A total of 41 (3.07%) metabolites are not produced by any reaction of the model: 2me4p_c, 2pglyc_c, 4gudbd_c, 5fthf_c, allphn_c, ...

Orphans are metabolites that are only consumed but not produced by reactions in the model. They may indicate the presence of network and knowledge gaps. Implementation: Find orphan metabolites structurally by considering only reaction equations and bounds. FBA is not carried out.

There are a total of 119 metabolites (8.91%) without a formula: __iYS854__12napdol_c, __iYS854__2mehbtpp_c, __iYS854__12diisgly_c, __iYS854__33hmeoxobut_c, __iYS854__3c1ht_c, ...

To be able to ensure that reactions are mass-balanced, all model metabolites ought to be provided with a chemical formula. Since it may be difficult to obtain formulas for certain metabolites this test serves as a mere report. Models can still be stoichiometrically consistent even when chemical formulas are not defined for each metabolite. Implementation: Check if each cobra.Metabolite has a non-empty "formula" attribute. This attribute is set by the parser if there is an fbc:chemicalFormula attribute for the corresponding species in the SBML.

This model contains 626 unconserved metabolites: for_e, pydx_c, mnl1p_c, hisp_c, pydx5p_c, ...

The list of unconserved metabolites is computed using the algorithm described in section 3.2 of "Detection of Stoichiometric Inconsistencies in Biomolecular Models." Bioinformatics 24, no. 19 (2008): 2245. doi: 10.1093/bioinformatics/btn425.