Rv0467 Isocitrate lyase (EC 4.1.3.1) / Methylisocitrate lyase (EC 4.1.3.30)

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv0467 icl1 Isocitrate lyase (EC 4.1.3.1) / Methylisocitrate lyase (EC 4.1.3.30) CDS 557527 558813 + 1 287 428 FALSE

Rv0467 (Isocitrate lyase (EC 4.1.3.1) / Methylisocitrate lyase (EC 4.1.3.30)) is predicted to be co-regulated in modules bicluster_0475 with residual 0.40 and bicluster_0528 with residual 0.42.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 9.10 for bicluster_0475 and 0.00 and 47.00 for bicluster_0528 respectively.

These modules are enriched for following go terms: fatty acid synthase activity .

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

Mutant available?: Yes

Last update: 10/16/2017 - 02:57
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-15740 MT0483 2812
Displaying 1 - 1 of 1
Gene Target Differential Expression Distance Expression pvalue Type
No results were found
Displaying 1 - 9 of 9
ChipSeq TF Differential Expression Distance Expression pvalue Type
transcriptional regulator, ArsR family
Induced 55 1.89 5.1e-16 Primary.TSS
Transcriptional regulator, TetR family
No -145 -0.27 0.650339 Primary.TSS
Lactate-responsive regulator LldR in Enterobacteria, GntR family
Repressed -9 -0.99 0.00151645 Primary.TSS
putative RNA polymerase sigma factor
No -66 -0.6 0.49522 Primary.TSS
No -99 0.68 0.110521 Primary.TSS
Beta-carotene ketolase (EC 1.14.-.-)
No -23 -0.02 0.999473 Primary.TSS
Transcriptional regulator, TetR family
No 3 -0.16 0.817337 Primary.TSS
Histone protein Lsr2
No -73 0.22 0.768494 Primary.TSS
Transcriptional regulator, AsnC family
No -38 0.1 0.961751 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0475
e.value: 
0.0014
Motif Bicluster: 
e.value: 
9.1
Motif Bicluster: 
0.40
bicluster_0528
e.value: 
0.00023
Motif Bicluster: 
e.value: 
47
Motif Bicluster: 
0.42
Product (LegacyBRC) Product (RefSeq)
Isocitrate lyase isocitrate lyase
Operon # Operon
313 Rv0467
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

KEGG

Glyoxylate and dicarboxylate metabolism

31
Total items in this category:  

KEGG

Metabolic pathways

601
Total items in this category:  

KEGG

Microbial metabolism in diverse environments

296
Total items in this category:  
BioCyc Gene Page Cellular Overview Map
Link to STRING STRING Network

STRING

GI Number Protein ID Blast Conserved Domains
57116734 YP_177728.1 Run
GO:0004451

isocitrate lyase activity

isocitrate lyase activity

Details: 
Catalysis of the reaction: isocitrate = glyoxylate + succinate.
GO Category: 
molecular_function
3
Total items in this category:  
GO:0001101

response to acid

response to acid

Details: 
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an acid stimulus.
GO Category: 
biological_process
11
Total items in this category:  
GO:0004451

isocitrate lyase activity

isocitrate lyase activity

Details: 
Catalysis of the reaction: isocitrate = glyoxylate + succinate.
GO Category: 
molecular_function
3
Total items in this category:  
GO:0005829

cytosol

cytosol

Details: 
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO Category: 
cellular_component
371
Total items in this category:  
GO:0005886

plasma membrane

plasma membrane

Details: 
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO Category: 
cellular_component
1284
Total items in this category:  
GO:0006097

glyoxylate cycle

glyoxylate cycle

Details: 
A modification of the TCA cycle occurring in some plants and microorganisms, in which isocitrate is cleaved to glyoxylate and succinate. Glyoxylate can then react with acetyl-CoA to form malate.
GO Category: 
biological_process
2
Total items in this category:  
GO:0009405

pathogenesis

pathogenesis

Details: 
The set of specific processes that generate the ability of an organism to cause disease in another.
GO Category: 
biological_process
65
Total items in this category:  
GO:0010034

response to acetate

response to acetate

Details: 
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an acetate stimulus.
GO Category: 
biological_process
1
Total items in this category:  
GO:0046421

methylisocitrate lyase activity

methylisocitrate lyase activity

Details: 
Catalysis of the reaction: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = pyruvate + succinate.
GO Category: 
molecular_function
2
Total items in this category:  
GO:0052572

response to host immune response

response to host immune response

Details: 
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of detecting the immune response of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
GO Category: 
biological_process
62
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 0.060000 0.09

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.