Pfam
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| 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 |
| Download URL | Pfam ftp Pfam ftp |
| Miscellaneous | |
| License | GNU Lesser General Public License |
| 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]
Contents
Features
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 is 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 on 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 current release of Pfam is "Pfam 28.0" (May 2015; 16,230 families).[8]
See also
- 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
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External links
- Pfam - Protein family database at EBI UK
- Pfam - Protein family database at Janelia Farm Research Campus USA
- Pfam - Protein family database at Stockholm Bioinformatics Centre Sweden
- iPfam - Interactions of Pfam domains in PDB
- PDBfam - Assignments of Pfam domains to sequences in the PDB at Fox Chase Cancer Center USA
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