Rv2642 Arsenical resistance operon repressor

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv2642 Arsenical resistance operon repressor CDS 2966533 2966913 + 381 126 TRUE

Rv2642 (Arsenical resistance operon repressor) is predicted to be co-regulated in modules bicluster_0008 with residual 0.62 and bicluster_0043 with residual 0.47.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 0.00 for bicluster_0008 and 0.00 and 0.01 for bicluster_0043 respectively.

These modules are enriched for following go terms: nucleic acid binding transcription facto..., sequence-specific DNA binding transcript....

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 15
Gene Target Differential Expression Distance Expression pvalue Type
Partial REP13E12 repeat protein
No -57 0.14 0.82682 CDS
No -44 -0.06 0.847987 Internal.TSS
No -112 -0.09 0.839267 Primary.TSS
PROBABLE CONSERVED TRANSMEMBRANE PROTEIN
No 19 -0.09 0.846867 CDS
Induced -77 0.65 0.0257658 Primary.TSS
Transcriptional regulatory protein
No -99 0.04 0.900602 Primary.TSS
Polyketide synthase
No -23 -0.14 0.676272 Primary.TSS
Maltose/maltodextrin ABC transporter, substrate binding periplasmic protein MalE
No -121 -0.01 0.984088 CDS
Possible membrane protein
No 43 0.09 0.829863 CDS
Universal stress protein UspA and related nucleotide-binding proteins
No -103 0.26 0.578048 Primary.TSS
Product (LegacyBRC) Product (RefSeq)
POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN [PROBABLY ARSR-FAMILY] ArsR family transcriptional regulator
Operon # Operon
1737 -
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
15609779 NP_217158.1 Run
GO:0003700

sequence-specific DNA binding transcription factor activity

sequence-specific DNA binding transcription factor activity

Details: 
Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
GO Category: 
molecular_function
17
Total items in this category:  
GO:0005622

intracellular

intracellular

Details: 
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
GO Category: 
cellular_component
65
Total items in this category:  
GO:0046688

response to copper ion

response to copper ion

Details: 
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a copper ion stimulus.
GO Category: 
biological_process
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 GSM1426845 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426846 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426847 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426848 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426849 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426845 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426846 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426847 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426848 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426849 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv2642_B207 UCSC Browser Tracks
Rv2642_B237 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.990000 1.27

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: 0.00000673892
p-value INH: 0.870774
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 13.02 U
D3I 3 3 3.83 13.30 I
D3U 3 3 3.83 13.11 U
D5I 9 5 6.00 12.25 I
D5U 17 5 6.00 11.81 U
D7I 18 7 8.14 14.05 I
D7U 19 7 8.14 12.69 U
D14I 4 14 15.63 13.84 I
D14U 4 14 15.63 11.45 U
D17I 3 17 19.15 14.68 I
D17U 3 17 19.15 11.03 U
D21I 4 21 23.23 14.81 I
D21U 4 21 23.23 11.30 U
D24I 3 24 26.60 15.83 I
D24U 3 24 26.60 10.78 U
D28I 4 28 30.61 15.57 I
D28U 4 28 30.61 10.87 U