Rv1395 Family assigned · medium auto-curated
H37Rv Rv1395 · MTBC0 - ·
344 aa · 1571047–1572081 (+) ·
RefSeq YP_177808.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | HTH-type transcriptional regulator |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | HTH-type transcriptional regulator. Pfam: Arabinose_bd (PF12625.13), HTH_18 (PF12833.14). |
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 |
P9WMJ1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized HTH-type transcriptional regulator Rv1395 |
UniProt still lists this protein as Uncharacterized HTH-type transcriptional regulator Rv1395; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| eggNOG description | Arabinose-binding domain of AraC transcription regulator, N-term |
| Orthologous group | COG2207 |
| Gene Ontology (72) |
GO:0003674, GO:0003676, GO:0003677, GO:0003700, GO:0003824, GO:0005488, GO:0006081, GO:0006082, GO:0006089, GO:0006355, GO:0008150, GO:0008152 +60 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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 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 |
|---|---|---|---|---|
Arabinose_bd | PF12625.13 | 3.8e-22 | 28–216 | Arabinose-binding domain of AraC transcription regulator, N-term |
HTH_18 | PF12833.14 | 4.5e-18 | 266–343 | Helix-turn-helix domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1393c (monoxygenase), high confidence from genomic context alone (score 829 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1393c |
monoxygenase | 829 | 829 ctx | neighborhood:784 |
Rv3833 |
AraC family transcriptional regulator | 823 | 816 | coexpression:743 |
Rv1190 hyp |
hypothetical protein | 814 | 814 | coexpression:783 |
Rv3736 |
AraC/XylS family transcriptional regulator | 810 | 811 | coexpression:732 |
Rv3082c virS |
HTH-type transcriptional regulator VirS | 810 | 810 | coexpression:731 |
Rv1674c |
transcriptional regulator | 817 | 808 | coexpression:803 |
Rv1931c |
transcriptional regulator | 813 | 803 | coexpression:732 |
Rv0624 vapC30 |
ribonuclease VapC30 | 800 | 800 | coexpression:800 |
Rv3167c |
TetR family transcriptional regulator | 800 | 797 | coexpression:797 |
Rv0273c |
transcriptional regulator | 799 | 796 | coexpression:796 |
Rv1189 sigI |
ECF RNA polymerase sigma factor SigI | 798 | 790 | coexpression:753 |
Rv1725c hyp |
hypothetical protein | 790 | 790 | coexpression:759 |
Rv3066 |
DeoR family transcriptional regulator | 815 | 789 | coexpression:736 |
Rv1960c parD1 |
antitoxin ParD1 | 788 | 788 | coexpression:788 |
Rv1985c lysG |
HTH-type transcriptional regulator | 786 | 776 | coexpression:746 |
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): HTH-type transcriptional regulator
- Pfam (hmmscan --cut_ga): Arabinose_bd PF12625.13 (E=4e-22), HTH_18 PF12833.14 (E=4e-18)
- (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 YP_177808.1)
- Domains: Pfam-A via hmmscan --cut_ga — Arabinose_bd (PF12625.13), HTH_18 (PF12833.14)
- 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
COG2207 - Curated reference: UniProt P9WMJ1 (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 —
60 functional partner(s); context anchor
Rv1393c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1395| MGHLPPPAEVRHPVYATRVLCEVANERGVPTADVLAGTAIEPADLDDPDAVVGALDEITAVRRLLARLPDDAGIGIDVGSRFALTHFGLFGFAVMSCGTLRELLTIAMRYFALTTMHVDITLFETADDCLVELDASHLPADVRGFFIERDIAGIIATTTSFALPLAAKYADQVSAELAVDAELLRPLLELVPVHDVAFGRAHNRVHFPRAMFDEPLPQADRHTLEMCIAQCDVLMQRNERRRGITALVRSKLFRDSGLFPTFTDVAGELDMHPRTLRRRLAEEGTSFRALLGEARSTVAVDLLRNVGLTVQQVSTRLGYTEVSTFSHAFKRWYGVAPSEYSRRG