dxr Resolved · high auto-curated
H37Rv Rv2870c · MTBC0 mtbc0_003052 ·
413 aa · 3202436–3203677 (-) ·
RefSeq NP_217386.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 1-deoxy-D-xylulose 5-phosphate reductoisomerase |
|---|---|
| MTBC0 PGAP re-annotation | 1-deoxy-D-xylulose-5-phosphate reductoisomerase |
| Revised (this work) | 1-deoxy-D-xylulose-5-phosphate reductoisomerase. Pfam: DXP_reductoisom (PF02670.23), DXP_redisom_C (PF08436.18), DXPR_C (PF13288.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WNS1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | 1-deoxy-D-xylulose 5-phosphate reductoisomerase |
| EC (curated) |
EC 1.1.1.267
|
| Curated function | Catalyzes the NADPH-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | dxr |
| eggNOG description | Catalyzes the NADP-dependent rearrangement and reduction of 1-deoxy-D-xylulose-5-phosphate (DXP) to 2-C-methyl-D-erythritol 4-phosphate (MEP) |
| Orthologous group | COG0743 |
| EC number |
EC 1.1.1.267
|
| KEGG orthology |
K00099
|
| KEGG pathways |
map00900, map01100, map01110, map01130
|
| KEGG modules |
M00096
|
| Gene Ontology (61) |
GO:0000166, GO:0000287, GO:0003674, GO:0003824, GO:0005488, GO:0006081, GO:0006082, GO:0006090, GO:0006629, GO:0006644, GO:0006720, GO:0006721 +49 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 | 0.092 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 1 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 |
|---|---|---|---|---|
DXP_reductoisom | PF02670.23 | 1.0e-35 | 15–135 | 1-deoxy-D-xylulose 5-phosphate reductoisomerase |
DXP_redisom_C | PF08436.18 | 2.5e-34 | 147–230 | 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal domain |
DXPR_C | PF13288.13 | 1.2e-36 | 263–380 | DXP reductoisomerase C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ispD (2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase), high confidence from genomic context alone (score 977 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3582c ispD |
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase | 998 | 977 ctx | cooccurence:762 database:900 textmining:957 |
Rv2682c dxs1 |
1-deoxy-D-xylulose 5-phosphate synthase | 998 | 977 ctx | cooccurence:747 database:900 textmining:931 |
Rv3379c dxs2 |
1-deoxy-D-xylulose-5-phosphate synthase | 993 | 974 ctx | cooccurence:729 database:900 textmining:742 |
Rv2868c gcpE |
4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (flavodoxin) | 997 | 968 ctx | neighborhood:865 cooccurence:772 textmining:928 |
Rv2869c rip |
zinc metalloprotease | 953 | 934 ctx | neighborhood:882 coexpression:464 |
Rv2867c |
GCN5-like N-acetyltransferase | 801 | 801 ctx | neighborhood:795 |
Rv3581c ispF |
2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 988 | 792 ctx | cooccurence:773 textmining:948 |
Rv1110 lytB2 |
4-hydroxy-3-methylbut-2-enyl diphosphate reductase | 907 | 781 ctx | cooccurence:766 textmining:594 |
Rv3382c lytB1 |
4-hydroxy-3-methylbut-2-enyl diphosphate reductase | 957 | 777 ctx | cooccurence:767 textmining:817 |
Rv1011 ispE |
4-diphosphocytidyl-2C-methyl-D-erythritol kinase | 987 | 772 ctx | cooccurence:758 textmining:948 |
Rv2361c uppS |
decaprenyl diphosphate synthase | 919 | 732 | coexpression:687 textmining:713 |
Rv2881c cdsA |
phosphatidate cytidylyltransferase | 816 | 714 | coexpression:666 |
Rv2873 mpt83 |
cell surface lipoprotein | 711 | 712 ctx | neighborhood:711 |
Rv1086 |
(2Z,6E)-farnesyl diphosphate synthase | 811 | 702 | coexpression:691 |
Rv1087A |
Rv1087A, len: 106 aa (fragment). Conserved hypothetical protein, highly similar to C-terminus of near ORF O53434|YA86_MYCTU|Rv1086|MT1118|MT | 725 | 696 | coexpression:685 |
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: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
- MTBC0 PGAP product: 1-deoxy-D-xylulose-5-phosphate reductoisomerase
- Pfam (hmmscan --cut_ga): DXP_reductoisom PF02670.23 (E=1e-35), DXP_redisom_C PF08436.18 (E=3e-34), DXPR_C PF13288.13 (E=1e-36)
- (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_217386.2)
- Domains: Pfam-A via hmmscan --cut_ga — DXP_reductoisom (PF02670.23), DXP_redisom_C (PF08436.18), DXPR_C (PF13288.13)
- 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
COG0743 - Curated reference: UniProt P9WNS1 (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 —
57 functional partner(s); context anchor
ispD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003052|Rv2870c|dxr MTNSTDGRADGRLRVVVLGSTGSIGTQALQVIADNPDRFEVVGLAAGGAHLDTLLRQRAQTGVTNIAVADEHAAQRVGDIPYHGSDAATRLVEQTEADVVLNALVGALGLRPTLAALKTGARLALANKESLVAGGSLVLRAARPGQIVPVDSEHSALAQCLRGGTPDEVAKLVLTASGGPFRGWSAADLEHVTPEQAGAHPTWSMGPMNTLNSASLVNKGLEVIETHLLFGIPYDRIDVVVHPQSIIHSMVTFIDGSTIAQASPPDMKLPISLALGWPRRVSGAAAACDFHTASSWEFEPLDTDVFPAVELARQAGVAGGCMTAVYNAANEEAAAAFLAGRIGFPAIVGIIADVLHAADQWAVEPATVDDVLDAQRWARERAQRAVSGMASVAIASTAKPGAAGRHASTLERS