Rv3291c Leucine-responsive regulatory protein, regulator for leucine (or lrp) regulon and high-affinity branched-chain amino acid transport system

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3291c lrpA Leucine-responsive regulatory protein, regulator for leucine (or lrp) regulon and high-affinity... CDS 3671845 3672297 - 453 150 TRUE

Rv3291c (Leucine-responsive regulatory protein, regulator for leucine (or lrp) regulon and high-affinity branched-chain amino acid transport system) is predicted to be co-regulated in modules bicluster_0063 with residual 0.56 and bicluster_0561 with residual 0.52.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.01 and 37.00 for bicluster_0063 and 0.03 and 9.50 for bicluster_0561 respectively.

These modules are enriched for following go terms: monovalent inorganic cation transport, metal ion transport, cation-transporting ATPase activity, metal ion transmembrane transporter acti..., monovalent inorganic cation transmembran..., ATPase activity, coupled to transmembran....

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 14
Gene Target Differential Expression Distance Expression pvalue Type
No -76 0.57 0.0813063 CDS
No -27 0.79 0.144735 CDS
Probable phiRV1 phage protein
No -43 0.3 0.664434 CDS
Probable phiRv1 integrase
No -13 0.27 0.549069 CDS
Probable phiRv1 integrase
No 5 0.27 0.549069 Internal.TSS
Partial REP13E12 repeat protein
No -14 0.01 0.982674 Antisense.TSS
Transcriptional repressor Mce3R, TetR family
No 43 0.34 0.44765 Primary.TSS
FIG055075: Possibly a cell division protein, antigen 84 in Mycobacteria
No 67 0.15 0.473668 Primary.TSS
No -24 -0.03 0.96413 CDS
No 2 -0.03 0.96413 Internal.TSS
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
No results were found
Motif 1 Motif 2 Residual
bicluster_0063
e.value: 
0.014
Motif Bicluster: 
e.value: 
37
Motif Bicluster: 
0.56
bicluster_0561
e.value: 
0.027
Motif Bicluster: 
e.value: 
9.5
Motif Bicluster: 
0.52
Product (LegacyBRC) Product (RefSeq)
PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN [PROBABLY ASNC-FAMILY] AsnC family transcriptional regulator
Operon # Operon
2151
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
15610427 NP_217808.1 Run
GO:0003677

DNA binding

DNA binding

Details: 
Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid).
GO Category: 
molecular_function
37
Total items in this category:  
GO:0051260

protein homooligomerization

protein homooligomerization

Details: 
The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
GO Category: 
biological_process
31
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 GSM1426971 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426972 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426973 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3291c_B152 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.690000 1.83

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: 0.145566
p-value INH: 0.860973
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 12.40 U
D3I 3 3 3.83 11.00 I
D3U 3 3 3.83 11.56 U
D5I 9 5 6.00 13.39 I
D5U 17 5 6.00 13.03 U
D7I 18 7 8.14 12.26 I
D7U 19 7 8.14 12.04 U
D14I 4 14 15.63 13.27 I
D14U 4 14 15.63 12.19 U
D17I 3 17 19.15 13.15 I
D17U 3 17 19.15 11.87 U
D21I 4 21 23.23 13.04 I
D21U 4 21 23.23 11.91 U
D24I 3 24 26.60 13.01 I
D24U 3 24 26.60 11.40 U
D28I 4 28 30.61 12.94 I
D28U 4 28 30.61 11.49 U