# Uniprot [Health: Active]

**Category:** 🗄️ Databases  
**Repository:** https://github.com/pipeworx-io/mcp-uniprot  
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**Directory Page:** https://allmcps.com/mcp/uniprot

## Description
UniProt MCP — protein sequence + function database.

## Tools
Capabilities this server exposes over MCP:

- **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.

## Claude Desktop Quick Installation
Install path detected from listing signals. Uses `npx` (confidence: high):

```json
"mcpServers": {
  "uniprot": {
    "command": "npx",
    "args": ["-y","@pipeworx/mcp-uniprot"]
  }
}
```

## Documentation

## What the Uniprot MCP server does

The Uniprot MCP server exposes selected UniProt data operations through the Model Context Protocol. UniProt provides protein sequence and function information, and the underlying public service is available at `https://rest.uniprot.org/` without an API key.

Its tools cover several common lookup tasks:

- Search UniProtKB with Lucene-style queries, with optional output format and result-size controls.
- Retrieve one record using a UniProt accession such as `P12345`.
- Search available proteomes.
- Search NCBI taxonomy as represented by UniProt.
- Retrieve information for a UniProt keyword ID.
- Summarize feature annotations for an accession, including categories such as domains and mutagens.

This makes the Uniprot MCP server suitable for agents that need to find proteins, inspect records, or retrieve related biological annotations rather than perform general database administration.

## How it works

The service has two connection modes. A remote MCP endpoint is available at `https://gateway.pipeworx.io/uniprot/mcp`. That endpoint exposes the Uniprot tools and also includes shared Pipeworx gateway tools. The gateway’s `ask_pipeworx` tool can route a plain-language request across the wider Pipeworx catalog, while the direct tools handle the UniProt operations listed above.

The same gateway also provides a full endpoint at `https://gateway.pipeworx.io/mcp`. The pack endpoint lists the Uniprot tools directly; the full endpoint lists tools from the broader catalog. The initialization response is the authoritative source for the exact tools exposed by a connection.

For direct HTTP use, tool calls can be sent to gateway routes such as `/v1/tools/uniprot_search` with a JSON request body. A tool definition can be inspected through the corresponding gateway endpoint.

## Setup and configuration

Add the remote MCP URL to a compatible client, or run the package locally with npx:

```json
{
  "mcpServers": {
    "uniprot": {
      "command": "npx",
      "args": ["-y", "@pipeworx/mcp-uniprot"]
    }
  }
}
```

The local package communicates over stdin and stdout and does not require a Pipeworx account or gateway round trip. It exposes only the pack’s UniProt tools, without the shared gateway meta-tools. The remote connection requires no account for initial calls according to the supplied documentation, and the data source itself is keyless.

## Limitations and notes

Remote pack connections include shared Pipeworx tools in addition to the pack-specific tools. As a result, the number shown by `tools/list` can be larger than the six UniProt operations documented here. There is no supported way to remove those shared tools from a pack endpoint.

The local and remote modes use the same source and provide the same pack-specific capabilities, but only the gateway mode provides Pipeworx-wide routing through `ask_pipeworx`. Results and query behavior depend on the public UniProt REST service and the query formats it accepts.

_Full upstream README: https://allmcps.com/mcp/uniprot/readme_