Rv2011c Family assigned · medium auto-curated
H37Rv Rv2011c · MTBC0 mtbc0_002139 ·
143 aa · 2282467–2282898 (-) ·
RefSeq NP_216527.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | MarR family winged helix-turn-helix transcriptional regulator |
| Revised (this work) | MarR family winged helix-turn-helix transcriptional regulator. Pfam: MarR_2 (PF12802.14). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WLM5
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Uncharacterized protein Rv2011c |
UniProt still lists this protein as Uncharacterized protein Rv2011c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | MarR family |
| 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 | 0.129 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 1 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.20% of strains (294) · 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 | 9.0e-11 | 33–86 | MarR family |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3167c |
TetR family transcriptional regulator | 769 | 769 | coexpression:731 |
Rv0767c |
HTH-type transcriptional regulator | 732 | 732 | coexpression:732 |
Rv2017 |
transcriptional regulator | 701 | 691 | coexpression:651 |
Rv2012 hyp |
hypothetical protein | 598 | 598 ctx | neighborhood:587 |
Rv0792c |
transcriptional regulator | 604 | 580 | coexpression:580 |
Rv3082c virS |
HTH-type transcriptional regulator VirS | 566 | 547 | coexpression:547 |
Rv3183 higA3 |
transcriptional regulator | 489 | 470 | coexpression:404 |
Rv0330c hyp |
hypothetical protein | 447 | 447 | |
Rv1674c |
transcriptional regulator | 454 | 423 | coexpression:404 |
Rv3066 |
DeoR family transcriptional regulator | 437 | 416 | |
Rv2621c |
transcriptional regulator | 414 | 415 | coexpression:415 |
Rv1395 |
HTH-type transcriptional regulator | 419 | 393 | |
Rv2642 |
ArsR family transcriptional regulator | 404 | 382 | |
Rv1985c lysG |
HTH-type transcriptional regulator | 405 | 379 | |
Rv3833 |
AraC family transcriptional regulator | 436 | 377 |
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: hypothetical protein
- MTBC0 PGAP product: MarR family winged helix-turn-helix transcriptional regulator
- Pfam (hmmscan --cut_ga): MarR_2 PF12802.14 (E=9e-11)
- (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_216527.1)
- Domains: Pfam-A via hmmscan --cut_ga — MarR_2 (PF12802.14)
- 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 P9WLM5 (SwissProt, reviewed; Inferred from homology)
- 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 — 18 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002139|Rv2011c| MSDEIARLVADVFELAGLLRRSGEVVAAREGHTQARWQLLSVVSDRALTVPQAARRLGVTRQGVQRVANDLVVCGLAELRHNPDHRTSPLLVLTENGRRVLQAITERAIVVNNRLADAVDPAALQATRDSLRRMIVALKAERP