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Kretaks
Dec 17, 2019, 5:23:42 AM12/17/19
to COBRA Toolbox
Hello,
I was using checkDuplicateRxn function ( [modelOut, removedRxnInd, keptRxnInd] = checkDuplicateRxn(model); )
Cobra gave me output
Var1 -> reaction for removed (MetaCyc identificator)
Var2 -> reaction for kept
Var3 -> equation for removed
Var4 -> equation for kept
I was wondering if everything is correct because most reactions are nowhere near similar
For example:
{'RXN-10938'} {'RXN-9615'} {'1-PHOSPHATIDYL-1D-MYO-INOSITOL-35-BISPH + WATER => CPD-177 + Pi'} {'AMMONIUM => AMMONIUM'}
I used function in loop while all duplicates were removed (separated by line of Var1-4)
Var1 Var2 Var3 Var4
______________________________ __________________________ ________________________________________________________________________________________________________________________ _________________________________________________________________________________________
{'GLYCERALDEHYDE-DEHYDRO-RXN'} {'RXN-15513' } {'GLYCERALD + Acceptor + WATER => GLYCERATE + Donor-H2 + PROTON' } {'2-PG <=> G3P' }
{'ERYTHRONOLIDE-SYNTHASE-RXN'} {'RXN0-5195' } {'PROPIONYL-COA + 6 D-METHYL-MALONYL-COA + 6 NADPH + 12 PROTON => CPD-428 + 7 CO-A + 6 CARBON-DIOXIDE + WATER + 6 NADP'} {'General-Protein-Substrates + WATER => 2 Peptides-holder + 2 PROTON' }
{'RXN-9557' } {'RXN0-5184' } {'R-3-hydroxy-cis-vaccenoyl-ACPs => cis-vaccen-2-enoyl-ACPs + WATER' } {'1-4-alpha-D-Glucan + Pi => 1-4-alpha-D-Glucan + GLC-1-P' }
{'RXN-12317' } {'RXN0-3221' } {'S-ADENOSYLMETHIONINE + Phosphatase-2A-leucine => ADENOSYL-HOMO-CYS + Phosphatase-2A-leucine-methyl-ester' } {'General-Protein-Substrates + WATER => 2 Peptides-holder' }
{'PROTOPORGENOXI-RXN' } {'DLACTDEHYDROGNAD-RXN' } {'PROTOPORPHYRINOGEN + 3 OXYGEN-MOLECULE => PROTOPORPHYRIN_IX + 3 HYDROGEN-PEROXIDE' } {'PYRUVATE + NADH + PROTON => D-LACTATE + NAD' }
{'R313-RXN' } {'CARNOSINE-SYNTHASE-RXN'} {'3-CYANOPYRIDINE + WATER => NIACINAMIDE' } {'B-ALANINE + HIS + ATP => PROTON + CARNOSINE + ADP + Pi' }
{'AKBLIG-RXN' } {'RXN-13697' } {'GLY + ACETYL-COA <=> AMINO-OXOBUT + CO-A' } {'L-ASPARTATE + 2-KETOGLUTARATE <=> GLT + OXALACETIC_ACID' }
{'RXN-8708' } {'AMINOACYLASE-RXN' } {'WATER + Aromatic-amino-acid-esters => 2 Aromatic-Amino-Acids' } {'N-Acylated-Aliphatic-Amino-Acids + WATER => Carboxylates + Aliphatic-L-Amino-Acids' }
{'3.4.11.18-RXN' } {'RXN-9556' } {'Protein-With-N-Terminal-Met + WATER => MET + Peptide-Holder-Alternative' } {'3-oxo-cis-vaccenoyl-ACPs + NADPH + PROTON => R-3-hydroxy-cis-vaccenoyl-ACPs + NADP' }
{'RXN-14666' } {'RXN-10660' } {'NovH-proteins + TYR + ATP => Tyr-S-NovH + AMP + PPI' } {'3-hydroxy-cis-D9-hexaecenoyl-ACPs => Trans-D3-cis-D9-hexadecenoyl-ACPs + WATER' }
{'RXN0-2142' } {'3.2.1.52-RXN' } {'b-Keto-cis-D5-dodecenoyl-ACPs + NADPH + PROTON => b-Hydroxy-cis-D5-dodecenoyl-ACPs + NADP' } {'N-Acetyl-beta-D-Hexosaminides + WATER => N-acetyl-beta-D-hexosamines + Alcohols' }
{'RXN-19711' } {'RXN-12127' } {'CPD0-2113 + WATER => CPD-16717 + Pi' } {'CPD-12575 + CHOLESTEROL => UDP + CPD-556 + PROTON' }
{'TRANS-RXN-131' } {'6.3.5.7-RXN' } {'GLYCEROL <=> GLYCEROL' } {'GLN + L-glutamyl-tRNAGln + ATP + WATER => GLT + Charged-GLN-tRNAs + Pi + ADP + PROTON'}
{'RXN-14224' } {'RXN-10756' } {'CPD-15163 + NAD + WATER => CPD-661 + NADH + 2 PROTON' } {'CPD6666-1 + WATER <=> OLEATE-CPD + AMMONIUM' }
Var1 Var2 Var3 Var4
_________________ _____________ ______________________________________________________________________________ ________________________________________________________________
{'RXN-12402' } {'RXN0-3221'} {'CPD0-1202 + WATER => Glucopyranose + XYLOSE' } {'General-Protein-Substrates + WATER => 2 Peptides-holder' }
{'XYLULOKIN-RXN'} {'RXN0-21' } {'D-XYLULOSE + ATP => PROTON + XYLULOSE-5-PHOSPHATE + ADP' } {'GLUTATHIONE + ATP + WATER => GLUTATHIONE + ADP + Pi + PROTON'}
{'RXN-17896' } {'RXN-9615' } {'S-ADENOSYLMETHIONINE + CPD-19220 => ADENOSYL-HOMO-CYS + CPD-18779 + PROTON'} {'AMMONIUM => AMMONIUM' }
Var1 Var2 Var3 Var4
_____________________________ _____________ _________________________________________________________________________________________________________ ________________________________________________________________
{'CYTOCHROME-C-OXIDASE-RXN' } {'RXN0-3221'} {'OXYGEN-MOLECULE + 8 PROTON + 4 Cytochromes-C-Reduced => 4 PROTON + 2 WATER + 4 Cytochromes-C-Oxidized'} {'General-Protein-Substrates + WATER => 2 Peptides-holder' }
{'RXN-17884' } {'RXN0-21' } {'S-NITROSOGLUTATHIONE + NADH + PROTON => CPD-19217 + NAD' } {'GLUTATHIONE + ATP + WATER => GLUTATHIONE + ADP + Pi + PROTON'}
{'RETINOL-DEHYDROGENASE-RXN'} {'RXN-9615' } {'CPD-13524 + NAD <=> RETINAL + NADH + PROTON' } {'AMMONIUM => AMMONIUM' }
Var1 Var2 Var3 Var4
_____________________________ _____________ __________________________________________________________________ ________________________________________________________________
{'RXN-12490' } {'RXN0-3221'} {'CPD0-2244 + NAD => CPD0-2123 + NADH + PROTON' } {'General-Protein-Substrates + WATER => 2 Peptides-holder' }
{'RXN-17916' } {'RXN0-21' } {'ATP + 5-Phospho-RNA + PROTON => A-5-prime-PP-5-prime-RNA + PPI'} {'GLUTATHIONE + ATP + WATER => GLUTATHIONE + ADP + Pi + PROTON'}
{'RETINOL-DEHYDROGENASE-RXN'} {'RXN-9615' } {'CPD-13524 + NAD <=> RETINAL + NADH + PROTON' } {'AMMONIUM => AMMONIUM' }
Var1 Var2 Var3 Var4
________________________ _____________ __________________________________________________________ ________________________________________________________________
{'RXN-12496' } {'RXN0-3221'} {'Carotenoid-psi-end-group => Carotenoid-beta-end-group' } {'General-Protein-Substrates + WATER => 2 Peptides-holder' }
{'RXN-18329' } {'RXN0-21' } {'DIHYDROLIPOAMIDE + NADP <=> LIPOAMIDE + NADPH + PROTON'} {'GLUTATHIONE + ATP + WATER => GLUTATHIONE + ADP + Pi + PROTON'}
{'DLACTDEHYDROGFAD-RXN'} {'RXN-9615' } {'Ubiquinones + D-LACTATE => Ubiquinols + PYRUVATE' } {'AMMONIUM => AMMONIUM' }
Var1 Var2 Var3 Var4
_____________ _____________ _____________________________________________________________ ________________________________________________________________
{'RXN-12529'} {'RXN0-3221'} {'GLUTATHIONE + CPD-211 => CPD-13498 + GLY' } {'General-Protein-Substrates + WATER => 2 Peptides-holder' }
{'RXN-18935'} {'RXN0-21' } {'CPD-12600 + WATER => ARACHIDONIC_ACID + GLYCEROL + PROTON'} {'GLUTATHIONE + ATP + WATER => GLUTATHIONE + ADP + Pi + PROTON'}
{'RXN-12413'} {'RXN-9615' } {'CPD-12321 + 5 Acceptor => CPD-12932 + 5 Donor-H2' } {'AMMONIUM => AMMONIUM' }
Var1 Var2 Var3 Var4
____________________________________ _____________ __________________________________________________________________________________________________________________________________ ________________________________________________________________
{'PROTEIN-TYROSINE-PHOSPHATASE-RXN'} {'RXN0-3221'} {'Protein-tyrosine-phosphates + WATER => Pi + Protein-Tyrosines' } {'General-Protein-Substrates + WATER => 2 Peptides-holder' }
{'RXN-13713' } {'RXN0-21' } {'CPD-7238 + 6 Reduced-adrenal-ferredoxins + 5 PROTON + 3 OXYGEN-MOLECULE => CPD-1834 + 6 Oxidized-adrenal-ferredoxins + 4 WATER'} {'GLUTATHIONE + ATP + WATER => GLUTATHIONE + ADP + Pi + PROTON'}
{'RXN-18328' } {'RXN-9615' } {'CPD-296 + NADP <=> LIPOIC-ACID + NADPH + PROTON' } {'AMMONIUM => AMMONIUM' }
Var1 Var2 Var3 Var4
_____________ _____________ ____________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ ________________________________________________________________
{'RXN-14957'} {'RXN0-3221'} {'2 S-ADENOSYLMETHIONINE + a-pyruvate-dehydrogenase-E2-protein-Nsup + 2 Sulfurated-Sulfur-Acceptors + 2 Reduced-2Fe-2S-Ferredoxins => Pyruvate-dehydrogenase-lipoate + 2 MET + 2 CH33ADO + 2 Unsulfurated-Sulfur-Acceptors + 2 Oxidized-2Fe-2S-Ferredoxins'} {'General-Protein-Substrates + WATER => 2 Peptides-holder' }
{'RXN-10870'} {'RXN0-21' } {'S-ADENOSYLMETHIONINE + L-DIHYDROXY-PHENYLALANINE => CPD-11496 + ADENOSYL-HOMO-CYS + PROTON' } {'GLUTATHIONE + ATP + WATER => GLUTATHIONE + ADP + Pi + PROTON'}
{'RXN-10477'} {'RXN-9615' } {'Thyroglobulin-L-thyroxines + WATER => L-THYROXINE + Unspecified-Degradation-Products' } {'AMMONIUM => AMMONIUM' }
Var1 Var2 Var3 Var4
_________________ ____________ ______________________________________________________________________________________________________ ________________________________________________________________
{'1.14.13.8-RXN'} {'RXN0-21' } {'NN-DIMETHYLANILINE + OXYGEN-MOLECULE + NADPH + PROTON => NN-DIMETHYLANILINE-N-OXIDE + WATER + NADP'} {'GLUTATHIONE + ATP + WATER => GLUTATHIONE + ADP + Pi + PROTON'}
{'RXN-18442' } {'RXN-9615'} {'CPD-4211 + CPD-19784 => PPI + CPD-19785 + PROTON' } {'AMMONIUM => AMMONIUM' }
Var1 Var2 Var3 Var4
_________________ ____________ __________________________________________________________________________________________________________________________________________________________________ ________________________________________________________________
{'1.14.13.8-RXN'} {'RXN0-21' } {'NN-DIMETHYLANILINE + OXYGEN-MOLECULE + NADPH + PROTON => NN-DIMETHYLANILINE-N-OXIDE + WATER + NADP' } {'GLUTATHIONE + ATP + WATER => GLUTATHIONE + ADP + Pi + PROTON'}
{'RXN-18490' } {'RXN-9615'} {'CPD-19821 + 2 Red-NADPH-Hemoprotein-Reductases + 2 OXYGEN-MOLECULE => 12-carboxyjasmonoyl-L-amino-acids + 2 Ox-NADPH-Hemoprotein-Reductases + 3 WATER + PROTON'} {'AMMONIUM => AMMONIUM' }
Var1 Var2 Var3 Var4
_____________ ____________ ___________________________________ ________________________________________________________________
{'RXN0-2421'} {'RXN0-21' } {'FE+2 + PROTON <=> FE+2 + PROTON'} {'GLUTATHIONE + ATP + WATER => GLUTATHIONE + ADP + Pi + PROTON'}
{'RXN-10644'} {'RXN-9615'} {'CPD-11447 => CPD-11446' } {'AMMONIUM => AMMONIUM' }
Var1 Var2 Var3 Var4
________________ ____________ ___________________________________________________________________________________________ ________________________________________________________________
{'1.17.1.1-RXN'} {'RXN0-21' } {'CPD-658 + NADH-P-OR-NOP + PROTON => CPD-1078 + NAD-P-OR-NOP + WATER' } {'GLUTATHIONE + ATP + WATER => GLUTATHIONE + ADP + Pi + PROTON'}
{'RXN-10780' } {'RXN-9615'} {'5-HYDROXYINDOLE_ACETALDEHYDE + NAD + WATER => 5-HYDROXYINDOLE_ACETATE + NADH + 2 PROTON'} {'AMMONIUM => AMMONIUM' }
Var1 Var2 Var3 Var4
_________________ ____________ ___________________________________________________________________________________________ ________________________________________________________________
{'TRANS-RXN-127'} {'RXN0-21' } {'TARTRATE + SUC <=> TARTRATE + SUC' } {'GLUTATHIONE + ATP + WATER => GLUTATHIONE + ADP + Pi + PROTON'}
{'RXN-18817' } {'RXN-9615'} {'Galactofuranosemannans + 5 WATER => Aspergilus-galactomannan-core + 5 D-galactofuransoe'} {'AMMONIUM => AMMONIUM' }
Var1 Var2 Var3 Var4
_____________ ____________ ____________________________________________________________________________________________________ ________________________________________________________________
{'RXN-12461'} {'RXN0-21' } {'S-ADENOSYLMETHIONINE + carbo-me-ur-34-tRNA => 5-2-me-oxy-2-oxo-et-ur-34-tRNA + ADENOSYL-HOMO-CYS'} {'GLUTATHIONE + ATP + WATER => GLUTATHIONE + ADP + Pi + PROTON'}
{'RXN-18818'} {'RXN-9615'} {'CPD-20117 + WATER => D-galactofuransoe + P-NITROPHENOL + PROTON' } {'AMMONIUM => AMMONIUM' }
Var1 Var2 Var3 Var4
_____________ ____________ ___________________________________________________________________ ________________________________________________________________
{'RXN-13927'} {'RXN0-21' } {'L-2-hydroxyacids + NAD <=> 2-Oxo-carboxylates + NADH + PROTON' } {'GLUTATHIONE + ATP + WATER => GLUTATHIONE + ADP + Pi + PROTON'}
{'RXN-18818'} {'RXN-9615'} {'CPD-20117 + WATER => D-galactofuransoe + P-NITROPHENOL + PROTON'} {'AMMONIUM => AMMONIUM' }
Var1 Var2 Var3 Var4
_____________ ____________ ____________________________________________________________________ ________________________
{'RXN-18912'} {'RXN-9615'} {'Man9GlcNAc2-proteins + WATER => Protein-L-Aspartates + CPD-20273'} {'AMMONIUM => AMMONIUM'}
Var1 Var2 Var3 Var4
_____________ ____________ ______________________________________________________________________________ ________________________
{'RXN-18917'} {'RXN-9615'} {'Man7GlcNAc2-protein-A123B3 + WATER => Man6GlcNAc2-protein-A123 + CPD-12601'} {'AMMONIUM => AMMONIUM'}
Var1 Var2 Var3 Var4
_____________ ____________ ______________________________________________________________ ________________________
{'RXN-19036'} {'RXN-9615'} {'HS + GLUTATHIONE + ETR-Quinones => CPD-11281 + ETR-Quinols'} {'AMMONIUM => AMMONIUM'}
Var1 Var2 Var3 Var4
_____________ ____________ ___________________________________________________________________ ________________________
{'RXN-10938'} {'RXN-9615'} {'1-PHOSPHATIDYL-1D-MYO-INOSITOL-35-BISPH + WATER => CPD-177 + Pi'} {'AMMONIUM => AMMONIUM'}
Var1 Var2 Var3 Var4
_____________ ____________ ____________________________________________________________________________________________________ ________________________
{'RXN-10958'} {'RXN-9615'} {'1-PHOSPHATIDYL-1D-MYO-INOSITOL-35-BISPH + WATER => 1-PHOSPHATIDYL-1D-MYO-INOSITOL-5-PHOSPHA + Pi'} {'AMMONIUM => AMMONIUM'}
Var1 Var2 Var3 Var4
________________ ____________ _________________________________________________ ________________________
{'1.1.1.39-RXN'} {'RXN-9615'} {'MAL + NAD => PYRUVATE + CARBON-DIOXIDE + NADH'} {'AMMONIUM => AMMONIUM'}
Var1 Var2 Var3 Var4
________________ ____________ ___________________________________________________________ ________________________
{'1.1.3.41-RXN'} {'RXN-9615'} {'XYLITOL + OXYGEN-MOLECULE => XYLOSE + HYDROGEN-PEROXIDE'} {'AMMONIUM => AMMONIUM'}
Var1 Var2 Var3 Var4
_________________ ____________ ________________________________________________________________________________________________ ________________________
{'1.14.11.2-RXN'} {'RXN-9615'} {'PROCOLLAGEN-L-PROLINE + 2-KETOGLUTARATE + OXYGEN-MOLECULE => CPD-6321 + SUC + CARBON-DIOXIDE'} {'AMMONIUM => AMMONIUM'}
Var1 Var2 Var3 Var4
__________________ ____________ ________________________________________________________________________________________________________________________________________ ________________________
{'1.14.13.36-RXN'} {'RXN-9615'} {'4-COUMAROYLQUINATE + OXYGEN-MOLECULE + Red-NADPH-Hemoprotein-Reductases => CAFFEOYLQUINATE + WATER + Ox-NADPH-Hemoprotein-Reductases'} {'AMMONIUM => AMMONIUM'}
Var1 Var2 Var3 Var4
__________________ ____________ ________________________________________________________________________________________________________________________________________ ________________________
{'1.14.13.36-RXN'} {'RXN-9615'} {'4-COUMAROYLQUINATE + OXYGEN-MOLECULE + Red-NADPH-Hemoprotein-Reductases => CAFFEOYLQUINATE + WATER + Ox-NADPH-Hemoprotein-Reductases'} {'AMMONIUM => AMMONIUM'}
Var1 Var2 Var3 Var4
_________________ ____________ ___________________________________________________________________________________________________________________________ ________________________
{'1.14.19.5-RXN'} {'RXN-9615'} {'ACYL-COA + 2 FERROCYTOCHROME-B5 + OXYGEN-MOLECULE + 2 PROTON => Cis-Delta-11-acyl-CoAs + 2 FERRICYTOCHROME-B5 + 2 WATER'} {'AMMONIUM => AMMONIUM'}
Var1 Var2 Var3 Var4
_________________ ____________ ___________________________________________________________________________________________________________________________ ________________________
{'1.14.19.5-RXN'} {'RXN-9615'} {'ACYL-COA + 2 FERROCYTOCHROME-B5 + OXYGEN-MOLECULE + 2 PROTON => Cis-Delta-11-acyl-CoAs + 2 FERRICYTOCHROME-B5 + 2 WATER'} {'AMMONIUM => AMMONIUM'}
Var1 Var2 Var3 Var4
_____________ ____________ _____________________________________________________________________________________________________________________________ ________________________
{'RXN-11126'} {'RXN-9615'} {'GLT + TYR + CPD-470 + 2 SER + ARG + 2 CPD-12097 + LYS + 2 THR + 11 ATP => CPD-12098 + WATER + 11 AMP + 11 PPI + 12 PROTON'} {'AMMONIUM => AMMONIUM'}
Var1 Var2 Var3 Var4
_____________ ____________ _______________________________________________________________________________________ ________________________
{'RXN-11135'} {'RXN-9615'} {'ATP + WATER + Supercoiled-Duplex-DNAs => ADP + Pi + PROTON + 2 Single-Stranded-DNAs'} {'AMMONIUM => AMMONIUM'}
Var1 Var2 Var3 Var4
_____________ ____________ ________________________________________________________ ________________________
{'RXN-19583'} {'RXN-9615'} {'CPD-21169 + WATER => CPD-21178 + PYRUVATE + AMMONIUM'} {'AMMONIUM => AMMONIUM'}
Var1 Var2 Var3 Var4
________________ ____________ _________________________________________________________________________ ________________________
{'3.1.26.4-RXN'} {'RXN-9615'} {'RNA-DNA-hybrids + n WATER => DNA-Holder + n Nucleoside-Monophosphates'} {'AMMONIUM => AMMONIUM'}
Var1 Var2 Var3 Var4
________________ ____________ _______________________________________________________________ ________________________
{'PYRUVDEH-RXN'} {'RXN-9615'} {'PYRUVATE + CO-A + NAD => ACETYL-COA + CARBON-DIOXIDE + NADH'} {'AMMONIUM => AMMONIUM'}
Var1 Var2 Var3 Var4
_____________ ____________ ____________________________________________________ ________________________
{'RXN-11192'} {'RXN-9615'} {'CPD-9776 + WATER => PROTON + CPD-9777 + BENZOATE'} {'AMMONIUM => AMMONIUM'}
Var1 Var2 Var3 Var4
_____________ ____________ _________________________________________________________________________________________________ ________________________
{'RXN-17905'} {'RXN-9615'} {'3-Prime-Phosphate-Terminated-RNAs + 5Prime-OH-Terminated-RNAs + GTP => RNA-Holder + GMP + PPI'} {'AMMONIUM => AMMONIUM'}
Var1 Var2 Var3 Var4
_____________ ____________ _____________________________________________________________________________________________________________________________________________________________________________________ ________________________
{'RXN-12465'} {'RXN-9615'} {'2 S-ADENOSYLMETHIONINE + 23S-rRNA-adenine-2503 + 2 Reduced-2Fe-2S-Ferredoxins => ADENOSYL-HOMO-CYS + MET + CH33ADO + 23S-rRNA-8-methyladenine2503 + 2 Oxidized-2Fe-2S-Ferredoxins'} {'AMMONIUM => AMMONIUM'}
Var1 Var2 Var3 Var4
_____________ ____________ _____________________________________________________________________________________________________________________________________________________________________________________ ________________________
{'RXN-11586'} {'RXN-9615'} {'2 S-ADENOSYLMETHIONINE + 23S-rRNA-adenine-2503 + 2 Reduced-2Fe-2S-Ferredoxins => ADENOSYL-HOMO-CYS + MET + CH33ADO + 23S-rRNA-2-methyladenine2503 + 2 Oxidized-2Fe-2S-Ferredoxins'} {'AMMONIUM => AMMONIUM'}
Var1 Var2 Var3 Var4
_____________ ____________ _______________________________________________________________________________________________________________ ________________________
{'RXN-11638'} {'RXN-9615'} {'S-ADENOSYLMETHIONINE + 16S-rRNA-cytidine1402 => ADENOSYL-HOMO-CYS + 16S-rRNA-N4-methylcytidine1402 + PROTON'} {'AMMONIUM => AMMONIUM'}
Var1 Var2 Var3 Var4
_____________ ____________ ________________________________________________________________________ ________________________
{'RXN0-7041'} {'RXN-9615'} {'THIAMINE-PYROPHOSPHATE + Pi + n PROTON => CPD-611 + WATER + n PROTON'} {'AMMONIUM => AMMONIUM'}
Var1 Var2 Var3 Var4
_____________ ____________ __________________________________________________________________________ ________________________
{'RXN-10039'} {'RXN-9615'} {'O-phospho-L-seryl-tRNASecs + SEPO3 + WATER => Charged-SEC-tRNAs + 2 Pi'} {'AMMONIUM => AMMONIUM'}
Var1 Var2 Var3 Var4
________________________________________ ____________ __________________________________________________________________________________________________________ ________________________
{'TRNA-URACIL-5--METHYLTRANSFERASE-RXN'} {'RXN-9615'} {'S-ADENOSYLMETHIONINE + Uracil-54-in-tRNA => tRNA-containing-5Me-uridine54 + ADENOSYL-HOMO-CYS + PROTON'} {'AMMONIUM => AMMONIUM'}
Var1 Var2 Var3 Var4
_____________ ____________ ______________________________________________________________________________________________________________ ________________________
{'RXN-12459'} {'RXN-9615'} {'S-ADENOSYLMETHIONINE + Guanine9-in-tRNA => tRNA-Containing-N1-Methylguanine-9 + ADENOSYL-HOMO-CYS + PROTON'} {'AMMONIUM => AMMONIUM'}
Ronan M.T. Fleming
Dec 18, 2019, 4:29:30 AM12/18/19
to COBRA Toolbox
Hi
the default behaviour is to check the S matrix for duplicate columns.
Could it be your S matrix has duplicates but the labels on the
reactions are incorrect?
https://github.com/opencobra/cobratoolbox/blob/master/src/reconstruction/modelGeneration/checkDuplicateRxn.m
Regards,
Ronan
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Division of Systems Biomedicine and Pharmacology,
Leiden Academic Centre for Drug Research,
Faculty of Science,
Leiden University.
https://www.universiteitleiden.nl/en/staffmembers/ronan-fleming
&
H2020 Project Coordinator,
Systems Medicine of Mitochondrial Parkinson’s Disease,
http://sysmedpd.eu
&
Adjunct Lecturer,
School of Medicine,
National University of Ireland, Galway.
----------------------------------------------------------------------------
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Mobile: +353 873 413 072
Skype: ronan.fleming
----------------------------------------------------------------------------
Upcoming course from 25-29 November 2019, at Leiden University on
"Constraint-based modelling: introduction and advanced topics".
https://www.biosb.nl/archive-courses/constraint-based-modelling-introduction-and-advanced-topics-2019/
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the default behaviour is to check the S matrix for duplicate columns.
Could it be your S matrix has duplicates but the labels on the
reactions are incorrect?
https://github.com/opencobra/cobratoolbox/blob/master/src/reconstruction/modelGeneration/checkDuplicateRxn.m
Regards,
Ronan
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--
--
Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.
----------------------------------------------------------------------------
Assistant Professor,
Division of Systems Biomedicine and Pharmacology,
Leiden Academic Centre for Drug Research,
Faculty of Science,
Leiden University.
https://www.universiteitleiden.nl/en/staffmembers/ronan-fleming
&
H2020 Project Coordinator,
Systems Medicine of Mitochondrial Parkinson’s Disease,
http://sysmedpd.eu
&
Adjunct Lecturer,
School of Medicine,
National University of Ireland, Galway.
----------------------------------------------------------------------------
Peer-reviewed publications: https://goo.gl/FZPG23
Mobile: +353 873 413 072
Skype: ronan.fleming
----------------------------------------------------------------------------
Upcoming course from 25-29 November 2019, at Leiden University on
"Constraint-based modelling: introduction and advanced topics".
https://www.biosb.nl/archive-courses/constraint-based-modelling-introduction-and-advanced-topics-2019/
----------------------------------------------------------------------------
(This message is confidential and may contain privileged information.
It is intended for the named recipient only. If you receive it in
error please notify me and permanently delete the original message and
any copies.)
Kretaks
Dec 20, 2019, 7:13:49 AM12/20/19
to COBRA Toolbox
Hi,
[modelOut, removedRxnInd, keptRxnInd] = checkDuplicateRxn(modelOut, 'S', 1, 1); prints out:
Checking for reaction duplicates by stoichiometry ...
61 duplicate reaction(s) (up to orientation)
Keep: RXN0-3221 General-Protein-Substrates + WATER -> 2 Peptides-holder
Duplicate: 3.4.21.53-RXN General-Protein-Substrates + WATER -> 2 Peptides-holder
Keep: RXN0-21 ATP + WATER -> ADP + PROTON + Pi
Duplicate: 3.6.3.3-RXN ATP + WATER -> ADP + PROTON + Pi
While disp(table(modelOut.rxns(removedRxnInd),modelOut.rxns(keptRxnInd),modelOut.equations(removedRxnInd),modelOut.equations(keptRxnInd)))
Var1 Var2 Var3 Var4
_________________ _____________ ______________________________________________________________________________ ________________________________________________________________
{'RXN-12402' } {'RXN0-3221'} {'CPD0-1202 + WATER => Glucopyranose + XYLOSE' } {'General-Protein-Substrates + WATER => 2 Peptides-holder' }
{'XYLULOKIN-RXN'} {'RXN0-21' } {'D-XYLULOSE + ATP => PROTON + XYLULOSE-5-PHOSPHATE + ADP' } {'GLUTATHIONE + ATP + WATER => GLUTATHIONE + ADP + Pi + PROTON'}
It seems that it's error in my code as modelOut.rxns(removedRxnInd) prints out wrong element as modelOut has changed already
Regards,
Kristaps
P.S. where could I get newest versions of reaction.lst and KEGG_dictionary.xls, are the newest versions included in Cobra toolbox?
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