Rv0555 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase (EC 188.8.131.52)
|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 184.108.40.206)||CDS||646298||647962||+||1 665||554||FALSE|
Rv0555 (2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase (EC 220.127.116.11)) 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 for growth on cholesterol.
|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|
|BioCyc Gene Page||Cellular Overview Map|
|t-test p-value||Cholesterol/Glycerol Ratio|
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.
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.