TOPDOM: Conservatively Located Domains and Motifs in Proteins

Search

Users can enter any identifier or part of an identifier that is indexed in UniTmp database at the top of the page (A), including PDB code, UniProt Identifier/Accession, or domains/motifs from the following databases also incorporated into InterPro: Gene3D, TIGRFAM, PANTHER, PRINTS, Pfam, ProSiteProfiles, SMART, SUPERFAMILY. Users can also search for protein names. The results will appear in four lines, and will show results from PDBTM, TOPDB, TOPDOM and HTP databases. By clicking on any of the four categoriges a new list will appear with all entries related to the given query.

Users can also restrict results to the TOPDOM database by selecting the scroll-down option "TOPDOM" and then performing the search (B).

Browse

Users can browse the content of the TOPDOM database using different filters using the browse button at the right of the search box. This includes localization, source database and number of supporting sequences (C).

List viewer

Once a search is performed, a list viewer page appears. In the case of searching in the whole UniTmp database, users first have to narrow down which source database they wish to use (D).

In the case of TOPDOM, the list includes panels for each result, showing some basic information about the protein: a small pictogram of the domain (blue for outside, red for inside), the identifier and the (human readable) name of the domain, and the number of supporting or contradicting evidence.

Downloads

Various download options are available in the download menu, in XML format: Users can download subsets, such as domains included in specific databases or with specific localizations. Download option is also available for the whole database.