Rv3095 Family assigned · medium auto-curated
H37Rv Rv3095 · MTBC0 mtbc0_003289 ·
158 aa · 3485337–3485813 (+) ·
RefSeq NP_217611.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | HTH-type transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | helix-turn-helix domain-containing protein |
| Revised (this work) | Helix-turn-helix domain-containing protein. Pfam: HxlR (PF01638.24), HTH_5 (PF01022.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMG3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized HTH-type transcriptional regulator Rv3095 |
UniProt still lists this protein as Uncharacterized HTH-type transcriptional regulator Rv3095; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | HxlR-like helix-turn-helix |
| Orthologous group | COG1733 |
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 | 0.362 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 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 |
|---|---|---|---|---|
HxlR | PF01638.24 | 5.1e-28 | 21–108 | HxlR-like helix-turn-helix |
HTH_5 | PF01022.27 | 9.5e-05 | 29–67 | Bacterial regulatory protein, arsR family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3093c (oxidoreductase), high confidence from genomic context alone (score 899 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3093c |
oxidoreductase | 898 | 899 ctx | neighborhood:636 coexpression:733 |
Rv3094c hyp |
hypothetical protein | 984 | 886 ctx | neighborhood:783 coexpression:494 textmining:870 |
Rv3092c |
integral membrane protein | 877 | 877 ctx | neighborhood:507 coexpression:761 |
Rv3096 hyp |
hypothetical protein | 670 | 671 ctx | neighborhood:652 |
Rv2405 hyp |
hypothetical protein | 555 | 555 | coexpression:554 |
Rv1931c |
transcriptional regulator | 468 | 468 ctx | cooccurence:465 |
Rv0659c mazF2 |
toxin MazF2 | 421 | 422 | coexpression:422 |
Rv0456A mazF1 |
toxin MazF1 | 416 | 417 | coexpression:417 |
Rv2801c mazF9 |
mRNA interferase MazF9 | 416 | 417 | coexpression:417 |
Rv1102c mazF3 |
mRNA interferase MazF3 | 416 | 417 | coexpression:417 |
Rv1942c mazF5 |
toxin MazF5 | 414 | 415 | coexpression:415 |
Rv1991c mazF6 |
mRNA interferase MazF6 | 414 | 415 | coexpression:415 |
Rv1495 mazF4 |
mRNA interferase MazF4 | 412 | 413 | coexpression:413 |
Rv2063A mazF7 |
mRNA interferase MazF7 | 412 | 413 | coexpression:413 |
Rv3098A |
PemK-like protein | 412 | 413 | coexpression: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: helix-turn-helix domain-containing protein
- Pfam (hmmscan --cut_ga): HxlR PF01638.24 (E=5e-28), HTH_5 PF01022.27 (E=1e-04)
- (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_217611.1)
- Domains: Pfam-A via hmmscan --cut_ga — HxlR (PF01638.24), HTH_5 (PF01022.27)
- 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
COG1733 - Curated reference: UniProt P9WMG3 (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 —
34 functional partner(s); context anchor
Rv3093c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003289|Rv3095| MAVSDLSHRFEGESVGRALELVGERWTLLILREAFFGVRRFGQLARNLGIPRPTLSSRLRMLVEVGLFDRVPYSSDPERHEYRLTEAGRDLFAAIVVLMQWGDEYLPRPEGPPIKLRHHTCGEHADPRLICTHCGEEITARNVTPEPGPGFKAKLASS