Rv0043c Family assigned · medium auto-curated
H37Rv Rv0043c · MTBC0 mtbc0_000048 ·
244 aa · 47465–48199 (-) ·
RefSeq NP_214557.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | HTH-type transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | GntR family transcriptional regulator |
| Revised (this work) | GntR family transcriptional regulator. Pfam: GntR (PF00392.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMG9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized HTH-type transcriptional regulator Rv0043c |
UniProt still lists this protein as Uncharacterized HTH-type transcriptional regulator Rv0043c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | transcriptional |
| Orthologous group | COG1802 |
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 | 2.684 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 7 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.13% of strains (182) · 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 |
|---|---|---|---|---|
GntR | PF00392.28 | 1.4e-12 | 11–71 | Bacterial regulatory proteins, gntR family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0044c (oxidoreductase), high confidence from genomic context alone (score 766 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3263 |
DNA methylase | 798 | 798 | coexpression:798 |
Rv1267c embR |
transcriptional regulator EmbR | 773 | 774 | coexpression:733 |
Rv3692 moxR2 |
methanol dehydrogenase transcriptional regulator MoxR | 767 | 767 | coexpression:767 |
Rv0044c |
oxidoreductase | 766 | 766 ctx | neighborhood:757 |
Rv3840 |
transcriptional regulator | 773 | 765 | coexpression:730 |
Rv3124 moaR1 |
transcriptional regulator MoaR | 764 | 764 | coexpression:716 |
Rv0042c |
transcriptional regulator | 775 | 763 ctx | neighborhood:748 |
Rv1556 |
HTH-type transcriptional regulator | 771 | 763 | coexpression:729 |
Rv3736 |
AraC/XylS family transcriptional regulator | 761 | 747 | coexpression:746 |
Rv0691c mftR |
mycofactocin biosynthesis transcriptional regulator MftR | 754 | 745 | coexpression:744 |
Rv0045c |
hydrolase | 731 | 732 ctx | neighborhood:696 |
Rv1674c |
transcriptional regulator | 731 | 731 | coexpression:731 |
Rv1453 |
transcriptional activator protein | 730 | 730 | coexpression:730 |
Rv0674 hyp |
hypothetical protein | 730 | 730 | coexpression:730 |
Rv0212c nadR |
transcriptional regulator NadR | 755 | 716 | coexpression:716 |
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: GntR family transcriptional regulator
- Pfam (hmmscan --cut_ga): GntR PF00392.28 (E=1e-12)
- (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_214557.1)
- Domains: Pfam-A via hmmscan --cut_ga — GntR (PF00392.28)
- 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
COG1802 - Curated reference: UniProt P9WMG9 (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
Rv0044c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000048|Rv0043c| MPKKYGVKEKDQVVAHILNLLLTGKLRSGDRVDRNEIAHGLGVSRVPIQEALVQLEHDGIVSTRYHRGAFIERFDVATILEHHELDGLLNGIASARAAANPTPRILGQLDAVMRSLRNSKESRAFAECVWEYRRTVNDEYAGPRLHATIRASQNLIPRVFWMTYQNSRDDVLPFYEEENAAIHRREPEAARAACIGRSELMAQTMLAELFRRRVLVPPEGACPGPFGAPIPGFARSYQPSSPVP