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ModelSEED / ModelSEEDDatabase

This repository contains the definitive copy of the biochemistry and metadata used to construct models using the ModelSEED/ProbAnno approach
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Possible bug with reported deltaG using NADPH #58

Open samseaver opened 7 years ago

samseaver commented 7 years ago

I've just discovered two pairs of reactions that use NADH and NADPH but deltaG is wrong for the second (NADPH) one:

seaver@twig:~/Projects/ModelSEEDDatabase/Biochemistry$ cat reactions.tsv | cut -f1,8,9,10,15,16 | grep rxn04113
rxn04113        (1) NADPH[0] + (1) H+[0] + (1) 1-Hydroxy-2-methyl-2-butenyl 4-diphosphate[0] <=> (1) H2O[0] + (1) NADP[0] + (1) Isopentenyldiphosphate[0]   >
        >       -16.86  1.23
seaver@twig:~/Projects/ModelSEEDDatabase/Biochemistry$ cat reactions.tsv | cut -f1,8,9,10,15,16 | grep rxn08756
rxn08756        (1) NADH[0] + (1) H+[0] + (1) 1-Hydroxy-2-methyl-2-butenyl 4-diphosphate[0] <=> (1) H2O[0] + (1) NAD[0] + (1) Isopentenyldiphosphate[0] <   <
        16.86   1.23

I now believe there might be a bug in my original code for heuristically handling phosphorylated compounds. I haven't got the time at the moment to follow up on this, but we will be migrating that code into Python, in this repository, and re-running it to double-check for any problems such as this one.