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Fig. 7 | BMC Systems Biology

Fig. 7

From: Systems biology of the structural proteome

Fig. 7

New structural systems biology applications using GEM-PRO. a The counts of different ligands from the Ligand Expo database (PDB) that are bound to holoenzyme protein structures in the E. coli GEM-PRO model and are linked to catalytic metabolic reactions. b An example of a highly promiscuous family of enzymes, transaminases, which have been shown to rescue the activity of another protein when its respective gene has been knocked out [6]. Pfam refers to shared protein fold family, '% id' refers to percent sequence identity, and '% align' refers to the 3D structural alignment of the two proteins. The plot in c demonstrates how the GEM-PRO model can be combined with experimental data, such as ribosomal profiling, to predict the in vivo abundance of proteins and their complex stoichiometry. The example shown here is that of ATP synthase, which indicates a high overlap between the complex stoichiometry stored in GEM-PRO and an experimental measurement

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