Worked example — how one UniProtKB entry demultiplexes across the four axes

Using P25888 (ATP-dependent RNA helicase RhlE, Escherichia coli K12) to illustrate how a single UniProtKB entry’s FT/CC annotations map onto the trait axes and categories.

Note. This is an illustration of the demultiplexing model, not a set of live records. Per-protein records like these are instance-level annotations, not reusable trait classes, so they are not seeded standalone; instead a real protein is attached as a canonical_example on the relevant class-level trait (via fetch_uniprot_examples.py). The mapping below — FT type → axis / category — is what the seeders and the README table encode.

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SEQUENCE (6 records)

# Trait Category UniProt evidence
1 Disordered C-terminal region, residues 373-454 SEQ_DISORDER FT REGION /note="Disordered" (MobiDB-lite)
2 Gly-rich composition bias 393-406 SEQ_COMPOSITION FT COMPBIAS /note="Gly residues"
3 Basic + acidic residues 424-434 SEQ_COMPOSITION FT COMPBIAS /note="Basic and acidic residues"
4 Basic residues 443-454 SEQ_COMPOSITION FT COMPBIAS /note="Basic residues"
5 Q motif 1-29 SEQ_MOTIF FT MOTIF /note="Q motif" (cross-refs PROSITE PS51195)
6 DEAD box 156-159 SEQ_MOTIF FT MOTIF /note="DEAD box" (cross-refs PROSITE PS00039)

STRUCTURE (3 records)

# Trait Category UniProt evidence
7 Helicase ATP-binding domain 32-208 STRUCT_DOMAIN FT DOMAIN /note="Helicase ATP-binding"
8 Helicase C-terminal domain 219-381 STRUCT_DOMAIN FT DOMAIN /note="Helicase C-terminal"
9 ATP binding site 45-52 STRUCT_BINDING_SITE FT BINDING /ligand="ATP" /ligand_id="ChEBI:CHEBI:30616"

FUNCTION (11 records)

FUNC_ENZYMATIC_ACTIVITY (3)

# Trait Source
10 ATP + H₂O → ADP + phosphate + H⁺ (EC 3.6.4.13, Rhea:13065) CC CATALYTIC ACTIVITY
11 ATP hydrolysis activity (GO:0016887) DR GO F:
12 RNA helicase activity (GO:0003724) DR GO F:

FUNC_BINDING_CAPACITY (2)

# Trait Source
13 ATP binding (GO:0005524) DR GO F: (complements the localised binding site #9)
14 RNA binding (GO:0003723) DR GO F:

FUNC_LOCALIZATION (2)

# Trait Source
15 Cytoplasm (with ribosome-associated note) CC SUBCELLULAR LOCATION
16 Cytosol (GO:0005829) DR GO C:

FUNC_ENVIRONMENTAL_RESPONSE (2)

# Trait Source
17 Response to cold shock (PubMed:14527658) CC INDUCTION — keyword scan matches “cold shock”
18 Response to heat (GO:0009408) DR GO P: response to heat

FUNC_INTERACTION_PARTNER (2)

# Trait Source
19 Interacts with PcnB (PubMed:10361280) CC SUBUNIT
20 Interacts in vitro with RNase E (PubMed:15554979) CC SUBUNIT

What’s captured, what’s still open

Captured automatically: identifiers, human-readable labels, cross-references to source ontologies, canonical exemplar (the source UniProt entry + NCBITaxon), evidence PMIDs where the flat file cites them.

Open for curator work:

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