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 for growth on cholesterol.

Mutant available?:

Product (LegacyBRC) Product (RefSeq)
1-deoxy-D-xylulose-5-phosphate synthase 1-deoxy-D-xylulose-5-phosphate synthase
Operon # Operon
1758
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:  
No TFOE experiment results were found

Quantitative Proteomics Data

t-test p-value Cholesterol/Glycerol Ratio
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.

TRIP log2 fold abundance change

reports the log2 abundance fold change of each TFI strain, relative to no induction, in absence or presence of drug, averaged across experimental replicates. Also reported are the accompanying z-scores and two-sided t-test p-values for each TFI strain under each condition. Please refer to Ma et al., 2020, Nature Microbiology for more information.

p-value Untreated:
p-value INH: