whiB7 Family assigned · medium auto-curated
H37Rv Rv3197A · MTBC0 - ·
92 aa · 3568401–3568679 (-) ·
RefSeq YP_177940.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator WhiB7 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Transcriptional regulator WhiB7. Pfam: Whib (PF02467.22), AT_hook (PF02178.25). |
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 |
Q6MX01
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable transcriptional regulator WhiB7 |
| Curated function | The apo- but not holo-form probably binds DNA (By similarity). Acts as a transcriptional regulator. Probably redox-responsive. Upon overproduction at least 10 other genes are up-regulated, among them are Rv1258c, Rv1988, Rv2301, Rv2416c, Rv2725c and whiB7 itself. Probably redox-responsive. The apo-form has been shown to act as a protein disulfide reductase. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | whiB7 |
| eggNOG description | Acts as a transcriptional regulator. Probably redox- responsive. The apo- but not holo-form probably binds DNA |
| Orthologous group | 2DMIS |
| KEGG orthology |
K18958
|
| Gene Ontology (9) |
GO:0001101, GO:0008150, GO:0010033, GO:0033993, GO:0042221, GO:0046677, GO:0050896, GO:0070542, GO:1901700
|
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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 5.94% of strains (8630) · 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 | 4.7e-14 | 20–68 | Transcription factor WhiB |
AT_hook | PF02178.25 | 5.9e-03 | 80–91 | AT hook motif |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1417 (membrane protein), medium confidence from genomic context alone (score 478 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2703 sigA |
RNA polymerase sigma factor SigA | 999 | 999 | experimental:999 |
Rv0668 rpoC |
DNA-directed RNA polymerase subunit beta' | 999 | 999 | experimental:999 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 965 | 899 | experimental:898 textmining:677 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 910 | 899 | experimental:898 |
Rv2050 rbpA |
RNA polymerase-binding protein RbpA | 902 | 899 | experimental:898 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 898 | 899 | experimental:898 |
Rv3583c carD |
RNA polymerase-binding transcription factor CarD | 898 | 898 | experimental:898 |
Rv2710 sigB |
RNA polymerase sigma factor SigB | 828 | 822 | experimental:821 |
Rv0487 hyp |
hypothetical protein | 596 | 596 ctx | cooccurence:595 |
Rv0801 hyp |
hypothetical protein | 513 | 513 ctx | cooccurence:513 |
Rv0498 hyp |
hypothetical protein | 510 | 511 ctx | cooccurence:508 |
Rv1417 |
membrane protein | 477 | 478 ctx | cooccurence:476 |
Rv0244c fadE5 |
acyl-CoA dehydrogenase FadE5 | 465 | 465 ctx | cooccurence:465 |
Rv3780 bpa hyp |
hypothetical protein | 432 | 432 ctx | cooccurence:432 |
Rv1467c fadE15 |
acyl-CoA dehydrogenase | 430 | 430 ctx | cooccurence:425 |
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 WhiB7
- Pfam (hmmscan --cut_ga): Whib PF02467.22 (E=5e-14), AT_hook PF02178.25 (E=6e-03)
- (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 YP_177940.1)
- Domains: Pfam-A via hmmscan --cut_ga — Whib (PF02467.22), AT_hook (PF02178.25)
- 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
2DMIS - Curated reference: UniProt Q6MX01 (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 —
36 functional partner(s); context anchor
Rv1417 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3197A|whiB7 MSVLTVPRQTPRQRLPVLPCHVGDPDLWFADTPAGLEVAKTLCVSCPIRRQCLAAALQRAEPWGVWGGEIFDQGSIVSHKRPRGRPRKDAVA