Rv0445c RNA polymerase sigma factor RpoE

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv0445c sigK RNA polymerase sigma factor RpoE CDS 533833 534396 - 564 187 TRUE

Rv0445c (RNA polymerase sigma factor RpoE) is predicted to be co-regulated in modules bicluster_0290 with residual 0.50 and bicluster_0415 with residual 0.48.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 58.00 and 8,200.00 for bicluster_0290 and 37.00 and 3,500.00 for bicluster_0415 respectively.

These modules are enriched for following go terms: response to stress.

This gene is found to be for growth on cholesterol.

Mutant available?: Yes

Last update: 11/20/2020 - 12:11
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-18196 MT0461 1698
Displaying 1 - 3 of 3
Gene Target Differential Expression Distance Expression pvalue Type
LSU ribosomal protein L30p (L7e)
No 11 0.13 0.956245 CDS
PE family protein
No -17 -0.27 0.966643 Primary.TSS
DNA-binding protein, CopG family
No 53 -0.15 0.969443 Primary.TSS
Product (LegacyBRC) Product (RefSeq)
RNA polymerase sigma factor sigK RNA polymerase sigma factor SigK
Operon # Operon
298
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics

PATRIC

Not assigned Not assigned
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

KEGG

RNA polymerase

17
Total items in this category:  
BioCyc Gene Page Cellular Overview Map
Link to STRING STRING Network

STRING

GI Number Protein ID Blast Conserved Domains
15607586 NP_214959.1 Run
GO:0005515

protein binding

protein binding

Details: 
Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
GO Category: 
molecular_function
135
Total items in this category:  
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 GSM1426477 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426478 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426479 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426477 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426478 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426479 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0445c_B418 UCSC Browser Tracks
Rv0445c_B533 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.350000 0.78

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: 0.0850813
p-value INH: 0.873582
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 8.65 U
D3I 3 3 3.83 7.49 I
D3U 3 3 3.83 6.47 U
D5I 9 5 6.00 7.12 I
D5U 17 5 6.00 7.09 U
D7I 18 7 8.14 7.97 I
D7U 19 7 8.14 7.51 U
D14I 4 14 15.63 4.51 I
D14U 4 14 15.63 4.12 U
D17I 3 17 19.15 2.57 I
D17U 3 17 19.15 2.27 U
D21I 4 21 23.23 4.19 I
D21U 4 21 23.23 4.91 U
D24I 3 24 26.60 3.08 I
D24U 3 24 26.60 U
D28I 4 28 30.61 4.85 I
D28U 4 28 30.61 4.52 U