Rv1460 Iron-sulfur cluster regulator SufR

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv1460 Iron-sulfur cluster regulator SufR CDS 1646186 1646992 + 807 268 TRUE

Rv1460 (Iron-sulfur cluster regulator SufR) is predicted to be co-regulated in modules bicluster_0446 with residual 0.47 and bicluster_0485 with residual 0.51.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 1,700.00 and 5,500.00 for bicluster_0446 and 0.00 and 0.07 for bicluster_0485 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?:

BASS Score Distance to Tuberculist Start Codon Internal TSS New Internal UTR Re-Annotated Start Tuberculist Annotated Start
-0.67 72 1646258 -120 1646138 1646186
Displaying 1 - 5 of 5
Gene Target Differential Expression Distance Expression pvalue Type
Programmed cell death toxin YdcE
No 57 0.07 0.965095 Primary.TSS
No results were found NA 57 Internal.TSS
No -58 0.23 0.856568 CDS
PE family protein
No -8 0.1 0.970855 Primary.TSS
Histone protein Lsr2
No 55 -0.19 0.85991 Primary.TSS
Displaying 1 - 6 of 6
ChipSeq TF Differential Expression Distance Expression pvalue Type
DNA-binding response regulator TrcR
No -67 0.38 0.338461 Internal.TSS
Phosphatidylinositol alpha-mannosyltransferase (EC 2.4.1.57)
NA -12 Internal.TSS
Mycofactocin system transcriptional regulator
No -22 -0.17 0.999588 Internal.TSS
DNA-binding response regulator TrcR
No 5 0.38 0.338461 CDS
Mycofactocin system transcriptional regulator
No 50 -0.17 0.999588 CDS
Phosphatidylinositol alpha-mannosyltransferase (EC 2.4.1.57)
NA 60 CDS
Product (LegacyBRC) Product (RefSeq)
PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN transcriptional regulatory protein
Operon # Operon
976 - - - - - -
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
57116868 NP_215976.2 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 GSM1426682 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426683 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426684 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv1460_B127 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.130000 0.01

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: 0.0282468
p-value INH: 0.832328
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 10.21 U
D3I 3 3 3.83 10.19 I
D3U 3 3 3.83 10.03 U
D5I 9 5 6.00 13.65 I
D5U 17 5 6.00 13.32 U
D7I 18 7 8.14 10.48 I
D7U 19 7 8.14 9.19 U
D14I 4 14 15.63 8.88 I
D14U 4 14 15.63 8.01 U
D17I 3 17 19.15 8.70 I
D17U 3 17 19.15 7.73 U
D21I 4 21 23.23 8.93 I
D21U 4 21 23.23 7.61 U
D24I 3 24 26.60 8.46 I
D24U 3 24 26.60 7.31 U
D28I 4 28 30.61 8.71 I
D28U 4 28 30.61 7.45 U