Rv0042c Family assigned · medium auto-curated
H37Rv Rv0042c · MTBC0 - ·
208 aa · 46581–47207 (-) ·
RefSeq NP_214556.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Transcriptional regulator. Pfam: MarR_2 (PF12802.14), Staph_reg_Sar_Rot (PF22381.3), MarR (PF01047.29), HTH_27 (PF13463.13). |
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 |
P71699
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible transcriptional regulatory protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | uspR |
| eggNOG description | transcriptional |
| Orthologous group | COG1846 |
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 | 0.38 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 4 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.67% of strains (976) · 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 |
|---|---|---|---|---|
MarR_2 | PF12802.14 | 3.1e-08 | 82–140 | MarR family |
Staph_reg_Sar_Rot | PF22381.3 | 8.9e-08 | 82–151 | Transcriptional regulator SarA/Rot |
MarR | PF01047.29 | 9.2e-18 | 83–141 | MarR family |
HTH_27 | PF13463.13 | 5.1e-05 | 112–149 | Winged helix DNA-binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0043c (HTH-type transcriptional regulator), high confidence from genomic context alone (score 763 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0043c |
HTH-type transcriptional regulator | 775 | 763 ctx | neighborhood:748 |
Rv0044c |
oxidoreductase | 682 | 683 ctx | neighborhood:678 |
Rv0045c |
hydrolase | 608 | 608 ctx | neighborhood:608 |
Rv0046c ino1 |
inositol-3-phosphate synthase | 521 | 522 ctx | neighborhood:520 |
Rv0049 hyp |
hypothetical protein | 463 | 273 | |
Rv2949c |
chorismate pyruvate-lyase | 518 | 56 | textmining:511 |
Rv3830c |
TetR family transcriptional regulator | 516 | 53 | textmining:511 |
Rv0903c prrA |
two component transcriptional regulator PrrA | 625 | 51 | textmining:621 |
Rv2299c htpG |
chaperone protein HtpG | 763 | 47 | textmining:762 |
Rv0126 treS |
trehalose synthase/amylase TreS | 514 | 47 | textmining:511 |
Rv2780 ald |
L-alanine dehydrogenase | 447 | 46 | textmining:445 |
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): transcriptional regulator
- Pfam (hmmscan --cut_ga): MarR_2 PF12802.14 (E=3e-08), Staph_reg_Sar_Rot PF22381.3 (E=9e-08), MarR PF01047.29 (E=9e-18), HTH_27 PF13463.13 (E=5e-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_214556.1)
- Domains: Pfam-A via hmmscan --cut_ga — MarR_2 (PF12802.14), Staph_reg_Sar_Rot (PF22381.3), MarR (PF01047.29), HTH_27 (PF13463.13)
- 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
COG1846 - Curated reference: UniProt P71699 (TrEMBL, unreviewed; 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 —
11 functional partner(s); context anchor
Rv0043c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0042c| MSVVRSIGKKMQRISGPNALAVKGRPTQVYGHTHVRLDCRFMADSEFTAPEVTQLAEGLHRALSKLISMLRRGDPNGAAAGDLTLAQLSILVTLLDQGPIRMTDLAAHERVRTPTTTVAIRRLEKIGLVKRSRDPSDLRAVLVDITPQGRAVHGESLANRRAALAALLSQLPRSDLETLRKALAPLERLASGEPASGPASNSPARKRA