Rv3316 Succinate dehydrogenase cytochrome b-556 subunit

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3316 sdhC Succinate dehydrogenase cytochrome b-556 subunit CDS 3704102 3704440 + 339 112 FALSE

Rv3316 (Succinate dehydrogenase cytochrome b-556 subunit) is predicted to be co-regulated in modules bicluster_0186 with residual 0.45 and bicluster_0469 with residual 0.61.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 0.18 for bicluster_0186 and 0.00 and 0.00 for bicluster_0469 respectively.

These modules are enriched for following go terms: generation of precursor metabolites and ..., oxidation-reduction process .

This gene is found to be non-essential for growth on cholesterol.

Mutant available?:

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_0186
e.value: 
0.00035
Motif Bicluster: 
e.value: 
0.18
Motif Bicluster: 
0.45
bicluster_0469
e.value: 
6.1e-25
Motif Bicluster: 
e.value: 
0.0000000000000038
Motif Bicluster: 
0.61
Product (LegacyBRC) Product (RefSeq)
PROBABLE SUCCINATE DEHYDROGENASE [CYTOCHROME B-556 SUBUNIT] SDHC [SUCCINIC DEHYDROGENASE] [FUMARATE REDUCTASE] [FUMARATE DEHYDROGENASE] [FUMARIC HYDROGENASE] succinate dehydrogenase cytochrome B-556 subunit
Operon # Operon
2166 Rv3316 - Rv3317
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics

PATRIC

Not assigned Not assigned
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

KEGG

Citrate cycle (TCA cycle)

35
Total items in this category:  

KEGG

Oxidative phosphorylation

47
Total items in this category:  

KEGG

Toluene degradation

13
Total items in this category:  

KEGG

Butanoate metabolism

63
Total items in this category:  

KEGG

Carbon fixation pathways in prokaryotes

42
Total items in this category:  

KEGG

Metabolic pathways

601
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
15610452 NP_217833.1 Run
GO:0000104

succinate dehydrogenase activity

succinate dehydrogenase activity

Details: 
Catalysis of the reaction: succinate + acceptor = fumarate + reduced acceptor.
GO Category: 
molecular_function
7
Total items in this category:  
GO:0006118

electron transport

electron transport

Details: 
OBSOLETE. The transport of electrons from an electron donor to an electron acceptor.
GO Category: 
biological_process
11
Total items in this category:  
GO:0006099

tricarboxylic acid cycle

tricarboxylic acid cycle

Details: 
A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
GO Category: 
biological_process
4
Total items in this category:  
GO:0016020

membrane

membrane

Details: 
Double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
GO Category: 
cellular_component
33
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
Cholesterol Essentiality t-test p-value Cholesterol/Glycerol Ratio
non-essential 0.050000 0.72

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.