Rv3173c Transcriptional regulator, TetR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv3173c Transcriptional regulator, TetR family CDS 3541443 3542045 - 603 200 TRUE

Rv3173c (Transcriptional regulator, TetR family) is predicted to be co-regulated in modules bicluster_0043 with residual 0.47 and bicluster_0069 with residual 0.54.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 0.01 for bicluster_0043 and 0.00 and 0.00 for bicluster_0069 respectively.

These modules are enriched for following go terms: nucleic acid binding transcription facto..., sequence-specific DNA binding transcript... .

This gene is found to be for growth on cholesterol.

Mutant available?:

BASS Score New Primary UTR Primary TSS Re-Annotated Start Tuberculist Annotated Start
-0.594 66 3542045 3541979 3542045
Displaying 1 - 8 of 8
Gene Target Differential Expression Distance Expression pvalue Type
Possible conserved exported protein
No -26 -0.5 0.708202 CDS
DNA-directed RNA polymerase beta subunit (EC 2.7.7.6)
No 2 0.02 0.975135 Primary.TSS
Transcriptional regulator, TetR family
Induced 45 1.79 1.95e-18 Primary.TSS
Putative oxidoreductase
No -12 -0.2 0.719634 Primary.TSS
Epoxide hydrolase (EC 3.3.2.9)
Repressed 32 -0.84 0.0237214 Primary.TSS
Hydrolase, alpha/beta fold family
No -14 -0.09 0.812018 Primary.TSS
ESX-1 secretion system protein (Rv3616c)
No -83 -0.15 0.882701 Primary.TSS
Antigen 85-C precursor (85C) (Antigen 85 complex C) (Ag85C) (Mycolyl transferase 85C) (EC 2.3.1.-)
No -60 0.17 0.883757 Primary.TSS
Displaying 1 - 2 of 2
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, TetR family
Induced 45 1.79 1.95e-18 Primary.TSS
No -39 0.12 0.999609 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0043
e.value: 
0.00000015
Motif Bicluster: 
e.value: 
0.0062
Motif Bicluster: 
0.47
bicluster_0069
e.value: 
0.0000000000000036
Motif Bicluster: 
e.value: 
0.0000025
Motif Bicluster: 
0.54
Product (LegacyBRC) Product (RefSeq)
PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN [PROBABLY TETR_ACRR-FAMILY] TetR/ACRR family transcriptional regulator
Operon # Operon
2067
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
15610309 NP_217689.1 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 GSM1426939 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426940 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426941 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3173c_B379 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.370000 3.59

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: 0.65748
p-value INH: 0.725941
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 13.88 U
D3I 3 3 3.83 13.69 I
D3U 3 3 3.83 13.31 U
D5I 9 5 6.00 14.84 I
D5U 17 5 6.00 14.63 U
D7I 18 7 8.14 13.28 I
D7U 19 7 8.14 13.24 U
D14I 4 14 15.63 7.43 I
D14U 4 14 15.63 13.26 U
D17I 3 17 19.15 5.05 I
D17U 3 17 19.15 12.93 U
D21I 4 21 23.23 4.04 I
D21U 4 21 23.23 12.77 U
D24I 3 24 26.60 2.98 I
D24U 3 24 26.60 12.83 U
D28I 4 28 30.61 2.89 I
D28U 4 28 30.61 12.54 U