uniprot

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)