What this entity is
Canonical name: UniProt. 1
Known aliases: UniProt accession; the report also refers to UniRef100 and UniParc identifiers as related identifier types, not as aliases of UniProt. 1
Stable external identifier: No stable external identifier was specified in this report. 1
UniProt is the protein-sequence identifier source used to bridge kbase-ke-pangenome gene clusters to AlphaFold MSA-depth records in kescience-alphafold. 1 The annotation-gap study refines this role by using UniProt’s reviewed bacterial sequences as homology exemplars for candidate gene assignment. 2 The BERDL Data Atlas inventories 215,130,942 UniProt proteins and recommends refdata UniProt alongside UniRef50, UniRef90, and UniRef100 as reference-protein resources. 3 This supports UniProt’s role as a large reference layer while refining the earlier accession-bridge view; across-tenant deduplication was not performed, so Refdata and KBase may contain the same UniProt entries through different cluster indices. 3
Evidence from alphafold_msa_annotation
The analysis joined kbase_ke_pangenome, Bakta annotations, interproscan domain annotations, and kescience-alphafold records. 1
Of 132,531,501 total gene clusters, 38,804,903 (29.3%) had a real UniProt accession. 1
A total of 38,051,842 gene cluster–UniProt pairs (28.7% of all gene clusters) bridged successfully to AlphaFold MSA depths. 1
The remaining 70.7% lacked UniRef100 IDs or had UniParc-only identifiers without an AlphaFold entry. 1
The analysed subset was biased toward better-studied organisms, so the report states that the annotation gap among the remaining 70.7% is likely larger, although that inference was not directly measured. 1
Across the 38,051,842 gene cluster–UniProt pairs, MSA depth and domain-hit count had Spearman ρ = 0.7563. 1
Mean domain hits increased from 0.59 for MSA depth < 10 to 10.83 for MSA depth ≥ 10,000, while mean distinct InterPro families increased from 0.059 to 4.601. 1
Across all 132,531,501 gene clusters, 111,035,431 (83.8%) had at least one InterProScan domain annotation, exceeding the 29.3% AlphaFold bridge coverage. 1
The report used a non-UPI UniProt accession as a requirement for AlphaFold MSA-depth lookup, which contributed to the limited bridge coverage. 1
The UniProt-to-AlphaFold bridge was based on a static version-6 KBase Data Lakehouse AlphaFold snapshot, and later UniProt deposits may change MSA depths. 1
Evidence from annotation_gap_discovery
The annotation-gap study supports UniProt’s role as a sequence-evidence resource: it retrieved 328 reviewed bacterial Swiss-Prot exemplar sequences through the UniProt REST API, covering 75/84 unique ECs, for DIAMOND homology searches. 2 Those searches identified 154 hits and contributed to the final 96 resolved reaction-organism pairs, although the full pipeline—not UniProt homology alone—provided the evidence triangulation. 2
Related pages
- AlphaFold MSA Depth as a Lens on the Bacterial Annotation Gap — source summary describing UniProt accession bridging, AlphaFold MSA depth, and annotation coverage. 1
- Annotation-Gap Discovery via Phenotype-Fitness-Pangenome-Gapfilling Integration — source summary describing UniProt/Swiss-Prot exemplar retrieval and homology-supported annotation-gap resolution. 2
- BERDL Data Atlas — Inventory, Topic Map, and Cross-Reference Synergies — atlas summary describing UniProt inventory scale, reference-data guidance, and cross-tenant deduplication caveats. 3
- kbase-ke-pangenome — gene-cluster dataset joined to UniProt identifiers. 1
- kescience-alphafold — AlphaFold dataset receiving the UniProt-linked MSA-depth lookups. 1
- interproscan — domain-annotation dataset compared with UniProt-linked MSA depth. 1
- swiss-prot — reviewed protein-sequence source used for annotation-gap homology exemplars. 2
- diamond — protein-sequence homology method used with UniProt/Swiss-Prot exemplars. 2
- pangenome-integration — cross-project concept covering pangenome structure and annotation coverage.