The Pfam database contains information about protein domains and families. For each entry a protein sequence alignment and a Hidden Markov Model is stored.
- Prefix
pfam- Alternative Prefixes
- PF
- Keywords
- biology domain protein
- License
- CC0-1.0
- Links
- Homepage
- Contact
- Alex Bateman 0000-0002-6982-4660
- Pattern for Local Unique Identifiers
-
Local identifiers in Pfam should match this regular expression:
^PF\d{5}$ - Example Local Unique Identifier
- PF11779 Resolve
- Pattern for CURIES
-
Compact URIs (CURIEs) constructed from Pfam should match this regular expression:
^pfam:PF\d{5}$ - Example CURIE
- pfam:PF11779
- Publications
-
- 1999 Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins
- 1998 Pfam: multiple sequence alignments and HMM-profiles of protein domains
- 1997 Pfam: a comprehensive database of protein domain families based on seed alignments
- 2024 The Pfam protein families database: embracing AI/ML
- 2021 Pfam: The protein families database in 2021
- 2019 The Pfam protein families database in 2019
- 2015 The Pfam protein families database: towards a more sustainable future
- 2013 Pfam: the protein families database
- 2011 The Pfam protein families database
- 2009 The Pfam protein families database
- 2007 The Pfam protein families database
- 2006 Pfam: clans, web tools and services
- 2004 The Pfam protein families database
- 2002 The Pfam protein families database
- 2000 The Pfam protein families database
- References
- Tweet https://twitter.com/PfamDB/status/1555149527228813314
Ontology
A summary of the relations in the Bioregistry schema can be found here.
- Provided By
- pandit
- In Collection
- Synapse.org external links
Metaregistry Pfam
The metaregistry provides mappings between the Bioregistry and other registries. There are 13 mappings to external registries for this resource with 7 unique external prefixes.
| Registry Name | Registry Metaprefix | External Prefix | Curate |
|---|---|---|---|
| BioContext | biocontext |
PFAM
|
|
EDAM
|
edam |
1138
|
|
FAIRSharing
|
fairsharing |
FAIRsharing.y3scf6
|
|
GO
|
go |
Pfam
|
|
Integbio
|
integbio |
nbdc00163
|
|
Identifiers.org
|
miriam |
pfam
|
|
N2T
|
n2t |
pfam
|
|
NCBI
|
ncbi |
PFAM
|
|
Prefix Commons
|
prefixcommons |
pfam
|
|
re3data
|
re3data |
r3d100012850
|
|
| TogoID | togoid |
Pfam
|
|
UniProt
|
uniprot |
DB-0073
|
|
Wikidata
|
wikidata |
P3519
|
Providers
A provider turns a local unique identifiers from a resource into a URI. Many providers are also resolvable as URLs (i.e., they can be used in a web browser).
The local unique identifier PF11779 is used to demonstrate the providers
available for Pfam. Some providers may use a different example, which is displayed in the table below.
A guide for curating additional providers can be found
here.
| Name | Metaprefix | URI |
|---|---|---|
| Pfam | pfam |
https://www.ebi.ac.uk/interpro/entry/pfam/PF11779 |
| Bioregistry | bioregistry |
https://bioregistry.io/pfam:PF11779 |
| Identifiers.org | miriam |
https://identifiers.org/pfam:PF11779 |
| Name-to-Thing | n2t |
https://n2t.net/pfam:PF11779 |
Extra Providers
Additional providers curated in the Bioregistry are listed here. These are typically inherited from Identifiers.org or Prefix Commons, and need extra curation.
| Code | Name | URL |
|---|---|---|
bio2rdf |
Bio2RDF | http://bio2rdf.org/pfam:PF11779 |
sanger |
Sanger Pfam Mirror | http://pfam.sanger.ac.uk/family?entry=PF11779 |
xfam |
Xfam | https://pfam.xfam.org/family?acc=PF11779 |