The InterPro database, an integrated documentation resource for protein families, domains and functional sites

Abstract

Signature databases are vital tools for identifying distant relationships in novel sequences and hence for inferring protein function. InterPro is an integrated documentation resource for protein families, domains and functional sites, which amalgamates the efforts of the PROSITE, PRINTS, Pfam and ProDom database projects. Each InterPro entry includes a functional description, annotation, literature references and links back to the relevant member database(s). Release 2.0 of InterPro (October 2000) contains over 3000 entries, representing families, domains, repeats and sites of post-translational modification encoded by a total of 6804 different regular expressions, profiles, fingerprints and Hidden Markov Models. Each InterPro entry lists all the matches against SWISS-PROT and TrEMBL (more than 1,000,000 hits from 462,500 proteins in SWISS-PROT and TrEMBL). The database is accessible for text- and sequence-based searches at http://www.ebi.ac.uk/interpro/. Questions can be emailed to interhelp@ebi.ac.uk.

Figure 1

Demonstration of relationships existing between InterPro entries. (Top) Parent–child relationship. This graphical view of three proteins shows IPR000663, which contains signatures describing the Natriuretic peptide family. Each protein has an additional InterPro entry associated with it, containing a fingerprint for more specific classes of Natriuretic peptide. These InterPro entries, IPR002406, IPR002407 and IPR002408 are the children or sub-families of IPR000663. (Bottom) Contains-found in relationship. In these three proteins, IPR000051, the SAM binding motif is a domain found in several different protein families, including IPR001737 (ribosomal RNA adenine dimethylase), IPR000682 (protein-l-isoaspartate(d-aspartate) O-methyltransferase) and IPR000339, a family of ubiqunone methyltransferases. They are not sub-families of the SAM binding domain.

Figure 1

Demonstration of relationships existing between InterPro entries. (Top) Parent–child relationship. This graphical view of three proteins shows IPR000663, which contains signatures describing the Natriuretic peptide family. Each protein has an additional InterPro entry associated with it, containing a fingerprint for more specific classes of Natriuretic peptide. These InterPro entries, IPR002406, IPR002407 and IPR002408 are the children or sub-families of IPR000663. (Bottom) Contains-found in relationship. In these three proteins, IPR000051, the SAM binding motif is a domain found in several different protein families, including IPR001737 (ribosomal RNA adenine dimethylase), IPR000682 (protein-l-isoaspartate(d-aspartate) O-methyltransferase) and IPR000339, a family of ubiqunone methyltransferases. They are not sub-families of the SAM binding domain.

Figure 2

An example of an InterPro entry. This is IPR000890, an entry containing signatures describing the acetate and butyrate kinase protein family. The ‘i’ information buttons have links to help files describing, for example, the ‘Family’ concept.