Rv0165c Predicted regulator PutR for proline utilization, GntR family

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv0165c mce1R Predicted regulator PutR for proline utilization, GntR family CDS 194144 194938 - 795 264 FALSE

Rv0165c (Predicted regulator PutR for proline utilization, GntR family) is predicted to be co-regulated in modules bicluster_0541 with residual 0.44 and bicluster_0565 with residual 0.53.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.02 and 0.19 for bicluster_0541 and 0.16 and 35.00 for bicluster_0565 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?: Yes

BASS Score New Primary UTR Primary TSS Re-Annotated Start Tuberculist Annotated Start
-0.689 296 194931 194635 194815
Last update: 11/20/2020 - 12:11
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-18383 MT0174 2148
Displaying 1 - 1 of 1
Gene Target Differential Expression Distance Expression pvalue Type
No results were found
Displaying 1 - 2 of 2
ChipSeq TF Differential Expression Distance Expression pvalue Type
transcriptional regulator, ArsR family
No 32 0.18 0.700787 Primary.TSS
Transcriptional regulator, ArsR family
No 48 -0.53 0.399481 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0541
e.value: 
0.021
Motif Bicluster: 
e.value: 
0.19
Motif Bicluster: 
0.44
bicluster_0565
e.value: 
0.16
Motif Bicluster: 
e.value: 
35
Motif Bicluster: 
0.53
Product (LegacyBRC) Product (RefSeq)
POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN [PROBABLY GNTR-FAMILY] GntR family transcriptional regulator
Operon # Operon
120
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
57116700 YP_177700.1 Run
GO:0075182

negative regulation of symbiont transcription in response to host

negative regulation of symbiont transcription in response to host

Details: 
Any process in which an organism stops, prevents, or reduces the frequency, rate or extent of its transcription as a result of detecting molecules of its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
GO Category: 
biological_process
1
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 GSM1426420 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426421 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426422 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0165c_B397 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.030000 0.81

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: 0.000592352
p-value INH: 0.988908
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 11.84 U
D3I 3 3 3.83 11.80 I
D3U 3 3 3.83 12.14 U
D5I 9 5 6.00 13.21 I
D5U 17 5 6.00 12.90 U
D7I 18 7 8.14 12.75 I
D7U 19 7 8.14 11.85 U
D14I 4 14 15.63 11.94 I
D14U 4 14 15.63 11.38 U
D17I 3 17 19.15 12.18 I
D17U 3 17 19.15 11.20 U
D21I 4 21 23.23 12.53 I
D21U 4 21 23.23 11.72 U
D24I 3 24 26.60 12.34 I
D24U 3 24 26.60 11.47 U
D28I 4 28 30.61 12.63 I
D28U 4 28 30.61 12.00 U