Rv2258c Possible transcriptional regulatory protein

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv2258c Possible transcriptional regulatory protein CDS 2530836 2531897 - 1 062 353 TRUE

Rv2258c (Possible transcriptional regulatory protein) is predicted to be co-regulated in modules bicluster_0359 with residual 0.50 and bicluster_0496 with residual 0.57.

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_0359 and 0.00 and 0.00 for bicluster_0496 respectively.

These modules are enriched for following go terms: sulfur compound metabolic process.

This gene is found to be for growth on cholesterol.

Mutant available?: Yes

Last update: 11/20/2020 - 12:12
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-17995 MT2319 1085
Product (LegacyBRC) Product (RefSeq)
Possible transcriptional regulatory protein transcriptional regulator
Operon # Operon
1483 -
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
15609395 NP_216774.1 Run
GO:0005886

plasma membrane

plasma membrane

Details: 
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO Category: 
cellular_component
1284
Total items in this category:  
GO:0071456

cellular response to hypoxia

cellular response to hypoxia

Details: 
Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
GO Category: 
biological_process
7
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 GSM1426808 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426809 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426810 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426811 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426808 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426809 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426810 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426811 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv2258c_B487 UCSC Browser Tracks
Rv2258c_B618 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.500000 0.97

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: 0.000165023
p-value INH: 0.175737
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 13.78 U
D3I 3 3 3.83 13.59 I
D3U 3 3 3.83 13.28 U
D5I 9 5 6.00 14.37 I
D5U 17 5 6.00 14.06 U
D7I 18 7 8.14 14.18 I
D7U 19 7 8.14 13.45 U
D14I 4 14 15.63 13.97 I
D14U 4 14 15.63 13.15 U
D17I 3 17 19.15 14.02 I
D17U 3 17 19.15 13.06 U
D21I 4 21 23.23 14.08 I
D21U 4 21 23.23 13.32 U
D24I 3 24 26.60 14.03 I
D24U 3 24 26.60 13.18 U
D28I 4 28 30.61 14.04 I
D28U 4 28 30.61 13.44 U