bpa Resolved · high auto-curated
H37Rv Rv3780 · MTBC0 mtbc0_004008 ·
178 aa · 4251110–4251646 (+) ·
RefSeq NP_218297.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | proteasome activator protein Bpa |
| Revised (this work) | Proteasome activator protein Bpa. Pfam: BPA (PF10759.15). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKX3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Bacterial proteasome activator |
| Curated function | Interacts with the core proteasome alpha-subunit (PrcA) through its C-terminal hydrophobic-tyrosine-X motif (HbYX motif). Interaction of Bpa with the proteasome stimulates proteasomal peptidase and casein degradation activity, which suggests Bpa could play a role in the removal of non-native or damaged proteins by influencing the conformation of the proteasome complex upon interaction. Can inhibit degradation of Pup-tagged substrates in vitro by competing with Mpa for association with the proteasome. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | bpa |
| eggNOG description | Interacts with the core proteasome alpha-subunit (PrcA) through its C-terminal hydrophobic-tyrosine-X motif (HbYX motif). Interaction of Bpa with the proteasome stimulates proteosomal peptidase and casein degradation activity, which suggests Bpa could play a role in the removal of non-native or damaged proteins by influencing the conformation of the proteasome complex upon interaction |
| Orthologous group | 291ZT |
| Gene Ontology (62) |
GO:0000502, GO:0003674, GO:0005488, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005886, GO:0008150, GO:0009893, GO:0009894, GO:0009896 +50 more
|
Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.
Conservation & selection (intra-MTBC, 145 209 strains)
| pN/pS | 0.33 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 missense, 0 nonsense, 0 frameshift |
pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.
Domains (Pfam, hmmscan --cut_ga)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
BPA | PF10759.15 | 7.6e-79 | 32–170 | Bacterial proteasome activator |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: prcA (proteasome subunit alpha), high confidence from genomic context alone (score 976 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2109c prcA |
proteasome subunit alpha | 981 | 976 ctx | cooccurence:766 experimental:900 |
Rv2115c mpa |
proteasome-associated ATPase | 984 | 971 ctx | cooccurence:724 database:900 textmining:466 |
Rv2110c prcB |
proteasome subunit beta | 960 | 949 ctx | cooccurence:754 experimental:800 |
Rv3781 rfbE |
O-antigen/lipopolysaccharide ABC transporter ATP-binding protein RfbE | 964 | 884 ctx | neighborhood:882 textmining:703 |
Rv3782 glfT1 |
galactofuranosyl transferase GlfT | 943 | 884 ctx | neighborhood:882 textmining:533 |
Rv3783 rfbD |
O-antigen/lipopolysaccharide ABC transporter permease RfbD | 962 | 882 ctx | neighborhood:881 textmining:694 |
Rv3779 |
transmembrane protein | 897 | 882 ctx | neighborhood:881 |
Rv2097c pafA |
proteasome accessory factor PafA | 777 | 713 ctx | cooccurence:709 |
Rv2112c dop |
pup deamidase/depupylase | 786 | 687 ctx | cooccurence:685 |
Rv2111c pup |
ubiquitin-like protein Pup | 694 | 681 ctx | cooccurence:679 |
Rv3778c |
aminotransferase | 639 | 639 ctx | neighborhood:636 |
Rv0738 hyp |
hypothetical protein | 567 | 567 ctx | cooccurence:566 |
Rv3660c ssd hyp |
hypothetical protein | 539 | 539 ctx | cooccurence:539 |
Rv3221A rshA |
anti-sigma factor RshA | 538 | 539 ctx | cooccurence:536 |
Rv3784 |
dTDP-glucose 4,6-dehydratase | 473 | 473 ctx | neighborhood:471 |
STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.
Evidence
- Legacy H37Rv annotation: hypothetical protein
- MTBC0 PGAP product: proteasome activator protein Bpa
- Pfam (hmmscan --cut_ga): BPA PF10759.15 (E=8e-79)
- (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)
Sources
- Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
- Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_218297.1)
- Domains: Pfam-A via hmmscan --cut_ga — BPA (PF10759.15)
- Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
- Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021,
doi:10.1093/molbev/msab293), eggNOG 5.0 DB
(Huerta-Cepas et al. 2019) — OG
291ZT - Curated reference: UniProt P9WKX3 (SwissProt, reviewed; Evidence at protein level)
- Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
- Interaction network: STRING v12.0 (Szklarczyk et al. 2023,
doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 —
22 functional partner(s); context anchor
prcA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004008|Rv3780|bpa MRKRMVIGLSTGSDDDDVEVIGGVDPRLIAVQENDSDESSLTDLVEQPAKVMRIGTMIKQLLEEVRAAPLDEASRNRLRDIHATSIRELEDGLAPELREELDRLTLPFNEDAVPSDAELRIAQAQLVGWLEGLFHGIQTALFAQQMAARAQLQQMRQGALPPGVGKSGQHGHGTGQYL