whiB1 Family assigned · medium auto-curated
H37Rv Rv3219 · MTBC0 - ·
84 aa · 3595713–3595967 (+) ·
RefSeq NP_217735.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator WhiB1 |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Transcriptional regulator WhiB1. 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 |
P9WF43
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Transcriptional regulator WhiB1 |
| Curated function | Acts as a transcriptional repressor, inhibiting expression in vitro. Probably redox-responsive. The apo- but not holo-form binds to its own promoter as well as that of groEL2. Oxidized apo-form and nitrosylated holo-form also bind DNA. The apo-form has been shown to act as a protein disulfide reductase, but also not to act as a protein disulfide reductase. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | whiB |
| eggNOG description | Acts as a transcriptional regulator. Probably redox- responsive. The apo- but not holo-form probably binds DNA |
| Orthologous group | 2DMIE |
| KEGG orthology |
K18955
|
| Gene Ontology (66) |
GO:0000302, GO:0003674, GO:0003676, GO:0003677, GO:0003824, GO:0005488, GO:0006355, GO:0006950, GO:0006979, GO:0008150, GO:0008152, GO:0009889 +54 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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 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 |
|---|---|---|---|---|
Whib | PF02467.22 | 5.5e-28 | 3–71 | Transcription factor WhiB |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1830 (HTH-type transcriptional regulator), high confidence from genomic context alone (score 775 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2703 sigA |
RNA polymerase sigma factor SigA | 999 | 999 | experimental:999 textmining:504 |
Rv2710 sigB |
RNA polymerase sigma factor SigB | 880 | 823 | experimental:821 |
Rv1830 |
HTH-type transcriptional regulator | 775 | 775 ctx | cooccurence:772 |
Rv2901c hyp |
hypothetical protein | 773 | 773 ctx | cooccurence:770 |
Rv1440 secG |
protein-export membrane protein SecG | 771 | 772 ctx | cooccurence:769 |
Rv1390 rpoZ |
DNA-directed RNA polymerase subunit omega | 768 | 768 ctx | cooccurence:758 |
Rv1321 nucS |
endonuclease NucS | 735 | 736 ctx | cooccurence:732 |
Rv3218 hyp |
hypothetical protein | 869 | 722 ctx | neighborhood:720 textmining:550 |
Rv3195 hyp |
hypothetical protein | 701 | 701 ctx | cooccurence:701 |
Rv2050 rbpA |
RNA polymerase-binding protein RbpA | 711 | 677 ctx | cooccurence:672 |
Rv1025 hyp |
hypothetical protein | 656 | 656 ctx | cooccurence:656 |
Rv3907c pcnA |
poly(A) polymerase PcnA | 640 | 640 ctx | cooccurence:640 |
Rv2699c hyp |
hypothetical protein | 636 | 637 ctx | cooccurence:633 |
Rv0525 hyp |
hypothetical protein | 629 | 629 ctx | cooccurence:627 |
Rv0807 hyp |
hypothetical protein | 621 | 621 ctx | cooccurence:621 |
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 WhiB1
- Pfam (hmmscan --cut_ga): Whib PF02467.22 (E=5e-28)
- (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_217735.1)
- 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
2DMIE - Curated reference: UniProt P9WF43 (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 —
55 functional partner(s); context anchor
Rv1830 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3219|whiB1 MDWRHKAVCRDEDPELFFPVGNSGPALAQIADAKLVCNRCPVTTECLSWALNTGQDSGVWGGMSEDERRALKRRNARTKARTGV