Rv3765c putative two-component system response regulator

Summary

Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3765c tcrX putative two-component system response regulator CDS 4211080 4211784 - 705 234 TRUE

Rv3765c (putative two-component system response regulator) is predicted to be co-regulated in modules bicluster_0352 with residual 0.50 and bicluster_0526 with residual 0.56.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.01 and 2,900.00 for bicluster_0352 and 450.00 and 8,100.00 for bicluster_0526 respectively.

These modules are enriched for following go terms: cellular biosynthetic process, organic substance biosynthetic process, translational elongation, macromolecule metabolic process, biosynthetic process, intracellular, macromolecular complex, translation elongation factor activity RNA binding.

This gene is found to be for growth on cholesterol.

Mutant available?:

BASS Score Distance to Tuberculist Start Codon Internal TSS New Internal UTR Primary TSS Re-Annotated Start Tuberculist Annotated Start
-0.566 344 4211440 -380 4211820 4211820 4211784
Displaying 1 - 10 of 49
Gene Target Differential Expression Distance Expression pvalue Type
2-amino-3-ketobutyrate coenzyme A ligase (EC 2.3.1.29)
No -49 0.04 0.956542 Primary.TSS
Partial REP13E12 repeat protein
Repressed -60 -1.43 0.000125734 CDS
GDP-mannose 4,6 dehydratase (EC 4.2.1.47)
Induced -71 0.97 0.0112293 Primary.TSS
Phosphoheptose isomerase (EC 5.3.1.-)
Induced -38 1.14 0.0000912 CDS
No -108 -0.1 0.831045 Primary.TSS
FIG030769: Probable conserved MCE associated membrane protein
No -110 0.06 0.75578 Primary.TSS
No -20 -0.19 0.693047 Primary.TSS
Possible conserved exported protein
Repressed -21 -1.12 0.0130848 CDS
PPE family protein
No 15 -0.56 0.0581963 Primary.TSS
Phosphoribosylglycinamide formyltransferase 2 (EC 2.1.2.-)
No -35 0.43 0.155457 Primary.TSS
Displaying 1 - 3 of 3
ChipSeq TF Differential Expression Distance Expression pvalue Type
DNA-binding response regulator TrcR
Repressed 44 -0.79 0.0378113 Primary.TSS
putative two-component system response regulator
Induced 30 2.76 1.56e-23 Primary.TSS
No -40 0.29 0.571003 Primary.TSS
Product (LegacyBRC) Product (RefSeq)
PROBABLE TWO COMPONENT TRANSCRIPTIONAL REGULATORY PROTEIN two component transcriptional regulatory protein
Operon # Operon
2461
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
15610901 NP_218282.1 Run
GO:0008150

biological_process

biological_process

Details: 
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
GO Category: 
biological_process
66
Total items in this category:  
GO:0008150

biological_process

biological_process

Details: 
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
GO Category: 
biological_process
66
Total items in this category:  
GO:0010106

cellular response to iron ion starvation

cellular response to iron ion starvation

Details: 
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of iron ions.
GO Category: 
biological_process
14
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 GSM1427035 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427036 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427037 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3765c_B344 UCSC Browser Tracks

Quantitative Proteomics Data

t-test p-value Cholesterol/Glycerol Ratio
0.500000 1.33

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: 0.0000000000897038
p-value INH: 0.000259814
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 13.83 U
D3I 3 3 3.83 13.94 I
D3U 3 3 3.83 13.91 U
D5I 9 5 6.00 9.27 I
D5U 17 5 6.00 12.09 U
D7I 18 7 8.14 9.96 I
D7U 19 7 8.14 13.67 U
D14I 4 14 15.63 4.75 I
D14U 4 14 15.63 11.47 U
D17I 3 17 19.15 3.15 I
D17U 3 17 19.15 10.90 U
D21I 4 21 23.23 3.00 I
D21U 4 21 23.23 9.45 U
D24I 3 24 26.60 I
D24U 3 24 26.60 9.26 U
D28I 4 28 30.61 1.73 I
D28U 4 28 30.61 7.66 U