Rv0555 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase (EC 2.2.1.9)

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv0555 menD 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase (EC 2.2.1.9) CDS 646298 647962 + 1 665 554 FALSE

Rv0555 (2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase (EC 2.2.1.9)) is predicted to be co-regulated in modules bicluster_0113 with residual 0.50 and bicluster_0438 with residual 0.51.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 3.20 and 170.00 for bicluster_0113 and 2.50 and 3,200.00 for bicluster_0438 respectively.

These modules are enriched for following go terms: exodeoxyribonuclease activity, exodeoxyribonuclease activity, producing..., exonuclease activity, active with either..., deoxyribonuclease activity porphyrin-containing compound metabolic ..., porphyrin-containing compound biosynthet..., cofactor biosynthetic process, sulfur amino acid biosynthetic process, sulfur amino acid metabolic process, cofactor metabolic 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
TetR/ACRR family transcriptional regulator
No -137 0.15 0.895306 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0113
e.value: 
3.2
Motif Bicluster: 
e.value: 
170
Motif Bicluster: 
0.50
bicluster_0438
e.value: 
2.5
Motif Bicluster: 
e.value: 
3200
Motif Bicluster: 
0.51
Product (LegacyBRC) Product (RefSeq)
2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase 2-succinyl-5-enolpyruvyl-6-hydroxy-3- cyclohexene-1-carboxylate synthase
Operon # Operon
374 Rv0555 - Rv0556
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

KEGG

Ubiquinone and other terpenoid-quinone biosynthesis

7
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:  
BioCyc Gene Page Cellular Overview Map
Link to STRING STRING Network

STRING

GI Number Protein ID Blast Conserved Domains
15607695 NP_215069.1 Run
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:0040007

growth

growth

Details: 
The increase in size or mass of an entire organism, a part of an organism or a cell.
GO Category: 
biological_process
621
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 NA NA

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.