Rv1019 Transcriptional regulator, TetR family

Summary

Product Feature Type Start End Strand Length AA Length is TF
Rv1019 Transcriptional regulator, TetR family CDS 1138315 1138908 + 594 197 TRUE

Rv1019 (Transcriptional regulator, TetR family) is predicted to be co-regulated in modules bicluster_0055 with residual 0.58 and bicluster_0511 with residual 0.52.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.58 and 9.50 for bicluster_0055 and 670.00 and 6,900.00 for bicluster_0511 respectively.

These modules are enriched for following go terms: phosphopantetheine binding, modified amino acid binding, amide binding, amino acid binding.

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 3 of 3
Gene Target Differential Expression Distance Expression pvalue Type
Flavodoxin reductases (ferredoxin-NADPH reductases) family 1
No 19 1.81 0.0899573 Primary.TSS
Acyl-CoA dehydrogenase (EC 1.3.99.-)
No 66 -0.09 0.944252 CDS
Transcriptional regulator kstR (Rv3574), TetR family
No -10 0.28 0.887369 Primary.TSS
Displaying 1 - 4 of 4
ChipSeq TF Differential Expression Distance Expression pvalue Type
DNA-binding response regulator TrcR
No -112 0.12 0.809725 Primary.TSS
Transcriptional regulator kstR (Rv3574), TetR family
No -111 -0.08 0.703638 Primary.TSS
Transcriptional regulatory protein
No -29 0.21 0.198458 Primary.TSS
Two component transcriptional regulatory protein DevR
No -103 -0.19 0.0736082 Primary.TSS
Product (LegacyBRC) Product (RefSeq)
PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN [PROBABLY TETR-FAMILY] TetR family transcriptional regulator
Operon # Operon
683
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
15608159 NP_215535.1 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 GSM1426601 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426602 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426603 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv1019_B431 UCSC Browser Tracks

Quantitative Proteomics Data

t-test p-value Cholesterol/Glycerol Ratio
0.460000 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: 0.00546197
p-value INH: 0.501382
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 12.21 U
D3I 3 3 3.83 10.71 I
D3U 3 3 3.83 10.83 U
D5I 9 5 6.00 13.94 I
D5U 17 5 6.00 13.58 U
D7I 18 7 8.14 12.65 I
D7U 19 7 8.14 11.85 U
D14I 4 14 15.63 9.48 I
D14U 4 14 15.63 9.28 U
D17I 3 17 19.15 8.28 I
D17U 3 17 19.15 8.62 U
D21I 4 21 23.23 8.48 I
D21U 4 21 23.23 9.02 U
D24I 3 24 26.60 7.43 I
D24U 3 24 26.60 8.32 U
D28I 4 28 30.61 7.84 I
D28U 4 28 30.61 8.66 U