Rv2711 Iron-dependent repressor IdeR/DtxR

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv2711 ideR Iron-dependent repressor IdeR/DtxR CDS 3023565 3024257 + 693 230 FALSE

Rv2711 (Iron-dependent repressor IdeR/DtxR) is predicted to be co-regulated in modules bicluster_0073 with residual 0.60 and bicluster_0335 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_0073 and 57.00 and 1,600.00 for bicluster_0335 respectively.

These modules are enriched for following go terms: .

This gene is found to be 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 - 1 of 1
ChipSeq TF Differential Expression Distance Expression pvalue Type
No results were found
Motif 1 Motif 2 Residual
bicluster_0073
e.value: 
0.0000015
Motif Bicluster: 
e.value: 
0.000047
Motif Bicluster: 
0.60
bicluster_0335
e.value: 
57
Motif Bicluster: 
e.value: 
1600
Motif Bicluster: 
0.58
Product (LegacyBRC) Product (RefSeq)
Iron-dependent repressor ideR IRON-dependent repressor and activator IDER
Operon # Operon
1780
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
15609848 NP_217227.1 Run
GO:0003677

DNA binding

DNA binding

Details: 
Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid).
GO Category: 
molecular_function
37
Total items in this category:  
GO:0005506

iron ion binding

iron ion binding

Details: 
Interacting selectively and non-covalently with iron (Fe) ions.
GO Category: 
molecular_function
13
Total items in this category:  
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:0006979

response to oxidative stress

response to oxidative stress

Details: 
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
GO Category: 
biological_process
13
Total items in this category:  
GO:0008198

ferrous iron binding

ferrous iron binding

Details: 
Interacting selectively and non-covalently with ferrous iron, Fe(II).
GO Category: 
molecular_function
1
Total items in this category:  
GO:0008270

zinc ion binding

zinc ion binding

Details: 
Interacting selectively and non-covalently with zinc (Zn) ions.
GO Category: 
molecular_function
15
Total items in this category:  
GO:0016151

nickel cation binding

nickel cation binding

Details: 
Interacting selectively and non-covalently with nickel (Ni) cations.
GO Category: 
molecular_function
6
Total items in this category:  
GO:0045892

negative regulation of transcription, DNA-dependent

negative regulation of transcription, DNA-dependent

Details: 
Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-dependent transcription.
GO Category: 
biological_process
10
Total items in this category:  
GO:0019290

siderophore biosynthetic process

siderophore biosynthetic process

Details: 
The chemical reactions and pathways resulting in the formation of siderophores, low molecular weight Fe(III)-chelating substances made by aerobic or facultatively anaerobic bacteria, especially when growing under iron deficient conditions. The complexes of Fe(3+)-siderophores have very high stability constants and are taken up by specific transport systems by microorganisms; the subsequent release of iron requires enzymatic action.
GO Category: 
biological_process
6
Total items in this category:  
GO:0030145

manganese ion binding

manganese ion binding

Details: 
Interacting selectively and non-covalently with manganese (Mn) ions.
GO Category: 
molecular_function
31
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 GSM1426856 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426857 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426858 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv2711_B191 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
NA NA

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: 0.0576462
p-value INH: 0.748902
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 11.42 U
D3I 3 3 3.83 10.43 I
D3U 3 3 3.83 9.96 U
D5I 9 5 6.00 11.87 I
D5U 17 5 6.00 11.42 U
D7I 18 7 8.14 11.43 I
D7U 19 7 8.14 10.79 U
D14I 4 14 15.63 8.89 I
D14U 4 14 15.63 8.21 U
D17I 3 17 19.15 8.53 I
D17U 3 17 19.15 7.41 U
D21I 4 21 23.23 8.85 I
D21U 4 21 23.23 7.80 U
D24I 3 24 26.60 7.70 I
D24U 3 24 26.60 6.85 U
D28I 4 28 30.61 8.30 I
D28U 4 28 30.61 7.04 U