Rv2887 Family assigned · medium auto-curated
H37Rv Rv2887 · MTBC0 mtbc0_003069 ·
139 aa · 3217260–3217679 (+) ·
RefSeq NP_217403.1
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), HTH_24 (PF13412.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WME9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | HTH-type transcriptional repressor Rv2887 |
| Curated function | Represses expression of the HQNO methyltransferase htm gene (Rv0560c) by binding to its promoter region. Also represses the expression of at least five other genes, including the methyltransferase Rv0558. Binds salicylate (SA), para-aminosalicylic acid (PAS) and gemfibrozil. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Transcriptional regulator |
| Orthologous group | COG1846 |
| Gene Ontology (27) |
GO:0001067, GO:0003674, GO:0003676, GO:0003677, GO:0005488, GO:0006355, GO:0008150, GO:0009889, GO:0010468, GO:0010556, GO:0019219, GO:0019222 +15 more
|
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 | 0.806 · 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 |
|---|---|---|---|---|
MarR_2 | PF12802.14 | 3.8e-11 | 31–90 | MarR family |
MarR | PF01047.29 | 1.6e-14 | 33–90 | MarR family |
HTH_24 | PF13412.13 | 3.0e-05 | 41–78 | Winged helix-turn-helix DNA-binding |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2885c (transposase), medium confidence from genomic context alone (score 576 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2885c |
transposase | 576 | 576 ctx | neighborhood:572 |
Rv2886c |
resolvase | 573 | 573 ctx | neighborhood:572 |
Rv2327 hyp |
hypothetical protein | 428 | 408 ctx | cooccurence:404 |
Rv3095 |
HTH-type transcriptional regulator | 490 | 276 | |
Rv0880 |
HTH-type transcriptional regulator | 836 | 163 | textmining:813 |
Rv0560c |
benzoquinone methyltransferase | 874 | 72 | textmining:870 |
Rv3094c hyp |
hypothetical protein | 534 | 54 | textmining:528 |
Rv1405c |
methyltransferase | 583 | 52 | textmining:578 |
Rv1404 |
transcriptional regulator | 870 | 44 | textmining:870 |
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=4e-11), MarR PF01047.29 (E=2e-14), HTH_24 PF13412.13 (E=3e-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_217403.1)
- Domains: Pfam-A via hmmscan --cut_ga — MarR_2 (PF12802.14), MarR (PF01047.29), HTH_24 (PF13412.13)
- 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 P9WME9 (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 —
9 functional partner(s); context anchor
Rv2885c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003069|Rv2887| MGLADDAPLGYLLYRVGAVLRPEVSAALSPLGLTLPEFVCLRMLSQSPGLSSAELARHASVTPQAMNTVLRKLEDAGAVARPASVSSGRSLPATLTARGRALAKRAEAVVRAADARVLARLTAPQQREFKRMLEKLGSD