Rv1049 Organic hydroperoxide resistance transcriptional regulator

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv1049 Organic hydroperoxide resistance transcriptional regulator CDS 1172386 1172832 + 447 148 TRUE

Rv1049 (Organic hydroperoxide resistance transcriptional regulator) is predicted to be co-regulated in modules bicluster_0283 with residual 0.50 and bicluster_0361 with residual 0.58.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.01 and 1.50 for bicluster_0283 and 0.00 and 0.14 for bicluster_0361 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 130
Gene Target Differential Expression Distance Expression pvalue Type
DNA gyrase subunit A (EC 5.99.1.3)
No 69 0.23 0.225915 CDS
No -130 -0.03 0.950999 Primary.TSS
2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29)
No -41 -0.11 0.888304 Primary.TSS
No -134 0.5 0.0807394 Internal.TSS
No -74 0.5 0.0807394 Internal.TSS
Replicative DNA helicase (EC 3.6.1.-) @ intein-containing
No -74 0.08 0.831439 Primary.TSS
Probable cation-transporting ATPase I (EC 3.6.3.-)
No 14 -0.11 0.778749 CDS
epoxide hydrolase
No -50 0.07 0.788004 Primary.TSS
Transcriptional regulator, TetR family
No -11 -0.48 0.00929958 Internal.TSS
No -59 -0.3 0.0995112 Primary.TSS
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
Organic hydroperoxide resistance transcriptional regulator
Induced -45 4.59 1.14e-39 Primary.TSS
Product (LegacyBRC) Product (RefSeq)
PROBABLE TRANSCRIPTIONAL REPRESSOR PROTEIN transcriptional repressor protein
Operon # Operon
703
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
15608189 NP_215565.1 Run
GO:0005829

cytosol

cytosol

Details: 
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO Category: 
cellular_component
371
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 GSM1426611 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426612 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426613 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426611 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426612 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426613 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv1049_B341 UCSC Browser Tracks
Rv1049_B401 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.420000 1.46

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: 0.00000000199904
p-value INH: 0.0478283
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 11.16 U
D3I 3 3 3.83 10.84 I
D3U 3 3 3.83 10.40 U
D5U 17 5 6.00 11.58 U
D5I 9 5 6.00 9.28 I
D7I 18 7 8.14 7.74 I
D7U 19 7 8.14 10.82 U
D14I 4 14 15.63 3.03 I
D14U 4 14 15.63 9.41 U
D17I 3 17 19.15 2.28 I
D17U 3 17 19.15 9.07 U
D21I 4 21 23.23 2.16 I
D21U 4 21 23.23 8.91 U
D24I 3 24 26.60 2.33 I
D24U 3 24 26.60 8.95 U
D28I 4 28 30.61 1.11 I
D28U 4 28 30.61 8.77 U