Rv3058c Family assigned · medium auto-curated
H37Rv Rv3058c · MTBC0 mtbc0_003250 ·
216 aa · 3440022–3440672 (-) ·
RefSeq NP_217574.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | TetR family transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | TetR/AcrR family transcriptional regulator |
| Revised (this work) | TetR/AcrR family transcriptional regulator. Pfam: TetR_N (PF00440.30), EthR_C (PF21313.3). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P95100
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible 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 | 0.664 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 2 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 | 2.4e-12 | 26–71 | Bacterial regulatory proteins, tetR family |
EthR_C | PF21313.3 | 1.2e-06 | 102–211 | Transcriptional regulator EthR, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3057c (short chain alcohol dehydrogenase/reductase), high confidence from genomic context alone (score 803 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3057c |
short chain alcohol dehydrogenase/reductase | 802 | 803 ctx | neighborhood:800 |
Rv3059 cyp136 |
cytochrome P450 Cyp136 | 755 | 754 ctx | neighborhood:751 |
Rv0273c |
transcriptional regulator | 717 | 717 ctx | cooccurence:713 |
Rv3810 pirG |
cell surface protein | 621 | 621 ctx | cooccurence:615 |
Rv3446c hyp |
hypothetical protein | 571 | 571 ctx | cooccurence:569 |
Rv3492c |
Mce associated protein | 510 | 510 ctx | cooccurence:502 |
Rv0164 TB18.5 hyp |
hypothetical protein | 507 | 508 ctx | cooccurence:502 |
Rv1836c hyp |
hypothetical protein | 494 | 494 ctx | cooccurence:488 |
Rv3499c mce4A |
Mce family protein Mce4A | 493 | 493 ctx | cooccurence:488 |
Rv0233 nrdB |
ribonucleoside-diphosphate reductase subunit beta NrdB | 479 | 479 ctx | cooccurence:473 |
Rv0262c aac |
aminoglycoside 2'-N-acetyltransferase | 476 | 476 ctx | cooccurence:473 |
Rv0290 eccD3 |
ESX-3 secretion system protein EccD | 475 | 476 ctx | cooccurence:474 |
Rv3035 hyp |
hypothetical protein | 448 | 446 ctx | cooccurence:443 |
Rv1254 |
acyltransferase | 429 | 429 ctx | cooccurence:429 |
Rv0518 hyp |
hypothetical protein | 425 | 426 ctx | cooccurence:425 |
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: TetR family transcriptional regulator
- MTBC0 PGAP product: TetR/AcrR family transcriptional regulator
- Pfam (hmmscan --cut_ga): TetR_N PF00440.30 (E=2e-12), EthR_C PF21313.3 (E=1e-06)
- (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_217574.1)
- Domains: Pfam-A via hmmscan --cut_ga — TetR_N (PF00440.30), EthR_C (PF21313.3)
- 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 P95100 (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 —
19 functional partner(s); context anchor
Rv3057c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003250|Rv3058c| MTSHAADEKQAAPPMRRRGDRHRQAILRAARELLEETPFAELSVRAISLRAGVARSGFYFYFDSKYSVLAQILAEATEELEEASQHFSARQPGESPEQFVNRMIGSVAAVYANNDPVLRACNAARQSDMEIRDILERQFQVLLRETIGVFEAEVKAGTAHPISEDLPTLVRTLAATTALMLTGDALLVGPDSDAARRVRVLEQMWLNALWGGGKAP