Pfam Database-
Pfam Database
Introduction-
Pfam is a database of curated protein families, each of which is defined by two alignments and a profile hidden Markov model (HMM). A high-quality seed alignment is essential, as it provides the basis for the position-specific amino-acid frequencies, gap and length parameters in the profile HMM. In Pfam, the profile HMM is searched against a large sequence collection, based on UniProt Knowledgebase (UniProtKB), to find all instances of the family.
Home Page of Pfam Database
History-
Pfam was founded in 1995 by Erik Sonhammer, Sean Eddy and Richard Durbin as a collection of commonly occurring protein domains that could be used to annotate the protein coding genes of multicellular animals.
The project was partly driven by the assertion in ‘One thousand families for the molecular biologist’ by Cyrus Chothia that there were around 1500 different families of proteins and that the majority of proteins fell into just 1000 of these.
Pfam database currently contains 16,306 entries corresponding to unique protein domains and families.
Pfam entries are classified in one of six ways:
Family: A collection of related protein regions
Domain: A structural unitRepeat:A short unit which is unstable in isolation but forms a stable structure when multiple copies are present
Motifs: A short unit found outside globular domains
Coiled-Coil: Regions that predominantly contain coiled-coil motifs, regions that typically contain alpha-helices that are coiled together in bundles of 2-7.
Disordered: Regions that are conserved, yet are either shown or predicted to contain bias sequence composition and/or are intrinsically disordered (non-globular).
Related Pfam entries are grouped together into clans; the relationship may be defined by similarity of sequence, structure or profile-HMM.
Uses-
The general purpose of the Pfam database is to provide a complete and accurate classification of protein families and domains.
Researching specific proteins, by structural biologists to identify new targets for structure determination, by computational biologists to organize sequences and by evolutionary biologists tracing the origins of proteins.
Early genome projects, such as human and fly used Pfam extensively for functional annotation of genomic data.
The Pfam website allows users to submit protein or DNA sequences to search for matches to families in the database.
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