Fig. 3.

Overlap of genes in draft reconstructions for Lactobacillus plantarum with those in the manually curated model. In total, 29 networks were reconstructed with 7 tools (CarveMe: CA; MetaDraft: MD; AuReMe: AU; Pathway Tools: PT; ModelSEED: MS; RAVEN: RA; Merlin: ME). Several reconstructions, which are represented with different sub-indices, were generated for each tool using different parameters settings. Numbers inside bars represent percentages with respect to the total number of genes in iLP728. The coverage (blue bars) ranged from 49.7 to 87.8% while the percentage of additional genes (yellow bars) ranged from 4.3 to 65.0%. Most of the genes that were not recovered (dark green bars) are related to very specific metabolic functions that were carefully incorporated during the manual curation of iLP728 such as polysaccharide biosynthesis and transport