query-uniprot

name	query-uniprot
description	Query UniProt protein database. Use when user asks about protein sequences, functions, annotations, domains, or protein identifiers. Triggers on "uniprot", "protein function", "protein sequence", "gene product", "protein info".

UniProt Protein Database Query

Query the UniProt REST API for protein information.

When to Use

• User asks about a protein's function, sequence, or annotation
• User provides a gene name and wants protein info
• User needs protein accession IDs
• User asks "what does gene X do" (protein level)

How to Execute

import requests
import json

BASE_URL = "https://rest.uniprot.org"

# 1. Search by gene name (default: human, reviewed/Swiss-Prot)
def search_uniprot(gene_name, organism_id=9606, max_results=5):
    url = f"{BASE_URL}/uniprotkb/search"
    params = {
        "query": f"gene_exact:{gene_name} AND organism_id:{organism_id} AND reviewed:true",
        "format": "json",
        "size": max_results,
        "fields": "accession,id,gene_names,protein_name,organism_name,length,cc_function,ft_domain,sequence"
    }
    r = requests.get(url, params=params)
    r.raise_for_status()
    return r.json()

# 2. Get by accession ID
def get_uniprot_entry(accession):
    url = f"{BASE_URL}/uniprotkb/{accession}.json"
    # Request an explicit field set so the response shape is deterministic.
    params = {"fields": "accession,id,gene_names,protein_name,organism_name,length,cc_function,ft_domain,sequence"}
    r = requests.get(url, params=params, timeout=30)
    r.raise_for_status()
    return r.json()

# 3. Get FASTA sequence
def get_fasta(accession):
    url = f"{BASE_URL}/uniprotkb/{accession}.fasta"
    r = requests.get(url)
    r.raise_for_status()
    return r.text

# Example usage
data = search_uniprot("TP53")
for entry in data.get("results", []):
    acc = entry["primaryAccession"]
    name = entry.get("proteinDescription", {}).get("recommendedName", {}).get("fullName", {}).get("value", "N/A")
    gene = entry.get("genes", [{}])[0].get("geneName", {}).get("value", "N/A")
    length = entry.get("sequence", {}).get("length", "N/A")
    
    # Extract function
    functions = [c["texts"][0]["value"] for c in entry.get("comments", []) if c["commentType"] == "FUNCTION"]
    func_text = functions[0][:200] if functions else "N/A"
    
    print(f"Accession: {acc}")
    print(f"Protein: {name}")
    print(f"Gene: {gene}")
    print(f"Length: {length} aa")
    print(f"Function: {func_text}")

Common Search Patterns

• By gene: gene_exact:BRCA1 AND organism_id:9606
• By keyword: keyword:kinase AND organism_id:9606
• By disease: cc_disease:cancer AND organism_id:9606
• By GO term: go:apoptosis AND organism_id:9606
• Species IDs: Human=9606, Mouse=10090, Rat=10116, Zebrafish=7955, Fly=7227, Yeast=559292

Output Format

Present: Accession, protein name, gene, organism, length, function summary, and UniProt link.

Follow-up Suggestions

• "Want me to get the AlphaFold structure for this protein?"
• "Should I check protein-protein interactions on STRING?"
• "Want me to BLAST this protein sequence?"