search_uniprot_entity
Search UniProt proteins using Solr-style queries, filtering by gene, organism, keyword, or sequence length. Returns TSV rows with accession, protein name, and organism.
Instructions
Search for a UniProt entity ID by query.
⚠️ Only the search string and limit are accepted. Extra parameters
like taxon, organism, reviewed, species, etc. are silently
dropped and have no effect — express such filters inside the Solr
query string instead (e.g., organism_id:9606 AND reviewed:true).
⚠️ An unrecognised FIELD NAME inside the query string is not silently
ignored: UniProt rejects it (HTTP 400, "'taxon' is not a valid search
field") and this tool returns the "Error:" string described below.
Common wrong guesses that fail this way: taxon, organism, species,
go_id. What CAN fail silently is a valid field given an ill-formed
value — it returns 0 rows, or rows you did not expect, with HTTP 200.
The search string can be passed as any of: query (canonical),
search, term, keyword, keywords, search_term, or name.
RETURNS a TSV string with columns: accession, protein_name, organism_name. On upstream/HTTP failure this tool does NOT raise — it returns a plain string beginning with "Error:" (not TSV). CHECK FOR the "Error:" prefix BEFORE parsing rows.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| name | No | ||
| term | No | ||
| limit | No | The maximum number of results to return. Default is 20. | |
| query | No | The Solr-style query string for the UniProtKB /search endpoint. QUERY SYNTAX: - Simple keyword: "rubisco" - Field-specific: "field:value" (e.g., "gene:BRCA1", "protein_name:rubisco") - Boolean operators: AND, OR, NOT (e.g., "gene:TP53 AND organism_id:9606") - Grouping with parentheses: "((gene:CTNNB1) AND (taxonomy_id:9606))" - Wildcards (* suffix): "gene:PRO*" matches any gene starting with PRO - Ranges: "length:[1000 TO 2000]" or open-ended "length:[5000 TO *]" KEY QUERY FIELDS: Identity / Name: accession UniProt primary accession (e.g., "accession:P04637") id UniProt entry name / mnemonic (e.g., "id:P53_HUMAN") protein_name Protein name, including synonyms (e.g., "protein_name:rubisco") gene Gene name with wildcard support (e.g., "gene:BRCA*") gene_exact Exact gene name match (e.g., "gene_exact:TP53") ec Enzyme Commission number (e.g., "ec:1.1.1.1") Taxonomy: organism_id NCBI taxonomy ID (e.g., "organism_id:9606" for human, "organism_id:10090" for mouse) organism_name Organism scientific or common name taxonomy_id Taxon ID including all descendants lineage Taxonomic lineage keyword Annotation status: reviewed true = Swiss-Prot (manually reviewed), false = TrEMBL (automatically annotated) ALWAYS add "reviewed:true" when seeking high-quality entries. Sequence properties: length Sequence length as a range (e.g., "length:[100 TO 500]") mass Molecular mass in Daltons (range supported) existence Protein existence level: 1 (protein), 2 (transcript), 3 (homology), 4 (predicted), 5 (uncertain) Functional annotation: keyword UniProt keyword name (e.g., "keyword:Kinase") keyword_id UniProt keyword ID (e.g., "keyword_id:KW-0418") go Gene Ontology term, by ID or by term name (e.g., "go:0043202", 'go:"lysosomal lumen"'). TWO behaviours to know: (1) the ID must be zero-padded to 7 digits — "go:43202" is a VALID field with an unmatchable value, so it returns 0 rows and no error; (2) the match includes the term's GO DESCENDANTS, so "go:0043202" also returns proteins annotated only to its children (acrosomal lumen, endolysosome lumen) — 192 reviewed entries carry the term directly, 214 once descendants are counted (2026-08-20). function Function free-text annotation family Protein family (e.g., "family:globin") organelle Subcellular organelle (e.g., "organelle:chloroplast") cc_subcellular_location Subcellular location comment Cross-references: database Database cross-reference (e.g., "database:PDB") xref Cross-reference ID (e.g., "xref:pdb-1A2B") chebi ChEBI ID (e.g., "chebi:15422") interactor UniProt accession of interacting protein Literature: lit_author Author surname (e.g., "lit_author:Smith") lit_pubmed PubMed ID lit_doi DOI EXAMPLES (structured queries): # Reviewed human TP53 protein "gene_exact:TP53 AND organism_id:9606 AND reviewed:true" # All human kinases manually reviewed "keyword:Kinase AND organism_id:9606 AND reviewed:true" # EGFR in human or mouse "gene_exact:EGFR AND (organism_id:9606 OR organism_id:10090) AND reviewed:true" # Long chloroplast proteins (>= 5000 aa) in any organism "organelle:chloroplast AND length:[5000 TO *]" # Proteins with PDB structures involved in apoptosis "database:PDB AND keyword:Apoptosis AND organism_id:9606 AND reviewed:true" # Proteins encoded by gene names starting with "PIK3" "gene:PIK3* AND organism_id:9606 AND reviewed:true" | |
| search | No | ||
| keyword | No | ||
| keywords | No | ||
| search_term | No |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| result | Yes |