Rv3581c 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12)

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3581c ispF 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) CDS 4023868 4024347 - 480 159 FALSE

Rv3581c (2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12)) is predicted to be co-regulated in modules bicluster_0470 with residual 0.49 and bicluster_0542 with residual 0.60.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 150.00 and 8,000.00 for bicluster_0470 and 0.02 and 150.00 for bicluster_0542 respectively.

These modules are enriched for following go terms: .

This gene is found to be 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
POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN
No -102 0.12 0.806571 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0470
e.value: 
150
Motif Bicluster: 
e.value: 
8000
Motif Bicluster: 
0.49
bicluster_0542
e.value: 
0.019
Motif Bicluster: 
e.value: 
150
Motif Bicluster: 
0.60
Product (LegacyBRC) Product (RefSeq)
2-C-methyl-D-erythritol 24-cyclodiphosphate synthase 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Operon # Operon
2333 - -
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
15610717 NP_218098.1 Run
GO:0008685

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity

2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity

Details: 
Catalysis of the reaction: 4-CDP-2-C-methyl-D-erythritol 2-phosphate = 2-C-methyl-D-erythritol 2,4-cyclic diphosphate + CMP.
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
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: