Rv2801c Programmed cell death toxin YdcE

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv2801c mazF9 Programmed cell death toxin YdcE CDS 3110167 3110523 - 357 118 FALSE

Rv2801c (Programmed cell death toxin YdcE) is predicted to be co-regulated in modules bicluster_0058 with residual 0.53 and bicluster_0375 with residual 0.45.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 3.10 for bicluster_0058 and 0.00 and 0.01 for bicluster_0375 respectively.

These modules are enriched for following go terms: acetyl-CoA C-acyltransferase activity .

This gene is found to be for growth on cholesterol.

Mutant available?:

BASS Score Re-Annotated Start Tuberculist Annotated Start
-0.855 3110520 3110523
Product (LegacyBRC) Product (RefSeq)
Putative uncharacterized protein
Operon # Operon
1839
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
15609938 NP_217317.1 Run
GO:0008150

biological_process

biological_process

Details: 
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
GO Category: 
biological_process
66
Total items in this category:  
GO:0008150

biological_process

biological_process

Details: 
Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
GO Category: 
biological_process
66
Total items in this category:  
GO:0004521

endoribonuclease activity

endoribonuclease activity

Details: 
Catalysis of the hydrolysis of ester linkages within ribonucleic acid by creating internal breaks.
GO Category: 
molecular_function
3
Total items in this category:  
GO:0006402

mRNA catabolic process

mRNA catabolic process

Details: 
The chemical reactions and pathways resulting in the breakdown of mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes.
GO Category: 
biological_process
3
Total items in this category:  
GO:0045926

negative regulation of growth

negative regulation of growth

Details: 
Any process that stops, prevents or reduces the rate or extent of growth, the increase in size or mass of all or part of an organism.
GO Category: 
biological_process
36
Total items in this category:  
No TFOE experiment results were found
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.340000 0.75

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: