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jotech / gapseq

Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
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Questions about the result of using customer medium Gapfilling #84

Closed zhouqCui closed 3 years ago

zhouqCui commented 3 years ago

Hello,

I try to build up the model by using my own medium. This medium has been published before and my target strains can grow in lab test (they did not grow as well as nutrient rich medium like LB). However, the result of Gapfilling showed "final growth rate:0". I try to use M9 medium to test my target strain for Gapfilling as a control which works well. The final growth rate is around 0.8. So I suppose the problem may caused by my medium? Below I have attached my medium file and the result of Gapfilling, would you give me some advice?

thank you very much!

MEDIUM: compounds | name | maxFlux cpd00027 | Glucose | 10 cpd00067 | H+ | 100 cpd00099 | Cl- | 100 cpd00205 | K+ | 100 cpd00254 | Mg | 100 cpd00971 | Na+ | 100 cpd00001 | H2O | 100 cpd00009 | Phosphate | 100 cpd00011 | CO2 | 100 cpd00013 | NH3 | 10 cpd00082 | D-Fructose | 1 cpd00129 | L-Proline | 0.1 cpd00132 | L-Asparagine | 0.1 cpd00053 | L-glutamine | 0.1 cpd00054 | L-Serine | 1 cpd00133 | Nicotinamide | 0.1 cpd00007 | O2 | 27 cpd10515 | Fe2+ | 100 cpd10516 | fe3 | 100 cpd00058 | Cu2+ | 100 cpd00063 | Ca2+ | 100 cpd00030 | Mn2+ | 100 cpd00034 | Zn2+ | 100 cpd00149 | Co2+ | 100

RESULT:

  1. Initial gapfilling: Make model grow on given media using all reactions Utilized candidate reactions: 391Warning message: In gapfill4(mod.orig = mod.orig, mod.full = mod, rxn.weights = copy(rxn.weights), : Final model Ea110_genome cannot produce enough target even when all candidate reactions are added! obj=9.16282921393675e-13 lp_stat=5

  2. Biomass gapfilling using core reactions only Gapfill summary: Filled components: 1 ( UTP-c0 ) Added reactions: 6 Final growth rate: 0

2b. Anaerobic biomass gapfilling using core reactions only Gapfill summary: Filled components: 0 ( ) Added reactions: 6 Final growth rate: 0

  1. Energy source gapfilling with core reactions only Gapfill summary: Filled components: 10 ( L-Lysine-e0,L-Leucine-e0,Xylose-e0,L-Valine-e0,Taurine-e0,L-Isoleucine-e0,GABA-e0,D-Serine-e0,L-Idonate-e0,Cholate-e0-e0 ) Added reactions: 232 Final growth rate: 0

  2. Checking for potential metabolic products with core reactions only Gapfill summary: Filled components: 2 ( D-Fructose-e0,Riboflavin-e0-e0 ) Added reactions: 2 Final growth rate: 0

Uptake at limit: Choline:0, H2S2O3:0, PAN:0, Maltodextrin:0, NAD:0

Waschina commented 3 years ago

Hi,

the medium does not contain any source of sulfur. You could try to add for example

I hope this solves the issue

Best Silvio

zhouqCui commented 3 years ago

Hello Silvio,

I have tried all of my strains and it works well!!! Thank you very much!

Zhouqi

On Jul 9, 2021, at 2:58 AM, Silvio Waschina @.***> wrote:

Hi,

the medium does not contain any source of sulfur. You could try to add for example

sulfate (cpd00048) H2S (cpd00239) I hope this solves the issue

Best Silvio

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Waschina commented 3 years ago

Perfect :)