Rv3405c Transcriptional regulator, TetR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv3405c Transcriptional regulator, TetR family CDS 3824702 3825268 - 567 188 TRUE

Rv3405c (Transcriptional regulator, TetR family) is predicted to be co-regulated in modules bicluster_0043 with residual 0.47 and bicluster_0058 with residual 0.53.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 0.01 for bicluster_0043 and 0.00 and 3.10 for bicluster_0058 respectively.

These modules are enriched for following go terms: nucleic acid binding transcription facto..., sequence-specific DNA binding transcript... acetyl-CoA C-acyltransferase activity.

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 5 of 5
Gene Target Differential Expression Distance Expression pvalue Type
DNA-directed RNA polymerase beta subunit (EC 2.7.7.6)
No -1 -0.09 0.89199 Primary.TSS
No -37 -0.33 0.717211 CDS
Transcriptional regulator, TetR family
Induced 26 4.61 0 CDS
Alpha-ketoglutarate-dependent taurine dioxygenase (EC 1.14.11.17)
No -36 -1.17 0.0555903 CDS
ESX-1 secretion system protein (Rv3616c)
No -61 0.34 0.731979 Primary.TSS
Displaying 1 - 3 of 3
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, TetR family
Induced 26 4.61 0 CDS
Transcriptional regulator, ArsR family
No 29 0.16 0.572837 CDS
DNA-binding response regulator TrcR
No 56 -0.31 0.655127 CDS
Product (LegacyBRC) Product (RefSeq)
Uncharacterized HTH-type transcriptional regulator Rv3405c_MT3513 transcriptional regulatory protein
Operon # Operon
2228
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
15610541 NP_217922.1 Run
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 GSM1426990 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426991 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426992 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3405c_B155 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.530000 0.28

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: 0.0138863
p-value INH: 0.988908
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D3I 3 3 3.83 10.38 I
D5I 9 5 6.00 11.83 I
D7I 18 7 8.14 10.42 I
D14I 4 14 15.63 9.84 I
D17I 3 17 19.15 9.64 I
D21I 4 21 23.23 9.69 I
D24I 3 24 26.60 9.32 I
D28I 4 28 30.61 9.40 I
D0U 27 0 0.00 9.71 U
D3U 3 3 3.83 10.11 U
D5U 17 5 6.00 11.56 U
D7U 19 7 8.14 9.43 U
D14U 4 14 15.63 9.44 U
D17U 3 17 19.15 9.37 U
D21U 4 21 23.23 9.63 U
D24U 3 24 26.60 9.19 U
D28U 4 28 30.61 9.63 U