dapB Resolved · high auto-curated
H37Rv Rv2773c · MTBC0 mtbc0_002952 ·
245 aa · 3104019–3104756 (-) ·
RefSeq NP_217289.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 4-hydroxy-tetrahydrodipicolinate reductase |
|---|---|
| MTBC0 PGAP re-annotation | 4-hydroxy-tetrahydrodipicolinate reductase |
| Revised (this work) | 4-hydroxy-tetrahydrodipicolinate reductase. Pfam: DapB_N (PF01113.27), DapB_C (PF05173.20). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WP23
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | 4-hydroxy-tetrahydrodipicolinate reductase |
| EC (curated) |
EC 1.17.1.8
|
| Curated function | Catalyzes the conversion of 4-hydroxy-tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate (Probable). Can use both NADH and NADPH as a reductant, with NADH being 6-fold as effective as NADPH. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | dapB |
| eggNOG description | Catalyzes the conversion of 4-hydroxy- tetrahydrodipicolinate (HTPA) to tetrahydrodipicolinate |
| Orthologous group | COG0289 |
| EC number |
EC 1.17.1.8
|
| KEGG orthology |
K00215
|
| KEGG pathways |
map00261, map00300, map01100, map01110, map01120, map01130, map01230
|
| KEGG modules |
M00016, M00525, M00526, M00527
|
| Gene Ontology (66) |
GO:0000166, GO:0003674, GO:0003824, GO:0005488, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0006082 +54 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 | 1.095 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
DapB_N | PF01113.27 | 3.8e-21 | 1–105 | Dihydrodipicolinate reductase, N-terminus |
DapB_C | PF05173.20 | 8.0e-33 | 108–240 | Dihydrodipicolinate reductase, C-terminus |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: dapA (4-hydroxy-tetrahydrodipicolinate synthase), high confidence from genomic context alone (score 990 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2753c dapA |
4-hydroxy-tetrahydrodipicolinate synthase | 997 | 990 ctx | cooccurence:772 coexpression:479 database:900 textmining:778 |
Rv1201c dapD |
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase | 987 | 951 | coexpression:416 database:900 textmining:767 |
Rv2772c |
transmembrane protein | 894 | 878 ctx | neighborhood:876 |
Rv1293 lysA |
diaminopimelate decarboxylase | 979 | 825 ctx | cooccurence:755 textmining:890 |
Rv2771c hyp |
hypothetical protein | 792 | 785 ctx | neighborhood:779 |
Rv3907c pcnA |
poly(A) polymerase PcnA | 779 | 779 | coexpression:761 |
Rv2774c hyp |
hypothetical protein | 776 | 777 ctx | neighborhood:776 |
Rv3708c asd |
aspartate-semialdehyde dehydrogenase | 937 | 744 ctx | cooccurence:466 coexpression:502 textmining:767 |
Rv2726c dapF |
diaminopimelate epimerase | 969 | 731 ctx | cooccurence:708 textmining:890 |
Rv3709c ask |
aspartokinase | 918 | 683 ctx | cooccurence:598 textmining:754 |
Rv1294 thrA |
homoserine dehydrogenase | 689 | 590 ctx | cooccurence:412 |
Rv1296 thrB |
homoserine kinase | 738 | 572 | coexpression:440 textmining:414 |
Rv2775 |
GCN5-like N-acetyltransferase | 541 | 537 ctx | neighborhood:535 |
Rv1178 dapC |
aminotransferase | 801 | 500 ctx | cooccurence:479 textmining:619 |
Rv2555c alaS |
alanine--tRNA ligase | 436 | 436 | coexpression:418 |
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 reductase
- MTBC0 PGAP product: 4-hydroxy-tetrahydrodipicolinate reductase
- Pfam (hmmscan --cut_ga): DapB_N PF01113.27 (E=4e-21), DapB_C PF05173.20 (E=8e-33)
- (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_217289.1)
- Domains: Pfam-A via hmmscan --cut_ga — DapB_N (PF01113.27), DapB_C (PF05173.20)
- 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
COG0289 - Curated reference: UniProt P9WP23 (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 —
54 functional partner(s); context anchor
dapA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002952|Rv2773c|dapB MRVGVLGAKGKVGATMVRAVAAADDLTLSAELDAGDPLSLLTDGNTEVVIDFTHPDVVMGNLEFLIDNGIHAVVGTTGFTAERFQQVESWLVAKPNTSVLIAPNFAIGAVLSMHFAKQAARFFDSAEVIELHHPHKADAPSGTAARTAKLIAEARKGLPPNPDATSTSLPGARGADVDGIPVHAVRLAGLVAHQEVLFGTEGETLTIRHDSLDRTSFVPGVLLAVRRIAERPGLTVGLEPLLDLH