dxs2 Resolved · high auto-curated
H37Rv Rv3379c · MTBC0 - ·
536 aa · 3793257–3794867 (-) ·
RefSeq NP_217896.1
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), 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 |
O50408
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | 1-deoxy-D-xylulose-5-phosphate synthase |
| EC (curated) |
EC 2.2.1.7
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | dxs |
| eggNOG description | 1-deoxy-D-xylulose-5-phosphate synthase |
| Orthologous group | COG1154 |
| EC number |
EC 2.2.1.7
|
| KEGG orthology |
K01662
|
| KEGG pathways |
map00730, map00900, map01100, map01110, map01130
|
| KEGG modules |
M00096
|
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 | 0.639 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 9 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 61.62% of strains (89472) · reference-fixed |
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 | 3.7e-50 | 1–128 | 1-deoxy-D-xylulose-5-phosphate synthase |
Transket_pyr | PF02779.30 | 2.2e-42 | 212–372 | Transketolase, pyrimidine binding domain |
Transketolase_C | PF02780.26 | 1.8e-23 | 396–509 | 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 974 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2870c dxr |
1-deoxy-D-xylulose 5-phosphate reductoisomerase | 993 | 974 ctx | cooccurence:729 database:900 textmining:742 |
Rv2682c dxs1 |
1-deoxy-D-xylulose 5-phosphate synthase | 908 | 905 | database:900 |
Rv0417 thiG |
thiazole synthase | 938 | 901 | database:900 textmining:410 |
Rv3382c lytB1 |
4-hydroxy-3-methylbut-2-enyl diphosphate reductase | 984 | 835 ctx | neighborhood:493 cooccurence:685 textmining:908 |
Rv3378c |
diterpene synthase | 934 | 803 ctx | neighborhood:801 textmining:680 |
Rv3377c |
type B diterpene cyclase | 937 | 801 ctx | neighborhood:801 textmining:697 |
Rv2868c gcpE |
4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase (flavodoxin) | 911 | 766 ctx | cooccurence:744 textmining:637 |
Rv3581c ispF |
2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase | 853 | 731 ctx | cooccurence:715 textmining:477 |
Rv1110 lytB2 |
4-hydroxy-3-methylbut-2-enyl diphosphate reductase | 818 | 707 ctx | cooccurence:688 textmining:408 |
Rv3582c ispD |
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase | 799 | 618 ctx | cooccurence:577 textmining:496 |
Rv1011 ispE |
4-diphosphocytidyl-2C-methyl-D-erythritol kinase | 835 | 529 ctx | cooccurence:514 textmining:666 |
Rv3383c idsB |
polyprenyl synthetase IdsB | 829 | 465 ctx | neighborhood:407 textmining:694 |
Rv1694 tlyA |
16S/23S rRNA (cytidine-2'-O)-methyltransferase TlyA | 455 | 455 | coexpression:424 |
Rv3380c |
Probable transposase; Rv3380c, (MTV004.38c), len: 328 aa. Probable transposase subunit for IS6110. Identical to many other M. tuberculosis I | 883 | 433 ctx | neighborhood:429 textmining:803 |
Rv3381c |
Rv3381c, (MTV004.39c), len: 108 aa. Putative Transposase for IS6110 (fragment). Identical to many other M. tuberculosis IS6110 transposase s | 431 | 431 ctx | neighborhood:429 |
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=4e-50), Transket_pyr PF02779.30 (E=2e-42), Transketolase_C PF02780.26 (E=2e-23)
- (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_217896.1)
- Domains: Pfam-A via hmmscan --cut_ga — DXP_synthase_N (PF13292.12), 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 O50408 (TrEMBL, unreviewed; Inferred from homology)
- 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 —
34 functional partner(s); context anchor
dxr - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3379c|dxs2 MFDTGHQTYPHKLLTGRGKDFATLRQADGLSGYPNRHESPHDWVENSHASVSLAWVDGIAKALALQGQCDRRVIAVIGDGALTGGVAWEGLNNLGAATRPVIVVLNDNGRSYDPTAGALAAHLEELRVGTPRGPNLFENMGFTYIGPVDGHNIPDTCAVLRKAAAAARPVVVHAVTSKGRGYPPAEADERDHMHACGVVDIATGLASTPSQRSWTDVFEDEIARIADDRSDVVGLTAAMRLPTGLGALSRRYPHRVFDSGIAEQHLLASAAGLAAAGTHPVVAVYSTFLHRAFDQLLFDIGLHRLPVTLVLDRAGVTGPDGPSHHGLWDLALLACVPGFQIACPRDAPRLRQQLRTAIATAAPTAVRFPKGAPGEPITAEHTIGGLDVLHTPPPHWRPDVLLVAVGAMSRPCMDAARCLSEEQIGVTVVDPQWVWPISPALTELAGRHRITVCVEDAIADVGIGAHLSHHIGRTHPRTRTYTLGLPPAYIPHASRDHILSSHGLTGPAIRIRCKSLLNALHEVPGPEDHPDSGDSY