Rv2682c 1-deoxy-D-xylulose 5-phosphate synthase (EC 2.2.1.7)

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv2682c dxs1 1-deoxy-D-xylulose 5-phosphate synthase (EC 2.2.1.7) CDS 2998052 2999968 - 1 917 638 FALSE

Rv2682c (1-deoxy-D-xylulose 5-phosphate synthase (EC 2.2.1.7)) is predicted to be co-regulated in modules bicluster_0165 with residual 0.44 and bicluster_0308 with residual 0.49.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.03 and 0.07 for bicluster_0165 and 0.00 and 0.32 for bicluster_0308 respectively.

These modules are enriched for following go terms: phosphate-containing compound metabolic ..., phosphorus metabolic process, NAD binding .

This gene is found to be non-essential for growth on cholesterol.

Mutant available?:

Displaying 1 - 1 of 1
Gene Target Differential Expression Distance Expression pvalue Type
No results were found
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
No results were found
Motif 1 Motif 2 Residual
bicluster_0165
e.value: 
0.025
Motif Bicluster: 
e.value: 
0.071
Motif Bicluster: 
0.44
bicluster_0308
e.value: 
0.00000028
Motif Bicluster: 
e.value: 
0.32
Motif Bicluster: 
0.49
Product (LegacyBRC) Product (RefSeq)
1-deoxy-D-xylulose-5-phosphate synthase 1-deoxy-D-xylulose-5-phosphate synthase
Operon # Operon
1758 Rv2682c
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics

PATRIC

1-deoxy-D-xylulose-5-phosphate synthase Terpenoid backbone biosynthesis
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

KEGG

Terpenoid backbone biosynthesis

27
Total items in this category:  

KEGG

Metabolic pathways

601
Total items in this category:  

KEGG

Biosynthesis of secondary metabolites

326
Total items in this category:  
BioCyc Gene Page Cellular Overview Map
Link to STRING STRING Network

STRING

GI Number Protein ID Blast Conserved Domains
57117013 YP_177898.1 Run
GO:0008661

1-deoxy-D-xylulose-5-phosphate synthase activity

1-deoxy-D-xylulose-5-phosphate synthase activity

Details: 
Catalysis of the reaction: D-glyceraldehyde 3-phosphate + H(+) + pyruvate = 1-deoxy-D-xylulose 5-phosphate + CO(2).
GO Category: 
molecular_function
2
Total items in this category:  
GO:0000287

magnesium ion binding

magnesium ion binding

Details: 
Interacting selectively and non-covalently with magnesium (Mg) ions.
GO Category: 
molecular_function
52
Total items in this category:  
GO:0008661

1-deoxy-D-xylulose-5-phosphate synthase activity

1-deoxy-D-xylulose-5-phosphate synthase activity

Details: 
Catalysis of the reaction: D-glyceraldehyde 3-phosphate + H(+) + pyruvate = 1-deoxy-D-xylulose 5-phosphate + CO(2).
GO Category: 
molecular_function
2
Total items in this category:  
GO:0019288

isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway

isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway

Details: 
The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway. Isopentenyl diphosphate (IPP) is the fundamental unit in isoprenoid biosynthesis and is biosynthesized from pyruvate and glyceraldehyde 3-phosphate via intermediates, including 1-deoxy-D-xylulose 5-phosphate.
GO Category: 
biological_process
1
Total items in this category:  
GO:0030145

manganese ion binding

manganese ion binding

Details: 
Interacting selectively and non-covalently with manganese (Mn) ions.
GO Category: 
molecular_function
31
Total items in this category:  
GO:0030975

thiamine binding

thiamine binding

Details: 
Interacting selectively and non-covalently with thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
GO Category: 
molecular_function
1
Total items in this category:  
GO:0040007

growth

growth

Details: 
The increase in size or mass of an entire organism, a part of an organism or a cell.
GO Category: 
biological_process
621
Total items in this category:  
Description:Expression data from transcription factor over expression experiments. TFOE are matched to the ChIP-seq experiment done simultaneously. This dataset is described in Rustad et al. 2014, Genome Biology.
Quantitative Proteomics Data
Cholesterol Essentiality t-test p-value Cholesterol/Glycerol Ratio
non-essential NA NA

How essentiality calculations were done?

The relative representation of each mutant was determined by calculating the fold change (sequence reads/insertion in cholesterol divided by sequence reads/insertion in glycerol) for each gene. Statistical significance was determined by t-test. Each insertion site in each replicate sample was treated as a separate data point. The hyperbola used for defining genes specifically required for growth in cholesterol was defined by the formula, y = 3.8/x+0.7. Genes above this line are annotated as required for growth on cholesterol.