Rv0302 Family assigned · medium auto-curated
H37Rv Rv0302 · MTBC0 mtbc0_000321 ·
210 aa · 367944–368576 (+) ·
RefSeq NP_214816.1
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_6 (PF13977.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O07229
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 | 0.345 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 | 3.4e-17 | 19–65 | Bacterial regulatory proteins, tetR family |
TetR_C_6 | PF13977.12 | 7.4e-08 | 89–203 | BetI-type transcriptional repressor, C-terminal |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0303 (dehydrogenase/reductase), high confidence from genomic context alone (score 836 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0303 |
dehydrogenase/reductase | 836 | 836 ctx | neighborhood:836 |
Rv0301 vapC2 |
ribonuclease VapC2 | 593 | 593 ctx | neighborhood:520 |
Rv1534 |
transcriptional regulator | 565 | 565 ctx | cooccurence:559 |
Rv3882c eccE1 |
ESX-1 secretion system protein EccE1 | 546 | 547 ctx | cooccurence:544 |
Rv0300 vapB2 |
antitoxin VapB2 | 532 | 532 ctx | neighborhood:520 |
Rv3877 eccD1 |
ESX-1 secretion system protein EccD1 | 468 | 468 ctx | cooccurence:465 |
Rv3160c |
TetR family transcriptional regulator | 438 | 438 ctx | cooccurence:422 |
Rv0299 |
toxin | 430 | 430 ctx | neighborhood:423 |
Rv0298 |
antitoxin | 426 | 427 ctx | neighborhood:423 |
Rv1014c pth |
peptidyl-tRNA hydrolase | 403 | 403 | coexpression:401 |
Rv0067c |
transcriptional regulator | 440 | 169 | |
Rv0377 |
HTH-type transcriptional regulator | 449 | 152 | |
Rv2282c |
LysR family HTH-type transcriptional regulator | 449 | 152 |
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=3e-17), TetR_C_6 PF13977.12 (E=7e-08)
- (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_214816.1)
- Domains: Pfam-A via hmmscan --cut_ga — TetR_N (PF00440.30), TetR_C_6 (PF13977.12)
- 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 O07229 (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 —
13 functional partner(s); context anchor
Rv0303 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000321|Rv0302| MGVPAKKKQQQGERSRESILDATERLMATKGYAATSISDIRDACGLAPSSIYWHFGSKEGVLAAMMERGAQRFFAAIPTWDEAHGPVEQRSERQLTELVSLQSQHPDFLRLFYLLSMERSQDPAVAAVVRRVRNTAIARFRDSITHLLPSDIPPGKADLVVAELTAFAVALSDGVYFAGHLEPDTTDVERMYRRLRQALEALIPVLLEET