Pfam Tools#

Configuration File: pfam_tools.json Tool Type: Local Tools Count: 6

This page contains all tools defined in the pfam_tools.json configuration file.

Available Tools#

Pfam_get_family_detail (Type: PfamTool)#

Get detailed information about a specific Pfam protein family by accession. Returns the full fami…

Pfam_get_family_detail tool specification

Tool Information:

  • Name: Pfam_get_family_detail

  • Type: PfamTool

  • Description: Get detailed information about a specific Pfam protein family by accession. Returns the full family name, short name, description, type (domain/family/repeat), protein/structure/taxa counts, clan (superfamily) membership, representative 3D structure, Wikipedia link, and GO terms. Pfam families are the fundamental units of protein classification - for example PF00001 (7tm_1) covers the rhodopsin-like GPCR superfamily with 432,000+ proteins, while PF00076 (RRM_1) is the RNA recognition motif found in 627,000+ proteins. Use this to understand what a Pfam family represents and its biological significance.

Parameters:

  • pfam_accession (string) (required) Pfam family accession. Examples: ‘PF00001’ (7tm_1, GPCR rhodopsin family), ‘PF00076’ (RRM_1, RNA recognition motif), ‘PF00069’ (Pkinase), ‘PF00096’ (zf-C2H2, zinc finger).

Example Usage:

query = {
    "name": "Pfam_get_family_detail",
    "arguments": {
        "pfam_accession": "example_value"
    }
}
result = tu.run(query)

Pfam_get_family_proteins (Type: PfamTool)#

Get proteins containing a specific Pfam domain, optionally filtered by species. Returns protein a…

Pfam_get_family_proteins tool specification

Tool Information:

  • Name: Pfam_get_family_proteins

  • Type: PfamTool

  • Description: Get proteins containing a specific Pfam domain, optionally filtered by species. Returns protein accessions, names, gene names, lengths, organisms, and exact domain positions. Results are cursor-paginated: when has_more is true, pass next_cursor as cursor with the same filters to retrieve the next page.

Parameters:

  • pfam_accession (string) (required) Pfam family accession. Examples: ‘PF00001’ (7tm_1 GPCR), ‘PF00076’ (RRM_1), ‘PF00069’ (Pkinase), ‘PF00125’ (Core histone).

  • max_results (integer) (optional) Maximum number of proteins to return (default 20, max 100).

  • cursor ([‘string’, ‘null’]) (optional) Opaque InterPro cursor returned as next_cursor by a previous call. Omit for the first page.

  • reviewed_only (boolean) (optional) If true (default), return only SwissProt-reviewed proteins. Set false for all UniProt proteins.

  • tax_id ([‘string’, ‘null’]) (optional) NCBI taxonomy ID to filter by species. Examples: ‘9606’ (human), ‘10090’ (mouse), ‘7227’ (Drosophila), ‘559292’ (S. cerevisiae).

Example Usage:

query = {
    "name": "Pfam_get_family_proteins",
    "arguments": {
        "pfam_accession": "example_value"
    }
}
result = tu.run(query)

Pfam_get_family_proteomes (Type: PfamTool)#

Get the proteome (organism) distribution for a Pfam protein family, including organism names, tax…

Pfam_get_family_proteomes tool specification

Tool Information:

  • Name: Pfam_get_family_proteomes

  • Type: PfamTool

  • Description: Get the proteome (organism) distribution for a Pfam protein family, including organism names, taxonomy IDs, and reference status. Results are cursor-paginated: when has_more is true, pass next_cursor as cursor to retrieve the next page.

Parameters:

  • pfam_accession (string) (required) Pfam family accession. Examples: ‘PF00001’ (7tm_1, found in 1890 proteomes), ‘PF00076’ (RRM_1, 6831 proteomes), ‘PF00069’ (Pkinase).

  • max_results (integer) (optional) Maximum number of proteomes to return (default 20, max 100).

  • cursor ([‘string’, ‘null’]) (optional) Opaque InterPro cursor returned as next_cursor by a previous call. Omit for the first page.

Example Usage:

query = {
    "name": "Pfam_get_family_proteomes",
    "arguments": {
        "pfam_accession": "example_value"
    }
}
result = tu.run(query)

Pfam_get_protein_annotations (Type: PfamTool)#

Get all Pfam domain annotations for a specific protein by its UniProt accession. Returns every Pf…

Pfam_get_protein_annotations tool specification

Tool Information:

  • Name: Pfam_get_protein_annotations

  • Type: PfamTool

  • Description: Get all Pfam domain annotations for a specific protein by its UniProt accession. Returns every Pfam domain found in the protein with exact start/end residue positions, E-values (scores), short names, and integrated InterPro entries. This provides the complete Pfam domain architecture of a protein. For example, P04637 (TP53) has 4 Pfam domains: PF08563 (P53_TAD, 6-30), PF18521 (P53_TAD2, 35-59), PF00870 (P53, 100-288), PF07710 (P53_tetramer, 319-357). Use this to understand the domain composition of any protein.

Parameters:

  • accession (string) (required) UniProt protein accession. Examples: ‘P04637’ (TP53, 4 domains), ‘P00533’ (EGFR), ‘P68431’ (Histone H3.1), ‘P38398’ (BRCA1), ‘P01308’ (Insulin).

Example Usage:

query = {
    "name": "Pfam_get_protein_annotations",
    "arguments": {
        "accession": "example_value"
    }
}
result = tu.run(query)

Pfam_search_clans (Type: PfamTool)#

Search and list Pfam clans (superfamilies) by keyword. Pfam clans group related families with a c…

Pfam_search_clans tool specification

Tool Information:

  • Name: Pfam_search_clans

  • Type: PfamTool

  • Description: Search and list Pfam clans (superfamilies) by keyword. Pfam clans group related families with a common evolutionary origin. If no query is given, lists all clans. Results are cursor-paginated: when has_more is true, pass next_cursor as cursor to retrieve the next page.

Parameters:

  • query (string) (optional) Search keyword for clan name. Examples: ‘kinase’, ‘EGF’, ‘RRM’, ‘immunoglobulin’. Leave empty to list all clans.

  • max_results (integer) (optional) Maximum number of clans to return (default 20, max 100).

  • cursor ([‘string’, ‘null’]) (optional) Opaque InterPro cursor returned as next_cursor by a previous call. Omit for the first page.

Example Usage:

query = {
    "name": "Pfam_search_clans",
    "arguments": {
    }
}
result = tu.run(query)

Pfam_search_families (Type: PfamTool)#

Search for Pfam protein family entries by keyword using the InterPro API. Pfam is the authoritati…

Pfam_search_families tool specification

Tool Information:

  • Name: Pfam_search_families

  • Type: PfamTool

  • Description: Search for Pfam protein family entries by keyword using the InterPro API. Pfam is the authoritative database of protein families, domains, and functional sites. Returns matching Pfam family accessions, names, types (domain, family, repeat, etc.), and integrated InterPro entries. Results are cursor-paginated: when has_more is true, pass next_cursor as cursor to retrieve the next page.

Parameters:

  • query (string) (required) Search keyword. Examples: ‘kinase’, ‘zinc finger’, ‘helicase’, ‘immunoglobulin’, ‘rhodopsin’, ‘RNA binding’.

  • max_results (integer) (optional) Maximum number of results to return (default 20, max 100).

  • cursor ([‘string’, ‘null’]) (optional) Opaque InterPro cursor returned as next_cursor by a previous call. Omit for the first page.

Example Usage:

query = {
    "name": "Pfam_search_families",
    "arguments": {
        "query": "example_value"
    }
}
result = tu.run(query)