ChiMera: an easy to use pipeline for bacterial genome based metabolic network reconstruction, evaluation and visualization

Table 1 MEMOTE evaluation metrics

Model ID	Balance metrics			Biomass constitution			Network topology
Model ID	Stoichiometric	Mass	Charge	Biomass constitution	Missing precursors in biomass	Blocked reactions	Orphan metabolites	Dead-end metabolites
P. putida iChiMera1716	99.8	99.9	80.2	1.00	1	19	0	0
iJN1463	0	99.6	99.7	0.98	2	247	56	85
E. coli iChiMera1657	99.6	99.9	83.2	1.00	1	18	0	1
iEC1344_C	100	100	74	1.54	30	0	0	1
B. subtilis iChiMera1182	100.0	99.9	82.1	1.03	1	54	1	1
iYO844	100.0	94.4	98.9	1.04	6	50	122	21

Parameters that can influence the precision of the predictions were selected to assay Chimera and BiGG curated models. Values in the range of 1±\(1{0}^{-3}\) in Biomass Constitution are necessary to indicate a realistic biomass function

ISSN: 1471-2105