menC Resolved · high auto-curated
H37Rv Rv0553 · MTBC0 mtbc0_000582 ·
326 aa · 648041–649021 (+) ·
RefSeq NP_215067.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | muconate cycloisomerase |
|---|---|
| MTBC0 PGAP re-annotation | o-succinylbenzoate synthase |
| Revised (this work) | O-succinylbenzoate synthase. Pfam: Enolase_like_N (PF18374.7), MR_MLE_C (PF13378.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJP3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | o-succinylbenzoate synthase |
| EC (curated) |
EC 4.2.1.113
|
| Curated function | Converts 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) to 2-succinylbenzoate (OSB). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | menC |
| eggNOG description | Converts 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1- carboxylate (SHCHC) to 2-succinylbenzoate (OSB) |
| Orthologous group | COG4948 |
| EC number |
EC 4.2.1.113
|
| KEGG orthology |
K02549
|
| KEGG pathways |
map00130, map01100, map01110
|
| KEGG modules |
M00116
|
| Gene Ontology (2) |
GO:0008150, 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 | 0.257 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
Enolase_like_N | PF18374.7 | 3.9e-27 | 17–68 | Enolase N-terminal domain-like |
MR_MLE_C | PF13378.13 | 4.0e-34 | 103–288 | Enolase C-terminal domain-like |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: menD (bifunctional 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase/2-oxoglutarate decarboxylase), high confidence from genomic context alone (score 960 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0555 menD |
bifunctional 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase/2-oxoglutarate decarboxylase | 997 | 960 ctx | neighborhood:817 cooccurence:598 database:500 textmining:945 |
Rv0542c menE |
2-succinylbenzoic acid--CoA ligase | 954 | 955 | database:900 |
Rv0552 hyp |
hypothetical protein | 902 | 902 ctx | neighborhood:881 |
Rv0554 bpoC |
non-heme bromoperoxidase BpoC | 887 | 882 ctx | neighborhood:882 |
Rv0548c menB |
1,4-dihydroxy-2-naphthoyl-CoA synthase | 974 | 862 ctx | neighborhood:631 cooccurence:641 textmining:825 |
Rv0551c fadD8 |
fatty-acid--CoA ligase FadD8 | 802 | 802 ctx | neighborhood:780 |
Rv0557 mgtA |
GDP-mannose-dependent alpha-mannosyltransferase | 756 | 756 ctx | neighborhood:756 |
Rv0556 |
transmembrane protein | 704 | 704 ctx | neighborhood:704 |
Rv0534c menA |
1,4-dihydroxy-2-naphthoate octaprenyltransferase | 720 | 650 ctx | cooccurence:589 |
Rv0558 menH |
demethylmenaquinone methyltransferase | 943 | 567 ctx | neighborhood:567 textmining:874 |
Rv1930c hyp |
hypothetical protein | 548 | 548 ctx | neighborhood:544 |
Rv1931c |
transcriptional regulator | 544 | 544 ctx | neighborhood:544 |
Rv0547c |
oxidoreductase | 542 | 542 ctx | neighborhood:539 |
Rv3683 hyp |
hypothetical protein | 433 | 433 ctx | cooccurence:433 |
Rv2033c hyp |
hypothetical protein | 401 | 401 |
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: muconate cycloisomerase
- MTBC0 PGAP product: o-succinylbenzoate synthase
- Pfam (hmmscan --cut_ga): Enolase_like_N PF18374.7 (E=4e-27), MR_MLE_C PF13378.13 (E=4e-34)
- (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_215067.1)
- Domains: Pfam-A via hmmscan --cut_ga — Enolase_like_N (PF18374.7), MR_MLE_C (PF13378.13)
- 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
COG4948 - Curated reference: UniProt P9WJP3 (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 —
26 functional partner(s); context anchor
menD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000582|Rv0553|menC MIPVLPPLEALLDRLYVVALPMRVRFRGITTREVALIEGPAGWGEFGAFVEYQSAQACAWLASAIETAYCAPPPVRRDRVPINATVPAVAAAQVGEVLARFPGARTAKVKVAEPGQSLADDIERVNAVRELVPMVRVDANGGWGVAEAVAAAAALTADGPLEYLEQPCATVAELAELRRRVDVPIAADESIRKAEDPLAVVRAQAADIAVLKVAPLGGISALLDIAARIAVPVVVSSALDSAVGIAAGLTAAAALPELDHACGLGTGGLFEEDVAEPAAPVDGFLAVARTTPDPARLQALGAPPQRRQWWIDRVKACYSLLVPSFG