Rv1963c Transcriptional repressor Mce3R, TetR family

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv1963c mce3R Transcriptional repressor Mce3R, TetR family CDS 2205582 2206802 - 1 221 406 TRUE

Rv1963c (Transcriptional repressor Mce3R, TetR family) is predicted to be co-regulated in modules bicluster_0434 with residual 0.58 and bicluster_0486 with residual 0.55.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 0.00 for bicluster_0434 and 500.00 and 840.00 for bicluster_0486 respectively.

These modules are enriched for following go terms: cellular macromolecule catabolic process, cellular protein metabolic process, coenzyme biosynthetic process, cofactor biosynthetic process DNA binding, nucleic acid binding.

This gene is found to be for growth on cholesterol.

Mutant available?:

BASS Score New Primary UTR Primary TSS Re-Annotated Start Tuberculist Annotated Start
-0.405 302 2207047 2206745 2206802
Displaying 1 - 1 of 1
Gene Target Differential Expression Distance Expression pvalue Type
No results were found
Displaying 1 - 10 of 15
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator kstR (Rv3574), TetR family
No 33 0.19 0.613192 Primary.TSS
Transcriptional regulatory protein
Induced 46 0.96 0.000990388 Primary.TSS
transcriptional regulator, ArsR family
Induced 43 0.67 0.00147623 Primary.TSS
Transcriptional repressor EthR, TetR family
No 40 0.32 0.828075 Primary.TSS
WhiB-type transcription regulator
No 39 0.05 0.999973 Primary.TSS
Transcriptional regulator, MarR family
Repressed 35 -0.84 0.00960828 Primary.TSS
Leucine-responsive regulatory protein, regulator for leucine (or lrp) regulon and high-affinity branched-chain amino acid transport system
No 43 0.34 0.44765 Primary.TSS
HTH-type transcriptional regulator
No 43 -0.3 0.486145 Primary.TSS
putative two-component system response regulator
No 38 -0.58 0.181669 Primary.TSS
Transcriptional regulator, PadR family
No 5 -0.07 0.982039 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0434
e.value: 
0.0000018
Motif Bicluster: 
e.value: 
0.000029
Motif Bicluster: 
0.58
bicluster_0486
e.value: 
500
Motif Bicluster: 
e.value: 
840
Motif Bicluster: 
0.55
Product (LegacyBRC) Product (RefSeq)
PROBABLE TRANSCRIPTIONAL REPRESSOR [PROBABLY TETR-FAMILY] MCE3R transcriptional repressor (probably TETR-family) MCE3R
Operon # Operon
1286
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
15609100 NP_216479.1 Run
GO:0003700

sequence-specific DNA binding transcription factor activity

sequence-specific DNA binding transcription factor activity

Details: 
Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
GO Category: 
molecular_function
17
Total items in this category:  
GO:0045892

negative regulation of transcription, DNA-dependent

negative regulation of transcription, DNA-dependent

Details: 
Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-dependent transcription.
GO Category: 
biological_process
10
Total items in this category:  
GO:0040007

growth

growth

Details: 
The increase in size or mass of an entire organism, a part of an organism or a cell.
GO Category: 
biological_process
621
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 GSM1426754 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426755 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426756 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv1963c_B417 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.000000 0.06

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: 0.0144205
p-value INH: 0.000824769
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 12.73 U
D3I 3 3 3.83 11.95 I
D3U 3 3 3.83 11.51 U
D5I 9 5 6.00 11.47 I
D5U 17 5 6.00 11.91 U
D7I 18 7 8.14 11.34 I
D7U 19 7 8.14 11.80 U
D14I 4 14 15.63 7.07 I
D14U 4 14 15.63 9.46 U
D17I 3 17 19.15 6.10 I
D17U 3 17 19.15 9.33 U
D21I 4 21 23.23 4.21 I
D21U 4 21 23.23 8.65 U
D24I 3 24 26.60 3.03 I
D24U 3 24 26.60 8.53 U
D28I 4 28 30.61 2.18 I
D28U 4 28 30.61 8.10 U