uniprot-protein

UniProt Protein Database API

Access the Universal Protein Resource (UniProt) to search and retrieve protein entries, sequences, functional annotations, and cross-references. No authentication required.

API Endpoints

Base: https://rest.uniprot.org

GET /uniprotkb/search -- Search protein entries

# Search for human insulin proteins (reviewed/Swiss-Prot only)
curl -s "https://rest.uniprot.org/uniprotkb/search?query=insulin+AND+organism_id:9606+AND+reviewed:true&format=json&size=5"

# Search by gene name exact match
curl -s "https://rest.uniprot.org/uniprotkb/search?query=gene_exact:TP53+AND+organism_id:9606&format=json"

# Search by EC number (enzyme classification)
curl -s "https://rest.uniprot.org/uniprotkb/search?query=ec:2.7.11.1+AND+reviewed:true&format=json&size=10"

Search by Gene Ontology term

curl -s "https://rest.uniprot.org/uniprotkb/search?query=go:0006915+AND+organism_id:9606&format=json&size=10"

### GET /uniprotkb/{accession} -- Retrieve a single protein entry
```bash
# Get full entry for human p53 (JSON)
curl -s "https://rest.uniprot.org/uniprotkb/P04637?format=json"

# Get entry in TSV with selected fields
curl -s "https://rest.uniprot.org/uniprotkb/search?query=accession:P04637&format=tsv&fields=accession,gene_names,protein_name,organism_name,length,go_p"

GET /uniprotkb/{accession}.fasta -- Download FASTA sequence

# Get FASTA sequence for human hemoglobin subunit alpha
curl -s "https://rest.uniprot.org/uniprotkb/P69905.fasta"

GET /uniref/search -- Search UniProt Reference Clusters

# Find UniRef90 clusters for a protein
curl -s "https://rest.uniprot.org/uniref/search?query=uniprot_id:P04637&format=json&size=5"

GET /uniparc/search -- Search UniProt Archive

# Search UniParc for cross-reference records
curl -s "https://rest.uniprot.org/uniparc/search?query=uniprotkb:P04637&format=json&size=5"

Query Syntax

UniProt supports a rich query language for the query parameter:

Field	Example	Description
gene_exact	gene_exact:BRCA1	Exact gene name match
organism_id	organism_id:9606	NCBI taxonomy ID (9606 = human)
ec	ec:3.4.21.5	Enzyme Commission number
go	go:0006915	Gene Ontology term ID
keyword	keyword:Phosphoprotein	UniProt keyword
reviewed	reviewed:true	Swiss-Prot (reviewed) entries only
length	length:[100 TO 500]	Sequence length range
structure_3d	structure_3d:true	Has 3D structure
accession	accession:P04637	UniProt accession

Combine with AND, OR, NOT. Use + for spaces in URL encoding.

Common Queries

# All reviewed human kinases
curl -s "https://rest.uniprot.org/uniprotkb/search?query=keyword:Kinase+AND+organism_id:9606+AND+reviewed:true&format=json&size=25"

# Proteins with disease association
curl -s "https://rest.uniprot.org/uniprotkb/search?query=keyword:Disease+AND+gene_exact:CFTR&format=json"

# Batch retrieve multiple accessions (TSV)
curl -s "https://rest.uniprot.org/uniprotkb/search?query=accession:P04637+OR+accession:P69905+OR+accession:P00533&format=tsv&fields=accession,gene_names,protein_name,length"

# Paginate results using cursor (check Link header for next page)
curl -sI "https://rest.uniprot.org/uniprotkb/search?query=organism_id:9606+AND+reviewed:true&size=25" | grep -i link

Best Practices

1. Always add reviewed:true when searching Swiss-Prot (curated) entries to avoid TrEMBL noise.
2. Use format=tsv&fields=... for tabular output when you only need specific fields.
3. Use format=json for programmatic parsing of full entry data.
4. Paginate with size parameter (max 500) and cursor-based pagination via the Link header.
5. No API key is needed, but be respectful with rate limits -- avoid rapid-fire batch requests.
6. Common organism IDs: human=9606, mouse=10090, rat=10116, E.coli=83333, yeast=559292.
7. Use .fasta suffix for quick sequence retrieval without parsing JSON.

Data Integrity Rule

NEVER fabricate database results from training data. Every protein ID, gene name, compound property, pathway ID, structure detail, and metadata MUST come from an actual API response in this conversation. If the API returns no results, errors, or partial data, report exactly what happened. Do not "fill in" missing data from memory or make up identifiers.