Rv0232 Family assigned · medium auto-curated
H37Rv Rv0232 · MTBC0 mtbc0_000247 ·
229 aa · 278280–278969 (+) ·
RefSeq NP_214746.1
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). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96415
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable transcriptional regulatory protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | tetR family |
| 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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 0 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 | 3.7e-12 | 18–60 | Bacterial regulatory proteins, tetR family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: nrdB (ribonucleoside-diphosphate reductase subunit beta NrdB), high confidence from genomic context alone (score 983 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0233 nrdB |
ribonucleoside-diphosphate reductase subunit beta NrdB | 982 | 983 ctx | neighborhood:882 coexpression:860 |
Rv0231 fadE4 |
acyl-CoA dehydrogenase FadE4 | 757 | 758 ctx | neighborhood:756 |
Rv0230c php |
phosphotriesterase | 749 | 749 ctx | neighborhood:697 |
Rv3830c |
TetR family transcriptional regulator | 566 | 553 ctx | cooccurence:549 |
Rv1354c hyp |
hypothetical protein | 519 | 476 ctx | cooccurence:407 |
Rv3829c |
dehydrogenase | 469 | 469 ctx | cooccurence:466 |
Rv0048c |
membrane protein | 461 | 461 ctx | cooccurence:461 |
Rv3773c hyp |
hypothetical protein | 453 | 454 ctx | cooccurence:446 |
Rv0128 |
transmembrane protein | 449 | 449 ctx | cooccurence:449 |
Rv1061 hyp |
hypothetical protein | 429 | 429 ctx | cooccurence:426 |
Rv0875c hyp |
hypothetical protein | 427 | 427 ctx | cooccurence:419 |
Rv1171 hyp |
hypothetical protein | 426 | 427 ctx | cooccurence:410 |
Rv0736 rslA |
anti-sigma-L factor RslA | 425 | 426 ctx | cooccurence:418 |
Rv1014c pth |
peptidyl-tRNA hydrolase | 403 | 403 | coexpression:401 |
Rv2434c |
transmembrane protein | 418 | 397 |
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=4e-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_214746.1)
- Domains: Pfam-A via hmmscan --cut_ga — TetR_N (PF00440.30)
- 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 P96415 (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 —
25 functional partner(s); context anchor
nrdB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000247|Rv0232| MPTVTWARVDPARRAAVVEAAEAEFGAHGFSRGSLNVIARRAGVAKGSLFQYFADKRDLYAFIADIASQRVRSYMEDLIRELDPNRPFFEFLTDLLDGWVAYFAEHPRERALHAAATLEVDTDARISVRSVLHRHYLDVLRPLVRDAHARGDLRADSDTGALMSLLLLIFPHLALAPYMRGLDPILGLDEPTPEQPALAVRRLVAVLAAAFDAQHPATNSAQTRSEEIT