Rv1189 putative RNA polymerase sigma factor

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv1189 sigI putative RNA polymerase sigma factor CDS 1332092 1332964 + 873 290 TRUE

Rv1189 (putative RNA polymerase sigma factor) is predicted to be co-regulated in modules bicluster_0151 with residual 0.47 and bicluster_0299 with residual 0.50.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 3,500.00 and 12,000.00 for bicluster_0151 and 0.00 and 48.00 for bicluster_0299 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 19
Gene Target Differential Expression Distance Expression pvalue Type
Serine hydroxymethyltransferase (EC 2.1.2.1)
No -120 0.32 0.692661 Primary.TSS
No -85 0.43 0.442326 Primary.TSS
Isocitrate lyase (EC 4.1.3.1) / Methylisocitrate lyase (EC 4.1.3.30)
No -66 -0.6 0.49522 Primary.TSS
DNA-directed RNA polymerase beta subunit (EC 2.7.7.6)
No -21 -0.01 0.987523 Primary.TSS
No -91 -0.41 0.514171 CDS
No -17 0.21 0.87899 Antisense.TSS
Probable phiRv1 integrase
No 18 -0.31 0.719287 Internal.TSS
Probable phiRv1 integrase
No 0 -0.31 0.719287 CDS
Partial REP13E12 repeat protein
No -1 -0.3 0.571125 Antisense.TSS
Chalcone synthase (EC 2.3.1.74)
No -59 -0.24 0.675824 Primary.TSS
Product (LegacyBRC) Product (RefSeq)
POSSIBLE ALTERNATIVE RNA POLYMERASE SIGMA FACTOR SIGI RNA polymerase sigma factor SigI
Operon # Operon
809 -
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
15608329 NP_215705.1 Run
GO:0009409

response to cold

response to cold

Details: 
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cold stimulus, a temperature stimulus below the optimal temperature for that organism.
GO Category: 
biological_process
3
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 GSM1426634 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426635 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426636 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426634 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426635 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426636 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv1189_B435 UCSC Browser Tracks
Rv1189_B553 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.260000 0.80

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: 0.00546197
p-value INH: 0.0355616
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 15.40 U
D3I 3 3 3.83 15.76 I
D3U 3 3 3.83 15.98 U
D5I 9 5 6.00 16.49 I
D5U 17 5 6.00 16.32 U
D7I 18 7 8.14 15.67 I
D7U 19 7 8.14 15.23 U
D14I 4 14 15.63 14.56 I
D14U 4 14 15.63 14.81 U
D17I 3 17 19.15 12.99 I
D17U 3 17 19.15 14.11 U
D21I 4 21 23.23 13.49 I
D21U 4 21 23.23 14.58 U
D24I 3 24 26.60 11.83 I
D24U 3 24 26.60 13.96 U
D28I 4 28 30.61 12.70 I
D28U 4 28 30.61 14.25 U