The genome-scale metabolic model iCY1106 reconstructed in this study included 1106 genes representing 9.51% of the 11631 protein-coding genes in the genome of M. alpina ATCC 32222. The model consisted of 1854 reactions and 1732 metabolites (Table 1). Compared with the previous model constructed by Vongsangnak [21], iCY1106 is more detailed and contains a higher degree of functional information that can be used in in silico simulations. During the construction of iCY1106, some missing gene were added from the Vongsangnak’s model such as MA-090-247, which encodes an asparaginase (EC: 3.5.1.1), and catalyzes the transformation of L-asparagine into L-aspartate. When compared with the existing model, many improvements in iCY1106 are apparent. (1) A total of 139 transport proteins were annotated based on TCDB and TransportDB. (2) A total of 216 exchange reactions were added into model iCY1106. (3) Biomass composition of M. alpina was calculated based on literature mining. (4) Additional chemical reactions were also included. (5) The reversibility of some reactions was redefined according to MetaCyc and BioPath databases. For example, in the published model, the reaction catalyzed by aldehyde dehydrogenase (EC: 1.2.1.3) was reversible, whereas this reaction is irreversible according to BioPath. The flux distribution of iCY1106 was normal following this change.
Table 1  General features of model i CY1106
Features  i CY1106  Existed model a
Genome feature
 Genome size (Mb) 38.38 38.38
 Total open reading frames (ORFs) 11631 11631
Metabolic model
 Total reactions 1854 1183
 Biochemical reactions 1391 1183
 Transport reactions 247 none
 Exchange reactions 216 none
 Metabolites 1732 1660
 ORFs associated in model 1106 1042
 ORF coverageb (%) 9.51 8.95
aThe existed model was constructed by Vongsangnak et al. [21]; bThe number of ORFs incorporated in model iCY1106 divided by the total number of ORFs.