jungeng / microbiota-d3 Goto Github PK

Description of the issue:

missing ATP cost for different biomass macromolecules.

Current feature/value/output:

How the reaction/metabolite/gene/simulation actually looks in the master branch. PLEASE DELETE THIS LINE.
code/Biomass/dna.py:
only A,T,C,G
but here should have ATP consume to construct DNA macromolecule

Description of the issue:

• Currently non-mapped metabolite ids in Biomass templates

Gram-negative template
BiGG Co-eff

• 1 2fe2s -0.000026
• 53 fe2 -0.006715
• 54 fe3 -0.007808
• 94 ni2 -0.000323
• 97 pe161 -0.075214
• 113 so4 -0.004338

Gram-positive template
BiGG Co-eff

• 24 cdlp_BS -0.000005
• 35 d12dg_BS -0.000110
• 54 fe3 -0.003450
• 55 gdp -0.000180
• 62 gtca1_45_BS -0.003624
• 63 gtca2_45_BS -0.002347
• 64 gtca3_45_BS -0.001819
• 76 lipo1_24_BS -0.000007
• 77 lipo2_24_BS -0.000006
• 78 lipo3_24_BS -0.000018
• 79 lipo4_24_BS -0.000015
• 86 mql7 -0.000266
• 99 peptido_BS -0.101817
• 100 pgly_BS -0.000176
• 107 psetha_BS -0.000560
• 115 t12dg_BS -0.000066
• 116 tcam_BS -0.003112

Archaea template
metacyc_id bigg_id comp seed_id iAF692

• 3 3hdpgpe c cpd15817 -0.002698
• 4 3hdpgpg c cpd15818 -0.01012
• 6 3hdpgps c cpd15820 -0.01147
• 9 adocblhbi c cpd15834 -0.00474
• 40 dpgpi c cpd15860 -0.002698
• 45 f420_2 c cpd00649 -4.3e-05
• 46 f420_3 c cpd15868 -2.6e-05
• 47 f420_4 c cpd15869 -0.000374
• 48 f420_5 c cpd15870 -0.000299
• 49 f420_6 c cpd15871 -1.1e-05
• 50 f420_7 c cpd15872 -1e-06
• 51 f430 c -0.002
• 56 gdpgpi c cpd15880 -0.01619
• 60 glycogen c cpd00155 -0.01543