interpro-domain-annotation

name	interpro_domain_annotation
description	InterPro domain/family annotation via VenusFactory download tools. Use when the user needs domain boundaries, family membership, or UniProt→InterPro annotations for engineering target selection. Do NOT use for pathway enrichment (string_database / kegg_database) or kinetic parameters (brenda_database).
license	Apache-2.0
metadata	{"version":"1.0","skill-author":"VenusFactory2"}

InterPro Domain Annotation

Overview

Retrieves InterPro entry metadata, UniProt-linked annotations, and protein lists. Prefer these hub tools over ad-hoc HTTP in agent_generated_code.

Project Tools (VenusFactory2)

Tool	Args	When
download_interpro_metadata_by_id	interpro_id, out_dir	Known IPR / entry id
download_interpro_annotations_by_uniprot_id	uniprot_id, out_dir	Domains on a protein
download_interpro_proteins_by_id	interpro_id, out_dir, pagination args	Members of a family
download_interpro_uniprot_list_by_id	interpro_id, out_dir	UniProt accessions for an entry
download_uniprot_meta_by_id	uniprot_id, out_path	Cross-check function/GO

Workflow

1. If user has UniProt accession → download_interpro_annotations_by_uniprot_id.
2. For a specific InterPro id → metadata + optional protein list.
3. Before proposing mutations in catalytic triads, confirm the domain via InterPro + UniProt meta.
4. Optional: map domains onto structure via protein_structure_pipeline + residue indices.

Common mistakes

• Treating InterPro ids as UniProt accessions.
• Editing conserved catalytic residues without reading annotation evidence.