Rv0158 Family assigned · medium auto-curated
H37Rv Rv0158 · MTBC0 mtbc0_000171 ·
214 aa · 187131–187775 (+) ·
RefSeq NP_214672.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 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_24 (PF17932.7), TetR_C_5 (PF08360.16). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53641
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable transcriptional regulatory protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Transcriptional regulator |
| Orthologous group | COG1309 |
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 | 0.23 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 synonymous, 5 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 | 1.4e-12 | 16–57 | Bacterial regulatory proteins, tetR family |
TetR_C_24 | PF17932.7 | 5.7e-21 | 81–196 | Tetracyclin repressor-like, C-terminal domain |
TetR_C_5 | PF08360.16 | 3.9e-04 | 81–195 | QacR-like protein, C-terminal region |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0238 (transcriptional regulator), medium confidence from genomic context alone (score 635 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3855 ethR |
HTH-type transcriptional repressor EthR | 869 | 869 | coexpression:802 |
Rv3557c kstR2 |
HTH-type transcriptional regulator KstR2 | 794 | 795 | coexpression:731 |
Rv3488 hyp |
hypothetical protein | 782 | 778 | coexpression:778 |
Rv3263 |
DNA methylase | 744 | 744 | coexpression:744 |
Rv3060c |
GntR family transcriptional regulator | 740 | 733 | coexpression:732 |
Rv0339c iniR |
transcriptional regulator | 733 | 733 | coexpression:733 |
Rv1176c hyp |
hypothetical protein | 737 | 732 | coexpression:732 |
Rv1985c lysG |
HTH-type transcriptional regulator | 726 | 722 | coexpression:687 |
Rv3183 higA3 |
transcriptional regulator | 703 | 703 | coexpression:703 |
Rv3840 |
transcriptional regulator | 651 | 651 | coexpression:651 |
Rv1561 vapC11 |
ribonuclease VapC11 | 651 | 651 | coexpression:651 |
Rv2760c vapB42 |
antitoxin VapB42 | 651 | 651 | coexpression:651 |
Rv1560 vapB11 |
antitoxin VapB11 | 651 | 651 | coexpression:651 |
Rv0238 |
transcriptional regulator | 634 | 635 ctx | cooccurence:445 |
Rv2506 |
TetR family transcriptional regulator | 620 | 621 | coexpression:431 |
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: transcriptional regulator
- MTBC0 PGAP product: TetR/AcrR family transcriptional regulator
- Pfam (hmmscan --cut_ga): TetR_N PF00440.30 (E=1e-12), TetR_C_24 PF17932.7 (E=6e-21), TetR_C_5 PF08360.16 (E=4e-04)
- (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_214672.1)
- Domains: Pfam-A via hmmscan --cut_ga — TetR_N (PF00440.30), TetR_C_24 (PF17932.7), TetR_C_5 (PF08360.16)
- 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 O53641 (TrEMBL, unreviewed; 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 —
21 functional partner(s); context anchor
Rv0238 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000171|Rv0158| MPSDTSPNGLSRREELLAVATKLFAARGYHGTRMDDVADVIGLNKATVYHYYASKSLILFDIYRQAAEGTLAAVHDDPSWTAREALYQYTVRLLTAIASNPERAAVYFQEQPYITEWFTSEQVAEVREKEQQVYEHVHGLIDRGIASGEFYECDSHVVALGYIGMTLGSYRWLRPSGRRTAKEIAAEFSTALLRGLIRDESIRNQSPLGTRKET