Pfam domains
E736821
Pfam domains are conserved protein regions defined in the Pfam database that represent functional and structural units shared across different proteins.
All labels observed (6)
| Label | Occurrences |
|---|---|
| Pfam | 1 |
| Pfam database | 1 |
| Pfam domains canonical | 1 |
| Pfam signatures | 1 |
| Pfam-A collection | 1 |
| Pfam-B collection | 1 |
How this entity was disambiguated
This entity first appeared as the object of triple T8482784 — resolving that mention is where its identity was fixed. The disambiguator weighed these candidate entities and picked the highlighted one (or “None”, minting a new entity). This is how homonymy is resolved: the same surface form can point to different entities.
NED1
Entity disambiguation (via context triple)
gpt-5-mini-2025-08-07
Target entity: Pfam domains Context triple: [UniProt protein sequences, linkedTo, Pfam domains]
-
A.
Conserved Domain Database
The Conserved Domain Database is an NCBI-curated resource that catalogs and annotates conserved protein domains to support functional and evolutionary analysis of protein sequences.
-
B.
Protein database
The Protein database is a curated collection of protein sequences and related functional, structural, and bibliographic information maintained by the National Center for Biotechnology Information (NCBI).
-
C.
EMBL-EBI AlphaFold Protein Structure Database
The EMBL-EBI AlphaFold Protein Structure Database is a publicly accessible resource providing predicted 3D structures of proteins generated by DeepMind’s AlphaFold system.
-
D.
Gene Ontology (GO)
Gene Ontology (GO) is a major bioinformatics initiative that provides a structured, controlled vocabulary to describe gene and gene product attributes across species in terms of their molecular functions, biological processes, and cellular components.
-
E.
UniProt protein sequences
UniProt protein sequences are a comprehensive, curated collection of protein sequence data that serves as a primary reference resource for protein information in biological and biomedical research.
- F. None of above. chosen
- G. Unsure - the case is ambiguous/there is not enough information to decide.
NED2
Entity disambiguation (via description)
gpt-5-mini-2025-08-07
Target entity: Pfam domains Target entity description: Pfam domains are conserved protein regions defined in the Pfam database that represent functional and structural units shared across different proteins.
-
A.
Conserved Domain Database
The Conserved Domain Database is an NCBI-curated resource that catalogs and annotates conserved protein domains to support functional and evolutionary analysis of protein sequences.
-
B.
Protein database
The Protein database is a curated collection of protein sequences and related functional, structural, and bibliographic information maintained by the National Center for Biotechnology Information (NCBI).
-
C.
EMBL-EBI AlphaFold Protein Structure Database
The EMBL-EBI AlphaFold Protein Structure Database is a publicly accessible resource providing predicted 3D structures of proteins generated by DeepMind’s AlphaFold system.
-
D.
Gene Ontology (GO)
Gene Ontology (GO) is a major bioinformatics initiative that provides a structured, controlled vocabulary to describe gene and gene product attributes across species in terms of their molecular functions, biological processes, and cellular components.
-
E.
UniProt protein sequences
UniProt protein sequences are a comprehensive, curated collection of protein sequence data that serves as a primary reference resource for protein information in biological and biomedical research.
- F. None of above. chosen
Statements (49)
| Predicate | Object |
|---|---|
| instanceOf |
conserved protein region
ⓘ
protein domain family ⓘ |
| definedIn |
Pfam database
ⓘ
linked to:
Pfam domains
|
| hasDatabaseAccessionPrefix | PF ⓘ |
| hasExample |
PF00005 (ABC transporter ATP-binding domain)
ⓘ
PF00069 (protein kinase domain) ⓘ PF00072 (response regulator receiver domain) ⓘ PF00076 (RNA recognition motif) ⓘ PF00096 (zinc finger C2H2 type) ⓘ |
| hasPrimaryAccessURL | https://pfam.xfam.org ⓘ |
| hasProperty |
associated with GO terms
ⓘ
associated with InterPro entries ⓘ associated with full alignment ⓘ associated with gathering threshold score ⓘ associated with noise cutoff score ⓘ associated with seed alignment ⓘ associated with sequence logos ⓘ associated with trusted cutoff score ⓘ can be found in different combinations in proteins ⓘ can be shared across different species ⓘ can occur in multiple copies within a protein ⓘ conserved across multiple proteins ⓘ curated by experts ⓘ linked to other protein family databases ⓘ often associated with specific 3D structure ⓘ often associated with specific biochemical function ⓘ |
| hasScope |
eukaryotic proteins
ⓘ
prokaryotic proteins ⓘ viral proteins ⓘ |
| isBasedOn | multiple sequence alignment ⓘ |
| isMaintainedBy |
European Bioinformatics Institute
ⓘ
Wellcome Sanger Institute ⓘ |
| isModeledBy | profile hidden Markov model ⓘ |
| isPartOf |
Pfam-A collection
ⓘ
linked to:
Pfam domains
Pfam-B collection ⓘ
linked to:
Pfam domains
XFAM resource ⓘ |
| isUsedFor |
comparative genomics
ⓘ
domain architecture analysis ⓘ evolutionary studies of proteins ⓘ protein domain annotation ⓘ protein family classification ⓘ protein function prediction ⓘ protein sequence analysis ⓘ |
| represents |
functional unit of protein
ⓘ
structural unit of protein ⓘ |
| usedBy |
Ensembl
ⓘ
InterPro ⓘ
linked to:
InterPro entries
NCBI protein annotation pipelines ⓘ UniProt ⓘ
linked to:
UniProt Knowledgebase
|
How these facts were elicited
The pipeline generated the facts above by prompting gpt-5.1 with this entity's name + description and the instruction below.
Instruction
You are a knowledge base construction expert. Given a subject entity and a description of it, return factual statements that you know for the subject as a JSON list of dictionaries(triples), where keys must be "subject", "predicate" and "object". The number of facts may be very high, between 25 to 50 or more, for very popular subjects. For less popular subjects, the number of facts can be very low, like 5 or 10. # Requirements - If you don't know the subject at all, return an empty list. - If the subject is not a named entity, return an empty list. - Include at least one triple where predicate is "instanceOf". - Do not get too wordy. - Separate several objects into multiple triples with one object.
Input
Subject: Pfam domains Description of subject: Pfam domains are conserved protein regions defined in the Pfam database that represent functional and structural units shared across different proteins.
Referenced by (6)
Full triples — surface form annotated when it differs from this entity's canonical label.
linked to: Pfam domains
subject linked to:
Pfam domains
linked to: Pfam domains
subject linked to:
Pfam domains
linked to: Pfam domains
subject linked to:
InterPro entries
linked to: Pfam domains