TOPDOM: Conservatively Located Domains and Motifs in Proteins

TOPDOM is

a collection of domains and sequence motifs located conservatively on one side of membranes either in transmembrane or globular proteins. The database was created by predicting the transmembrane status and topology of all protein sequences in UniProt (SwissProt) database by the CCTOP algorithm and scanning by specific domain or motif detecting algorithms. The identified domain or motif was added to the database if it was uniformly annotated in the same side of the membrane of the various proteins in UniProt (SwissProt) database. The sequences in the UniProt (SwissProt) database were scanned by InterProScan algorithm for domains and motifs from Gene3D, TIGRFAM/NCBIfam, PANTHER, PRINTS, Pfam, ProSiteProfiles, SMART, SUPERFAMILY. For further details refer to our manuscripts.

TOPDOM can be

downloaded either the whole database or various subsets of the database in XML format. The database can be searched by keywords, gen names or identifiers.

TOPDOM is part of

the UNIfied database of TransMembrane Proteins (UniTmp), that is a comprehensive and freely accessible resource of transmembrane protein topology and structural information. UniTmp bridges the gap between TOPDB (Topology Data Bank of Transmembrane Proteins), TOPDOM (database of conservatively located domains and motifs in proteins), PDBTM (Protein Data Bank of Transmembrane Proteins) and HTP (Human Transmembrane Proteome) databases.

These resources stand for over 15 years by now and they provide structural information at different levels. The goal of UniTmp was to serve a solid background for all this information, by integrating these resources using a shared SQL based database. This way UniTmp provides up-to-date and consistent data, while keeping up the old usual interface of the original websites.