Rv1511 \GDP-mannose 4,6-dehydratase (EC 4.2.1.47)\\\""

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv1511 gmdA \GDP-mannose 4,6-dehydratase (EC 4.2.1.47)\\\"" CDS 1703074 1704096 + 1 023 340 FALSE

Rv1511 (\GDP-mannose 4,6-dehydratase (EC 4.2.1.47)\\\"") is predicted to be co-regulated in modules bicluster_0025 with residual 0.54 and bicluster_0153 with residual 0.56.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.31 and 8.20 for bicluster_0025 and 0.01 and 20.00 for bicluster_0153 respectively.

These modules are enriched for following go terms: nucleotide-sugar metabolic process nucleotide metabolic process.

This gene is found to be for growth on cholesterol.

Mutant available?: Yes

Last update: 10/16/2017 - 11:39
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-13627 MT1561 1022
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
TetR/ACRR family transcriptional regulator
Repressed -29 -2.26 1.20512e-43 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0025
e.value: 
0.31
Motif Bicluster: 
e.value: 
8.2
Motif Bicluster: 
0.54
bicluster_0153
e.value: 
0.0083
Motif Bicluster: 
e.value: 
20
Motif Bicluster: 
0.56
Product (LegacyBRC) Product (RefSeq)
GDP-D-mannose dehydratase gmdA [GDP-mannose 46 dehydratase] [GMD] GDP-D-mannose dehydratase gmdA (GDP-mannose 4,6 dehydratase) (GMD)
Operon # Operon
1007 - -
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

KEGG

Fructose and mannose metabolism

18
Total items in this category:  

KEGG

Amino sugar and nucleotide sugar metabolism

28
Total items in this category:  

KEGG

Metabolic pathways

601
Total items in this category:  
BioCyc Gene Page Cellular Overview Map
Link to STRING STRING Network

STRING

GI Number Protein ID Blast Conserved Domains
15608649 NP_216027.1 Run
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:0071456

cellular response to hypoxia

cellular response to hypoxia

Details: 
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
GO Category: 
biological_process
7
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
0.630000 1.43

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: