Rv0042c Transcriptional regulator, MarR family

Summary

Product Feature Type Start End Strand Length AA Length is TF
Rv0042c Transcriptional regulator, MarR family CDS 46581 47207 - 627 208 TRUE

Rv0042c (Transcriptional regulator, MarR family) is predicted to be co-regulated in modules bicluster_0293 with residual 0.53 and bicluster_0511 with residual 0.52.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.01 and 0.78 for bicluster_0293 and 670.00 and 6,900.00 for bicluster_0511 respectively.

These modules are enriched for following go terms: phosphopantetheine binding, modified amino acid binding, amide binding, amino acid binding.

This gene is found to be for growth on cholesterol.

Mutant available?:

BASS Score Distance to Tuberculist Start Codon Internal TSS Re-Annotated Start Tuberculist Annotated Start
-0.8 123 47084 47084 47207
Displaying 1 - 4 of 4
Gene Target Differential Expression Distance Expression pvalue Type
GDP-mannose 4,6 dehydratase (EC 4.2.1.47)
No -58 -0.15 0.893668 Primary.TSS
O-Methyltransferase involved in polyketide biosynthesis
No 6 -0.43 0.519251 Primary.TSS
PE family protein
No -18 0.01 0.990747 Primary.TSS
PPE family protein
No 43 -0.57 0.433942 CDS
Displaying 1 - 6 of 6
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, TetR family
Repressed -87 -0.65 0.00416848 CDS
Two component transcriptional regulatory protein DevR
No 65 -0.4 0.00134156 Internal.TSS
Transcriptional regulator, TetR family
Repressed 36 -0.65 0.00416848 Internal.TSS
Two component transcriptional regulatory protein DevR
No -58 -0.4 0.00134156 CDS
Transcriptional regulator, MerR family
No 16 0.03 0.979622 CDS
Beta-carotene ketolase (EC 1.14.-.-)
No 18 0.15 0.999473 CDS
Product (LegacyBRC) Product (RefSeq)
POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN [PROBABLY MARR-FAMILY] MarR family transcriptional regulator
Operon # Operon
27
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
15607184 NP_214556.1 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 GSM1426381 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426382 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426383 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0042c_B391 UCSC Browser Tracks

Quantitative Proteomics Data

t-test p-value Cholesterol/Glycerol Ratio
0.440000 0.77

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: 0.992639
p-value INH: 0.520276
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 11.92 U
D3I 3 3 3.83 11.64 I
D3U 3 3 3.83 12.19 U
D5I 9 5 6.00 10.74 I
D5U 17 5 6.00 10.62 U
D7I 18 7 8.14 11.79 I
D7U 19 7 8.14 11.76 U
D14I 4 14 15.63 11.92 I
D14U 4 14 15.63 12.15 U
D17I 3 17 19.15 12.05 I
D17U 3 17 19.15 12.55 U
D21I 4 21 23.23 11.82 I
D21U 4 21 23.23 12.43 U
D24I 3 24 26.60 11.15 I
D24U 3 24 26.60 12.41 U
D28I 4 28 30.61 11.26 I
D28U 4 28 30.61 12.14 U