Pfam 28.0 (May 2015, 16230 families). The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs) .ifferent 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. Pfam also generates higher-level groupings of related families, known as clans.