Rv0252 Nitrite reductase [NAD(P)H] large subunit (EC 1.7.1.4)

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv0252 nirB Nitrite reductase [NAD(P)H] large subunit (EC 1.7.1.4) CDS 302866 305427 + 2 562 853 FALSE

Rv0252 (Nitrite reductase [NAD(P)H] large subunit (EC 1.7.1.4)) is predicted to be co-regulated in modules bicluster_0021 with residual 0.46 and bicluster_0134 with residual 0.52.

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_0021 and 0.00 and 9.50 for bicluster_0134 respectively.

These modules are enriched for following go terms: oxidoreductase activity, acting on other....

This gene is found to be for growth on cholesterol.

Mutant available?: Yes

BASS Score Distance to Tuberculist Start Codon Internal TSS Re-Annotated Start Tuberculist Annotated Start
-0.25 592 303458 302917 302866
Last update: 10/16/2017 - 17:54
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-17901 MT0266 511
Displaying 1 - 1 of 1
Gene Target Differential Expression Distance Expression pvalue Type
No results were found
Displaying 1 - 7 of 7
ChipSeq TF Differential Expression Distance Expression pvalue Type
DNA-binding response regulator
Induced -147 2.27 1.63e-19 CDS
WhiB-type transcription regulator
No -135 0.65 0.999973 CDS
HspR, transcriptional repressor of DnaK operon
No -130 -0.14 0.771506 CDS
Phosphate regulon transcriptional regulatory protein PhoB (SphR)
Induced -64 3.85 8.41e-40 CDS
Transcriptional regulator, TetR family
No 47 -0.05 0.971241 Internal.TSS
DNA-binding response regulator mtrA
No -92 0.64 0.339144 CDS
Repressed -65 -1.11 0.00117096 CDS
Motif 1 Motif 2 Residual
bicluster_0021
e.value: 
0.000000033
Motif Bicluster: 
e.value: 
0.0039
Motif Bicluster: 
0.46
bicluster_0134
e.value: 
0.00003
Motif Bicluster: 
e.value: 
9.5
Motif Bicluster: 
0.52
Product (LegacyBRC) Product (RefSeq)
PROBABLE NITRITE REDUCTASE [NAD[P]H] LARGE SUBUNIT [FAD FLAVOPROTEIN] NIRB nitrite reductase large subunit
Operon # Operon
176 -
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics

PATRIC

Nitrite reductase (NAD(P)H) Nitrogen metabolism
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

KEGG

Nitrogen metabolism

24
Total items in this category:  

KEGG

Microbial metabolism in diverse environments

296
Total items in this category:  
BioCyc Gene Page Cellular Overview Map
Link to STRING STRING Network

STRING

GI Number Protein ID Blast Conserved Domains
15607393 NP_214766.1 Run
GO:0008942

nitrite reductase [NAD(P)H] activity

nitrite reductase [NAD(P)H] activity

Details: 
Catalysis of the reaction: ammonium hydroxide + 3 NAD(P)+ + H2O = nitrite + 3 NAD(P)H + 3 H+.
GO Category: 
molecular_function
2
Total items in this category:  
GO:0005829

cytosol

cytosol

Details: 
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO Category: 
cellular_component
371
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:0042128

nitrate assimilation

nitrate assimilation

Details: 
The nitrogen metabolic process that encompasses the uptake of nitrate from the environment and reduction to ammonia, and results in the incorporation of nitrogen derived from nitrate into cellular substances.
GO Category: 
biological_process
3
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.
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.420000 1.35

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:
p-value INH: