hmmtop/) | TMPro | PONGO | TMHMM (http://www.cbs.dtu.dk/services/TMHMM/) | SOSUI (http://harrier.nagahama-i-bio.ac.jp/sosui/) | TMBETA-DISC | TMBETA-SVM | TMBETA-RBF (http://rbf.bioinfo.tw/~sachen/OMPpredict/TMBETADISC-RBF.php) | TMBETA-NET | ProfTMB | Transfold (http://bioinformatics.bc.edu/clotelab/transFold) | TMB-Hunt | PRED-TMBB (http://bioinformatics.biol.uoa.gr/PRED-TMBB) | TBB-Pred (http://www.imtech.res.in/raghava/tbbpred) | PUBMED (http://www.ncbi.nlm.nih.gov)
Published papers (PubMed IDs)pmid:18842639
Operational StatusArchived