Rv3681c WhiB-type transcription regulator

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3681c whiB4 WhiB-type transcription regulator CDS 4121198 4121554 - 357 118 TRUE

Rv3681c (WhiB-type transcription regulator) is predicted to be co-regulated in modules bicluster_0400 with residual 0.51 and bicluster_0421 with residual 0.58.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.01 and 0.12 for bicluster_0400 and 360.00 and 130.00 for bicluster_0421 respectively.

These modules are enriched for following go terms: carboxypeptidase activity, thiosulfate sulfurtransferase activity, unfolded protein binding, exopeptidase activity .

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 56
Gene Target Differential Expression Distance Expression pvalue Type
GDP-mannose 4,6 dehydratase (EC 4.2.1.47)
No -83 0.24 0.999973 Primary.TSS
Nitrite reductase [NAD(P)H] large subunit (EC 1.7.1.4)
No -135 0.65 0.999973 CDS
No -144 -0.43 0.40191 Primary.TSS
DNA-binding response regulator
Induced -12 1.01 0.00000192 Primary.TSS
Long-chain-fatty-acid--CoA ligase (EC 6.2.1.3)
No -71 0.14 0.999973 Primary.TSS
PPE family protein
No 69 -0.01 0.999973 CDS
Death on curing protein, Doc toxin
No -3 -0.1 0.999973 Primary.TSS
Prevent host death protein, Phd antitoxin
No -3 -0.18 0.999973 Internal.TSS
Prevent host death protein, Phd antitoxin
No -86 -0.18 0.999973 CDS
Carboxylesterase (EC 3.1.1.1)
No -94 -0.17 0.999973 Primary.TSS
Displaying 1 - 5 of 5
ChipSeq TF Differential Expression Distance Expression pvalue Type
DNA-binding response regulator mtrA
No -3 -0.2 0.624012 Primary.TSS
transcriptional regulator, ArsR family
No -27 0.51 0.00000035 Primary.TSS
Transcriptional regulator, ArsR family
Repressed -8 -2.06 1.12104e-44 Primary.TSS
DNA-binding response regulator TrcR
Induced -45 0.63 0.000131331 Primary.TSS
cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases
No -63 0.37 0.0771035 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0400
e.value: 
0.0052
Motif Bicluster: 
e.value: 
0.12
Motif Bicluster: 
0.51
bicluster_0421
e.value: 
360
Motif Bicluster: 
e.value: 
130
Motif Bicluster: 
0.58
Product (LegacyBRC) Product (RefSeq)
PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN WHIB-LIKE WHIB4 transcriptional regulatory protein WHIB-like WHIB4
Operon # Operon
2397 - -
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
57117144 NP_218198.2 Run
GO:0005618

cell wall

cell wall

Details: 
The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan.
GO Category: 
cellular_component
320
Total items in this category:  
GO:0042803

protein homodimerization activity

protein homodimerization activity

Details: 
Interacting selectively and non-covalently with an identical protein to form a homodimer.
GO Category: 
molecular_function
83
Total items in this category:  
GO:0047134

protein-disulfide reductase activity

protein-disulfide reductase activity

Details: 
Catalysis of the reaction: protein-dithiol + NAD(P)+ = protein-disulfide + NAD(P)H + H+.
GO Category: 
molecular_function
2
Total items in this category:  
GO:0051539

4 iron, 4 sulfur cluster binding

4 iron, 4 sulfur cluster binding

Details: 
Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
GO Category: 
molecular_function
5
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 GSM1427023 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427024 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427025 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3681c_B128 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.610000 1.94

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: