Rv0494 Lactate-responsive regulator LldR in Enterobacteria, GntR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv0494 Lactate-responsive regulator LldR in Enterobacteria, GntR family CDS 584695 585423 + 729 242 TRUE

Rv0494 (Lactate-responsive regulator LldR in Enterobacteria, GntR family) is predicted to be co-regulated in modules bicluster_0160 with residual 0.59 and bicluster_0441 with residual 0.47.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.01 and 5,000.00 for bicluster_0160 and 75.00 and 120.00 for bicluster_0441 respectively.

These modules are enriched for following go terms: calcium- and calmodulin-responsive adeny..., adenylate cyclase activity, cyclase activity.

This gene is found to be for growth on cholesterol.

Mutant available?:

BASS Score Re-Annotated Start Tuberculist Annotated Start
-0.988 584707 584695
Displaying 1 - 10 of 25
Gene Target Differential Expression Distance Expression pvalue Type
Adenylosuccinate synthetase (EC 6.3.4.4)
No 50 -0.14 0.639079 CDS
Orotate phosphoribosyltransferase (EC 2.4.2.10)
No -40 -0.11 0.608889 CDS
PPE family protein
No -88 -0.03 0.914503 Primary.TSS
Isocitrate lyase (EC 4.1.3.1) / Methylisocitrate lyase (EC 4.1.3.30)
Repressed -9 -0.99 0.00151645 Primary.TSS
Repressed 65 -1.39 0.0000000285 CDS
Lactate-responsive regulator LldR in Enterobacteria, GntR family
Induced 60 5.68 0 CDS
Methoxy mycolic acid synthase 1 MmaA1 (EC 2.1.1.-)
No 28 0.05 0.872286 CDS
Methoxy mycolic acid synthase 1 MmaA1 (EC 2.1.1.-)
No 38 0.05 0.872286 Antisense.TSS
Mrp protein homolog
No -59 -0.02 0.899548 Antisense.TSS
Phosphopantothenoylcysteine decarboxylase (EC 4.1.1.36) / Phosphopantothenoylcysteine synthetase (EC 6.3.2.5)
No -101 -0.15 0.253851 CDS
Displaying 1 - 3 of 3
ChipSeq TF Differential Expression Distance Expression pvalue Type
Lactate-responsive regulator LldR in Enterobacteria, GntR family
Induced 60 5.68 0 CDS
Transcriptional regulator, TetR family
Repressed 3 -0.76 0.0468208 CDS
transcriptional regulator, ArsR family
No 13 0.5 0.0155666 CDS
Product (LegacyBRC) Product (RefSeq)
Uncharacterized HTH-type transcriptional regulator Rv0494_MT0514 GntR family transcriptional regulator
Operon # Operon
336
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
57116742 NP_215008.2 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 GSM1426501 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426502 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426503 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426504 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426501 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426502 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426503 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426504 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0494_B150 UCSC Browser Tracks
Rv0494_B557 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.230000 0.77

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: 0.00161226
p-value INH: 0.252572
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 11.80 U
D3I 3 3 3.83 12.00 I
D3U 3 3 3.83 11.73 U
D5I 9 5 6.00 12.69 I
D5U 17 5 6.00 12.13 U
D7I 18 7 8.14 13.41 I
D7U 19 7 8.14 12.10 U
D14I 4 14 15.63 12.76 I
D14U 4 14 15.63 11.29 U
D17I 3 17 19.15 13.16 I
D17U 3 17 19.15 11.06 U
D21I 4 21 23.23 13.64 I
D21U 4 21 23.23 11.63 U
D24I 3 24 26.60 13.94 I
D24U 3 24 26.60 11.40 U
D28I 4 28 30.61 14.14 I
D28U 4 28 30.61 11.89 U