Rv3574 Transcriptional regulator kstR (Rv3574), TetR family

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3574 kstR Transcriptional regulator kstR (Rv3574), TetR family CDS 4016484 4017083 + 600 199 TRUE

Rv3574 (Transcriptional regulator kstR (Rv3574), TetR family) is predicted to be co-regulated in modules bicluster_0199 with residual 0.54 and bicluster_0200 with residual 0.45.

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_0199 and 0.00 and 0.16 for bicluster_0200 respectively.

These modules are enriched for following go terms: coenzyme binding, oxidoreductase 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-15132 MT3679 1413
Displaying 1 - 10 of 138
Gene Target Differential Expression Distance Expression pvalue Type
Lead, cadmium, zinc and mercury transporting ATPase (EC 3.6.3.3) (EC 3.6.3.5); Copper-translocating P-type ATPase (EC 3.6.3.4)
No 45 -0.13 0.485165 Primary.TSS
No -73 0.07 0.857796 CDS
No 25 -0.26 0.611914 Primary.TSS
Transcriptional regulator, TetR family
Repressed -75 -0.64 0.027632 Primary.TSS
MCE-family protein Mce1C
No -73 0.36 0.246627 CDS
FIG033285: Conserved MCE associated transmembrane protein
No -62 -0.11 0.527064 Internal.TSS
FIG034772: Probable conserved MCE associated protein
No -62 -0.05 0.775024 Primary.TSS
Possible membrane protein
No -2 0.34 0.1075 Antisense.TSS
Nitrate/nitrite transporter
No -60 0.26 0.159946 CDS
Cytochrome P450 135A1
No -116 0.12 0.63827 CDS
Displaying 1 - 10 of 10
ChipSeq TF Differential Expression Distance Expression pvalue Type
No -3 0.37 0.384637 Primary.TSS
Transcriptional regulator, AsnC family
No 48 0.15 0.924573 Primary.TSS
Transcriptional regulator kstR (Rv3574), TetR family
Induced -1 3.36 0 Primary.TSS
Transcriptional regulator, MarR family
No -39 0.73 0.0997296 Primary.TSS
Histone protein Lsr2
No -9 0.27 0.605592 Primary.TSS
Transcriptional regulator, ArsR family
Induced -8 0.92 0.00000267 Primary.TSS
transcriptional regulator, ArsR family
No -5 0.41 0.0538045 Primary.TSS
Transcriptional regulatory protein
No -12 0.17 0.61049 Primary.TSS
Phenylacetic acid degradation operon negative regulatory protein PaaX
No 2 0.14 0.951168 Primary.TSS
Transcriptional regulator, TetR family
No -10 0.28 0.887369 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0199
e.value: 
0.000000000000001
Motif Bicluster: 
e.value: 
0.000000085
Motif Bicluster: 
0.54
bicluster_0200
e.value: 
8.3e-28
Motif Bicluster: 
e.value: 
0.16
Motif Bicluster: 
0.45
Product (LegacyBRC) Product (RefSeq)
TRANSCRIPTIONAL REGULATORY PROTEIN [PROBABLY TETR-FAMILY] transcriptional regulatory protein TetR-family
Operon # Operon
2328
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
15610710 NP_218091.1 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: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:  
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 GSM1427008 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427009 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427010 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427011 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427012 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427008 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427009 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427010 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427011 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427012 GSE59086 25232098 GEO Tiling Array RNA
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.110000 0.75

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: 0.00000872796
p-value INH: 0.852778
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 12.17 U
D3I 3 3 3.83 11.79 I
D3U 3 3 3.83 10.90 U
D5I 9 5 6.00 10.89 I
D5U 17 5 6.00 11.76 U
D7I 18 7 8.14 10.15 I
D7U 19 7 8.14 11.31 U
D14I 4 14 15.63 4.32 I
D14U 4 14 15.63 8.47 U
D17I 3 17 19.15 2.30 I
D17U 3 17 19.15 7.41 U
D21I 4 21 23.23 2.50 I
D21U 4 21 23.23 7.03 U
D24I 3 24 26.60 I
D24U 3 24 26.60 5.82 U
D28I 4 28 30.61 I
D28U 4 28 30.61 5.94 U