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Fig. 2 | BMC Systems Biology

Fig. 2

From: Systems biology of the structural proteome

Fig. 2

a The new GEM-PRO model for T. maritima (TM). Displayed in the pie chart on the left is the coverage of genes by a PDB structure or homology model, and a comparison of those structures available in 2009 versus 2015. In the pie chart on the right, the available PDB structures are further classified into three groups based on the overall quality of the structure: (i) high quality structures that have no mutations in the interior of the protein (112 genes involved in 210 reactions; in teal); (ii) high quality structures that have some mutations and require minimal modification to revert back to wild-type sequence (24 genes involved in 49 reactions; in light green) and low quality structures (13 genes involved in 20 reactions; blue) that may have large gaps of unresolved sections of the protein or a large number of mutations at the interior of the protein and require further homology modeling (in light blue). Determining the quality of a PDB is explained in detail in the section entitled Quality control and quality assessment of all structures. The same quality assessment evaluations were carried out for E. coli in (b)

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