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 with page sizes from 1 to 1000 and exposes its cursor pagination: when metadata.has_more is true, pass metadata.next_cursor unchanged in the next call. Metadata reports exact total_results, returned, and page_size. Returns accession numbers, names, types, and InterPro cross-references.

Parameters:

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

  • limit (integer) (optional) Number of results per page (1-1000). Values outside this range are rejected rather than silently clamped.

  • cursor (string) (optional) Opaque InterPro pagination cursor. Omit for the first page; for later pages, pass metadata.next_cursor from the preceding response unchanged.

Example Usage:

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