Rv2009

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv2009 vapB15 CDS 2258030 2258272 + 243 80 TRUE

Rv2009 () is predicted to be co-regulated in modules bicluster_0129 with residual 0.53 and bicluster_0304 with residual 0.58.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 2.40 for bicluster_0129 and 0.36 and 78.00 for bicluster_0304 respectively.

These modules are enriched for following go terms: cellular ketone metabolic process.

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 15
Gene Target Differential Expression Distance Expression pvalue Type
No -111 -0.09 0.999734 Primary.TSS
FIG030769: Probable conserved MCE associated membrane protein
No -118 0.01 0.999734 Primary.TSS
Possible lipoprotein LprO
No 68 0.1 0.999734 Primary.TSS
Glycerophosphoryl diester phosphodiesterase (EC 3.1.4.46)
No -60 -0.03 0.999734 Primary.TSS
lipoprotein, putative
No 67 0.16 0.999734 CDS
PPE family protein
No 6 0.08 0.999734 CDS
Type VII secretion integral membrane protein EccD
No -62 0.03 0.999734 Primary.TSS
No -9 0.53 0.999734 CDS
No -24 0.53 0.999734 Internal.TSS
Toxin 1, PIN domain
Induced -24 1.05 0.00797688 Primary.TSS
Displaying 1 - 6 of 6
ChipSeq TF Differential Expression Distance Expression pvalue Type
No -9 0.53 0.999734 CDS
DNA-binding response regulator TrcR
No -19 0.13 0.907943 Internal.TSS
No -24 0.53 0.999734 Internal.TSS
DNA-binding response regulator TrcR
No -4 0.13 0.907943 CDS
transcriptional regulator, ArsR family
No -16 0.37 0.0835178 Internal.TSS
transcriptional regulator, ArsR family
No -1 0.37 0.0835178 CDS
Motif 1 Motif 2 Residual
bicluster_0129
e.value: 
0.0000044
Motif Bicluster: 
e.value: 
2.4
Motif Bicluster: 
0.53
bicluster_0304
e.value: 
0.36
Motif Bicluster: 
e.value: 
78
Motif Bicluster: 
0.58
Product (LegacyBRC) Product (RefSeq)
Uncharacterized protein Rv2009_MT20641
Operon # Operon
1319 -
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
15609146 NP_216525.1 Run
GO:0001666

response to hypoxia

response to hypoxia

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 stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
GO Category: 
biological_process
37
Total items in this category:  
GO:0045927

positive regulation of growth

positive regulation of growth

Details: 
Any process that activates or increases the rate or extent of growth, the increase in size or mass of all or part of an organism.
GO Category: 
biological_process
31
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 GSM1426771 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426772 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426773 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv2009_B368 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.950000 1.23

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: 0.00102776
p-value INH: 0.0235794
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 13.58 U
D3I 3 3 3.83 13.92 I
D3U 3 3 3.83 13.75 U
D5I 9 5 6.00 12.63 I
D5U 17 5 6.00 12.27 U
D7I 18 7 8.14 13.70 I
D7U 19 7 8.14 13.24 U
D14I 4 14 15.63 15.95 I
D14U 4 14 15.63 14.56 U
D17I 3 17 19.15 16.19 I
D17U 3 17 19.15 14.57 U
D21I 4 21 23.23 15.86 I
D21U 4 21 23.23 14.23 U
D24I 3 24 26.60 15.99 I
D24U 3 24 26.60 14.03 U
D28I 4 28 30.61 15.76 I
D28U 4 28 30.61 13.58 U