dapA Resolved · high auto-curated
H37Rv Rv2753c · MTBC0 mtbc0_002930 ·
300 aa · 3088637–3089539 (-) ·
RefSeq NP_217269.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 4-hydroxy-tetrahydrodipicolinate synthase |
|---|---|
| MTBC0 PGAP re-annotation | 4-hydroxy-tetrahydrodipicolinate synthase |
| Revised (this work) | 4-hydroxy-tetrahydrodipicolinate synthase. Pfam: DHDPS (PF00701.29). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WP25
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | 4-hydroxy-tetrahydrodipicolinate synthase |
| EC (curated) |
EC 4.3.3.7
|
| Curated function | Catalyzes the condensation of (S)-aspartate-beta-semialdehyde [(S)-ASA] and pyruvate to 4-hydroxy-tetrahydrodipicolinate (HTPA). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | dapA |
| eggNOG description | Catalyzes the condensation of (S)-aspartate-beta- semialdehyde (S)-ASA and pyruvate to 4-hydroxy- tetrahydrodipicolinate (HTPA) |
| Orthologous group | COG0329 |
| EC number |
EC 4.3.3.7
|
| KEGG orthology |
K01714
|
| KEGG pathways |
map00261, map00300, map01100, map01110, map01120, map01130, map01230
|
| KEGG modules |
M00016, M00525, M00526, M00527
|
| Gene Ontology (43) |
GO:0003674, GO:0003824, GO:0005575, GO:0005623, GO:0005886, GO:0006082, GO:0006520, GO:0006553, GO:0006807, GO:0008150, GO:0008152, GO:0008652 +31 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 | 0.376 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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 |
|---|---|---|---|---|
DHDPS | PF00701.29 | 3.6e-77 | 13–295 | Dihydrodipicolinate synthetase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: dapB (4-hydroxy-tetrahydrodipicolinate reductase), high confidence from genomic context alone (score 990 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2773c dapB |
4-hydroxy-tetrahydrodipicolinate reductase | 997 | 990 ctx | cooccurence:772 coexpression:479 database:900 textmining:778 |
Rv3708c asd |
aspartate-semialdehyde dehydrogenase | 996 | 972 ctx | cooccurence:497 coexpression:450 database:900 textmining:877 |
Rv1294 thrA |
homoserine dehydrogenase | 962 | 939 | database:900 textmining:409 |
Rv2752c rnj |
ribonuclease J | 934 | 885 ctx | neighborhood:839 textmining:449 |
Rv2754c thyX |
thymidylate synthase ThyX | 861 | 822 ctx | neighborhood:795 |
Rv1293 lysA |
diaminopimelate decarboxylase | 961 | 817 ctx | cooccurence:752 textmining:800 |
Rv2726c dapF |
diaminopimelate epimerase | 965 | 730 ctx | cooccurence:697 textmining:877 |
Rv3709c ask |
aspartokinase | 959 | 722 ctx | cooccurence:523 textmining:862 |
Rv3012c gatC |
glutamyl-tRNA(GLN) amidotransferase subunit C | 736 | 721 | coexpression:698 |
Rv2785c rpsO |
30S ribosomal protein S15 | 699 | 699 | coexpression:653 |
Rv2756c hsdM |
type I restriction/modification system DNA methylase HsdM | 681 | 682 ctx | neighborhood:677 |
Rv0948c |
chorismate mutase | 688 | 669 | coexpression:650 |
Rv1885c |
chorismate mutase | 687 | 669 | coexpression:650 |
Rv0706 rplV |
50S ribosomal protein L22 | 662 | 662 | coexpression:654 |
Rv2762c hyp |
hypothetical protein | 755 | 655 ctx | neighborhood:643 |
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: 4-hydroxy-tetrahydrodipicolinate synthase
- MTBC0 PGAP product: 4-hydroxy-tetrahydrodipicolinate synthase
- Pfam (hmmscan --cut_ga): DHDPS PF00701.29 (E=4e-77)
- (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_217269.1)
- Domains: Pfam-A via hmmscan --cut_ga — DHDPS (PF00701.29)
- 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
COG0329 - Curated reference: UniProt P9WP25 (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 —
71 functional partner(s); context anchor
dapB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002930|Rv2753c|dapA MTTVGFDVAARLGTLLTAMVTPFSGDGSLDTATAARLANHLVDQGCDGLVVSGTTGESPTTTDGEKIELLRAVLEAVGDRARVIAGAGTYDTAHSIRLAKACAAEGAHGLLVVTPYYSKPPQRGLQAHFTAVADATELPMLLYDIPGRSAVPIEPDTIRALASHPNIVGVKDAKADLHSGAQIMADTGLAYYSGDDALNLPWLAMGATGFISVIAHLAAGQLRELLSAFGSGDIATARKINIAVAPLCNAMSRLGGVTLSKAGLRLQGIDVGDPRLPQVAATPEQIDALAADMRAASVLR