| Name | TMFunction |
|---|
| Aliases | None |
|---|
| Description | TMFunction is a database of functional residues in alpha-helical and beta-barrel membrane proteins (cited from the original site). |
|---|
| Type | DB |
|---|
| Main Institutes of management | Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST) |
|---|
| Country of the Institute | Japan |
|---|
| URL of the site | https://dbarchive.biosciencedbc.jp/jp/tmfunction/desc.html |
|---|
| Interface | GUI |
|---|
| Input example | Click "Search" munu, then Push the "Search" button. |
|---|
| Keyword | functional 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 type | Protein-structure , functional residues |
|---|
| Biological species in the main concern | Homo 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 use | CC 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 products | N/A |
|---|
| How to make a link to get access to each IDs. | None |
|---|
| external databases to which this database/tool have links | PDB (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 Status | Archived |
|---|
