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. 2020 May 30;11:e00132. doi: 10.1016/j.mec.2020.e00132

Fig. 2.

Fig. 2

Characteristics of iDT1278. A) Comparison among the template models (Escherichia coli str. K-12 substr. MG1655, Klebsiella pneumoniae subsp. pneumoniae MGH 78578, Geobacter metallireducens GS-15, Clostridium ljungdahlii DSM 13528 and Methanosarcina barkeri str. Fusaro) and iDT1278 reactions. The six models share 208 core metabolic reactions. A. vinelandii DJ model contains 112 unique reactions related to aromatic compounds metabolism, alginate and PHB production, etc. B) Number of reactions in the template models and A. vinelandii DJ. C) Change in the number of reactions, metabolites and genes at the different stages of the reconstruction process/manual curation of A. vinelandii DJ. D) Reactions distribution through the subsystems in the genome-scale model; subsystems were grouped into 11 groups summarizing the complete metabolism of A. vinelandii DJ. Nitrogen fixation, PHB, and alginate production are highlighted in the condensed pathway diagrams. Alginate accumulation occurs in the extracellular space meanwhile PHB storage happens in the cytoplasm compartment. Nitrogen fixation in A. vinelandii can be performed by different specialized nitrogenases.