Pfam

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Pfam
Pfam logo.gif
Content
Description The Pfam database provides alignments and hidden Markov models for protein domains.
Data types
captured
Protein families
Organisms all
Contact
Research center EBI
Primary citation PMID 19920124
Access
Data format Stockholm format
Website pfam.xfam.org
Download URL FTP 1 FTP 2
Miscellaneous
License GNU Lesser General Public License
Version 30.0
Bookmarkable
entities
yes

Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models.[1][2][3]

Features[edit]

For each family in Pfam one can:

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

The descriptions of Pfam families are managed by the general public using Wikipedia.

Nearly 80% of protein sequences in the UniProt Knowledgebase have at least one match to Pfam.[4] This number is called the sequence coverage.

The Pfam database contains information about protein domains and families. Pfam-A is the manually curated portion of the database that contains over 16,000 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 was provided called Pfam-B. Pfam-B contains a large number of small families derived from clusters produced by an algorithm called ADDA.[5] Although of lower quality, Pfam-B families can be useful when no Pfam-A families are found. Pfam-B was discontinued as of release 28.0.[6]

The database iPfam[7] 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.

The most recent version, Pfam 30.0, was released in July 2016 and contains 16,306 families.[8]

See also[edit]

  • TrEMBL Database performing an automated protein sequence annotation
  • InterPro Integration of protein domain and protein family databases
  • PDBfam — thorough assignment of Pfam domains to sequences in the Protein Data Bank (PDB)[9][10]

References[edit]

  1. ^ Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A (2008). "The Pfam protein families database". Nucleic Acids Res. 36 (Database issue): D281–8. doi:10.1093/nar/gkm960. PMC 2238907free to read. PMID 18039703. 
  2. ^ Finn, R. D.; Mistry, J.; Schuster-Böckler, B.; Griffiths-Jones, S.; Hollich, V.; Lassmann, T.; Moxon, S.; Marshall, M.; Khanna, A.; Durbin, R.; Eddy, S. R.; Sonnhammer, E. L.; Bateman, A. (Jan 2006). "Pfam: clans, web tools and services" (Free full text). Nucleic Acids Research. 34 (Database issue): D247–D251. doi:10.1093/nar/gkj149. ISSN 0305-1048. PMC 1347511free to read. PMID 16381856. 
  3. ^ Bateman, A.; Coin, L.; Durbin, R.; Finn, R. D.; Hollich, V.; Griffiths-Jones, S.; Khanna, A.; Marshall, M.; Moxon, S.; Sonnhammer, E. L.; Studholme, D. J.; Yeats, C.; Eddy, S. R. (2004). "The Pfam protein families database". Nucleic Acids Research. 32 (Database issue): 138D–1141. doi:10.1093/nar/gkh121. ISSN 0305-1048. PMC 308855free to read. PMID 14681378.  open access publication - free to read
  4. ^ Punta, M.; Coggill, P. C.; Eberhardt, R. Y.; Mistry, J.; Tate, J.; Boursnell, C.; Pang, N.; Forslund, K.; Ceric, G. (2011). "The Pfam protein families database". Nucleic Acids Research. 40 (D1): D290–D301. doi:10.1093/nar/gkr1065. ISSN 0305-1048. PMC 3245129free to read. PMID 22127870. 
  5. ^ Heger, A.; Wilton, C. A.; Sivakumar, A.; Holm, L. (Jan 2005). "ADDA: a domain database with global coverage of the protein universe" (Free full text). Nucleic Acids Research. 33 (Database issue): D188–D191. doi:10.1093/nar/gki096. ISSN 0305-1048. PMC 540050free to read. PMID 15608174. 
  6. ^ "Pfam 28.0 release notes". Retrieved 30 June 2015. 
  7. ^ Finn, R. D.; Marshall, M.; Bateman, A. (Feb 2005). "IPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions" (Free full text). Bioinformatics (Oxford, England). 21 (3): 410–412. doi:10.1093/bioinformatics/bti011. ISSN 1367-4803. PMID 15353450. 
  8. ^ Finn, Rob; Mistry, Jaina (1 July 2016). "Pfam 30.0 is available". Xfam Blog. Retrieved 29 July 2016. 
  9. ^ Dunbrack, Roland. "PDBfam". PDBfam. Fox Chase Cancer Center. Retrieved 9 March 2013. 
  10. ^ Xu, Qifang; Dunbrack, Roland (2012). "Assignment of protein sequences to existing domain and family classification systems: Pfam and the PDB". Bioinformatics. 28 (21): 2763–72. doi:10.1093/bioinformatics/bts533. PMC 3476341free to read. PMID 22942020. 

External links[edit]