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. 2019 Aug 7;20:158. doi: 10.1186/s13059-019-1769-1

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© The Author(s). 2019

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Fig. 5 — Overlap of reactions in draft reconstructions for Lactobacillus plantarum with those in the manually curated model. In total, 29 networks were reconstructed with 7 tools (CarveMe: C, MetaDraft: D, AuReMe: A, Pathway Tools: P, ModelSEED: S, RAVEN: R, Merlin: E). 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 corrected number of reactions in iLP728, which is the total number of reactions in iLP728 minus the biomass-related reactions (light green). We observed a wide variation in the coverage (blue bars) and the percentage of additional reactions (yellow bars). In addition, a considerable number of reactions in the networks build with ModelSEED, RAVEN (KEGG), and Merlin contained different stoichiometry for protons than those in iLP728 (dark green bars)