Rv0196 Family assigned · medium auto-curated
H37Rv Rv0196 · MTBC0 mtbc0_000210 ·
194 aa · 231997–232581 (+) ·
RefSeq NP_214710.1
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_13 (PF16925.11), TetR_C_13_2 (PF21993.2). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WME1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized HTH-type transcriptional regulator Rv0196 |
UniProt still lists this protein as Uncharacterized HTH-type transcriptional regulator Rv0196; 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 (41) |
GO:0000976, GO:0001067, GO:0003674, GO:0003676, GO:0003677, GO:0003690, GO:0003700, GO:0005488, GO:0005575, GO:0005622, GO:0005623, GO:0005737 +29 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 | 0.365 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.23% of strains (341) · 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 |
|---|---|---|---|---|
TetR_N | PF00440.30 | 5.5e-06 | 12–52 | Bacterial regulatory proteins, tetR family |
TetR_C_13 | PF16925.11 | 8.7e-08 | 73–180 | Tetracyclin repressor-like, C-terminal domain |
TetR_C_13_2 | PF21993.2 | 8.1e-26 | 75–180 | Transcriptional regulator LmrA/YxaF-like, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0197 (oxidoreductase), high confidence from genomic context alone (score 986 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0197 |
oxidoreductase | 992 | 986 ctx | neighborhood:881 coexpression:860 textmining:512 |
Rv3055 |
TetR family transcriptional regulator | 564 | 564 ctx | cooccurence:564 |
Rv0195 |
two component transcriptional regulator | 528 | 527 ctx | neighborhood:526 |
Rv1014c pth |
peptidyl-tRNA hydrolase | 403 | 403 | coexpression:401 |
Rv3095 |
HTH-type transcriptional regulator | 404 | 390 | |
Rv0097 |
oxidoreductase | 516 | 176 | textmining:438 |
Rv0784 hyp |
hypothetical protein | 824 | 159 | textmining:800 |
Rv2339 mmpL9 |
transmembrane transport protein MmpL9 | 554 | 53 | textmining:549 |
Rv1057 hyp |
hypothetical protein | 436 | 47 | textmining:433 |
Rv2781c |
oxidoreductase | 803 | 45 | textmining:803 |
Rv1139c hyp |
hypothetical protein | 802 | 41 | textmining:802 |
Rv3572 hyp |
hypothetical protein | 618 | 41 | textmining:618 |
Rv2638 hyp |
hypothetical protein | 439 | 41 | textmining:439 |
Rv0820 phoT |
phosphate ABC transporter ATP-binding protein PhoT | 436 | 41 | textmining:436 |
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=5e-06), TetR_C_13 PF16925.11 (E=9e-08), TetR_C_13_2 PF21993.2 (E=8e-26)
- (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_214710.1)
- Domains: Pfam-A via hmmscan --cut_ga — TetR_N (PF00440.30), TetR_C_13 (PF16925.11), TetR_C_13_2 (PF21993.2)
- 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 P9WME1 (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 —
14 functional partner(s); context anchor
Rv0197 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000210|Rv0196| MQGPRERMVVSAALLIRERGAHATAISDVLQHSGAPRGSAYHYFPGGRTQLLCEAVDYAGEHVAAMINEAEGGLELLDALIDKYRQQLLSTDFRAGCPIAAVSVEAGDEQDRERMAPVIARAAAVFDRWSDLTAQRFIADGIPPDRAHELAVLATSTLEGAILLARVRRDLTPLDLVHRQLRNLLLAELPERSR