Pfam is a collection of protein families and domains. Pfam contains multiple protein alignments and profile-HMMs of these families. Pfam is a semiautomatic protein family database, which aims to be comprehensive as well as accurate.
References
Bateman A, Birney E, Durbin R, Eddy SR, Finn RD, Sonnhammer ELL (1999) Pfam 3.1: 1313 multiple alignments match the majority of proteins, Nucleic Acids Research 27:260-262 (link)
Sonnhammer ELL, Eddy SR, Birney E, Bateman A, Durbin R (1998) Pfam: multiple sequence alignments and HMM-profiles of protein domains, Nucleic Acids Research 26:320-322
Sonnhammer ELL, Eddy SR, Durbin R (1997) Pfam: A Comprehensive Database of Protein Families Based on Seed Alignments, Proteins 28:405-420
is a collection of protein families and domains.