Rv3833 Transcriptional regulator, AraC family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv3833 Transcriptional regulator, AraC family CDS 4306867 4307658 + 792 263 TRUE

Rv3833 (Transcriptional regulator, AraC family) is predicted to be co-regulated in modules bicluster_0027 with residual 0.56 and bicluster_0059 with residual 0.54.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 0.04 for bicluster_0027 and 0.07 and 75.00 for bicluster_0059 respectively.

These modules are enriched for following go terms: disaccharide metabolic process, trehalose metabolic process, trehalose biosynthetic process, disaccharide biosynthetic process, carbohydrate biosynthetic process pigment metabolic process, pigment biosynthetic process.

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-18253 MT3941 1860
Displaying 1 - 2 of 2
Gene Target Differential Expression Distance Expression pvalue Type
No 0 0.65 0.672214 CDS
Transcriptional regulator, AraC family
Induced -56 4.46 8.40779e-45 CDS
Displaying 1 - 2 of 2
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, PadR family
No -13 0.24 0.962221 CDS
Transcriptional regulator, AraC family
Induced -56 4.46 8.40779e-45 CDS
Product (LegacyBRC) Product (RefSeq)
TRANSCRIPTIONAL REGULATORY PROTEIN [PROBABLY ARAC-FAMILY] AraC family transcriptional regulator
Operon # Operon
2508
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
15610969 NP_218350.1 Run
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 GSM1427041 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427042 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427043 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3833_B643 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.080000 0.71

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: 0.909512
p-value INH: 0.873582
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 14.64 U
D3I 3 3 3.83 14.54 I
D3U 3 3 3.83 14.04 U
D5I 9 5 6.00 13.60 I
D5U 17 5 6.00 13.46 U
D7I 18 7 8.14 14.49 I
D7U 19 7 8.14 14.48 U
D14I 4 14 15.63 13.88 I
D14U 4 14 15.63 14.20 U
D17I 3 17 19.15 13.45 I
D17U 3 17 19.15 14.00 U
D21I 4 21 23.23 13.39 I
D21U 4 21 23.23 14.31 U
D24I 3 24 26.60 12.63 I
D24U 3 24 26.60 13.92 U
D28I 4 28 30.61 12.57 I
D28U 4 28 30.61 13.83 U