uniprot

name	uniprot
description	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, use pdb. For sequence design, use proteinmpnn.
license	MIT
category	utilities
tags	["database","sequence","annotation"]
source	https://github.com/adaptyvbio/protein-design-skills

UniProt Database Access

Note: Uses UniProt REST API directly. No Modal needed.

Fetching Sequences

# FASTA format
curl "https://rest.uniprot.org/uniprotkb/P00533.fasta"

# JSON format with annotations
curl "https://rest.uniprot.org/uniprotkb/P00533.json"

import requests

def get_uniprot_sequence(accession):
    url = f"https://rest.uniprot.org/uniprotkb/{accession}.fasta"
    response = requests.get(url)
    if response.ok:
        lines = response.text.strip().split('\n')
        return lines[0], ''.join(lines[1:])
    return None, None

def get_uniprot_entry(accession):
    url = f"https://rest.uniprot.org/uniprotkb/{accession}.json"
    response = requests.get(url)
    return response.json() if response.ok else None

Getting Annotations

Domain boundaries

def get_domains(accession):
    entry = get_uniprot_entry(accession)
    return [
        {'name': f.get('description', ''),
         'start': f['location']['start']['value'],
         'end': f['location']['end']['value']}
        for f in entry.get('features', [])
        if f['type'] == 'Domain'
    ]

PDB cross-references

def get_pdb_references(accession):
    entry = get_uniprot_entry(accession)
    return [
        {'pdb_id': xref['id']}
        for xref in entry.get('uniProtKBCrossReferences', [])
        if xref['database'] == 'PDB'
    ]

Searching UniProt

def search_uniprot(query, organism=None, limit=10):
    params = {"query": query, "format": "json", "size": limit}
    if organism:
        params["query"] += f" AND organism_id:{organism}"
    response = requests.get("https://rest.uniprot.org/uniprotkb/search", params=params)
    return response.json()['results']

# Search for human EGFR
results = search_uniprot("EGFR", organism=9606)

API Reference

Endpoint	Description
/uniprotkb/{id}.fasta	FASTA sequence
/uniprotkb/{id}.json	Full entry JSON
/uniprotkb/search	Search entries

Next: Use sequence with esm for embeddings or pdb for structure.