UniProt — Protein Database

UniProt — Protein Database

Overview

UniProt is the most comprehensive protein sequence and functional annotation database, containing 250M+ entries. This skill covers programmatic access via the UniProt REST API for protein search, sequence retrieval, ID mapping, and annotation queries. Swiss-Prot entries are manually curated; TrEMBL entries are computationally predicted.

When to Use

• Searching for proteins by gene name, accession, organism, or function keywords
• Retrieving protein sequences in FASTA format for downstream analysis
• Mapping identifiers between databases (UniProt ↔ Ensembl, PDB, RefSeq, KEGG)
• Accessing protein annotations: GO terms, domains, post-translational modifications
• Batch retrieving multiple protein entries for comparative analysis
• Downloading reviewed (Swiss-Prot) protein datasets for a specific organism
• For unified access to 40+ databases, use bioservices instead
• For protein 3D structures, use alphafold-database-access or pdb-database

Prerequisites

pip install requests pandas

API Rate Limits: UniProt REST API has no strict rate limit but recommends adding time.sleep(0.5) between batch requests. For large queries (>10k results), use the streaming endpoint instead of paginated search. Maximum 100,000 IDs per ID mapping job.

Quick Start

import requests

# Search for human insulin proteins (reviewed/Swiss-Prot only)
url = "https://rest.uniprot.org/uniprotkb/search"
params = {"query": "insulin AND organism_id:9606 AND reviewed:true", "format": "tsv",
          "fields": "accession,gene_names,protein_name,length"}
response = requests.get(url, params=params)
print(response.text[:500])
# accession  gene_names  protein_name  length
# P01308     INS         Insulin       110