Read entry_type, function, GO terms and feature positions off each entry, then follow cross_references to PDB, ChEMBL and AlphaFold or fold the sequence.

The search returns protein entries with annotations, GO terms, features, and cross-references. When the amino acid sequence is included, it feeds directly into ESMFold structure prediction, a BLAST similarity search, or a Target Passport.

Output structure

UniProt Search returns a JSON object containing matched protein entries with annotations and metadata.

Top-level fields

Field	Type	Description
`total_results`	integer	Total matching entries in UniProt
`returned_count`	integer	Number of entries returned in this response
`query_info`	object	Search parameters used
`entries`	array	List of protein entry objects

Protein entry fields

Each entry in the entries array contains:

Field	Type	Description
`accession`	string	UniProt accession ID (e.g., "P00533")
`entry_name`	string	UniProt entry name (e.g., "EGFR_HUMAN")
`entry_type`	string	"Swiss-Prot" (reviewed) or "TrEMBL" (unreviewed)
`protein_name`	string	Recommended protein name
`gene_name`	string	Primary gene symbol
`organism`	string	Source organism scientific name
`function`	string	Functional annotation summary
`disease_associations`	string[]	Known disease links
`subcellular_location`	string	Where the protein is found in the cell
`go_terms`	object	Gene Ontology annotations (see below)
`features`	object[]	Protein features (included unless you ask to leave them out)
`sequence`	string	Full amino acid sequence (when you ask for the sequence)
`sequence_length`	integer	Number of amino acids
`cross_references`	object	Links to external databases

GO terms object

Field	Type	Description
`molecular_function`	string[]	What the protein does (e.g., "protein tyrosine kinase activity")
`biological_process`	string[]	Pathways and processes (e.g., "signal transduction")
`cellular_component`	string[]	Where in the cell (e.g., "plasma membrane")

Feature object fields

Field	Type	Description
`type`	string	Feature type (Domain, Active site, Binding site, Modified residue, etc.)
`description`	string	Feature description
`start`	integer	Start position in the sequence
`end`	integer	End position in the sequence
`evidence`	string	Evidence code (experimental, predicted, etc.)

Common feature types:

Type	Meaning
Domain	Structural or functional domain (e.g., "Protein kinase")
Active site	Catalytically active residue
Binding site	Substrate or cofactor binding residue
Modified residue	Post-translational modification site (phosphorylation, glycosylation, etc.)
Signal peptide	N-terminal signal sequence
Transmembrane	Membrane-spanning region
Disulfide bond	Cysteine-cysteine bond
Mutagenesis	Known mutation with phenotypic effect

Cross-references object

Field	Type	Description
`pdb_ids`	string[]	Associated PDB structure IDs
`chembl_id`	string	ChEMBL target identifier
`alphafold_url`	string	AlphaFold predicted structure URL
`pfam_domains`	string[]	Pfam domain family IDs
`interpro_ids`	string[]	InterPro family identifiers
`gene_id`	string	NCBI Gene ID

Entry type interpretation

Entry type	Meaning	Reliability
Swiss-Prot	Manually curated by expert biologists	High — experimental evidence reviewed
TrEMBL	Computationally annotated	Variable — functional predictions may be incomplete

Always check the entry type when assessing annotation quality. Swiss-Prot entries have undergone expert review, while TrEMBL entries are automatically generated.

Example output

{
  "total_results": 1,
  "returned_count": 1,
  "entries": [
    {
      "accession": "P00533",
      "entry_name": "EGFR_HUMAN",
      "entry_type": "Swiss-Prot",
      "protein_name": "Epidermal growth factor receptor",
      "gene_name": "EGFR",
      "organism": "Homo sapiens",
      "function": "Receptor tyrosine kinase binding ligands of the EGF family and activating several signaling cascades to convert extracellular cues into appropriate cellular responses.",
      "disease_associations": ["Lung cancer", "Glioblastoma"],
      "subcellular_location": "Cell membrane; Single-pass type I membrane protein",
      "go_terms": {
        "molecular_function": ["protein tyrosine kinase activity", "ATP binding"],
        "biological_process": ["signal transduction", "cell proliferation"],
        "cellular_component": ["plasma membrane", "receptor complex"]
      },
      "features": [
        {
          "type": "Domain",
          "description": "Protein kinase",
          "start": 712,
          "end": 979
        },
        {
          "type": "Active site",
          "description": "Proton acceptor",
          "start": 837,
          "end": 837
        }
      ],
      "sequence": "MRPSGTAGAALLALLAAL...",
      "sequence_length": 1210,
      "cross_references": {
        "pdb_ids": ["1M17", "1NQL", "2GS6", "3POZ", "4HJO"],
        "chembl_id": "CHEMBL203",
        "alphafold_url": "https://alphafold.ebi.ac.uk/entry/P00533",
        "pfam_domains": ["PF07714", "PF00069"],
        "gene_id": "1956"
      }
    }
  ]
}

Canvas visualization

When UniProt Search results appear on the canvas:

Border color: Blue-grey (#607D8B)
Tier 2 metrics: Entry count, organism, sequence length, annotation count

Interpreting canvas metrics

Metric	Meaning
Swiss-Prot entry type	High-quality, manually reviewed annotations
Many PDB cross-references	Well-studied protein with experimental structures available
Long feature list	Rich annotation with many known domains and sites
Sequence included	Ready for downstream structure prediction or similarity search

Field	Type	Description
`error`	string	Error message describing the failure
`suggestion`	string	Guidance for resolving the issue

Common error values:

"Provide accession, gene, or query" — No accession, gene, or query was given
"No entries found" — Query matched zero proteins
"UniProt API timeout" — API did not respond in time; retry
"Invalid accession format" — Accession ID does not match expected pattern

UniProt Search outputs

Output structure

Top-level fields

Protein entry fields

GO terms object

Feature object fields

Cross-references object

Entry type interpretation

Example output

Canvas visualization

Interpreting canvas metrics

Downstream data use

Chaining into ESMFold

Chaining into BLAST

Chaining into Target Passport

Error responses

Read next

UniProt Search inputs and parameters

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