TOPDOM: Conservatively Located Domains and Motifs in Proteins

Description of TOPDOM server

Protein domains are functional units that fold independently from other parts of the protein. These functional units may appear in different proteins, as their function may be important for several processes. Certain domains may only function in their appropriate environment, therefore they will also appear in the same cellular compartment.

The TOPDOM database is a collection of domains and sequence motifs located conservatively on one side of membranes either in transmembrane or globular proteins.

The TOPDOM database was created by predicting the transmembrane topology of sequences in UniProt (SwissProt) database by the CCTOP algorithm for transmembrane proteins and by adding curated annotations from UniProt (SwissProt) for non-TM proteins. 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. The identified domain or motif was added to the database if it occurred at least 10 times in UniProt (SwissProt) and in at least 99% of the cases it was annotated in the same side of the membrane (inside/outside). For further details refer to our manuscripts.

The UNIfied database of TransMembrane Proteins (UniTmp) 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 10 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.