Rv2488c Adenylyl cyclase class-3/4/guanylyl cyclase / Disease resistance domain-containing protein / Tetratricopeptide repeat-containing protein / Transcriptional regulator, LuxR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv2488c Adenylyl cyclase class-3/4/guanylyl cyclase / Disease resistance domain-containing protein /... CDS 2797467 2800880 - 3 414 1 137 TRUE

Rv2488c (Adenylyl cyclase class-3/4/guanylyl cyclase / Disease resistance domain-containing protein / Tetratricopeptide repeat-containing protein / Transcriptional regulator, LuxR family) is predicted to be co-regulated in modules bicluster_0514 with residual 0.49 and bicluster_0549 with residual 0.51.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 1,700.00 and 4,200.00 for bicluster_0514 and 0.28 and 340.00 for bicluster_0549 respectively.

These modules are enriched for following go terms: monocarboxylic acid binding.

This gene is found to be for growth on cholesterol.

Mutant available?: Yes

BASS Score Distance to Tuberculist Start Codon Internal TSS New Internal UTR Re-Annotated Start Tuberculist Annotated Start
-0.571 92 2800788 -8 2800796 2800880
Last update: 11/20/2020 - 12:12
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-18139 MT2563 1522
Displaying 1 - 1 of 1
Gene Target Differential Expression Distance Expression pvalue Type
Transcriptional regulator, TetR family
No -1 -0.22 0.999776 Primary.TSS
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, PadR family
No -86 0.04 0.987476 Internal.TSS
Product (LegacyBRC) Product (RefSeq)
PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN [LUXR-FAMILY] LuxR family transcriptional regulator
Operon # Operon
1640 -
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
15609625 NP_217004.1 Run
GO:0005829

cytosol

cytosol

Details: 
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO Category: 
cellular_component
371
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 GSM1426830 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426831 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv2488c_B488 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.010000 0.87

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: 0.0494605
p-value INH: 0.988908
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 13.29 U
D3I 3 3 3.83 13.23 I
D3U 3 3 3.83 13.02 U
D5I 9 5 6.00 15.61 I
D5U 17 5 6.00 15.22 U
D7I 18 7 8.14 13.83 I
D7U 19 7 8.14 12.53 U
D14I 4 14 15.63 11.67 I
D14U 4 14 15.63 10.86 U
D17I 3 17 19.15 11.55 I
D17U 3 17 19.15 10.30 U
D21I 4 21 23.23 11.77 I
D21U 4 21 23.23 10.57 U
D24I 3 24 26.60 11.39 I
D24U 3 24 26.60 9.96 U
D28I 4 28 30.61 11.64 I
D28U 4 28 30.61 10.44 U