dapD Resolved · high auto-curated
H37Rv Rv1201c · MTBC0 mtbc0_001289 ·
317 aa · 1352658–1353611 (-) ·
RefSeq NP_215717.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | 2%2C3%2C4%2C5-tetrahydropyridine-2%2C6-dicarboxylate N-succinyltransferase |
| Revised (this work) | 2%2C3%2C4%2C5-tetrahydropyridine-2%2C6-dicarboxylate N-succinyltransferase. Pfam: THDPS_M (PF14789.12), Hexapep_2 (PF14602.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WP21
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase |
| EC (curated) |
EC 2.3.1.117
|
| Curated function | Catalyzes the conversion of the cyclic tetrahydrodipicolinate (THDP) into the acyclic N-succinyl-L-2-amino-6-oxopimelate using succinyl-CoA. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | dapD |
| eggNOG description | Catalyzes the conversion of the cyclic tetrahydrodipicolinate (THDP) into the acyclic N-succinyl-L-2- amino-6-oxopimelate using succinyl-CoA |
| Orthologous group | COG2171 |
| EC number |
EC 2.3.1.117
|
| KEGG orthology |
K00674
|
| KEGG pathways |
map00300, map01100, map01120, map01230
|
| KEGG modules |
M00016
|
| Gene Ontology (28) |
GO:0000287, GO:0003674, GO:0003824, GO:0005488, GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0008150, GO:0008666, GO:0016020, GO:0016410 +16 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 | 0.304 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 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 |
|---|---|---|---|---|
THDPS_M | PF14789.12 | 7.1e-21 | 111–150 | Tetrahydrodipicolinate N-succinyltransferase middle |
Hexapep_2 | PF14602.13 | 2.6e-16 | 232–264 | Hexapeptide repeat of succinyl-transferase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: dapE (succinyl-diaminopimelate desuccinylase DapE), high confidence from genomic context alone (score 890 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2773c dapB |
4-hydroxy-tetrahydrodipicolinate reductase | 987 | 951 | coexpression:416 database:900 textmining:767 |
Rv0858c dapC |
N-succinyldiaminopimelate aminotransferase DapC | 988 | 905 | database:900 textmining:880 |
Rv1655 argD |
acetylornithine aminotransferase | 911 | 904 | database:900 |
Rv1202 dapE |
succinyl-diaminopimelate desuccinylase DapE | 996 | 890 ctx | neighborhood:782 cooccurence:509 textmining:965 |
Rv3396c guaA |
GMP synthase | 812 | 709 | coexpression:704 |
Rv3305c amiA1 |
N-acyl-L-amino acid amidohydrolase AmiA | 492 | 457 | coexpression:426 |
Rv1240 mdh |
malate dehydrogenase | 489 | 457 | coexpression:440 |
Rv3306c amiB1 |
amidase AmiB | 492 | 456 | coexpression:425 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 612 | 454 | coexpression:452 |
Rv3834c serS |
serine--tRNA ligase | 510 | 443 | coexpression:424 |
Rv3661 hyp |
hypothetical protein | 435 | 436 ctx | cooccurence:407 |
Rv2524c fas |
fatty acid synthase | 581 | 434 | coexpression:418 |
Rv1093 glyA1 |
serine hydroxymethyltransferase | 466 | 434 | coexpression:419 |
Rv0070c glyA2 |
serine hydroxymethyltransferase | 463 | 430 | coexpression:415 |
Rv2448c valS |
valine--tRNA ligase | 472 | 421 | coexpression:421 |
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: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
- MTBC0 PGAP product: 2%2C3%2C4%2C5-tetrahydropyridine-2%2C6-dicarboxylate N-succinyltransferase
- Pfam (hmmscan --cut_ga): THDPS_M PF14789.12 (E=7e-21), Hexapep_2 PF14602.13 (E=3e-16)
- (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_215717.1)
- Domains: Pfam-A via hmmscan --cut_ga — THDPS_M (PF14789.12), Hexapep_2 (PF14602.13)
- 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
COG2171 - Curated reference: UniProt P9WP21 (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 —
44 functional partner(s); context anchor
dapE - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001289|Rv1201c|dapD MSTVTGAAGIGLATLAADGSVLDTWFPAPELTESGTSATSRLAVSDVPVELAALIGRDDDRRTETIAVRTVIGSLDDVAADPYDAYLRLHLLSHRLVAPHGLNAGGLFGVLTNVVWTNHGPCAIDGFEAVRARLRRRGPVTVYGVDKFPRMVDYVVPTGVRIADADRVRLGAHLAPGTTVMHEGFVNYNAGTLGASMVEGRISAGVVVGDGSDVGGGASIMGTLSGGGTHVISIGKRCLLGANSGLGISLGDDCVVEAGLYVTAGTRVTMPDSNSVKARELSGSSNLLFRRNSVSGAVEVLARDGQGIALNEDLHAN