Rv0560c Resolved · high auto-curated
H37Rv Rv0560c · MTBC0 - ·
241 aa · 650779–651504 (-) ·
RefSeq NP_215074.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | benzoquinone methyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Benzoquinone methyltransferase. Pfam: TPMT (PF05724.18), MTS (PF05175.21), Methyltransf_23 (PF13489.13), PrmA (PF06325.20), Ubie_methyltran (PF01209.25), Methyltransf_25 (PF13649.13), Methyltransf_31 (PF13847.13), Methyltransf_11 (PF08241.19), Methyltransf_12 (PF08242.19). |
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 |
P9WKL5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | 2-heptyl-1-hydroxyquinolin-4(1H)-one methyltransferase |
| EC (curated) |
EC 2.1.1.374
|
| Curated function | Involved in cellular response to chemical stress and may contribute to resistance toward antimicrobial natural compounds as well as drugs (Probable). Catalyzes the methylation and detoxification of the P.aeruginosa toxin 2-heptyl-1-hydroxy-4(1H)-quinolinone (HQNO) to 2-heptyl-1-methoxy-4(1H)-quinolinone (HMOQ). Can also methylate 3-bromo-2-heptyl-1-hydroxy-4(1H)-quinolinone, and shows much lower activity with 1-hydroxyquinolin-4(1H)-one, quercetin, 4-hydroxyquinolin-2(1H)-one (DHQ) and 4-hydroxyisoquinolin-1(2H)-one. In addition, N-methylates and abolishes the mycobactericidal activity of 3-me. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| eggNOG description | Thiopurine S-methyltransferase (TPMT) |
| Orthologous group | COG0500 |
| Gene Ontology (63) |
GO:0001101, GO:0001666, GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0006873, GO:0006875, GO:0006879 +51 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 | 0.258 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 3 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.13% of strains (186) · clonal |
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 |
|---|---|---|---|---|
TPMT | PF05724.18 | 1.6e-12 | 48–200 | Thiopurine S-methyltransferase (TPMT) |
MTS | PF05175.21 | 3.1e-08 | 61–157 | Methyltransferase small domain |
Methyltransf_23 | PF13489.13 | 9.4e-11 | 63–171 | Methyltransferase domain |
PrmA | PF06325.20 | 2.9e-05 | 63–133 | Ribosomal protein L11 methyltransferase (PrmA) |
Ubie_methyltran | PF01209.25 | 2.8e-05 | 64–174 | ubiE/COQ5 methyltransferase family |
Methyltransf_25 | PF13649.13 | 4.1e-19 | 66–160 | Methyltransferase domain |
Methyltransf_31 | PF13847.13 | 8.9e-19 | 66–169 | Methyltransferase domain |
Methyltransf_11 | PF08241.19 | 1.0e-14 | 67–164 | Methyltransferase domain |
Methyltransf_12 | PF08242.19 | 4.9e-12 | 67–161 | Methyltransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: menJ (oxidoreductase), high confidence from genomic context alone (score 745 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3160c |
TetR family transcriptional regulator | 759 | 759 | coexpression:731 |
Rv0561c menJ |
oxidoreductase | 901 | 745 ctx | neighborhood:707 textmining:630 |
Rv0559c hyp |
hypothetical protein | 951 | 668 ctx | neighborhood:668 textmining:860 |
Rv0562 grcC1 |
polyprenyl-diphosphate synthase GrcC | 556 | 540 ctx | neighborhood:529 |
Rv0290 eccD3 |
ESX-3 secretion system protein EccD | 524 | 524 ctx | cooccurence:522 |
Rv0676c mmpL5 |
transmembrane transport protein MmpL5 | 512 | 347 | |
Rv0652 rplL |
50S ribosomal protein L7/L12 | 407 | 155 | |
Rv3692 moxR2 |
methanol dehydrogenase transcriptional regulator MoxR | 461 | 93 | textmining:431 |
Rv1938 ephB |
epoxide hydrolase EphB | 403 | 89 | |
Rv3164c moxR3 |
methanol dehydrogenase transcriptional regulator MoxR | 672 | 82 | textmining:658 |
Rv2887 |
HTH-type transcriptional regulator | 874 | 72 | textmining:870 |
Rv3215 entC |
isochorismate synthase | 551 | 71 | textmining:537 |
Rv0534c menA |
1,4-dihydroxy-2-naphthoate octaprenyltransferase | 465 | 61 | textmining:454 |
Rv0880 |
HTH-type transcriptional regulator | 520 | 59 | textmining:512 |
Rv3648c cspA |
cold shock protein A | 530 | 58 | textmining:522 |
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): benzoquinone methyltransferase
- Pfam (hmmscan --cut_ga): TPMT PF05724.18 (E=2e-12), MTS PF05175.21 (E=3e-08), Methyltransf_23 PF13489.13 (E=9e-11), PrmA PF06325.20 (E=3e-05), Ubie_methyltran PF01209.25 (E=3e-05), Methyltransf_25 PF13649.13 (E=4e-19), Methyltransf_31 PF13847.13 (E=9e-19), Methyltransf_11 PF08241.19 (E=1e-14), Methyltransf_12 PF08242.19 (E=5e-12)
- (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_215074.1)
- Domains: Pfam-A via hmmscan --cut_ga — TPMT (PF05724.18), MTS (PF05175.21), Methyltransf_23 (PF13489.13), PrmA (PF06325.20), Ubie_methyltran (PF01209.25), Methyltransf_25 (PF13649.13), Methyltransf_31 (PF13847.13), Methyltransf_11 (PF08241.19), Methyltransf_12 (PF08242.19)
- 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
COG0500 - Curated reference: UniProt P9WKL5 (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 —
28 functional partner(s); context anchor
menJ - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0560c| MSTVLTYIRAVDIYEHMTESLDLEFESAYRGESVAFGEGVRPPWSIGEPQPELAALIVQGKFRGDVLDVGCGEAAISLALAERGHTTVGLDLSPAAVELARHEAAKRGLANASFEVADASSFTGYDGRFDTIVDSTLFHSMPVESREGYLQSIVRAAAPGASYFVLVFDRAAIPEGPINAVTEDELRAAVSKYWIIDEIKPARLYARFPAGFAGMPALLDIREEPNGLQSIGGWLLSAHLG