Table 1.

Comparison of model properties of Recon 2, Recon 2Q, Recon 2.2, Recon 2M.1, and Recon 2M.2

PropertyRecon 2Recon 2QRecon 2.2Recon 2M.1Recon 2M.2
Total no. of reactions7,4407,3277,7855,8255,842
Total no. of metabolites5,0634,9625,3243,3683,368
No. of unique metabolites2,6262,5312,6521,7351,735
No. of transcripts2,1942,167N/A15,692 (Ensembl)15,597 (Ensembl)
4,028 (RefSeq)4,005 (RefSeq)
14,094 (UCSC)14,004 (UCSC)
No. of unique genes1,7891,7751,6741,6821,663
No. of blocked reactions (% of all reactions)1,603 (21.5%)1,546 (21.1%)1,863 (23.9%)744 (12.8%)737 (12.6%)
No. of dead-end metabolites (% of all metabolites)1,176 (23.2%)1,066 (21.5%)1,088 (20.4%)239 (7.1%)240 (7.1%)
No. of balanced reactions (% of all reactions)6,340 (85.2%)6,242 (85.2%)7,035 (90.4%)4,568 (78.4%)4,574 (78.3%)
No. of gene-mediated reactions (% of all reactions)3,918 (52.7%)3,879 (52.9%)4,727 (60.7%)3,914 (67.2%)3,940 (67.4%)
No. of metabolites with chemical formula (% of all metabolites)4,877 (96.3%)4,807 (96.9%)5,318 (99.9%)3,310 (98.3%)3,310 (98.3%)
No. of metabolites with compound IDs of ChEBI, HMDB, HumanCyc and/or KEGG (% of all metabolites)3,081 (60.9%)3,341 (67.3%)3,274 (61.0%)2,321 (68.9%)2,321 (68.9%)
No. of metabolites with structural information using InChI and/or SMILES (% of all metabolites)2,914 (57.6%)3,023 (60.9%)3,360 (63.1%)2,333 (69.3%)2,333 (69.3%)