Rv0653c Family assigned · medium auto-curated
H37Rv Rv0653c · MTBC0 mtbc0_000691 ·
231 aa · 753320–754015 (-) ·
RefSeq NP_215167.1
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_33 (PF13305.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96941
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible 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 | 1.078 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 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 | 1.8e-11 | 11–57 | Bacterial regulatory proteins, tetR family |
TetR_C_33 | PF13305.12 | 7.4e-16 | 81–198 | Tetracyclin repressor-like, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0654 (carotenoid cleavage oxygenase), high confidence from genomic context alone (score 785 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1167c |
transcriptional regulator | 833 | 833 | coexpression:810 |
Rv1019 |
transcriptional regulator | 823 | 824 | coexpression:772 |
Rv1985c lysG |
HTH-type transcriptional regulator | 825 | 822 | coexpression:800 |
Rv3736 |
AraC/XylS family transcriptional regulator | 811 | 808 | coexpression:780 |
Rv3167c |
TetR family transcriptional regulator | 806 | 806 | coexpression:806 |
Rv1931c |
transcriptional regulator | 806 | 806 | coexpression:767 |
Rv0452 |
transcriptional regulator | 801 | 801 | coexpression:761 |
Rv0691c mftR |
mycofactocin biosynthesis transcriptional regulator MftR | 805 | 800 | coexpression:800 |
Rv3263 |
DNA methylase | 800 | 800 | coexpression:800 |
Rv0603 hyp |
hypothetical protein | 799 | 799 | coexpression:799 |
Rv3840 |
transcriptional regulator | 799 | 799 | coexpression:799 |
Rv1359 |
transcriptional regulator | 797 | 797 | coexpression:797 |
Rv3328c sigJ |
ECF RNA polymerase sigma factor SigJ | 791 | 792 | coexpression:732 |
Rv0654 |
carotenoid cleavage oxygenase | 785 | 785 ctx | neighborhood:785 |
Rv1674c |
transcriptional regulator | 788 | 780 | coexpression:780 |
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=2e-11), TetR_C_33 PF13305.12 (E=7e-16)
- (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_215167.1)
- Domains: Pfam-A via hmmscan --cut_ga — TetR_N (PF00440.30), TetR_C_33 (PF13305.12)
- 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 P96941 (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 —
46 functional partner(s); context anchor
Rv0654 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000691|Rv0653c| MTSQTGVRDELLHAGVRLLDDHGPDALQTRKVAAAAGTSTMAVYTHFGGMRGLIAAIAEEGLRQFDVALTVPQTADPVADLLAIGTAYRRYAIERPHMYRLMFGSTSAHGINVPARDVLTLKVAEIEHQHPSFAHVVRAVHRCLLAGRFATALGADDDTAIVATAAQFWSQIHGFVMLELAGFYGDRGAAVEPVLAAMTVNLLVALGDSPERAQCSLRAEQTQKNTLGRAT