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Do traditional gap filling on the model #45

Closed hgscott closed 7 months ago

hgscott commented 8 months ago

We just want the model to grow so that we can estimate CUE again.

hgscott commented 8 months ago

I need to make media files for glucose, acetate, and 3-hydroxybutyrate.

hgscott commented 8 months ago

I found existing media files from my original pass at gap filling: Image

Image

Image

hgscott commented 8 months ago

I tried gap filling for all three and none of them worked- I must be missing some essential components. Image

hgscott commented 8 months ago

Based on the blocked biomass components that MEMOTE found, I decided what I should add to the media.

ID Name Already in (Glucose) Media? Add to Media?
cpd00220_c0 Riboflavin [c0] No Yes- but check with Mary Ann/Rogier
cpd00201_c0 10-Formyltetrahydrofolate [c0] No No
cpd15352_c0 2-Demethylmenaquinone 8 [c0] No No
cpd00056_c0 TPP [c0] No No
cpd00345_c0 5-Methyltetrahydrofolate [c0] No No
cpd00010_c0 CoA [c0] No No
cpd00118_c0 Putrescine [c0] No No
cpd00254_c0 Mg [c0] Yes -
cpd00099_c0 Cl- [c0] Yes -
cpd15500_c0 Menaquinone 8 [c0] No No
cpd00149_c0 Co2+ [c0] Yes -
cpd15793_c0 Stearoylcardiolipin (B. subtilis) [c0] No No
cpd00557_c0 Siroheme [c0] No No
cpd11493_c0 ACP [c0] No No
cpd10515_c0 Fe2+ [c0] Yes -
cpd00087_c0 Tetrahydrofolate [c0] No No
cpd11463_c0 Protein [c0] No Definitely not
cpd02229_c0 Bactoprenyl diphosphate [c0] No No
cpd15665_c0 Peptidoglycan polymer (n subunits) [c0] No Definitely not
cpd00264_c0 Spermidine [c0] No No
cpd15560_c0 Ubiquinone-8 [c0] No No
cpd00015_c0 FAD [c0] No No

I tried just adding Riboflavin, and that wasn't enough to get growth.

hgscott commented 8 months ago

I also tried a different minimal glucose media, and that also failed at gap filling. Image Image

hgscott commented 7 months ago

Osnat's PROMM acetate media also failed: Image

hgscott commented 7 months ago

But it did work with the old gapfilling app: Image

hgscott commented 7 months ago

When I tried the old app with C-D-Glucose, I got an error: Image

hgscott commented 7 months ago

Got the same error with the C-acetate media and the C-3-hydroxybutanoate media.

hgscott commented 7 months ago

I tried the new app but with the model before I remove the K+ transport reaction, and I got the same comment as before ("Gapfilling failed for media C-D-Glucose. Database lacks reactions to grow on media or media is missing essential nutrients.").

hgscott commented 7 months ago

I want to make a complete media with all of the blocked biomass components in it directly to check that it works.

So I need to add:

hgscott commented 7 months ago

I made a new media with adding all of those components: Image

hgscott commented 7 months ago

But when I ran the model in that media, it still didn't grow: Image

But that isn't surprising- even though all those things are in the media, there aren't transporters for all of those things.

hgscott commented 7 months ago

Gapfilling on my complete media failed.

hgscott commented 7 months ago

Osnat says to:

Ilija says to:

Daniel says to:

DSher says to:

hgscott commented 7 months ago

Look what is in the KBase logs (ChatGPT may help) before opening a KBase ticket.

hgscott commented 7 months ago

Daniel says to stop using KBase and instead use our own code for gap filling, including trying Shany's ReFill algorithm (https://github.com/C-CoMP-STC/GEM-mit1002/issues/52).

hgscott commented 7 months ago

Or I could manually add reactions?

hgscott commented 7 months ago

The KBase "Complete" Media, seems to be totally empty: Image

But gap filling with it still added 66 reactions: Image

Here are all the reactions that were added.

Reaction ID Reaction Name Media Direction Target Gapfilling Sensitivity ID Gapfilling Sensitivity Name
EX_cpd00149_e0 Exchange for Co2+ [e0] Complete < bio1 cpd00149_c0 Co2+ [c0]
EX_cpd00137_e0 Exchange for Citrate [e0] Complete < bio1 cpd00149_c0; cpd00254_c0; cpd03422_c0 Co2+ [c0]; Mg [c0]; Cobinamide [c0]
EX_cpd00254_e0 Exchange for Mg [e0] Complete < bio1 cpd00254_c0; cpd03422_c0 Mg [c0]; Cobinamide [c0]
EX_cpd00099_e0 Exchange for Cl- [e0] Complete < bio1 cpd00099_c0; cpd03422_c0; cpd11493_c0 Cl- [c0]; Cobinamide [c0]; ACP [c0]
rxn08333_c0 1,4-dihydroxy-2-naphthoate octaprenyltransferase Complete > bio1 cpd15352_c0; cpd15500_c0 2-Demethylmenaquinone 8 [c0]; Menaquinone 8 [c0]
rxn02898_c0 O-Succinylbenzoyl-CoA 1,4-dihydroxy-2-naphthoate-lyase Complete > bio1 cpd11493_c0; cpd15352_c0; cpd15500_c0; cpd15665_c0 ACP [c0]; 2-Demethylmenaquinone 8 [c0]; Menaquinone 8 [c0]; Peptidoglycan polymer (n subunits) [c0]
rxn10336_c0 stearoyl-cardiolipin synthase Complete > bio1 cpd15665_c0; cpd15793_c0 Peptidoglycan polymer (n subunits) [c0]; Stearoylcardiolipin (B. subtilis) [c0]
rxn00068_c0 Fe2+:NAD+ oxidoreductase Complete < bio1 cpd00557_c0; cpd10515_c0 Siroheme [c0]; Fe2+ [c0]
rxn05522_c0 citrate transport in via Co complex Complete > bio1 cpd00149_c0; cpd03422_c0; cpd15666_c0 Co2+ [c0]; Cobinamide [c0]; Peptidoglycan polymer (n-1 subunits) [c0]
rxn05039_c0 R07280 Complete > bio1 cpd00015_c0; cpd00220_c0; cpd03422_c0; cpd15666_c0 FAD [c0]; Riboflavin [c0]; Cobinamide [c0]; Peptidoglycan polymer (n-1 subunits) [c0]
rxn03536_c0 R05221 Complete > bio1 cpd01997_c0; cpd03422_c0; cpd15666_c0 Dimethylbenzimidazole [c0]; Cobinamide [c0]; Peptidoglycan polymer (n-1 subunits) [c0]
rxn03397_c0 UDP-L-rhamnose:flavonol-3-O-D-glucoside L-rhamnosyltransferase Complete > bio1 cpd15560_c0 Ubiquinone-8 [c0]
rxn00979_c0 glycolaldehyde:NAD+ oxidoreductase Complete > bio1 cpd00087_c0; cpd00201_c0; cpd00345_c0; cpd03422_c0 Tetrahydrofolate [c0]; 10-Formyltetrahydrofolate [c0]; 5-Methyltetrahydrofolate [c0]; Cobinamide [c0]
rxn11703_c0 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase Complete > bio1 cpd03422_c0; cpd12370_c0; cpd15352_c0; cpd15500_c0; cpd15666_c0 Cobinamide [c0]; apo-ACP [c0]; 2-Demethylmenaquinone 8 [c0]; Menaquinone 8 [c0]; Peptidoglycan polymer (n-1 subunits) [c0]
rxn03537_c0 R05222 Complete > bio1 cpd01997_c0; cpd03422_c0; cpd15665_c0 Dimethylbenzimidazole [c0]; Cobinamide [c0]; Peptidoglycan polymer (n subunits) [c0]
rxn10094_c0 S-adenosylmethione:2-demethylmenaquinone methyltransferase Complete > bio1 cpd15500_c0 Menaquinone 8 [c0]
rxn00333_c0 Glycolate:oxygen 2-oxidoreductase Complete > bio1 cpd00087_c0; cpd00201_c0; cpd00345_c0; cpd03422_c0 Tetrahydrofolate [c0]; 10-Formyltetrahydrofolate [c0]; 5-Methyltetrahydrofolate [c0]; Cobinamide [c0]
rxn03150_c0 R04594 Complete > bio1 cpd01997_c0; cpd03422_c0; cpd15666_c0 Dimethylbenzimidazole [c0]; Cobinamide [c0]; Peptidoglycan polymer (n-1 subunits) [c0]
rxn03087_c0 N-Succinyl-L-2,6-diaminoheptanedioate:2-oxoglutarate amino-transferase Complete < bio1 cpd15665_c0; cpd15666_c0; cpd00039_c0 Peptidoglycan polymer (n subunits) [c0]; Peptidoglycan polymer (n-1 subunits) [c0]; L-Lysine [c0]
rxn03538_c0 R05223 Complete > bio1 cpd01997_c0; cpd03422_c0 Dimethylbenzimidazole [c0]; Cobinamide [c0]
rxn01213_c0 GPPSYN-RXN Complete > bio1 cpd02229_c0; cpd15352_c0; cpd15500_c0; cpd15560_c0 Bactoprenyl diphosphate [c0]; 2-Demethylmenaquinone 8 [c0]; Menaquinone 8 [c0]; Ubiquinone-8 [c0]
rxn01265_c0 Nicotinate D-ribonucleotide:diphosphate phosphoribosyltransferase Complete < bio1 cpd01997_c0; cpd03422_c0; cpd15666_c0 Dimethylbenzimidazole [c0]; Cobinamide [c0]; Peptidoglycan polymer (n-1 subunits) [c0]
rxn00599_c0 succinyl-CoA:glycine C-succinyltransferase (decarboxylating) Complete > bio1 cpd00557_c0 Siroheme [c0]
rxn11702_c0 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase Complete > bio1 cpd03422_c0; cpd15352_c0; cpd15500_c0 Cobinamide [c0]; 2-Demethylmenaquinone 8 [c0]; Menaquinone 8 [c0]
rxn05214_c0 Citrate-Mg2+:H+ symporter Complete > bio1 cpd00254_c0; cpd11493_c0 Mg [c0]; ACP [c0]
rxn00346_c0 L-aspartate 1-carboxy-lyase (beta-alanine-forming) Complete > bio1 cpd00010_c0; cpd03422_c0; cpd11493_c0; cpd12370_c0; cpd15666_c0 CoA [c0]; Cobinamide [c0]; ACP [c0]; apo-ACP [c0]; Peptidoglycan polymer (n-1 subunits) [c0]
rxn02897_c0 Nicotinate-nucleotide:dimethylbenzimidazole phospho-D-ribosyltransferase Complete > bio1 cpd01997_c0; cpd03422_c0; cpd15666_c0 Dimethylbenzimidazole [c0]; Cobinamide [c0]; Peptidoglycan polymer (n-1 subunits) [c0]
rxn02831_c0 O-Succinylbenzoate:CoA ligase (AMP-forming) Complete > bio1 cpd15352_c0; cpd15500_c0 2-Demethylmenaquinone 8 [c0]; Menaquinone 8 [c0]
rxn01258_c0 chorismate hydroxymutase Complete > bio1 cpd15352_c0; cpd15500_c0; cpd15666_c0 2-Demethylmenaquinone 8 [c0]; Menaquinone 8 [c0]; Peptidoglycan polymer (n-1 subunits) [c0]
rxn01538_c0 ATP:thiamine phosphotransferase Complete > bio1 cpd00056_c0; cpd12370_c0; cpd15665_c0 TPP [c0]; apo-ACP [c0]; Peptidoglycan polymer (n subunits) [c0]
rxn02832_c0 (1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate hydrolyase (2-succinylbenzoate-forming) Complete < bio1 cpd15352_c0; cpd15500_c0 2-Demethylmenaquinone 8 [c0]; Menaquinone 8 [c0]
rxn00467_c0 L-Ornithine:2-oxo-acid aminotransferase Complete < bio1 cpd00118_c0; cpd00264_c0; cpd03422_c0; cpd15666_c0; cpd00051_c0 Putrescine [c0]; Spermidine [c0]; Cobinamide [c0]; Peptidoglycan polymer (n-1 subunits) [c0]; L-Arginine [c0]
rxn08234_c0 chloride (Cl-1) transport via diffusion (extracellular to periplasm) Complete > bio1 cpd00099_c0; cpd03422_c0 Cl- [c0]; Cobinamide [c0]
hgscott commented 7 months ago

I tested how that gapfilled model runs on my 3 media files:

It does not grow on C-D-Glucose: Image

Or acetate: Image

Or on 3-hydroxybutyrate: Image

hgscott commented 7 months ago

Per KBase's suggestion- I tried gapfilling and not selecting for "ATP Safe", but I still got the same message.

hgscott commented 7 months ago

But if I gapfill for glucose after gapfilling for complete media it works!

It added these reactions (on top of what was added for the complete media):

Reaction ID Reaction Name Media Direction Target Gapfilling Sensitivity ID Gapfilling Sensitivity Name
rxn05211_c0 Transport of citrate, extracellular C-D-Glucose < bio1 cpd00149_c0; cpd00254_c0 Co2+ [c0]; Mg [c0]
rxn09429_c0 fatty acid synthase (n-C18:0) C-D-Glucose > bio1 cpd15533_c0; cpd15540_c0; cpd15793_c0 phosphatidylethanolamine dioctadecanoyl [c0]; Phosphatidylglycerol dioctadecanoyl [c0]; Stearoylcardiolipin (B. subtilis) [c0]
rxn12376_c0 transport of 4-hydroxybenzyl alcohol extraorganism-cytosol C-D-Glucose < bio1 cpd00056_c0 TPP [c0]
rxn09310_c0 thiazole phosphate synthesis C-D-Glucose > bio1 cpd00056_c0; cpd03422_c0; cpd15665_c0 TPP [c0]; Cobinamide [c0]; Peptidoglycan polymer (n subunits) [c0]
rxn02304_c0 protoporphyrinogen-IX:oxygen oxidoreductase C-D-Glucose > bio1 cpd00028_c0; cpd03422_c0; cpd11493_c0; cpd15666_c0 Heme [c0]; Cobinamide [c0]; ACP [c0]; Peptidoglycan polymer (n-1 subunits) [c0]
rxn02185_c0 2-Acetolactate pyruvate-lyase (carboxylating) C-D-Glucose < bio1 cpd00010_c0; cpd03422_c0; cpd11463_c0; cpd11493_c0; cpd12370_c0 CoA [c0]; Cobinamide [c0]; Protein [c0]; ACP [c0]; apo-ACP [c0]
hgscott commented 7 months ago

Then I gapfilled the complete gapfilled model with all three media at once: Image

Which got growth on all three: Image

With the following reactions added:

Reaction ID Reaction Name Media Direction Target Gapfilling Sensitivity ID Gapfilling Sensitivity Name
rxn05211_c0 Transport of citrate, extracellular C-D-Glucose; C-acetate; C-3-hydroxy-butyrate < bio1 cpd00149_c0; cpd00254_c0 Co2+ [c0]; Mg [c0]
rxn09429_c0 fatty acid synthase (n-C18:0) C-D-Glucose; C-acetate; C-3-hydroxy-butyrate > bio1 cpd15533_c0; cpd15540_c0; cpd15793_c0 phosphatidylethanolamine dioctadecanoyl [c0]; Phosphatidylglycerol dioctadecanoyl [c0]; Stearoylcardiolipin (B. subtilis) [c0]
rxn12376_c0 transport of 4-hydroxybenzyl alcohol extraorganism-cytosol C-D-Glucose; C-acetate; C-3-hydroxy-butyrate < bio1 cpd00056_c0 TPP [c0]
rxn09310_c0 thiazole phosphate synthesis C-D-Glucose; C-acetate; C-3-hydroxy-butyrate > bio1 cpd00056_c0 TPP [c0]
rxn02304_c0 protoporphyrinogen-IX:oxygen oxidoreductase C-D-Glucose; C-acetate; C-3-hydroxy-butyrate > bio1 cpd00028_c0; cpd12370_c0 Heme [c0]; apo-ACP [c0]
rxn02185_c0 2-Acetolactate pyruvate-lyase (carboxylating) C-D-Glucose; C-acetate; C-3-hydroxy-butyrate < bio1 cpd00010_c0; cpd00166_c0; cpd03422_c0; cpd11463_c0; cpd11493_c0; cpd12370_c0 CoA [c0]; Calomide [c0]; Cobinamide [c0]; Protein [c0]; ACP [c0]; apo-ACP [c0]
rxn04656_c0 rxn04656 C-3-hydroxy-butyrate > bio1 cpd00003_c0; cpd00006_c0; cpd00010_c0; cpd00015_c0; cpd00016_c0; cpd00017_c0; cpd00028_c0; cpd00042_c0; cpd00056_c0; cpd00058_c0; cpd00087_c0; cpd00118_c0; cpd00166_c0; cpd00201_c0; cpd00220_c0; cpd00264_c0; cpd00345_c0; cpd00557_c0; cpd01997_c0; cpd02229_c0; cpd03422_c0; cpd03736_c0; cpd10515_c0; cpd10516_c0; cpd11462_c0; cpd11463_c0; cpd11493_c0; cpd12370_c0; cpd15352_c0; cpd15500_c0; cpd15533_c0; cpd15540_c0; cpd15560_c0; cpd15665_c0; cpd15666_c0; cpd15793_c0; cpd00115_c0; cpd00241_c0; cpd00356_c0; cpd00357_c0; cpd11461_c0; cpd00084_c0 NAD [c0]; NADP [c0]; CoA [c0]; FAD [c0]; Pyridoxal phosphate [c0]; S-Adenosyl-L-methionine [c0]; Heme [c0]; GSH [c0]; TPP [c0]; Cu2+ [c0]; Tetrahydrofolate [c0]; Putrescine [c0]; Calomide [c0]; 10-Formyltetrahydrofolate [c0]; Riboflavin [c0]; Spermidine [c0]; 5-Methyltetrahydrofolate [c0]; Siroheme [c0]; Dimethylbenzimidazole [c0]; Bactoprenyl diphosphate [c0]; Cobinamide [c0]; Lauroyl-KDO2-lipid IV(A) [c0]; Fe2+ [c0]; fe3 [c0]; mRNA [c0]; Protein [c0]; ACP [c0]; apo-ACP [c0]; 2-Demethylmenaquinone 8 [c0]; Menaquinone 8 [c0]; phosphatidylethanolamine dioctadecanoyl [c0]; Phosphatidylglycerol dioctadecanoyl [c0]; Ubiquinone-8 [c0]; Peptidoglycan polymer (n subunits) [c0]; Peptidoglycan polymer (n-1 subunits) [c0]; Stearoylcardiolipin (B. subtilis) [c0]; dATP [c0]; dGTP [c0]; dCTP [c0]; TTP [c0]; DNA [c0]; L-Cysteine [c0]
rxn04657_c0 N2-acetyl-L-aminoadipate kinase C-3-hydroxy-butyrate > bio1 cpd00003_c0; cpd00006_c0; cpd00010_c0; cpd00015_c0; cpd00016_c0; cpd00017_c0; cpd00028_c0; cpd00042_c0; cpd00056_c0; cpd00058_c0; cpd00087_c0; cpd00118_c0; cpd00166_c0; cpd00201_c0; cpd00220_c0; cpd00264_c0; cpd00345_c0; cpd00557_c0; cpd01997_c0; cpd02229_c0; cpd03422_c0; cpd03736_c0; cpd10515_c0; cpd10516_c0; cpd11462_c0; cpd11463_c0; cpd11493_c0; cpd12370_c0; cpd15352_c0; cpd15500_c0; cpd15533_c0; cpd15540_c0; cpd15560_c0; cpd15665_c0; cpd15666_c0; cpd15793_c0; cpd00115_c0; cpd00241_c0; cpd00356_c0; cpd00357_c0; cpd11461_c0; cpd00084_c0 NAD [c0]; NADP [c0]; CoA [c0]; FAD [c0]; Pyridoxal phosphate [c0]; S-Adenosyl-L-methionine [c0]; Heme [c0]; GSH [c0]; TPP [c0]; Cu2+ [c0]; Tetrahydrofolate [c0]; Putrescine [c0]; Calomide [c0]; 10-Formyltetrahydrofolate [c0]; Riboflavin [c0]; Spermidine [c0]; 5-Methyltetrahydrofolate [c0]; Siroheme [c0]; Dimethylbenzimidazole [c0]; Bactoprenyl diphosphate [c0]; Cobinamide [c0]; Lauroyl-KDO2-lipid IV(A) [c0]; Fe2+ [c0]; fe3 [c0]; mRNA [c0]; Protein [c0]; ACP [c0]; apo-ACP [c0]; 2-Demethylmenaquinone 8 [c0]; Menaquinone 8 [c0]; phosphatidylethanolamine dioctadecanoyl [c0]; Phosphatidylglycerol dioctadecanoyl [c0]; Ubiquinone-8 [c0]; Peptidoglycan polymer (n subunits) [c0]; Peptidoglycan polymer (n-1 subunits) [c0]; Stearoylcardiolipin (B. subtilis) [c0]; dATP [c0]; dGTP [c0]; dCTP [c0]; TTP [c0]; DNA [c0]; L-Cysteine [c0]
rxn04659_c0 RXN-5184.c C-3-hydroxy-butyrate > bio1 cpd00003_c0; cpd00006_c0; cpd00010_c0; cpd00015_c0; cpd00016_c0; cpd00017_c0; cpd00028_c0; cpd00042_c0; cpd00056_c0; cpd00058_c0; cpd00087_c0; cpd00118_c0; cpd00166_c0; cpd00201_c0; cpd00220_c0; cpd00264_c0; cpd00345_c0; cpd00557_c0; cpd01997_c0; cpd02229_c0; cpd03422_c0; cpd03736_c0; cpd10515_c0; cpd10516_c0; cpd11462_c0; cpd11463_c0; cpd11493_c0; cpd12370_c0; cpd15352_c0; cpd15500_c0; cpd15533_c0; cpd15540_c0; cpd15560_c0; cpd15665_c0; cpd15666_c0; cpd15793_c0; cpd00115_c0; cpd00241_c0; cpd00356_c0; cpd00357_c0; cpd11461_c0; cpd00084_c0 NAD [c0]; NADP [c0]; CoA [c0]; FAD [c0]; Pyridoxal phosphate [c0]; S-Adenosyl-L-methionine [c0]; Heme [c0]; GSH [c0]; TPP [c0]; Cu2+ [c0]; Tetrahydrofolate [c0]; Putrescine [c0]; Calomide [c0]; 10-Formyltetrahydrofolate [c0]; Riboflavin [c0]; Spermidine [c0]; 5-Methyltetrahydrofolate [c0]; Siroheme [c0]; Dimethylbenzimidazole [c0]; Bactoprenyl diphosphate [c0]; Cobinamide [c0]; Lauroyl-KDO2-lipid IV(A) [c0]; Fe2+ [c0]; fe3 [c0]; mRNA [c0]; Protein [c0]; ACP [c0]; apo-ACP [c0]; 2-Demethylmenaquinone 8 [c0]; Menaquinone 8 [c0]; phosphatidylethanolamine dioctadecanoyl [c0]; Phosphatidylglycerol dioctadecanoyl [c0]; Ubiquinone-8 [c0]; Peptidoglycan polymer (n subunits) [c0]; Peptidoglycan polymer (n-1 subunits) [c0]; Stearoylcardiolipin (B. subtilis) [c0]; dATP [c0]; dGTP [c0]; dCTP [c0]; TTP [c0]; DNA [c0]; L-Cysteine [c0]
rxn02226_c0 L-2-Aminoadipate-6-semialdehyde:NAD+ 6-oxidoreductase C-3-hydroxy-butyrate > bio1 cpd00003_c0; cpd00006_c0; cpd00010_c0; cpd00015_c0; cpd00016_c0; cpd00017_c0; cpd00028_c0; cpd00042_c0; cpd00056_c0; cpd00058_c0; cpd00087_c0; cpd00118_c0; cpd00166_c0; cpd00201_c0; cpd00220_c0; cpd00264_c0; cpd00345_c0; cpd00557_c0; cpd01997_c0; cpd02229_c0; cpd03422_c0; cpd03736_c0; cpd10515_c0; cpd10516_c0; cpd11462_c0; cpd11463_c0; cpd11493_c0; cpd12370_c0; cpd15352_c0; cpd15500_c0; cpd15533_c0; cpd15540_c0; cpd15560_c0; cpd15665_c0; cpd15666_c0; cpd15793_c0; cpd00115_c0; cpd00241_c0; cpd00356_c0; cpd00357_c0; cpd11461_c0; cpd00084_c0 NAD [c0]; NADP [c0]; CoA [c0]; FAD [c0]; Pyridoxal phosphate [c0]; S-Adenosyl-L-methionine [c0]; Heme [c0]; GSH [c0]; TPP [c0]; Cu2+ [c0]; Tetrahydrofolate [c0]; Putrescine [c0]; Calomide [c0]; 10-Formyltetrahydrofolate [c0]; Riboflavin [c0]; Spermidine [c0]; 5-Methyltetrahydrofolate [c0]; Siroheme [c0]; Dimethylbenzimidazole [c0]; Bactoprenyl diphosphate [c0]; Cobinamide [c0]; Lauroyl-KDO2-lipid IV(A) [c0]; Fe2+ [c0]; fe3 [c0]; mRNA [c0]; Protein [c0]; ACP [c0]; apo-ACP [c0]; 2-Demethylmenaquinone 8 [c0]; Menaquinone 8 [c0]; phosphatidylethanolamine dioctadecanoyl [c0]; Phosphatidylglycerol dioctadecanoyl [c0]; Ubiquinone-8 [c0]; Peptidoglycan polymer (n subunits) [c0]; Peptidoglycan polymer (n-1 subunits) [c0]; Stearoylcardiolipin (B. subtilis) [c0]; dATP [c0]; dGTP [c0]; dCTP [c0]; TTP [c0]; DNA [c0]; L-Cysteine [c0]
rxn04660_c0 RXN-5185.c C-3-hydroxy-butyrate > bio1 cpd00003_c0; cpd00006_c0; cpd00010_c0; cpd00015_c0; cpd00016_c0; cpd00017_c0; cpd00028_c0; cpd00042_c0; cpd00056_c0; cpd00058_c0; cpd00087_c0; cpd00118_c0; cpd00166_c0; cpd00201_c0; cpd00220_c0; cpd00264_c0; cpd00345_c0; cpd00557_c0; cpd01997_c0; cpd02229_c0; cpd03422_c0; cpd03736_c0; cpd10515_c0; cpd10516_c0; cpd11462_c0; cpd11463_c0; cpd11493_c0; cpd12370_c0; cpd15352_c0; cpd15500_c0; cpd15533_c0; cpd15540_c0; cpd15560_c0; cpd15665_c0; cpd15666_c0; cpd15793_c0; cpd00115_c0; cpd00241_c0; cpd00356_c0; cpd00357_c0; cpd11461_c0; cpd00084_c0 NAD [c0]; NADP [c0]; CoA [c0]; FAD [c0]; Pyridoxal phosphate [c0]; S-Adenosyl-L-methionine [c0]; Heme [c0]; GSH [c0]; TPP [c0]; Cu2+ [c0]; Tetrahydrofolate [c0]; Putrescine [c0]; Calomide [c0]; 10-Formyltetrahydrofolate [c0]; Riboflavin [c0]; Spermidine [c0]; 5-Methyltetrahydrofolate [c0]; Siroheme [c0]; Dimethylbenzimidazole [c0]; Bactoprenyl diphosphate [c0]; Cobinamide [c0]; Lauroyl-KDO2-lipid IV(A) [c0]; Fe2+ [c0]; fe3 [c0]; mRNA [c0]; Protein [c0]; ACP [c0]; apo-ACP [c0]; 2-Demethylmenaquinone 8 [c0]; Menaquinone 8 [c0]; phosphatidylethanolamine dioctadecanoyl [c0]; Phosphatidylglycerol dioctadecanoyl [c0]; Ubiquinone-8 [c0]; Peptidoglycan polymer (n subunits) [c0]; Peptidoglycan polymer (n-1 subunits) [c0]; Stearoylcardiolipin (B. subtilis) [c0]; dATP [c0]; dGTP [c0]; dCTP [c0]; TTP [c0]; DNA [c0]; L-Cysteine [c0]
rxn04658_c0 RXN-5183.c C-3-hydroxy-butyrate > bio1 cpd00003_c0; cpd00006_c0; cpd00010_c0; cpd00015_c0; cpd00016_c0; cpd00017_c0; cpd00028_c0; cpd00042_c0; cpd00056_c0; cpd00058_c0; cpd00087_c0; cpd00118_c0; cpd00166_c0; cpd00201_c0; cpd00220_c0; cpd00264_c0; cpd00345_c0; cpd00557_c0; cpd01997_c0; cpd02229_c0; cpd03422_c0; cpd03736_c0; cpd10515_c0; cpd10516_c0; cpd11462_c0; cpd11463_c0; cpd11493_c0; cpd12370_c0; cpd15352_c0; cpd15500_c0; cpd15533_c0; cpd15540_c0; cpd15560_c0; cpd15665_c0; cpd15666_c0; cpd15793_c0; cpd00115_c0; cpd00241_c0; cpd00356_c0; cpd00357_c0; cpd11461_c0; cpd00084_c0 NAD [c0]; NADP [c0]; CoA [c0]; FAD [c0]; Pyridoxal phosphate [c0]; S-Adenosyl-L-methionine [c0]; Heme [c0]; GSH [c0]; TPP [c0]; Cu2+ [c0]; Tetrahydrofolate [c0]; Putrescine [c0]; Calomide [c0]; 10-Formyltetrahydrofolate [c0]; Riboflavin [c0]; Spermidine [c0]; 5-Methyltetrahydrofolate [c0]; Siroheme [c0]; Dimethylbenzimidazole [c0]; Bactoprenyl diphosphate [c0]; Cobinamide [c0]; Lauroyl-KDO2-lipid IV(A) [c0]; Fe2+ [c0]; fe3 [c0]; mRNA [c0]; Protein [c0]; ACP [c0]; apo-ACP [c0]; 2-Demethylmenaquinone 8 [c0]; Menaquinone 8 [c0]; phosphatidylethanolamine dioctadecanoyl [c0]; Phosphatidylglycerol dioctadecanoyl [c0]; Ubiquinone-8 [c0]; Peptidoglycan polymer (n subunits) [c0]; Peptidoglycan polymer (n-1 subunits) [c0]; Stearoylcardiolipin (B. subtilis) [c0]; dATP [c0]; dGTP [c0]; dCTP [c0]; TTP [c0]; DNA [c0]; L-Cysteine [c0]
rxn00317_c0 L-Lysine:2-oxoglutarate 6-aminotransferase C-3-hydroxy-butyrate > bio1 cpd00003_c0; cpd00006_c0; cpd00010_c0; cpd00015_c0; cpd00016_c0; cpd00017_c0; cpd00028_c0; cpd00042_c0; cpd00056_c0; cpd00058_c0; cpd00087_c0; cpd00118_c0; cpd00166_c0; cpd00201_c0; cpd00220_c0; cpd00264_c0; cpd00345_c0; cpd00557_c0; cpd01997_c0; cpd02229_c0; cpd03422_c0; cpd03736_c0; cpd10515_c0; cpd10516_c0; cpd11462_c0; cpd11463_c0; cpd11493_c0; cpd12370_c0; cpd15352_c0; cpd15500_c0; cpd15533_c0; cpd15540_c0; cpd15560_c0; cpd15665_c0; cpd15666_c0; cpd15793_c0; cpd00115_c0; cpd00241_c0; cpd00356_c0; cpd00357_c0; cpd11461_c0; cpd00084_c0 NAD [c0]; NADP [c0]; CoA [c0]; FAD [c0]; Pyridoxal phosphate [c0]; S-Adenosyl-L-methionine [c0]; Heme [c0]; GSH [c0]; TPP [c0]; Cu2+ [c0]; Tetrahydrofolate [c0]; Putrescine [c0]; Calomide [c0]; 10-Formyltetrahydrofolate [c0]; Riboflavin [c0]; Spermidine [c0]; 5-Methyltetrahydrofolate [c0]; Siroheme [c0]; Dimethylbenzimidazole [c0]; Bactoprenyl diphosphate [c0]; Cobinamide [c0]; Lauroyl-KDO2-lipid IV(A) [c0]; Fe2+ [c0]; fe3 [c0]; mRNA [c0]; Protein [c0]; ACP [c0]; apo-ACP [c0]; 2-Demethylmenaquinone 8 [c0]; Menaquinone 8 [c0]; phosphatidylethanolamine dioctadecanoyl [c0]; Phosphatidylglycerol dioctadecanoyl [c0]; Ubiquinone-8 [c0]; Peptidoglycan polymer (n subunits) [c0]; Peptidoglycan polymer (n-1 subunits) [c0]; Stearoylcardiolipin (B. subtilis) [c0]; dATP [c0]; dGTP [c0]; dCTP [c0]; TTP [c0]; DNA [c0]; L-Cysteine [c0]
hgscott commented 7 months ago

Even though KBase saw growth on 3-hydroxybutyrate, when I downloaded the model, and ran it in COBRApy, I got that there was no exchange reaction for it.

I also, saw growth on a lot of things where there isn't supposed to be any growth: Image

And I got growth when there is no C in the media.

hgscott commented 7 months ago

With that, I am going to close this issue and try to tackle those three issues in #12, #53, #54.