menA Resolved · high auto-curated
H37Rv Rv0534c · MTBC0 mtbc0_000563 ·
292 aa · 629113–629991 (-) ·
RefSeq NP_215048.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 1,4-dihydroxy-2-naphthoate octaprenyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | 1%2C4-dihydroxy-2-naphthoate polyprenyltransferase |
| Revised (this work) | 1%2C4-dihydroxy-2-naphthoate polyprenyltransferase. Pfam: UbiA (PF01040.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIP3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | 1,4-dihydroxy-2-naphthoate octaprenyltransferase |
| EC (curated) |
EC 2.5.1.74
|
| Curated function | Conversion of 1,4-dihydroxy-2-naphthoate (DHNA) to demethylmenaquinone (DMK). Can use a variety of allylic isoprenyl diphosphates as substrates but has a requirement for at least three isoprene units. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | menA |
| eggNOG description | Belongs to the MenA family. Type 1 subfamily |
| Orthologous group | COG1575 |
| EC number |
EC 2.5.1.74
|
| KEGG orthology |
K02548
|
| KEGG pathways |
map00130, map01100, map01110
|
| KEGG modules |
M00116
|
| Gene Ontology (35) |
GO:0003674, GO:0003824, GO:0004659, GO:0006732, GO:0006733, GO:0006743, GO:0006744, GO:0006766, GO:0006775, GO:0008150, GO:0008152, GO:0009058 +23 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 | 0.808 · 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 |
|---|---|---|---|---|
UbiA | PF01040.24 | 8.7e-25 | 20–250 | UbiA prenyltransferase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: menB (1,4-dihydroxy-2-naphthoyl-CoA synthase), high confidence from genomic context alone (score 810 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1847 |
esterase | 981 | 904 | database:900 textmining:813 |
Rv0558 menH |
demethylmenaquinone methyltransferase | 961 | 904 | database:900 textmining:614 |
Rv0548c menB |
1,4-dihydroxy-2-naphthoyl-CoA synthase | 938 | 810 ctx | cooccurence:767 textmining:688 |
Rv0555 menD |
bifunctional 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase/2-oxoglutarate decarboxylase | 850 | 800 ctx | cooccurence:766 |
Rv0535 pnp |
5'-methylthioadenosine phosphorylase | 792 | 792 ctx | neighborhood:791 |
Rv0536 galE3 |
UDP-glucose 4-epimerase GalE | 792 | 792 ctx | neighborhood:791 |
Rv0533c fabH |
3-oxoacyl-ACP synthase III | 790 | 790 ctx | neighborhood:785 |
Rv0553 menC |
muconate cycloisomerase | 720 | 650 ctx | cooccurence:589 |
Rv0542c menE |
2-succinylbenzoic acid--CoA ligase | 809 | 469 | textmining:657 |
Rv3215 entC |
isochorismate synthase | 640 | 222 | textmining:556 |
Rv1602 hisH |
imidazole glycerol phosphate synthase subunit HisH | 408 | 203 | |
Rv0561c menJ |
oxidoreductase | 708 | 186 | textmining:656 |
Rv2715 |
hydrolase | 806 | 153 | textmining:781 |
Rv1938 ephB |
epoxide hydrolase EphB | 697 | 151 | textmining:658 |
Rv0560c |
benzoquinone methyltransferase | 465 | 61 | textmining:454 |
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: 1,4-dihydroxy-2-naphthoate octaprenyltransferase
- MTBC0 PGAP product: 1%2C4-dihydroxy-2-naphthoate polyprenyltransferase
- Pfam (hmmscan --cut_ga): UbiA PF01040.24 (E=9e-25)
- (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_215048.1)
- Domains: Pfam-A via hmmscan --cut_ga — UbiA (PF01040.24)
- 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
COG1575 - Curated reference: UniProt P9WIP3 (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 —
18 functional partner(s); context anchor
menB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000563|Rv0534c|menA MASFAQWVSGARPRTLPNAIAPVVAGTGAAAWLHAAVWWKALLALAVAVALVIGVNYANDYSDGIRGTDDDRVGPVRLVGSRLATPRSVLTAAMTSLALGALAGLVLALLSAPWLIAVGAICIAGAWLYTGGSKPYGYAGFGELAVFVFFGPVAVLGTQYTQALRVDWVGLAQAVATGALSCSVLVANNLRDIPTDARADKITLAVRLGDARTRMLYQGLLAVAGVLTFVLMLATPWCVVGLVAAPLALRAAGPVRSGRGGRELIPVLRDTGLAMLVWALAVAGALAFGQLS