Rv1560

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv1560 vapB11 CDS 1764755 1764973 + 219 72 FALSE

Rv1560 () is predicted to be co-regulated in modules bicluster_0061 with residual 0.63 and bicluster_0084 with residual 0.58.

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_0061 and 0.64 and 170.00 for bicluster_0084 respectively.

These modules are enriched for following go terms: isomerase activity nucleobase-containing compound kinase ac....

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

Mutant available?:

Displaying 1 - 1 of 1
Gene Target Differential Expression Distance Expression pvalue Type
No results were found
Displaying 1 - 4 of 4
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, TetR family
No -20 -0.28 0.363486 Internal.TSS
Transcriptional regulator, PadR family
No -6 -0.01 0.991765 Internal.TSS
Transcriptional regulator, TetR family
No -5 -0.28 0.363486 CDS
Transcriptional regulator, PadR family
No 9 -0.01 0.991765 CDS
Motif 1 Motif 2 Residual
bicluster_0061
e.value: 
3e-23
Motif Bicluster: 
e.value: 
0.000000000000051
Motif Bicluster: 
0.63
bicluster_0084
e.value: 
0.64
Motif Bicluster: 
e.value: 
170
Motif Bicluster: 
0.58
Product (LegacyBRC) Product (RefSeq)
Uncharacterized protein Rv1560_MT1611
Operon # Operon
1035 Rv1557 - Rv1558 - Rv1559 - Rv1560 - Rv1561
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics
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
15608698 NP_216076.1 Run
GO:0015643

toxin binding

toxin binding

Details: 
Interacting selectively and non-covalently with a toxin, a poisonous substance that causes damage to biological systems.
GO Category: 
molecular_function
8
Total items in this category:  
GO:0045727

positive regulation of translation

positive regulation of translation

Details: 
Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA.
GO Category: 
biological_process
3
Total items in this category:  
GO:0045927

positive regulation of growth

positive regulation of growth

Details: 
Any process that activates or increases the rate or extent of growth, the increase in size or mass of all or part of an organism.
GO Category: 
biological_process
31
Total items in this category:  
GO:0075136

response to host

response to host

Details: 
Any process that results in a change in state or activity of the symbiont or its cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of detecting molecules of its host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
GO Category: 
biological_process
12
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 GSM1426696 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426697 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426698 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv1560_B363 UCSC Browser Tracks
Quantitative Proteomics Data
Cholesterol Essentiality t-test p-value Cholesterol/Glycerol Ratio
non-essential 0.500000 0.11

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 15.11 U
D3I 3 3 3.83 15.42 I
D3U 3 3 3.83 16.44 U
D5I 9 5 6.00 15.29 I
D5U 17 5 6.00 15.26 U
D7I 18 7 8.14 14.81 I
D7U 19 7 8.14 14.65 U
D14I 4 14 15.63 16.40 I
D14U 4 14 15.63 16.02 U
D17I 3 17 19.15 16.18 I
D17U 3 17 19.15 16.19 U
D21I 4 21 23.23 15.79 I
D21U 4 21 23.23 15.85 U
D24I 3 24 26.60 15.30 I
D24U 3 24 26.60 15.73 U
D28I 4 28 30.61 15.18 I
D28U 4 28 30.61 15.31 U