APIbase

UniProt — Search Proteins

science.uniprot.search

Read-onlyIdempotent

Search UniProt protein sequences by name, gene, or organism to retrieve accessions, annotations, and review status for protein research.

Instructions

Search the UniProt protein sequence database for proteins by name, gene, or organism. UniProt is the world's leading repository for protein sequences and functional annotations, covering 250M+ sequences from Swiss-Prot (reviewed) and TrEMBL (unreviewed). Returns accession, protein name, organism, gene names, sequence length, review status, and annotation score. Supports field-specific queries (gene:TP53, organism:9606) and free-text search. Use reviewed:true to restrict to Swiss-Prot's manually curated, high-quality entries. CC BY 4.0 — Universal Protein Resource (UniProt Consortium)

Input Schema

Name	Required	Description
`gene`	No	Gene name filter (exact or partial). E.g. "TP53", "EGFR", "BRAC1". Combined with query using AND logic
`limit`	No	Number of results to return (1–25, default 5)
`query`	Yes	Protein or gene search term — e.g. "insulin", "hemoglobin", "BRCA1". Supports UniProt query syntax: field:value pairs (e.g. "protein_name:kinase")
`reviewed`	No	If true, restrict to Swiss-Prot (manually reviewed) entries only. Swiss-Prot has higher quality annotations than TrEMBL (unreviewed)
`organism_id`	No	NCBI taxonomy ID to filter by organism. Common IDs: 9606 (human), 10090 (mouse), 10116 (rat), 7227 (fruit fly), 6239 (C. elegans), 3702 (A. thaliana)

Output Schema

Name	Required	Description	Default
`error`	No	Present only when the call failed. Includes error code, message, request_id, and any provider-specific extras.
`result`	No	Tool response payload. Shape varies per tool — consult the tool description and inputSchema. May be an object, array, string, or number depending on the upstream provider response.

Schema Changelog

Changes observed during successful MCP inspections.

Addedv2.2.0Oct 29, 2026

TDQS

A3.9/5.0

Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already mark this read-only/idempotent/non-destructive. The description adds behavioral detail beyond that: response fields, field-specific query syntax, the reviewed/unreviewed distinction, and the data source coverage. It doesn't describe pagination/rate limits, but the schema and output schema cover the essentials.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Front-loaded action sentence, then useful return-field and query-syntax detail. Some non-operational context (250M+ sequences, CC BY 4.0) could be trimmed, but the overall structure is efficient and scannable.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness4/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given rich annotations, full parameter descriptions, and an output schema, the description is sufficient for an agent to select the tool and construct common searches. It lacks sibling routing (e.g., 'for a known accession use entry'), but this doesn't block correct use for search.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema coverage is 100%, so baseline is 3. The description adds query-syntax examples (gene:TP53, organism:9606) and free-text search, but the schema already documents each parameter with examples and AND logic; the description mostly reinforces rather than clarifies the parameters.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

Opens with a specific verb and resource: 'Search the UniProt protein sequence database for proteins by name, gene, or organism,' and enumerates returned fields. It does not explicitly differentiate itself from sibling tools like science.uniprot.entry or science.uniprot.features, so it stops short of a 5.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Gives clear context: free-text vs field-specific queries, and the reviewed:true filter for Swiss-Prot is a concrete condition for a common variant. It doesn't explicitly exclude the sibling entry/features tools, but the search use case is unambiguous.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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