Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

(d)NTP <-> (d)NMP + PPi Reactions Should Be Irreversible #527

Closed
Devlin-Moyer opened this issue Apr 5, 2023 · 8 comments
Closed

(d)NTP <-> (d)NMP + PPi Reactions Should Be Irreversible #527

Devlin-Moyer opened this issue Apr 5, 2023 · 8 comments
Labels
bug

Comments

@Devlin-Moyer
Copy link
Collaborator

Devlin-Moyer commented Apr 5, 2023 •
edited
Loading

Technically, the reaction ATP + H2O <-> AMP + PPi is almost perfectly reversible at physiological temperatures and pHs, but all cells express pyrophosphatases that rapidly hydrolyze all pyrophosphate into free inorganic phosphates (PPi + H2O -> 2 Pi; a very irreversible reaction), specifically so that all of these pyrophosphate-producing reactions are driven in the pyrophosphate-producing direction and wind up being effectively irreversible (source).
In Human1, most reactions that have a (d)NTP on one side and pyrophosphate on the other are reversible, and while this is technically not wrong, it allows FBA to predict very large ATP-producing fluxes from unrealistic sources, because FBA is under no obligation to ensure that most of the pyrophosphate produced from (d)NTPs winds up going through the pyrophosphatase reactions (MAR03975, MAR03977, MAR03979, MAR06912, MAR07794) if it can also run all these ATP <-> AMP + PPi reactions in the ATP-producing direction.
There are quite a few reactions like this, so I used this bit of code to find all of them and set either the upper or lower bound to zero:

for r in model.reactions:
    # skip the pyrophosphate exchange and pyrophosphatase reactions
    pi_in_rxn = any(m.id.startswith('MAM02751') for m in r.metabolites)
    # also skip reactions that are already irreversible
    if (r not in model.boundary) and not pi_in_rxn and r.reversibility:
        # figure out if pyrophosphate is a product or reactant (or both)
        ppi_prod = any(m.id.startswith('MAM02759') for m in r.products)
        ppi_reac = any(m.id.startswith('MAM02759') for m in r.reactants)
        if ppi_prod and not ppi_reac:
            r.lower_bound = 0
        elif ppi_reac and not ppi_prod:
            r.upper_bound = 0
Upper Bounds Should Be Zero MAR00156 MAR00165 MAR00168 MAR00171 MAR00174 MAR00177 MAR00180 MAR00184 MAR00188 MAR00192 MAR00196 MAR00209 MAR00213 MAR00217 MAR00226 MAR00233 MAR00237 MAR00245 MAR00249 MAR00259 MAR00267 MAR00271 MAR00279 MAR00283 MAR00293 MAR00301 MAR00305 MAR00309 MAR00313 MAR00319 MAR00323 MAR00327 MAR00331 MAR00337 MAR00341 MAR00345 MAR00349 MAR00353 MAR00357 MAR00361 MAR00365 MAR00377 MAR00397 MAR00401 MAR00405 MAR00409 MAR00413 MAR00437 MAR01157 MAR01158 MAR01159 MAR01160 MAR01200 MAR01201 MAR01202 MAR01203 MAR01263 MAR01264 MAR01265 MAR01266 MAR01290 MAR01465 MAR01532 MAR01726 MAR01727 MAR01841 MAR01842 MAR01844 MAR01848 MAR02942 MAR02943 MAR02944 MAR02945 MAR02948 MAR02949 MAR02951 MAR02952 MAR02954 MAR02956 MAR02957 MAR02961 MAR02963 MAR02965 MAR02966 MAR02967 MAR02970 MAR02971 MAR02972 MAR02973 MAR02974 MAR02975 MAR02976 MAR02977 MAR02978 MAR02979 MAR02980 MAR02981 MAR02982 MAR02983 MAR02984 MAR02985 MAR02988 MAR02991 MAR02992 MAR02994 MAR02996 MAR02998 MAR03480 MAR03482 MAR03493 MAR03797 MAR04085 MAR04086 MAR04262 MAR04401 MAR04418 MAR04452 MAR04532 MAR04536 MAR04577
Lower Bounds Should Be Zero MAR00200 MAR00204 MAR00241 MAR00255 MAR00275 MAR00289 MAR00297 MAR00369 MAR00373 MAR00381 MAR00385 MAR00389 MAR00393 MAR00417 MAR00421 MAR00425 MAR00429 MAR00433 MAR00737 MAR00740 MAR01248 MAR01249 MAR01250 MAR01251 MAR01832 MAR01833 MAR02026 MAR02120 MAR02147 MAR02946 MAR02947 MAR02955 MAR02962 MAR02964 MAR02968 MAR02969 MAR02986 MAR02987 MAR02989 MAR02990 MAR02999 MAR03000 MAR03001 MAR03002 MAR03003 MAR03387 MAR03389 MAR03489 MAR03801 MAR03803 MAR03805 MAR03846 MAR03872 MAR03874 MAR04254 MAR04257 MAR04276 MAR04460 MAR04727 MAR08990
@feiranl
Copy link
Collaborator

feiranl commented Apr 9, 2023 •
edited
Loading

Here is one example for this: MAR00156 AMP [c] + PPi [c] + butyryl-CoA [c] ⇔ ATP [c] + CoA [c] + butyrate [c], while in MetatCyc curated rxn, the reaction is irreversible with the direction of ATP consumption.

Please go ahead and make the changes and commits. Instead of setting the upper bound to be 0, I would suggest to revert the rxn and set the lb to be 0 and ub to be 1000 for consistence.

@Devlin-Moyer
Copy link
Collaborator Author

I would love to, except I don't really know how; I've only ever made these changes to a local copy of Human1 using Cobrapy, and after looking at all the changes made in #525, it seems like a pretty different process than editing a Cobrapy Model object.

@haowang-bioinfo
Copy link
Member

I would love to, except I don't really know how; I've only ever made these changes to a local copy of Human1 using Cobrapy

@Devlin-Moyer how about first list the reactions you locally changed under this issue, probably as a table for double check

@Devlin-Moyer
Copy link
Collaborator Author

like this?

reaction ID reaction change
MAR00200 (9E)-tetradecenoic acid + ATP + CoA <-> (9E)-tetradecenoyl-CoA + AMP + PPi set lower bound to 0
MAR00204 (7Z)-tetradecenoic acid + ATP + CoA <-> (7Z)-tetradecenoyl-CoA + AMP + PPi set lower bound to 0
MAR00241 (10Z)-heptadecenoic acid + ATP + CoA <-> (10Z)-heptadecenoyl-CoA + AMP + PPi set lower bound to 0
MAR00255 (13Z)-octadecenoic acid + ATP + CoA <-> (13Z)-octadecenoyl-CoA + AMP + PPi set lower bound to 0
MAR00275 (6Z,9Z)-octadecadienoic acid + ATP + CoA <-> (6Z,9Z)-octadecadienoyl-CoA + AMP + PPi set lower bound to 0
MAR00289 (13Z)-eicosenoic acid + ATP + CoA <-> (13Z)-eicosenoyl-CoA + AMP + PPi set lower bound to 0
MAR00297 9-eicosenoic acid + ATP + CoA <-> 9-eicosenoyl-CoA + AMP + PPi set lower bound to 0
MAR00369 (9Z,12Z,15Z,18Z,21Z)-TPA + ATP + CoA <-> (9Z,12Z,15Z,18Z,21Z)-tetracosapentaenoyl-CoA + AMP + PPi set lower bound to 0
MAR00373 (6Z,9Z,12Z,15Z,18Z,21Z)-THA + ATP + CoA <-> (6Z,9Z,12Z,15Z,18Z,21Z)-tetracosahexaenoyl-CoA + AMP + PPi set lower bound to 0
MAR00381 (11Z,14Z,17Z)-eicosatrienoic acid + ATP + CoA <-> (11Z,14Z,17Z)-eicosatrienoyl-CoA + AMP + PPi set lower bound to 0
MAR00385 13,16,19-docosatrienoic acid + ATP + CoA <-> 13,16,19-docosatrienoyl-CoA + AMP + PPi set lower bound to 0
MAR00389 10,13,16,19-docosatetraenoic acid + ATP + CoA <-> 10,13,16,19-docosatetraenoyl-CoA + AMP + PPi set lower bound to 0
MAR00393 12,15,18,21-tetracosatetraenoic acid + ATP + CoA <-> 12,15,18,21-tetracosatetraenoyl-CoA + AMP + PPi set lower bound to 0
MAR00417 (9Z,12Z,15Z,18Z)-TTA + ATP + CoA <-> (9Z,12Z,15Z,18Z)-tetracosatetraenoyl-CoA + AMP + PPi set lower bound to 0
MAR00421 (6Z,9Z,12Z,15Z,18Z)-TPA + ATP + CoA <-> (6Z,9Z,12Z,15Z,18Z)-tetracosapentaenoyl-CoA + AMP + PPi set lower bound to 0
MAR00425 (4Z,7Z,10Z,13Z,16Z)-DPA + ATP + CoA <-> (4Z,7Z,10Z,13Z,16Z)-docosapentaenoyl-CoA + AMP + PPi set lower bound to 0
MAR00429 (11Z,14Z)-eicosadienoic acid + ATP + CoA <-> (11Z,14Z)-eicosadienoyl-CoA + AMP + PPi set lower bound to 0
MAR00433 (13Z,16Z)-docosadienoic acid + ATP + CoA <-> (13Z,16Z)-docosadienoyl-CoA + AMP + PPi set lower bound to 0
MAR00737 ATP + CoA + elaidate <-> (2E)-octadecenoyl-CoA + AMP + PPi set lower bound to 0
MAR00740 ATP + CoA + Phytanate <-> AMP + phytanoyl-CoA + PPi set lower bound to 0
MAR01248 20-COOH-LTB4 + ATP + CoA <-> 20-CoA-20-oxo-LTB4 + AMP + PPi set lower bound to 0
MAR01249 20-COOH-LTB4 + ATP + CoA <-> 20-CoA-20-oxo-LTB4 + AMP + PPi set lower bound to 0
MAR01250 20-COOH-LTB4 + ATP + CoA <-> 20-CoA-20-oxo-LTB4 + AMP + PPi set lower bound to 0
MAR01251 20-COOH-LTB4 + ATP + CoA <-> 20-CoA-20-oxo-LTB4 + AMP + PPi set lower bound to 0
MAR01832 3alpha,12alpha-dihydroxy-5beta-cholanate + ATP + CoA <-> AMP + deoxycholoyl-CoA + PPi set lower bound to 0
MAR01833 3alpha,12alpha-dihydroxy-5beta-cholanate + ATP + CoA <-> AMP + deoxycholoyl-CoA + PPi set lower bound to 0
MAR02026 2 farnesyl-PP <-> PPi + presqualene-PP set lower bound to 0
MAR02120 dGTP + H2O <-> dGMP + H+ + PPi set lower bound to 0
MAR02147 H+ + NADPH + presqualene-PP <-> NADP+ + PPi + squalene set lower bound to 0
MAR02946 (9E)-tetradecenoic acid + ATP + CoA <-> (9E)-tetradecenoyl-CoA + AMP + PPi set lower bound to 0
MAR02947 (7Z)-tetradecenoic acid + ATP + CoA <-> (7Z)-tetradecenoyl-CoA + AMP + PPi set lower bound to 0
MAR02955 (10Z)-heptadecenoic acid + ATP + CoA <-> (10Z)-heptadecenoyl-CoA + AMP + PPi set lower bound to 0
MAR02962 (13Z)-octadecenoic acid + ATP + CoA <-> (13Z)-octadecenoyl-CoA + AMP + PPi set lower bound to 0
MAR02964 (6Z,9Z)-octadecadienoic acid + ATP + CoA <-> (6Z,9Z)-octadecadienoyl-CoA + AMP + PPi set lower bound to 0
MAR02968 (13Z)-eicosenoic acid + ATP + CoA <-> (13Z)-eicosenoyl-CoA + AMP + PPi set lower bound to 0
MAR02969 9-eicosenoic acid + ATP + CoA <-> 9-eicosenoyl-CoA + AMP + PPi set lower bound to 0
MAR02986 (9Z,12Z,15Z,18Z,21Z)-TPA + ATP + CoA <-> (9Z,12Z,15Z,18Z,21Z)-tetracosapentaenoyl-CoA + AMP + PPi set lower bound to 0
MAR02987 (6Z,9Z,12Z,15Z,18Z,21Z)-THA + ATP + CoA <-> (6Z,9Z,12Z,15Z,18Z,21Z)-tetracosahexaenoyl-CoA + AMP + PPi set lower bound to 0
MAR02989 (11Z,14Z,17Z)-eicosatrienoic acid + ATP + CoA <-> (11Z,14Z,17Z)-eicosatrienoyl-CoA + AMP + PPi set lower bound to 0
MAR02990 13,16,19-docosatrienoic acid + ATP + CoA <-> 13,16,19-docosatrienoyl-CoA + AMP + PPi set lower bound to 0
MAR02999 (9Z,12Z,15Z,18Z)-TTA + ATP + CoA <-> (9Z,12Z,15Z,18Z)-tetracosatetraenoyl-CoA + AMP + PPi set lower bound to 0
MAR03000 (6Z,9Z,12Z,15Z,18Z)-TPA + ATP + CoA <-> (6Z,9Z,12Z,15Z,18Z)-tetracosapentaenoyl-CoA + AMP + PPi set lower bound to 0
MAR03001 (4Z,7Z,10Z,13Z,16Z)-DPA + ATP + CoA <-> (4Z,7Z,10Z,13Z,16Z)-docosapentaenoyl-CoA + AMP + PPi set lower bound to 0
MAR03002 (11Z,14Z)-eicosadienoic acid + ATP + CoA <-> (11Z,14Z)-eicosadienoyl-CoA + AMP + PPi set lower bound to 0
MAR03003 (13Z,16Z)-docosadienoic acid + ATP + CoA <-> (13Z,16Z)-docosadienoyl-CoA + AMP + PPi set lower bound to 0
MAR03387 ATP + CoA + pristanic acid <-> (2S)-pristanoyl-CoA + AMP + PPi set lower bound to 0
MAR03389 ATP + CoA + phytanic acid <-> AMP + PPi + 3(S)-Phytanoyl Coenzyme A set lower bound to 0
MAR03489 (2R,6S,10S)-pristanate + ATP + CoA <-> (2S)-pristanoyl-CoA + AMP + PPi set lower bound to 0
MAR03801 6,7-dihydro-5-oxo-12-epi-LTB4 + ATP + CoA <-> 5-oxo-12(R)-hydroxy-eicosa-(8E,10E,14Z)-trienoyl-CoA + AMP + PPi set lower bound to 0
MAR03803 6,7-dihydro-5-oxo-12-epi-LTB4 + ATP + CoA <-> 5-oxo-12(R)-hydroxy-eicosa-(8E,10E,14Z)-trienoyl-CoA + AMP + PPi set lower bound to 0
MAR03805 6,7-dihydro-5-oxo-12-epi-LTB4 + ATP + CoA <-> 5-oxo-12(R)-hydroxy-eicosa-(8E,10E,14Z)-trienoyl-CoA + AMP + PPi set lower bound to 0
MAR03846 10,11-dihydro-12-epi-LTB4 + ATP + CoA <-> 10,11-dihydro-LTB4-CoA + AMP + PPi set lower bound to 0
MAR03872 10,11-dihydro-12-epi-LTB4 + ATP + CoA <-> 10,11-dihydro-LTB4-CoA + AMP + PPi set lower bound to 0
MAR03874 10,11-dihydro-12-epi-LTB4 + ATP + CoA <-> 10,11-dihydro-LTB4-CoA + AMP + PPi set lower bound to 0
MAR04254 H+ + nicotinate + PRPP <-> nicotinate ribonucleotide + PPi set lower bound to 0
MAR04257 ATP + H+ + nicotinate ribonucleotide <-> deamido-NAD + PPi set lower bound to 0
MAR04276 ATP + H+ + nicotinate ribonucleotide <-> deamido-NAD + PPi set lower bound to 0
MAR04460 ATP + H+ + propanoate <-> PPi + propinol adenylate set lower bound to 0
MAR04727 ATP + H+ + phosphopantetheine <-> dephospho-CoA + PPi set lower bound to 0
MAR08990 ATP + H+ + phosphopantetheine <-> dephospho-CoA + PPi set lower bound to 0
MAR00156 AMP + butyryl-CoA + PPi <-> ATP + butyrate + CoA swap products & reactants, then set lower bound to 0
MAR00165 AMP + pentanoyl-CoA + PPi <-> ATP + CoA + valeric acid swap products & reactants, then set lower bound to 0
MAR00168 AMP + hexanoyl-CoA + PPi <-> ATP + CoA + hexanoic acid swap products & reactants, then set lower bound to 0
MAR00171 AMP + heptanoyl-CoA + PPi <-> ATP + CoA + heptylic acid swap products & reactants, then set lower bound to 0
MAR00174 AMP + octanoyl-CoA + PPi <-> ATP + CoA + octanoic acid swap products & reactants, then set lower bound to 0
MAR00177 AMP + nonanoyl-CoA + PPi <-> ATP + CoA + nonanoic acid swap products & reactants, then set lower bound to 0
MAR00180 AMP + decanoyl-CoA + PPi <-> ATP + CoA + decanoic acid swap products & reactants, then set lower bound to 0
MAR00184 AMP + PPi + undecanoyl-CoA <-> ATP + CoA + undecylic acid swap products & reactants, then set lower bound to 0
MAR00188 AMP + lauroyl-CoA + PPi <-> ATP + CoA + lauric acid swap products & reactants, then set lower bound to 0
MAR00192 AMP + PPi + tridecanoyl-CoA <-> ATP + CoA + tridecylic acid swap products & reactants, then set lower bound to 0
MAR00196 AMP + myristoyl-CoA + PPi <-> ATP + CoA + myristic acid swap products & reactants, then set lower bound to 0
MAR00209 5-tetradecenoyl-CoA + AMP + PPi <-> ATP + CoA + physeteric acid swap products & reactants, then set lower bound to 0
MAR00213 AMP + pentadecanoyl-CoA + PPi <-> ATP + CoA + pentadecylic acid swap products & reactants, then set lower bound to 0
MAR00217 AMP + palmitoyl-CoA + PPi <-> ATP + CoA + palmitate swap products & reactants, then set lower bound to 0
MAR00226 AMP + palmitoleoyl-CoA + PPi <-> ATP + CoA + palmitolate swap products & reactants, then set lower bound to 0
MAR00233 7-hexadecenoyl-CoA + AMP + PPi <-> 7-palmitoleic acid + ATP + CoA swap products & reactants, then set lower bound to 0
MAR00237 AMP + heptadecanoyl-CoA + PPi <-> ATP + CoA + margaric acid swap products & reactants, then set lower bound to 0
MAR00245 9-heptadecenoyl-CoA + AMP + PPi <-> 9-heptadecylenic acid + ATP + CoA swap products & reactants, then set lower bound to 0
MAR00249 AMP + PPi + stearoyl-CoA <-> ATP + CoA + stearate swap products & reactants, then set lower bound to 0
MAR00259 AMP + cis-vaccenoyl-CoA + PPi <-> ATP + cis-vaccenic acid + CoA swap products & reactants, then set lower bound to 0
MAR00267 (9E)-octadecenoyl-CoA + AMP + PPi <-> ATP + CoA + elaidate swap products & reactants, then set lower bound to 0
MAR00271 (13Z)-octadecenoyl-CoA + AMP + PPi <-> (7Z)-octadecenoic acid + ATP + CoA swap products & reactants, then set lower bound to 0
MAR00279 AMP + nonadecanoyl-CoA + PPi <-> ATP + CoA + nonadecylic acid swap products & reactants, then set lower bound to 0
MAR00283 AMP + eicosanoyl-CoA + PPi <-> ATP + CoA + eicosanoate swap products & reactants, then set lower bound to 0
MAR00293 (11Z)-eicosenoyl-CoA + AMP + PPi <-> ATP + cis-gondoic acid + CoA swap products & reactants, then set lower bound to 0
MAR00301 (8Z,11Z)-eicosadienoyl-CoA + AMP + PPi <-> 8,11-eicosadienoic acid + ATP + CoA swap products & reactants, then set lower bound to 0
MAR00305 (5Z,8Z,11Z)-eicosatrienoyl-CoA + AMP + PPi <-> ATP + CoA + mead acid swap products & reactants, then set lower bound to 0
MAR00309 AMP + heneicosanoyl-CoA + PPi <-> ATP + CoA + henicosanoic acid swap products & reactants, then set lower bound to 0
MAR00313 AMP + docosanoyl-CoA + PPi <-> ATP + behenic acid + CoA swap products & reactants, then set lower bound to 0
MAR00319 (13Z)-docosenoyl-CoA + AMP + PPi <-> ATP + cis-erucic acid + CoA swap products & reactants, then set lower bound to 0
MAR00323 (11Z)-docosenoyl-CoA + AMP + PPi <-> ATP + cis-cetoleic acid + CoA swap products & reactants, then set lower bound to 0
MAR00327 AMP + PPi + tricosanoyl-CoA <-> ATP + CoA + tricosanoic acid swap products & reactants, then set lower bound to 0
MAR00331 AMP + PPi + tetracosanoyl-CoA <-> ATP + CoA + lignocerate swap products & reactants, then set lower bound to 0
MAR00337 (15Z)-tetracosenoyl-CoA + AMP + PPi <-> ATP + CoA + nervonic acid swap products & reactants, then set lower bound to 0
MAR00341 AMP + hexacosanoyl-CoA + PPi <-> ATP + cerotic acid + CoA swap products & reactants, then set lower bound to 0
MAR00345 AMP + hexacosenoyl-CoA + PPi <-> ATP + CoA + ximenic acid swap products & reactants, then set lower bound to 0
MAR00349 AMP + linolenoyl-CoA + PPi <-> ATP + CoA + linolenate swap products & reactants, then set lower bound to 0
MAR00353 (6Z,9Z,12Z,15Z)-octadecatetraenoyl-CoA + AMP + PPi <-> ATP + CoA + stearidonic acid swap products & reactants, then set lower bound to 0
MAR00357 (8Z,11Z,14Z,17Z)-eicosatetraenoyl-CoA + AMP + PPi <-> ATP + CoA + omega-3-arachidonic acid swap products & reactants, then set lower bound to 0
MAR00361 (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA + AMP + PPi <-> ATP + CoA + EPA swap products & reactants, then set lower bound to 0
MAR00365 (7Z,10Z,13Z,16Z,19Z)-docosapentaenoyl-CoA + AMP + PPi <-> ATP + CoA + DPA swap products & reactants, then set lower bound to 0
MAR00377 (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoyl-CoA + AMP + PPi <-> ATP + CoA + DHA swap products & reactants, then set lower bound to 0
MAR00397 AMP + linoleoyl-CoA + PPi <-> ATP + CoA + linoleate swap products & reactants, then set lower bound to 0
MAR00401 AMP + gamma-linolenoyl-CoA + PPi <-> ATP + CoA + gamma-linolenate swap products & reactants, then set lower bound to 0
MAR00405 AMP + dihomo-gamma-linolenoyl-CoA + PPi <-> ATP + CoA + dihomo-gamma-linolenate swap products & reactants, then set lower bound to 0
MAR00409 AMP + arachidonyl-CoA + PPi <-> arachidonate + ATP + CoA swap products & reactants, then set lower bound to 0
MAR00413 (7Z,10Z,13Z,16Z)-docosatetraenoyl-CoA + AMP + PPi <-> adrenic acid + ATP + CoA swap products & reactants, then set lower bound to 0
MAR00437 10,13,16-docosatrienoyl-CoA + AMP + PPi <-> 10,13,16-docosatriynoic acid + ATP + CoA swap products & reactants, then set lower bound to 0
MAR01157 5-oxo-12(R)-hydroxy-eicosa-(8E,10E,14Z)-trienoyl-CoA + AMP + PPi <-> 6,7-dihydro-5-oxo-LTB4 + ATP + CoA swap products & reactants, then set lower bound to 0
MAR01158 5-oxo-12(R)-hydroxy-eicosa-(8E,10E,14Z)-trienoyl-CoA + AMP + PPi <-> 6,7-dihydro-5-oxo-LTB4 + ATP + CoA swap products & reactants, then set lower bound to 0
MAR01159 5-oxo-12(R)-hydroxy-eicosa-(8E,10E,14Z)-trienoyl-CoA + AMP + PPi <-> 6,7-dihydro-5-oxo-LTB4 + ATP + CoA swap products & reactants, then set lower bound to 0
MAR01160 5-oxo-12(R)-hydroxy-eicosa-(8E,10E,14Z)-trienoyl-CoA + AMP + PPi <-> 6,7-dihydro-5-oxo-LTB4 + ATP + CoA swap products & reactants, then set lower bound to 0
MAR01200 5-oxo-12(S)-hydroxy-eicosa-(8E,10E,14Z)-trienoyl-CoA + AMP + PPi <-> 6,7-dihydro-5-oxo-12-epi-LTB4 + ATP + CoA swap products & reactants, then set lower bound to 0
MAR01201 5-oxo-12(S)-hydroxy-eicosa-(8E,10E,14Z)-trienoyl-CoA + AMP + PPi <-> 6,7-dihydro-5-oxo-12-epi-LTB4 + ATP + CoA swap products & reactants, then set lower bound to 0
MAR01202 5-oxo-12(S)-hydroxy-eicosa-(8E,10E,14Z)-trienoyl-CoA + AMP + PPi <-> 6,7-dihydro-5-oxo-12-epi-LTB4 + ATP + CoA swap products & reactants, then set lower bound to 0
MAR01203 5-oxo-12(S)-hydroxy-eicosa-(8E,10E,14Z)-trienoyl-CoA + AMP + PPi <-> 6,7-dihydro-5-oxo-12-epi-LTB4 + ATP + CoA swap products & reactants, then set lower bound to 0
MAR01263 10,11-dihydro-LTB4-CoA + AMP + PPi <-> 10,11-dihydro-LTB4 + ATP + CoA swap products & reactants, then set lower bound to 0
MAR01264 10,11-dihydro-LTB4-CoA + AMP + PPi <-> 10,11-dihydro-LTB4 + ATP + CoA swap products & reactants, then set lower bound to 0
MAR01265 10,11-dihydro-LTB4-CoA + AMP + PPi <-> 10,11-dihydro-LTB4 + ATP + CoA swap products & reactants, then set lower bound to 0
MAR01266 10,11-dihydro-LTB4-CoA + AMP + PPi <-> 10,11-dihydro-LTB4 + ATP + CoA swap products & reactants, then set lower bound to 0
MAR01290 20-COOH-LTE4-CoA + AMP + PPi <-> 20-COOH-LTE4 + ATP + CoA swap products & reactants, then set lower bound to 0
MAR01465 PPi + presqualene-PP <-> 2 farnesyl-PP swap products & reactants, then set lower bound to 0
MAR01532 PPi + trans,trans,cis-geranyl-geranyl-pp <-> dimethylallyl-PP + farnesyl-PP swap products & reactants, then set lower bound to 0
MAR01726 AMP + chenodeoxycholoyl-CoA + PPi <-> ATP + chenodiol + CoA swap products & reactants, then set lower bound to 0
MAR01727 AMP + chenodeoxycholoyl-CoA + PPi <-> ATP + chenodiol + CoA swap products & reactants, then set lower bound to 0
MAR01841 AMP + H+ + PPi + taurolithocholate <-> ATP + lithocholate + taurine swap products & reactants, then set lower bound to 0
MAR01842 AMP + H+ + PPi + taurolithocholate <-> ATP + lithocholate + taurine swap products & reactants, then set lower bound to 0
MAR01844 AMP + glycolithocholate + H+ + PPi <-> ATP + glycine + lithocholate swap products & reactants, then set lower bound to 0
MAR01848 AMP + choloyl-CoA + PPi <-> ATP + cholate + CoA swap products & reactants, then set lower bound to 0
MAR02942 AMP + lauroyl-CoA + PPi <-> ATP + CoA + lauric acid swap products & reactants, then set lower bound to 0
MAR02943 AMP + PPi + tridecanoyl-CoA <-> ATP + CoA + tridecylic acid swap products & reactants, then set lower bound to 0
MAR02944 AMP + myristoyl-CoA + PPi <-> ATP + CoA + myristic acid swap products & reactants, then set lower bound to 0
MAR02945 5-tetradecenoyl-CoA + AMP + PPi <-> ATP + CoA + physeteric acid swap products & reactants, then set lower bound to 0
MAR02948 AMP + pentadecanoyl-CoA + PPi <-> ATP + CoA + pentadecylic acid swap products & reactants, then set lower bound to 0
MAR02949 AMP + palmitoyl-CoA + PPi <-> ATP + CoA + palmitate swap products & reactants, then set lower bound to 0
MAR02951 7-hexadecenoyl-CoA + AMP + PPi <-> 7-palmitoleic acid + ATP + CoA swap products & reactants, then set lower bound to 0
MAR02952 AMP + palmitoleoyl-CoA + PPi <-> ATP + CoA + palmitolate swap products & reactants, then set lower bound to 0
MAR02954 AMP + heptadecanoyl-CoA + PPi <-> ATP + CoA + margaric acid swap products & reactants, then set lower bound to 0
MAR02956 9-heptadecenoyl-CoA + AMP + PPi <-> 9-heptadecylenic acid + ATP + CoA swap products & reactants, then set lower bound to 0
MAR02957 AMP + PPi + stearoyl-CoA <-> ATP + CoA + stearate swap products & reactants, then set lower bound to 0
MAR02961 (9E)-octadecenoyl-CoA + AMP + PPi <-> ATP + CoA + elaidate swap products & reactants, then set lower bound to 0
MAR02963 AMP + cis-vaccenoyl-CoA + PPi <-> ATP + cis-vaccenic acid + CoA swap products & reactants, then set lower bound to 0
MAR02965 AMP + nonadecanoyl-CoA + PPi <-> ATP + CoA + nonadecylic acid swap products & reactants, then set lower bound to 0
MAR02966 AMP + eicosanoyl-CoA + PPi <-> ATP + CoA + eicosanoate swap products & reactants, then set lower bound to 0
MAR02967 (11Z)-eicosenoyl-CoA + AMP + PPi <-> ATP + cis-gondoic acid + CoA swap products & reactants, then set lower bound to 0
MAR02970 (8Z,11Z)-eicosadienoyl-CoA + AMP + PPi <-> 8,11-eicosadienoic acid + ATP + CoA swap products & reactants, then set lower bound to 0
MAR02971 (5Z,8Z,11Z)-eicosatrienoyl-CoA + AMP + PPi <-> ATP + CoA + mead acid swap products & reactants, then set lower bound to 0
MAR02972 AMP + heneicosanoyl-CoA + PPi <-> ATP + CoA + henicosanoic acid swap products & reactants, then set lower bound to 0
MAR02973 AMP + docosanoyl-CoA + PPi <-> ATP + behenic acid + CoA swap products & reactants, then set lower bound to 0
MAR02974 (13Z)-docosenoyl-CoA + AMP + PPi <-> ATP + cis-erucic acid + CoA swap products & reactants, then set lower bound to 0
MAR02975 (11Z)-docosenoyl-CoA + AMP + PPi <-> ATP + cis-cetoleic acid + CoA swap products & reactants, then set lower bound to 0
MAR02976 AMP + PPi + tricosanoyl-CoA <-> ATP + CoA + tricosanoic acid swap products & reactants, then set lower bound to 0
MAR02977 AMP + PPi + tetracosanoyl-CoA <-> ATP + CoA + lignocerate swap products & reactants, then set lower bound to 0
MAR02978 (15Z)-tetracosenoyl-CoA + AMP + PPi <-> ATP + CoA + nervonic acid swap products & reactants, then set lower bound to 0
MAR02979 AMP + hexacosanoyl-CoA + PPi <-> ATP + cerotic acid + CoA swap products & reactants, then set lower bound to 0
MAR02980 AMP + hexacosenoyl-CoA + PPi <-> ATP + CoA + ximenic acid swap products & reactants, then set lower bound to 0
MAR02981 AMP + linolenoyl-CoA + PPi <-> ATP + CoA + linolenate swap products & reactants, then set lower bound to 0
MAR02982 (6Z,9Z,12Z,15Z)-octadecatetraenoyl-CoA + AMP + PPi <-> ATP + CoA + stearidonic acid swap products & reactants, then set lower bound to 0
MAR02983 (8Z,11Z,14Z,17Z)-eicosatetraenoyl-CoA + AMP + PPi <-> ATP + CoA + omega-3-arachidonic acid swap products & reactants, then set lower bound to 0
MAR02984 (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoyl-CoA + AMP + PPi <-> ATP + CoA + EPA swap products & reactants, then set lower bound to 0
MAR02985 (7Z,10Z,13Z,16Z,19Z)-docosapentaenoyl-CoA + AMP + PPi <-> ATP + CoA + DPA swap products & reactants, then set lower bound to 0
MAR02988 (4Z,7Z,10Z,13Z,16Z,19Z)-docosahexaenoyl-CoA + AMP + PPi <-> ATP + CoA + DHA swap products & reactants, then set lower bound to 0
MAR02991 AMP + linoleoyl-CoA + PPi <-> ATP + CoA + linoleate swap products & reactants, then set lower bound to 0
MAR02992 AMP + gamma-linolenoyl-CoA + PPi <-> ATP + CoA + gamma-linolenate swap products & reactants, then set lower bound to 0
MAR02994 AMP + dihomo-gamma-linolenoyl-CoA + PPi <-> ATP + CoA + dihomo-gamma-linolenate swap products & reactants, then set lower bound to 0
MAR02996 AMP + arachidonyl-CoA + PPi <-> arachidonate + ATP + CoA swap products & reactants, then set lower bound to 0
MAR02998 (7Z,10Z,13Z,16Z)-docosatetraenoyl-CoA + AMP + PPi <-> adrenic acid + ATP + CoA swap products & reactants, then set lower bound to 0
MAR03480 AMP + phytanoyl-CoA + PPi <-> ATP + CoA + phytanic acid swap products & reactants, then set lower bound to 0
MAR03482 AMP + phytanoyl-CoA + PPi <-> ATP + CoA + phytanic acid swap products & reactants, then set lower bound to 0
MAR03493 (2R)-pristanoyl-CoA + AMP + PPi <-> ATP + CoA + pristanic acid swap products & reactants, then set lower bound to 0
MAR03797 AMP + PPi + propanoyl-CoA <-> ATP + CoA + propanoate swap products & reactants, then set lower bound to 0
MAR04085 AMP + PPi <-> adenine + PRPP swap products & reactants, then set lower bound to 0
MAR04086 AMP + PPi <-> adenine + PRPP swap products & reactants, then set lower bound to 0
MAR04262 nicotinamide D-ribonucleotide + PPi <-> H+ + nicotinamide + PRPP swap products & reactants, then set lower bound to 0
MAR04401 GDP-L-fucose + PPi <-> GTP + H+ + L-fucose-1-phosphate swap products & reactants, then set lower bound to 0
MAR04418 IMP + PPi <-> hypoxanthine + PRPP swap products & reactants, then set lower bound to 0
MAR04452 GMP + PPi <-> guanine + PRPP swap products & reactants, then set lower bound to 0
MAR04532 CMP-neuNGc + PPi <-> CTP + neungc swap products & reactants, then set lower bound to 0
MAR04536 CMP-N-acetylneuraminate + PPi <-> CTP + N-acetylneuraminate swap products & reactants, then set lower bound to 0
MAR04577 orotidine-5-phosphate + PPi <-> orotate + PRPP swap products & reactants, then set lower bound to 0

@haowang-bioinfo
Copy link
Member

great job - will look into this

@Devlin-Moyer Devlin-Moyer mentioned this issue May 8, 2023
Merged
3 tasks
@haowang-bioinfo
Copy link
Member

fixed in #557

@Devlin-Moyer
Copy link
Collaborator Author

Devlin-Moyer commented Jun 14, 2023 •
edited
Loading

(moved to #648)

@Devlin-Moyer Devlin-Moyer reopened this Jun 14, 2023
@Devlin-Moyer Devlin-Moyer mentioned this issue Jun 14, 2023
Merged
3 tasks
@haowang-bioinfo
Copy link
Member

better move these new ones to a separate issue

@haowang-bioinfo haowang-bioinfo mentioned this issue Jun 17, 2023
Merged
@Devlin-Moyer Devlin-Moyer mentioned this issue Jun 20, 2023
Closed
@pranasag pranasag mentioned this issue Aug 9, 2023
Closed
@haowang-bioinfo haowang-bioinfo mentioned this issue Sep 25, 2023
Merged
@pranasag pranasag mentioned this issue Oct 30, 2023
Merged
3 tasks
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
bug
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
3 participants
@haowang-bioinfo @feiranl @Devlin-Moyer