UniProt Download

How to download a UniProt sequence as FASTA?

ProteinIQ retrieves a UniProtKB record from its accession and returns the available FASTA, JSON, mapped experimental structure files, and summary metadata. Enter an accession such as P00533, select FASTA for sequence files, or choose All formats for annotations and linked structures too, then download the returned files or copy their text content for sequence and annotation workflows.

For Q8W3K0 with Output format set to FASTA, the two output files are:

uniprot-Q8W3K0-fasta.fasta
uniprot-Q8W3K0-protein-sequence.fasta

The first retains the UniProt header. The second uses a compact header generated by ProteinIQ; both contain the sequence for the retrieved record.

What is UniProt Download?

UniProt Download is a direct-record retrieval tool for UniProtKB, the protein knowledgebase maintained by the UniProt Consortium. A UniProt accession identifies one protein record and its associated sequence, annotation, identifiers, and cross-references. The tool retrieves that record as FASTA or JSON, rather than searching a collection of gene names or protein descriptions.

That distinction matters for reproducibility. An accession such as P00533 identifies the human epidermal growth factor receptor record, while a gene symbol or protein name can match multiple organisms, entries, or isoforms. Use the database search page to discover a record when its accession is not known, then use this tool to keep a specific record with an analysis.

Input

Six- and ten-character UniProt accessions are supported. Accessions are normalized to uppercase before the record is requested. A not-found result means that UniProtKB did not return a record for that exact identifier.

Settings

Results and downloads

CIF does not represent a structure predicted from the UniProt sequence. It is an experimental-structure cross-reference recorded by UniProt and fetched from the Protein Data Bank. A record can therefore return no CIF files, or several when multiple PDB structures are cross-referenced. For a known archive entry, PDB Download retrieves its coordinate and sequence files directly.

The Files panel preserves the file label, generated filename, format, and source URL. FASTA and JSON are loaded into the browser when available. Linked CIF files remain download links and are fetched when downloaded, so a record with hundreds of PDB cross-references does not load every structure when the lookup runs.

Choosing the right file for a protein workflow

The two FASTA outputs often contain the same amino-acid sequence, but they serve slightly different purposes. The UniProt FASTA carries the provider's complete record header, which is useful when retaining the original provenance. The generated Protein sequence FASTA is deliberately compact and is convenient when a downstream program needs a simple sequence file.

JSON is the better choice when the workflow needs more than the sequence. It retains structured fields that may include the protein name, organism, gene names, entry status, sequence length, functional comments, and cross-references. Field availability depends on the selected UniProt record, so downstream parsing should not assume that every annotation category is present.

For sequence comparison, send the FASTA file to Clustal Omega. For rapid quality checks before an analysis, protein parameters and amino acid composition calculate complementary sequence properties. A linked CIF file is appropriate for inspecting an already deposited experimental model; an AlphaFold Database model is a separate, predicted structure resource.

Interpreting record status and structure links

UniProt labels entries as reviewed or unreviewed. A reviewed UniProtKB/Swiss-Prot record has undergone manual curation, while an unreviewed UniProtKB/TrEMBL record is computationally analyzed and awaits manual review. The JSON record retains this status in entryType; keep it when comparing annotations or assembling a reference dataset.

PDB cross-references indicate that the UniProt record is linked to one or more structural archive entries. They do not mean that the full UniProt sequence was resolved in each deposited model. Experimental constructs can omit termini, contain mutations, or cover only one domain. Compare sequence coverage and experimental metadata in the PDB record before treating a linked coordinate file as a full-length structural representation.

When direct UniProt download is the right starting point

Direct retrieval is best for a known accession that needs to be carried into a reproducible analysis, such as P69905 before a multiple sequence alignment or a saved JSON record accompanying a functional-annotation review. It is not a bulk proteome downloader, a gene-name disambiguation service, or a structure-prediction method. Search first when the identifier is uncertain, and use a structure-prediction tool only when no suitable experimental or database model answers the biological question.

Download availability

Enter one identifier or compound name on a single line, up to 200 characters. Surrounding spaces are ignored. These lookups need an internet connection: ProteinIQ retrieves the record from the selected database, and file downloads contact its file service.

If a text file cannot be loaded in the browser, a warning appears and its download link stays available. A listed link does not guarantee that the database currently serves that file. Retry the download or check the original database record; a connection failure is different from an unknown entry.