Rv0244c 3-methylmercaptopropionyl-CoA dehydrogenase (DmdC)

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv0244c fadE5 3-methylmercaptopropionyl-CoA dehydrogenase (DmdC) CDS 293798 295633 - 1 836 611 FALSE

Rv0244c (3-methylmercaptopropionyl-CoA dehydrogenase (DmdC)) is predicted to be co-regulated in modules bicluster_0331 with residual 0.41 and bicluster_0475 with residual 0.40.

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_0331 and 0.00 and 9.10 for bicluster_0475 respectively.

These modules are enriched for following go terms: primary metabolic process, cellular metabolic process, cellular process, organic substance metabolic process, cell, cell part, large ribosomal subunit, small ribosomal subunit fatty acid synthase activity.

This gene is found to be for growth on cholesterol.

Mutant available?: Yes

Last update: 10/16/2017 - 17:54
BEI Mutant Available BEI Mutant ID BEI MT Number BEI Target ID Order from BEI
Yes NR-18418 MT0258 2234
Displaying 1 - 1 of 1
Gene Target Differential Expression Distance Expression pvalue Type
No results were found
Displaying 1 - 9 of 9
ChipSeq TF Differential Expression Distance Expression pvalue Type
Transcriptional regulator, ArsR family
No 55 -0.03 0.969299 Primary.TSS
Transcriptional regulatory protein
Induced 30 1.37 0.0019303 Primary.TSS
Histone protein Lsr2
No 42 0.45 0.585389 Primary.TSS
Phosphate regulon transcriptional regulatory protein PhoB (SphR)
Repressed -3 -2 0.00000523 Primary.TSS
Transcriptional regulator, IclR family
No 48 0.12 0.941083 Primary.TSS
Transcriptional regulator, PadR family
No 32 -0.44 0.618727 Primary.TSS
No -118 0.16 0.821668 Primary.TSS
Transcriptional regulator, MarR family
No 58 -0.73 0.449138 Primary.TSS
Mycofactocin system transcriptional regulator
No -48 0.27 0.999588 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0331
e.value: 
0.0000000081
Motif Bicluster: 
e.value: 
0.00082
Motif Bicluster: 
0.41
bicluster_0475
e.value: 
0.0014
Motif Bicluster: 
e.value: 
9.1
Motif Bicluster: 
0.40
Product (LegacyBRC) Product (RefSeq)
PROBABLE ACYL-CoA DEHYDROGENASE FADE5 acyl-CoA dehydrogenase FADE5
Operon # Operon
170
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
15607385 NP_214758.1 Run
GO:0005576

extracellular region

extracellular region

Details: 
The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
GO Category: 
cellular_component
272
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:0052572

response to host immune response

response to host immune response

Details: 
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of detecting the immune response of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction.
GO Category: 
biological_process
62
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 0.13

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: