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SKILL.md
InterPro Database
Overview
InterPro (https://www.ebi.ac.uk/interpro/) is a comprehensive resource for protein family and domain classification maintained by EMBL-EBI. It integrates signatures from 13 member databases including Pfam, PANTHER, PRINTS, ProSite, SMART, TIGRFAM, SUPERFAMILY, CDD, and others, providing a unified view of protein functional annotations for over 100 million protein sequences.
InterPro classifies proteins into:
Families: Groups of proteins sharing common ancestry and function
Domains: Independently folding structural/functional units
Homologous superfamilies: Structurally similar protein regions
def get_protein_entries(uniprot_id):
"""Get all InterPro entries that match a UniProt protein."""
data = interpro_get(f"protein/UniProt/{uniprot_id}/entry/InterPro/")
return data
# Example: Human p53 (TP53)
result = get_protein_entries("P04637")
entries = result.get("results", [])
for entry in entries:
meta = entry["metadata"]
print(f" {meta['accession']} ({meta['type']}): {meta['name']}")
# e.g., IPR011615 (domain): p53, tetramerisation domain
# IPR010991 (domain): p53, DNA-binding domain
# IPR013872 (family): p53 family
3. Get Specific InterPro Entry
def get_entry(interpro_id):
"""Fetch details for an InterPro entry."""
return interpro_get(f"entry/InterPro/{interpro_id}/")
# Example: Get Pfam domain PF00397 (WW domain)
ww_entry = get_entry("IPR001202")
print(f"Name: {ww_entry['metadata']['name']}")
print(f"Type: {ww_entry['metadata']['type']}")
# Also supports member database IDs:
def get_pfam_entry(pfam_id):
return interpro_get(f"entry/Pfam/{pfam_id}/")
pfam = get_pfam_entry("PF00397")
4. Search Proteins by InterPro Entry
def get_proteins_for_entry(interpro_id, database="UniProt", page_size=25):
"""Get all proteins annotated with an InterPro entry."""
params = {"page_size": page_size}
data = interpro_get(f"entry/InterPro/{interpro_id}/protein/{database}/", params)
return data
# Example: Find all human kinase-domain proteins
kinase_proteins = get_proteins_for_entry("IPR000719") # Protein kinase domain
print(f"Total proteins: {kinase_proteins['count']}")
5. Domain Architecture
def get_domain_architecture(uniprot_id):
"""Get the complete domain architecture of a protein."""
data = interpro_get(f"protein/UniProt/{uniprot_id}/")
return data
# Example: Get full domain architecture for EGFR
egfr = get_domain_architecture("P00533")
# The response includes locations of all matching entries on the sequence
for entry in egfr.get("entries", []):
for fragment in entry.get("entry_protein_locations", []):
for loc in fragment.get("fragments", []):
print(f" {entry['accession']}: {loc['start']}-{loc['end']}")
6. GO Term Mapping
def get_go_terms_for_protein(uniprot_id):
"""Get GO terms associated with a protein via InterPro."""
data = interpro_get(f"protein/UniProt/{uniprot_id}/")
# GO terms are embedded in the entry metadata
go_terms = []
for entry in data.get("entries", []):
go = entry.get("metadata", {}).get("go_terms", [])
go_terms.extend(go)
# Deduplicate
seen = set()
unique_go = []
for term in go_terms:
if term["identifier"] not in seen:
seen.add(term["identifier"])
unique_go.append(term)
return unique_go
# GO terms include:
# {"identifier": "GO:0004672", "name": "protein kinase activity", "category": {"code": "F", "name": "Molecular Function"}}
7. Batch Protein Lookup
def batch_lookup_proteins(uniprot_ids, database="UniProt"):
"""Look up multiple proteins and collect their InterPro entries."""
import time
results = {}
for uid in uniprot_ids:
try:
data = interpro_get(f"protein/{database}/{uid}/entry/InterPro/")
entries = data.get("results", [])
results[uid] = [
{
"accession": e["metadata"]["accession"],
"name": e["metadata"]["name"],
"type": e["metadata"]["type"]
}
for e in entries
]
except Exception as e:
results[uid] = {"error": str(e)}
time.sleep(0.3) # Rate limiting
return results
# Example
proteins = ["P04637", "P00533", "P38398", "Q9Y6I9"]
domain_info = batch_lookup_proteins(proteins)
for uid, entries in domain_info.items():
print(f"\n{uid}:")
for e in entries[:3]:
print(f" - {e['accession']} ({e['type']}): {e['name']}")
8. Search by Text or Taxonomy
def search_entries(query, entry_type=None, taxonomy_id=None):
"""Search InterPro entries by text."""
params = {"search": query, "page_size": 20}
if entry_type:
params["type"] = entry_type # family, domain, homologous_superfamily, etc.
endpoint = "entry/InterPro/"
if taxonomy_id:
endpoint = f"entry/InterPro/taxonomy/UniProt/{taxonomy_id}/"
return interpro_get(endpoint, params)
# Search for kinase-related entries
kinase_entries = search_entries("kinase", entry_type="domain")
Look up each InterPro entry for biological context
Get GO terms from associated InterPro entries for functional inference
# After running InterProScan and getting a UniProt ID:
def characterize_protein(uniprot_id):
"""Complete characterization workflow."""
# 1. Get all annotations
entries = get_protein_entries(uniprot_id)
# 2. Group by type
by_type = {}
for e in entries.get("results", []):
t = e["metadata"]["type"]
by_type.setdefault(t, []).append({
"accession": e["metadata"]["accession"],
"name": e["metadata"]["name"]
})
# 3. Get GO terms
go_terms = get_go_terms_for_protein(uniprot_id)
return {
"families": by_type.get("family", []),
"domains": by_type.get("domain", []),
"superfamilies": by_type.get("homologous_superfamily", []),
"go_terms": go_terms
}
Workflow 2: Find All Members of a Protein Family
Identify the InterPro family entry ID (e.g., IPR000719 for protein kinases)
Query all UniProt proteins annotated with that entry
Filter by organism/taxonomy if needed
Download FASTA sequences for phylogenetic analysis
Workflow 3: Comparative Domain Analysis
Collect proteins of interest (e.g., all paralogs)
Get domain architecture for each protein
Compare domain compositions and orders
Identify domain gain/loss events
API Endpoint Summary
Endpoint
Description
/protein/UniProt/{id}/
Full annotation for a protein
/protein/UniProt/{id}/entry/InterPro/
InterPro entries for a protein
/entry/InterPro/{id}/
Details of an InterPro entry
/entry/Pfam/{id}/
Pfam entry details
/entry/InterPro/{id}/protein/UniProt/
Proteins with an entry
/entry/InterPro/
Search/list InterPro entries
/taxonomy/UniProt/{tax_id}/
Proteins from a taxon
/structure/PDB/{pdb_id}/
Structures mapped to InterPro
Member Databases
Database
Focus
Pfam
Protein domains (HMM profiles)
PANTHER
Protein families and subfamilies
PRINTS
Protein fingerprints
ProSitePatterns
Amino acid patterns
ProSiteProfiles
Protein profile patterns
SMART
Protein domain analysis
TIGRFAM
JCVI curated protein families
SUPERFAMILY
Structural classification
CDD
Conserved Domain Database (NCBI)
HAMAP
Microbial protein families
NCBIfam
NCBI curated TIGRFAMs
Gene3D
CATH structural classification
PIRSR
PIR site rules
Best Practices
Use UniProt accession numbers (not gene names) for the most reliable lookups
Distinguish types: family gives broad classification; domain gives specific structural/functional units
InterProScan is faster for novel sequences: For sequences not in UniProt, submit to the web service
Handle pagination: Large result sets require iterating through pages
Combine with UniProt data: InterPro entries often include links to UniProt, PDB, and GO
