Rv0967

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv0967 csoR CDS 1077975 1078334 + 360 119 TRUE

Rv0967 () is predicted to be co-regulated in modules bicluster_0053 with residual 0.49 and bicluster_0389 with residual 0.58.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 3.20 and 1,200.00 for bicluster_0053 and 0.00 and 0.02 for bicluster_0389 respectively.

These modules are enriched for following go terms: mitochondrial electron transport, NADH t..., mitochondrial ATP synthesis coupled elec....

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 186
Gene Target Differential Expression Distance Expression pvalue Type
No -24 0.08 0.999609 CDS
Multimodular transpeptidase-transglycosylase (EC 2.4.1.129) (EC 3.4.-.-)
No -116 0.14 0.999609 CDS
Possible membrane protein
No 65 -0.07 0.999609 Primary.TSS
Hydrogen peroxide-inducible genes activator
No -53 -0.19 0.999609 Primary.TSS
Trehalose synthase (EC 5.4.99.16)
No 33 0.04 0.999609 Primary.TSS
NAD(P) transhydrogenase alpha subunit (EC 1.6.1.2)
No 22 0.19 0.999609 CDS
Possible membrane protein
No -73 -0.04 0.999609 Primary.TSS
Glycosyltransferase (EC 2.4.1.-)
Repressed 56 -1.31 5.99e-26 Primary.TSS
Possible membrane protein
No 45 0.1 0.999609 CDS
Acyl-CoA dehydrogenase, short-chain specific (EC 1.3.99.2)
No -94 -0.15 0.999609 Primary.TSS
Displaying 1 - 3 of 3
ChipSeq TF Differential Expression Distance Expression pvalue Type
Phosphatidylinositol alpha-mannosyltransferase (EC 2.4.1.57)
NA -66 Primary.TSS
transcriptional regulator, ArsR family
Induced -90 1.43 0.000000000464 Primary.TSS
Transcriptional regulator, AsnC family
No 69 -0.13 0.947396 Primary.TSS
Product (LegacyBRC) Product (RefSeq)
Copper-sensing transcriptional repressor csoR
Operon # Operon
646
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
15608107 NP_215482.1 Run
GO:0003677

DNA binding

DNA binding

Details: 
Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid).
GO Category: 
molecular_function
37
Total items in this category:  
GO:0005507

copper ion binding

copper ion binding

Details: 
Interacting selectively and non-covalently with copper (Cu) ions.
GO Category: 
molecular_function
2
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:  
GO:0010272

response to silver ion

response to silver ion

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 silver ion stimulus.
GO Category: 
biological_process
1
Total items in this category:  
GO:0042803

protein homodimerization activity

protein homodimerization activity

Details: 
Interacting selectively and non-covalently with an identical protein to form a homodimer.
GO Category: 
molecular_function
83
Total items in this category:  
GO:0046688

response to copper ion

response to copper ion

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 copper ion stimulus.
GO Category: 
biological_process
5
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 GSM1426593 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426594 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426595 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0967_B386 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.250000 0.24

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: 0.308039
p-value INH: 0.988908
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 10.92 U
D3I 3 3 3.83 10.17 I
D3U 3 3 3.83 10.03 U
D5I 9 5 6.00 11.01 I
D5U 17 5 6.00 10.79 U
D7I 18 7 8.14 10.18 I
D7U 19 7 8.14 9.74 U
D14I 4 14 15.63 7.85 I
D14U 4 14 15.63 8.17 U
D17I 3 17 19.15 6.98 I
D17U 3 17 19.15 7.23 U
D21I 4 21 23.23 7.38 I
D21U 4 21 23.23 7.69 U
D24I 3 24 26.60 5.64 I
D24U 3 24 26.60 6.84 U
D28I 4 28 30.61 6.75 I
D28U 4 28 30.61 7.10 U