Rv3416 Sporulation regulatory protein WhiD

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3416 whiB3 Sporulation regulatory protein WhiD CDS 3834892 3835200 + 309 102 TRUE

Rv3416 (Sporulation regulatory protein WhiD) is predicted to be co-regulated in modules bicluster_0486 with residual 0.55 and bicluster_0524 with residual 0.54.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 500.00 and 840.00 for bicluster_0486 and 0.00 and 1.00 for bicluster_0524 respectively.

These modules are enriched for following go terms: DNA binding, nucleic acid binding .

This gene is found to be for growth on cholesterol.

Mutant available?: Yes

Last update: 11/20/2020 - 12:12
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-15101 MT3525 2601
Displaying 1 - 10 of 10
Gene Target Differential Expression Distance Expression pvalue Type
Partial REP13E12 repeat protein
No -49 0.04 0.938344 CDS
Repressed -112 -0.88 0.000149398 Primary.TSS
PROBABLE CONSERVED TRANSMEMBRANE PROTEIN
No 13 0.29 0.320601 CDS
Phage peptidoglycan binding endopeptidase
Induced 12 1.32 0.00000000139 Primary.TSS
Undecaprenyl-diphosphatase (EC 3.6.1.27)
No 30 0.51 0.00856777 Primary.TSS
No 30 0.48 0.135235 Internal.TSS
No -75 0.48 0.135235 CDS
No -5 0.48 0.135235 Antisense.TSS
Lipoprotein LppL
No -5 -0.03 0.935696 Primary.TSS
No 16 0.14 0.545405 Primary.TSS
Displaying 1 - 2 of 2
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, TetR family
No -121 -0.05 0.947884 Primary.TSS
ESX-1 secreted protein regulator EspR
No -108 0.06 0.839832 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0486
e.value: 
500
Motif Bicluster: 
e.value: 
840
Motif Bicluster: 
0.55
bicluster_0524
e.value: 
0.00036
Motif Bicluster: 
e.value: 
1
Motif Bicluster: 
0.54
Product (LegacyBRC) Product (RefSeq)
TRANSCRIPTIONAL REGULATORY PROTEIN WHIB-LIKE WHIB3 transcriptional regulatory protein WHIB-like WHIB3
Operon # Operon
2234
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
15610552 NP_217933.1 Run
GO:0005515

protein binding

protein binding

Details: 
Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
GO Category: 
molecular_function
135
Total items in this category:  
GO:0015035

protein disulfide oxidoreductase activity

protein disulfide oxidoreductase activity

Details: 
Catalysis of the reaction: a protein with reduced sulfide groups = a protein with oxidized disulfide bonds.
GO Category: 
molecular_function
7
Total items in this category:  
GO:0051536

iron-sulfur cluster binding

iron-sulfur cluster binding

Details: 
Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
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 GSM1426996 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426997 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426998 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3416_B403 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.010000 0.28

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: 0.00000877142
p-value INH: 0.000065193
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 14.72 U
D3I 3 3 3.83 15.28 I
D3U 3 3 3.83 14.99 U
D5I 9 5 6.00 13.25 I
D5U 17 5 6.00 14.84 U
D7I 18 7 8.14 12.59 I
D7U 19 7 8.14 15.13 U
D14I 4 14 15.63 6.36 I
D14U 4 14 15.63 14.82 U
D17I 3 17 19.15 3.33 I
D17U 3 17 19.15 15.27 U
D21I 4 21 23.23 3.39 I
D21U 4 21 23.23 14.36 U
D24I 3 24 26.60 2.90 I
D24U 3 24 26.60 15.60 U
D28I 4 28 30.61 2.66 I
D28U 4 28 30.61 14.80 U