menE Resolved · high auto-curated
H37Rv Rv0542c · MTBC0 mtbc0_000571 ·
362 aa · 637967–639055 (-) ·
RefSeq NP_215056.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 2-succinylbenzoic acid--CoA ligase |
|---|---|
| MTBC0 PGAP re-annotation | o-succinylbenzoate--CoA ligase |
| Revised (this work) | O-succinylbenzoate--CoA ligase. Pfam: AMP-binding (PF00501.35), AMP-binding_C (PF13193.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQ39
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable 2-succinylbenzoate--CoA ligase |
| EC (curated) |
EC 6.2.1.26
|
| Curated function | Converts 2-succinylbenzoate (OSB) to 2-succinylbenzoyl-CoA (OSB-CoA). May be involved in the biosynthesis of menaquinone (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolismQ Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| Preferred name | menE |
| eggNOG description | O-succinylbenzoic acid--CoA ligase |
| Orthologous group | COG0318 |
| EC number |
EC 4.2.1.113, EC 6.2.1.26
|
| KEGG orthology |
K01911, K02549
|
| KEGG pathways |
map00130, map01100, map01110
|
| KEGG modules |
M00116
|
| Gene Ontology (9) |
GO:0003674, GO:0003824, GO:0008150, GO:0008756, GO:0016405, GO:0016874, GO:0016877, GO:0016878, GO:0040007
|
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 | 0.1 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 1 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 |
|---|---|---|---|---|
AMP-binding | PF00501.35 | 2.6e-21 | 30–193 | AMP-binding enzyme |
AMP-binding_C | PF13193.13 | 1.4e-15 | 271–346 | AMP-binding enzyme C-terminal domain |
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 971 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0548c menB |
1,4-dihydroxy-2-naphthoyl-CoA synthase | 994 | 971 ctx | cooccurence:569 database:900 textmining:816 |
Rv0553 menC |
muconate cycloisomerase | 954 | 955 | database:900 |
Rv0541c |
integral membrane protein | 934 | 935 ctx | neighborhood:876 coexpression:494 |
Rv0543c hyp |
hypothetical protein | 806 | 807 ctx | neighborhood:795 |
Rv0545c pitA |
low-affinity inorganic phosphate transporter | 753 | 753 ctx | neighborhood:741 |
Rv1713 engA |
GTPase Der | 736 | 736 | coexpression:734 |
Rv3506 fadD17 |
long-chain-fatty-acid--CoA ligase FadD17 | 728 | 728 ctx | cooccurence:727 |
Rv0544c |
transmembrane protein | 698 | 698 ctx | neighborhood:690 |
Rv0719 rplF |
50S ribosomal protein L6 | 698 | 698 | experimental:402 database:510 |
Rv2380c mbtE |
peptide synthetase | 704 | 691 | experimental:465 |
Rv2048c pks12 |
polyketide synthase | 712 | 688 | |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 708 | 683 | |
Rv3825c pks2 |
phthioceranic/hydroxyphthioceranic acid synthase | 706 | 681 | |
Rv2933 ppsC |
phthiocerol synthesis polyketide synthase type I PpsC | 706 | 681 | |
Rv1527c pks5 |
polyketide synthase | 706 | 681 |
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: 2-succinylbenzoic acid--CoA ligase
- MTBC0 PGAP product: o-succinylbenzoate--CoA ligase
- Pfam (hmmscan --cut_ga): AMP-binding PF00501.35 (E=3e-21), AMP-binding_C PF13193.13 (E=1e-15)
- (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_215056.1)
- Domains: Pfam-A via hmmscan --cut_ga — AMP-binding (PF00501.35), AMP-binding_C (PF13193.13)
- 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
COG0318 - Curated reference: UniProt P9WQ39 (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 —
100 functional partner(s); context anchor
menB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000571|Rv0542c|menE MLGGSDPALVAVPTQHESLLGALRVGEQIDDDVALVVTTSGTTGPPKGAMLTAAALTASASAAHDRLGGPGSWLLAVPPYHIAGLAVLVRSVIAGSVPVELNVSAGFDVTELPNAIKRLGSGRRYTSLVAAQLAKALTDPAATAALAELDAVLIGGGPAPRPILDAAAAAGITVVRTYGMSETSGGCVYDGVPLDGVRLRVLAGGRIAIGGATLAKGYRNPVSPDPFAEPGWFHTDDLGALESGDSGVLTVLGRADEAISTGGFTVLPQPVEAALGTHPAVRDCAVFGLADDRLGQRVVAAIVVGDGCPPPTLEALRAHVARTLDVTAAPRELHVVNVLPRRGIGKVDRAALVRRFAGEADQ