How is protein family membership assigned in UniProtKB?

Last modified February 15, 2010

How is protein family membership assigned in UniProtKB?

The task of assigning proteins to families makes use of a range of sources including protein family databases, sequence analysis tools, scientific literature and sequence similarity search tools.

InterPro integrates predictive signatures representing protein domains, families and functional sites into a single resource from a number of family and domain databases: Gene3D, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART, SUPERFAMILY and TIGRFAMs. Use is made of InterPro and its member databases in assigning UniProtKB proteins to families.

Protein families for which no predictive signatures exist are defined through sequence similarity searches combined with use of scientific literature and sequence analysis tools. Factors such as end-to-end similarity with other family members and shared organisation such as common domain order and topology are considered. These newly identified families are passed to InterPro and its member databases to facilitate creation of new signatures which in turn leads to detection of additional family members.

The full list of protein families in UniProtKB and the entries which belong to each family is available here.