UniProt Bacterial Protein Records - By Taxon, Per Record

Every bacterial protein in UniProtKB - each UniProtKB entry under the Bacteria superkingdom (taxonomy_id:2) - as one clean, flat record: accession, protein and gene names, organism, taxonomic lineage, function summary and keywords. Reproduced verbatim from the UniProt REST API, values unmodified, no literature-author or contact field ever read.

What one record represents

The source is UniProt (the UniProtKB REST API), filtered to taxonomy_id:2 - the Bacteria superkingdom. Each record is one protein entry: its primary accession and entry name, the recommended protein name, gene name(s), organism and NCBI taxonomy id, the taxonomic lineage, whether the entry is reviewed (Swiss-Prot) or unreviewed (TrEMBL), the protein-existence evidence level, a function summary and the UniProt keywords.

Coverage and volume

The live bacterial set is 74,201,400 UniProtKB entries (measured at build time from the API's x-total-results). Because that is far too large for a single pull, a partition is required: you supply a UniProt query fragment - reviewed:true (Swiss-Prot bacteria), a genus or species taxonomy id such as taxonomy_id:1279 (Staphylococcus) or taxonomy_id:562 (E. coli) - and the Actor AND-s it onto taxonomy_id:2. The full-set figure is the capacity line; you always work within a partition.

Sol's Wave-3 index put this door at about 74,117,227 records; measured live at build time the bacterial set is 74,201,400 - the live figure is what this listing quotes.

The Actor pages the UniProt REST API using its cursor (the Link header's rel="next"), 500 entries at a time, and stops as soon as your Maximum records cap is met.

Distinctness from the other UniProt cells

Bacteria and human are disjoint clades, so this cell shares zero records with the human-proteome cell. About 337,294 bacterial entries are reviewed (Swiss-Prot) and so also appear in the reviewed-protein cell; the reviewed cell is all organisms, this one is Bacteria only, so they overlap exactly on reviewed bacterial entries and nowhere else. The enzyme cell overlaps only on bacterial enzymes. Stating these boundaries means the cells combine without double-counting.

Licence and attribution

UniProt data is released under Creative Commons Attribution 4.0 (CC BY 4.0) - free to use and redistribute with attribution. The full notice travels on every record:

UniProt (UniProtKB), CC BY 4.0. Attribution required; reproduced from the UniProt REST API, values unmodified. No literature-author, submitter or contact field is read.

The required attribution - UniProt Consortium (https://www.uniprot.org) - is present on every record.

Person-data policy

This Actor requests only protein, gene, organism and function fields. UniProt's literature-references section with author and submitter names is never requested and never delivered, and a per-record assertion rejects any author, submitter or contact field (verified with a planted-field test). No natural-person data is processed.

Interpretation caveat

UniProtKB entries under the Bacteria superkingdom (taxonomy_id:2): accession, protein/gene names, organism, lineage, function and keywords. The full bacterial set is ~74.2M entries, so a partition (reviewed:true, a genus/species taxon id) is required and AND-ed onto taxonomy_id:2. Disjoint from the human cell; ~337,294 are reviewed.

Values are reproduced verbatim from the API; the Actor never rewrites a field. The function field is the first UniProt function comment, which may cite PubMed identifiers - those are literature references, not author names. The taxonomic_lineage lets you filter or group within Bacteria without a second query.

Data quality and freshness

reviewed is a real boolean and organism_id a real number. Delivery is keyed on the stable accession, so the dataset is safe to diff, deduplicate or upsert. Every run re-reads the live API, so the data is as fresh as UniProt publishes, and each record's observed_at stamp dates the snapshot. The run's RUN_RECEIPT records the partition, the API's total result count, and how many records were delivered and charged.

Provenance and compliance

Every run reads rest.uniprot.org/robots.txt at runtime; the gate result (URL, status, byte length, SHA-256 of the policy) is written to the run's RUN_RECEIPT, and the search path is confirmed crawlable before any data request. The API is keyless. The Actor never bypasses a block or fetches through a mirror.

Inputs

• Partition (partition, required) - a UniProt query fragment AND-ed onto taxonomy_id:2. Prefilled with reviewed:true.
• Maximum records (maxRecords) - hard cap on protein records delivered and billed within the partition.

Output

Records land in the Actor's default dataset and export as JSON, CSV, Excel or via the Apify API. A tabular overview view surfaces accession, entry name, protein and gene names, organism, review status, protein-existence and keywords.

Fields in detail

The record leads with accession and entry_name, then protein_name, gene_names, organism, organism_id, taxonomic_lineage, the boolean reviewed (and the verbatim entry_type), protein_existence, function and keywords. The provenance block closes every record. Because the accession is UniProt's stable primary key, this dataset joins cleanly onto any system that references UniProt accessions, and onto the fleet's other UniProt cells.

Typical uses

Bioprocess, antimicrobial-resistance and microbiome teams use this cell to assemble a bacterial protein reference for a target clade - a genus, a species, or the reviewed Swiss-Prot core - as one flat table, without parsing UniProt's nested JSON. Because the taxonomy id and lineage are first-class fields, the dataset joins onto strain collections, AMR gene panels and metagenomic pipelines. A scheduled run per partition keeps a downstream reference current with UniProt's release cycle, and the stable accession key makes it safe to upsert.

Scaling and limits

Set Maximum records low to sample cheaply or high to pull a full partition. The Actor pages the API with its cursor (500 entries per request) and delivers incrementally, so memory stays flat regardless of how many records you request, and you are billed only for what is delivered. The cursor is stable across a run, so even a large partition proceeds without gaps or duplicates. Choose the partition to match your question - a single species, a genus, or reviewed-only - and re-run to keep the reference current.

Working with the Bacteria scope

The Bacteria superkingdom is enormous and overwhelmingly unreviewed, so the partition is where the work happens. For a curated core, reviewed:true gives the ~337,000 Swiss-Prot bacterial entries - hand-checked, richly annotated, and small enough to pull whole. For a single organism, a species taxonomy id (taxonomy_id:1280 for Staphylococcus aureus, taxonomy_id:562 for E. coli) narrows to that clade including its unreviewed entries. The taxonomic_lineage field on every record lets you filter or group within a pull without a second query - collect by phylum, class or genus after the fact. Because the accession is stable and the lineage travels on the row, a bacterial reference assembled here upserts cleanly and re-groups without re-fetching.

Why the partition is required

A door of 74 million records is not a single dataset you pull once; it is a corpus you query. Making the partition a required input is a deliberate guard - it stops an accidental full-corpus run and forces the buyer to name the clade or the review status they actually want, which is nearly always a few thousand to a few hundred thousand records rather than tens of millions. The full-set figure stands as the capacity line so you know the ceiling, but every run is scoped, bounded and billed only for what it delivers.

Sibling Actors

It sits beside the fleet's UniProt reviewed-protein, human-proteome, enzyme and disease-annotation records - the same door at different scopes. It shares its engineering - the runtime robots gate, cursor paging, push-then-charge billing and verbatim-value discipline - with the fleet's other UniProt records Actors, from which it stays distinct by its Bacteria scope and taxonomic lineage.