Rv3249c Transcriptional regulator, TetR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv3249c Transcriptional regulator, TetR family CDS 3629752 3630387 - 636 211 TRUE

Rv3249c (Transcriptional regulator, TetR family) is predicted to be co-regulated in modules bicluster_0063 with residual 0.56 and bicluster_0167 with residual 0.51.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.01 and 37.00 for bicluster_0063 and 0.00 and 49.00 for bicluster_0167 respectively.

These modules are enriched for following go terms: .

This gene is found to be non-essential for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 129
Gene Target Differential Expression Distance Expression pvalue Type
DNA gyrase subunit A (EC 5.99.1.3)
No 24 0 0.997072 CDS
Possible membrane protein
No 69 -0.06 0.899495 Primary.TSS
No 26 -0.07 0.865588 Internal.TSS
No -27 -0.07 0.865588 Internal.TSS
Partial REP13E12 repeat protein
No -141 0.4 0.433576 CDS
Oxidoreductase
Induced -23 1.34 0.000624759 CDS
Oxalyl-CoA decarboxylase (EC 4.1.1.8)
No -62 -0.11 0.839933 Primary.TSS
putative oxidoreductase
No -58 0.19 0.711307 CDS
MCE-family protein Mce1D
No -96 0.07 0.89104 Antisense.TSS
No 16 0.18 0.656076 Primary.TSS
Displaying 1 - 2 of 2
ChipSeq TF Differential Expression Distance Expression pvalue Type
putative two-component system response regulator
No 42 0.06 0.914454 Primary.TSS
transcriptional regulator, ArsR family
No 53 0.47 0.0115598 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0063
e.value: 
0.014
Motif Bicluster: 
e.value: 
37
Motif Bicluster: 
0.56
bicluster_0167
e.value: 
0.0021
Motif Bicluster: 
e.value: 
49
Motif Bicluster: 
0.51
Product (LegacyBRC) Product (RefSeq)
POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN [PROBABLY TETR-FAMILY] TetR family transcriptional regulator
Operon # Operon
2128 Rv3249c - Rv3250c - Rv3251c - Rv3252c
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
15610385 NP_217766.1 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 GSM1426960 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426961 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426962 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426963 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426964 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426960 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426961 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426962 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426963 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426964 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3249c_B256 UCSC Browser Tracks
Rv3249c_B317 UCSC Browser Tracks
Rv3249c_B561 UCSC Browser Tracks
Quantitative Proteomics Data
Cholesterol Essentiality t-test p-value Cholesterol/Glycerol Ratio
non-essential 0.040000 16.80

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.

Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 13.44 U
D3I 3 3 3.83 13.39 I
D3U 3 3 3.83 13.06 U
D5I 9 5 6.00 13.87 I
D5U 17 5 6.00 13.73 U
D7I 18 7 8.14 13.67 I
D7U 19 7 8.14 13.15 U
D14I 4 14 15.63 11.79 I
D14U 4 14 15.63 11.70 U
D17I 3 17 19.15 10.81 I
D17U 3 17 19.15 10.88 U
D21I 4 21 23.23 10.36 I
D21U 4 21 23.23 11.06 U
D24I 3 24 26.60 9.00 I
D24U 3 24 26.60 9.91 U
D28I 4 28 30.61 8.76 I
D28U 4 28 30.61 10.03 U