dprE2 Resolved · high auto-curated
H37Rv Rv3791 · MTBC0 - ·
254 aa · 4237165–4237929 (+) ·
RefSeq NP_218308.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | decaprenylphosphoryl-D-2-keto erythropentose reductase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Decaprenylphosphoryl-D-2-keto erythropentose reductase. Pfam: adh_short (PF00106.32), KR (PF08659.17), adh_short_C2 (PF13561.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WGS9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Decaprenylphosphoryl-2-keto-beta-D-erythro-pentose reductase |
| EC (curated) |
EC 1.1.1.333
|
| Curated function | Component of the DprE1-DprE2 complex that catalyzes the 2-step epimerization of decaprenyl-phospho-ribose (DPR) to decaprenyl-phospho-arabinose (DPA), a key precursor that serves as the arabinose donor required for the synthesis of cell-wall arabinans. DprE1 catalyzes the first step of epimerization, namely FAD-dependent oxidation of the C2' hydroxyl of DPR to yield the keto intermediate decaprenyl-phospho-2'-keto-D-arabinose (DPX). The intermediate DPX is then transferred to DprE2 subunit of the epimerase complex, most probably through a 'substrate channel' at the interface of DprE1-DprE2 com. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolismQ Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| Preferred name | dprE2 |
| eggNOG description | Dehydrogenase |
| Orthologous group | COG1028 |
| EC number |
EC 1.1.1.333
|
| KEGG orthology |
K16652
|
| Gene Ontology (39) |
GO:0000271, GO:0005575, GO:0005623, GO:0005886, GO:0005975, GO:0005976, GO:0008150, GO:0008152, GO:0009058, GO:0009059, GO:0009987, GO:0010383 +27 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 | 0.683 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 |
|---|---|---|---|---|
adh_short | PF00106.32 | 8.0e-28 | 10–203 | short chain dehydrogenase |
KR | PF08659.17 | 9.6e-06 | 11–188 | KR domain |
adh_short_C2 | PF13561.13 | 3.5e-19 | 20–205 | Enoyl-(Acyl carrier protein) reductase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: dprE1 (decaprenylphosphoryl-beta-D-ribose oxidase), high confidence from genomic context alone (score 988 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3790 dprE1 |
decaprenylphosphoryl-beta-D-ribose oxidase | 999 | 988 ctx | neighborhood:881 cooccurence:774 database:500 textmining:947 |
Rv3789 |
GtrA family protein | 966 | 957 ctx | neighborhood:823 cooccurence:764 |
Rv3793 embC |
arabinosyltransferase C | 961 | 937 ctx | neighborhood:881 cooccurence:485 textmining:405 |
Rv3792 aftA |
arabinofuranosyltransferase | 957 | 905 ctx | neighborhood:881 textmining:573 |
Rv3794 embA |
arabinosyltransferase A | 935 | 896 ctx | neighborhood:628 cooccurence:469 database:500 textmining:405 |
Rv3795 embB |
arabinosyltransferase B | 913 | 887 ctx | neighborhood:580 cooccurence:493 database:500 |
Rv3806c ubiA |
decaprenyl-phosphate phosphoribosyltransferase | 896 | 788 ctx | cooccurence:773 textmining:531 |
Rv3788 hyp |
hypothetical protein | 735 | 736 ctx | neighborhood:732 |
Rv2036 hyp |
hypothetical protein | 587 | 587 ctx | neighborhood:516 |
Rv3796 hyp |
hypothetical protein | 439 | 439 ctx | neighborhood:434 |
Rv3805c aftB |
terminal beta-(1->2)-arabinofuranosyltransferase | 473 | 358 | |
Rv3807c |
decaprenylphosphoryl-5-phosphoribose phosphatase | 800 | 304 | textmining:726 |
Rv1017c prsA |
ribose-phosphate pyrophosphokinase | 563 | 75 | textmining:548 |
Rv0308 |
integral membrane protein | 674 | 53 | textmining:670 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): decaprenylphosphoryl-D-2-keto erythropentose reductase
- Pfam (hmmscan --cut_ga): adh_short PF00106.32 (E=8e-28), KR PF08659.17 (E=1e-05), adh_short_C2 PF13561.13 (E=4e-19)
- (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_218308.1)
- Domains: Pfam-A via hmmscan --cut_ga — adh_short (PF00106.32), KR (PF08659.17), adh_short_C2 (PF13561.13)
- 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
COG1028 - Curated reference: UniProt P9WGS9 (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 —
14 functional partner(s); context anchor
dprE1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3791|dprE2 MVLDAVGNPQTVLLLGGTSEIGLAICERYLHNSAARIVLACLPDDPRREDAAAAMKQAGARSVELIDFDALDTDSHPKMIEAAFSGGDVDVAIVAFGLLGDAEELWQNQRKAVQIAEINYTAAVSVGVLLAEKMRAQGFGQIIAMSSAAGERVRRANFVYGSTKAGLDGFYLGLSEALREYGVRVLVIRPGQVRTRMSAHLKEAPLTVDKEYVANLAVTASAKGKELVWAPAAFRYVMMVLRHIPRSIFRKLPI