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Table 11 False gene essentiality predictions for genes representing systems beyond the scope of the EcoCyc–18.0–GEM biomass function

From: A genome-scale metabolic flux model of Escherichia coli K–12 derived from the EcoCyc database

Gene HT Sim Conv Citations Comments
der + [131133] Der is essential for maintenance of 50S ribosomal subunit stability. Der’s GTPase activity regulates the specificity of its interactions with the ribosomal subunit. Regulatory GTPase activities, such as those of Der, are beyond the current scope of EcoCyc–18.0–GEM.
mrdA + [134, 135] MrdA and FtsI, often referred to as penicillin-binding proteins 2 and 3, are essential for cell division
ftsI +   and maintenance of cell shape. Ogura et al.[135] determined mrdA to be essential in K–12, while [134] determined ftsI to be essential. Modeling of the unique roles of mrdA and ftsI is beyond the current scope of EcoCyc–18.0–GEM.
suhB + [136] Wang et al.[136] studied suhB null mutants, which exhibit a cold-sensitive phenotype, and reported that they were unable to grow at 30°C, but grew well at 42°C. Growth was studied at 37°C, but not described. Heat and cold sensitivity are beyond the current scope of EcoCyc–18.0–GEM.
  1. Examples of these systems include cold response and cell envelope maintenance. The EcoCyc GEM biomass function will be expanded to incorporate the operation of these systems in future versions. See Table 7 caption for a description of column headings.