Rv0238 Transcriptional regulator, TetR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv0238 Transcriptional regulator, TetR family CDS 288428 289042 + 615 204 TRUE

Rv0238 (Transcriptional regulator, TetR family) is predicted to be co-regulated in modules bicluster_0030 with residual 0.60 and bicluster_0060 with residual 0.34.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.05 and 0.81 for bicluster_0030 and 1,700.00 and 1,700.00 for bicluster_0060 respectively.

These modules are enriched for following go terms: single-organism metabolic process, single-organism cellular process, biosynthetic process, cellular nitrogen compound metabolic pro..., nitrogen compound metabolic process, membrane part .

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 6 of 6
Gene Target Differential Expression Distance Expression pvalue Type
3-oxoacyl-[acyl-carrier protein] reductase (EC 1.1.1.100)
Repressed -14 -1.15 0.00000801 Primary.TSS
3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)
Repressed -34 -1.07 0.00000229 Primary.TSS
Electron transfer flavoprotein, beta subunit
Repressed 13 -0.74 0.0000000482 Primary.TSS
Methyltransferase (EC 2.1.1.-)
Repressed -139 -0.9 0.000078 Primary.TSS
COG1180: Radical SAM, Pyruvate-formate lyase-activating enzyme like
No 35 -0.65 0.112464 Antisense.TSS
Acyl-CoA dehydrogenase, short-chain specific (EC 1.3.99.2)
Repressed -16 -2.04 0.000000000152 Primary.TSS
Displaying 1 - 2 of 2
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, TetR family
No 47 -0.43 0.54078 Primary.TSS
Transcriptional regulator, TetR family
Repressed -7 -0.75 0.0234615 Primary.TSS
Product (LegacyBRC) Product (RefSeq)
POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN [PROBABLY TETR-FAMILY] TetR family transcriptional regulator
Operon # Operon
166
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
15607379 NP_214752.1 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 GSM1426437 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426438 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426439 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0238_B407 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.580000 1.27

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: 0.000000857254
p-value INH: 0.988908
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 14.57 U
D3I 3 3 3.83 14.72 I
D3U 3 3 3.83 14.91 U
D5I 9 5 6.00 14.29 I
D5U 17 5 6.00 13.92 U
D7I 18 7 8.14 15.83 I
D7U 19 7 8.14 14.52 U
D14I 4 14 15.63 15.16 I
D14U 4 14 15.63 13.47 U
D17I 3 17 19.15 14.83 I
D17U 3 17 19.15 12.70 U
D21I 4 21 23.23 15.32 I
D21U 4 21 23.23 13.22 U
D24I 3 24 26.60 15.11 I
D24U 3 24 26.60 12.53 U
D28I 4 28 30.61 15.58 I
D28U 4 28 30.61 12.85 U