Rv3398c Dimethylallyltransferase (EC 2.5.1.1); Geranyltranstransferase (farnesyldiphosphate synthase) (EC 2.5.1.10); Geranylgeranyl pyrophosphate synthetase (EC 2.5.1.29)

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3398c idsA1 Dimethylallyltransferase (EC 2.5.1.1); Geranyltranstransferase (farnesyldiphosphate synthase) (EC 2... CDS 3815027 3816106 - 1 080 359 FALSE

Rv3398c (Dimethylallyltransferase (EC 2.5.1.1); Geranyltranstransferase (farnesyldiphosphate synthase) (EC 2.5.1.10); Geranylgeranyl pyrophosphate synthetase (EC 2.5.1.29)) is predicted to be co-regulated in modules bicluster_0534 with residual 0.58 and bicluster_0536 with residual 0.53.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 0.02 for bicluster_0534 and 0.60 and 130.00 for bicluster_0536 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
transcriptional regulator, ArsR family
No 36 -0.02 0.920365 CDS
Motif 1 Motif 2 Residual
bicluster_0534
e.value: 
0.0000000021
Motif Bicluster: 
e.value: 
0.017
Motif Bicluster: 
0.58
bicluster_0536
e.value: 
0.6
Motif Bicluster: 
e.value: 
130
Motif Bicluster: 
0.53
Product (LegacyBRC) Product (RefSeq)
Rv3398c multifunctional dimethylallyltransferase/farnesyl diphosphate synthetase/ farnesyltranstransferase
Operon # Operon
2223 - -
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
57117104 YP_177970.1 Run
GO:0008150

biological_process

biological_process

Details: 
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
GO Category: 
biological_process
66
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:0004161

dimethylallyltranstransferase activity

dimethylallyltranstransferase activity

Details: 
Catalysis of the reaction: dimethylallyl diphosphate + isopentenyl diphosphate = diphosphate + geranyl diphosphate.
GO Category: 
molecular_function
1
Total items in this category:  
GO:0005506

iron ion binding

iron ion binding

Details: 
Interacting selectively and non-covalently with iron (Fe) ions.
GO Category: 
molecular_function
13
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: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
0.270000 3.83

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: