Rv0674 Phenylacetic acid degradation operon negative regulatory protein PaaX

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv0674 Phenylacetic acid degradation operon negative regulatory protein PaaX CDS 774064 774786 + 723 240 TRUE

Rv0674 (Phenylacetic acid degradation operon negative regulatory protein PaaX) is predicted to be co-regulated in modules bicluster_0299 with residual 0.50 and bicluster_0464 with residual 0.52.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 48.00 for bicluster_0299 and 0.03 and 2.20 for bicluster_0464 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 2 of 2
Gene Target Differential Expression Distance Expression pvalue Type
Acyl-CoA dehydrogenase (EC 1.3.99.3)
Repressed -28 -2.18 2.65e-22 Primary.TSS
Transcriptional regulator kstR (Rv3574), TetR family
No 2 0.14 0.951168 Primary.TSS
Product (LegacyBRC) Product (RefSeq)
Putative uncharacterized protein
Operon # Operon
452 - - -
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
15607814 NP_215188.1 Run
GO:0005576

extracellular region

extracellular region

Details: 
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
GO Category: 
cellular_component
272
Total items in this category:  
GO:0040007

growth

growth

Details: 
The increase in size or mass of an entire organism, a part of an organism or a cell.
GO Category: 
biological_process
621
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 GSM1426529 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426530 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426531 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0674_B351 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.280000 0.05

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: 0.049674
p-value INH: 0.988908
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 12.77 U
D3I 3 3 3.83 12.19 I
D3U 3 3 3.83 12.28 U
D5I 9 5 6.00 13.17 I
D5U 17 5 6.00 13.03 U
D7I 18 7 8.14 12.37 I
D7U 19 7 8.14 11.60 U
D14I 4 14 15.63 8.55 I
D14U 4 14 15.63 9.07 U
D17I 3 17 19.15 7.59 I
D17U 3 17 19.15 8.06 U
D21I 4 21 23.23 7.39 I
D21U 4 21 23.23 8.20 U
D24I 3 24 26.60 5.59 I
D24U 3 24 26.60 6.96 U
D28I 4 28 30.61 6.07 I
D28U 4 28 30.61 7.43 U