What is InterPro?

InterPro provides functional analysis of proteins by classifying them into families and predicting the presence of important domains and sites. It does this by combining predictive models known as protein signatures from a number of different databases (referred to as member databases) into a single searchable resource. InterPro integrates the signatures, providing names, descriptive abstracts, and whenever possible, adding Gene Ontology (GO) terms, structural links and external database links. Together, the protein signatures combined within InterPro provide matches to ~ 80% of proteins in the UniProt database.

What are protein signatures?

Protein signatures are obtained by modelling the conservation of amino acids at specific positions within a group of related proteins (i.e., a protein family), or within the domains/sites shared by a group of proteins. InterPro’s different member databases use different computational methods to produce protein signatures, and they each have their own particular focus of interest: homologous superfamilies, structural and/or functional domains, protein families, or protein features such as active sites or binding sites (see Figure 1).

The protein signatures in InterPro are regularly run against the UniProt database of protein sequences, and all significant matches are reported on the InterPro website, allowing users to check which proteins match a particular signature. This information is also used to aid UniProt curators in their annotation of Swiss-Prot proteins and by the automatic systems that add annotation to TrEMBL (the non-reviewed protein sequences of UniProtKB).

InterPro entry types

The signatures provided by the member databases are integrated into InterPro entries. Each InterPro entry is assigned a type (see Figure 2): homologous superfamily, family, domain, repeat, or site (which can be a conserved site, active site, binding site or post-translational modification site).

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