Rv0472c Family assigned · medium auto-curated
H37Rv Rv0472c · MTBC0 mtbc0_000497 ·
234 aa · 566088–566792 (-) ·
RefSeq NP_214986.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | HTH-type transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | TetR/AcrR family transcriptional regulator |
| Revised (this work) | TetR/AcrR family transcriptional regulator. Pfam: TetR_N (PF00440.30), TetR_C_32 (PF19344.5). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMD9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized HTH-type transcriptional regulator Rv0472c |
UniProt still lists this protein as Uncharacterized HTH-type transcriptional regulator Rv0472c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Transcriptional regulator |
| Orthologous group | COG1309 |
| Gene Ontology (24) |
GO:0003674, GO:0003700, GO:0005575, GO:0005576, GO:0006355, GO:0008150, GO:0009889, GO:0010468, GO:0010556, GO:0019219, GO:0019222, GO:0031323 +12 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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 2 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 |
|---|---|---|---|---|
TetR_N | PF00440.30 | 3.2e-08 | 32–74 | Bacterial regulatory proteins, tetR family |
TetR_C_32 | PF19344.5 | 4.2e-07 | 89–207 | Tetracyclin repressor-like, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: hbhA (heparin binding hemagglutinin HbhA), high confidence from genomic context alone (score 738 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0471c hyp |
hypothetical protein | 883 | 883 ctx | neighborhood:882 |
Rv0470A hyp |
hypothetical protein | 801 | 801 ctx | neighborhood:800 |
Rv0475 hbhA |
heparin binding hemagglutinin HbhA | 738 | 738 ctx | neighborhood:595 |
Rv0473 |
transmembrane protein | 667 | 668 ctx | neighborhood:660 |
Rv1836c hyp |
hypothetical protein | 642 | 643 ctx | cooccurence:625 |
Rv0476 |
transmembrane protein | 584 | 584 | |
Rv0499 hyp |
hypothetical protein | 578 | 579 ctx | cooccurence:576 |
Rv2905 lppW |
lipoprotein LppW | 550 | 551 ctx | cooccurence:544 |
Rv3626c hyp |
hypothetical protein | 541 | 542 ctx | cooccurence:537 |
Rv0250c hyp |
hypothetical protein | 529 | 530 ctx | cooccurence:524 |
Rv0431 |
tuberculin-like peptide | 515 | 515 ctx | cooccurence:512 |
Rv0241c htdX |
3-hydroxyacyl-thioester dehydratase HtdX | 514 | 514 ctx | cooccurence:499 |
Rv0383c ttfA hyp |
hypothetical protein | 500 | 501 ctx | cooccurence:499 |
Rv0470c pcaA |
cyclopropane mycolic acid synthase | 744 | 500 ctx | neighborhood:488 textmining:510 |
Rv0242c fabG4 |
3-oxoacyl-ACP reductase FabG | 498 | 498 ctx | cooccurence:482 |
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: HTH-type transcriptional regulator
- MTBC0 PGAP product: TetR/AcrR family transcriptional regulator
- Pfam (hmmscan --cut_ga): TetR_N PF00440.30 (E=3e-08), TetR_C_32 PF19344.5 (E=4e-07)
- (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_214986.1)
- Domains: Pfam-A via hmmscan --cut_ga — TetR_N (PF00440.30), TetR_C_32 (PF19344.5)
- 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
COG1309 - Curated reference: UniProt P9WMD9 (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 —
45 functional partner(s); context anchor
hbhA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000497|Rv0472c| MAERIPAVTVKTDGRKRRWHQHKVERRNELVDGTIEAIRRHGRFLSMDEIAAEIGVSKTVLYRYFVDKNDLTTAVMMRFTQTTLIPNMIAALSADMDGFELTREIIRVYVETVAAQPEPYRFVMANSSASKSKVIADSERIIARMLAVMLRRRMQEAGMDTGGVEPWAYLIVGGVQLATHSWMSDPRMSSDELIDYLTMLSWSALCGIVEAGGSLEKFREQPHPSPIVPAWGQV