gap filling in a metabolic network

[Bhabuk Koirala]

Hi all,

I have the following network (glycolysis till pyruvate) in xls format. I feed this model to MATLAB cobra toolbox and try to do FBA. however, the solution is 0. I used gap find function to find gaps in metabolic network since metabolite accumulation is not allowed in stoichiometric models. It gives me several gaps in my network but the root gap is only one reaction. I do not know how to fill in the gap in the network. Can anyone help me on this? Thank you in advance.

gapfind output: 

[allGaps,rootGaps,downstreamGaps] = gapFind(model)

allGaps = 

    'G6P[c]+PYR[c]'

    'H[c]'

    'ADP[c]+H[c]+PEP[c]'

    'PYR[c]'

rootGaps = 

    'ADP[c]+H[c]+PEP[c]'

downstreamGaps = 

    'G6P[c]+PYR[c]'

    'H[c]'

    'PYR[c]'

Reactions:

Metabolites: Abbreviation Name Formulas (neutral) Formulas  Charge Compartment KEGG ID PubChem ID ChEBI ID BPG[c]  3_Phospho_D_glyceroyl_phosphate C3H4O10P2 -4 cytosol 2PG[c] D_Glycerate_2_phosphate C3H4O7P -3 cytosol 3PG[c]  3_Phospho_D_glycerate C3H4O7P  -3 cytosol ADP[c] ADP C10H12N5O10P2 -3 cytosol ATP[c] ATP C10H12N5O13P3 -4 cytosol DHAP[c] Dihydroxyacetone_phosphate C3H5O6P -2 cytosol F6P[c] F6P C6H11O9P -2 cytosol FBP FBP C6H11O9P2 -4 cytosol G3P[c] G3P C3H5O6P -2 cytosol G6P[c] G6P C6H11O9P -2 cytosol GLC[c] Glucose C6H12O6 0 cytosol GLC[e] Glucose C6H12O6 0 extracellular H[c] H H 1 cytosol H[e] H H 1 extracellular H2O[c] H2O H2O 0 cytosol NAD[c] NAD C21H26N7O14P2  -1 cytosol NADH[c] NADH C21H27N7O14P2 -2 cytosol PEP[c] PEP C3H2O6P -3 cytosol PI[c] PI HO4P -2 cytosol PI[e] PI HOP4 -2 extracellular PYR[c] Pyruvate  C3H3O3 -1 cytosol PYR[e] Pyruvate  C3H3O3 -1 extracellular

Reactions:

Reaction name	Reaction description	Formula	Gene reaction association	Genes	Proteins	Subsystem	Reversible	Lower bound	Upper bound	Objective
GLCe	GLCt	GLC[e] <=>					1	-1000	1000	0
GLCt	GLCt	GLC[e] <=> GLC[c]					1	-1000	1000	0
GLk2	GLK2	GLC[c] + PEP[c] -> G6P[c]+PYR[c]					0	-1000	1000	0
PGI	PGI	G6P[c] <=> F6P[c]					1	-1000	1000	0
PFK	PFK	F6P[c] + ATP[c] -> FBP[c] + ADP[c] + H[c]					0	-1000	1000	0
FBA	FBA	FBP[c] <=> G3P[c] + DHAP[c]					1	-1000	1000	0
TPI	TPI	DHAP[c]<=>G3P[c]					1	-1000	1000	0
GAPDH	GAPDH	G3P[c] + PI[c] + NAD[c] <=> BPG[c] + NADH[c]					1	-1000	1000	0
NAD	NAD	NADH[c]<=>NAD[c]					1	-1000	1000	0
PGK	PGK	BPG[c] + ADP[c] <=> 3PGA[c] + ATP[c]					1	-1000	1000	0
PMG	PMG	3PGA[c]<=>2PG[c]					1	-1000	1000	0
ENO	ENO	2PG[c]  <=> H2O[c] + PEP[c]					1	-1000	1000	0
H2Ot	H2Ot	ATP[c]+H2O[c]<=>ADP[c]+PI[c]+H[c]					1	-1000	1000	0
PYK	PYK	ADP[c]+H[c]+PEP[c] -> ATP[c] + PYR[c]					0	-1000	1000	0
He	He	H[e]<=>					1	-1000	1000	0
Ht	Ht	H[e]<=>H[c]					1	-1000	1000	0
Pie	pie	PI[e] <=>					1	-1000	1000	0
Pit	Pit	PI[c]<=> PI[e]					1	-1000	1000	0
PYRt	PYRt	H[c]+PYR[c]<=> H[e]+PYR[e]					1	-1000	1000	0
PYRe Sincerely, Bhabuk	PYRe	PYR[e] <=>					1	-1000	1000	1