whiB6 Family assigned · medium auto-curated
H37Rv Rv3862c · MTBC0 - ·
116 aa · 4338171–4338521 (-) ·
RefSeq NP_218379.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator WhiB6 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Transcriptional regulator WhiB6. Pfam: Whib (PF02467.22). |
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 |
P9WF37
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable transcriptional regulator WhiB6 |
| Curated function | Acts as a transcriptional regulator. Probably redox-responsive. The apo- but not holo-form probably binds DNA (By similarity). The apo-form has been shown to act as a protein disulfide reductase. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | whiB6 |
| eggNOG description | Transcription factor WhiB |
| Orthologous group | 2AJEQ |
| KEGG orthology |
K18957
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 9 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.23% of strains (328) · 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 |
|---|---|---|---|---|
Whib | PF02467.22 | 1.1e-06 | 38–79 | Transcription factor WhiB |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3863 hyp |
hypothetical protein | 408 | 408 | |
Rv3875 esxA |
ESAT-6 protein EsxA | 500 | 155 | textmining:433 |
Rv3416 whiB3 |
redox-responsive transcriptional regulator WhiB3 | 440 | 54 | textmining:433 |
Rv0726c |
S-adenosylmethionine-dependent methyltransferase | 444 | 50 | textmining:439 |
Rv0757 phoP |
two component system response transcriptional positive regulator PhoP | 654 | 47 | textmining:652 |
Rv3219 whiB1 |
transcriptional regulator WhiB1 | 550 | 45 | textmining:549 |
Rv3849 espR |
ESX-1 transcriptional regulator EspR | 433 | 41 | textmining:433 |
Rv3616c espA |
ESX-1 secretion-associated protein EspA | 431 | 41 | textmining:431 |
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): transcriptional regulator WhiB6
- Pfam (hmmscan --cut_ga): Whib PF02467.22 (E=1e-06)
- (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_218379.1)
- Domains: Pfam-A via hmmscan --cut_ga — Whib (PF02467.22)
- 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
2AJEQ - Curated reference: UniProt P9WF37 (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 — 8 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3862c|whiB6 MRYAFAAEATTCNAFWRNVDMTVTALYEVPLGVCTQDPDRWTTTPDDEAKTLCRACPRRWLCARDAVESAGAEGLWAGVVIPESGRARAFALGQLRSLAERNGYPVRDHRVSAQSA