Rv3066 Family assigned · medium auto-curated
H37Rv Rv3066 · MTBC0 mtbc0_003258 ·
202 aa · 3452071–3452679 (+) ·
RefSeq NP_217582.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | DeoR 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), TetR_C_31 (PF17940.7). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6X658
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable transcriptional regulatory protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Bacterial regulatory proteins, tetR family |
| Orthologous group | COG3226 |
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 | 0.373 · 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 | 5.0e-07 | 19–64 | Bacterial regulatory proteins, tetR family |
TetR_C_31 | PF17940.7 | 1.5e-09 | 87–183 | Tetracyclin repressor-like, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: mmr (multidrug resistance protein Mmr), high confidence from genomic context alone (score 885 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3065 mmr |
multidrug resistance protein Mmr | 959 | 885 ctx | neighborhood:881 textmining:660 |
Rv3183 higA3 |
transcriptional regulator | 857 | 857 | coexpression:833 |
Rv2788 sirR |
transcriptional repressor SirR | 830 | 830 | coexpression:830 |
Rv1725c hyp |
hypothetical protein | 827 | 827 | coexpression:804 |
Rv0691c mftR |
mycofactocin biosynthesis transcriptional regulator MftR | 822 | 823 | coexpression:800 |
Rv1167c |
transcriptional regulator | 804 | 805 | coexpression:805 |
Rv1674c |
transcriptional regulator | 801 | 801 | coexpression:801 |
Rv1151c cobB |
NAD-dependent protein deacylase | 800 | 800 | coexpression:800 |
Rv3736 |
AraC/XylS family transcriptional regulator | 799 | 800 | coexpression:800 |
Rv0494 |
HTH-type transcriptional regulator | 799 | 799 | coexpression:799 |
Rv3167c |
TetR family transcriptional regulator | 798 | 799 | coexpression:799 |
Rv1267c embR |
transcriptional regulator EmbR | 796 | 796 | coexpression:796 |
Rv0212c nadR |
transcriptional regulator NadR | 790 | 791 | coexpression:746 |
Rv1395 |
HTH-type transcriptional regulator | 815 | 789 | coexpression:736 |
Rv0674 hyp |
hypothetical protein | 788 | 788 | coexpression:788 |
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: DeoR family transcriptional regulator
- MTBC0 PGAP product: TetR/AcrR family transcriptional regulator
- Pfam (hmmscan --cut_ga): TetR_N PF00440.30 (E=5e-07), TetR_C_31 PF17940.7 (E=1e-09)
- (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_217582.1)
- Domains: Pfam-A via hmmscan --cut_ga — TetR_N (PF00440.30), TetR_C_31 (PF17940.7)
- 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
COG3226 - Curated reference: UniProt I6X658 (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 —
77 functional partner(s); context anchor
mmr - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003258|Rv3066| MTAGSDRRPRDPAGRRQAIVEAAERVIARQGLGGLSHRRVAAEANVPVGSTTYYFNDLDALREAALAHAANASADLLAQWRSDLDKDRDLAATLARLTTVYLADQDRYRTLNELYMAAAHRPELQRLARLWPDGLLALLEPRIGRRAANAVTVFFDGATLHALITGTPLSTDELTDAIARLVADGPEQREVGQSAHAGRTPD