Pfam protein domain families database

Many databases provide information on functional annotation of the genomes of organisms. One such high-quality standard database is Pfam (19). Pfam is fundamentally a protein domain family database derived based on sequence similarity. Pfam provides details on the functional properties of protein domains of known function. Out of 1,590, 1,495, and 1,536 proteins encoded in the genomes of 26695, J99, and HPAG1 strains of H. pylori, respectively, 1,113, 1,130, and 1,143 proteins have at least 1 protein domain associated (defined by Pfam) with the amino acid sequence. Therefore, for these domains of H. pylori proteins, preliminary indication of their functions is available. 

Sonnhammer, E.L., Eddy, S.R., Durbin, R. Pfam a comprehensive database of protein domain families based on seed alignments. Proteins 28 405-420, 1997. 

The specific format for cross references to the PROSITE and Pfam protein domain and family databases is ... 

It can be difficult if not impossible to find the domain structure of a protein of interest from the primary literature. The sequence may contain many common domains, but these are usually not apparent from searches of literature. Articles defining new domains may include the protein, but only in an alignment figure, which are not searchable. Perhaps, with the advent of online access to articles, the full text including figures may become searchable. Fortunately there have been several attempts to make this hidden information available in away that can be easily searched. These resources, called domain family databases, are exemplified by Prosite, Pfam, Prints, and SMART. These databases gather information from the literature about common domains and make it searchable in a variety of ways. They usually allow a researcher to look at the domain organization of proteins in the sequence database that have been precalculated and also provide a way to search new sequences... 

A comprehensive description of the databases and methods for domain, family, and pattern identification is available in chapter 2. Therefore, in this chapter, the discussion of the application of family and domain information to function assignment will be limited to Pfam, the virtual standard in protein domain/family classification, and to InterPro and CDD, two resources that integrate multiple domain databases. In addition, I discuss tools that can be used to scan those databases, namely HMMER,... 

The PROSITE database is used to determine the domain and the family of the protein sequences that, in turn, are based on biologically significant sites, patterns, and profiles.This database is similar to the HOMologous STRucture Alignment Database " (HOMSTRAD) and the Protein family (Pfam) database, both of which contain domain and family information for proteins. HOMSTRAD uses sequence and structure to group proteins into domains and families. Pfam classifies protein domains and families, based... 

PFAM is a database of Hidden Markov Models of protein families and domains, maintained at the Sanger Centre in Cambridge1651. The concept of PFAM is comparable to that of the PROSITE profile section. Similar to the profiles, the HMMs in PFAM have been derived by the iterative refinement procedure mentioned in Sect. 5.2.4. Unlike the PROSITE profiles, which all have been created manually by the curators, the HMMs in PFAM are generated semi-automatically, which accounts for a slightly lower sensitivity. However, this lack is more than compensated for by the facilitated update procedure, allowing the database to grow much faster than PROSITE and to have a shorter generation cycle. Currently, PFAM holds 2727 entries. 

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