bpoB Resolved · high auto-curated
H37Rv Rv1123c · MTBC0 - ·
302 aa · 1246144–1247052 (-) ·
RefSeq NP_215639.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | peroxidase BpoB |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Peroxidase BpoB. Pfam: Hydrolase_4 (PF12146.16), Abhydrolase_1 (PF00561.27), Abhydrolase_6 (PF12697.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
O06575
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible peroxidase BpoB |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | bpoB |
| eggNOG description | Alpha beta hydrolase |
| Orthologous group | COG0596 |
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) pseudogene candidate
| pN/pS | 0.85 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 5 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 5.92% of strains (8598) · clonal |
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 |
|---|---|---|---|---|
Hydrolase_4 | PF12146.16 | 2.0e-09 | 49–148 | Serine aminopeptidase, S33 |
Abhydrolase_1 | PF00561.27 | 1.5e-16 | 50–281 | alpha/beta hydrolase fold |
Abhydrolase_6 | PF12697.14 | 7.3e-14 | 52–290 | Alpha/beta hydrolase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ephC (epoxide hydrolase EphC), medium confidence from genomic context alone (score 662 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1124 ephC |
epoxide hydrolase EphC | 662 | 662 ctx | neighborhood:553 |
Rv1125 hyp |
hypothetical protein | 608 | 608 ctx | neighborhood:554 |
Rv2048c pks12 |
polyketide synthase | 529 | 501 | experimental:441 |
Rv3825c pks2 |
phthioceranic/hydroxyphthioceranic acid synthase | 528 | 501 | experimental:441 |
Rv1527c pks5 |
polyketide synthase | 528 | 501 | experimental:441 |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 526 | 498 | experimental:441 |
Rv2933 ppsC |
phthiocerol synthesis polyketide synthase type I PpsC | 526 | 498 | experimental:441 |
Rv0216 |
hydratase | 483 | 483 ctx | cooccurence:473 |
Rv2627c hyp |
hypothetical protein | 499 | 481 | |
Rv2946c pks1 |
polyketide synthase | 486 | 455 | |
Rv0144 |
transcriptional regulator | 447 | 447 ctx | cooccurence:436 |
Rv1661 pks7 |
polyketide synthase | 457 | 433 | |
Rv1181 pks4 |
polyketide beta-ketoacyl synthase | 452 | 427 | |
Rv1663 pks17 |
polyketide synthase | 436 | 416 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): peroxidase BpoB
- Pfam (hmmscan --cut_ga): Hydrolase_4 PF12146.16 (E=2e-09), Abhydrolase_1 PF00561.27 (E=1e-16), Abhydrolase_6 PF12697.14 (E=7e-14)
- (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_215639.1)
- Domains: Pfam-A via hmmscan --cut_ga — Hydrolase_4 (PF12146.16), Abhydrolase_1 (PF00561.27), Abhydrolase_6 (PF12697.14)
- 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
COG0596 - Curated reference: UniProt O06575 (TrEMBL, unreviewed; Predicted)
- 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 —
14 functional partner(s); context anchor
ephC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1123c|bpoB MTIWRVPSKVTSGPVSAVSSSPQAVAFSGARGITLVADEWNRGAAAADRPTILMLHGGGQNRFSWKNTGQILADEGHHVVALDTRGPGDSDRAPGADYAVETPTTDVLHVVEAIGRRVVVVEASMGGLTGILVAERAGPQTVNGLVLVDVVPRYEKEGNARIRDFMLGNIDGFGSLEEAADAVAEYLPHRDKPRSPEGLKRNLRLRDGRWHWHWDPAMMTAPGHDPQLRTENFERAAMGLTIPVLLIRGKLSDVVSSDGARDFLAKVPNAEFVELSNAGRTAAGDDNDAFTDVVVDFVRRLS