Rv2988c 3-isopropylmalate dehydratase large subunit (EC 4.2.1.33)

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv2988c leuC 3-isopropylmalate dehydratase large subunit (EC 4.2.1.33) CDS 3344654 3346075 - 1 422 473 FALSE

Rv2988c (3-isopropylmalate dehydratase large subunit (EC 4.2.1.33)) is predicted to be co-regulated in modules bicluster_0286 with residual 0.44 and bicluster_0344 with residual 0.49.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 4.30 and 5.80 for bicluster_0286 and 0.10 and 8.00 for bicluster_0344 respectively.

These modules are enriched for following go terms: branched-chain amino acid biosynthetic p..., branched-chain amino acid metabolic proc..., cytosol, cytosolic part .

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 - 4 of 4
ChipSeq TF Differential Expression Distance Expression pvalue Type
DNA-binding response regulator TrcR
No -2 -0.9 0.454516 Primary.TSS
Transcriptional regulator, IclR family
No 2 -1.72 0.152484 Primary.TSS
Organic hydroperoxide resistance transcriptional regulator
No -86 1.1 0.244211 Primary.TSS
Transcriptional regulator, IclR family
No -31 -0.09 0.967609 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0286
e.value: 
4.3
Motif Bicluster: 
e.value: 
5.8
Motif Bicluster: 
0.44
bicluster_0344
e.value: 
0.1
Motif Bicluster: 
e.value: 
8
Motif Bicluster: 
0.49
Product (LegacyBRC) Product (RefSeq)
3-isopropylmalate dehydratase large subunit isopropylmalate isomerase large subunit
Operon # Operon
1950 Rv2987c - Rv2988c
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics

PATRIC

3-isopropylmalate dehydratase Valine, leucine and isoleucine biosynthesis
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

KEGG

Valine, leucine and isoleucine biosynthesis

21
Total items in this category:  

KEGG

C5-Branched dibasic acid metabolism

9
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
15610125 NP_217504.1 Run
GO:0003861

3-isopropylmalate dehydratase activity

3-isopropylmalate dehydratase activity

Details: 
Catalysis of the reaction: 3-isopropylmalate = 2-isopropylmaleate + H2O.
GO Category: 
molecular_function
2
Total items in this category:  
GO:0005618

cell wall

cell wall

Details: 
The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan.
GO Category: 
cellular_component
320
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.