Rv2989 Transcriptional regulator, IclR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv2989 Transcriptional regulator, IclR family CDS 3346147 3346848 + 702 233 TRUE

Rv2989 (Transcriptional regulator, IclR family) is predicted to be co-regulated in modules bicluster_0286 with residual 0.44 and bicluster_0344 with residual 0.49.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 4.30 and 5.80 for bicluster_0286 and 0.10 and 8.00 for bicluster_0344 respectively.

These modules are enriched for following go terms: branched-chain amino acid biosynthetic p..., branched-chain amino acid metabolic proc..., cytosol, cytosolic part .

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 72
Gene Target Differential Expression Distance Expression pvalue Type
DNA recombination and repair protein RecF
No 47 0 0.999076 Primary.TSS
FIG018426: putative septation inhibitor protein
No -2 -0.17 0.810662 Primary.TSS
FIG215594: Membrane spanning protein
No 16 -0.14 0.697686 Primary.TSS
Phosphoheptose isomerase (EC 5.3.1.-)
No -27 0.06 0.955092 CDS
Phosphoenolpyruvate carboxykinase [GTP] (EC 4.1.1.32)
No 28 -0.7 0.131562 Primary.TSS
3-methylmercaptopropionyl-CoA dehydrogenase (DmdC)
No 48 0.12 0.941083 Primary.TSS
PE family protein
No 42 -0.28 0.624113 CDS
PPE family protein
No -97 0.86 0.205143 CDS
Chaperone protein DnaK
No -26 -0.47 0.574557 Primary.TSS
PPE family protein
No 57 0.8 0.193684 Primary.TSS
Displaying 1 - 4 of 4
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, IclR family
No -30 -0.33 0.817589 Primary.TSS
Transcriptional regulator, IclR family
Induced 3 1.78 0.0215465 Primary.TSS
Organic hydroperoxide resistance transcriptional regulator
No -85 0.72 0.382576 Primary.TSS
DNA-binding response regulator TrcR
No -1 -0.77 0.409496 Primary.TSS
Product (LegacyBRC) Product (RefSeq)
PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN transcriptional regulatory protein
Operon # Operon
1951
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
15610126 NP_217505.1 Run
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 GSM1426892 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426893 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426894 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426892 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426893 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426894 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426892 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426893 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426894 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv2989_B138 UCSC Browser Tracks
Rv2989_B546 UCSC Browser Tracks
Rv2989_B631 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.370000 0.03

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: 0.0000683817
p-value INH: 0.302193
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D17I 3 17 19.15 5.52 I
D17U 3 17 19.15 9.61 U
D24I 3 24 26.60 4.03 I
D24U 3 24 26.60 8.97 U
D3I 3 3 3.83 12.29 I
D3U 3 3 3.83 12.15 U
D14I 4 14 15.63 6.98 I
D14U 4 14 15.63 9.98 U
D21I 4 21 23.23 5.39 I
D21U 4 21 23.23 9.29 U
D28I 4 28 30.61 4.56 I
D28U 4 28 30.61 9.30 U
D5I 9 5 6.00 9.55 I
D5U 17 5 6.00 10.00 U
D7I 18 7 8.14 10.53 I
D7U 19 7 8.14 11.10 U
D0U 27 0 0.00 11.99 U