Rv3488 Transcriptional regulator, PadR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv3488 Transcriptional regulator, PadR family CDS 3907667 3907990 + 324 107 TRUE

Rv3488 (Transcriptional regulator, PadR family) is predicted to be co-regulated in modules bicluster_0247 with residual 0.41 and bicluster_0340 with residual 0.51.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 430.00 and 9,100.00 for bicluster_0247 and 1,100.00 and 2,300.00 for bicluster_0340 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 91
Gene Target Differential Expression Distance Expression pvalue Type
Transcriptional regulator, PadR family
No 12 0.35 0.962221 Primary.TSS
Butyryl-CoA dehydrogenase (EC 1.3.99.2)
Repressed 8 -0.98 0.000000177 Primary.TSS
No 63 0.08 0.967221 Internal.TSS
Esterase LipW
No -138 0.17 0.962221 Primary.TSS
Cell division protein DivIC (FtsB), stabilizes FtsL against RasP cleavage
No 2 -0.04 0.976996 Internal.TSS
Cell division protein DivIC (FtsB), stabilizes FtsL against RasP cleavage
No 67 -0.04 0.976996 Internal.TSS
Cell division protein DivIC (FtsB), stabilizes FtsL against RasP cleavage
No -80 -0.04 0.976996 CDS
Transcriptional regulator, TetR family
No 0 0.18 0.962221 Primary.TSS
No -12 0.25 0.962221 Primary.TSS
PROBABLE CONSERVED INTEGRAL MEMBRANE PROTEIN
No -106 -0.13 0.962221 CDS
Displaying 1 - 5 of 5
ChipSeq TF Differential Expression Distance Expression pvalue Type
WhiB-type transcription regulator
No -120 0.44 0.999973 CDS
Transcriptional regulator, PadR family
Induced -32 4.22 0 CDS
DNA-binding response regulator TrcR
No -132 0.3 0.631856 CDS
DNA-binding response regulator
No -113 -0.22 0.486799 CDS
ESX-1 secreted protein regulator EspR
No -137 0.14 0.687178 CDS
Motif 1 Motif 2 Residual
bicluster_0247
e.value: 
430
Motif Bicluster: 
e.value: 
9100
Motif Bicluster: 
0.41
bicluster_0340
e.value: 
1100
Motif Bicluster: 
e.value: 
2300
Motif Bicluster: 
0.51
Product (LegacyBRC) Product (RefSeq)
Putative uncharacterized protein
Operon # Operon
2282
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
15610624 NP_218005.1 Run
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 GSM1427002 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427003 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427004 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3488_B382 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.280000 0.75

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: 0.96184
p-value INH: 0.530397
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 11.56 U
D3I 3 3 3.83 12.02 I
D3U 3 3 3.83 11.61 U
D5I 9 5 6.00 12.99 I
D5U 17 5 6.00 12.50 U
D7I 18 7 8.14 11.24 I
D7U 19 7 8.14 11.07 U
D14I 4 14 15.63 10.86 I
D14U 4 14 15.63 11.79 U
D17I 3 17 19.15 8.64 I
D17U 3 17 19.15 11.20 U
D21I 4 21 23.23 7.88 I
D21U 4 21 23.23 11.17 U
D24I 3 24 26.60 4.80 I
D24U 3 24 26.60 10.80 U
D28I 4 28 30.61 5.11 I
D28U 4 28 30.61 10.81 U