Metabolites are not as expected #270
Description
Hello, I gapfilled the draft of Limosilactobacillus reuteri.
This is my code and customized culture medium composition:
gapseq fill -m LR-draft.RDS -c LR-rxnWeigths.RDS -g LR-rxnXgenes.RDS -n MRS.csv
MRS.csv
compounds name maxFlux
cpd00027 D-Glucose 10
cpd00007 O2 0
cpd00051 L-Arginine 100
cpd00084 L-Cysteine 100
cpd00119 L-Histidine 100
cpd00322 L-Isoleucine 100
cpd00107 L-Leucine 100
cpd00060 L-Methionine 100
cpd00066 L-Phenylalanine 100
cpd00129 L-Proline 100
cpd00054 L-Serine 100
cpd00161 L-Threonine 100
cpd00065 L-Tryptophan 100
cpd00069 L-Tyrosine 100
cpd00156 L-Valine 100
cpd00305 Thiamine 100
cpd00220 Riboflavin 100
cpd00218 Niacin 100
cpd00644 Pantothenate 100
cpd00263 Pyridoxine 100
cpd00104 Biotin 100
cpd00393 Folate 100
cpd00009 Phosphate 100
cpd00205 K+ 100
cpd00971 Na+ 100
cpd00013 Ammonium 100
cpd00254 Mg 100
cpd00048 Sulfate 100
cpd00030 Mn2+ 100
cpd10515 Fe2+ 100
cpd00034 Zn2+ 100
cpd00058 Cu2+ 100
cpd00149 Co2+ 100
cpd00244 Ni2+ 100
cpd00099 Cl- 100
cpd00001 H2O 100
cpd00067 H+ 100
cpd00063 Ca2+ 100
cpd10516 Fe3+ 100
Then I checked all the metabolites produced by Limosilactobacillus reuteri.
getMetaboliteProduction <- function(mod) {
require(cobrar)
require(data.table)
MTF
sol.mtf <- pfba(mod)
dt.mtf <- data.table(ex = mod@react_id,
name = mod@react_name,
mtf.flux = sol.mtf@fluxes)
FVA
sol.fv <- fva(mod, react = mod@react_id[grep("^EX_cpd[0-9]+_e0", mod@react_id)])
sol.fv$growth.fraction <- NULL
dt <- merge(dt.mtf, sol.fv, by.x = "ex", by.y = "react")
dt <- dt[mtf.flux > 1e-6]
return(dt[order(-mtf.flux)])
}
library(cobrar)
Loading required package: Matrix
cobrar uses...
- libSBML (v. 5.20.5)
- glpk (v. 5.0)
LR<- readRDS("LR.RDS")
getMetaboliteProduction(LR)[1:15]
Loading required package: data.table
data.table 1.17.6 using 52 threads (see ?getDTthreads). Latest news: r-datatable.com
ex name mtf.flux min.flux
1: EX_cpd00013_e0 NH3-e0 Exchange 161.90500325 161.90500327
2: EX_cpd00067_e0 H+-e0 Exchange 126.61995400 107.15105918
3: EX_cpd00141_e0 Propionate-e0 Exchange 125.66107697 104.28746925
4: EX_cpd00047_e0 Formate-e0 Exchange 120.57660046 90.15823113
5: EX_cpd00011_e0 CO2-e0 Exchange 53.34354442 0.00000000
6: EX_cpd00029_e0 Acetate-e0 Exchange 46.51438770 44.05229863
7: EX_cpd00035_e0 L-Alanine-e0 Exchange 40.81407021 0.00000000
8: EX_cpd00324_e0 MTTL-e0 Exchange 21.37360772 0.00000000
9: EX_cpd00033_e0 Glycine-e0 Exchange 4.12058349 0.00000000
10: EX_cpd00036_e0 Succinate-e0 Exchange 0.04469337 0.04469337
11: EX_cpd00239_e0 H2S-e0 Exchange 0.02979558 0.02979558
12: EX_cpd01981_e0 5-Methylthio-D-ribose-e0 Exchange 0.01489779 0.01489779
I am very confused about why there is no lactic acid in the metabolites of Limosilactobacillus reuteri, which is a common lactic acid bacterium.
I want to know the lactic acid production of Limosilactobacillus reuteri. How can I achieve this?
My gapseq version is 1.4.0.
The cobrar version is 0.2.0.