Rv0195 Resolved · high auto-curated
H37Rv Rv0195 · MTBC0 mtbc0_000209 ·
211 aa · 231249–231884 (+) ·
RefSeq NP_214709.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | two component transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | response regulator transcription factor |
| Revised (this work) | Response regulator transcription factor. Pfam: GerE (PF00196.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53646
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Possible two component transcriptional regulatory protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Bacterial regulatory proteins, luxR family |
| Orthologous group | COG2197 |
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 | 0.712 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 4 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 6.00% of strains (8709) · 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 |
|---|---|---|---|---|
GerE | PF00196.26 | 2.4e-12 | 150–205 | Bacterial regulatory proteins, luxR family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: narS (sensor histidine kinase NarS), high confidence from genomic context alone (score 818 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0194 |
multidrug ABC transporter ATPase/permease | 866 | 831 | coexpression:826 |
Rv0845 narS |
sensor histidine kinase NarS | 839 | 818 ctx | cooccurence:662 |
Rv0193c hyp |
hypothetical protein | 903 | 732 | coexpression:731 textmining:655 |
Rv0844c narL |
nitrate/nitrite response transcriptional regulator NarL | 712 | 713 ctx | cooccurence:708 |
Rv3133c devR |
two component transcriptional regulator DevR | 780 | 704 ctx | cooccurence:703 |
Rv2027c dosT |
two component sensor histidine kinase DosT | 749 | 650 | |
Rv3132c devS |
two component sensor histidine kinase DevS | 725 | 642 | |
Rv0197 |
oxidoreductase | 542 | 527 ctx | neighborhood:526 |
Rv0196 |
HTH-type transcriptional regulator | 528 | 527 ctx | neighborhood:526 |
Rv1674c |
transcriptional regulator | 509 | 478 | coexpression:476 |
Rv3840 |
transcriptional regulator | 433 | 426 | |
Rv0601c |
two component sensor kinase HK2 | 417 | 395 | |
Rv1675c cmr |
HTH-type transcriptional regulator Cmr | 424 | 394 | |
Rv1189 sigI |
ECF RNA polymerase sigma factor SigI | 408 | 387 | |
Rv0494 |
HTH-type transcriptional regulator | 406 | 383 |
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: two component transcriptional regulator
- MTBC0 PGAP product: response regulator transcription factor
- Pfam (hmmscan --cut_ga): GerE PF00196.26 (E=2e-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_214709.1)
- Domains: Pfam-A via hmmscan --cut_ga — GerE (PF00196.26)
- 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
COG2197 - Curated reference: UniProt O53646 (TrEMBL, unreviewed; Predicted)
- 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 —
28 functional partner(s); context anchor
narS - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000209|Rv0195| MAPVNVISVAVVASDPLTRDGALARLSSHRELDVRAWQAGCETSVLLVLATTITAPLLCQIEDVQKDGPSHAPKLVVVADEFSAEQVFRMIKLGLTGLLYRSQSTFDCIVETIRLSAEGRLRLPERVQRYLVGRIKSTPTAEPDTPCAAALAEREVAVLRLLADGLSTHQVAVQLNYCERTIKNIVHDIVTRLKLRNRTHAVAHALRAGLI