Rv0818 Phosphate regulon transcriptional regulatory protein PhoB (SphR)

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv0818 Phosphate regulon transcriptional regulatory protein PhoB (SphR) CDS 910972 911739 + 768 255 TRUE

Rv0818 (Phosphate regulon transcriptional regulatory protein PhoB (SphR)) is predicted to be co-regulated in modules bicluster_0509 with residual 0.59 and bicluster_0558 with residual 0.61.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 53.00 and 2,600.00 for bicluster_0509 and 0.00 and 0.69 for bicluster_0558 respectively.

These modules are enriched for following go terms: response to stress, S-methyltransferase activity, O-acyltransferase activity.

This gene is found to be for growth on cholesterol.

Mutant available?:

BASS Score Distance to Tuberculist Start Codon Internal TSS New Internal UTR New Primary UTR Primary TSS Re-Annotated Start Tuberculist Annotated Start
-0.323 47 911019 -44 37 910938 910975 910972
Displaying 1 - 10 of 16
Gene Target Differential Expression Distance Expression pvalue Type
Hydrolase
No -57 -0.21 0.428538 Primary.TSS
3-methylmercaptopropionyl-CoA dehydrogenase (DmdC)
Repressed -3 -2 0.00000523 Primary.TSS
Nitrilotriacetate monooxygenase component B (EC 1.14.13.-)
No 22 -0.31 0.220251 Primary.TSS
Nitrite reductase [NAD(P)H] large subunit (EC 1.7.1.4)
Induced -64 3.85 8.41e-40 CDS
POSSIBLE MYCOLIC ACID SYNTHASE UMAA1
No -1 -0.29 0.228551 Primary.TSS
UDP-glucose 4-epimerase (EC 5.1.3.2)
Induced -21 1.2 1.28e-24 Primary.TSS
Methylmalonyl-CoA epimerase (EC 5.1.99.1); Ethylmalonyl-CoA epimerase
Repressed -34 -2.05 3.52e-29 Primary.TSS
PE family protein
Repressed -75 -3.25 1.71e-41 CDS
Cyanoglobin; Hemoglobin-like protein HbN
Induced 15 6.04 0 CDS
PE FAMILY PROTEIN
Induced 29 1.43 0.00000000403 Primary.TSS
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
No results were found
Motif 1 Motif 2 Residual
bicluster_0509
e.value: 
53
Motif Bicluster: 
e.value: 
2600
Motif Bicluster: 
0.59
bicluster_0558
e.value: 
0.00041
Motif Bicluster: 
e.value: 
0.69
Motif Bicluster: 
0.61
Product (LegacyBRC) Product (RefSeq)
TRANSCRIPTIONAL REGULATORY PROTEIN transcriptional regulatory protein
Operon # Operon
541 -
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
15607958 NP_215333.1 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:  
GO:0042128

nitrate assimilation

nitrate assimilation

Details: 
The nitrogen metabolic process that encompasses the uptake of nitrate from the environment and reduction to ammonia, and results in the incorporation of nitrogen derived from nitrate into cellular substances.
GO Category: 
biological_process
3
Total items in this category:  
GO:0045893

positive regulation of transcription, DNA-dependent

positive regulation of transcription, DNA-dependent

Details: 
Any process that activates or increases the frequency, rate or extent of cellular DNA-dependent transcription.
GO Category: 
biological_process
14
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 GSM1426564 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426565 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426566 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0818_B610 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.700000 1.05

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: 0.000000000350584
p-value INH: 0.0355616
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 14.51 U
D3I 3 3 3.83 14.18 I
D3U 3 3 3.83 13.69 U
D5I 9 5 6.00 11.26 I
D5U 17 5 6.00 14.39 U
D7I 18 7 8.14 10.31 I
D7U 19 7 8.14 14.59 U
D14I 4 14 15.63 4.41 I
D14U 4 14 15.63 14.95 U
D17I 3 17 19.15 3.55 I
D17U 3 17 19.15 16.10 U
D21I 4 21 23.23 3.35 I
D21U 4 21 23.23 14.02 U
D24I 3 24 26.60 3.10 I
D24U 3 24 26.60 16.22 U
D28I 4 28 30.61 2.64 I
D28U 4 28 30.61 14.05 U