Rv1776c Transcriptional regulator, TetR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv1776c Transcriptional regulator, TetR family CDS 2009995 2010555 - 561 186 TRUE

Rv1776c (Transcriptional regulator, TetR family) is predicted to be co-regulated in modules bicluster_0160 with residual 0.59 and bicluster_0332 with residual 0.53.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.01 and 5,000.00 for bicluster_0160 and 0.02 and 590.00 for bicluster_0332 respectively.

These modules are enriched for following go terms: purine nucleotide biosynthetic process, purine nucleotide metabolic process, purine-containing compound biosynthetic ....

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 29
Gene Target Differential Expression Distance Expression pvalue Type
DNA polymerase III beta subunit (EC 2.7.7.7)
No -13 0.09 0.861457 Primary.TSS
No -116 0.28 0.377159 Primary.TSS
2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29)
No -13 0.05 0.956681 Primary.TSS
Proline-rich 28 kDa antigen
No -85 -0.46 0.181544 Primary.TSS
No 31 -0.51 0.0346309 Primary.TSS
ADP-ribose 1-phosphate phophatase related protein
No -39 0.05 0.918073 Primary.TSS
Oxidoreductase
No -5 0 0.99851 CDS
No -108 -0.01 0.997101 CDS
Phosphoheptose isomerase (EC 5.3.1.-)
No -25 -0.27 0.643054 CDS
Possible membrane protein
No -147 -0.22 0.726421 CDS
Displaying 1 - 2 of 2
ChipSeq TF Differential Expression Distance Expression pvalue Type
Possible oxidoreductase subunit
No 4 -0.56 0.00301764 Primary.TSS
Two component DNA binding Transcriptional regulatory protein TcrA
Repressed 9 -0.64 0.0144308 Primary.TSS
Product (LegacyBRC) Product (RefSeq)
POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN transcriptional regulatory protein
Operon # Operon
1160
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
15608914 NP_216292.1 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 GSM1426723 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426724 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426725 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv1776c_B459 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.890000 2.19

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: 0.00000000222975
p-value INH: 0.863117
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 11.32 U
D3I 3 3 3.83 10.57 I
D3U 3 3 3.83 10.99 U
D5I 9 5 6.00 7.59 I
D5U 17 5 6.00 9.96 U
D7I 18 7 8.14 7.88 I
D7U 19 7 8.14 11.07 U
D14I 4 14 15.63 2.57 I
D14U 4 14 15.63 9.96 U
D17I 3 17 19.15 I
D17U 3 17 19.15 9.94 U
D21I 4 21 23.23 2.50 I
D21U 4 21 23.23 8.61 U
D24I 3 24 26.60 1.96 I
D24U 3 24 26.60 8.97 U
D28I 4 28 30.61 1.56 I
D28U 4 28 30.61 7.65 U