Rv3246c DNA-binding response regulator mtrA

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3246c mtrA DNA-binding response regulator mtrA CDS 3626663 3627349 - 687 228 TRUE

Rv3246c (DNA-binding response regulator mtrA) is predicted to be co-regulated in modules bicluster_0316 with residual 0.52 and bicluster_0393 with residual 0.48.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.49 and 70.00 for bicluster_0316 and 0.00 and 14.00 for bicluster_0393 respectively.

These modules are enriched for following go terms: nucleotide biosynthetic process, nucleoside phosphate biosynthetic proces..., nucleotide metabolic process, hydroxymethyl-, formyl- and related tran... .

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 82
Gene Target Differential Expression Distance Expression pvalue Type
Proline-rich 28 kDa antigen
No 48 0.28 0.657558 Primary.TSS
Leucyl-tRNA synthetase (EC 6.1.1.4)
No -104 0.07 0.930314 Primary.TSS
Phosphoheptose isomerase (EC 5.3.1.-)
No -148 0.05 0.973722 CDS
Possible membrane protein
No -45 0.09 0.927176 Primary.TSS
Antigen 85-C precursor (85C) (Antigen 85 complex C) (Ag85C) (Mycolyl transferase 85C) (EC 2.3.1.-)
No 66 -0.03 0.977699 Primary.TSS
Probable enoyl-CoA hydratase 1 (EC 4.2.1.17)
No -111 0.36 0.750174 Primary.TSS
Possible lipoprotein LprO
No 58 0.15 0.792925 Primary.TSS
PROBABLE CONSERVED TRANSMEMBRANE PROTEIN
No -2 0.14 0.856043 CDS
tRNA (guanine46-N7-)-methyltransferase (EC 2.1.1.33)
No 29 0.35 0.30427 Internal.TSS
tRNA (guanine46-N7-)-methyltransferase (EC 2.1.1.33)
No 11 0.35 0.30427 CDS
Displaying 1 - 6 of 6
ChipSeq TF Differential Expression Distance Expression pvalue Type
Beta-carotene ketolase (EC 1.14.-.-)
No 19 0.01 0.999473 Internal.TSS
Transcriptional regulator, TetR family
No -88 0.2 0.605928 Internal.TSS
DNA-binding response regulator mtrA
No 14 0.52 0.190415 Internal.TSS
Transcriptional regulator, AsnC family
No 30 -0.47 0.124339 CDS
Transcriptional regulator, AsnC family
No 39 -0.47 0.124339 Internal.TSS
Beta-carotene ketolase (EC 1.14.-.-)
No 10 0.01 0.999473 CDS
Motif 1 Motif 2 Residual
bicluster_0316
e.value: 
0.49
Motif Bicluster: 
e.value: 
70
Motif Bicluster: 
0.52
bicluster_0393
e.value: 
0.00043
Motif Bicluster: 
e.value: 
14
Motif Bicluster: 
0.48
Product (LegacyBRC) Product (RefSeq)
Rv3246c two component sensory transduction transcriptional regulatory protein MTRA
Operon # Operon
2125
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
15610382 NP_217763.1 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:0006468

protein phosphorylation

protein phosphorylation

Details: 
The process of introducing a phosphate group on to a protein.
GO Category: 
biological_process
2
Total items in this category:  
GO:0044117

growth of symbiont in host

growth of symbiont in host

Details: 
The increase in size or mass of an organism, occurring within the cells or tissues of the host organism. This may (but not necessarily) include a filamentous growth form, and also can include secretion of proteases and lipases to break down host tissue. The host is defined as the larger of the organisms involved in a symbiotic interaction.
GO Category: 
biological_process
36
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 GSM1426957 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426958 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426959 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3246c_B208 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
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.

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: 0.0686262
p-value INH: 0.873582
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D3I 3 3 3.83 13.01 I
D5I 9 5 6.00 13.63 I
D7I 18 7 8.14 13.33 I
D14I 4 14 15.63 13.86 I
D17I 3 17 19.15 13.69 I
D21I 4 21 23.23 13.56 I
D24I 3 24 26.60 12.96 I
D28I 4 28 30.61 13.07 I
D0U 27 0 0.00 13.04 U
D3U 3 3 3.83 13.45 U
D5U 17 5 6.00 13.32 U
D7U 19 7 8.14 13.14 U
D14U 4 14 15.63 13.31 U
D17U 3 17 19.15 13.48 U
D21U 4 21 23.23 13.32 U
D24U 3 24 26.60 13.07 U
D28U 4 28 30.61 12.83 U