| name | brenda_database |
| description | BRENDA enzyme kinetics via VenusFactory download tools (SOAP). Use for Km/kcat, reactions, organism comparison, environmental optima by EC number. Do NOT use for pathway maps alone (kegg_database) or protein sequence fetch (uniprot_database). Requires BRENDA_EMAIL and BRENDA_PASSWORD. |
| license | Unknown |
| metadata | {"version":"1.2","skill-author":"VenusFactory2"} |
BRENDA Database
Overview
Agent exposes download-only tools that write JSON/CSV to disk. Configure BRENDA_EMAIL + BRENDA_PASSWORD in the environment.
Project Tools (VenusFactory2)
| Tool | Key args | Purpose |
|---|
| download_brenda_km_values_by_ec_number | ec_number, out_path, optional organism/substrate | Km values |
| download_brenda_reactions_by_ec_number | ec_number, out_path | Reactions |
| download_brenda_enzymes_by_substrate | substrate, out_path, limit | Enzymes by substrate |
| download_brenda_compare_organisms_by_ec_number | ec_number, organisms, out_path | Cross-organism |
| download_brenda_environmental_parameters_by_ec_number | ec_number, out_path | pH / temperature |
| download_brenda_kinetic_data_by_ec_number | ec_number, out_path, format | Kinetic export |
| download_brenda_pathway_report | pathway (dict), out_path | Pathway report file |
Returns rich JSON with status + file_info (not {success, file_path}). Tools live in src/tools/database/tools_agent.py.
Workflow
- Resolve EC number (user / UniProt / KEGG).
- Pick the matching download tool; set session-scoped
out_path.
- Parse saved file; plot kinetics if useful (
nature_figure for publication).
When NOT to use
- Gene→pathway wiring without kinetics →
kegg_database / string_database
- Empty files usually mean missing BRENDA credentials
Common mistakes
- Importing
query_brenda_* as hub tools (not registered — use download_*)
- Putting SOAP payloads in chat instead of reading
file_info.file_path
- Wrong path docs pointing at
search/tools_agent.py
References (progressive disclosure)
Trust order: SKILL.md (hub tools & envelopes) → topic refs → references/legacy_guide.md (archived; may be outdated).
read_skill(skill_id="brenda_database", relative_path="references/legacy_guide.md")
Load legacy only after the hub workflow in this file is insufficient.
