Rv3563 Acyl-CoA dehydrogenase, short-chain specific (EC 1.3.99.2)

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3563 fadE32 Acyl-CoA dehydrogenase, short-chain specific (EC 1.3.99.2) CDS 4004291 4005250 + 960 319 FALSE

Rv3563 (Acyl-CoA dehydrogenase, short-chain specific (EC 1.3.99.2)) is predicted to be co-regulated in modules bicluster_0181 with residual 0.51 and bicluster_0497 with residual 0.53.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 88.00 for bicluster_0181 and 310.00 and 800.00 for bicluster_0497 respectively.

These modules are enriched for following go terms: oxidoreductase activity, acting on the C..., flavin adenine dinucleotide binding 3-hydroxyacyl-CoA dehydrogenase activity.

This gene is found to be for growth on cholesterol.

Mutant available?:

BASS Score Re-Annotated Start Tuberculist Annotated Start
-0.653 4004297 4004291
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_0181
e.value: 
0.000000000000033
Motif Bicluster: 
e.value: 
88
Motif Bicluster: 
0.51
bicluster_0497
e.value: 
310
Motif Bicluster: 
e.value: 
800
Motif Bicluster: 
0.53
Product (LegacyBRC) Product (RefSeq)
PROBABLE ACYL-CoA DEHYDROGENASE FADE32 acyl-CoA dehydrogenase FADE32
Operon # Operon
2323 - - - -
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics

PATRIC

Not assigned Not assigned
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

KEGG

Geraniol degradation

52
Total items in this category:  

KEGG

Naphthalene degradation

40
Total items in this category:  

KEGG

Biosynthesis of secondary metabolites

326
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
15610699 NP_218080.1 Run
GO:0004085

butyryl-CoA dehydrogenase activity

butyryl-CoA dehydrogenase activity

Details: 
Catalysis of the reaction: butanoyl-CoA + electron-transfer flavoprotein = 2-butenoyl-CoA + reduced electron-transfer flavoprotein.
GO Category: 
molecular_function
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.
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.000000 0.10

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: