Rv3058c Transcriptional regulator, TetR family

Summary

Product Feature Type Start End Strand Length AA Length is TF
Rv3058c Transcriptional regulator, TetR family CDS 3418726 3419376 - 651 216 TRUE

Rv3058c (Transcriptional regulator, TetR family) is predicted to be co-regulated in modules bicluster_0298 with residual 0.51 and bicluster_0433 with residual 0.52.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 0.69 for bicluster_0298 and 0.00 and 0.00 for bicluster_0433 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?: Yes

Last update: 11/20/2020 - 12:12
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-14980 MT3144 398
Displaying 1 - 1 of 1
Gene Target Differential Expression Distance Expression pvalue Type
POSSIBLE LIPOPROTEIN LPQQ
No 32 0.41 0.118686 Primary.TSS
Displaying 1 - 2 of 2
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, ArsR family
Repressed 39 -1.9 0 Primary.TSS
No -31 -0.46 0.0422255 Primary.TSS
Product (LegacyBRC) Product (RefSeq)
POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN [PROBABLY TETR-FAMILY] TetR family transcriptional regulator
Operon # Operon
2002
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
15610195 NP_217574.1 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 GSM1426901 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426902 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426903 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3058c_B633 UCSC Browser Tracks

Quantitative Proteomics Data

t-test p-value Cholesterol/Glycerol Ratio
0.260000 0.56

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: 0.00000000000103042
p-value INH: 0.860973
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 12.63 U
D3I 3 3 3.83 12.52 I
D3U 3 3 3.83 12.13 U
D5I 9 5 6.00 10.53 I
D5U 17 5 6.00 12.58 U
D7I 18 7 8.14 9.43 I
D7U 19 7 8.14 13.17 U
D14I 4 14 15.63 10.02 I
D14U 4 14 15.63 12.05 U
D17I 3 17 19.15 3.15 I
D17U 3 17 19.15 11.66 U
D21I 4 21 23.23 5.48 I
D21U 4 21 23.23 12.02 U
D24I 3 24 26.60 I
D24U 3 24 26.60 11.61 U
D28I 4 28 30.61 5.63 I
D28U 4 28 30.61 12.00 U