dxs1 Resolved · high auto-curated
H37Rv Rv2682c · MTBC0 - ·
638 aa · 2998052–2999968 (-) ·
RefSeq YP_177898.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 1-deoxy-D-xylulose 5-phosphate synthase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | 1-deoxy-D-xylulose 5-phosphate synthase. Pfam: DXP_synthase_N (PF13292.12), TPP_enzyme_C (PF02775.27), Transket_pyr (PF02779.30), Transketolase_C (PF02780.26). |
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 |
P9WNS3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | 1-deoxy-D-xylulose-5-phosphate synthase |
| EC (curated) |
EC 2.2.1.7
|
| Curated function | Catalyzes the acyloin condensation reaction between C atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-xylulose-5-phosphate (DXP). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | dxs |
| eggNOG description | Catalyzes the acyloin condensation reaction between C atoms 2 and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-xylulose-5-phosphate (DXP) |
| Orthologous group | COG1154 |
| EC number |
EC 2.2.1.7
|
| KEGG orthology |
K01662
|
| KEGG pathways |
map00730, map00900, map01100, map01110, map01130
|
| KEGG modules |
M00096
|
| Gene Ontology (52) |
GO:0000287, GO:0003674, GO:0003824, GO:0005488, GO:0006081, GO:0006082, GO:0006090, GO:0006629, GO:0006644, GO:0006720, GO:0006793, GO:0006796 +40 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 | 0.095 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 11 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 |
|---|---|---|---|---|
DXP_synthase_N | PF13292.12 | 1.4e-108 | 2–278 | 1-deoxy-D-xylulose-5-phosphate synthase |
TPP_enzyme_C | PF02775.27 | 1.1e-04 | 106–174 | Thiamine pyrophosphate enzyme, C-terminal TPP binding domain |
Transket_pyr | PF02779.30 | 6.0e-45 | 315–476 | Transketolase, pyrimidine binding domain |
Transketolase_C | PF02780.26 | 4.7e-26 | 500–612 | Transketolase, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: dxr (1-deoxy-D-xylulose 5-phosphate reductoisomerase), high confidence from genomic context alone (score 977 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2870c dxr |
1-deoxy-D-xylulose 5-phosphate reductoisomerase | 998 | 977 ctx | cooccurence:747 database:900 textmining:931 |
Rv3379c dxs2 |
1-deoxy-D-xylulose-5-phosphate synthase | 908 | 905 | database:900 |
Rv0417 thiG |
thiazole synthase | 963 | 900 | database:900 textmining:650 |
Rv1110 lytB2 |
4-hydroxy-3-methylbut-2-enyl diphosphate reductase | 935 | 830 ctx | cooccurence:706 coexpression:415 textmining:635 |
Rv2868c gcpE |
4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (flavodoxin) | 942 | 776 ctx | cooccurence:752 textmining:755 |
Rv3581c ispF |
2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 971 | 756 ctx | cooccurence:735 textmining:889 |
Rv3382c lytB1 |
4-hydroxy-3-methylbut-2-enyl diphosphate reductase | 929 | 721 ctx | cooccurence:701 textmining:756 |
Rv3582c ispD |
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase | 969 | 659 ctx | cooccurence:619 textmining:915 |
Rv2683 hyp |
hypothetical protein | 644 | 645 ctx | neighborhood:645 |
Rv1011 ispE |
4-diphosphocytidyl-2C-methyl-D-erythritol kinase | 937 | 590 ctx | cooccurence:575 textmining:853 |
Rv2684 arsA |
arsenic-transport integral membrane protein ArsA | 543 | 543 ctx | neighborhood:542 |
Rv1694 tlyA |
16S/23S rRNA (cytidine-2'-O)-methyltransferase TlyA | 469 | 469 | coexpression:439 |
Rv2685 arsB1 |
arsenic-transport integral membrane protein ArsB | 420 | 421 ctx | neighborhood:412 |
Rv1695 ppnK |
inorganic polyphosphate/ATP-NAD kinase | 615 | 414 | |
Rv1415 ribA2 |
bifunctional riboflavin biosynthesis GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase | 466 | 197 |
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): 1-deoxy-D-xylulose 5-phosphate synthase
- Pfam (hmmscan --cut_ga): DXP_synthase_N PF13292.12 (E=1e-108), TPP_enzyme_C PF02775.27 (E=1e-04), Transket_pyr PF02779.30 (E=6e-45), Transketolase_C PF02780.26 (E=5e-26)
- (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 YP_177898.1)
- Domains: Pfam-A via hmmscan --cut_ga — DXP_synthase_N (PF13292.12), TPP_enzyme_C (PF02775.27), Transket_pyr (PF02779.30), Transketolase_C (PF02780.26)
- 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
COG1154 - Curated reference: UniProt P9WNS3 (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 —
37 functional partner(s); context anchor
dxr - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2682c|dxs1 MLQQIRGPADLQHLSQAQLRELAAEIREFLIHKVAATGGHLGPNLGVVELTLALHRVFDSPHDPIIFDTGHQAYVHKMLTGRSQDFATLRKKGGLSGYPSRAESEHDWVESSHASAALSYADGLAKAFELTGHRNRHVVAVVGDGALTGGMCWEALNNIAASRRPVIIVVNDNGRSYAPTIGGVADHLATLRLQPAYEQALETGRDLVRAVPLVGGLWFRFLHSVKAGIKDSLSPQLLFTDLGLKYVGPVDGHDERAVEVALRSARRFGAPVIVHVVTRKGMGYPPAEADQAEQMHSTVPIDPATGQATKVAGPGWTATFSDALIGYAQKRRDIVAITAAMPGPTGLTAFGQRFPDRLFDVGIAEQHAMTSAAGLAMGGLHPVVAIYSTFLNRAFDQIMMDVALHKLPVTMVLDRAGITGSDGASHNGMWDLSMLGIVPGIRVAAPRDATRLREELGEALDVDDGPTALRFPKGDVGEDISALERRGGVDVLAAPADGLNHDVLLVAIGAFAPMALAVAKRLHNQGIGVTVIDPRWVLPVSDGVRELAVQHKLLVTLEDNGVNGGAGSAVSAALRRAEIDVPCRDVGLPQEFYEHASRSEVLADLGLTDQDVARRITGWVAALGTGVCASDAIPEHLD