Rv3562 Acyl-CoA dehydrogenase, short-chain specific (EC 1.3.99.2)

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3562 fadE31 Acyl-CoA dehydrogenase, short-chain specific (EC 1.3.99.2) CDS 4003161 4004294 + 1 134 377 FALSE

Rv3562 (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?: Yes

Last update: 10/16/2017 - 15:33
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-14928 MT3667 280
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 FADE31 acyl-CoA dehydrogenase FADE31
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
15610698 NP_218079.1 Run
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
0.110000 0.02

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: