Rv3455c tRNA pseudouridine synthase A (EC 4.2.1.70)

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3455c truA tRNA pseudouridine synthase A (EC 4.2.1.70) CDS 3876052 3876945 - 894 297 FALSE

Rv3455c (tRNA pseudouridine synthase A (EC 4.2.1.70)) is predicted to be co-regulated in modules bicluster_0321 with residual 0.54 and bicluster_0528 with residual 0.42.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 380.00 and 15,000.00 for bicluster_0321 and 0.00 and 47.00 for bicluster_0528 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?:

BASS Score New Primary UTR Primary TSS Re-Annotated Start Tuberculist Annotated Start
-0.513 433 3877132 3876699 3876822
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_0321
e.value: 
380
Motif Bicluster: 
e.value: 
15000
Motif Bicluster: 
0.54
bicluster_0528
e.value: 
0.00023
Motif Bicluster: 
e.value: 
47
Motif Bicluster: 
0.42
Product (LegacyBRC) Product (RefSeq)
tRNA pseudouridine synthase A tRNA pseudouridine synthase A
Operon # Operon
2259
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics

PATRIC

Pseudouridylate synthase Pyrimidine metabolism
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
161352460 NP_217972.2 Run
GO:0004730

pseudouridylate synthase activity

pseudouridylate synthase activity

Details: 
Catalysis of the reaction: D-ribose 5-phosphate + uracil = H(2)O + pseudouridine 5'-phosphate.
GO Category: 
molecular_function
2
Total items in this category:  
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:  
GO:0040007

growth

growth

Details: 
The increase in size or mass of an entire organism, a part of an organism or a cell.
GO Category: 
biological_process
621
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
0.500000 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.

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: