Rv1816 Family assigned · medium auto-curated
H37Rv Rv1816 · MTBC0 - ·
234 aa · 2058256–2058960 (+) ·
RefSeq NP_216332.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | HTH-type transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | HTH-type 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.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WMC9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | HTH-type transcriptional regulator Rv1816 |
| Curated function | May participate in the regulatory network that controls the expression of MmpL lipid transporters. Binds to intragenic and/or promoter regions of rv1816, mmpL3, rv0204, mmpL11, mmpL7, kasA and mmpS3. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | tetR family |
| Orthologous group | COG1309 |
| Gene Ontology (22) |
GO:0003674, GO:0003700, GO:0006355, GO:0008150, GO:0009889, GO:0010468, GO:0010556, GO:0019219, GO:0019222, GO:0031323, GO:0031326, GO:0050789 +10 more
|
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) pseudogene candidate
| pN/pS | 0.698 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 4 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 5.77% of strains (8384) · clonal |
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 | 1.7e-06 | 21–64 | Bacterial regulatory proteins, tetR family |
TetR_C_33 | PF13305.12 | 4.2e-21 | 96–225 | Tetracyclin repressor-like, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: eccD2 (ESX-2 secretion system protein EccD), medium confidence from genomic context alone (score 559 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1815 hyp |
hypothetical protein | 938 | 938 ctx | neighborhood:700 coexpression:802 |
Rv2423 hyp |
hypothetical protein | 606 | 606 ctx | cooccurence:606 |
Rv3899c hyp |
hypothetical protein | 590 | 590 ctx | cooccurence:586 |
Rv2067c hyp |
hypothetical protein | 565 | 566 ctx | cooccurence:560 |
Rv3887c eccD2 |
ESX-2 secretion system protein EccD | 558 | 559 ctx | cooccurence:556 |
Rv1817 |
flavoprotein | 546 | 546 ctx | neighborhood:544 |
Rv0736 rslA |
anti-sigma-L factor RslA | 531 | 531 ctx | cooccurence:523 |
Rv3435c |
transmembrane protein | 487 | 488 ctx | cooccurence:480 |
Rv1748 hyp |
hypothetical protein | 482 | 482 ctx | cooccurence:482 |
Rv1814 erg3 |
membrane-bound C-5 sterol desaturase | 475 | 475 ctx | neighborhood:475 |
Rv1014c pth |
peptidyl-tRNA hydrolase | 404 | 404 | coexpression:402 |
Rv0827c kmtR |
HTH-type transcriptional regulator KmtR | 521 | 56 | textmining:514 |
Rv1423 whiA |
transcriptional regulator WhiA | 662 | 55 | textmining:657 |
Rv3246c mtrA |
two component DNA-binding response regulator MtrA | 552 | 55 | textmining:546 |
Rv1828 |
HTH-type transcriptional regulator | 813 | 53 | textmining:811 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): HTH-type transcriptional regulator
- Pfam (hmmscan --cut_ga): TetR_N PF00440.30 (E=2e-06), TetR_C_33 PF13305.12 (E=4e-21)
- (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_216332.1)
- 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 P9WMC9 (SwissProt, reviewed; 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 —
20 functional partner(s); context anchor
eccD2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1816| MCQTCRVGKRRDAREQIEAKIVELGRRQLLDHGAAGLSLRAIARNLGMVSSAVYRYVSSRDELLTLLLVDAYSDLADTVDRARDDTVADSWSDDVIAIARAVRGWAVTNPARWALLYGSPVPGYHAPPDRTAGVATRVVGAFFDAIAAGIATGDIRLTDDVAPQPMSSDFEKIRQEFGFPGDDRVVTKCFLLWAGVVGAISLEVFGQYGADMLTDPGVVFDAQTRLLVAVLAEH