Pfam

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Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families. For each family in Pfam you can:

Look at multiple alignments
View protein domain architectures
Examine species distribution
Follow links to other databases
View known protein structures

Pfam can be used to view the domain organisation of proteins. A typical example is shown below. Notice that a single protein can belong to several Pfam families.

74% of protein sequences have at least one match to Pfam. This number is called the sequence coverage and is shown in the pie chart on the right.

The Pfam database contains information about protein domains and families. Pfam-A is the manually curated portion of the database that contains over 9,000 entries. For each entry a protein sequence alignment and a hidden Markov model is stored. These hidden Markov models can be used to search sequence databases with the HMMER package written by Sean Eddy. Because the entries in Pfam-A do not cover all known proteins an automatically generated supplement is provided called Pfam-B. Pfam-B contains a large number of small families derived from the PRODOM[1] database. Although of lower quality Pfam-B families can be useful when no Pfam-A families are found.

The database iPfam builds on the domain description of Pfam. It investigates if different proteins described together in the protein structure database PDB are close enough to potentially interact.

[edit] See also

TrEMBL Database performing an automated protein sequence annotation
InterPro Integration of protein domain and protein family databases

[edit] References

Finn RD, Mistry J, Schuster-Bockler B, Griffiths-Jones S, Hollich V, Lassmann T, Moxon S, Marshall M, Khanna A, Durbin R, Eddy SR, Sonnhammer EL, Bateman A (2006). "Pfam: clans, web tools and services". Nucleic Acids Res. 34: D247–D251. doi:10.1093/nar/gkj149. PMID 16381856.

Finn RD, Marshall M, Bateman A (2005). "iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions". Bioinformatics 21: 410–412. doi:10.1093/bioinformatics/bti011. PMID 15353450.

Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR (2004). "The Pfam protein families database". Nucleic Acids Res. 32(Database issue): D138–D141. doi:10.1093/nar/gkh121. PMID 14681378.