Tcdb Tools#

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

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

Available Tools#

TCDB_get_transporter (Type: TCDBTool)#

Look up a membrane transporter protein in TCDB (Transporter Classification Database) by UniProt a…

TCDB_get_transporter tool specification

Tool Information:

  • Name: TCDB_get_transporter

  • Type: TCDBTool

  • Description: Look up a membrane transporter protein in TCDB (Transporter Classification Database) by UniProt accession. Returns TC classification number(s), family description, associated PDB structures, and human gene info if applicable. TC# format: class.subclass.family.subfamily.protein (e.g., 2.A.1.1.28 for human GLUT1).

Parameters:

  • uniprot_accession (string) (required) UniProt accession ID of the transporter protein (e.g., P11166 for GLUT1, P08183 for P-glycoprotein/MDR1). Aliases: uniprot_id, accession.

Example Usage:

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

TCDB_search_by_substrate (Type: TCDBTool)#

Search TCDB for transporters that transport a given substrate. Returns TC numbers, family descrip…

TCDB_search_by_substrate tool specification

Tool Information:

  • Name: TCDB_search_by_substrate

  • Type: TCDBTool

  • Description: Search TCDB for transporters that transport a given substrate. Returns TC numbers, family descriptions, and matching substrate ChEBI IDs. Useful for finding which transporters handle a specific molecule (e.g., glucose, sodium, chloride, ATP).

Parameters:

  • substrate_name (string) (required) Name of the substrate to search for (e.g., ‘glucose’, ‘sodium’, ‘chloride’, ‘ATP’). Case-insensitive partial match. Aliases: substrate.

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

Example Usage:

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

TCDB_search_family (Type: TCDBTool)#

Search TCDB transporter families by TC family ID prefix or family name text. Returns matching fam…

TCDB_search_family tool specification

Tool Information:

  • Name: TCDB_search_family

  • Type: TCDBTool

  • Description: Search TCDB transporter families by TC family ID prefix or family name text. Returns matching family descriptions and member counts. Use family_id for hierarchical browsing (e.g., ‘2.A.1’ for MFS superfamily, ‘1.A’ for all alpha-type channels) or family_name for text search (e.g., ‘Major Facilitator’, ‘ABC’).

Parameters:

  • family_id (string) (optional) TC family ID or prefix to search (e.g., ‘2.A.1’ for Major Facilitator Superfamily, ‘1.A.1’ for VIC superfamily). Matches all families starting with this prefix. Either family_id or family_name is required.

  • family_name (string) (optional) Text to search in family descriptions (e.g., ‘Major Facilitator’, ‘ABC’, ‘glucose’). Case-insensitive. Either family_id or family_name is required.

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

Example Usage:

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