Uniprot

UniProt MCP — protein sequence + function database.

Part of Pipeworx — an MCP gateway connecting AI agents to 965+ live data sources.

Tools

Tool	Description
search	"Find protein [name]" / "look up [gene] in UniProt" / "BRCA1 / TP53 / insulin protein info" / "all proteins for [organism]" — UniProtKB search via Lucene-style queries (e.g. "gene:BRCA1 AND organism_id:9606" for human BRCA1). UniProt is the authoritative protein-sequence-and-function database — use for protein characterization, function annotation, sequence retrieval, and cross-references to PDB/GO/PubMed.
get	"Fetch protein [P12345]" / "UniProt entry for [accession]" / "FASTA sequence for [protein]" — single UniProtKB entry by accession (e.g. P12345 or P38398 for BRCA1_HUMAN). Returns full protein record: sequence, function annotations, GO terms, cross-refs, post-translational modifications, variants. Pass format=fasta for sequence only.
proteomes_search	"Reference proteome for [organism]" / "complete protein set of [species]" — search UniProt reference proteomes (the curated representative protein set per organism). Use as a starting point for genome-scale protein analyses.
taxonomy_search	"NCBI taxonomy ID for [organism]" / "taxid for [species]" / "look up [Latin name] in NCBI taxonomy" — search NCBI Taxonomy via UniProt's mirror. Returns taxonomic IDs you can use as organism_id filters in search (9606 = human, 10090 = mouse, 7227 = D. melanogaster, etc).
keyword	"UniProt keyword KW-N info" / "what does keyword [X] mean" — fetch a UniProt controlled-vocabulary keyword by ID. Use to look up annotation tags like "Kinase" / "Membrane" / "Disease-associated".
feature_summary	"Domain map of [protein]" / "annotated features of [accession]" / "what regions / sites does [protein] have" — annotated features (domains, active sites, transmembrane regions, mutagenesis sites, glycosylation, disulfide bonds, etc.) for a UniProt accession. Use for structural/functional analysis without pulling the full protein record.

Quick Start

Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):

{
  "mcpServers": {
    "uniprot": {
      "url": "https://gateway.pipeworx.io/uniprot/mcp"
    }
  }
}

Or connect to the full Pipeworx gateway for access to all 965+ data sources:

{
  "mcpServers": {
    "pipeworx": {
      "url": "https://gateway.pipeworx.io/mcp"
    }
  }
}

Using with ask_pipeworx

Instead of calling tools directly, you can ask questions in plain English:

ask_pipeworx({ question: "your question about Uniprot data" })

The gateway picks the right tool and fills the arguments automatically.

More

• All tools and guides
• pipeworx.io

License

MIT