Rv1994c Transcriptional regulator, ArsR family

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv1994c cmtR Transcriptional regulator, ArsR family CDS 2237628 2237984 - 357 118 TRUE

Rv1994c (Transcriptional regulator, ArsR family) is predicted to be co-regulated in modules bicluster_0073 with residual 0.60 and bicluster_0337 with residual 0.50.

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_0073 and 0.00 and 0.00 for bicluster_0337 respectively.

These modules are enriched for following go terms: aspartate carbamoyltransferase activity.

This gene is found to be for growth on cholesterol.

Mutant available?: Yes

Last update: 11/20/2020 - 12:12
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-15096 MT2050 2239
Displaying 1 - 10 of 69
Gene Target Differential Expression Distance Expression pvalue Type
No -58 -0.12 0.380643 Primary.TSS
Serine hydroxymethyltransferase (EC 2.1.2.1)
Repressed 42 -0.91 0.00017917 Primary.TSS
Retron-type RNA-directed DNA polymerase (EC 2.7.7.49)
No -130 -0.21 0.394628 CDS
Cystathionine beta-lyase, type II (EC 4.4.1.8)
No 62 -0.04 0.91624 CDS
Oxidoreductase
Induced -31 1.22 0.00110388 CDS
Transcriptional regulator, TetR family
Repressed -93 -1.83 0.0000000132 CDS
No -39 0.31 0.0873022 Internal.TSS
FIG033285: Conserved MCE associated transmembrane protein
No -11 -0.07 0.72359 Internal.TSS
FIG034772: Probable conserved MCE associated protein
No -11 -0.25 0.0774612 Primary.TSS
PROBABLE CONSERVED TRANSMEMBRANE PROTEIN
No 19 0.27 0.340311 CDS
Displaying 1 - 7 of 7
ChipSeq TF Differential Expression Distance Expression pvalue Type
Histone protein Lsr2
No 32 0.16 0.818968 Primary.TSS
Transcriptional regulatory protein
Induced 11 1.12 0.00015683 Primary.TSS
Transcriptional regulator, ArsR family
Induced 17 2.43 5.18e-25 Primary.TSS
Transcriptional regulator, TetR family
No -83 0.18 0.813101 Primary.TSS
Transcriptional regulator, TetR family
No -147 0.39 0.505423 Primary.TSS
Transcriptional regulator, ArsR family
Repressed 12 -1.6 0.0000000000000173 Primary.TSS
DNA-binding response regulator TrcR
No 24 0.02 0.987569 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0073
e.value: 
0.0000015
Motif Bicluster: 
e.value: 
0.000047
Motif Bicluster: 
0.60
bicluster_0337
e.value: 
1.2e-19
Motif Bicluster: 
e.value: 
0.000000026
Motif Bicluster: 
0.50
Product (LegacyBRC) Product (RefSeq)
Uncharacterized HTH-type transcriptional regulator Rv1994c_MT2050 transcriptional regulatory protein
Operon # Operon
1306
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
15609131 NP_216510.1 Run
GO:0010288

response to lead ion

response to lead ion

Details: 
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lead ion stimulus.
GO Category: 
biological_process
1
Total items in this category:  
GO:0016564

transcription repressor activity

transcription repressor activity

Details: 
OBSOLETE. Any transcription regulator activity that prevents or downregulates transcription.
GO Category: 
molecular_function
2
Total items in this category:  
GO:0032791

lead ion binding

lead ion binding

Details: 
Interacting selectively and non-covalently with lead (Pb) ions.
GO Category: 
molecular_function
1
Total items in this category:  
GO:0042803

protein homodimerization activity

protein homodimerization activity

Details: 
Interacting selectively and non-covalently with an identical protein to form a homodimer.
GO Category: 
molecular_function
83
Total items in this category:  
GO:0046686

response to cadmium ion

response to cadmium ion

Details: 
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cadmium (Cd) ion stimulus.
GO Category: 
biological_process
2
Total items in this category:  
GO:0046870

cadmium ion binding

cadmium ion binding

Details: 
Interacting selectively and non-covalently with cadmium (Cd) ions.
GO Category: 
molecular_function
2
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 GSM1426766 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426767 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426768 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426769 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426770 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv1994c_B187 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.890000 1.47

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: 0.00000061849
p-value INH: 0.294669
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 13.86 U
D3I 3 3 3.83 13.72 I
D3U 3 3 3.83 14.28 U
D5I 9 5 6.00 10.48 I
D5U 17 5 6.00 12.38 U
D7I 18 7 8.14 10.13 I
D7U 19 7 8.14 13.44 U
D14I 4 14 15.63 6.80 I
D14U 4 14 15.63 13.42 U
D17I 3 17 19.15 4.03 I
D17U 3 17 19.15 13.51 U
D21I 4 21 23.23 4.95 I
D21U 4 21 23.23 13.33 U
D24I 3 24 26.60 2.76 I
D24U 3 24 26.60 13.28 U
D28I 4 28 30.61 4.96 I
D28U 4 28 30.61 12.95 U