Rv3050c Transcriptional regulator, TetR family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv3050c Transcriptional regulator, TetR family CDS 3411217 3411957 - 741 246 TRUE

Rv3050c (Transcriptional regulator, TetR family) is predicted to be co-regulated in modules bicluster_0030 with residual 0.60 and bicluster_0458 with residual 0.58.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.05 and 0.81 for bicluster_0030 and 0.15 and 30,000.00 for bicluster_0458 respectively.

These modules are enriched for following go terms: single-organism metabolic process, single-organism cellular process, biosynthetic process, cellular nitrogen compound metabolic pro..., nitrogen compound metabolic process, membrane part organonitrogen compound metabolic proces..., primary metabolic process, small molecule metabolic process, small molecule biosynthetic process, single-organism biosynthetic process, organonitrogen compound biosynthetic pro....

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

Mutant available?:

Displaying 1 - 7 of 7
Gene Target Differential Expression Distance Expression pvalue Type
Phosphoheptose isomerase (EC 5.3.1.-)
Repressed -81 -0.81 0.0199056 CDS
possible transmembrane protein
Repressed -20 -1.9 0.00000000941 Primary.TSS
No -67 -0.21 0.601008 CDS
FIG055075: Possibly a cell division protein, antigen 84 in Mycobacteria
No 49 0 0.997658 Primary.TSS
Monooxygenase, flavin-binding family
No 4 -0.5 0.0931228 Primary.TSS
ESX-1 secretion system protein (Rv3616c)
No -141 0.06 0.908887 Primary.TSS
ATP/GTP binding protein
No -133 -0.35 0.286445 Primary.TSS
Displaying 1 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
No results were found
Motif 1 Motif 2 Residual
bicluster_0030
e.value: 
0.052
Motif Bicluster: 
e.value: 
0.81
Motif Bicluster: 
0.60
bicluster_0458
e.value: 
0.15
Motif Bicluster: 
e.value: 
30000
Motif Bicluster: 
0.58
Product (LegacyBRC) Product (RefSeq)
PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN [PROBABLY ASNC-FAMILY] AsnC family transcriptional regulator
Operon # Operon
1996 Rv3050c
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
15610187 NP_217566.1 Run
GO:0005618

cell wall

cell wall

Details: 
The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan.
GO Category: 
cellular_component
320
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 GSM1426895 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426896 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426897 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3050c_B334 UCSC Browser Tracks
Quantitative Proteomics Data
Cholesterol Essentiality t-test p-value Cholesterol/Glycerol Ratio
essential 0.050000 0.03

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 13.56 U
D3I 3 3 3.83 13.46 I
D3U 3 3 3.83 12.90 U
D5I 9 5 6.00 14.32 I
D5U 17 5 6.00 14.43 U
D7I 18 7 8.14 13.82 I
D7U 19 7 8.14 13.64 U
D14I 4 14 15.63 11.38 I
D14U 4 14 15.63 12.95 U
D17I 3 17 19.15 10.59 I
D17U 3 17 19.15 13.02 U
D21I 4 21 23.23 10.63 I
D21U 4 21 23.23 13.28 U
D24I 3 24 26.60 9.30 I
D24U 3 24 26.60 13.04 U
D28I 4 28 30.61 9.69 I
D28U 4 28 30.61 13.58 U