Prosite Tools

Configuration File: prosite_tools.json Tool Type: Local Tools Count: 3

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

Available Tools

PROSITE_get_entry (Type: PROSITETool)

Retrieve a PROSITE protein motif/domain entry by its accession number. Returns the entry name, de…

PROSITE_get_entry tool specification

Tool Information:

  • Name: PROSITE_get_entry

  • Type: PROSITETool

  • Description: Retrieve a PROSITE protein motif/domain entry by its accession number. Returns the entry name, description, type (PATTERN or MATRIX/profile), consensus pattern, functional site annotations, cross-references to UniProt proteins, and documentation links. PROSITE (ExPASy/SIB) contains 1,800+ patterns and profiles describing protein domains, families, and functional sites. Pattern accessions start with PS000xx (e.g., PS00001 for N-glycosylation, PS00028 for zinc finger C2H2). Use this to understand what a PROSITE motif means after finding it via ScanProsite_scan_protein.

Parameters:

  • accession (string) (required) PROSITE accession number starting with ‘PS’. Examples: ‘PS00001’ (N-glycosylation site), ‘PS00028’ (zinc finger C2H2 signature), ‘PS00348’ (p53 tumor suppressor family), ‘PS51420’ (Rho GTPase domain profile), ‘PS00262’ (insulin family signature).

Example Usage:

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

PROSITE_scan_sequence (Type: PROSITETool)

Scan a raw protein amino acid sequence against all PROSITE patterns and profiles to find matching…

PROSITE_scan_sequence tool specification

Tool Information:

  • Name: PROSITE_scan_sequence

  • Type: PROSITETool

  • Description: Scan a raw protein amino acid sequence against all PROSITE patterns and profiles to find matching motifs and domains. Returns PROSITE signature accessions, names, positions, and confidence scores. This is the sequence-based alternative to ScanProsite_scan_protein (which accepts UniProt accessions). Use this when you have a novel or modified sequence not in UniProt. By default, skips frequent/low-information patterns (like N-glycosylation); set skip_frequent=false to include all matches.

Parameters:

  • sequence (string) (required) Protein amino acid sequence in single-letter code (e.g., ‘MKTAYIAKQRQ…’). Must contain only standard amino acid letters.

  • skip_frequent (boolean) (optional) If true (default), skip frequent low-information patterns like glycosylation sites. Set to false to include all matches.

Example Usage:

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

PROSITE_search (Type: PROSITETool)

Search the PROSITE database for protein motifs, domains, and functional site patterns by keyword….

PROSITE_search tool specification

Tool Information:

  • Name: PROSITE_search

  • Type: PROSITETool

  • Description: Search the PROSITE database for protein motifs, domains, and functional site patterns by keyword. Uses the EBI InterPro API which indexes all PROSITE entries. Returns accession numbers, names, types, and InterPro cross-references. Useful for finding PROSITE patterns related to a biological function (e.g., ‘kinase’, ‘zinc finger’, ‘glycosylation’). Follow up with PROSITE_get_entry to get full details of any result.

Parameters:

  • query (string) (required) Search keyword(s) for PROSITE entries. Examples: ‘zinc finger’, ‘kinase’, ‘glycosylation’, ‘insulin’, ‘p53’, ‘EGF-like domain’.

  • limit (integer) (optional) Maximum number of results to return (default: 10, max: 50).

Example Usage:

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