Rv1404 Transcriptional regulator, MarR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv1404 Transcriptional regulator, MarR family CDS 1580591 1581073 + 483 160 TRUE

Rv1404 (Transcriptional regulator, MarR family) is predicted to be co-regulated in modules bicluster_0434 with residual 0.58 and bicluster_0487 with residual 0.48.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 0.00 for bicluster_0434 and 0.00 and 3.50 for bicluster_0487 respectively.

These modules are enriched for following go terms: cellular macromolecule catabolic process, cellular protein metabolic process, coenzyme biosynthetic process, cofactor biosynthetic process .

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 48
Gene Target Differential Expression Distance Expression pvalue Type
FIG018426: putative septation inhibitor protein
No -89 0.06 0.94572 Primary.TSS
FIG215594: Membrane spanning protein
No -71 -0.16 0.671562 Primary.TSS
Single-stranded DNA-binding protein
No -9 0.16 0.818339 CDS
Transcriptional regulator, LuxR family
No -2 -0.22 0.706417 Primary.TSS
3-methylmercaptopropionyl-CoA dehydrogenase (DmdC)
No 58 -0.73 0.449138 Primary.TSS
POSSIBLE MYCOLIC ACID SYNTHASE UMAA1
No 8 -0.39 0.382875 Primary.TSS
Transcriptional regulator, ArsR family
No -75 0.36 0.282708 Primary.TSS
Mycofactocin system heme/flavin dehydrogenase
No -12 -0.01 0.98857 Antisense.TSS
PE-PGRS virulence associated protein
Repressed -55 -1.82 0.000000634 CDS
PE-PGRS FAMILY PROTEIN
Repressed 25 -1.2 0.0114134 Primary.TSS
Displaying 1 - 3 of 3
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, MarR family
Induced -48 1.41 7.34e-18 Primary.TSS
DNA-binding response regulator TrcR
No -31 -0.1 0.860458 Primary.TSS
No 42 -0.25 0.999609 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0434
e.value: 
0.0000018
Motif Bicluster: 
e.value: 
0.000029
Motif Bicluster: 
0.58
bicluster_0487
e.value: 
0.0000000000079
Motif Bicluster: 
e.value: 
3.5
Motif Bicluster: 
0.48
Product (LegacyBRC) Product (RefSeq)
PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN transcriptional regulatory protein
Operon # Operon
942
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
15608542 NP_215920.1 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:  
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 GSM1426673 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426674 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426675 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv1404_B440 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: 0.0000427602
p-value INH: 0.182577
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 12.35 U
D3I 3 3 3.83 12.55 I
D3U 3 3 3.83 12.22 U
D5I 9 5 6.00 11.38 I
D5U 17 5 6.00 11.81 U
D7I 18 7 8.14 11.25 I
D7U 19 7 8.14 12.46 U
D14I 4 14 15.63 6.98 I
D14U 4 14 15.63 11.85 U
D17I 3 17 19.15 3.95 I
D17U 3 17 19.15 11.53 U
D21I 4 21 23.23 9.54 I
D21U 4 21 23.23 11.65 U
D24I 3 24 26.60 2.50 I
D24U 3 24 26.60 11.47 U
D28I 4 28 30.61 4.03 I
D28U 4 28 30.61 11.43 U