Rv1453

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv1453 CDS 1638381 1639646 + 1 266 421 FALSE

Rv1453 () is predicted to be co-regulated in modules bicluster_0008 with residual 0.62 and bicluster_0430 with residual 0.49.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 0.00 for bicluster_0008 and 2,000.00 and 5,600.00 for bicluster_0430 respectively.

These modules are enriched for following go terms: primary metabolic process, cellular metabolic process, cellular process, organic substance metabolic process.

This gene is found to be for growth on cholesterol.

Mutant available?: Yes

BASS Score Distance to Tuberculist Start Codon Internal TSS New Primary UTR Primary TSS Re-Annotated Start Tuberculist Annotated Start
-0.115 1074 1639455 123 1638225 1638348 1638381
Last update: 11/20/2020 - 12:11
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-15046 MT1500 1245
Product (LegacyBRC) Product (RefSeq)
POSSIBLE TRANSCRIPTIONAL ACTIVATOR PROTEIN transcriptional activator protein
Operon # Operon
970
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics
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
57116867 NP_215969.2 Run
GO:0005618

cell wall

cell wall

Details: 
The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan.
GO Category: 
cellular_component
320
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 GSM1426679 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426680 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426681 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv1453_B443 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.560000 1.18

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: 0.733065
p-value INH: 0.832328
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 12.52 U
D7U 19 7 8.14 13.03 U
D7I 18 7 8.14 13.21 I
D5U 17 5 6.00 15.12 U
D5I 9 5 6.00 15.08 I
D14I 4 14 15.63 10.28 I
D14U 4 14 15.63 11.41 U
D21I 4 21 23.23 9.34 I
D21U 4 21 23.23 11.62 U
D28I 4 28 30.61 8.36 I
D28U 4 28 30.61 12.07 U
D17I 3 17 19.15 9.56 I
D17U 3 17 19.15 11.26 U
D24I 3 24 26.60 8.41 I
D24U 3 24 26.60 11.50 U
D3I 3 3 3.83 12.89 I
D3U 3 3 3.83 12.67 U