Rv3539 PPE family protein

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3539 PPE63 PPE family protein CDS 3978059 3979498 + 1 440 479 FALSE

Rv3539 (PPE family protein) is predicted to be co-regulated in modules bicluster_0124 with residual 0.56 and bicluster_0434 with residual 0.58.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.06 and 1,200.00 for bicluster_0124 and 0.00 and 0.00 for bicluster_0434 respectively.

These modules are enriched for following go terms: cellular macromolecule catabolic process, cellular protein metabolic process, coenzyme biosynthetic process, cofactor biosynthetic process.

This gene is found to be for growth on cholesterol.

Mutant available?: Yes

Last update: 10/16/2017 - 15:33
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-15715 MT3643 1550
Displaying 1 - 1 of 1
Gene Target Differential Expression Distance Expression pvalue Type
No results were found
Displaying 1 - 2 of 2
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, PadR family
No 4 0.15 0.962221 Antisense.TSS
No -100 0.06 0.737811 CDS
Motif 1 Motif 2 Residual
bicluster_0124
e.value: 
0.059
Motif Bicluster: 
e.value: 
1200
Motif Bicluster: 
0.56
bicluster_0434
e.value: 
0.0000018
Motif Bicluster: 
e.value: 
0.000029
Motif Bicluster: 
0.58
Product (LegacyBRC) Product (RefSeq)
PPE FAMILY PROTEIN PPE family protein
Operon # Operon
2311
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
57117123 YP_177987.1 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:  
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
0.150000 1.26

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: