dapC Resolved · high auto-curated
H37Rv Rv1178 · MTBC0 mtbc0_001267 ·
362 aa · 1317805–1318893 (+) ·
RefSeq NP_215694.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | aminotransferase |
|---|---|
| MTBC0 PGAP re-annotation | succinyldiaminopimelate transaminase |
| Revised (this work) | Succinyldiaminopimelate transaminase. Pfam: Aminotran_1_2 (PF00155.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O50434
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable aminotransferase Rv1178 |
| EC (curated) |
EC 2.6.1.-
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | dapC |
| eggNOG description | Aminotransferase |
| Orthologous group | COG0436 |
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 | 0.516 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
Aminotran_1_2 | PF00155.28 | 8.7e-44 | 27–360 | Aminotransferase class I and II |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fdxC (ferredoxin FdxC), high confidence from genomic context alone (score 903 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1177 fdxC |
ferredoxin FdxC | 950 | 903 ctx | neighborhood:833 fusion:405 textmining:510 |
Rv0511 hemD |
uroporphyrin-III C-methyltransferase | 769 | 760 | coexpression:755 |
Rv1293 lysA |
diaminopimelate decarboxylase | 876 | 759 ctx | cooccurence:595 coexpression:409 textmining:510 |
Rv1176c hyp |
hypothetical protein | 730 | 731 ctx | neighborhood:727 |
Rv1202 dapE |
succinyl-diaminopimelate desuccinylase DapE | 903 | 706 ctx | cooccurence:663 textmining:684 |
Rv2726c dapF |
diaminopimelate epimerase | 898 | 685 ctx | cooccurence:581 textmining:691 |
Rv3709c ask |
aspartokinase | 752 | 582 | textmining:432 |
Rv3797 fadE35 |
acyl-CoA dehydrogenase FadE35 | 556 | 554 ctx | neighborhood:544 |
Rv0884c serC |
phosphoserine aminotransferase | 589 | 550 ctx | cooccurence:437 |
Rv1294 thrA |
homoserine dehydrogenase | 561 | 520 | |
Rv2753c dapA |
4-hydroxy-tetrahydrodipicolinate synthase | 785 | 519 ctx | cooccurence:485 textmining:572 |
Rv1175c fadH |
NADPH dependent 2,4-dienoyl-CoA reductase FadH | 564 | 510 ctx | neighborhood:487 |
Rv2773c dapB |
4-hydroxy-tetrahydrodipicolinate reductase | 801 | 500 ctx | cooccurence:479 textmining:619 |
Rv1600 hisC1 |
histidinol-phosphate aminotransferase | 524 | 497 ctx | cooccurence:434 |
Rv2173 idsA2 |
geranylgeranyl pyrophosphate synthetase IdsA | 410 | 384 |
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: aminotransferase
- MTBC0 PGAP product: succinyldiaminopimelate transaminase
- Pfam (hmmscan --cut_ga): Aminotran_1_2 PF00155.28 (E=9e-44)
- (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_215694.1)
- Domains: Pfam-A via hmmscan --cut_ga — Aminotran_1_2 (PF00155.28)
- 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 O50434 (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 —
36 functional partner(s); context anchor
fdxC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001267|Rv1178|dapC MSASLPVFPWDTLADAKALAGAHPDGIVDLSVGTPVDPVAPLIQEALAAASAAPGYPATAGTARLRESVVAALARRYGITRLTEAAVLPVIGTKELIAWLPTLLGLGGADLVVVPELAYPTYDVGARLAGTRVLRADALTQLGPQSPALLYLNSPSNPTGRVLGVDHLRKVVEWARGRGVLVVSDECYLGLGWDAEPVSVLHPSVCDGDHTGLLAVHSLSKSSSLAGYRAGFVVGDLEIVAELLAVRKHAGMMVPAPVQAAMVAALDDDAHERQQRERYAQRRAALLPALGSAGFAVDYSDAGLYLWATRGEPCRDSVAWLAQRGILVAPGDFYGPGGAQHVRVALTATDERVAAAVGRLTC