Rv0047c Transcriptional regulator, PadR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv0047c Transcriptional regulator, PadR family CDS 51185 51727 - 543 180 TRUE

Rv0047c (Transcriptional regulator, PadR family) is predicted to be co-regulated in modules bicluster_0402 with residual 0.39 and bicluster_0509 with residual 0.59.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 650.00 for bicluster_0402 and 53.00 and 2,600.00 for bicluster_0509 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 229
Gene Target Differential Expression Distance Expression pvalue Type
DNA gyrase subunit A (EC 5.99.1.3)
No 48 0.09 0.729306 CDS
Inositol-1-phosphate synthase (EC 5.5.1.4)
Repressed -99 -1.17 0.00013167 Primary.TSS
Transcriptional regulator, PadR family
Induced 7 2.56 4.75e-25 Primary.TSS
No -54 0.22 0.58419 CDS
ADP-ribose 1-phosphate phophatase related protein
No -28 0.22 0.487799 Primary.TSS
Cystathionine beta-lyase, type II (EC 4.4.1.8)
No -1 0.11 0.796662 CDS
Formate hydrogenlyase subunit 11
No 16 0.31 0.680718 Primary.TSS
Oxidoreductase
Induced -131 1.24 0.0319232 Internal.TSS
Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
Induced 68 1.14 0.00948805 CDS
Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
Induced -137 1.14 0.00948805 Internal.TSS
Displaying 1 - 2 of 2
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, PadR family
No 12 0.35 0.962221 Primary.TSS
Transcriptional regulator, PadR family
Induced 7 2.56 4.75e-25 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0402
e.value: 
0.0017
Motif Bicluster: 
e.value: 
650
Motif Bicluster: 
0.39
bicluster_0509
e.value: 
53
Motif Bicluster: 
e.value: 
2600
Motif Bicluster: 
0.59
Product (LegacyBRC) Product (RefSeq)
Putative uncharacterized protein
Operon # Operon
31
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
15607189 NP_214561.1 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 GSM1426387 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426388 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426389 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0047c_B348 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.020000 0.21

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: 0.0399685
p-value INH: 0.832328
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 11.48 U
D3I 3 3 3.83 10.97 I
D3U 3 3 3.83 11.73 U
D5I 9 5 6.00 8.66 I
D5U 17 5 6.00 9.71 U
D7I 18 7 8.14 9.30 I
D7U 19 7 8.14 10.18 U
D14I 4 14 15.63 4.10 I
D14U 4 14 15.63 8.10 U
D17I 3 17 19.15 I
D17U 3 17 19.15 6.35 U
D21I 4 21 23.23 1.11 I
D21U 4 21 23.23 6.04 U
D24I 3 24 26.60 I
D24U 3 24 26.60 4.50 U
D28I 4 28 30.61 I
D28U 4 28 30.61 4.49 U