Correct grRules, metFormula, additional annotation (InChi, ChEBI, KEGG)

* Removed incorrect annotation of FAD:ubiquinone oxidoreductse (yli0053), while allowing flux through NADH:ubiquinone oxidoreductse (773).
* Some complex grRules were incorrect. Some metFormula gave error message when loaded as SBML.
* Cytosolic and mitochondrial branched-chain amino-acid transaminases are encoded by different genes (BAT2 and BAT1, respectively).
* Metabolite annotation (InChi, ChEBI, KEGG) that were previously lost during conversion from RAVEN to COBRA format are now included by exporting the file in RAVEN format. This format is now fully COBRA compatible.

iYali4.txt

@@ -1,7 +1,7 @@
 Rxn name	Rxn description	Formula	Gene-reaction association	Reversible	LB	UB	Objective
-1	(R)-lactate:ferricytochrome-c 2-oxidoreductase	m1[cy] + 2 m2[mi]  -> 2 m3[mi] + m4[cy] 	(YALI0D09273g and YALI0E03212g) or (YALI0C06446g)	0	  0.00	1000.00	  0.00
-2	(R)-lactate:ferricytochrome-c 2-oxidoreductase	2 m2[mi] + m5[mi]  -> 2 m3[mi] + m6[mi] 	(YALI0E03212g and YALI0D09273g)	0	  0.00	1000.00	  0.00
-4	(S)-lactate:ferricytochrome-c 2-oxidoreductase	2 m2[mi] + m7[cy]  -> 2 m3[mi] + m4[cy] 	(YALI0E03212g and YALI0D09273g)	0	  0.00	1000.00	  0.00
+1	(R)-lactate:ferricytochrome-c 2-oxidoreductase	m1[cy] + 2 m2[mi]  -> 2 m3[mi] + m4[cy] 	(YALI0C06446g and YALI0D09273g) or (YALI0E03212g and YALI0D09273g)	0	  0.00	1000.00	  0.00
+2	(R)-lactate:ferricytochrome-c 2-oxidoreductase	2 m2[mi] + m5[mi]  -> 2 m3[mi] + m6[mi] 	(YALI0C06446g and YALI0D09273g) or (YALI0E03212g and YALI0D09273g)	0	  0.00	1000.00	  0.00
+4	(S)-lactate:ferricytochrome-c 2-oxidoreductase	2 m2[mi] + m7[cy]  -> 2 m3[mi] + m4[cy] 	(YALI0E21307g and YALI0D09273g)	0	  0.00	1000.00	  0.00
 5	1,3-beta-glucan synthase	m8[cy]  -> m9[en] + m10[cy] + m11[cy] 	(YALI0C01411g) or (YALI0E21021g)	0	  0.00	1000.00	  0.00
 6	(1-6)-beta-glucan synthase	m8[cy]  -> m10[cy] + m11[cy] + m12[en] 	(YALI0C14190g)	0	  0.00	1000.00	  0.00
 7	1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase	m13[cy]  -> m14[cy] 	(YALI0F05192g)	0	  0.00	1000.00	  0.00
@@ -24,8 +24,8 @@ Rxn name	Rxn description	Formula	Gene-reaction association	Reversible	LB	UB	Obje
 26	2-keto-4-methylthiobutyrate transamination	m33[cy] + m50[cy]  -> m51[cy] + m74[cy] 		0	  0.00	1000.00	  0.00
 27	2-methylcitrate dehydratase	m75[mi]  <=> m26[mi] + m76[mi] 	(YALI0E02728g)	1	-1000.00	1000.00	  0.00
 28	2-methylcitrate synthase	m26[mi] + m77[mi] + m78[mi]  -> m28[mi] + m73[mi] + m79[mi] 	(YALI0E00638g) or (YALI0E02684g)	0	  0.00	1000.00	  0.00
-29	2-oxo-4-methyl-3-carboxypentanoate decarboxylation	m10[cy] + m80[cy]  -> m81[cy] + m82[cy] 	(YALI0D01265g)	0	  0.00	  0.00	  0.00
-30	2-oxo-4-methyl-3-carboxypentanoate decarboxylation	m28[mi] + m83[mi]  -> m44[mi] + m84[mi] 	(YALI0D01265g)	0	  0.00	1000.00	  0.00
+29	2-oxo-4-methyl-3-carboxypentanoate decarboxylation	m10[cy] + m80[cy]  -> m81[cy] + m82[cy] 	(YALI0F19910g)	0	-1000.00	1000.00	  0.00
+30	2-oxo-4-methyl-3-carboxypentanoate decarboxylation	m28[mi] + m83[mi]  -> m44[mi] + m84[mi] 	(YALI0D01265g)	0	-1000.00	1000.00	  0.00
 32	3',5'-bisphosphate nucleotidase	m32[cy] + m85[cy]  -> m35[cy] + m86[cy] 	(YALI0F27665g)	0	  0.00	1000.00	  0.00
 33	3',5'-cyclic-nucleotide phosphodiesterase	m32[cy] + m87[cy]  -> m10[cy] + m86[cy] 	(YALI0E32527g) or (YALI0A08041g)	0	  0.00	1000.00	  0.00
 34	3',5'-cyclic-nucleotide phosphodiesterase	m32[cy] + m88[cy]  -> m10[cy] + m89[cy] 	(YALI0A08041g)	0	  0.00	1000.00	  0.00
@@ -141,7 +141,7 @@ Rxn name	Rxn description	Formula	Gene-reaction association	Reversible	LB	UB	Obje
 191	allophanate hydrolase	3 m10[cy] + m32[cy] + m288[cy]  -> 2 m38[cy] + 2 m82[cy] 	(YALI0B14619g) or (YALI0E07271g) or (YALI0E35156g)	0	  0.00	1000.00	  0.00
 192	alpha 1,2-mannosyltransferase	m289[go] + m290[go]  -> m291[go] + m292[go] + m293[go] 	(YALI0A06589g) or (YALI0B01672g) or (YALI0E01892g) or (YALI0F25817g)	0	  0.00	1000.00	  0.00
 194	alpha,alpha-trehalase	m32[cy] + m294[cy]  -> 2 m295[cy] 	(YALI0D15598g)	0	  0.00	1000.00	  0.00
-195	alpha,alpha-trehalose-phosphate synthase (UDP-forming)	m8[cy] + m296[cy]  -> m10[cy] + m11[cy] + m297[cy] 	(YALI0D14476g and YALI0E14685g and YALI0E31086g)	0	  0.00	1000.00	  0.00
+195	alpha,alpha-trehalose-phosphate synthase (UDP-forming)	m8[cy] + m296[cy]  -> m10[cy] + m11[cy] + m297[cy] 	(YALI0E14685g and YALI0D14476g and YALI0E31086g)	0	  0.00	1000.00	  0.00
 199	amidase	m32[cy] + m298[cy]  -> m38[cy] + m299[cy] 	(YALI0F23441g)	0	  0.00	1000.00	  0.00
 200	Aminoacetone:oxygen oxidoreductase(deaminating)(flavin-containing)	m32[cy] + m109[cy] + m300[cy]  -> m38[cy] + m301[cy] + m302[cy] 		0	  0.00	1000.00	  0.00
 201	Aminobutyraldehyde dehydrogenase	m26[mi] + m27[mi] + m303[mi]  -> 2 m28[mi] + m30[mi] + m304[mi] 	(YALI0C03025g) or (YALI0D07942g) or (YALI0E00264g) or (YALI0F04444g)	0	  0.00	1000.00	  0.00
@@ -169,7 +169,7 @@ Rxn name	Rxn description	Formula	Gene-reaction association	Reversible	LB	UB	Obje
 223	ATP adenylyltransferase	m10[cy] + m143[cy] + m266[cy]  -> m35[cy] + m339[cy] 	(YALI0F30349g)	0	  0.00	1000.00	  0.00
 224	ATP adenylyltransferase	m10[cy] + m266[cy] + m268[cy]  -> m35[cy] + m340[cy] 	(YALI0F30349g)	0	  0.00	1000.00	  0.00
 225	ATP phosphoribosyltransferase	m141[cy] + m253[cy]  -> m203[cy] + m341[cy] 	(YALI0C05170g)	0	  0.00	1000.00	  0.00
-226	ATP synthase	3 m10[cy] + m58[mi] + m197[mi]  -> m26[mi] + 2 m28[mi] + m46[mi] 	(NP_075432 and NP_075433 and NP_075437 and YALI0F03179g and YALI0F02893g and YALI0D22022g and YALI0D12584g and YALI0D11814g and YALI0B06831g and YALI0F04774g and YALI0B03982g and YALI0D17490g and YALI0F20306g and YALI0E32164g) or (YALI0B21527g)	0	  0.00	1000.00	  0.00
+226	ATP synthase	3 m10[cy] + m58[mi] + m197[mi]  -> m26[mi] + 2 m28[mi] + m46[mi] 	(NP_075432 and NP_075433 and NP_075437 and YALI0F03179g and YALI0F02893g and YALI0D22022g and YALI0D12584g and YALI0D11814g and YALI0B06831g and YALI0F04774g and YALI0B03982g and YALI0D17490g and YALI0F20306g and YALI0E32164g)	0	  0.00	1000.00	  0.00
 227	ATPase, cytosolic	m32[cy] + m141[cy]  -> m35[cy] + m143[cy] + m342[ex] 	(YALI0B22066g)	0	  0.00	1000.00	  0.00
 228	beta-1,4 mannosyltransferase	m343[cy] + m344[cy]  -> m268[cy] + m345[cy] 	(YALI0E34133g)	0	  0.00	1000.00	  0.00
 229	biotin synthase	m346[cy] + m347[cy]  <=> 2 m10[cy] + m348[cy] 	(YALI0D15400g)	1	-1000.00	1000.00	  0.00
@@ -337,7 +337,7 @@ Rxn name	Rxn description	Formula	Gene-reaction association	Reversible	LB	UB	Obje
 478	glutaminyl-tRNA synthetase	m130[cy] + m141[cy] + m553[cy]  -> m86[cy] + m203[cy] + m554[cy] 	(YALI0C03674g)	0	  0.00	1000.00	  0.00
 479	glutamyl-tRNA synthetase	m50[cy] + m141[cy] + m555[cy]  -> m86[cy] + m203[cy] + m556[cy] 	(YALI0E28468g)	0	  0.00	1000.00	  0.00
 480	glutamyl-tRNA synthetase	m29[mi] + m46[mi] + m557[mi]  -> m48[mi] + m204[mi] + m558[mi] 	(YALI0E17919g)	0	  0.00	1000.00	  0.00
-481	glutathione oxidoreductase	m10[cy] + m40[cy] + m559[cy]  -> m41[cy] + 2 m530[cy] 	(YALI0B13398g) or (YALI0C05467g and YALI0E18029g)	0	  0.00	1000.00	  0.00
+481	glutathione oxidoreductase	m10[cy] + m40[cy] + m559[cy]  -> m41[cy] + 2 m530[cy] 	(YALI0C05467g and YALI0E18029g) or (YALI0B13398g and YALI0E18029g)	0	  0.00	1000.00	  0.00
 482	glutathione oxidoreductase	m28[mi] + m176[mi] + m560[mi]  -> m178[mi] + 2 m561[mi] 	(YALI0E18029g and YALI0F21219g)	0	  0.00	1000.00	  0.00
 483	glutathione peridoxase	m301[cy] + 2 m530[cy]  <=> 2 m32[cy] + m559[cy] 	(YALI0C05467g) or (YALI0E02310g)	1	-1000.00	1000.00	  0.00
 484	glutathione peroxidase, mitochondria	m526[mi] + 2 m561[mi]  <=> 2 m26[mi] + m560[mi] 	(YALI0F21219g)	1	-1000.00	1000.00	  0.00
@@ -401,7 +401,7 @@ Rxn name	Rxn description	Formula	Gene-reaction association	Reversible	LB	UB	Obje
 548	homoserine kinase	m141[cy] + m630[cy]  -> m10[cy] + m143[cy] + m631[cy] 	(YALI0F13453g)	0	  0.00	1000.00	  0.00
 549	homoserine O-trans-acetylase	m68[cy] + m630[cy]  -> m69[cy] + m444[cy] 	(YALI0E00836g)	0	  0.00	1000.00	  0.00
 550	hydrogen peroxide reductase (thioredoxin)	m301[cy] + m632[cy]  -> 2 m32[cy] + m633[cy] 	(YALI0B15125g and YALI0F01496g)	0	  0.00	1000.00	  0.00
-551	hydrogen peroxide reductase (thioredoxin)	m526[mi] + m634[mi]  -> 2 m26[mi] + m635[mi] 	(YALI0F08195g and YALI0F01496g) or (YALI0E23540g)	0	  0.00	1000.00	  0.00
+551	hydrogen peroxide reductase (thioredoxin)	m526[mi] + m634[mi]  -> 2 m26[mi] + m635[mi] 	(YALI0E23540g) or (YALI0F08195g and YALI0F01496g)	0	  0.00	1000.00	  0.00
 552	hydrogen peroxide reductase (thioredoxin)	m222[pe] + m636[pe]  -> 2 m375[pe] + m637[pe] 	(YALI0E25091g and YALI0F01496g)	0	  0.00	1000.00	  0.00
 553	hydroxyacylglutathione hydrolase	m32[cy] + m638[cy]  -> m1[cy] + m10[cy] + m530[cy] 	(YALI0D06974g)	0	  0.00	1000.00	  0.00
 554	hydroxyacylglutathione hydrolase	m26[mi] + m639[mi]  -> m5[mi] + m28[mi] + m561[mi] 	(YALI0D06974g)	0	  0.00	1000.00	  0.00
@@ -489,7 +489,7 @@ Rxn name	Rxn description	Formula	Gene-reaction association	Reversible	LB	UB	Obje
 659	isocitrate dehydrogenase (NADP)	m41[cy] + m738[cy]  <=> m40[cy] + m51[cy] + m82[cy] 	(YALI0F04095g)	1	-1000.00	1000.00	  0.00
 661	isocitrate dehydrogenase (NADP+), peroxisomal	m739[pe] + m740[pe]  <=> m330[pe] + m741[pe] + m742[pe] 	(YALI0F04095g)	1	-1000.00	1000.00	  0.00
 662	isocitrate lyase	m738[cy]  -> m271[cy] + m541[cy] 	(YALI0C16885g) or (YALI0F31999g)	0	  0.00	1000.00	  0.00
-663	isoleucine transaminase	m51[cy] + m743[cy]  <=> m50[cy] + m744[cy] 	(YALI0D01265g)	1	  0.00	  0.00	  0.00
+663	isoleucine transaminase	m51[cy] + m743[cy]  <=> m50[cy] + m744[cy] 	(YALI0F19910g)	1	-1000.00	1000.00	  0.00
 664	isoleucine transaminase	m219[mi] + m745[mi]  <=> m29[mi] + m489[mi] 	(YALI0D01265g)	1	-1000.00	1000.00	  0.00
 665	isoleucyl-tRNA synthetase	m141[cy] + m743[cy] + m746[cy]  -> m86[cy] + m203[cy] + m747[cy] 	(YALI0A00264g)	0	  0.00	1000.00	  0.00
 666	isoleucyl-tRNA synthetase	m46[mi] + m745[mi] + m748[mi]  -> m48[mi] + m204[mi] + m749[mi] 	(YALI0C10780g)	0	  0.00	1000.00	  0.00
@@ -518,7 +518,7 @@ Rxn name	Rxn description	Formula	Gene-reaction association	Reversible	LB	UB	Obje
 696	lactaldehyde dehydrogenase	m32[cy] + m122[cy] + m766[cy]  -> m7[cy] + 2 m10[cy] + m123[cy] 		0	  0.00	1000.00	  0.00
 697	lactoylglutathione lyase	m302[cy] + m530[cy]  -> m638[cy] 	(YALI0E24057g)	0	  0.00	1000.00	  0.00
 698	lanosterol synthase	m774[cy]  -> m449[cy] 	(YALI0F04378g)	0	  0.00	1000.00	  0.00
-699	leucine transaminase	m51[cy] + m775[cy]  <=> m50[cy] + m81[cy] 	(YALI0D01265g)	1	  0.00	  0.00	  0.00
+699	leucine transaminase	m51[cy] + m775[cy]  <=> m50[cy] + m81[cy] 	(YALI0F19910g)	1	-1000.00	1000.00	  0.00
 700	leucine transaminase	m219[mi] + m776[mi]  <=> m29[mi] + m84[mi] 	(YALI0D01265g)	1	-1000.00	1000.00	  0.00
 701	leucyl-tRNA synthetase	m141[cy] + m775[cy] + m777[cy]  -> m86[cy] + m203[cy] + m778[cy] 	(YALI0E24607g)	0	  0.00	1000.00	  0.00
 702	leucyl-tRNA synthetase	m46[mi] + m776[mi] + m779[mi]  -> m48[mi] + m204[mi] + m780[mi] 	(YALI0F02299g)	0	  0.00	1000.00	  0.00
@@ -571,7 +571,7 @@ Rxn name	Rxn description	Formula	Gene-reaction association	Reversible	LB	UB	Obje
 770	NADH dehydrogenase, cytosolic/mitochondrial	m10[cy] + m123[cy] + m468[mi]  -> m122[cy] + m471[mi] 	(YALI0F25135g)	0	  0.00	1000.00	  0.00
 771	NADH kinase	m123[cy] + m141[cy]  -> m10[cy] + m40[cy] + m143[cy] 	(YALI0E23991g) or (YALI0E27874g)	0	  0.00	1000.00	  0.00
 772	NADH kinase mitochondrial	m30[mi] + m46[mi]  -> m28[mi] + m176[mi] + m197[mi] 	(YALI0E23991g) or (YALI0E27874g) or (YALI0E17963g)	0	  0.00	1000.00	  0.00
-773	NADH:ubiquinone oxidoreductase	m28[mi] + m30[mi] + m468[mi]  -> m27[mi] + m471[mi] 	(YALI0F25135g)	0	  0.00	  0.00	  0.00
+773	NADH:ubiquinone oxidoreductase	m28[mi] + m30[mi] + m468[mi]  -> m27[mi] + m471[mi] 	(YALI0F25135g)	0	  0.00	1000.00	  0.00
 774	NAPRtase	m10[cy] + m253[cy] + m824[cy]  -> m203[cy] + m825[cy] 	(YALI0B00220g)	0	  0.00	1000.00	  0.00
 775	NAPRtase	m28[mi] + m826[mi] + m827[mi]  -> m204[mi] + m828[mi] 	(YALI0B00220g)	0	  0.00	1000.00	  0.00
 781	nicotinamidase	m32[cy] + m829[cy]  -> m38[cy] + m824[cy] 	(YALI0A21153g)	0	  0.00	1000.00	  0.00
@@ -795,7 +795,7 @@ Rxn name	Rxn description	Formula	Gene-reaction association	Reversible	LB	UB	Obje
 1084	UTP-glucose-1-phosphate uridylyltransferase	m10[cy] + m439[cy] + m589[cy]  <=> m8[cy] + m203[cy] 	(YALI0A02310g)	1	-1000.00	1000.00	  0.00
 1085	V-ATPase, Golgi	m10[cy] + m32[cy] + m141[cy]  -> m35[cy] + m143[cy] + 2 m293[go] 	(YALI0A11143g and YALI0E11355g and YALI0D00583g and YALI0E08617g and YALI0A09900g and YALI0F15631g and YALI0E16192g and YALI0F24475g and YALI0F16181g and YALI0E31471g and YALI0E27346g and YALI0E09933g) or (YALI0F31119g and YALI0F09405g)	0	  0.00	1000.00	  0.00
 1086	V-ATPase, vacuole	m10[cy] + m32[cy] + m141[cy]  -> m35[cy] + m143[cy] + 2 m1007[va] 	(YALI0A11143g and YALI0E11355g and YALI0D00583g and YALI0E08617g and YALI0A09900g and YALI0F15631g and YALI0E16192g and YALI0F24475g and YALI0F16181g and YALI0E31471g and YALI0E27346g and YALI0E09933g) or (YALI0F31119g and YALI0F09405g)	0	  0.00	  0.00	  0.00
-1087	valine transaminase	m51[cy] + m1008[cy]  <=> m50[cy] + m67[cy] 	(YALI0D01265g)	1	  0.00	  0.00	  0.00
+1087	valine transaminase	m51[cy] + m1008[cy]  <=> m50[cy] + m67[cy] 	(YALI0F19910g)	1	-1000.00	1000.00	  0.00
 1088	valine transaminase, mitochondiral	m219[mi] + m1009[mi]  <=> m29[mi] + m70[mi] 	(YALI0D01265g)	1	-1000.00	1000.00	  0.00
 1089	valyl-tRNA synthetase	m141[cy] + m1008[cy] + m1010[cy]  -> m86[cy] + m203[cy] + m1011[cy] 	(YALI0F20218g)	0	  0.00	1000.00	  0.00
 1090	valyl-tRNA synthetase	m46[mi] + m1009[mi] + m1012[mi]  -> m48[mi] + m204[mi] + m1013[mi] 	(YALI0F20218g)	0	  0.00	1000.00	  0.00
@@ -1981,7 +1981,6 @@ yli0049	3-methylglutaconyl-CoA dehydratase	m26[mi] + m1832[mi]  -> m648[mi] 		0
 yli0050	hydroxymethylglutaryl-CoA lyase	m648[mi]  -> m71[mi] + m1812[mi] 	(YALI0B22550g)	0	  0.00	1000.00	  0.00
 yli0051	2-oxoadipate dehydrogenase	m27[mi] + m73[mi] + m629[mi]  -> m30[mi] + m44[mi] + m1833[mi] 	(YALI0F23749g)	0	  0.00	1000.00	  0.00
 yli0052	glutaryl-CoA dehydrogenase	m563[mi] + m1833[mi]  -> m44[mi] + m566[mi] + m1834[mi] 	(YALI0E33517g and YALI0E16929g and YALI0D20768g)	0	  0.00	1000.00	  0.00
-yli0053	FAD:ubiquinone oxidoreductase	m468[mi] + m566[mi]  -> m471[mi] + m563[mi] 	(YALI0F23749g)	0	  0.00	1000.00	  0.00
 yli0054	crotonyl-CoA hydratase	m26[mi] + m1834[mi]  <=> m1835[mi] 	(YALI0B10406g)	1	-1000.00	1000.00	  0.00
 yli0055	(S)-3-Hydroxybutanoyl-CoA oxidoreductase	m27[mi] + m1835[mi]  -> m28[mi] + m30[mi] + m190[mi] 	(YALI0C08811g)	0	  0.00	1000.00	  0.00
 Metabolite name	Metabolite description	Metabolite formula
@@ -1994,7 +1993,7 @@ m6[mi]	pyruvate	C3H4O3
 m7[cy]	(S)-lactate	C3H6O3
 m8[cy]	UDP-D-glucose	C15H22N2O17P2
 m9[en]	(1-3)-beta-D-glucan	
-m10[cy]	H+	p+1
+m10[cy]	H+	H
 m11[cy]	UDP	C9H14N2O12P2
 m12[en]	(1-6)-beta-D-glucan	
 m13[cy]	1-(5-phospho-D-ribosyl)-5-[(5-phospho-D-ribosylamino)methylideneamino]imidazole-4-carboxamide	C15H21N5O15P2
@@ -2003,16 +2002,16 @@ m15[vm]	1-phosphatidyl-1D-myo-inositol 3-phosphate
 m16[vm]	ATP	C10H16N5O13P3
 m17[vm]	1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate	
 m18[vm]	ADP	C10H15N5O10P2
-m19[vm]	H+	p+1
+m19[vm]	H+	H
 m20[en]	1-phosphatidyl-1D-myo-inositol 3-phosphate	
 m21[en]	ATP	C10H16N5O13P3
 m22[en]	1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate	
 m23[en]	ADP	C10H15N5O10P2
-m24[en]	H+	p+1
+m24[en]	H+	H
 m25[mi]	1-pyrroline-5-carboxylate	C5H6NO2
 m26[mi]	H2O	H2O
 m27[mi]	NAD	C21H27N7O14P2
-m28[mi]	H+	p+1
+m28[mi]	H+	H
 m29[mi]	L-glutamate	C5H9NO4
 m30[mi]	NADH	C21H29N7O14P2
 m31[cy]	5-(methylsulfanyl)-2,3-dioxopentyl phosphate	C6H9O6PS
@@ -2086,7 +2085,7 @@ m98[cy]	3-dehydroquinate	C7H10O6
 m99[cy]	3-dehydroshikimate	C7H8O5
 m100[cy]	7-phospho-2-dehydro-3-deoxy-D-arabino-heptonic acid	C7H10O10P
 m101[er]	3-ketosphinganine	C18H38NO2
-m102[er]	H+	p+1
+m102[er]	H+	H
 m103[er]	NADPH	C21H30N7O17P3
 m104[er]	NADP(+)	C21H28N7O17P3
 m105[er]	sphinganine	C18H39NO2
@@ -2102,7 +2101,7 @@ m114[cy]	L-alanine	C3H7NO2
 m115[pe]	(R)-3-hydroxytetradecanoyl-CoA	
 m116[pe]	NAD	C21H27N7O14P2
 m117[pe]	3-oxotetradecanoyl-CoA	C35H60N7O18P3S
-m118[pe]	H+	p+1
+m118[pe]	H+	H
 m119[pe]	NADH	C21H29N7O14P2
 m120[cy]	2-amino-3-carboxymuconate-6-semialdehyde	
 m121[cy]	(2R,3S)-3-isopropylmalate	C7H12O5
@@ -2277,7 +2276,7 @@ m289[go]	beta-D-mannosyldiacetylchitobiosyldiphosphodolichol	C37H66N2O22P2
 m290[go]	GDP-alpha-D-mannose	C16H23N5O16P2
 m291[go]	alpha-D-mannosyl-beta-D-mannosyldiacetylchitobiosyldiphosphodolichol	C38H68N2O27P2(C5H8)n
 m292[go]	GDP	C10H15N5O11P2
-m293[go]	H+	p+1
+m293[go]	H+	H
 m294[cy]	trehalose	C12H22O11
 m295[cy]	D-glucose	C6H12O6
 m296[cy]	D-glucose 6-phosphate	C6H13O9P
@@ -2326,7 +2325,7 @@ m338[mi]	Asp-tRNA(Asp)	C14H22NO13PR2(C5H8O6PR)n
 m339[cy]	P1-(5'-adenosyl),P4-(5'-guanosyl) tetraphosphate	
 m340[cy]	P(1),P(4)-bis(5'-guanosyl) tetraphosphate	
 m341[cy]	5-phosphoribosyl-ATP	C15H19N5O20P4
-m342[ex]	H+	p+1
+m342[ex]	H+	H
 m343[cy]	GDP-alpha-D-mannose	C16H23N5O16P2
 m344[cy]	N,N'-diacetylchitobiosyldiphosphodolichol	
 m345[cy]	beta-D-mannosyldiacetylchitobiosyldiphosphodolichol	C37H66N2O22P2
@@ -2361,12 +2360,12 @@ m373[mi]	O-acetylcarnitine	C9H17NO4
 m374[mi]	(R)-carnitine	C7H15NO3
 m375[pe]	H2O	H2O
 m376[em]	CTP	C9H16N3O14P3
-m377[em]	H+	p+1
+m377[em]	H+	H
 m378[em]	phosphatidate	
 m379[em]	CDP-diacylglycerol	
 m380[em]	diphosphate	H4O7P2
 m381[mm]	CTP	C9H16N3O14P3
-m382[mm]	H+	p+1
+m382[mm]	H+	H
 m383[mm]	phosphatidate	
 m384[mm]	CDP-diacylglycerol	
 m385[mm]	diphosphate	H4O7P2
@@ -2611,7 +2610,7 @@ m623[cy]	N(pros)-methyl-L-histidine	C7H11N3O2
 m624[mi]	homoisocitrate	C7H10O7
 m625[nu]	2-oxoglutarate	C5H6O5
 m626[nu]	H2O	H2O
-m627[nu]	H+	p+1
+m627[nu]	H+	H
 m628[nu]	homocitrate	C7H10O7
 m629[mi]	2-oxoadipic acid	C6H6O5
 m630[cy]	L-homoserine	C4H9NO3
@@ -2855,7 +2854,7 @@ m867[cy]	5'-phosphoribosyl-5-aminoimidazole	C8H13N3O7P
 m868[mm]	phosphatidyl-L-serine	C8H11NO10PR2
 m869[mm]	carbon dioxide	CO2
 m870[mm]	phosphatidylethanolamine	C7H12NO8PR2
-m871[gm]	H+	p+1
+m871[gm]	H+	H
 m872[gm]	phosphatidyl-L-serine	C8H11NO10PR2
 m873[gm]	carbon dioxide	CO2
 m874[gm]	phosphatidylethanolamine	C7H12NO8PR2
@@ -2991,7 +2990,7 @@ m1003[nu]	UDP	C9H14N2O12P2
 m1004[nu]	dUMP	C9H13N2O8P
 m1005[nu]	dUDP	C9H14N2O11P2
 m1006[cy]	uroporphyrinogen III	C40H44N4O16
-m1007[va]	H+	p+1
+m1007[va]	H+	H
 m1008[cy]	L-valine	C5H11NO2
 m1009[mi]	L-valine	C5H11NO2
 m1010[cy]	tRNA(Val)	
@@ -3083,16 +3082,16 @@ m1095[ex]	nicotinate	C6H5NO2
 m1096[cy]	stearate	C18H36O2
 m1097[ex]	ornithine	C5H13N2O2
 m1098[ex]	(R)-pantothenate	C9H17NO5
-m1099[ex]	potassium	K.H
-m1100[cy]	potassium	K.H
+m1099[ex]	potassium	KH
+m1100[cy]	potassium	KH
 m1101[ex]	putrescine	C4H12N2
 m1102[va]	putrescine	C4H12N2
 m1103[ex]	pyruvate	C3H4O3
 m1104[ex]	S-adenosyl-L-methionine	C15H22N6O5S
 m1105[ex]	S-methyl-L-methionine	C6H13NO2S
 m1106[cy]	S-methyl-L-methionine	C6H13NO2S
-m1107[cy]	sodium	Na.H
-m1108[ex]	sodium	Na.H
+m1107[cy]	sodium	NaH
+m1108[ex]	sodium	NaH
 m1109[ex]	spermidine	C7H19N3
 m1110[va]	spermidine	C7H19N3
 m1111[ex]	spermine	C10H26N4
@@ -3164,7 +3163,7 @@ m1237[ex]	glutathione disulfide	C20H32N6O12S2
 m1242[ex]	glycolaldehyde	C2H4O2
 m1244[ex]	glyoxylate	C2H2O3
 m1247[ex]	guanosine	C10H13N5O5
-m1249[lp]	H+	p+1
+m1249[lp]	H+	H
 m1251[cy]	hexacosanoyl-CoA	C47H86N7O17P3S
 m1252[ex]	hexadecanal	C16H32O
 m1254[ex]	palmitate	C16H32O2