Rv3571 Phenylacetate-CoA oxygenase/reductase, PaaK subunit

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3571 kshB Phenylacetate-CoA oxygenase/reductase, PaaK subunit CDS 4012417 4013493 + 1 077 358 FALSE

Rv3571 (Phenylacetate-CoA oxygenase/reductase, PaaK subunit) is predicted to be co-regulated in modules bicluster_0331 with residual 0.41 and bicluster_0337 with residual 0.50.

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_0331 and 0.00 and 0.00 for bicluster_0337 respectively.

These modules are enriched for following go terms: primary metabolic process, cellular metabolic process, cellular process, organic substance metabolic process, cell, cell part, large ribosomal subunit, small ribosomal subunit aspartate carbamoyltransferase activity.

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 1 of 1
Gene Target Differential Expression Distance Expression pvalue Type
No results were found
Displaying 1 - 6 of 6
ChipSeq TF Differential Expression Distance Expression pvalue Type
transcriptional regulator, ArsR family
Induced 24 0.87 0.000000152 Primary.TSS
DNA-binding response regulator TrcR
No 67 0.3 0.598028 Primary.TSS
HTH-type transcriptional regulator
No 31 -0.19 0.582385 Primary.TSS
Transcriptional regulator, TetR family
No 60 0.64 0.159629 Primary.TSS
Induced 28 1.49 0.00000000000432 Primary.TSS
Histone protein Lsr2
No 58 0.03 0.96887 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0331
e.value: 
0.0000000081
Motif Bicluster: 
e.value: 
0.00082
Motif Bicluster: 
0.41
bicluster_0337
e.value: 
1.2e-19
Motif Bicluster: 
e.value: 
0.000000026
Motif Bicluster: 
0.50
Product (LegacyBRC) Product (RefSeq)
POSSIBLE HEMOGLOBINE-RELATED PROTEIN HMP hemoglobine-like protein
Operon # Operon
2326 -
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
15610707 NP_218088.1 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:0051409

response to nitrosative stress

response to nitrosative stress

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 nitrosative stress stimulus. Nitrosative stress is a state often resulting from exposure to high levels of nitric oxide (NO) or the highly reactive oxidant peroxynitrite, which is produced following interaction of NO with superoxide anions.
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.
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.000000 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:
p-value INH: