a. The average transcription rate is about 50 nucleotide per second in E.coli. The transcription rate of each transcript is calculated according to their lengths.
b. The average translation rate is about 15 amino acids per second in E.coli. The translation rate of each protein is calculated according to their amino acid numbers.
c. The average half-life of mRNAs is set to 10 min. The degradation rate is calculated according to the half-life value.
d. The average half-life of proteins is set to 2 h. The degradation rate is calculated according to the half-life value.
e. There are no data about the degradation rate constant, kinetic parameters of hdnoR. Because hdnoR is homologous to TetR protein, so the parameters related to hdnoR is from the experiment data of TetR
f. We add SrrA tag to the end of GFP, so the degradation rate is 10 times faster than the normal condition.
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