Rv0880 Family assigned · medium auto-curated
H37Rv Rv0880 · MTBC0 mtbc0_000935 ·
143 aa · 982148–982579 (+) ·
RefSeq NP_215395.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | HTH-type transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | MarR family transcriptional regulator |
| Revised (this work) | MarR family transcriptional regulator. Pfam: MarR_2 (PF12802.14), MarR (PF01047.29). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMF1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | HTH-type transcriptional regulator Rv0880 |
| Curated function | Part of a regulatory network that coordinates tolerance to the antitubercular drug bedaquiline. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| 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) | 2 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 |
|---|---|---|---|---|
MarR_2 | PF12802.14 | 2.9e-07 | 32–89 | MarR family |
MarR | PF01047.29 | 4.0e-14 | 33–90 | MarR family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0882 (transmembrane protein), high confidence from genomic context alone (score 883 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0882 |
transmembrane protein | 883 | 883 ctx | neighborhood:882 |
Rv0881 |
tRNA/rRNA methyltransferase | 883 | 882 ctx | neighborhood:882 |
Rv0879c |
transmembrane protein | 766 | 766 ctx | neighborhood:765 |
Rv2175c |
DNA-binding protein | 730 | 730 | coexpression:730 |
Rv0744c |
transcriptional regulator | 651 | 651 | coexpression:651 |
Rv0653c |
transcriptional regulator | 580 | 580 | coexpression:580 |
Rv3143 |
response regulator | 528 | 510 | |
Rv3692 moxR2 |
methanol dehydrogenase transcriptional regulator MoxR | 495 | 495 | coexpression:494 |
Rv2738c hyp |
hypothetical protein | 449 | 450 ctx | cooccurence:448 |
Rv0430 hyp |
hypothetical protein | 435 | 435 ctx | cooccurence:430 |
Rv3291c lrpA |
transcriptional regulator LrpA | 457 | 432 | coexpression:432 |
Rv0452 |
transcriptional regulator | 415 | 415 | coexpression:415 |
Rv2096c pafB |
proteasome accessory factor B | 428 | 414 | |
Rv3830c |
TetR family transcriptional regulator | 409 | 409 | coexpression:409 |
Rv2199c ctaF |
cytochrome c oxidase polypeptide 4 | 524 | 222 | textmining:413 |
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
- MTBC0 PGAP product: MarR family transcriptional regulator
- Pfam (hmmscan --cut_ga): MarR_2 PF12802.14 (E=3e-07), MarR PF01047.29 (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_215395.1)
- Domains: Pfam-A via hmmscan --cut_ga — MarR_2 (PF12802.14), MarR (PF01047.29)
- 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 P9WMF1 (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 —
35 functional partner(s); context anchor
Rv0882 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000935|Rv0880| MLDSDARLASDLSLAVMRLSRQLRFRNPSSPVSLSQLSALTTLANEGAMTPGALAIRERVRPPSMTRVIASLADMGFVDRAPHPIDGRQVLVSVSESGAELVKAARRARQEWLAERLATLNRSERDILRSAADLMLALVDESP