How to search the Protein Family Model database
How to search the Protein Family Model database
The Protein Family Model database can be queried using a variety of terms, including any name known for the model, the full name or a substring of the name of a protein, a gene symbol, a publication, or the type of model (Sparcle or Conserved domain architecture, BlastRule, or HMM).
Examples
- "IniC" returns protein family models where the term IniC appears in the model name, its description, gene symbol, or a publication title.
- "iniC[GeneSymbol]" returns protein family models with the gene symbol iniC
- "isoniazid[Description] AND blastrule[Method]" returns any BlastRule where the text describing the BlastRule contains the term "isoniazid".
Commonly used search terms
| Search term | Applies to | Description | Example |
|---|
| EC | All | Enzyme Commission number associated with the family model | "2 8 1 4 "[ECNumber] |
| ECTitle | All | Enzyme Commission name or part of name associated with the family model | sulfurtransferase[ECTitle] |
| FamilyAccession | All | NCBI Accession | nf003559[FamilyAccession] |
| FamilyAccessionOrig | HMMs | Accession in source database (Pfam PF14200.6, PRK PRK05234) | prk05234[FamilyAccessionOrig] |
| GeneDescription | Sparcle | Name or part of name of gene associated with the family model | sulfur[GeneDescription] |
| GeneSymbol | All | Gene symbol associated with the family model | mgsA[GeneSymbol] |
| Method | All | Family model type (blastrule, hmm, or sparcle) | sparcle[Method] |
| ProductName | All | Name or part of a name associated with the family model | "methylglyoxal synthase"[ProductName] |
| PubmedID | All | Pubmed publication ID associated with the family model | 1704886[PubmedID] |
| PublishDate | All | Family Model publication date or date range | ("2020/01/01"[PublicationDate] : "2020/02/01"[PublicationDate]) |
| ReviewLevel | Sparcle | Curated, autonamed, or named by domain | reviewed[ReviewLevel] |
Search results
The Search results include the following information for each model matching the search:
- The model name, encapsulating the function of the proteins in the family represented by the model
- A description of the function of proteins in the family or of the biological process in which proteins in the family are involved (if available).
- The date on which the family model was published
- The model accession number for the family
- The type of model (HMM, BlastRule, or Sparcle)
Individual records
Clicking on a search result opens a page that is specific for the model that was selected.
Information displayed in these records is different for HMM, BlastRules, and Conserved domain architectures. For more information, see the help documentation linked from the individual records.
Accessing the protein family models
Protein family models are available for download:
Revised 20 October 2020
