Rv0653c Transcriptional regulator, TetR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv0653c Transcriptional regulator, TetR family CDS 749234 749929 - 696 231 TRUE

Rv0653c (Transcriptional regulator, TetR family) is predicted to be co-regulated in modules bicluster_0007 with residual 0.55 and bicluster_0043 with residual 0.47.

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_0007 and 0.00 and 0.01 for bicluster_0043 respectively.

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

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

Mutant available?:

Displaying 1 - 10 of 19
Gene Target Differential Expression Distance Expression pvalue Type
Cystathionine beta-lyase, type II (EC 4.4.1.8)
No -9 0.21 0.429273 CDS
Short-chain dehydrogenase/reductase SDR
No -36 -0.26 0.0626995 CDS
Phospholipid/glycerol acyltransferase
No -133 0.07 0.688806 Primary.TSS
No 11 0.12 0.729469 CDS
Transcriptional regulator, TetR family
Induced 38 4.4 0 CDS
\Lignostilbene-alpha,beta-dioxygenase and related enzymes\\\""
Repressed 0 -0.85 0.00565818 Primary.TSS
PE family protein
No 29 0.08 0.88716 Primary.TSS
LSU ribosomal protein L25p
No -46 -0.17 0.560509 Primary.TSS
Nucleoside triphosphate pyrophosphohydrolase MazG (EC 3.6.1.8)
No -66 0.05 0.865794 CDS
PPE family protein
No -12 -0.12 0.731862 Internal.TSS
Displaying 1 - 7 of 7
ChipSeq TF Differential Expression Distance Expression pvalue Type
DNA-binding response regulator TrcR
No 45 0.29 0.732406 CDS
DNA-binding response regulator mtrA
No 44 0.57 0.446092 CDS
transcriptional regulator, ArsR family
No 44 0.27 0.283457 CDS
No 31 -0.1 0.84163 CDS
Transcriptional regulator, IclR family
No 58 -0.54 0.461213 CDS
Transcriptional regulator, TetR family
Induced 38 4.4 0 CDS
Histone protein Lsr2
No 59 0.01 0.995325 CDS
Motif 1 Motif 2 Residual
bicluster_0007
e.value: 
0.0000000091
Motif Bicluster: 
e.value: 
0.00042
Motif Bicluster: 
0.55
bicluster_0043
e.value: 
0.00000015
Motif Bicluster: 
e.value: 
0.0062
Motif Bicluster: 
0.47
Product (LegacyBRC) Product (RefSeq)
POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN [PROBABLY TETR-FAMILY] TetR family transcriptional regulator
Operon # Operon
440 Rv0653c
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
15607793 NP_215167.1 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 GSM1426524 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426525 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426526 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426527 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426528 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv0653c_B157 UCSC Browser Tracks
Quantitative Proteomics Data
Cholesterol Essentiality t-test p-value Cholesterol/Glycerol Ratio
non-essential 0.420000 0.96

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 9.10 U
D3I 3 3 3.83 8.01 I
D3U 3 3 3.83 8.86 U
D5I 9 5 6.00 12.75 I
D5U 17 5 6.00 12.35 U
D7I 18 7 8.14 9.07 I
D7U 19 7 8.14 8.45 U
D14I 4 14 15.63 7.39 I
D14U 4 14 15.63 7.10 U
D17I 3 17 19.15 6.41 I
D17U 3 17 19.15 6.55 U
D21I 4 21 23.23 6.80 I
D21U 4 21 23.23 6.96 U
D24I 3 24 26.60 6.24 I
D24U 3 24 26.60 6.19 U
D28I 4 28 30.61 6.41 I
D28U 4 28 30.61 6.74 U