menB Resolved · high auto-curated
H37Rv Rv0548c · MTBC0 - ·
314 aa · 639012–639956 (-) ·
RefSeq NP_215062.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 1,4-dihydroxy-2-naphthoyl-CoA synthase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | 1,4-dihydroxy-2-naphthoyl-CoA synthase. Pfam: ECH_1 (PF00378.26), ECH_2 (PF16113.11). |
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 |
P9WNP5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | 1,4-dihydroxy-2-naphthoyl-CoA synthase |
| EC (curated) |
EC 4.1.3.36
|
| Curated function | Converts o-succinylbenzoyl-CoA (OSB-CoA) to 1,4-dihydroxy-2-naphthoyl-CoA (DHNA-CoA). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | menB |
| eggNOG description | Belongs to the enoyl-CoA hydratase isomerase family. MenB subfamily |
| Orthologous group | COG0447 |
| EC number |
EC 4.1.3.36
|
| KEGG orthology |
K01661
|
| KEGG pathways |
map00130, map01100, map01110
|
| KEGG modules |
M00116
|
| Gene Ontology (40) |
GO:0003674, GO:0003824, GO:0005575, GO:0005623, GO:0005886, GO:0006732, GO:0008150, GO:0008152, GO:0008935, GO:0009058, GO:0009108, GO:0009233 +28 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, 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 |
|---|---|---|---|---|
ECH_1 | PF00378.26 | 5.9e-48 | 48–308 | Enoyl-CoA hydratase/isomerase |
ECH_2 | PF16113.11 | 4.9e-14 | 49–249 | Enoyl-CoA hydratase/isomerase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: menE (2-succinylbenzoic acid--CoA ligase), high confidence from genomic context alone (score 971 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0542c menE |
2-succinylbenzoic acid--CoA ligase | 994 | 971 ctx | cooccurence:569 database:900 textmining:816 |
Rv1847 |
esterase | 974 | 927 | database:900 textmining:659 |
Rv0555 menD |
bifunctional 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase/2-oxoglutarate decarboxylase | 992 | 881 ctx | neighborhood:419 cooccurence:770 textmining:935 |
Rv0553 menC |
muconate cycloisomerase | 974 | 862 ctx | neighborhood:631 cooccurence:641 textmining:825 |
Rv0534c menA |
1,4-dihydroxy-2-naphthoate octaprenyltransferase | 938 | 810 ctx | cooccurence:767 textmining:688 |
Rv0544c |
transmembrane protein | 677 | 677 ctx | neighborhood:667 |
Rv0547c |
oxidoreductase | 662 | 662 ctx | neighborhood:657 |
Rv0551c fadD8 |
fatty-acid--CoA ligase FadD8 | 670 | 656 ctx | neighborhood:654 |
Rv0554 bpoC |
non-heme bromoperoxidase BpoC | 642 | 629 ctx | neighborhood:623 |
Rv0552 hyp |
hypothetical protein | 614 | 615 ctx | neighborhood:615 |
Rv3039c echA17 |
enoyl-CoA hydratase EchA17 | 587 | 587 ctx | cooccurence:584 |
Rv0456c echA2 |
enoyl-CoA hydratase EchA2 | 547 | 547 ctx | cooccurence:546 |
Rv3373 echA18 |
enoyl-CoA hydratase | 494 | 494 ctx | cooccurence:489 |
Rv1449c tkt |
transketolase | 432 | 433 | coexpression:433 |
Rv0545c pitA |
low-affinity inorganic phosphate transporter | 430 | 430 |
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): 1,4-dihydroxy-2-naphthoyl-CoA synthase
- Pfam (hmmscan --cut_ga): ECH_1 PF00378.26 (E=6e-48), ECH_2 PF16113.11 (E=5e-14)
- (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_215062.1)
- Domains: Pfam-A via hmmscan --cut_ga — ECH_1 (PF00378.26), ECH_2 (PF16113.11)
- 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
COG0447 - Curated reference: UniProt P9WNP5 (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 —
29 functional partner(s); context anchor
menE - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0548c|menB MVAPAGEQGRSSTALSDNPFDAKAWRLVDGFDDLTDITYHRHVDDATVRVAFNRPEVRNAFRPHTVDELYRVLDHARMSPDVGVVLLTGNGPSPKDGGWAFCSGGDQRIRGRSGYQYASGDTADTVDVARAGRLHILEVQRLIRFMPKVVICLVNGWAAGGGHSLHVVCDLTLASREYARFKQTDADVGSFDGGYGSAYLARQVGQKFAREIFFLGRTYTAEQMHQMGAVNAVAEHAELETVGLQWAAEINAKSPQAQRMLKFAFNLLDDGLVGQQLFAGEATRLAYMTDEAVEGRDAFLQKRPPDWSPFPRYF