The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).
Proteins are generally composed of one or more functional regions, commonly termed domains. Different combinations of domains give rise to the diverse range of proteins found in nature. The identification of domains that occur within proteins can therefore provide insights into their function.
There are two components to Pfam: Pfam-A and Pfam-B. Pfam-A entries are high quality, manually curated families. Although these Pfam-A entries cover a large proportion of the sequences in the underlying sequence database, in order to give a more comprehensive coverage of known proteins we also generate a supplement using the PRODOM database. These automatically generated entries are called Pfam-B. Although of lower quality, Pfam-B families can be useful for identifying functionally conserved regions when no Pfam-A entries are found.
Pfam also generates higher-level groupings of related families, known as clans. A clan is a collection of Pfam-A entries which are related by similarity of sequence, structure or profile-HMM.
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