search

C-CoMP-STC / GEM-mit1002

Creative Commons Attribution 4.0 International
0 stars 0 forks source link

Check bounds of reactions making ATP #9

Closed hgscott closed 9 months ago

hgscott commented 1 year ago

There may be some reactions that are producing ATP when they shouldn't.

hgscott commented 1 year ago

I printed the information of reactions where ATP is a product, or where ATP is a reactant and the lower bound is less than 0:

rxn00225_c0 | ACKr | Bounds: [-1000.0, 0.0] | ATP:acetate phosphotransferase_c0 | -1.0 ATP_c0 (cpd00002_c0) + -1.0 Acetate_c0 (cpd00029_c0) + 1.0 ADP_c0 (cpd00008_c0) + 1.0 Acetylphosphate_c0 (cpd00196_c0)
rxn00148_c0 | ['CDC19', 'PYK', 'PYK2'] | Bounds: [-1000.0, 0.0] | ATP:pyruvate 2-O-phosphotransferase_c0 | -1.0 ATP_c0 (cpd00002_c0) + -1.0 Pyruvate_c0 (cpd00020_c0) + 1.0 ADP_c0 (cpd00008_c0) + 1.0 Phosphoenolpyruvate_c0 (cpd00061_c0) + 1.0 H+_c0 (cpd00067_c0)
rxn01100_c0 | ['PGK1', 'PGK'] | Bounds: [-1000.0, 1000.0] | ATP:3-phospho-D-glycerate 1-phosphotransferase_c0 | -1.0 ATP_c0 (cpd00002_c0) + -1.0 3-Phosphoglycerate_c0 (cpd00169_c0) + 1.0 ADP_c0 (cpd00008_c0) + 1.0 1,3-Bisphospho-D-glycerate_c0 (cpd00203_c0)
rxn00770_c0 | No BiGG ID | Bounds: [-1000.0, 1000.0] | ATP:D-ribose-5-phosphate diphosphotransferase_c0 | -1.0 ATP_c0 (cpd00002_c0) + -1.0 ribose-5-phosphate_c0 (cpd00101_c0) + 1.0 AMP_c0 (cpd00018_c0) + 1.0 H+_c0 (cpd00067_c0) + 1.0 PRPP_c0 (cpd00103_c0)
rxn00216_c0 | ['HXK1_2', 'GLK1_1', 'HXK2_2', 'HEX1'] | Bounds: [-1000.0, 1000.0] | ATP:D-glucose 6-phosphotransferase_c0 | -1.0 ATP_c0 (cpd00002_c0) + -1.0 D-Glucose_c0 (cpd00027_c0) + 1.0 ADP_c0 (cpd00008_c0) + 1.0 H+_c0 (cpd00067_c0) + 1.0 D-glucose-6-phosphate_c0 (cpd00079_c0)
rxn00077_c0 | ['YEL041W_2', 'UTR1_1', 'YEL041W_1', 'NADK', 'POS5_1', 'UTR1_2', 'NADKm', 'POS5_2'] | Bounds: [-1000.0, 1000.0] | ATP:NAD+ 2'-phosphotransferase_c0 | -1.0 ATP_c0 (cpd00002_c0) + -1.0 NAD_c0 (cpd00003_c0) + 1.0 NADP_c0 (cpd00006_c0) + 1.0 ADP_c0 (cpd00008_c0) + 1.0 H+_c0 (cpd00067_c0)
rxn08173_c0 | ['ATPS4r', 'ATPS4rpp'] | Bounds: [0.0, 1000.0] | F(1)-ATPase_c0 | -1.0 Phosphate_c0 (cpd00009_c0) + -4.0 H+_e0 (cpd00067_e0) + -1.0 ADP_c0 (cpd00008_c0) + 3.0 H+_c0 (cpd00067_c0) + 1.0 ATP_c0 (cpd00002_c0) + 1.0 H2O_c0 (cpd00001_c0)
rxn01673_c0 | ['YNK1_5', 'NDPK7'] | Bounds: [-1000.0, 1000.0] | ATP:dCDP phosphotransferase_c0 | -1.0 ATP_c0 (cpd00002_c0) + -1.0 dCDP_c0 (cpd00533_c0) + 1.0 ADP_c0 (cpd00008_c0) + 1.0 dCTP_c0 (cpd00356_c0)
rxn08137_c0 | AP5AH | Bounds: [-1000.0, 1000.0] | P1,P5-bis(5'-adenosyl)pentaphosphate nucleotidohydrolase (ATP-forming)_c0 | -1.0 H2O_c0 (cpd00001_c0) + -1.0 Bis(5'-adenosyl) pentaphosphate_c0 (cpd02511_c0) + 1.0 ATP_c0 (cpd00002_c0) + 1.0 ADP_c0 (cpd00008_c0)
rxn00789_c0 | ['ATPPRT', 'HIS1', 'ATPPRTr'] | Bounds: [-1000.0, 0.0] | 1-(5-phospho-D-ribosyl)-ATP:diphosphate phospho-alpha-D-ribosyl-transferase_c0 | -1.0 PPi_c0 (cpd00012_c0) + -1.0 H+_c0 (cpd00067_c0) + -1.0 Phosphoribosyl-ATP_c0 (cpd01775_c0) + 1.0 ATP_c0 (cpd00002_c0) + 1.0 PRPP_c0 (cpd00103_c0)
rxn00097_c0 | ['ADK2_1', 'ADK1_1', 'ADK1m', 'ADK1'] | Bounds: [-1000.0, 1000.0] | ATP:AMP phosphotransferase_c0 | -1.0 ATP_c0 (cpd00002_c0) + -1.0 AMP_c0 (cpd00018_c0) + -1.0 H+_c0 (cpd00067_c0) + 2.0 ADP_c0 (cpd00008_c0)
rxn00237_c0 | ['YNK1_8', 'NDPK1'] | Bounds: [-1000.0, 1000.0] | ATP:GDP phosphotransferase_c0 | -1.0 ATP_c0 (cpd00002_c0) + -1.0 GDP_c0 (cpd00031_c0) + 1.0 ADP_c0 (cpd00008_c0) + 1.0 GTP_c0 (cpd00038_c0)
rxn01509_c0 | ['GUK1_2', 'DGK1'] | Bounds: [-1000.0, 1000.0] | ATP:dGMP phosphotransferase_c0 | -1.0 ATP_c0 (cpd00002_c0) + -1.0 H+_c0 (cpd00067_c0) + -1.0 dGMP_c0 (cpd00296_c0) + 1.0 ADP_c0 (cpd00008_c0) + 1.0 dGDP_c0 (cpd00295_c0)
rxn09176_c0 | PPKr | Bounds: [-1000.0, 1000.0] | polyphosphate kinase_c0 | -1.0 ATP_c0 (cpd00002_c0) + -1.0 Phosphate_c0 (cpd00009_c0) + 1.0 ADP_c0 (cpd00008_c0) + 1.0 PPi_c0 (cpd00012_c0)
rxn01678_c0 | ['YNK1_4', 'NDPK6'] | Bounds: [-1000.0, 1000.0] | ATP:dUDP phosphotransferase_c0 | -1.0 ATP_c0 (cpd00002_c0) + -1.0 dUDP_c0 (cpd00978_c0) + 1.0 ADP_c0 (cpd00008_c0) + 1.0 dUTP_c0 (cpd00358_c0)
rxn00515_c0 | ['NDPK9', 'YNK1_9'] | Bounds: [-1000.0, 1000.0] | ATP:IDP phosphotransferase_c0 | -1.0 ATP_c0 (cpd00002_c0) + -1.0 IDP_c0 (cpd00090_c0) + 1.0 ADP_c0 (cpd00008_c0) + 1.0 ITP_c0 (cpd00068_c0)
rxn01353_c0 | ['NDPK5', 'YNK1_3'] | Bounds: [-1000.0, 1000.0] | ATP:dGDP phosphotransferase_c0 | -1.0 ATP_c0 (cpd00002_c0) + -1.0 dGDP_c0 (cpd00295_c0) + 1.0 ADP_c0 (cpd00008_c0) + 1.0 dGTP_c0 (cpd00241_c0)
rxn02155_c0 | ['NNAT', 'YLR328W_2', 'NNATr', 'YLR328W_1', 'NNATm'] | Bounds: [-1000.0, 1000.0] | ATP:nicotinamide-nucleotide adenylyltransferase_c0 | -1.0 ATP_c0 (cpd00002_c0) + -1.0 Nicotinate ribonucleotide_c0 (cpd00873_c0) + 1.0 PPi_c0 (cpd00012_c0) + 1.0 Deamido-NAD_c0 (cpd00638_c0)
rxn01987_c0 | ['DRBK', 'RBK1_2', 'DRBKr'] | Bounds: [-1000.0, 1000.0] | R02750_c0 | -1.0 ADP_c0 (cpd00008_c0) + -1.0 H+_c0 (cpd00067_c0) + -1.0 deoxyribose-5-phosphate_c0 (cpd00510_c0) + 1.0 ATP_c0 (cpd00002_c0) + 1.0 Thyminose_c0 (cpd01242_c0)
rxn01512_c0 | ['YNK1_6', 'NDPK4'] | Bounds: [-1000.0, 1000.0] | ATP:dTDP phosphotransferase_c0 | -1.0 ATP_c0 (cpd00002_c0) + -1.0 dTDP_c0 (cpd00297_c0) + 1.0 ADP_c0 (cpd00008_c0) + 1.0 TTP_c0 (cpd00357_c0)
rxn01127_c0 | ['DADK', 'U19'] | Bounds: [-1000.0, 1000.0] | ATP:dAMP phosphotransferase_c0 | -1.0 ATP_c0 (cpd00002_c0) + -1.0 H+_c0 (cpd00067_c0) + -1.0 dAMP_c0 (cpd00294_c0) + 1.0 ADP_c0 (cpd00008_c0) + 1.0 dADP_c0 (cpd00177_c0)
rxn00119_c0 | ['UMPK', 'URA6_1', 'URIDK1', 'UMPKURIDK1', 'URA6_2', 'UMPKn'] | Bounds: [-1000.0, 1000.0] | ATP:UMP phosphotransferase_c0 | -1.0 ATP_c0 (cpd00002_c0) + -1.0 H+_c0 (cpd00067_c0) + -1.0 UMP_c0 (cpd00091_c0) + 1.0 ADP_c0 (cpd00008_c0) + 1.0 UDP_c0 (cpd00014_c0)
rxn00409_c0 | ['YNK1_2', 'NDPK3'] | Bounds: [-1000.0, 1000.0] | ATP:CDP phosphotransferase_c0 | -1.0 ATP_c0 (cpd00002_c0) + -1.0 CDP_c0 (cpd00096_c0) + 1.0 ADP_c0 (cpd00008_c0) + 1.0 CTP_c0 (cpd00052_c0)
rxn02517_c0 | No BiGG ID | Bounds: [-1000.0, 1000.0] | ATP:dIDP phosphotransferase_c0 | -1.0 ATP_c0 (cpd00002_c0) + -1.0 dIDP_c0 (cpd00976_c0) + 1.0 ADP_c0 (cpd00008_c0) + 1.0 dITP_c0 (cpd00977_c0)
rxn00239_c0 | ['GK1', 'GUK1_1'] | Bounds: [-1000.0, 1000.0] | ATP:GMP phosphotransferase_c0 | -1.0 ATP_c0 (cpd00002_c0) + -1.0 H+_c0 (cpd00067_c0) + -1.0 GMP_c0 (cpd00126_c0) + 1.0 ADP_c0 (cpd00008_c0) + 1.0 GDP_c0 (cpd00031_c0)
rxn00104_c0 | ['PPK2r', 'PPK2', 'PPIK'] | Bounds: [-1000.0, 1000.0] | polyphosphate kinase_c0 | -1.0 ATP_c0 (cpd00002_c0) + -1.0 PPi_c0 (cpd00012_c0) + -1.0 H+_c0 (cpd00067_c0) + 1.0 ADP_c0 (cpd00008_c0) + 1.0 Triphosphate_c0 (cpd00421_c0)
rxn00117_c0 | ['NDPK2', 'YNK1_1'] | Bounds: [-1000.0, 1000.0] | ATP:UDP phosphotransferase_c0 | -1.0 ATP_c0 (cpd00002_c0) + -1.0 UDP_c0 (cpd00014_c0) + 1.0 ADP_c0 (cpd00008_c0) + 1.0 UTP_c0 (cpd00062_c0)
rxn00839_c0 | ['NDPK8', 'YNK1_7'] | Bounds: [-1000.0, 1000.0] | ATP:dADP phosphotransferase_c0 | -1.0 ATP_c0 (cpd00002_c0) + -1.0 dADP_c0 (cpd00177_c0) + 1.0 ADP_c0 (cpd00008_c0) + 1.0 dATP_c0 (cpd00115_c0)
rxn42230_c0 | No BiGG ID | Bounds: [-1000.0, 1000.0] | rxn42230_c0 | -2.0 ATP_c0 (cpd00002_c0) + -1.0 Reduced-Flavoproteins_c0 (cpd28070_c0) + -2.0 Cbi(II)_c0 (cpd33817_c0) + 3.0 H+_c0 (cpd00067_c0) + 2.0 Triphosphate_c0 (cpd00421_c0) + 2.0 Adenosyl cobinamide_c0 (cpd03918_c0) + 1.0 Oxidized-Flavoproteins_c0 (cpd27744_c0)
rxn16574_c0 | No BiGG ID | Bounds: [-1000.0, 1000.0] | ATP:molybdopterin adenylyltransferase_c0 | -1.0 ATP_c0 (cpd00002_c0) + -1.0 Molybdopterin_c0 (cpd03520_c0) + 1.0 PPi_c0 (cpd00012_c0) + 1.0 Adenylated molybdopterin_c0 (cpd21090_c0)
rxn05148_c0 | HEMEti | Bounds: [-1000.0, 1000.0] | Heme transport via ABC system_c0 | -1.0 ATP_c0 (cpd00002_c0) + -1.0 H2O_c0 (cpd00001_c0) + -1.0 Heme_e0 (cpd00028_e0) + 1.0 H+_c0 (cpd00067_c0) + 1.0 Phosphate_c0 (cpd00009_c0) + 1.0 Heme_c0 (cpd00028_c0) + 1.0 ADP_c0 (cpd00008_c0)
rxn08192_c0 | ['CBL1abc', 'CBL1abcpp'] | Bounds: [-1000.0, 1000.0] | ABC-5-RXN.cp_c0 | -1.0 Cbl_e0 (cpd00635_e0) + -1.0 ATP_c0 (cpd00002_c0) + -1.0 H2O_c0 (cpd00001_c0) + 1.0 H+_c0 (cpd00067_c0) + 1.0 Phosphate_c0 (cpd00009_c0) + 1.0 Cbl_c0 (cpd00635_c0) + 1.0 ADP_c0 (cpd00008_c0)
rxn01517_c0 | ['URIDK3', 'URIDK2rn', 'URIDK2r', 'URIDK2', 'URA6_3'] | Bounds: [-1000.0, 0.0] | ATP:dUMP phosphotransferase_c0 | -1.0 H+_c0 (cpd00067_c0) + -1.0 dUMP_c0 (cpd00299_c0) + -1.0 ATP_c0 (cpd00002_c0) + 1.0 ADP_c0 (cpd00008_c0) + 1.0 dUDP_c0 (cpd00978_c0)
rxn10663_c0 | FAO11 | Bounds: [-1000.0, 0.0] | Fatty acid oxidation (n-C16:1)_c0 | -1.0 hexadecenoate_c0 (cpd15237_c0) + -6.0 FAD_c0 (cpd00015_c0) + -1.0 ATP_c0 (cpd00002_c0) + -8.0 CoA_c0 (cpd00010_c0) + -7.0 NAD_c0 (cpd00003_c0) + -7.0 H2O_c0 (cpd00001_c0) + 1.0 AMP_c0 (cpd00018_c0) + 1.0 PPi_c0 (cpd00012_c0) + 2.0 H+_c0 (cpd00067_c0) + 8.0 Acetyl-CoA_c0 (cpd00022_c0) + 7.0 NADH_c0 (cpd00004_c0) + 6.0 FADH2_c0 (cpd00982_c0)
hgscott commented 1 year ago

I looked up all the reactions in the E. coli model and found the following reactions whose bounds did not match the bounds in E. coli:

There were also a few reactions that were not present in the E. coli model.

hgscott commented 1 year ago

I ran the model with those updated bounds, but am still getting significant flux making ATP through 2 reactions.

hgscott commented 1 year ago

I tried blocking any reaction other than ATPase from making ATP and that caused 0 growth.

hgscott commented 11 months ago

Cannot make progress on this until the new MS2 model can grow on the expected carbon source(s).

hgscott commented 11 months ago

For the new MS2 model, before there is growth, check the bounds manually. Check the delta G value (can get from the ModelSEED database json file), or even ask ChatGPT if that reaction should be reversible.

Josh Goldford (sp?) in his Nature Ecology paper did something similar?

hgscott commented 10 months ago

I don't think I need to do this anymore since using the MEMOTE tool and then fixing the cycle I found fixed any erroneous ATP generation.