kmtR Resolved · high auto-curated
H37Rv Rv0827c · MTBC0 mtbc0_000876 ·
130 aa · 923808–924200 (-) ·
RefSeq NP_215342.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | HTH-type transcriptional regulator KmtR |
|---|---|
| MTBC0 PGAP re-annotation | Ni(II)/Co(II)-sensing metalloregulatory transcriptional repressor KmtR |
| Revised (this work) | Ni(II)/Co(II)-sensing metalloregulatory transcriptional repressor KmtR. Pfam: HTH_20 (PF12840.14), HTH_5 (PF01022.27), MarR_2 (PF12802.14), HTH_IclR (PF09339.17). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53838
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | HTH-type transcriptional regulator KmtR |
| Curated function | Represses expression of Rv2025c and its own expression. Acts by binding to the promoter regions. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | kmtR |
| eggNOG description | regulatory protein, arsR |
| Orthologous group | COG0640 |
| Gene Ontology (13) |
GO:0003674, GO:0003676, GO:0003677, GO:0005488, GO:0008150, GO:0010035, GO:0010038, GO:0010045, GO:0032025, GO:0042221, GO:0050896, GO:0097159 +1 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 | 1.024 · 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 |
|---|---|---|---|---|
HTH_20 | PF12840.14 | 1.2e-09 | 25–74 | Helix-turn-helix domain |
HTH_5 | PF01022.27 | 2.6e-13 | 27–72 | Bacterial regulatory protein, arsR family |
MarR_2 | PF12802.14 | 2.7e-06 | 29–77 | MarR family |
HTH_IclR | PF09339.17 | 6.0e-05 | 38–74 | IclR helix-turn-helix domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0830 (S-adenosylmethionine-dependent methyltransferase), medium confidence from genomic context alone (score 681 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2359 zur |
zinc uptake regulation protein | 819 | 792 | coexpression:785 |
Rv1267c embR |
transcriptional regulator EmbR | 788 | 788 | coexpression:788 |
Rv0117 oxyS |
oxidative stress response regulatory protein OxyS | 788 | 780 | coexpression:780 |
Rv0377 |
HTH-type transcriptional regulator | 763 | 754 | coexpression:754 |
Rv3082c virS |
HTH-type transcriptional regulator VirS | 756 | 747 | coexpression:744 |
Rv1931c |
transcriptional regulator | 736 | 737 | coexpression:737 |
Rv2488c |
LuxR family transcriptional regulator | 742 | 733 | coexpression:733 |
Rv1027c kdpE |
transcriptional regulator KdpE | 741 | 732 | coexpression:732 |
Rv0830 |
S-adenosylmethionine-dependent methyltransferase | 681 | 681 ctx | neighborhood:680 |
Rv0828c |
deaminase | 675 | 675 ctx | neighborhood:675 |
Rv3167c |
TetR family transcriptional regulator | 584 | 557 | coexpression:557 |
Rv2025c |
cation efflux system protein | 912 | 539 | textmining:817 |
Rv1674c |
transcriptional regulator | 768 | 533 | textmining:525 |
Rv2642 |
ArsR family transcriptional regulator | 627 | 513 ctx | cooccurence:484 |
Rv1725c hyp |
hypothetical protein | 470 | 469 | coexpression:463 |
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 KmtR
- MTBC0 PGAP product: Ni(II)/Co(II)-sensing metalloregulatory transcriptional repressor KmtR
- Pfam (hmmscan --cut_ga): HTH_20 PF12840.14 (E=1e-09), HTH_5 PF01022.27 (E=3e-13), MarR_2 PF12802.14 (E=3e-06), HTH_IclR PF09339.17 (E=6e-05)
- (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_215342.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_20 (PF12840.14), HTH_5 (PF01022.27), MarR_2 (PF12802.14), HTH_IclR (PF09339.17)
- 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
COG0640 - Curated reference: UniProt O53838 (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 —
36 functional partner(s); context anchor
Rv0830 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000876|Rv0827c|kmtR MYADSGPDPLPDDQVCLVVEVFRMLADATRVQVLWSLADREMSVNELAEQVGKPAPSVSQHLAKLRMARLVRTRRDGTTIFYRLENEHVRQLVIDAVFNAEHAGPGIPRHHRAAGGLQSVAKASATKDVG