Scanprosite Tools#

Configuration File: scanprosite_tools.json Tool Type: Local Tools Count: 2

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

Available Tools#

ScanProsite_find_proteins_with_motif (Type: PROSITETool)#

Reverse PROSITE motif scan with recoverable pagination over every match present in the ScanProsit…

ScanProsite_find_proteins_with_motif tool specification

Tool Information:

  • Name: ScanProsite_find_proteins_with_motif

  • Type: PROSITETool

  • Description: Reverse PROSITE motif scan with recoverable pagination over every match present in the ScanProsite response. Continue with next_offset while has_more is true. If capped is true, the remote database scan itself is incomplete even after all available pages are consumed; complete_database_result and capped_note make this explicit.

Parameters:

  • signature_ac (string) (required) PROSITE signature accession starting with ‘PS’. Examples: ‘PS00029’ (LEUCINE_ZIPPER), ‘PS00107’ (PROTEIN_KINASE_ATP), ‘PS00028’ (ZINC_FINGER_C2H2_1). Use PROSITE_search or PROSITE_get_entry to discover signature accessions.

  • db (string) (optional) Sequence database to search: ‘sprot’ = Swiss-Prot (reviewed, default), ‘trembl’ = TrEMBL (unreviewed), ‘uniprot’ = both.

  • skip_frequent (boolean) (optional) If true (default), skip very frequent low-information signatures (SKIP-FLAG=TRUE patterns such as PS00005, PS00008). Set to false to force ScanProsite to include them; note these can produce extremely large or truncated responses across the whole proteome.

  • max_results (integer) (optional) Maximum response matches to return on this page (default 50, max 1000).

  • offset (integer) (optional) Zero-based offset within matches available in this ScanProsite response.

Example Usage:

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

ScanProsite_scan_protein (Type: BaseRESTTool)#

Scan a protein against the PROSITE database of protein motifs, domains, and families. Given a Uni…

ScanProsite_scan_protein tool specification

Tool Information:

  • Name: ScanProsite_scan_protein

  • Type: BaseRESTTool

  • Description: Scan a protein against the PROSITE database of protein motifs, domains, and families. Given a UniProt accession (e.g., P04637 for TP53, P01308 for insulin), identifies all PROSITE pattern matches in the protein sequence. Returns matched PROSITE signature accessions and IDs with start/end positions. PROSITE is part of the ExPASy/SIB suite and contains 1,800+ patterns and profiles for protein functional sites and domains. Essential for identifying conserved motifs like zinc fingers, kinase activation loops, or receptor binding sites. Note: only patterns (PS00xxx) are scanned; profile matches require the ScanProsite web interface.

Parameters:

  • seq (string) (required) UniProt accession to scan for PROSITE motifs. Examples: ‘P04637’ (TP53, returns PS00348 p53 signature), ‘P01308’ (insulin, returns PS00262 insulin family), ‘Q9UHC1’ (MLH3, returns PS00058 DNA mismatch repair). Can also accept a raw amino acid sequence.

Example Usage:

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