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 | ... More
  • 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