moxR3 Family assigned · medium auto-curated
H37Rv Rv3164c · MTBC0 mtbc0_003363 ·
320 aa · 3557791–3558753 (-) ·
RefSeq NP_217680.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | methanol dehydrogenase transcriptional regulator MoxR |
|---|---|
| MTBC0 PGAP re-annotation | MoxR family ATPase |
| Revised (this work) | MoxR family ATPase. Pfam: bpMoxR (PF20030.6), Sigma54_activat (PF00158.33), AAA_3 (PF07726.18), AAA_5 (PF07728.21), AAA (PF00004.36), AAA_lid_2 (PF17863.8). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53314
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable methanol dehydrogenase transcriptional regulatory protein MoxR3 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | moxR3 |
| eggNOG description | associated with various cellular activities |
| Orthologous group | COG0714 |
| KEGG orthology |
K03924
|
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 | 0.354 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 4 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 |
|---|---|---|---|---|
bpMoxR | PF20030.6 | 1.3e-07 | 13–203 | MoxR domain in the MoxR-vWA-beta-propeller ternary systems |
Sigma54_activat | PF00158.33 | 2.3e-04 | 32–152 | Sigma-54 interaction domain |
AAA_3 | PF07726.18 | 5.8e-63 | 42–171 | ATPase family associated with various cellular activities (AAA) |
AAA_5 | PF07728.21 | 6.0e-11 | 48–170 | AAA domain (dynein-related subfamily) |
AAA | PF00004.36 | 3.9e-04 | 49–176 | ATPase family associated with various cellular activities (AAA) |
AAA_lid_2 | PF17863.8 | 2.2e-19 | 236–294 | AAA lid domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3162c (integral membrane protein), high confidence from genomic context alone (score 843 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3163c hyp |
hypothetical protein | 923 | 919 ctx | neighborhood:841 cooccurence:402 |
Rv3165c hyp |
hypothetical protein | 882 | 882 ctx | neighborhood:881 |
Rv3166c hyp |
hypothetical protein | 881 | 882 ctx | neighborhood:881 |
Rv3162c |
integral membrane protein | 843 | 843 ctx | neighborhood:841 |
Rv2488c |
LuxR family transcriptional regulator | 839 | 840 | coexpression:836 |
Rv0273c |
transcriptional regulator | 827 | 827 | coexpression:827 |
Rv1725c hyp |
hypothetical protein | 827 | 827 | coexpression:824 |
Rv0377 |
HTH-type transcriptional regulator | 828 | 822 | coexpression:822 |
Rv1027c kdpE |
transcriptional regulator KdpE | 806 | 806 | coexpression:806 |
Rv3263 |
DNA methylase | 802 | 803 | coexpression:803 |
Rv1675c cmr |
HTH-type transcriptional regulator Cmr | 803 | 801 | coexpression:801 |
Rv3736 |
AraC/XylS family transcriptional regulator | 799 | 799 | coexpression:799 |
Rv0117 oxyS |
oxidative stress response regulatory protein OxyS | 803 | 796 | coexpression:796 |
Rv3328c sigJ |
ECF RNA polymerase sigma factor SigJ | 796 | 796 | coexpression:796 |
Rv0339c iniR |
transcriptional regulator | 794 | 794 | coexpression:793 |
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: methanol dehydrogenase transcriptional regulator MoxR
- MTBC0 PGAP product: MoxR family ATPase
- Pfam (hmmscan --cut_ga): bpMoxR PF20030.6 (E=1e-07), Sigma54_activat PF00158.33 (E=2e-04), AAA_3 PF07726.18 (E=6e-63), AAA_5 PF07728.21 (E=6e-11), AAA PF00004.36 (E=4e-04), AAA_lid_2 PF17863.8 (E=2e-19)
- (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_217680.1)
- Domains: Pfam-A via hmmscan --cut_ga — bpMoxR (PF20030.6), Sigma54_activat (PF00158.33), AAA_3 (PF07726.18), AAA_5 (PF07728.21), AAA (PF00004.36), AAA_lid_2 (PF17863.8)
- 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
COG0714 - Curated reference: UniProt O53314 (TrEMBL, unreviewed; 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 —
59 functional partner(s); context anchor
Rv3162c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003363|Rv3164c|moxR3 MIMPAATTTAHCEAVLDEIERVVVGKRSALTLILTAVLARGHVLIEDLPGLGKTLIARSFAAALGLDFTRVQFTPDLLPADLLGSTIYDMQSGRFEFRAGPIFTNLLLADEINRTPPKTQAALLEAMAEGQVSIDGQTHKLAMPFIVLATDNPIEYEGTYPLPEAQLDRFAIRLELRYLSERDETSMLRRRLERGSADPTVNQVVDCHDLLAMRESVEQVTVHEDVLHYVVSLANATRHHPQVAVGASPRAELDLVQLSRARALLLGRDYVIPEDVKELATAAVAHRITLRPEMWVRKIAGADVVSELLRRLPVPRISGT