Rv0602c Two component DNA binding Transcriptional regulatory protein TcrA

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv0602c tcrA Two component DNA binding Transcriptional regulatory protein TcrA CDS 699038 699799 - 762 253 TRUE

Rv0602c (Two component DNA binding Transcriptional regulatory protein TcrA) is predicted to be co-regulated in modules bicluster_0067 with residual 0.54 and bicluster_0207 with residual 0.51.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 180.00 and 34.00 for bicluster_0067 and 150.00 and 95.00 for bicluster_0207 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?:

BASS Score Re-Annotated Start Tuberculist Annotated Start
-1.173 699733 699799
Displaying 1 - 10 of 75
Gene Target Differential Expression Distance Expression pvalue Type
NAD(P) transhydrogenase subunit beta (EC 1.6.1.2)
No 30 -0.17 0.648928 CDS
PROBABLE CONSERVED TRANSMEMBRANE PROTEIN
No 5 -0.27 0.573151 CDS
tRNA (guanine46-N7-)-methyltransferase (EC 2.1.1.33)
No -1 0.08 0.841587 Internal.TSS
Enoyl-CoA hydratase (EC 4.2.1.17)
No -16 0.01 0.984889 CDS
Oxidoreductase (flavoprotein)
No 32 -0.46 0.380726 Primary.TSS
Possible membrane protein
No -4 0.14 0.744155 CDS
Iron-regulated heparin binding hemagglutinin HbhA (Adhesin)
No -13 -0.38 0.140415 CDS
Phosphoglycerate mutase (EC 5.4.2.1)
No -33 -0.14 0.663382 Primary.TSS
Two component DNA binding Transcriptional regulatory protein TcrA
Induced -55 6.99 0 CDS
POSSIBLE EXPORTED PROTEIN
Induced -112 5.61 0 CDS
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
Two component DNA binding Transcriptional regulatory protein TcrA
Induced -55 6.99 0 CDS
Motif 1 Motif 2 Residual
bicluster_0067
e.value: 
180
Motif Bicluster: 
e.value: 
34
Motif Bicluster: 
0.54
bicluster_0207
e.value: 
150
Motif Bicluster: 
e.value: 
95
Motif Bicluster: 
0.51
Product (LegacyBRC) Product (RefSeq)
PROBABLE TWO COMPONENT DNA BINDING TRANSCRIPTIONAL REGULATORY PROTEIN TCRA two component DNA binding transcriptional regulatory protein TCRA
Operon # Operon
403
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
15607742 NP_215116.1 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:0005886

plasma membrane

plasma membrane

Details: 
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO Category: 
cellular_component
1284
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 GSM1426515 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426516 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426517 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426515 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426516 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426517 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0602c_B135 UCSC Browser Tracks
Rv0602c_B339 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.030000 0.54

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: 0.27403
p-value INH: 0.988908
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 12.65 U
D3I 3 3 3.83 12.79 I
D3U 3 3 3.83 12.36 U
D5I 9 5 6.00 11.69 I
D5U 17 5 6.00 11.43 U
D7I 18 7 8.14 13.10 I
D7U 19 7 8.14 12.80 U
D14I 4 14 15.63 12.54 I
D14U 4 14 15.63 12.31 U
D17I 3 17 19.15 12.39 I
D17U 3 17 19.15 12.14 U
D21I 4 21 23.23 12.26 I
D21U 4 21 23.23 12.11 U
D24I 3 24 26.60 12.19 I
D24U 3 24 26.60 12.21 U
D28I 4 28 30.61 11.71 I
D28U 4 28 30.61 12.00 U