kstR2 Family assigned · medium auto-curated
H37Rv Rv3557c · MTBC0 mtbc0_003774 ·
200 aa · 4020706–4021308 (-) ·
RefSeq NP_218074.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | HTH-type transcriptional regulator KstR2 |
|---|---|
| MTBC0 PGAP re-annotation | TetR family transcriptional regulator KstR2 |
| Revised (this work) | TetR family transcriptional regulator KstR2. Pfam: TetR_N (PF00440.30), TetR_C_24 (PF17932.7). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMB9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | HTH-type transcriptional repressor KstR2 |
| Curated function | Controls the expression of a small regulon that may play a role in the utilization of cholesterol. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | kstR2 |
| eggNOG description | transcriptional |
| Orthologous group | COG1309 |
| KEGG orthology |
K22108
|
| Gene Ontology (35) |
GO:0003674, GO:0003676, GO:0003677, GO:0003700, GO:0005488, GO:0005515, GO:0006355, GO:0008150, GO:0009889, GO:0010468, GO:0010556, GO:0010565 +23 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)
| pN/pS | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 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 | 3.5e-17 | 15–61 | Bacterial regulatory proteins, tetR family |
TetR_C_24 | PF17932.7 | 1.7e-19 | 81–195 | Tetracyclin repressor-like, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadA6 (acetyl-CoA acetyltransferase FadA), high confidence from genomic context alone (score 810 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3556c fadA6 |
acetyl-CoA acetyltransferase FadA | 930 | 810 ctx | neighborhood:799 textmining:648 |
Rv0158 |
transcriptional regulator | 794 | 795 | coexpression:731 |
Rv3855 ethR |
HTH-type transcriptional repressor EthR | 791 | 778 | coexpression:748 |
Rv3060c |
GntR family transcriptional regulator | 743 | 736 | coexpression:735 |
Rv3555c hyp |
hypothetical protein | 485 | 485 ctx | neighborhood:480 |
Rv3574 kstR |
HTH-type transcriptional regulator KstR | 961 | 460 ctx | cooccurence:453 textmining:931 |
Rv3521 hyp |
hypothetical protein | 459 | 459 ctx | cooccurence:456 |
Rv3552 |
CoA-transferase subunit beta | 511 | 454 ctx | cooccurence:436 |
Rv3542c chsH2 hyp |
hypothetical protein | 451 | 451 ctx | cooccurence:448 |
Rv3541c chsH1 hyp |
hypothetical protein | 468 | 448 ctx | cooccurence:445 |
Rv3558 PPE64 |
PPE family protein PPE64 | 436 | 436 ctx | neighborhood:434 |
Rv3560c fadE30 |
acyl-CoA dehydrogenase FadE30 | 866 | 427 | textmining:777 |
Rv1176c hyp |
hypothetical protein | 419 | 408 | |
Rv1014c pth |
peptidyl-tRNA hydrolase | 400 | 401 | |
Rv3551 |
CoA-transferase subunit alpha | 612 | 400 |
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: HTH-type transcriptional regulator KstR2
- MTBC0 PGAP product: TetR family transcriptional regulator KstR2
- Pfam (hmmscan --cut_ga): TetR_N PF00440.30 (E=4e-17), TetR_C_24 PF17932.7 (E=2e-19)
- (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_218074.1)
- Domains: Pfam-A via hmmscan --cut_ga — TetR_N (PF00440.30), TetR_C_24 (PF17932.7)
- 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
COG1309 - Curated reference: UniProt P9WMB9 (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 —
42 functional partner(s); context anchor
fadA6 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003774|Rv3557c|kstR2 MDRVAGQVNSRRGELLELAAAMFAERGLRATTVRDIADGAGILSGSLYHHFASKEEMVDELLRGFLDWLFARYRDIVDSTANPLERLQGLFMASFEAIEHHHAQVVIYQDEAQRLASQPRFSYIEDRNKQQRKMWVDVLNQGIEEGYFRPDLDVDLVYRFIRDTTWVSVRWYRPGGPLTAQQVGQQYLAIVLGGITKEGV