Rv3208 Transcriptional regulator, TetR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv3208 Transcriptional regulator, TetR family CDS 3585004 3585690 + 687 228 FALSE

Rv3208 (Transcriptional regulator, TetR family) is predicted to be co-regulated in modules bicluster_0229 with residual 0.54 and bicluster_0244 with residual 0.55.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 170.00 and 860.00 for bicluster_0229 and 0.00 and 0.00 for bicluster_0244 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 1 of 1
Gene Target Differential Expression Distance Expression pvalue Type
No results were found
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
No results were found
Motif 1 Motif 2 Residual
bicluster_0229
e.value: 
170
Motif Bicluster: 
e.value: 
860
Motif Bicluster: 
0.54
bicluster_0244
e.value: 
0.00000047
Motif Bicluster: 
e.value: 
0.00000089
Motif Bicluster: 
0.55
Product (LegacyBRC) Product (RefSeq)
PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN [PROBABLY TETR-FAMILY] TetR family transcriptional regulator
Operon # Operon
2095
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
15610344 NP_217724.1 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 GSM1426948 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426949 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426950 GSE59086 25232098 GEO Tiling Array RNA
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: 0.00222263
p-value INH: 0.275581
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 12.37 U
D3I 3 3 3.83 12.18 I
D3U 3 3 3.83 11.77 U
D5I 9 5 6.00 13.40 I
D5U 17 5 6.00 13.17 U
D7I 18 7 8.14 12.49 I
D7U 19 7 8.14 11.98 U
D14I 4 14 15.63 10.90 I
D14U 4 14 15.63 10.89 U
D17I 3 17 19.15 9.76 I
D17U 3 17 19.15 10.28 U
D21I 4 21 23.23 10.01 I
D21U 4 21 23.23 10.65 U
D24U 3 24 26.60 9.87 U
D24I 3 24 26.60 9.13 I
D28I 4 28 30.61 9.52 I
D28U 4 28 30.61 10.37 U