dapE Resolved · high auto-curated
H37Rv Rv1202 · MTBC0 - ·
354 aa · 1345260–1346324 (+) ·
RefSeq YP_177796.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | succinyl-diaminopimelate desuccinylase DapE |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Succinyl-diaminopimelate desuccinylase DapE. Pfam: Peptidase_M28 (PF04389.23), Peptidase_M20 (PF01546.34), M20_dimer (PF07687.20). |
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 |
P9WHS9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative succinyl-diaminopimelate desuccinylase DapE |
| EC (curated) |
EC 3.5.1.18
|
| Curated function | Catalyzes the hydrolysis of N-succinyl-L,L-diaminopimelic acid (SDAP), forming succinate and LL-2,6-diaminoheptanedioate (DAP), an intermediate involved in the bacterial biosynthesis of lysine and meso-diaminopimelic acid. |
UniProt still lists this protein as Putative succinyl-diaminopimelate desuccinylase DapE; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | dapE |
| eggNOG description | succinyl-diaminopimelate desuccinylase |
| Orthologous group | COG0624 |
| EC number |
EC 3.5.1.18
|
| KEGG orthology |
K01439
|
| KEGG pathways |
map00300, map01100, map01120, map01230
|
| KEGG modules |
M00016
|
| 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 | 0.215 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 3 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 |
|---|---|---|---|---|
Peptidase_M28 | PF04389.23 | 5.8e-07 | 54–126 | Peptidase family M28 |
Peptidase_M20 | PF01546.34 | 1.3e-21 | 65–352 | Peptidase family M20/M25/M40 |
M20_dimer | PF07687.20 | 7.5e-11 | 166–264 | Peptidase dimerisation domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: dapF (diaminopimelate epimerase), high confidence from genomic context alone (score 959 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2726c dapF |
diaminopimelate epimerase | 997 | 959 ctx | cooccurence:557 database:900 textmining:949 |
Rv1655 argD |
acetylornithine aminotransferase | 911 | 906 | database:900 |
Rv0858c dapC |
N-succinyldiaminopimelate aminotransferase DapC | 988 | 903 | database:900 textmining:881 |
Rv1201c dapD |
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase | 996 | 890 ctx | neighborhood:782 cooccurence:509 textmining:965 |
Rv1178 dapC |
aminotransferase | 903 | 706 ctx | cooccurence:663 textmining:684 |
Rv1652 argC |
N-acetyl-gamma-glutamyl-phoshate reductase | 656 | 620 | |
Rv1658 argG |
argininosuccinate synthase | 570 | 466 | |
Rv3436c glmS |
glucosamine--fructose-6-phosphate aminotransferase | 495 | 441 | experimental:419 |
Rv0884c serC |
phosphoserine aminotransferase | 494 | 423 | |
Rv3257c pmmA |
phosphomannomutase PmmA | 430 | 396 | |
Rv1208 gpgS |
glucosyl-3-phosphoglycerate synthase | 713 | 323 | textmining:595 |
Rv2773c dapB |
4-hydroxy-tetrahydrodipicolinate reductase | 850 | 310 | textmining:792 |
Rv1315 murA |
UDP-N-acetylglucosamine 1-carboxyvinyltransferase | 717 | 244 | textmining:642 |
Rv3709c ask |
aspartokinase | 800 | 226 | textmining:753 |
Rv2141c hyp |
hypothetical protein | 504 | 199 | textmining:407 |
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): succinyl-diaminopimelate desuccinylase DapE
- Pfam (hmmscan --cut_ga): Peptidase_M28 PF04389.23 (E=6e-07), Peptidase_M20 PF01546.34 (E=1e-21), M20_dimer PF07687.20 (E=7e-11)
- (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 YP_177796.1)
- Domains: Pfam-A via hmmscan --cut_ga — Peptidase_M28 (PF04389.23), Peptidase_M20 (PF01546.34), M20_dimer (PF07687.20)
- 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
COG0624 - Curated reference: UniProt P9WHS9 (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
dapF - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv1202|dapE MLDLRGDPIELTAALIDIPSESRKEARIADEVEAALRAQASGFEIIRNGNAVLARTKLNRSSRVLLAGHLDTVPVAGNLPSRRENDQLHGCGAADMKSGDAVFLHLAATLAEPTHDLTLVFYDCEEIDSAANGLGRIQRELPDWLSADVAILGEPTAGCIEAGCQGTLRVVLSVTGTRAHSARSWLGDNAIHKLGAVLDRLAVYRARSVDIDGCTYREGLSAVRVAGGVAGNVIPDAASVTINYRFAPDRSVAAALQHVHDVFDGLDVQIEQTDAAAGALPGLSEPAAKALVEAAGGQVRAKYGWTDVSRFAALGIPAVNYGPGDPNLAHCRDERVPVGNITAAVDLLRRYLGG