dapC Resolved · high auto-curated
H37Rv Rv0858c · MTBC0 mtbc0_000913 ·
397 aa · 956877–958070 (-) ·
RefSeq NP_215373.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | N-succinyldiaminopimelate aminotransferase DapC |
|---|---|
| MTBC0 PGAP re-annotation | pyridoxal phosphate-dependent aminotransferase |
| Revised (this work) | Pyridoxal phosphate-dependent aminotransferase. Pfam: Aminotran_1_2 (PF00155.28), Aminotran_5 (PF00266.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPZ5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable N-succinyldiaminopimelate aminotransferase DapC |
| EC (curated) |
EC 2.6.1.17
|
| Curated function | Involved in the lysine biosynthetic pathways. It catalyzes the transfer of an amino group from L-glutamate to N-succinyl-2-l-amino-6-oxoheptanedioate (N-succinyl-2-l-amino-6-ketopimelate) in a PLP-dependent reaction, yielding as products N-succinyl-l-2,6-diaminoheptanedioate (N-succinyl-diaminopimelate) and 2-oxoglutarate (Probable). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | dapC |
| eggNOG description | Aminotransferase |
| Orthologous group | COG0436 |
| EC number |
EC 2.6.1.1, EC 2.6.1.17, EC 2.6.1.2, EC 2.6.1.66
|
| KEGG orthology |
K00812, K14260, K14267
|
| KEGG pathways |
map00220, map00250, map00270, map00290, map00300, map00330, map00350, map00360, map00400, map00401, map00950, map00960, map01100, map01110, map01120, map01130, map01210, map01230
|
| KEGG modules |
M00016
|
| Gene Ontology (6) |
GO:0005575, GO:0005618, GO:0005623, GO:0030312, GO:0044464, GO:0071944
|
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 | 0.719 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 8 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 |
|---|---|---|---|---|
Aminotran_1_2 | PF00155.28 | 4.4e-63 | 27–388 | Aminotransferase class I and II |
Aminotran_5 | PF00266.26 | 4.6e-07 | 84–199 | Aminotransferase class-V |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadA (acyltransferase), high confidence from genomic context alone (score 707 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1201c dapD |
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase | 988 | 905 | database:900 textmining:880 |
Rv1655 argD |
acetylornithine aminotransferase | 909 | 905 | database:900 |
Rv1202 dapE |
succinyl-diaminopimelate desuccinylase DapE | 988 | 903 | database:900 textmining:881 |
Rv0859 fadA |
acyltransferase | 711 | 707 ctx | neighborhood:699 |
Rv0860 fadB |
fatty oxidation protein FadB | 707 | 693 ctx | neighborhood:687 |
Rv3838c pheA |
prephenate dehydratase | 540 | 515 ctx | fusion:486 |
Rv1293 lysA |
diaminopimelate decarboxylase | 730 | 422 | coexpression:402 textmining:553 |
Rv3667 acs |
acetyl-CoAsynthetase | 455 | 420 | |
Rv0728c serA2 |
D-3-phosphoglycerate dehydrogenase SerA | 431 | 396 | |
Rv2996c serA1 |
D-3-phosphoglycerate dehydrogenase | 405 | 368 | |
Rv3709c ask |
aspartokinase | 774 | 319 | textmining:682 |
Rv2726c dapF |
diaminopimelate epimerase | 871 | 311 | textmining:821 |
Rv3708c asd |
aspartate-semialdehyde dehydrogenase | 771 | 303 | textmining:686 |
Rv3859c gltB |
glutamate synthase large subunit | 598 | 284 | textmining:462 |
Rv2152c murC |
UDP-N-acetylmuramate--alanine ligase | 586 | 106 | textmining:556 |
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: N-succinyldiaminopimelate aminotransferase DapC
- MTBC0 PGAP product: pyridoxal phosphate-dependent aminotransferase
- Pfam (hmmscan --cut_ga): Aminotran_1_2 PF00155.28 (E=4e-63), Aminotran_5 PF00266.26 (E=5e-07)
- (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_215373.1)
- Domains: Pfam-A via hmmscan --cut_ga — Aminotran_1_2 (PF00155.28), Aminotran_5 (PF00266.26)
- 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
COG0436 - Curated reference: UniProt P9WPZ5 (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 —
19 functional partner(s); context anchor
fadA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000913|Rv0858c|dapC MTVSRLRPYATTVFAEMSALATRIGAVNLGQGFPDEDGPPKMLQAAQDAIAGGVNQYPPGPGSAPLRRAIAAQRRRHFGVDYDPETEVLVTVGATEAIAAAVLGLVEPGSEVLLIEPFYDSYSPVVAMAGAHRVTVPLVPDGRGFALDADALRRAVTPRTRALIINSPHNPTGAVLSATELAAIAEIAVAANLVVITDEVYEHLVFDHARHLPLAGFDGMAERTITISSAAKMFNCTGWKIGWACGPAELIAGVRAAKQYLSYVGGAPFQPAVALALDTEDAWVAALRNSLRARRDRLAAGLTEIGFAVHDSYGTYFLCADPRPLGYDDSTEFCAALPEKVGVAAIPMSAFCDPAAGQASQQADVWNHLVRFTFCKRDDTLDEAIRRLSVLAERPAT