uniprot
Access UniProt for protein sequence and annotation retrieval. Use this skill when: (1) Looking up protein sequences by accession, (2) Finding functional annotations, (3) Getting domain boundaries, (4) Finding homologs and variants, (5) Cross-referencing to PDB structures. For structure retrieval, us
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UniProt Database Access
Note: This skill uses the UniProt REST API directly. No Modal deployment needed - all operations run locally via HTTP requests.
Fetching Sequences
By Accession
# FASTA format
curl "https://rest.uniprot.org/uniprotkb/P00533.fasta"
# JSON format with annotations
curl "https://rest.uniprot.org/uniprotkb/P00533.json"
Using Python
import requests
def get_uniprot_sequence(accession):
"""Fetch sequence from UniProt."""
url = f"https://rest.uniprot.org/uniprotkb/{accession}.fasta"
response = requests.get(url)
if response.ok:
lines = response.text.strip().split('\n')
header = lines[0]
sequence = ''.join(lines[1:])
return header, sequence
return None, None
Getting Annotations
Full Entry
def get_uniprot_entry(accession):
"""Fetch full UniProt entry as JSON."""
url = f"https://rest.uniprot.org/uniprotkb/{accession}.json"
response = requests.get(url)
return response.json() if response.ok else None
entry = get_uniprot_entry("P00533")
print(f"Protein: {entry['proteinDescription']['recommendedName']['fullName']['value']}")
Domain Boundaries
def get_domains(accession):
"""Extract domain annotations."""
entry = get_uniprot_entry(accession)
domains = []
for feature in entry.get('features', []):
if feature['type'] == 'Domain':
domains.append({
'name': feature.get('description', ''),
'start': feature['location']['start']['value'],
'end': feature['location']['end']['value']
})
return domains
# Example: EGFR domains
domains = get_domains("P00533")
# [{'name': 'Kinase', 'start': 712, 'end': 979}, ...]
Searching UniProt
By Gene Name
def search_uniprot(query, organism=None, limit=10):
"""Search UniProt by query."""
url = "https://rest.uniprot.org/uniprotkb/search"
params = {
"query": query,
"format": "json",
"size": limit
}
if organism:
params["query"] += f" AND organism_id:{organism}"
response = requests.get(url, params=params)
return response.json()['results']
# Search for human EGFR
results = search_uniprot("EGFR", organism=9606)
By Sequence Similarity (BLAST)
# Use UniProt BLAST
# https://www.uniprot.org/blast