The KEGGID version:
UL=['C00001','C00002','C00003','C00004','C00005','C00006','C00007','C00008','C00009','C00010', 'C00011', 'C00013','C00014','C00015','C00020', 'C00024','C00080 ', 'C00362', 'C00144', 'C00209', 'C00282', 'C00044', 'C00361', 'C00286', 'C00063', 'C00112', 'C00131', 'C00206', 'C00360', 'C00460', 'C00075', 'C00105', 'C00804', 'C00048', 'C00153', 'C00387', 'C05985', 'C00035', 'C00455', 'C00215', 'C00067', 'C00575', 'C03248', 'C00704', 'C00027', 'C01346', 'C00365', 'C00055', 'C00058'],
% Alkylphosphonate/PH2O4R [Annotation], PH2O4R [ConceptName] 


Using following regular expression in Ondex: 
^[d][A|U|G][M|D|T]P$|^[A|C|U|G][M|D|T]P$|h2o|^nicotinamide|H\+|^[h|H]ydrogen$|^\|NAD\(P\)\|$|^[H|h]2O2$|^\|NAD\(P\)H\|$|^\|Donor-H2\|$|^\|Acceptor\|$|^Phosphate$|^\|Pi\|$|^Coenzyme A$|^Acetyl-CoA$|^Ammonium$|^[a|A]mmonia$|^\|acceptor\|$|^O2$|^Diphosphate$|^CO2$|^[o|O]xygen$|^NAD\(P\)H$|^NAD\(P\)\+|NAD-P-OR-NOP$

Following list of Ubiquitoud compounds were removed from the model:kegg_rno-PreferredFirstNameFiltered-Mapped-RelationsCollapsed.xml.gz

H2O	H2O [Annotation], H2O [ConceptName] 	
Orthophosphate	Phosphate [ConceptName] 	
ADP	ADP [ConceptName], ADP (PDB) [ConceptAccession] 	
ATP	ATP [ConceptName], ATP (PDB) [ConceptAccession] 	
Acetyl-CoA	Acetyl-CoA [ConceptName] 	
Diphosphate	Diphosphate [ConceptName] 	
Oxygen	O2 [Annotation], O2 [ConceptName], Oxygen [ConceptName] 	
NADH	Nicotinamide adenine dinucleotide [ConceptName] 	
NAD+	Nicotinamide adenine dinucleotide [ConceptName] 	
H+	H+ [ConceptName] 	
dGMP	dGMP [ConceptName] 	
GMP	GMP [ConceptName] 	
Guanosine	GMP (PDB) [ConceptAccession] 	
2-Propyn-1-al	C3H2O [Annotation], C3H2O [ConceptName] 	
GDP	GDP [ConceptName], GDP (PDB) [ConceptAccession] 	
Nicotinamide D-ribonucleotide	Nicotinamide mononucleotide [ConceptName], Nicotinamide ribonucleotide [ConceptName], Nicotinamide nucleotide [ConceptName], Nicotinamide D-ribonucleotide [ConceptName] 	
NADPH	NADPH [ConceptName]	 
CoA	Coenzyme A [ConceptName] 	
dGDP	dGDP [ConceptName] 	
dGTP	dGTP [ConceptName] 	
Formaldehyde	CH2O [Annotation], CH2O [ConceptName] 	
3',5'-Cyclic AMP	CMP (PDB) [ConceptAccession] 	
GTP	GTP [ConceptName], GTP (PDB) [ConceptAccession] 	
Oxalate	C2H2O4 [Annotation], C2H2O4 [ConceptName] 	
Hydrogen	Hydrogen [ConceptName] 	
Acetylenedicarboxylate	C4H2O4 [Annotation], C4H2O4 [ConceptName] 	
O2.-	O2 [Annotation], O2 [ConceptName] 	
H2O2	H2O2 [Annotation], H2O2 [ConceptName] 	
dUTP	dUTP [ConceptName] 	
dUDP	dUDP [ConceptName] 	
dUMP	dUMP [ConceptName], UMP (PDB) [ConceptAccession] 	
CMP	CMP [ConceptName] 	
Formate	CH2O2 [Annotation], CH2O2 [ConceptName] 	
CDP	CDP [ConceptName], CDP (PDB) [ConceptAccession] 	
dATP	dATP [ConceptName] 	
dADP	dADP [ConceptName] 	
dAMP	dAMP [ConceptName] 	
AMP	AMP [ConceptName], AMP (PDB) [ConceptAccession] 	
Alkylphosphonate	PH2O4R [Annotation], PH2O4R [ConceptName] 	
CTP	CTP [ConceptName], CTP (PDB) [ConceptAccession] 	
UTP	UTP [ConceptName], UTP (PDB) [ConceptAccession] 	
UMP	UMP [ConceptName] 	
UDP	UDP [ConceptName] 	
Propynoate	C3H2O2 [Annotation], C3H2O2 [ConceptName] 	
Glyoxylate	C2H2O3 [Annotation], C2H2O3 [ConceptName] 	
NADP+	Nicotinamide adenine dinucleotide phosphate [ConceptName] 	
CO2	CO2 [Annotation], CO2 [ConceptName], CO2 (PDB) [ConceptAccession] 	
NH3	Ammonia [ConceptName] 	
Nicotinamide	Nicotinamide [ConceptName] 	
