Rv3133c Two component transcriptional regulatory protein DevR

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3133c devR / DosR Two component transcriptional regulatory protein DevR CDS 3499262 3499915 - 654 217 TRUE

Rv3133c (Two component transcriptional regulatory protein DevR) is predicted to be co-regulated in modules bicluster_0182 with residual 0.43 and bicluster_0417 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 0.32 for bicluster_0182 and 0.00 and 0.00 for bicluster_0417 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 151
Gene Target Differential Expression Distance Expression pvalue Type
Transcriptional regulator, MarR family
No 65 -0.4 0.00134156 Internal.TSS
Transcriptional regulator, MarR family
No -58 -0.4 0.00134156 CDS
Multimodular transpeptidase-transglycosylase (EC 2.4.1.129) (EC 3.4.-.-)
No 66 0.04 0.710974 CDS
Induced -39 3.47 7.49e-18 Primary.TSS
Probable cation-transporting ATPase I (EC 3.6.3.-)
No 25 0.29 0.0174762 CDS
Possible membrane protein
Repressed -6 -0.61 0.000189237 Primary.TSS
Hydrogen peroxide-inducible genes activator
No -124 -0.21 0.297718 Primary.TSS
Transcriptional regulator, TetR family
No -51 -0.56 0.00739666 Primary.TSS
MCE-family protein Mce1D
No -78 0.17 0.344312 Antisense.TSS
Lysophospholipid acyltransferase
No 53 0.11 0.256927 CDS
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, ArsR family
No 43 0.56 0.0272709 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0182
e.value: 
2.1e-23
Motif Bicluster: 
e.value: 
0.32
Motif Bicluster: 
0.43
bicluster_0417
e.value: 
3.9e-21
Motif Bicluster: 
e.value: 
0.00018
Motif Bicluster: 
0.42
Product (LegacyBRC) Product (RefSeq)
TWO COMPONENT TRANSCRIPTIONAL REGULATORY PROTEIN DEVR [PROBABLY LUXR_UHPA-FAMILY] two component transcriptional regulatory protein DevR
Operon # Operon
2048 Rv3132c - Rv3133c - Rv3134c
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics

PATRIC

Not assigned Not assigned
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

KEGG

Two-component system

53
Total items in this category:  
BioCyc Gene Page Cellular Overview Map
Link to STRING STRING Network

STRING

GI Number Protein ID Blast Conserved Domains
15610269 NP_217649.1 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:0001666

response to hypoxia

response to hypoxia

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 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
37
Total items in this category:  
GO:0003677

DNA binding

DNA binding

Details: 
Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid).
GO Category: 
molecular_function
37
Total items in this category:  
GO:0003700

sequence-specific DNA binding transcription factor activity

sequence-specific DNA binding transcription factor activity

Details: 
Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
GO Category: 
molecular_function
17
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: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: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:  
GO:0071500

cellular response to nitrosative stress

cellular response to nitrosative stress

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 nitrosative stress stimulus. Nitrosative stress is a state often resulting from exposure to high levels of nitric oxide (NO) or the highly reactive oxidant peroxynitrite, which is produced following interaction of NO with superoxide anions.
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 GSM1426924 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426925 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426926 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426924 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426925 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426926 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426924 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426925 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426926 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426924 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3133c_B121 UCSC Browser Tracks
Rv3133c_B172 UCSC Browser Tracks
Rv3133c_B226 UCSC Browser Tracks
Rv3133c_B238 UCSC Browser Tracks
Rv3133c_B239 UCSC Browser Tracks
Rv3133c_B253 UCSC Browser Tracks
Rv3133c_B481 UCSC Browser Tracks
Rv3133c_B491 UCSC Browser Tracks
Rv3133c_B492 UCSC Browser Tracks
Rv3133c_B493 UCSC Browser Tracks
Quantitative Proteomics Data
Cholesterol Essentiality t-test p-value Cholesterol/Glycerol Ratio
No results were found 0.080000 0.67

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.

Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 14.12 U
D3I 3 3 3.83 14.30 I
D3U 3 3 3.83 14.27 U
D5I 9 5 6.00 12.47 I
D5U 17 5 6.00 13.00 U
D7I 18 7 8.14 12.94 I
D7U 19 7 8.14 14.46 U
D14I 4 14 15.63 10.33 I
D14U 4 14 15.63 14.09 U
D17I 3 17 19.15 7.28 I
D17U 3 17 19.15 13.81 U
D21I 4 21 23.23 6.55 I
D21U 4 21 23.23 13.76 U
D24I 3 24 26.60 3.76 I
D24U 3 24 26.60 13.46 U
D28I 4 28 30.61 6.20 I
D28U 4 28 30.61 13.30 U