InterPro

What InterPro is

InterPro is a database that classifies protein sequences into families, domains, functional sites, repeats, and homologous superfamilies. It integrates diagnostic models from 13 consortium member databases, combining distinct methods such as hidden Markov models, position-specific scoring matrices, and regular expressions into a unified classification system.

Analysing uncharacterised protein sequences typically requires consulting multiple disparate resources spanning structural classifications, sequence alignments, and curated subfamilies. InterPro addresses this by providing a single resource where equivalent signatures from member databases are merged into shared entries, complete with curated descriptions, standardised nomenclature, and Gene Ontology annotations.

How it is organised

InterPro collates signatures—including profile hidden Markov models, fingerprints, and regular expressions—from 13 member databases: CATH-Gene3D, CDD, HAMAP, MobiDB, PANTHER, Pfam, PIRSF, PRINTS, PROSITE, SMART, SUPERFAMILY, SFLD, and TIGRFAMs. Entries are evaluated against UniProtKB protein sequences. Signatures that describe identical domains, sites, or families are integrated into single InterPro entries based on the comparative overlap and sequence locations of their protein matches.

Entries are divided into five types: Homologous Superfamily, Family, Domain, Repeat, and Site. Matches against proteins from UniProtKB, splice variants, UniParc, and UniMES are updated every eight weeks alongside UniProtKB releases. Users can also scan uncharacterised nucleotide or amino acid sequences against these integrated signatures using the InterProScan software package or web APIs.

Key facts

What you can use it for

Genome-wide protein characterisation

Annotating newly sequenced genomes with InterProScan to obtain a rapid initial functional profile for predicted protein sets.

Protein domain architecture analysis

Identifying the locations of evolutionary domains, repeats, and mobile sequence modules across unknown protein sequences.

Functional site identification

Detecting specific functional features, including post-translational modification sites, binding sites, and catalytic active sites.

Gene Ontology mapping

Assigning consistent Gene Ontology terms and pathway contexts to proteins via integrated family and subfamily matches.

Query it here

The research agent queries InterPro directly — no account, no API key — and every answer links back to the record it came from. Ask in plain language and it writes the query.

Strengths and limits

Questions