Rv1152 Family assigned · medium auto-curated
H37Rv Rv1152 · MTBC0 mtbc0_001238 ·
121 aa · 1288096–1288461 (+) ·
RefSeq NP_215668.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | GntR family transcriptional regulator |
| Revised (this work) | GntR family transcriptional regulator. Pfam: GntR (PF00392.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06550
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | HTH-type transcriptional regulator Rv1152 |
| Curated function | Transcriptional regulator that modulates resistance to vancomycin and aminoglycosides. Negatively regulates the expression of several genes responsive to vancomycin, resulting in decreased susceptibility of bacteria to vancomycin. Negatively regulates the expression of genes encoding the ribosome binding protein Hsp, the small subunit of sulfate adenylyltransferase CysD, the L-lysine-epsilon aminotransferase LAT and the protease HtpX. Also modulates purine metabolism and aminoglycoside antibiotic resistance. Negatively regulates the expression of purine metabolism-related genes and the accumul. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | transcriptional |
| Orthologous group | COG1725 |
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 | 0.728 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 2 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 |
|---|---|---|---|---|
GntR | PF00392.28 | 4.2e-14 | 21–80 | Bacterial regulatory proteins, gntR family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cobB (NAD-dependent protein deacylase), high confidence from genomic context alone (score 923 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1151c cobB |
NAD-dependent protein deacylase | 923 | 923 ctx | neighborhood:789 coexpression:651 |
Rv1019 |
transcriptional regulator | 850 | 845 | coexpression:845 |
Rv1725c hyp |
hypothetical protein | 803 | 803 | coexpression:803 |
Rv1267c embR |
transcriptional regulator EmbR | 798 | 798 | coexpression:798 |
Rv0691c mftR |
mycofactocin biosynthesis transcriptional regulator MftR | 804 | 797 | coexpression:797 |
Rv0038 hyp |
hypothetical protein | 781 | 781 | coexpression:780 |
Rv1931c |
transcriptional regulator | 775 | 775 | coexpression:734 |
Rv2788 sirR |
transcriptional repressor SirR | 764 | 764 | coexpression:761 |
Rv0212c nadR |
transcriptional regulator NadR | 757 | 757 | coexpression:757 |
Rv0275c |
transcriptional regulator | 755 | 746 | coexpression:746 |
Rv1985c lysG |
HTH-type transcriptional regulator | 753 | 740 | coexpression:740 |
Rv1674c |
transcriptional regulator | 748 | 739 | coexpression:738 |
Rv2359 zur |
zinc uptake regulation protein | 749 | 735 | coexpression:735 |
Rv3167c |
TetR family transcriptional regulator | 743 | 734 | coexpression:734 |
Rv3263 |
DNA methylase | 734 | 734 | coexpression:734 |
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: GntR family transcriptional regulator
- Pfam (hmmscan --cut_ga): GntR PF00392.28 (E=4e-14)
- (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_215668.1)
- Domains: Pfam-A via hmmscan --cut_ga — GntR (PF00392.28)
- 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
COG1725 - Curated reference: UniProt O06550 (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 —
47 functional partner(s); context anchor
cobB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001238|Rv1152| MELRDWLRVDVKAGKPLFDQLRTQVIDGVRAGALPPGTRLPTVRDLAGQLGVAANTVARAYRELESAAIVETRGRFGTFISRFDPTDAAMAAAAKEYVGVARALGLTKSDAMRYLTHVPDD