Rv0757 DNA-binding response regulator

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv0757 phoP DNA-binding response regulator CDS 851608 852351 + 744 247 TRUE

Rv0757 (DNA-binding response regulator) is predicted to be co-regulated in modules bicluster_0144 with residual 0.61 and bicluster_0543 with residual 0.58.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.02 and 13.00 for bicluster_0144 and 0.00 and 0.00 for bicluster_0543 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?: Yes

Last update: 11/20/2020 - 12:11
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-14776 MT0782 186
Displaying 1 - 10 of 96
Gene Target Differential Expression Distance Expression pvalue Type
Cell division protein FtsW
No 32 -0.05 0.730957 Internal.TSS
No -102 0.13 0.602485 Primary.TSS
2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29)
No -44 0.11 0.800996 Primary.TSS
No -90 -0.38 0.0700584 Internal.TSS
No 60 -0.38 0.0700584 Internal.TSS
No -150 -0.38 0.0700584 Internal.TSS
Replicative DNA helicase (EC 3.6.1.-) @ intein-containing
No -90 -0.48 0.00158228 Primary.TSS
Phosphoheptose isomerase (EC 5.3.1.-)
No -55 0.26 0.40791 CDS
Repressed -104 -0.68 0.00163255 Primary.TSS
tRNA (guanine46-N7-)-methyltransferase (EC 2.1.1.33)
No 7 -0.27 0.0964239 Internal.TSS
Displaying 1 - 10 of 11
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, MarR family
No -10 -0.01 0.99008 Primary.TSS
transcriptional regulator, ArsR family
No -15 0.14 0.344343 Primary.TSS
Repressed -53 -1.01 0.0000000889 Primary.TSS
TetR/ACRR family transcriptional regulator
No -9 -0.47 0.298119 Primary.TSS
WhiB-type transcription regulator
Induced -12 1.01 0.00000192 Primary.TSS
DNA-binding response regulator
Induced -23 1.38 1.86e-19 Primary.TSS
Transcriptional regulator, IclR family
No -36 0.07 0.916112 Primary.TSS
Transcriptional regulator, TetR family
Repressed -10 -1.34 0.0000000000000726 Primary.TSS
Transcriptional regulator, MarR family
Repressed -16 -1.46 6.04e-16 Primary.TSS
Histone protein Lsr2
No -37 0.12 0.742544 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0144
e.value: 
0.022
Motif Bicluster: 
e.value: 
13
Motif Bicluster: 
0.61
bicluster_0543
e.value: 
0.000000012
Motif Bicluster: 
e.value: 
0.00095
Motif Bicluster: 
0.58
Product (LegacyBRC) Product (RefSeq)
POSSIBLE TWO COMPONENT SYSTEM RESPONSE TRANSCRIPTIONAL POSITIVE REGULATOR PHOP two component system response transcriptional positive regulator PHOP
Operon # Operon
503
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics

PATRIC

Not assigned Not assigned
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

KEGG

not assigned to any KEGG Pathway.
BioCyc Gene Page Cellular Overview Map
Link to STRING STRING Network

STRING

GI Number Protein ID Blast Conserved Domains
15607897 NP_215271.1 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: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: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:0006979

response to oxidative stress

response to oxidative stress

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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
GO Category: 
biological_process
13
Total items in this category:  
GO:0009247

glycolipid biosynthetic process

glycolipid biosynthetic process

Details: 
The chemical reactions and pathways resulting in the formation of glycolipid, a class of 1,2-di-O-acylglycerols joined at oxygen 3 by a glycosidic linkage to a carbohydrate part (usually a mono-, di- or tri-saccharide).
GO Category: 
biological_process
17
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:0045892

negative regulation of transcription, DNA-dependent

negative regulation of transcription, DNA-dependent

Details: 
Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-dependent transcription.
GO Category: 
biological_process
10
Total items in this category:  
GO:0045893

positive regulation of transcription, DNA-dependent

positive regulation of transcription, DNA-dependent

Details: 
Any process that activates or increases the frequency, rate or extent of cellular DNA-dependent transcription.
GO Category: 
biological_process
14
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.
BioProject Accession GEO Series References Repository Sample Method Sample Type
PRJNA254351 GSM1426552 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426553 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426554 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426555 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426552 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426553 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426554 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426555 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0757_B167 UCSC Browser Tracks
Rv0757_B169 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.640000 0.32

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: 0.303872
p-value INH: 0.044751
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 13.70 U
D3I 3 3 3.83 13.88 I
D3U 3 3 3.83 13.53 U
D5I 9 5 6.00 14.03 I
D5U 17 5 6.00 13.83 U
D7I 18 7 8.14 13.74 I
D7U 19 7 8.14 13.58 U
D14I 4 14 15.63 13.81 I
D14U 4 14 15.63 13.00 U
D17I 3 17 19.15 14.21 I
D17U 3 17 19.15 12.79 U
D21I 4 21 23.23 14.04 I
D21U 4 21 23.23 12.81 U
D24I 3 24 26.60 14.59 I
D24U 3 24 26.60 12.65 U
D28I 4 28 30.61 14.27 I
D28U 4 28 30.61 12.71 U