Rv2282c Family assigned · medium auto-curated
H37Rv Rv2282c · MTBC0 mtbc0_002423 ·
312 aa · 2579685–2580623 (-) ·
RefSeq NP_216798.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | LysR family HTH-type transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | LysR family transcriptional regulator |
| Revised (this work) | LysR family transcriptional regulator. Pfam: HTH_1 (PF00126.34), LysR_substrate (PF03466.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMF3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized HTH-type transcriptional regulator Rv2282c |
UniProt still lists this protein as Uncharacterized HTH-type transcriptional regulator Rv2282c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Bacterial regulatory helix-turn-helix protein, lysR family |
| Orthologous group | COG0583 |
| Gene Ontology (8) |
GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0044424, GO:0044444, GO:0044464
|
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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 2 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.15% of strains (222) · 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 |
|---|---|---|---|---|
HTH_1 | PF00126.34 | 1.0e-19 | 13–68 | Bacterial regulatory helix-turn-helix protein, lysR family |
LysR_substrate | PF03466.26 | 4.1e-36 | 95–306 | LysR substrate binding domain |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1675c cmr |
HTH-type transcriptional regulator Cmr | 869 | 862 | coexpression:862 |
Rv0691c mftR |
mycofactocin biosynthesis transcriptional regulator MftR | 853 | 851 | coexpression:833 |
Rv3840 |
transcriptional regulator | 854 | 848 | coexpression:848 |
Rv0117 oxyS |
oxidative stress response regulatory protein OxyS | 846 | 847 | coexpression:803 |
Rv1674c |
transcriptional regulator | 848 | 839 | coexpression:812 |
Rv3736 |
AraC/XylS family transcriptional regulator | 845 | 837 | coexpression:837 |
Rv3830c |
TetR family transcriptional regulator | 836 | 834 | coexpression:813 |
Rv3167c |
TetR family transcriptional regulator | 836 | 831 | coexpression:810 |
Rv1267c embR |
transcriptional regulator EmbR | 833 | 827 | coexpression:827 |
Rv2488c |
LuxR family transcriptional regulator | 835 | 826 | coexpression:826 |
Rv1556 |
HTH-type transcriptional regulator | 830 | 825 | coexpression:803 |
Rv1151c cobB |
NAD-dependent protein deacylase | 823 | 824 | coexpression:823 |
Rv1189 sigI |
ECF RNA polymerase sigma factor SigI | 820 | 813 | coexpression:813 |
Rv1776c |
transcriptional regulator | 864 | 811 | coexpression:788 |
Rv1027c kdpE |
transcriptional regulator KdpE | 820 | 810 | coexpression:810 |
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: LysR family HTH-type transcriptional regulator
- MTBC0 PGAP product: LysR family transcriptional regulator
- Pfam (hmmscan --cut_ga): HTH_1 PF00126.34 (E=1e-19), LysR_substrate PF03466.26 (E=4e-36)
- (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_216798.1)
- Domains: Pfam-A via hmmscan --cut_ga — HTH_1 (PF00126.34), LysR_substrate (PF03466.26)
- 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
COG0583 - Curated reference: UniProt P9WMF3 (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 — 70 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002423|Rv2282c| MPLSSRMPGLTCFEIFLAIAEAGSLGGAARELGLTQQAVSRRLASMEAQIGVRLAIRTTRGSQLTPAGIVVAEWAARLLEVADEIDAGLGSLRTEGRQRIRVVASQTIAEQLMPHWMLSLRAADMRRGGTVPEVILTATNSEHAIAAVRDGIADLGFIENPCPPTGLGSVVVARDELVVVVPPGHKWARRSRVVSARELAQTPLVTREPNSGIRDSLTAALRDTLGEDMQQAPPVLELSSAAAVRAAVLAGAGPAAMSRLAIADDLAFGRLLAVDIPALNLRRQLRAIWVGGRTPPAGAIRDLLSHITSRST