Rfer_0007	PWY-5392	reductive TCA cycle II
Rfer_0007	PWY-5537	pyruvate fermentation to acetate V
Rfer_0007	PWY-5538	pyruvate fermentation to acetate VI
Rfer_0007	PWY-5690	TCA cycle II (plants and fungi)
Rfer_0007	PWY-5913	TCA cycle VI (obligate autotrophs)
Rfer_0007	PWY-6728	methylaspartate cycle
Rfer_0007	PWY-6969	TCA cycle V (2-oxoglutarate:ferredoxin oxidoreductase)
Rfer_0007	PWY-7384	anaerobic energy metabolism (invertebrates, mitochondrial)
Rfer_0014	PWY-6123	inosine-5'-phosphate biosynthesis I
Rfer_0014	PWY-6124	inosine-5'-phosphate biosynthesis II
Rfer_0014	PWY-7219	adenosine ribonucleotides <i>de novo</i> biosynthesis
Rfer_0014	PWY-7234	inosine-5'-phosphate biosynthesis III
Rfer_0077	PWY-5269	cardiolipin biosynthesis II
Rfer_0077	PWY-5668	cardiolipin biosynthesis I
Rfer_0088	PWY-241	C4 photosynthetic carbon assimilation cycle, NADP-ME type
Rfer_0088	PWY-6549	L-glutamine biosynthesis III
Rfer_0088	PWY-7115	C4 photosynthetic carbon assimilation cycle, NAD-ME type
Rfer_0088	PWY-7117	C4 photosynthetic carbon assimilation cycle, PEPCK type
Rfer_0093	PWY-1281	sulfoacetaldehyde degradation I
Rfer_0093	PWY-241	C4 photosynthetic carbon assimilation cycle, NADP-ME type
Rfer_0093	PWY-5482	pyruvate fermentation to acetate II
Rfer_0093	PWY-5485	pyruvate fermentation to acetate IV
Rfer_0093	PWY-5497	purine nucleobases degradation II (anaerobic)
Rfer_0093	PWY-6637	sulfolactate degradation II
Rfer_0093	PWY-7117	C4 photosynthetic carbon assimilation cycle, PEPCK type
Rfer_0106	PWY-7219	adenosine ribonucleotides <i>de novo</i> biosynthesis
Rfer_0108	PWY-7219	adenosine ribonucleotides <i>de novo</i> biosynthesis
Rfer_0121	PWY-1801	formaldehyde oxidation II (glutathione-dependent)
Rfer_0121	PWY-3162	L-tryptophan degradation V (side chain pathway)
Rfer_0121	PWY-5057	L-valine degradation II
Rfer_0121	PWY-5076	L-leucine degradation III
Rfer_0121	PWY-5078	L-isoleucine degradation II
Rfer_0121	PWY-5079	L-phenylalanine degradation III
Rfer_0121	PWY-5082	L-methionine degradation III
Rfer_0121	PWY-5480	pyruvate fermentation to ethanol I
Rfer_0121	PWY-5486	pyruvate fermentation to ethanol II
Rfer_0121	PWY-5751	phenylethanol biosynthesis
Rfer_0121	PWY-6028	acetoin degradation
Rfer_0121	PWY-6313	serotonin degradation
Rfer_0121	PWY-6333	acetaldehyde biosynthesis I
Rfer_0121	PWY-6342	noradrenaline and adrenaline degradation
Rfer_0121	PWY-6587	pyruvate fermentation to ethanol III
Rfer_0121	PWY-6802	salidroside biosynthesis
Rfer_0121	PWY-6871	3-methylbutanol biosynthesis
Rfer_0121	PWY-7013	L-1,2-propanediol degradation
Rfer_0121	PWY-7111	pyruvate fermentation to isobutanol (engineered)
Rfer_0121	PWY-7118	chitin degradation to ethanol
Rfer_0121	PWY-7396	butanol and isobutanol biosynthesis (engineered)
Rfer_0121	PWY-7557	dehydrodiconiferyl alcohol degradation
Rfer_0122	PWY-1801	formaldehyde oxidation II (glutathione-dependent)
Rfer_0139	PWY-7399	methylphosphonate degradation II
Rfer_0140	PWY-7399	methylphosphonate degradation II
Rfer_0142	PWY-7399	methylphosphonate degradation II
Rfer_0145	PWY-7399	methylphosphonate degradation II
Rfer_0147	PWY-5532	adenosine nucleotides degradation IV
Rfer_0148	PWY-5532	adenosine nucleotides degradation IV
Rfer_0165	PWY-5691	urate degradation to allantoin I
Rfer_0165	PWY-7394	urate degradation to allantoin II
Rfer_0191	PWY-5265	peptidoglycan biosynthesis II (staphylococci)
Rfer_0191	PWY-6471	peptidoglycan biosynthesis IV (Enterococcus faecium)
Rfer_0197	PWY-6123	inosine-5'-phosphate biosynthesis I
Rfer_0197	PWY-7234	inosine-5'-phosphate biosynthesis III
Rfer_0203	PWY-6123	inosine-5'-phosphate biosynthesis I
Rfer_0203	PWY-6124	inosine-5'-phosphate biosynthesis II
Rfer_0203	PWY-7234	inosine-5'-phosphate biosynthesis III
Rfer_0204	PWY-1042	glycolysis IV (plant cytosol)
Rfer_0204	PWY-1861	formaldehyde assimilation II (RuMP Cycle)
Rfer_0204	PWY-5484	glycolysis II (from fructose 6-phosphate)
Rfer_0204	PWY-6142	gluconeogenesis II (<i>Methanobacterium thermoautotrophicum</i>)
Rfer_0204	PWY-7385	1,3-propanediol biosynthesis (engineered)
Rfer_0205	PWY-1042	glycolysis IV (plant cytosol)
Rfer_0205	PWY-2221	Entner-Doudoroff pathway III (semi-phosphorylative)
Rfer_0205	PWY-5484	glycolysis II (from fructose 6-phosphate)
Rfer_0205	PWY-5723	Rubisco shunt
Rfer_0205	PWY-6142	gluconeogenesis II (<i>Methanobacterium thermoautotrophicum</i>)
Rfer_0205	PWY-6886	1-butanol autotrophic biosynthesis
Rfer_0205	PWY-6901	superpathway of glucose and xylose degradation
Rfer_0205	PWY-7003	glycerol degradation to butanol
Rfer_0205	PWY-7218	photosynthetic 3-hydroxybutanoate biosynthesis (engineered)
Rfer_0205	PWY-7383	anaerobic energy metabolism (invertebrates, cytosol)
Rfer_0219	PWY-6163	chorismate biosynthesis from 3-dehydroquinate
Rfer_0220	PWY-1361	benzoyl-CoA degradation I (aerobic)
Rfer_0221	PWY-1361	benzoyl-CoA degradation I (aerobic)
Rfer_0222	PWY-101	photosynthesis light reactions
Rfer_0222	PWY-1361	benzoyl-CoA degradation I (aerobic)
Rfer_0222	PWY-7230	ubiquinol-6 biosynthesis from 4-aminobenzoate (eukaryotic)
Rfer_0224	PWY-1361	benzoyl-CoA degradation I (aerobic)
Rfer_0224	PWY-5109	2-methylbutanoate biosynthesis
Rfer_0224	PWY-5136	fatty acid &beta;-oxidation II (peroxisome)
Rfer_0224	PWY-5138	unsaturated, even numbered fatty acid &beta;-oxidation
Rfer_0224	PWY-5177	glutaryl-CoA degradation
Rfer_0224	PWY-5789	3-hydroxypropanoate/4-hydroxybutanate cycle
Rfer_0224	PWY-6435	4-hydroxybenzoate biosynthesis V
Rfer_0224	PWY-6583	pyruvate fermentation to butanol I
Rfer_0224	PWY-6863	pyruvate fermentation to hexanol
Rfer_0224	PWY-6883	pyruvate fermentation to butanol II
Rfer_0224	PWY-6944	androstenedione degradation
Rfer_0224	PWY-6945	cholesterol degradation to androstenedione I (cholesterol oxidase)
Rfer_0224	PWY-6946	cholesterol degradation to androstenedione II (cholesterol dehydrogenase)
Rfer_0224	PWY-7007	methyl ketone biosynthesis
Rfer_0224	PWY-7046	4-coumarate degradation (anaerobic)
Rfer_0224	PWY-7094	fatty acid salvage
Rfer_0224	PWY-7216	(R)- and (S)-3-hydroxybutanoate biosynthesis
Rfer_0224	PWY-735	jasmonic acid biosynthesis
Rfer_0224	PWY-7401	crotonate fermentation (to acetate and cyclohexane carboxylate)
Rfer_0226	PWY-1361	benzoyl-CoA degradation I (aerobic)
Rfer_0226	PWY-2361	3-oxoadipate degradation
Rfer_0226	PWY-6185	4-methylcatechol degradation (<i>ortho</i> cleavage)
Rfer_0228	PWY-1361	benzoyl-CoA degradation I (aerobic)
Rfer_0242	PWY-621	sucrose degradation III (sucrose invertase)
Rfer_0252	PWY-5674	nitrate reduction IV (dissimilatory)
Rfer_0259	PWY-5674	nitrate reduction IV (dissimilatory)
Rfer_0262	PWY-1281	sulfoacetaldehyde degradation I
Rfer_0262	PWY-5482	pyruvate fermentation to acetate II
Rfer_0262	PWY-5485	pyruvate fermentation to acetate IV
Rfer_0262	PWY-5497	purine nucleobases degradation II (anaerobic)
Rfer_0262	PWY-6637	sulfolactate degradation II
Rfer_0331	PWY-6216	3-chlorobenzoate degradation II (via protocatechuate)
Rfer_0331	PWY-6217	3,4-dichlorobenzoate degradation
Rfer_0339	PWY-6215	4-chlorobenzoate degradation
Rfer_0346	PWY-40	putrescine biosynthesis I
Rfer_0346	PWY-6305	putrescine biosynthesis IV
Rfer_0350	PWY-381	nitrate reduction II (assimilatory)
Rfer_0350	PWY-5675	nitrate reduction V (assimilatory)
Rfer_0350	PWY-6549	L-glutamine biosynthesis III
Rfer_0350	PWY-6963	ammonia assimilation cycle I
Rfer_0350	PWY-6964	ammonia assimilation cycle II
Rfer_0359	PWY-6825	phosphatidylcholine biosynthesis V
Rfer_0362	PWY-1042	glycolysis IV (plant cytosol)
Rfer_0362	PWY-1861	formaldehyde assimilation II (RuMP Cycle)
Rfer_0362	PWY-5484	glycolysis II (from fructose 6-phosphate)
Rfer_0362	PWY-6531	mannitol cycle
Rfer_0362	PWY-7385	1,3-propanediol biosynthesis (engineered)
Rfer_0368	PWY-7187	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis II
Rfer_0368	PWY-7220	adenosine deoxyribonucleotides <i>de novo</i> biosynthesis II
Rfer_0368	PWY-7222	guanosine deoxyribonucleotides <i>de novo</i> biosynthesis II
Rfer_0372	PWY-5642	2,4-dinitrotoluene degradation
Rfer_0372	PWY-6373	acrylate degradation
Rfer_0406	PWY-5344	L-homocysteine biosynthesis
Rfer_0419	PWY-6825	phosphatidylcholine biosynthesis V
Rfer_0436	PWY-6386	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis II (lysine-containing)
Rfer_0436	PWY-6387	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis I (<i>meso</i>-diaminopimelate containing)
Rfer_0454	PWY-5162	2-oxopentenoate degradation
Rfer_0455	PWY-5162	2-oxopentenoate degradation
Rfer_0455	PWY-5436	L-threonine degradation IV
Rfer_0455	PWY-5480	pyruvate fermentation to ethanol I
Rfer_0455	PWY-6587	pyruvate fermentation to ethanol III
Rfer_0455	PWY-7085	triethylamine degradation
Rfer_0455	PWY-7180	2'-deoxy-&alpha;-D-ribose 1-phosphate degradation
Rfer_0456	PWY-5101	L-isoleucine biosynthesis II
Rfer_0456	PWY-5103	L-isoleucine biosynthesis III
Rfer_0456	PWY-5104	L-isoleucine biosynthesis IV
Rfer_0456	PWY-7111	pyruvate fermentation to isobutanol (engineered)
Rfer_0466	PWY-2201	folate transformations I
Rfer_0466	PWY-3841	folate transformations II
Rfer_0480	PWY-6386	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis II (lysine-containing)
Rfer_0480	PWY-6387	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis I (<i>meso</i>-diaminopimelate containing)
Rfer_0482	PWY-1269	CMP-3-deoxy-D-<I>manno</I>-octulosonate biosynthesis I
Rfer_0482	PWY-5111	CMP-3-deoxy-D-<i>manno</i>-octulosonate biosynthesis II (from D-arabinose 5-phosphate)
Rfer_0482	PWY-6164	3-dehydroquinate biosynthesis I
Rfer_0485	PWY-2582	brassinosteroid biosynthesis II
Rfer_0485	PWY-6945	cholesterol degradation to androstenedione I (cholesterol oxidase)
Rfer_0485	PWY-6946	cholesterol degradation to androstenedione II (cholesterol dehydrogenase)
Rfer_0485	PWY-6948	sitosterol degradation to androstenedione
Rfer_0485	PWY-699	brassinosteroid biosynthesis I
Rfer_0485	PWY-7299	progesterone biosynthesis
Rfer_0488	PWY-7383	anaerobic energy metabolism (invertebrates, cytosol)
Rfer_0506	PWY-5057	L-valine degradation II
Rfer_0506	PWY-5076	L-leucine degradation III
Rfer_0506	PWY-5078	L-isoleucine degradation II
Rfer_0506	PWY-5101	L-isoleucine biosynthesis II
Rfer_0506	PWY-5103	L-isoleucine biosynthesis III
Rfer_0506	PWY-5104	L-isoleucine biosynthesis IV
Rfer_0506	PWY-5108	L-isoleucine biosynthesis V
Rfer_0511	PWY-5941	glycogen degradation II (eukaryotic)
Rfer_0511	PWY-622	starch biosynthesis
Rfer_0511	PWY-6731	starch degradation III
Rfer_0511	PWY-6737	starch degradation V
Rfer_0511	PWY-7238	sucrose biosynthesis II
Rfer_0512	PWY-622	starch biosynthesis
Rfer_0513	PWY-622	starch biosynthesis
Rfer_0514	PWY-5941	glycogen degradation II (eukaryotic)
Rfer_0514	PWY-6724	starch degradation II
Rfer_0514	PWY-6737	starch degradation V
Rfer_0514	PWY-7238	sucrose biosynthesis II
Rfer_0518	PWY-5081	L-tryptophan degradation VIII (to tryptophol)
Rfer_0525	PWY-6803	phosphatidylcholine acyl editing
Rfer_0525	PWY-7409	phospholipid remodeling (phosphatidylethanolamine, yeast)
Rfer_0525	PWY-7416	phospholipid remodeling (phosphatidylcholine, yeast)
Rfer_0525	PWY-7417	phospholipid remodeling (phosphatidate, yeast)
Rfer_0529	PWY-6893	thiamin diphosphate biosynthesis II (Bacillus)
Rfer_0529	PWY-6894	thiamin diphosphate biosynthesis I (E. coli)
Rfer_0529	PWY-6896	thiamin salvage I
Rfer_0529	PWY-6897	thiamin salvage II
Rfer_0532	PWY-1861	formaldehyde assimilation II (RuMP Cycle)
Rfer_0532	PWY-5723	Rubisco shunt
Rfer_0553	PWY-7219	adenosine ribonucleotides <i>de novo</i> biosynthesis
Rfer_0572	PWY-3722	glycine betaine biosynthesis II (Gram-positive bacteria)
Rfer_0572	PWY-7494	choline degradation IV
Rfer_0597	PWY-40	putrescine biosynthesis I
Rfer_0597	PWY-6305	putrescine biosynthesis IV
Rfer_0606	PWY-6386	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis II (lysine-containing)
Rfer_0606	PWY-6387	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis I (<i>meso</i>-diaminopimelate containing)
Rfer_0607	PWY-5669	phosphatidylethanolamine biosynthesis I
Rfer_0609	PWY-2201	folate transformations I
Rfer_0609	PWY-5497	purine nucleobases degradation II (anaerobic)
Rfer_0626	PWY-6700	queuosine biosynthesis
Rfer_0628	PWY-6700	queuosine biosynthesis
Rfer_0652	PWY-5041	<i>S</i>-adenosyl-L-methionine cycle II
Rfer_0654	PWY-2201	folate transformations I
Rfer_0654	PWY-3841	folate transformations II
Rfer_0663	PWY-7335	UDP-<i>N</i>-acetyl-&alpha;-D-mannosaminouronate biosynthesis
Rfer_0673	PWY-7346	UDP-&alpha;-D-glucuronate biosynthesis (from UDP-glucose)
Rfer_0711	PWY-5659	GDP-mannose biosynthesis
Rfer_0711	PWY-6073	alginate biosynthesis I (algal)
Rfer_0711	PWY-6082	alginate biosynthesis II (bacterial)
Rfer_0711	PWY-882	L-ascorbate biosynthesis I (L-galactose pathway)
Rfer_0713	PWY-3821	galactose degradation III
Rfer_0713	PWY-6317	galactose degradation I (Leloir pathway)
Rfer_0713	PWY-6397	mycolyl-arabinogalactan-peptidoglycan complex biosynthesis
Rfer_0713	PWY-6527	stachyose degradation
Rfer_0713	PWY-7328	superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis
Rfer_0713	PWY-7344	UDP-D-galactose biosynthesis
Rfer_0715	PWY-3221	dTDP-L-rhamnose biosynthesis II
Rfer_0715	PWY-6808	dTDP-D-forosamine biosynthesis
Rfer_0715	PWY-6942	dTDP-D-desosamine biosynthesis
Rfer_0715	PWY-6953	dTDP-3-acetamido-3,6-dideoxy-&alpha;-D-galactose biosynthesis
Rfer_0715	PWY-6973	dTDP-D-olivose, dTDP-D-oliose and dTDP-D-mycarose biosynthesis
Rfer_0715	PWY-6974	dTDP-L-olivose biosynthesis
Rfer_0715	PWY-6976	dTDP-L-mycarose biosynthesis
Rfer_0715	PWY-7104	dTDP-L-megosamine biosynthesis
Rfer_0715	PWY-7301	dTDP-&beta;-L-noviose biosynthesis
Rfer_0715	PWY-7312	dTDP-D-&beta;-fucofuranose biosynthesis
Rfer_0715	PWY-7315	dTDP-<i>N</i>-acetylthomosamine biosynthesis
Rfer_0715	PWY-7316	dTDP-<i>N</i>-acetylviosamine biosynthesis
Rfer_0715	PWY-7318	dTDP-3-acetamido-3,6-dideoxy-&alpha;-D-glucose biosynthesis
Rfer_0715	PWY-7413	dTDP-6-deoxy-&alpha;-D-allose biosynthesis
Rfer_0715	PWY-7414	dTDP-&alpha;-D-mycaminose biosynthesis
Rfer_0715	PWY-7440	dTDP-&beta;-L-4-<i>epi</i>-vancosamine biosynthesis
Rfer_0717	PWY-2723	trehalose degradation V
Rfer_0717	PWY-5384	sucrose degradation IV (sucrose phosphorylase)
Rfer_0717	PWY-5661	GDP-glucose biosynthesis
Rfer_0717	PWY-5940	streptomycin biosynthesis
Rfer_0717	PWY-621	sucrose degradation III (sucrose invertase)
Rfer_0717	PWY-622	starch biosynthesis
Rfer_0717	PWY-6731	starch degradation III
Rfer_0717	PWY-6737	starch degradation V
Rfer_0717	PWY-6981	chitin biosynthesis
Rfer_0717	PWY-7238	sucrose biosynthesis II
Rfer_0717	PWY-7343	UDP-glucose biosynthesis
Rfer_0734	PWY-5381	pyridine nucleotide cycling (plants)
Rfer_0734	PWY-5695	urate biosynthesis/inosine 5'-phosphate degradation
Rfer_0734	PWY-6596	adenosine nucleotides degradation I
Rfer_0734	PWY-6606	guanosine nucleotides degradation II
Rfer_0734	PWY-6607	guanosine nucleotides degradation I
Rfer_0734	PWY-6608	guanosine nucleotides degradation III
Rfer_0734	PWY-7185	UTP and CTP dephosphorylation I
Rfer_0736	PWY-6703	preQ<sub>0</sub> biosynthesis
Rfer_0743	PWY-6825	phosphatidylcholine biosynthesis V
Rfer_0755	PWY-2941	L-lysine biosynthesis II
Rfer_0755	PWY-2942	L-lysine biosynthesis III
Rfer_0755	PWY-5097	L-lysine biosynthesis VI
Rfer_0786	PWY-6825	phosphatidylcholine biosynthesis V
Rfer_0814	PWY-6147	6-hydroxymethyl-dihydropterin diphosphate biosynthesis I
Rfer_0814	PWY-6148	tetrahydromethanopterin biosynthesis
Rfer_0814	PWY-6797	6-hydroxymethyl-dihydropterin diphosphate biosynthesis II (archaea)
Rfer_0814	PWY-7539	6-hydroxymethyl-dihydropterin diphosphate biosynthesis III (Chlamydia)
Rfer_0821	PWY-5531	chlorophyllide <i>a</i> biosynthesis II (anaerobic)
Rfer_0821	PWY-7159	chlorophyllide <i>a</i> biosynthesis III (aerobic, light independent)
Rfer_0825	PWY-6386	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis II (lysine-containing)
Rfer_0825	PWY-6387	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis I (<i>meso</i>-diaminopimelate containing)
Rfer_0827	PWY-5381	pyridine nucleotide cycling (plants)
Rfer_0920	PWY-5265	peptidoglycan biosynthesis II (staphylococci)
Rfer_0920	PWY-6471	peptidoglycan biosynthesis IV (Enterococcus faecium)
Rfer_0929	PWY-7383	anaerobic energy metabolism (invertebrates, cytosol)
Rfer_0937	PWY-7130	L-glucose degradation
Rfer_0938	PWY-2221	Entner-Doudoroff pathway III (semi-phosphorylative)
Rfer_0938	PWY-6507	4-deoxy-L-<i>threo</i>-hex-4-enopyranuronate degradation
Rfer_0938	PWY-7242	D-fructuronate degradation
Rfer_0938	PWY-7310	D-glucosaminate degradation
Rfer_0947	PWY-7242	D-fructuronate degradation
Rfer_0949	PWY-7130	L-glucose degradation
Rfer_0950	PWY-2221	Entner-Doudoroff pathway III (semi-phosphorylative)
Rfer_0950	PWY-6507	4-deoxy-L-<i>threo</i>-hex-4-enopyranuronate degradation
Rfer_0950	PWY-7242	D-fructuronate degradation
Rfer_0950	PWY-7310	D-glucosaminate degradation
Rfer_0956	PWY-5530	sorbitol biosynthesis II
Rfer_0956	PWY-6163	chorismate biosynthesis from 3-dehydroquinate
Rfer_0961	PWY-2221	Entner-Doudoroff pathway III (semi-phosphorylative)
Rfer_0961	PWY-6507	4-deoxy-L-<i>threo</i>-hex-4-enopyranuronate degradation
Rfer_0961	PWY-7242	D-fructuronate degradation
Rfer_0961	PWY-7310	D-glucosaminate degradation
Rfer_0962	PWY-7130	L-glucose degradation
Rfer_0964	PWY-7383	anaerobic energy metabolism (invertebrates, cytosol)
Rfer_0977	PWY-7383	anaerobic energy metabolism (invertebrates, cytosol)
Rfer_0989	PWY-5921	glutaminyl-tRNA<sup>gln</sup> biosynthesis via transamidation
Rfer_1008	PWY-723	alkylnitronates degradation
Rfer_1034	PWY-1361	benzoyl-CoA degradation I (aerobic)
Rfer_1034	PWY-2361	3-oxoadipate degradation
Rfer_1034	PWY-6185	4-methylcatechol degradation (<i>ortho</i> cleavage)
Rfer_1038	PWY-6386	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis II (lysine-containing)
Rfer_1038	PWY-6387	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis I (<i>meso</i>-diaminopimelate containing)
Rfer_1063	PWY-3841	folate transformations II
Rfer_1063	PWY-7184	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis I
Rfer_1063	PWY-7187	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis II
Rfer_1063	PWY-7198	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis IV
Rfer_1063	PWY-7199	pyrimidine deoxyribonucleosides salvage
Rfer_1063	PWY-7210	pyrimidine deoxyribonucleotides biosynthesis from CTP
Rfer_1074	PWY-6749	CMP-legionaminate biosynthesis I
Rfer_1083	PWY-5514	UDP-<i>N</i>-acetyl-D-galactosamine biosynthesis II
Rfer_1102	PWY-3121	linamarin degradation
Rfer_1102	PWY-5176	coumarin biosynthesis (via 2-coumarate)
Rfer_1102	PWY-6002	lotaustralin degradation
Rfer_1102	PWY-6788	cellulose degradation II (fungi)
Rfer_1102	PWY-7089	taxiphyllin bioactivation
Rfer_1102	PWY-7091	linustatin bioactivation
Rfer_1102	PWY-7092	neolinustatin bioactivation
Rfer_1111	PWY-3121	linamarin degradation
Rfer_1111	PWY-5176	coumarin biosynthesis (via 2-coumarate)
Rfer_1111	PWY-6002	lotaustralin degradation
Rfer_1111	PWY-6788	cellulose degradation II (fungi)
Rfer_1111	PWY-7089	taxiphyllin bioactivation
Rfer_1111	PWY-7091	linustatin bioactivation
Rfer_1111	PWY-7092	neolinustatin bioactivation
Rfer_1122	PWY-5659	GDP-mannose biosynthesis
Rfer_1122	PWY-6073	alginate biosynthesis I (algal)
Rfer_1122	PWY-6082	alginate biosynthesis II (bacterial)
Rfer_1122	PWY-882	L-ascorbate biosynthesis I (L-galactose pathway)
Rfer_1125	PWY-7268	NAD/NADP-NADH/NADPH cytosolic interconversion (yeast)
Rfer_1126	PWY-1861	formaldehyde assimilation II (RuMP Cycle)
Rfer_1126	PWY-5723	Rubisco shunt
Rfer_1127	PWY-3801	sucrose degradation II (sucrose synthase)
Rfer_1127	PWY-5054	sorbitol biosynthesis I
Rfer_1127	PWY-5384	sucrose degradation IV (sucrose phosphorylase)
Rfer_1127	PWY-5514	UDP-<i>N</i>-acetyl-D-galactosamine biosynthesis II
Rfer_1127	PWY-5659	GDP-mannose biosynthesis
Rfer_1127	PWY-6142	gluconeogenesis II (<i>Methanobacterium thermoautotrophicum</i>)
Rfer_1127	PWY-621	sucrose degradation III (sucrose invertase)
Rfer_1127	PWY-622	starch biosynthesis
Rfer_1127	PWY-6531	mannitol cycle
Rfer_1127	PWY-6981	chitin biosynthesis
Rfer_1127	PWY-7238	sucrose biosynthesis II
Rfer_1127	PWY-7347	sucrose biosynthesis III
Rfer_1127	PWY-7385	1,3-propanediol biosynthesis (engineered)
Rfer_1145	PWY-2723	trehalose degradation V
Rfer_1145	PWY-3801	sucrose degradation II (sucrose synthase)
Rfer_1145	PWY-5384	sucrose degradation IV (sucrose phosphorylase)
Rfer_1145	PWY-5661	GDP-glucose biosynthesis
Rfer_1145	PWY-5661-1	Rfer_1145|Rfer_1145|REF_jgi:Rfer_1145|GeneID:3963451
Rfer_1145	PWY-5940	streptomycin biosynthesis
Rfer_1145	PWY-5941	glycogen degradation II (eukaryotic)
Rfer_1145	PWY-622	starch biosynthesis
Rfer_1145	PWY-6731	starch degradation III
Rfer_1145	PWY-6737	starch degradation V
Rfer_1145	PWY-6749	CMP-legionaminate biosynthesis I
Rfer_1145	PWY-7238	sucrose biosynthesis II
Rfer_1145	PWY-7343	UDP-glucose biosynthesis
Rfer_1161	PWY-7219	adenosine ribonucleotides <i>de novo</i> biosynthesis
Rfer_1168	PWY-7219	adenosine ribonucleotides <i>de novo</i> biosynthesis
Rfer_1235	PWY-66	GDP-L-fucose biosynthesis I (from GDP-D-mannose)
Rfer_1237	PWY-5738	GDP-6-deoxy-D-talose biosynthesis
Rfer_1237	PWY-5739	GDP-D-perosamine biosynthesis
Rfer_1237	PWY-5740	GDP-L-colitose biosynthesis
Rfer_1237	PWY-66	GDP-L-fucose biosynthesis I (from GDP-D-mannose)
Rfer_1242	PWY-1269	CMP-3-deoxy-D-<I>manno</I>-octulosonate biosynthesis I
Rfer_1242	PWY-5111	CMP-3-deoxy-D-<i>manno</i>-octulosonate biosynthesis II (from D-arabinose 5-phosphate)
Rfer_1247	PWY-6164	3-dehydroquinate biosynthesis I
Rfer_1250	PWY-5833	CDP-4-dehydro-3,6-dideoxy-D-glucose biosynthesis
Rfer_1250	PWY-5940	streptomycin biosynthesis
Rfer_1251	PWY-5833	CDP-4-dehydro-3,6-dideoxy-D-glucose biosynthesis
Rfer_1281	PWY-5188	tetrapyrrole biosynthesis I (from glutamate)
Rfer_1288	PWY-6386	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis II (lysine-containing)
Rfer_1288	PWY-6387	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis I (<i>meso</i>-diaminopimelate containing)
Rfer_1291	PWY-5839	menaquinol-7 biosynthesis
Rfer_1291	PWY-5844	menaquinol-9 biosynthesis
Rfer_1291	PWY-5849	menaquinol-6 biosynthesis
Rfer_1291	PWY-5890	menaquinol-10 biosynthesis
Rfer_1291	PWY-5891	menaquinol-11 biosynthesis
Rfer_1291	PWY-5892	menaquinol-12 biosynthesis
Rfer_1291	PWY-5895	menaquinol-13 biosynthesis
Rfer_1301	PWY-5663	tetrahydrobiopterin biosynthesis I
Rfer_1301	PWY-5664	tetrahydrobiopterin biosynthesis II
Rfer_1301	PWY-6147	6-hydroxymethyl-dihydropterin diphosphate biosynthesis I
Rfer_1301	PWY-6703	preQ<sub>0</sub> biosynthesis
Rfer_1301	PWY-6983	tetrahydrobiopterin biosynthesis III
Rfer_1301	PWY-7442	drosopterin and aurodrosopterin biosynthesis
Rfer_1309	PWY-1622	formaldehyde assimilation I (serine pathway)
Rfer_1309	PWY-5484	glycolysis II (from fructose 6-phosphate)
Rfer_1313	PWY-5667	CDP-diacylglycerol biosynthesis I
Rfer_1313	PWY-5981	CDP-diacylglycerol biosynthesis III
Rfer_1314	PWY-7052	cyanophycin metabolism
Rfer_1315	PWY-7052	cyanophycin metabolism
Rfer_1318	PWY-5316	nicotine biosynthesis
Rfer_1318	PWY-5381	pyridine nucleotide cycling (plants)
Rfer_1318	PWY-5653	NAD biosynthesis from 2-amino-3-carboxymuconate semialdehyde
Rfer_1318	PWY-7342	superpathway of nicotine biosynthesis
Rfer_1319	PWY-5316	nicotine biosynthesis
Rfer_1319	PWY-7342	superpathway of nicotine biosynthesis
Rfer_1323	PWY-702	L-methionine biosynthesis II
Rfer_1327	PWY-5344	L-homocysteine biosynthesis
Rfer_1327	PWY-7174	<i>S</i>-methyl-5-thio-&alpha;-D-ribose 1-phosphate degradation II
Rfer_1332	PWY-7560	methylerythritol phosphate pathway II
Rfer_1334	PWY-723	alkylnitronates degradation
Rfer_1335	PWY-6969	TCA cycle V (2-oxoglutarate:ferredoxin oxidoreductase)
Rfer_1351	PWY-4381	fatty acid biosynthesis initiation I
Rfer_1351	PWY-5743	3-hydroxypropanoate cycle
Rfer_1351	PWY-5744	glyoxylate assimilation
Rfer_1351	PWY-5789	3-hydroxypropanoate/4-hydroxybutanate cycle
Rfer_1351	PWY-6679	jadomycin biosynthesis
Rfer_1351	PWY-7388	octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)
Rfer_1353	PWY-2941	L-lysine biosynthesis II
Rfer_1353	PWY-2942	L-lysine biosynthesis III
Rfer_1353	PWY-5097	L-lysine biosynthesis VI
Rfer_1353	PWY-6559	spermidine biosynthesis II
Rfer_1353	PWY-6562	norspermidine biosynthesis
Rfer_1353	PWY-7153	grixazone biosynthesis
Rfer_1369	PWY-5188	tetrapyrrole biosynthesis I (from glutamate)
Rfer_1380	PWY-5686	UMP biosynthesis
Rfer_1381	PWY-5686	UMP biosynthesis
Rfer_1391	PWY-5532	adenosine nucleotides degradation IV
Rfer_1391	PWY-5723	Rubisco shunt
Rfer_1392	PWY-5723	Rubisco shunt
Rfer_1393	PWY-5484	glycolysis II (from fructose 6-phosphate)
Rfer_1404	PWY-6829	tRNA methylation (yeast)
Rfer_1404	PWY-7285	methylwyosine biosynthesis
Rfer_1404	PWY-7286	7-(3-amino-3-carboxypropyl)-wyosine biosynthesis
Rfer_1410	PWY-7158	L-phenylalanine degradation V
Rfer_1424	PWY-1281	sulfoacetaldehyde degradation I
Rfer_1424	PWY-241	C4 photosynthetic carbon assimilation cycle, NADP-ME type
Rfer_1424	PWY-5482	pyruvate fermentation to acetate II
Rfer_1424	PWY-5485	pyruvate fermentation to acetate IV
Rfer_1424	PWY-5497	purine nucleobases degradation II (anaerobic)
Rfer_1424	PWY-6637	sulfolactate degradation II
Rfer_1424	PWY-7117	C4 photosynthetic carbon assimilation cycle, PEPCK type
Rfer_1433	PWY-5523	5,6-dimethylbenzimidazole biosynthesis
Rfer_1433	PWY-6167	flavin biosynthesis II (archaea)
Rfer_1433	PWY-6168	flavin biosynthesis III (fungi)
Rfer_1441	PWY-7204	pyridoxal 5'-phosphate salvage II (plants)
Rfer_1441	PWY-7282	4-amino-2-methyl-5-phosphomethylpyrimidine biosynthesis (yeast)
Rfer_1462	PWY-5386	methylglyoxal degradation I
Rfer_1466	PWY-6823	molybdenum cofactor biosynthesis
Rfer_1467	PWY-5964	guanylyl molybdenum cofactor biosynthesis
Rfer_1468	PWY-6823	molybdenum cofactor biosynthesis
Rfer_1477	PWY-6386	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis II (lysine-containing)
Rfer_1477	PWY-6387	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis I (<i>meso</i>-diaminopimelate containing)
Rfer_1478	PWY-5508	adenosylcobalamin biosynthesis from cobyrinate <i>a,c</i>-diamide II
Rfer_1478	PWY-5509	adenosylcobalamin biosynthesis from cobyrinate <i>a,c</i>-diamide I
Rfer_1478	PWY-6268	adenosylcobalamin salvage from cobalamin
Rfer_1478	PWY-6269	adenosylcobalamin salvage from cobinamide II
Rfer_1479	PWY-1042	glycolysis IV (plant cytosol)
Rfer_1479	PWY-1861	formaldehyde assimilation II (RuMP Cycle)
Rfer_1479	PWY-5484	glycolysis II (from fructose 6-phosphate)
Rfer_1479	PWY-7385	1,3-propanediol biosynthesis (engineered)
Rfer_1491	PWY-1042	glycolysis IV (plant cytosol)
Rfer_1491	PWY-5484	glycolysis II (from fructose 6-phosphate)
Rfer_1491	PWY-6142	gluconeogenesis II (<i>Methanobacterium thermoautotrophicum</i>)
Rfer_1491	PWY-7003	glycerol degradation to butanol
Rfer_1505	PWY-3781	aerobic respiration I (cytochrome c)
Rfer_1505	PWY-4302	aerobic respiration III (alternative oxidase pathway)
Rfer_1505	PWY-5083	NAD/NADH phosphorylation and dephosphorylation
Rfer_1505	PWY-6692	Fe(II) oxidation
Rfer_1509	PWY-5022	4-aminobutanoate degradation V
Rfer_1509	PWY-6728	methylaspartate cycle
Rfer_1509	PWY-7126	ethylene biosynthesis IV
Rfer_1535	PWY-2781	<i>cis</i>-zeatin biosynthesis
Rfer_1567	PWY-6163	chorismate biosynthesis from 3-dehydroquinate
Rfer_1567	PWY-7205	CMP phosphorylation
Rfer_1568	PWY-7303	3-dimethylallyl-4-hydroxybenzoate biosynthesis
Rfer_1569	PWY-3461	L-tyrosine biosynthesis II
Rfer_1569	PWY-3462	L-phenylalanine biosynthesis II
Rfer_1569	PWY-6120	L-tyrosine biosynthesis III
Rfer_1569	PWY-6627	salinosporamide A biosynthesis
Rfer_1569	PWY-7432	L-phenylalanine biosynthesis III (cytosolic, plants)
Rfer_1582	PWY-6123	inosine-5'-phosphate biosynthesis I
Rfer_1582	PWY-6124	inosine-5'-phosphate biosynthesis II
Rfer_1582	PWY-7234	inosine-5'-phosphate biosynthesis III
Rfer_1613	PWY-6281	L-selenocysteine biosynthesis II (archaea and eukaryotes)
Rfer_1630	PWY-7206	pyrimidine deoxyribonucleotides dephosphorylation
Rfer_1649	PWY-6121	5-aminoimidazole ribonucleotide biosynthesis I
Rfer_1649	PWY-6613	tetrahydrofolate salvage from 5,10-methenyltetrahydrofolate
Rfer_1651	PWY-5083	NAD/NADH phosphorylation and dephosphorylation
Rfer_1651	PWY-7268	NAD/NADP-NADH/NADPH cytosolic interconversion (yeast)
Rfer_1651	PWY-7269	NAD/NADP-NADH/NADPH mitochondrial interconversion (yeast)
Rfer_1659	PWY-7560	methylerythritol phosphate pathway II
Rfer_1681	PWY-3781	aerobic respiration I (cytochrome c)
Rfer_1681	PWY-4521	arsenite oxidation I (respiratory)
Rfer_1681	PWY-6692	Fe(II) oxidation
Rfer_1681	PWY-7279	aerobic respiration II (cytochrome c) (yeast)
Rfer_1708	PWY-6890	4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis
Rfer_1710	PWY-4983	L-citrulline-nitric oxide cycle
Rfer_1710	PWY-4984	urea cycle
Rfer_1710	PWY-5	canavanine biosynthesis
Rfer_1710	PWY-5154	L-arginine biosynthesis III (via <i>N</i>-acetyl-L-citrulline)
Rfer_1710	PWY-7400	L-arginine biosynthesis IV (archaebacteria)
Rfer_1714	PWY-1622	formaldehyde assimilation I (serine pathway)
Rfer_1714	PWY-241	C4 photosynthetic carbon assimilation cycle, NADP-ME type
Rfer_1714	PWY-5913	TCA cycle VI (obligate autotrophs)
Rfer_1714	PWY-6142	gluconeogenesis II (<i>Methanobacterium thermoautotrophicum</i>)
Rfer_1714	PWY-6146	<i>Methanobacterium thermoautotrophicum</i> biosynthetic metabolism
Rfer_1714	PWY-6549	L-glutamine biosynthesis III
Rfer_1714	PWY-7115	C4 photosynthetic carbon assimilation cycle, NAD-ME type
Rfer_1714	PWY-7117	C4 photosynthetic carbon assimilation cycle, PEPCK type
Rfer_1714	PWY-7124	ethylene biosynthesis V (engineered)
Rfer_1715	PWY-5188	tetrapyrrole biosynthesis I (from glutamate)
Rfer_1715	PWY-5189	tetrapyrrole biosynthesis II (from glycine)
Rfer_1716	PWY-5188	tetrapyrrole biosynthesis I (from glutamate)
Rfer_1716	PWY-5189	tetrapyrrole biosynthesis II (from glycine)
Rfer_1730	PWY-4381	fatty acid biosynthesis initiation I
Rfer_1731	PWY-4381	fatty acid biosynthesis initiation I
Rfer_1731	PWY-6799	fatty acid biosynthesis (plant mitochondria)
Rfer_1731	PWY-7388	octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)
Rfer_1732	PWY-5367	petroselinate biosynthesis
Rfer_1732	PWY-5971	palmitate biosynthesis II (bacteria and plants)
Rfer_1732	PWY-5973	<i>cis</i>-vaccenate biosynthesis
Rfer_1732	PWY-5989	stearate biosynthesis II (bacteria and plants)
Rfer_1732	PWY-5994	palmitate biosynthesis I (animals and fungi)
Rfer_1732	PWY-6113	superpathway of mycolate biosynthesis
Rfer_1732	PWY-6282	palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate)
Rfer_1732	PWY-6519	8-amino-7-oxononanoate biosynthesis I
Rfer_1732	PWY-6951	Rfer_1732|Rfer_1732|REF_jgi:Rfer_1732|GeneID:3964031
Rfer_1732	PWY-7053	docosahexaenoate biosynthesis I (lower eukaryotes)
Rfer_1732	PWY-7388	octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)
Rfer_1732	PWYG-321	mycolate biosynthesis
Rfer_1753	PWY-6012	acyl carrier protein metabolism I
Rfer_1753	PWY-6012-1	acyl carrier protein metabolism II (mammalian)
Rfer_1786	PWY-4381	fatty acid biosynthesis initiation I
Rfer_1786	PWY-5743	3-hydroxypropanoate cycle
Rfer_1786	PWY-5744	glyoxylate assimilation
Rfer_1786	PWY-5789	3-hydroxypropanoate/4-hydroxybutanate cycle
Rfer_1786	PWY-6679	jadomycin biosynthesis
Rfer_1786	PWY-7388	octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)
Rfer_1792	PWY-2941	L-lysine biosynthesis II
Rfer_1792	PWY-2942	L-lysine biosynthesis III
Rfer_1792	PWY-5097	L-lysine biosynthesis VI
Rfer_1792	PWY-5154	L-arginine biosynthesis III (via <i>N</i>-acetyl-L-citrulline)
Rfer_1792	PWY-6559	spermidine biosynthesis II
Rfer_1792	PWY-6562	norspermidine biosynthesis
Rfer_1792	PWY-7153	grixazone biosynthesis
Rfer_1792	PWY-7400	L-arginine biosynthesis IV (archaebacteria)
Rfer_1793	PWY-7396	butanol and isobutanol biosynthesis (engineered)
Rfer_1798	PWY-3781	aerobic respiration I (cytochrome c)
Rfer_1798	PWY-4302	aerobic respiration III (alternative oxidase pathway)
Rfer_1798	PWY-561	superpathway of glyoxylate cycle and fatty acid degradation
Rfer_1798	PWY-5690	TCA cycle II (plants and fungi)
Rfer_1798	PWY-6728	methylaspartate cycle
Rfer_1798	PWY-6969	TCA cycle V (2-oxoglutarate:ferredoxin oxidoreductase)
Rfer_1798	PWY-7254	TCA cycle VII (acetate-producers)
Rfer_1798	PWY-7279	aerobic respiration II (cytochrome c) (yeast)
Rfer_1799	PWY-3781	aerobic respiration I (cytochrome c)
Rfer_1799	PWY-4302	aerobic respiration III (alternative oxidase pathway)
Rfer_1799	PWY-561	superpathway of glyoxylate cycle and fatty acid degradation
Rfer_1799	PWY-5690	TCA cycle II (plants and fungi)
Rfer_1799	PWY-6728	methylaspartate cycle
Rfer_1799	PWY-6969	TCA cycle V (2-oxoglutarate:ferredoxin oxidoreductase)
Rfer_1799	PWY-7254	TCA cycle VII (acetate-producers)
Rfer_1799	PWY-7279	aerobic respiration II (cytochrome c) (yeast)
Rfer_1803	PWY-1622	formaldehyde assimilation I (serine pathway)
Rfer_1803	PWY-5392	reductive TCA cycle II
Rfer_1803	PWY-561	superpathway of glyoxylate cycle and fatty acid degradation
Rfer_1803	PWY-5690	TCA cycle II (plants and fungi)
Rfer_1803	PWY-5913	TCA cycle VI (obligate autotrophs)
Rfer_1803	PWY-6728	methylaspartate cycle
Rfer_1803	PWY-6969	TCA cycle V (2-oxoglutarate:ferredoxin oxidoreductase)
Rfer_1803	PWY-7115	C4 photosynthetic carbon assimilation cycle, NAD-ME type
Rfer_1803	PWY-7383	anaerobic energy metabolism (invertebrates, cytosol)
Rfer_1806	PWY-5747	2-methylcitrate cycle II
Rfer_1823	PWY-5188	tetrapyrrole biosynthesis I (from glutamate)
Rfer_1843	PWY-5794	malonate degradation I (biotin-independent)
Rfer_1843	PWY-6060	malonate degradation II (biotin-dependent)
Rfer_1845	PWY-4381	fatty acid biosynthesis initiation I
Rfer_1845	PWY-5743	3-hydroxypropanoate cycle
Rfer_1845	PWY-5744	glyoxylate assimilation
Rfer_1845	PWY-5789	3-hydroxypropanoate/4-hydroxybutanate cycle
Rfer_1845	PWY-6060	malonate degradation II (biotin-dependent)
Rfer_1845	PWY-6679	jadomycin biosynthesis
Rfer_1845	PWY-7388	octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)
Rfer_1846	PWY-6060	malonate degradation II (biotin-dependent)
Rfer_1847	PWY-5796	malonate decarboxylase activation
Rfer_1848	PWY-5796	malonate decarboxylase activation
Rfer_1863	PWY-6823	molybdenum cofactor biosynthesis
Rfer_1863	PWY-6891	thiazole biosynthesis II (Bacillus)
Rfer_1863	PWY-6892	thiazole biosynthesis I (E. coli)
Rfer_1863	PWY-7250	[2Fe-2S] iron-sulfur cluster biosynthesis
Rfer_1886	PWY-3781	aerobic respiration I (cytochrome c)
Rfer_1886	PWY-4521	arsenite oxidation I (respiratory)
Rfer_1886	PWY-6692	Fe(II) oxidation
Rfer_1886	PWY-7279	aerobic respiration II (cytochrome c) (yeast)
Rfer_1915	PWY-6823	molybdenum cofactor biosynthesis
Rfer_1917	PWY-6823	molybdenum cofactor biosynthesis
Rfer_1921	PWY-5101	L-isoleucine biosynthesis II
Rfer_1921	PWY-5103	L-isoleucine biosynthesis III
Rfer_1921	PWY-5104	L-isoleucine biosynthesis IV
Rfer_1921	PWY-7111	pyruvate fermentation to isobutanol (engineered)
Rfer_1930	PWY-3781	aerobic respiration I (cytochrome c)
Rfer_1930	PWY-4521	arsenite oxidation I (respiratory)
Rfer_1930	PWY-6692	Fe(II) oxidation
Rfer_1930	PWY-7279	aerobic respiration II (cytochrome c) (yeast)
Rfer_1931	PWY-3781	aerobic respiration I (cytochrome c)
Rfer_1931	PWY-4521	arsenite oxidation I (respiratory)
Rfer_1931	PWY-6692	Fe(II) oxidation
Rfer_1931	PWY-7279	aerobic respiration II (cytochrome c) (yeast)
Rfer_1960	PWY-723	alkylnitronates degradation
Rfer_1962	PWY-1801	formaldehyde oxidation II (glutathione-dependent)
Rfer_1984	PWY-6938	NADH repair
Rfer_1988	PWY-5921	glutaminyl-tRNA<sup>gln</sup> biosynthesis via transamidation
Rfer_1994	PWY-7560	methylerythritol phosphate pathway II
Rfer_1999	PWY-5971	palmitate biosynthesis II (bacteria and plants)
Rfer_1999	PWY-5973	<i>cis</i>-vaccenate biosynthesis
Rfer_1999	PWY-5989	stearate biosynthesis II (bacteria and plants)
Rfer_1999	PWY-5994	palmitate biosynthesis I (animals and fungi)
Rfer_1999	PWY-6113	superpathway of mycolate biosynthesis
Rfer_1999	PWY-6282	palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate)
Rfer_1999	PWY-6519	8-amino-7-oxononanoate biosynthesis I
Rfer_1999	PWY-7388	octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)
Rfer_1999	PWYG-321	mycolate biosynthesis
Rfer_2004	PWY-5154	L-arginine biosynthesis III (via <i>N</i>-acetyl-L-citrulline)
Rfer_2004	PWY-5686	UMP biosynthesis
Rfer_2004	PWY-7400	L-arginine biosynthesis IV (archaebacteria)
Rfer_2006	PWY-5154	L-arginine biosynthesis III (via <i>N</i>-acetyl-L-citrulline)
Rfer_2006	PWY-5686	UMP biosynthesis
Rfer_2006	PWY-7400	L-arginine biosynthesis IV (archaebacteria)
Rfer_2012	PWY-6614	tetrahydrofolate biosynthesis
Rfer_2013	PWY-6749	CMP-legionaminate biosynthesis I
Rfer_2059	PWY-7204	pyridoxal 5'-phosphate salvage II (plants)
Rfer_2059	PWY-7282	4-amino-2-methyl-5-phosphomethylpyrimidine biosynthesis (yeast)
Rfer_2060	PWY-5101	L-isoleucine biosynthesis II
Rfer_2060	PWY-5103	L-isoleucine biosynthesis III
Rfer_2060	PWY-5104	L-isoleucine biosynthesis IV
Rfer_2060	PWY-7111	pyruvate fermentation to isobutanol (engineered)
Rfer_2061	PWY-2221	Entner-Doudoroff pathway III (semi-phosphorylative)
Rfer_2061	PWY-6507	4-deoxy-L-<i>threo</i>-hex-4-enopyranuronate degradation
Rfer_2061	PWY-7242	D-fructuronate degradation
Rfer_2061	PWY-7310	D-glucosaminate degradation
Rfer_2073	PWY-7183	pyrimidine nucleobases salvage I
Rfer_2076	PWY-6121	5-aminoimidazole ribonucleotide biosynthesis I
Rfer_2076	PWY-6122	5-aminoimidazole ribonucleotide biosynthesis II
Rfer_2076	PWY-6277	superpathway of 5-aminoimidazole ribonucleotide biosynthesis
Rfer_2077	PWY-5531	chlorophyllide <i>a</i> biosynthesis II (anaerobic)
Rfer_2077	PWY-7159	chlorophyllide <i>a</i> biosynthesis III (aerobic, light independent)
Rfer_2078	PWY-5381	pyridine nucleotide cycling (plants)
Rfer_2078	PWY-5653	NAD biosynthesis from 2-amino-3-carboxymuconate semialdehyde
Rfer_2097	PWY-2941	L-lysine biosynthesis II
Rfer_2097	PWY-2942	L-lysine biosynthesis III
Rfer_2097	PWY-5097	L-lysine biosynthesis VI
Rfer_2105	PWY-5154	L-arginine biosynthesis III (via <i>N</i>-acetyl-L-citrulline)
Rfer_2113	PWY-7377	cob(II)yrinate <i>a,c</i>-diamide biosynthesis I (early cobalt insertion)
Rfer_2116	PWY-5988	wound-induced proteolysis I
Rfer_2116	PWY-6018	seed germination protein turnover
Rfer_2120	PWY-4981	L-proline biosynthesis II (from arginine)
Rfer_2120	PWY-4984	urea cycle
Rfer_2120	PWY-7400	L-arginine biosynthesis IV (archaebacteria)
Rfer_2127	PWY-5971	palmitate biosynthesis II (bacteria and plants)
Rfer_2127	PWY-5973	<i>cis</i>-vaccenate biosynthesis
Rfer_2127	PWY-5989	stearate biosynthesis II (bacteria and plants)
Rfer_2127	PWY-6113	superpathway of mycolate biosynthesis
Rfer_2127	PWY-6282	palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate)
Rfer_2127	PWY-6519	8-amino-7-oxononanoate biosynthesis I
Rfer_2127	PWY-7096	triclosan resistance
Rfer_2127	PWYG-321	mycolate biosynthesis
Rfer_2156	PWY-2661	trehalose biosynthesis V
Rfer_2156	PWY-5941	glycogen degradation II (eukaryotic)
Rfer_2156	PWY-6724	starch degradation II
Rfer_2156	PWY-6737	starch degradation V
Rfer_2156	PWY-7238	sucrose biosynthesis II
Rfer_2157	PWY-2661	trehalose biosynthesis V
Rfer_2160	PWY-2622	trehalose biosynthesis IV
Rfer_2162	PWY-5067	glycogen biosynthesis II (from UDP-D-Glucose)
Rfer_2162	PWY-622	starch biosynthesis
Rfer_2172	PWY-5839	menaquinol-7 biosynthesis
Rfer_2172	PWY-5844	menaquinol-9 biosynthesis
Rfer_2172	PWY-5849	menaquinol-6 biosynthesis
Rfer_2172	PWY-5890	menaquinol-10 biosynthesis
Rfer_2172	PWY-5891	menaquinol-11 biosynthesis
Rfer_2172	PWY-5892	menaquinol-12 biosynthesis
Rfer_2172	PWY-5895	menaquinol-13 biosynthesis
Rfer_2174	PWY-5913	TCA cycle VI (obligate autotrophs)
Rfer_2174	PWY-6318	L-phenylalanine degradation IV (mammalian, via side chain)
Rfer_2174	PWY-6638	sulfolactate degradation III
Rfer_2174	PWY-6642	(<i>R</i>)-cysteate degradation
Rfer_2174	PWY-6643	coenzyme M biosynthesis II
Rfer_2174	PWY-7115	C4 photosynthetic carbon assimilation cycle, NAD-ME type
Rfer_2174	PWY-7117	C4 photosynthetic carbon assimilation cycle, PEPCK type
Rfer_2174	PWY-7383	anaerobic energy metabolism (invertebrates, cytosol)
Rfer_2177	PWY-6823	molybdenum cofactor biosynthesis
Rfer_2177	PWY-6891	thiazole biosynthesis II (Bacillus)
Rfer_2177	PWY-6892	thiazole biosynthesis I (E. coli)
Rfer_2177	PWY-7250	[2Fe-2S] iron-sulfur cluster biosynthesis
Rfer_2191	PWY-5484	glycolysis II (from fructose 6-phosphate)
Rfer_2197	PWY-6545	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis III
Rfer_2197	PWY-7184	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis I
Rfer_2197	PWY-7198	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis IV
Rfer_2197	PWY-7210	pyrimidine deoxyribonucleotides biosynthesis from CTP
Rfer_2197	PWY-7220	adenosine deoxyribonucleotides <i>de novo</i> biosynthesis II
Rfer_2197	PWY-7222	guanosine deoxyribonucleotides <i>de novo</i> biosynthesis II
Rfer_2197	PWY-7226	guanosine deoxyribonucleotides <i>de novo</i> biosynthesis I
Rfer_2197	PWY-7227	adenosine deoxyribonucleotides <i>de novo</i> biosynthesis
Rfer_2205	PWY-5686	UMP biosynthesis
Rfer_2206	PWY-1861	formaldehyde assimilation II (RuMP Cycle)
Rfer_2206	PWY-5723	Rubisco shunt
Rfer_2209	PWY-1722	formate reduction to 5,10-methylenetetrahydrofolate
Rfer_2209	PWY-2201	folate transformations I
Rfer_2209	PWY-3841	folate transformations II
Rfer_2209	PWY-5030	L-histidine degradation III
Rfer_2209	PWY-5497	purine nucleobases degradation II (anaerobic)
Rfer_2209	PWY-6613	tetrahydrofolate salvage from 5,10-methenyltetrahydrofolate
Rfer_2212	PWY-6891	thiazole biosynthesis II (Bacillus)
Rfer_2212	PWY-6892	thiazole biosynthesis I (E. coli)
Rfer_2212	PWY-7560	methylerythritol phosphate pathway II
Rfer_2214	PWY-5046	2-oxoisovalerate decarboxylation to isobutanoyl-CoA
Rfer_2214	PWY-5084	2-oxoglutarate decarboxylation to succinyl-CoA
Rfer_2241	PWY-7181	pyrimidine deoxyribonucleosides degradation
Rfer_2245	PWY-5269	cardiolipin biosynthesis II
Rfer_2245	PWY-5668	cardiolipin biosynthesis I
Rfer_2255	PWY-6545	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis III
Rfer_2255	PWY-7184	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis I
Rfer_2255	PWY-7187	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis II
Rfer_2255	PWY-7197	pyrimidine deoxyribonucleotide phosphorylation
Rfer_2255	PWY-7198	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis IV
Rfer_2255	PWY-7210	pyrimidine deoxyribonucleotides biosynthesis from CTP
Rfer_2272	PWY-1361	benzoyl-CoA degradation I (aerobic)
Rfer_2272	PWY-5109	2-methylbutanoate biosynthesis
Rfer_2272	PWY-5136	fatty acid &beta;-oxidation II (peroxisome)
Rfer_2272	PWY-5138	unsaturated, even numbered fatty acid &beta;-oxidation
Rfer_2272	PWY-5177	glutaryl-CoA degradation
Rfer_2272	PWY-5789	3-hydroxypropanoate/4-hydroxybutanate cycle
Rfer_2272	PWY-6435	4-hydroxybenzoate biosynthesis V
Rfer_2272	PWY-6583	pyruvate fermentation to butanol I
Rfer_2272	PWY-6863	pyruvate fermentation to hexanol
Rfer_2272	PWY-6883	pyruvate fermentation to butanol II
Rfer_2272	PWY-6944	androstenedione degradation
Rfer_2272	PWY-6945	cholesterol degradation to androstenedione I (cholesterol oxidase)
Rfer_2272	PWY-6946	cholesterol degradation to androstenedione II (cholesterol dehydrogenase)
Rfer_2272	PWY-7007	methyl ketone biosynthesis
Rfer_2272	PWY-7046	4-coumarate degradation (anaerobic)
Rfer_2272	PWY-7094	fatty acid salvage
Rfer_2272	PWY-7216	(R)- and (S)-3-hydroxybutanoate biosynthesis
Rfer_2272	PWY-735	jasmonic acid biosynthesis
Rfer_2272	PWY-7401	crotonate fermentation (to acetate and cyclohexane carboxylate)
Rfer_2287	PWY-7221	guanosine ribonucleotides <i>de novo</i> biosynthesis
Rfer_2288	PWY-5695	urate biosynthesis/inosine 5'-phosphate degradation
Rfer_2288	PWY-6596	adenosine nucleotides degradation I
Rfer_2288	PWY-7221	guanosine ribonucleotides <i>de novo</i> biosynthesis
Rfer_2292	PWY-7380	biotin biosynthesis from 8-amino-7-oxononanoate II
Rfer_2296	PWY-7219	adenosine ribonucleotides <i>de novo</i> biosynthesis
Rfer_2307	PWY-7560	methylerythritol phosphate pathway II
Rfer_2311	PWY-6545	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis III
Rfer_2311	PWY-7176	UTP and CTP <i>de novo</i> biosynthesis
Rfer_2311	PWY-7184	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis I
Rfer_2311	PWY-7187	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis II
Rfer_2311	PWY-7197	pyrimidine deoxyribonucleotide phosphorylation
Rfer_2311	PWY-7198	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis IV
Rfer_2311	PWY-7205	CMP phosphorylation
Rfer_2311	PWY-7210	pyrimidine deoxyribonucleotides biosynthesis from CTP
Rfer_2311	PWY-7220	adenosine deoxyribonucleotides <i>de novo</i> biosynthesis II
Rfer_2311	PWY-7221	guanosine ribonucleotides <i>de novo</i> biosynthesis
Rfer_2311	PWY-7222	guanosine deoxyribonucleotides <i>de novo</i> biosynthesis II
Rfer_2311	PWY-7224	purine deoxyribonucleosides salvage
Rfer_2311	PWY-7226	guanosine deoxyribonucleotides <i>de novo</i> biosynthesis I
Rfer_2311	PWY-7227	adenosine deoxyribonucleotides <i>de novo</i> biosynthesis
Rfer_2319	PWY-5046	2-oxoisovalerate decarboxylation to isobutanoyl-CoA
Rfer_2319	PWY-5084	2-oxoglutarate decarboxylation to succinyl-CoA
Rfer_2320	PWY-5084	2-oxoglutarate decarboxylation to succinyl-CoA
Rfer_2321	PWY-5084	2-oxoglutarate decarboxylation to succinyl-CoA
Rfer_2322	PWY-3941	&beta;-alanine biosynthesis II
Rfer_2322	PWY-5104	L-isoleucine biosynthesis IV
Rfer_2322	PWY-5747	2-methylcitrate cycle II
Rfer_2332	PWY-6386	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis II (lysine-containing)
Rfer_2332	PWY-6387	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis I (<i>meso</i>-diaminopimelate containing)
Rfer_2333	PWY-4261	glycerol degradation I
Rfer_2333	PWY-6118	glycerol-3-phosphate shuttle
Rfer_2333	PWY-6952	glycerophosphodiester degradation
Rfer_2334	PWY-4261	glycerol degradation I
Rfer_2335	PWY-6386	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis II (lysine-containing)
Rfer_2335	PWY-6387	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis I (<i>meso</i>-diaminopimelate containing)
Rfer_2345	PWY-6871	3-methylbutanol biosynthesis
Rfer_2352	PWY-5392	reductive TCA cycle II
Rfer_2352	PWY-5537	pyruvate fermentation to acetate V
Rfer_2352	PWY-5538	pyruvate fermentation to acetate VI
Rfer_2352	PWY-5690	TCA cycle II (plants and fungi)
Rfer_2352	PWY-5913	TCA cycle VI (obligate autotrophs)
Rfer_2352	PWY-6728	methylaspartate cycle
Rfer_2352	PWY-6969	TCA cycle V (2-oxoglutarate:ferredoxin oxidoreductase)
Rfer_2352	PWY-7384	anaerobic energy metabolism (invertebrates, mitochondrial)
Rfer_2364	PWY-7545	pyruvate to cytochrome <i>bd</i> terminal oxidase electron transfer
Rfer_2365	PWY-5392	reductive TCA cycle II
Rfer_2365	PWY-561	superpathway of glyoxylate cycle and fatty acid degradation
Rfer_2365	PWY-5690	TCA cycle II (plants and fungi)
Rfer_2365	PWY-5913	TCA cycle VI (obligate autotrophs)
Rfer_2365	PWY-6728	methylaspartate cycle
Rfer_2365	PWY-6969	TCA cycle V (2-oxoglutarate:ferredoxin oxidoreductase)
Rfer_2365	PWY-7254	TCA cycle VII (acetate-producers)
Rfer_2365	PWY-7384	anaerobic energy metabolism (invertebrates, mitochondrial)
Rfer_2370	PWY-6700	queuosine biosynthesis
Rfer_2378	PWY-6936	seleno-amino acid biosynthesis
Rfer_2381	PWY-6163	chorismate biosynthesis from 3-dehydroquinate
Rfer_2381	PWY-6416	quinate degradation II
Rfer_2381	PWY-6707	gallate biosynthesis
Rfer_2386	PWY-1361	benzoyl-CoA degradation I (aerobic)
Rfer_2386	PWY-5109	2-methylbutanoate biosynthesis
Rfer_2386	PWY-5136	fatty acid &beta;-oxidation II (peroxisome)
Rfer_2386	PWY-5138	unsaturated, even numbered fatty acid &beta;-oxidation
Rfer_2386	PWY-5177	glutaryl-CoA degradation
Rfer_2386	PWY-5789	3-hydroxypropanoate/4-hydroxybutanate cycle
Rfer_2386	PWY-6435	4-hydroxybenzoate biosynthesis V
Rfer_2386	PWY-6583	pyruvate fermentation to butanol I
Rfer_2386	PWY-6863	pyruvate fermentation to hexanol
Rfer_2386	PWY-6883	pyruvate fermentation to butanol II
Rfer_2386	PWY-6944	androstenedione degradation
Rfer_2386	PWY-6945	cholesterol degradation to androstenedione I (cholesterol oxidase)
Rfer_2386	PWY-6946	cholesterol degradation to androstenedione II (cholesterol dehydrogenase)
Rfer_2386	PWY-7007	methyl ketone biosynthesis
Rfer_2386	PWY-7046	4-coumarate degradation (anaerobic)
Rfer_2386	PWY-7094	fatty acid salvage
Rfer_2386	PWY-7216	(R)- and (S)-3-hydroxybutanoate biosynthesis
Rfer_2386	PWY-735	jasmonic acid biosynthesis
Rfer_2386	PWY-7401	crotonate fermentation (to acetate and cyclohexane carboxylate)
Rfer_2403	PWY-1622	formaldehyde assimilation I (serine pathway)
Rfer_2403	PWY-5392	reductive TCA cycle II
Rfer_2403	PWY-561	superpathway of glyoxylate cycle and fatty acid degradation
Rfer_2403	PWY-5690	TCA cycle II (plants and fungi)
Rfer_2403	PWY-5913	TCA cycle VI (obligate autotrophs)
Rfer_2403	PWY-6728	methylaspartate cycle
Rfer_2403	PWY-6969	TCA cycle V (2-oxoglutarate:ferredoxin oxidoreductase)
Rfer_2403	PWY-7115	C4 photosynthetic carbon assimilation cycle, NAD-ME type
Rfer_2403	PWY-7383	anaerobic energy metabolism (invertebrates, cytosol)
Rfer_2405	PWY-5796	malonate decarboxylase activation
Rfer_2407	PWY-6038	citrate degradation
Rfer_2408	PWY-5392	reductive TCA cycle II
Rfer_2408	PWY-6038	citrate degradation
Rfer_2420	PWY-6121	5-aminoimidazole ribonucleotide biosynthesis I
Rfer_2420	PWY-6122	5-aminoimidazole ribonucleotide biosynthesis II
Rfer_2420	PWY-6277	superpathway of 5-aminoimidazole ribonucleotide biosynthesis
Rfer_2436	PWY-7204	pyridoxal 5'-phosphate salvage II (plants)
Rfer_2436	PWY-7282	4-amino-2-methyl-5-phosphomethylpyrimidine biosynthesis (yeast)
Rfer_2456	PWY-6683	sulfate reduction III (assimilatory)
Rfer_2459	PWY-5278	sulfite oxidation III
Rfer_2459	PWY-5340	sulfate activation for sulfonation
Rfer_2459	PWY-6683	sulfate reduction III (assimilatory)
Rfer_2459	PWY-6932	selenate reduction
Rfer_2460	PWY-5278	sulfite oxidation III
Rfer_2460	PWY-5340	sulfate activation for sulfonation
Rfer_2460	PWY-6683	sulfate reduction III (assimilatory)
Rfer_2460	PWY-6932	selenate reduction
Rfer_2462	PWY-101	photosynthesis light reactions
Rfer_2462	PWY-7230	ubiquinol-6 biosynthesis from 4-aminobenzoate (eukaryotic)
Rfer_2466	PWY-6891	thiazole biosynthesis II (Bacillus)
Rfer_2466	PWY-6892	thiazole biosynthesis I (E. coli)
Rfer_2467	PWY-6893	thiamin diphosphate biosynthesis II (Bacillus)
Rfer_2467	PWY-6894	thiamin diphosphate biosynthesis I (E. coli)
Rfer_2467	PWY-6897	thiamin salvage II
Rfer_2467	PWY-6907	thiamin diphosphate biosynthesis III (Staphylococcus)
Rfer_2467	PWY-6908	thiamin diphosphate biosynthesis IV (eukaryotes)
Rfer_2467	PWY-7353	4-methyl-5(&beta;-hydroxyethyl)thiazole salvage (yeast)
Rfer_2467	PWY-7357	thiamin formation from pyrithiamine and oxythiamine (yeast)
Rfer_2470	PWY-6910	hydroxymethylpyrimidine salvage
Rfer_2470	PWY-7356	thiamin salvage IV (yeast)
Rfer_2470	PWY-7357	thiamin formation from pyrithiamine and oxythiamine (yeast)
Rfer_2471	PWY-6893	thiamin diphosphate biosynthesis II (Bacillus)
Rfer_2471	PWY-6894	thiamin diphosphate biosynthesis I (E. coli)
Rfer_2471	PWY-6897	thiamin salvage II
Rfer_2471	PWY-6907	thiamin diphosphate biosynthesis III (Staphylococcus)
Rfer_2471	PWY-6908	thiamin diphosphate biosynthesis IV (eukaryotes)
Rfer_2471	PWY-7353	4-methyl-5(&beta;-hydroxyethyl)thiazole salvage (yeast)
Rfer_2471	PWY-7357	thiamin formation from pyrithiamine and oxythiamine (yeast)
Rfer_2472	PWY-6897	thiamin salvage II
Rfer_2472	PWY-7353	4-methyl-5(&beta;-hydroxyethyl)thiazole salvage (yeast)
Rfer_2472	PWY-7357	thiamin formation from pyrithiamine and oxythiamine (yeast)
Rfer_2496	PWY-5669	phosphatidylethanolamine biosynthesis I
Rfer_2508	PWY-6147	6-hydroxymethyl-dihydropterin diphosphate biosynthesis I
Rfer_2508	PWY-6148	tetrahydromethanopterin biosynthesis
Rfer_2508	PWY-6797	6-hydroxymethyl-dihydropterin diphosphate biosynthesis II (archaea)
Rfer_2508	PWY-7539	6-hydroxymethyl-dihydropterin diphosphate biosynthesis III (Chlamydia)
Rfer_2512	PWY-6121	5-aminoimidazole ribonucleotide biosynthesis I
Rfer_2512	PWY-6122	5-aminoimidazole ribonucleotide biosynthesis II
Rfer_2512	PWY-6277	superpathway of 5-aminoimidazole ribonucleotide biosynthesis
Rfer_2552	PWY-5386	methylglyoxal degradation I
Rfer_2557	PWY-6683	sulfate reduction III (assimilatory)
Rfer_2560	PWY-5676	acetyl-CoA fermentation to butanoate II
Rfer_2560	PWY-5741	ethylmalonyl-CoA pathway
Rfer_2560	PWY-7216	(R)- and (S)-3-hydroxybutanoate biosynthesis
Rfer_2581	PWY-6672	<i>cis</i>-genanyl-CoA degradation
Rfer_2581	PWY-7118	chitin degradation to ethanol
Rfer_2583	PWY-5392	reductive TCA cycle II
Rfer_2583	PWY-561	superpathway of glyoxylate cycle and fatty acid degradation
Rfer_2583	PWY-5690	TCA cycle II (plants and fungi)
Rfer_2583	PWY-5913	TCA cycle VI (obligate autotrophs)
Rfer_2583	PWY-6728	methylaspartate cycle
Rfer_2583	PWY-6969	TCA cycle V (2-oxoglutarate:ferredoxin oxidoreductase)
Rfer_2583	PWY-7254	TCA cycle VII (acetate-producers)
Rfer_2583	PWY-7384	anaerobic energy metabolism (invertebrates, mitochondrial)
Rfer_2595	PWY-1361	benzoyl-CoA degradation I (aerobic)
Rfer_2595	PWY-5109	2-methylbutanoate biosynthesis
Rfer_2595	PWY-5136	fatty acid &beta;-oxidation II (peroxisome)
Rfer_2595	PWY-5138	unsaturated, even numbered fatty acid &beta;-oxidation
Rfer_2595	PWY-5177	glutaryl-CoA degradation
Rfer_2595	PWY-5789	3-hydroxypropanoate/4-hydroxybutanate cycle
Rfer_2595	PWY-6435	4-hydroxybenzoate biosynthesis V
Rfer_2595	PWY-6583	pyruvate fermentation to butanol I
Rfer_2595	PWY-6863	pyruvate fermentation to hexanol
Rfer_2595	PWY-6883	pyruvate fermentation to butanol II
Rfer_2595	PWY-6944	androstenedione degradation
Rfer_2595	PWY-6945	cholesterol degradation to androstenedione I (cholesterol oxidase)
Rfer_2595	PWY-6946	cholesterol degradation to androstenedione II (cholesterol dehydrogenase)
Rfer_2595	PWY-7007	methyl ketone biosynthesis
Rfer_2595	PWY-7046	4-coumarate degradation (anaerobic)
Rfer_2595	PWY-7094	fatty acid salvage
Rfer_2595	PWY-7216	(R)- and (S)-3-hydroxybutanoate biosynthesis
Rfer_2595	PWY-735	jasmonic acid biosynthesis
Rfer_2595	PWY-7401	crotonate fermentation (to acetate and cyclohexane carboxylate)
Rfer_2597	PWY-6386	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis II (lysine-containing)
Rfer_2597	PWY-6387	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis I (<i>meso</i>-diaminopimelate containing)
Rfer_2609	PWY-5508	adenosylcobalamin biosynthesis from cobyrinate <i>a,c</i>-diamide II
Rfer_2609	PWY-5509	adenosylcobalamin biosynthesis from cobyrinate <i>a,c</i>-diamide I
Rfer_2609	PWY-6269	adenosylcobalamin salvage from cobinamide II
Rfer_2610	PWY-5508	adenosylcobalamin biosynthesis from cobyrinate <i>a,c</i>-diamide II
Rfer_2610	PWY-5509	adenosylcobalamin biosynthesis from cobyrinate <i>a,c</i>-diamide I
Rfer_2610	PWY-6269	adenosylcobalamin salvage from cobinamide II
Rfer_2611	PWY-5508	adenosylcobalamin biosynthesis from cobyrinate <i>a,c</i>-diamide II
Rfer_2611	PWY-5509	adenosylcobalamin biosynthesis from cobyrinate <i>a,c</i>-diamide I
Rfer_2611	PWY-6269	adenosylcobalamin salvage from cobinamide II
Rfer_2614	PWY-6703	preQ<sub>0</sub> biosynthesis
Rfer_2617	PWY-5508	adenosylcobalamin biosynthesis from cobyrinate <i>a,c</i>-diamide II
Rfer_2617	PWY-5523	5,6-dimethylbenzimidazole biosynthesis
Rfer_2618	PWY-5508	adenosylcobalamin biosynthesis from cobyrinate <i>a,c</i>-diamide II
Rfer_2618	PWY-5509	adenosylcobalamin biosynthesis from cobyrinate <i>a,c</i>-diamide I
Rfer_2618	PWY-6268	adenosylcobalamin salvage from cobalamin
Rfer_2618	PWY-6269	adenosylcobalamin salvage from cobinamide II
Rfer_2622	PWY-5508	adenosylcobalamin biosynthesis from cobyrinate <i>a,c</i>-diamide II
Rfer_2622	PWY-5509	adenosylcobalamin biosynthesis from cobyrinate <i>a,c</i>-diamide I
Rfer_2622	PWY-6269	adenosylcobalamin salvage from cobinamide II
Rfer_2646	PWY-6545	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis III
Rfer_2646	PWY-7184	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis I
Rfer_2646	PWY-7187	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis II
Rfer_2646	PWY-7206	pyrimidine deoxyribonucleotides dephosphorylation
Rfer_2648	PWY-7176	UTP and CTP <i>de novo</i> biosynthesis
Rfer_2648	PWY-7177	UTP and CTP dephosphorylation II
Rfer_2648	PWY-7185	UTP and CTP dephosphorylation I
Rfer_2649	PWY-1269	CMP-3-deoxy-D-<I>manno</I>-octulosonate biosynthesis I
Rfer_2649	PWY-5111	CMP-3-deoxy-D-<i>manno</i>-octulosonate biosynthesis II (from D-arabinose 5-phosphate)
Rfer_2650	PWY-1042	glycolysis IV (plant cytosol)
Rfer_2650	PWY-1622	formaldehyde assimilation I (serine pathway)
Rfer_2650	PWY-2221	Entner-Doudoroff pathway III (semi-phosphorylative)
Rfer_2650	PWY-5484	glycolysis II (from fructose 6-phosphate)
Rfer_2650	PWY-5723	Rubisco shunt
Rfer_2650	PWY-6142	gluconeogenesis II (<i>Methanobacterium thermoautotrophicum</i>)
Rfer_2650	PWY-6886	1-butanol autotrophic biosynthesis
Rfer_2650	PWY-6901	superpathway of glucose and xylose degradation
Rfer_2650	PWY-7003	glycerol degradation to butanol
Rfer_2650	PWY-7124	ethylene biosynthesis V (engineered)
Rfer_2650	PWY-7218	photosynthetic 3-hydroxybutanoate biosynthesis (engineered)
Rfer_2658	PWY-1622	formaldehyde assimilation I (serine pathway)
Rfer_2658	PWY-181	photorespiration
Rfer_2658	PWY-2161	folate polyglutamylation
Rfer_2658	PWY-2201	folate transformations I
Rfer_2658	PWY-3661	glycine betaine degradation I
Rfer_2658	PWY-3661-1	glycine betaine degradation II (mammalian)
Rfer_2658	PWY-3841	folate transformations II
Rfer_2658	PWY-5497	purine nucleobases degradation II (anaerobic)
Rfer_2667	PWY-6167	flavin biosynthesis II (archaea)
Rfer_2667	PWY-6168	flavin biosynthesis III (fungi)
Rfer_2667	PWY-7219	adenosine ribonucleotides <i>de novo</i> biosynthesis
Rfer_2668	PWY-6167	flavin biosynthesis II (archaea)
Rfer_2668	PWY-6168	flavin biosynthesis III (fungi)
Rfer_2668	PWY-7539	6-hydroxymethyl-dihydropterin diphosphate biosynthesis III (Chlamydia)
Rfer_2669	PWY-6167	flavin biosynthesis II (archaea)
Rfer_2669	PWY-6168	flavin biosynthesis III (fungi)
Rfer_2677	PWY-3221	dTDP-L-rhamnose biosynthesis II
Rfer_2677	PWY-6808	dTDP-D-forosamine biosynthesis
Rfer_2677	PWY-6942	dTDP-D-desosamine biosynthesis
Rfer_2677	PWY-6953	dTDP-3-acetamido-3,6-dideoxy-&alpha;-D-galactose biosynthesis
Rfer_2677	PWY-6973	dTDP-D-olivose, dTDP-D-oliose and dTDP-D-mycarose biosynthesis
Rfer_2677	PWY-6974	dTDP-L-olivose biosynthesis
Rfer_2677	PWY-6976	dTDP-L-mycarose biosynthesis
Rfer_2677	PWY-7104	dTDP-L-megosamine biosynthesis
Rfer_2677	PWY-7301	dTDP-&beta;-L-noviose biosynthesis
Rfer_2677	PWY-7312	dTDP-D-&beta;-fucofuranose biosynthesis
Rfer_2677	PWY-7315	dTDP-<i>N</i>-acetylthomosamine biosynthesis
Rfer_2677	PWY-7316	dTDP-<i>N</i>-acetylviosamine biosynthesis
Rfer_2677	PWY-7318	dTDP-3-acetamido-3,6-dideoxy-&alpha;-D-glucose biosynthesis
Rfer_2677	PWY-7413	dTDP-6-deoxy-&alpha;-D-allose biosynthesis
Rfer_2677	PWY-7414	dTDP-&alpha;-D-mycaminose biosynthesis
Rfer_2677	PWY-7440	dTDP-&beta;-L-4-<i>epi</i>-vancosamine biosynthesis
Rfer_2681	PWY-5188	tetrapyrrole biosynthesis I (from glutamate)
Rfer_2683	PWY-6121	5-aminoimidazole ribonucleotide biosynthesis I
Rfer_2683	PWY-6122	5-aminoimidazole ribonucleotide biosynthesis II
Rfer_2683	PWY-6277	superpathway of 5-aminoimidazole ribonucleotide biosynthesis
Rfer_2683	PWY-7282	4-amino-2-methyl-5-phosphomethylpyrimidine biosynthesis (yeast)
Rfer_2686	PWY-2161	folate polyglutamylation
Rfer_2689	PWY-4983	L-citrulline-nitric oxide cycle
Rfer_2689	PWY-4984	urea cycle
Rfer_2689	PWY-5	canavanine biosynthesis
Rfer_2689	PWY-5154	L-arginine biosynthesis III (via <i>N</i>-acetyl-L-citrulline)
Rfer_2689	PWY-7400	L-arginine biosynthesis IV (archaebacteria)
Rfer_2691	PWY-6386	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis II (lysine-containing)
Rfer_2691	PWY-6387	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis I (<i>meso</i>-diaminopimelate containing)
Rfer_2704	PWY-5484	glycolysis II (from fructose 6-phosphate)
Rfer_2739	PWY-5674	nitrate reduction IV (dissimilatory)
Rfer_2754	PWY-1361	benzoyl-CoA degradation I (aerobic)
Rfer_2754	PWY-5109	2-methylbutanoate biosynthesis
Rfer_2754	PWY-5136	fatty acid &beta;-oxidation II (peroxisome)
Rfer_2754	PWY-5138	unsaturated, even numbered fatty acid &beta;-oxidation
Rfer_2754	PWY-5177	glutaryl-CoA degradation
Rfer_2754	PWY-5789	3-hydroxypropanoate/4-hydroxybutanate cycle
Rfer_2754	PWY-6435	4-hydroxybenzoate biosynthesis V
Rfer_2754	PWY-6583	pyruvate fermentation to butanol I
Rfer_2754	PWY-6863	pyruvate fermentation to hexanol
Rfer_2754	PWY-6883	pyruvate fermentation to butanol II
Rfer_2754	PWY-6944	androstenedione degradation
Rfer_2754	PWY-6945	cholesterol degradation to androstenedione I (cholesterol oxidase)
Rfer_2754	PWY-6946	cholesterol degradation to androstenedione II (cholesterol dehydrogenase)
Rfer_2754	PWY-7007	methyl ketone biosynthesis
Rfer_2754	PWY-7046	4-coumarate degradation (anaerobic)
Rfer_2754	PWY-7094	fatty acid salvage
Rfer_2754	PWY-7216	(R)- and (S)-3-hydroxybutanoate biosynthesis
Rfer_2754	PWY-735	jasmonic acid biosynthesis
Rfer_2754	PWY-7401	crotonate fermentation (to acetate and cyclohexane carboxylate)
Rfer_2761	PWY-5913	TCA cycle VI (obligate autotrophs)
Rfer_2761	PWY-6549	L-glutamine biosynthesis III
Rfer_2761	PWY-6728	methylaspartate cycle
Rfer_2761	PWY-6969	TCA cycle V (2-oxoglutarate:ferredoxin oxidoreductase)
Rfer_2761	PWY-7124	ethylene biosynthesis V (engineered)
Rfer_2761	PWY-7254	TCA cycle VII (acetate-producers)
Rfer_2761	PWY-7268	NAD/NADP-NADH/NADPH cytosolic interconversion (yeast)
Rfer_2770	PWY-4381	fatty acid biosynthesis initiation I
Rfer_2782	PWY-5381	pyridine nucleotide cycling (plants)
Rfer_2782	PWY-5695	urate biosynthesis/inosine 5'-phosphate degradation
Rfer_2782	PWY-6596	adenosine nucleotides degradation I
Rfer_2782	PWY-6606	guanosine nucleotides degradation II
Rfer_2782	PWY-6607	guanosine nucleotides degradation I
Rfer_2782	PWY-6608	guanosine nucleotides degradation III
Rfer_2782	PWY-7185	UTP and CTP dephosphorylation I
Rfer_2803	PWY-4381	fatty acid biosynthesis initiation I
Rfer_2803	PWY-5743	3-hydroxypropanoate cycle
Rfer_2803	PWY-5744	glyoxylate assimilation
Rfer_2803	PWY-5789	3-hydroxypropanoate/4-hydroxybutanate cycle
Rfer_2803	PWY-6679	jadomycin biosynthesis
Rfer_2803	PWY-7388	octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)
Rfer_2805	PWY-5743	3-hydroxypropanoate cycle
Rfer_2805	PWY-5789	3-hydroxypropanoate/4-hydroxybutanate cycle
Rfer_2805	PWY-6728	methylaspartate cycle
Rfer_2805	PWY-7384	anaerobic energy metabolism (invertebrates, mitochondrial)
Rfer_2811	PWY-5737	(5<i>R</i>)-carbapenem carboxylate biosynthesis
Rfer_2811	PWY-6853	ethylene biosynthesis II (microbes)
Rfer_2811	PWY-6922	L-<i>N<sup>&delta;</sup></i>-acetylornithine biosynthesis
Rfer_2818	PWY-4381	fatty acid biosynthesis initiation I
Rfer_2818	PWY-5743	3-hydroxypropanoate cycle
Rfer_2818	PWY-5744	glyoxylate assimilation
Rfer_2818	PWY-5789	3-hydroxypropanoate/4-hydroxybutanate cycle
Rfer_2818	PWY-6679	jadomycin biosynthesis
Rfer_2818	PWY-7388	octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)
Rfer_2828	PWY-5855	ubiquinol-7 biosynthesis (prokaryotic)
Rfer_2828	PWY-5856	ubiquinol-9 biosynthesis (prokaryotic)
Rfer_2828	PWY-5857	ubiquinol-10 biosynthesis (prokaryotic)
Rfer_2828	PWY-5870	ubiquinol-8 biosynthesis (eukaryotic)
Rfer_2828	PWY-5871	ubiquinol-9 biosynthesis (eukaryotic)
Rfer_2828	PWY-5872	ubiquinol-10 biosynthesis (eukaryotic)
Rfer_2828	PWY-5873	ubiquinol-7 biosynthesis (eukaryotic)
Rfer_2828	PWY-6708	ubiquinol-8 biosynthesis (prokaryotic)
Rfer_2828	PWY-7230	ubiquinol-6 biosynthesis from 4-aminobenzoate (eukaryotic)
Rfer_2828	PWY-7233	ubiquinol-6 bypass biosynthesis (eukaryotic)
Rfer_2829	PWY-181	photorespiration
Rfer_2844	PWY-6281	L-selenocysteine biosynthesis II (archaea and eukaryotes)
Rfer_2875	PWY-6891	thiazole biosynthesis II (Bacillus)
Rfer_2875	PWY-6892	thiazole biosynthesis I (E. coli)
Rfer_2875	PWY-7560	methylerythritol phosphate pathway II
Rfer_2883	PWY-5194	siroheme biosynthesis
Rfer_2883	PWY-7377	cob(II)yrinate <i>a,c</i>-diamide biosynthesis I (early cobalt insertion)
Rfer_2890	PWY-6936	seleno-amino acid biosynthesis
Rfer_2890	PWY-7274	D-cycloserine biosynthesis
Rfer_2892	PWY-2301	<i>myo</i>-inositol biosynthesis
Rfer_2892	PWY-4702	phytate degradation I
Rfer_2892	PWY-6363	D-<i>myo</i>-inositol (1,4,5)-trisphosphate degradation
Rfer_2899	PWY-7219	adenosine ribonucleotides <i>de novo</i> biosynthesis
Rfer_2910	PWY-5154	L-arginine biosynthesis III (via <i>N</i>-acetyl-L-citrulline)
Rfer_2916	PWY-2941	L-lysine biosynthesis II
Rfer_2916	PWY-2942	L-lysine biosynthesis III
Rfer_2916	PWY-5097	L-lysine biosynthesis VI
Rfer_2925	PWY-6163	chorismate biosynthesis from 3-dehydroquinate
Rfer_2926	PWY-6164	3-dehydroquinate biosynthesis I
Rfer_2944	PWY-6386	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis II (lysine-containing)
Rfer_2944	PWY-6387	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis I (<i>meso</i>-diaminopimelate containing)
Rfer_2961	PWY-5663	tetrahydrobiopterin biosynthesis I
Rfer_2961	PWY-5664	tetrahydrobiopterin biosynthesis II
Rfer_2961	PWY-6147	6-hydroxymethyl-dihydropterin diphosphate biosynthesis I
Rfer_2961	PWY-6703	preQ<sub>0</sub> biosynthesis
Rfer_2961	PWY-6983	tetrahydrobiopterin biosynthesis III
Rfer_2961	PWY-7442	drosopterin and aurodrosopterin biosynthesis
Rfer_2964	PWY-3781	aerobic respiration I (cytochrome c)
Rfer_2964	PWY-6692	Fe(II) oxidation
Rfer_2964	PWY-7082	ammonia oxidation IV (autotrophic ammonia oxidizers)
Rfer_2964	PWY-7279	aerobic respiration II (cytochrome c) (yeast)
Rfer_2974	PWY-1281	sulfoacetaldehyde degradation I
Rfer_2974	PWY-5482	pyruvate fermentation to acetate II
Rfer_2974	PWY-5485	pyruvate fermentation to acetate IV
Rfer_2974	PWY-5497	purine nucleobases degradation II (anaerobic)
Rfer_2974	PWY-6637	sulfolactate degradation II
Rfer_2975	PWY-5482	pyruvate fermentation to acetate II
Rfer_2975	PWY-5485	pyruvate fermentation to acetate IV
Rfer_2975	PWY-5497	purine nucleobases degradation II (anaerobic)
Rfer_2979	PWY-381	nitrate reduction II (assimilatory)
Rfer_2979	PWY-5675	nitrate reduction V (assimilatory)
Rfer_2979	PWY-6549	L-glutamine biosynthesis III
Rfer_2979	PWY-6963	ammonia assimilation cycle I
Rfer_2979	PWY-6964	ammonia assimilation cycle II
Rfer_2985	PWY-3841	folate transformations II
Rfer_2985	PWY-6614	tetrahydrofolate biosynthesis
Rfer_2986	PWY-3841	folate transformations II
Rfer_2986	PWY-7184	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis I
Rfer_2986	PWY-7187	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis II
Rfer_2986	PWY-7198	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis IV
Rfer_2986	PWY-7199	pyrimidine deoxyribonucleosides salvage
Rfer_2986	PWY-7210	pyrimidine deoxyribonucleotides biosynthesis from CTP
Rfer_2989	PWY-6386	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis II (lysine-containing)
Rfer_2989	PWY-6387	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis I (<i>meso</i>-diaminopimelate containing)
Rfer_2999	PWY-6749	CMP-legionaminate biosynthesis I
Rfer_3011	PWY-6545	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis III
Rfer_3011	PWY-7184	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis I
Rfer_3011	PWY-7198	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis IV
Rfer_3011	PWY-7210	pyrimidine deoxyribonucleotides biosynthesis from CTP
Rfer_3011	PWY-7220	adenosine deoxyribonucleotides <i>de novo</i> biosynthesis II
Rfer_3011	PWY-7222	guanosine deoxyribonucleotides <i>de novo</i> biosynthesis II
Rfer_3011	PWY-7226	guanosine deoxyribonucleotides <i>de novo</i> biosynthesis I
Rfer_3011	PWY-7227	adenosine deoxyribonucleotides <i>de novo</i> biosynthesis
Rfer_3015	PWY-5755	4-hydroxybenzoate biosynthesis II (microbes)
Rfer_3015	PWY-5870	ubiquinol-8 biosynthesis (eukaryotic)
Rfer_3015	PWY-6148	tetrahydromethanopterin biosynthesis
Rfer_3031	PWY-5316	nicotine biosynthesis
Rfer_3031	PWY-7342	superpathway of nicotine biosynthesis
Rfer_3032	PWY-5155	&beta;-alanine biosynthesis III
Rfer_3033	PWY-6654	phosphopantothenate biosynthesis III
Rfer_3084	PWY-7429	arsenite oxidation II (respiratory)
Rfer_3085	PWY-7429	arsenite oxidation II (respiratory)
Rfer_3106	PWY-5154	L-arginine biosynthesis III (via <i>N</i>-acetyl-L-citrulline)
Rfer_3108	PWY-6386	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis II (lysine-containing)
Rfer_3108	PWY-6387	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis I (<i>meso</i>-diaminopimelate containing)
Rfer_3147	PWY-7221	guanosine ribonucleotides <i>de novo</i> biosynthesis
Rfer_3151	PWY-6854	ethylene biosynthesis III (microbes)
Rfer_3157	PWY-1269	CMP-3-deoxy-D-<I>manno</I>-octulosonate biosynthesis I
Rfer_3157	PWY-5111	CMP-3-deoxy-D-<i>manno</i>-octulosonate biosynthesis II (from D-arabinose 5-phosphate)
Rfer_3158	PWY-7219	adenosine ribonucleotides <i>de novo</i> biosynthesis
Rfer_3160	PWY-5344	L-homocysteine biosynthesis
Rfer_3160	PWY-7174	<i>S</i>-methyl-5-thio-&alpha;-D-ribose 1-phosphate degradation II
Rfer_3161	PWY-6163	chorismate biosynthesis from 3-dehydroquinate
Rfer_3199	PWY-6748	nitrate reduction VII (denitrification)
Rfer_3199	PWY-7084	nitrifier denitrification
Rfer_3243	PWY-6281	L-selenocysteine biosynthesis II (archaea and eukaryotes)
Rfer_3248	PWY-7560	methylerythritol phosphate pathway II
Rfer_3269	PWY-1881	formate oxidation to CO<sub>2</sub>
Rfer_3269	PWY-5497	purine nucleobases degradation II (anaerobic)
Rfer_3269	PWY-6696	oxalate degradation III
Rfer_3293	PWY-7187	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis II
Rfer_3295	PWY-5497	purine nucleobases degradation II (anaerobic)
Rfer_3295	PWY-6606	guanosine nucleotides degradation II
Rfer_3295	PWY-6608	guanosine nucleotides degradation III
Rfer_3295	PWY-7442	drosopterin and aurodrosopterin biosynthesis
Rfer_3297	PWY-6610	adenine and adenosine salvage IV
Rfer_3314	PWY-5958	acridone alkaloid biosynthesis
Rfer_3314	PWY-6660	2-heptyl-3-hydroxy-4(1<i>H</i>)-quinolone biosynthesis
Rfer_3314	PWY-6661	4-hydroxy-2(1<i>H</i>)-quinolone biosynthesis
Rfer_3322	PWY-5101	L-isoleucine biosynthesis II
Rfer_3322	PWY-5103	L-isoleucine biosynthesis III
Rfer_3322	PWY-5104	L-isoleucine biosynthesis IV
Rfer_3322	PWY-5938	(<i>R</i>)-acetoin biosynthesis I
Rfer_3322	PWY-5939	(<i>R</i>)-acetoin biosynthesis II
Rfer_3322	PWY-6389	(<i>S</i>)-acetoin biosynthesis
Rfer_3322	PWY-7111	pyruvate fermentation to isobutanol (engineered)
Rfer_3323	PWY-5101	L-isoleucine biosynthesis II
Rfer_3323	PWY-5103	L-isoleucine biosynthesis III
Rfer_3323	PWY-5104	L-isoleucine biosynthesis IV
Rfer_3323	PWY-5938	(<i>R</i>)-acetoin biosynthesis I
Rfer_3323	PWY-5939	(<i>R</i>)-acetoin biosynthesis II
Rfer_3323	PWY-6389	(<i>S</i>)-acetoin biosynthesis
Rfer_3323	PWY-7111	pyruvate fermentation to isobutanol (engineered)
Rfer_3324	PWY-5101	L-isoleucine biosynthesis II
Rfer_3324	PWY-5103	L-isoleucine biosynthesis III
Rfer_3324	PWY-5104	L-isoleucine biosynthesis IV
Rfer_3324	PWY-7111	pyruvate fermentation to isobutanol (engineered)
Rfer_3325	PWY-5669	phosphatidylethanolamine biosynthesis I
Rfer_3347	PWY-6545	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis III
Rfer_3347	PWY-7184	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis I
Rfer_3347	PWY-7198	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis IV
Rfer_3347	PWY-7210	pyrimidine deoxyribonucleotides biosynthesis from CTP
Rfer_3347	PWY-7220	adenosine deoxyribonucleotides <i>de novo</i> biosynthesis II
Rfer_3347	PWY-7222	guanosine deoxyribonucleotides <i>de novo</i> biosynthesis II
Rfer_3347	PWY-7226	guanosine deoxyribonucleotides <i>de novo</i> biosynthesis I
Rfer_3347	PWY-7227	adenosine deoxyribonucleotides <i>de novo</i> biosynthesis
Rfer_3348	PWY-6545	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis III
Rfer_3348	PWY-7184	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis I
Rfer_3348	PWY-7198	pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis IV
Rfer_3348	PWY-7210	pyrimidine deoxyribonucleotides biosynthesis from CTP
Rfer_3348	PWY-7220	adenosine deoxyribonucleotides <i>de novo</i> biosynthesis II
Rfer_3348	PWY-7222	guanosine deoxyribonucleotides <i>de novo</i> biosynthesis II
Rfer_3348	PWY-7226	guanosine deoxyribonucleotides <i>de novo</i> biosynthesis I
Rfer_3348	PWY-7227	adenosine deoxyribonucleotides <i>de novo</i> biosynthesis
Rfer_3367	PWY-1269	CMP-3-deoxy-D-<I>manno</I>-octulosonate biosynthesis I
Rfer_3367	PWY-5111	CMP-3-deoxy-D-<i>manno</i>-octulosonate biosynthesis II (from D-arabinose 5-phosphate)
Rfer_3367	PWY-6164	3-dehydroquinate biosynthesis I
Rfer_3386	PWY-4041	&gamma;-glutamyl cycle
Rfer_3386	PWY-5826	hypoglycin biosynthesis
Rfer_3399	PWY-5704	urea degradation II
Rfer_3400	PWY-5704	urea degradation II
Rfer_3402	PWY-5704	urea degradation II
Rfer_3413	PWY-6163	chorismate biosynthesis from 3-dehydroquinate
Rfer_3423	PWY-6386	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis II (lysine-containing)
Rfer_3423	PWY-6387	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis I (<i>meso</i>-diaminopimelate containing)
Rfer_3424	PWY-6386	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis II (lysine-containing)
Rfer_3424	PWY-6387	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis I (<i>meso</i>-diaminopimelate containing)
Rfer_3425	PWY-5265	peptidoglycan biosynthesis II (staphylococci)
Rfer_3425	PWY-6385	peptidoglycan biosynthesis III (mycobacteria)
Rfer_3425	PWY-6470	peptidoglycan biosynthesis V (&beta;-lactam resistance)
Rfer_3425	PWY-6471	peptidoglycan biosynthesis IV (Enterococcus faecium)
Rfer_3427	PWY-6386	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis II (lysine-containing)
Rfer_3427	PWY-6387	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis I (<i>meso</i>-diaminopimelate containing)
Rfer_3428	PWY-5265	peptidoglycan biosynthesis II (staphylococci)
Rfer_3428	PWY-6470	peptidoglycan biosynthesis V (&beta;-lactam resistance)
Rfer_3428	PWY-6471	peptidoglycan biosynthesis IV (Enterococcus faecium)
Rfer_3429	PWY-6386	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis II (lysine-containing)
Rfer_3429	PWY-6387	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis I (<i>meso</i>-diaminopimelate containing)
Rfer_3444	PWY-2941	L-lysine biosynthesis II
Rfer_3444	PWY-5097	L-lysine biosynthesis VI
Rfer_3460	PWY-6936	seleno-amino acid biosynthesis
Rfer_3464	PWY-5686	UMP biosynthesis
Rfer_3487	PWY-6123	inosine-5'-phosphate biosynthesis I
Rfer_3487	PWY-6124	inosine-5'-phosphate biosynthesis II
Rfer_3487	PWY-7219	adenosine ribonucleotides <i>de novo</i> biosynthesis
Rfer_3487	PWY-7234	inosine-5'-phosphate biosynthesis III
Rfer_3515	PWY-5839	menaquinol-7 biosynthesis
Rfer_3515	PWY-5844	menaquinol-9 biosynthesis
Rfer_3515	PWY-5849	menaquinol-6 biosynthesis
Rfer_3515	PWY-5890	menaquinol-10 biosynthesis
Rfer_3515	PWY-5891	menaquinol-11 biosynthesis
Rfer_3515	PWY-5892	menaquinol-12 biosynthesis
Rfer_3515	PWY-5895	menaquinol-13 biosynthesis
Rfer_3517	PWY-1361	benzoyl-CoA degradation I (aerobic)
Rfer_3517	PWY-5109	2-methylbutanoate biosynthesis
Rfer_3517	PWY-5136	fatty acid &beta;-oxidation II (peroxisome)
Rfer_3517	PWY-5138	unsaturated, even numbered fatty acid &beta;-oxidation
Rfer_3517	PWY-5177	glutaryl-CoA degradation
Rfer_3517	PWY-5789	3-hydroxypropanoate/4-hydroxybutanate cycle
Rfer_3517	PWY-6435	4-hydroxybenzoate biosynthesis V
Rfer_3517	PWY-6583	pyruvate fermentation to butanol I
Rfer_3517	PWY-6863	pyruvate fermentation to hexanol
Rfer_3517	PWY-6883	pyruvate fermentation to butanol II
Rfer_3517	PWY-6944	androstenedione degradation
Rfer_3517	PWY-6945	cholesterol degradation to androstenedione I (cholesterol oxidase)
Rfer_3517	PWY-6946	cholesterol degradation to androstenedione II (cholesterol dehydrogenase)
Rfer_3517	PWY-7007	methyl ketone biosynthesis
Rfer_3517	PWY-7046	4-coumarate degradation (anaerobic)
Rfer_3517	PWY-7094	fatty acid salvage
Rfer_3517	PWY-7216	(R)- and (S)-3-hydroxybutanoate biosynthesis
Rfer_3517	PWY-735	jasmonic acid biosynthesis
Rfer_3517	PWY-7401	crotonate fermentation (to acetate and cyclohexane carboxylate)
Rfer_3524	PWY-5154	L-arginine biosynthesis III (via <i>N</i>-acetyl-L-citrulline)
Rfer_3524	PWY-7400	L-arginine biosynthesis IV (archaebacteria)
Rfer_3554	PWY-5046	2-oxoisovalerate decarboxylation to isobutanoyl-CoA
Rfer_3569	PWY-6617	adenosine nucleotides degradation III
Rfer_3571	PWY-6840	homoglutathione biosynthesis
Rfer_3571	PWY-7255	ergothioneine biosynthesis I (bacteria)
Rfer_3581	PWY-6728	methylaspartate cycle
Rfer_3581	PWY-6969	TCA cycle V (2-oxoglutarate:ferredoxin oxidoreductase)
Rfer_3581	PWY-7118	chitin degradation to ethanol
Rfer_3581	PWY-7294	xylose degradation IV
Rfer_3581	PWY-7295	L-arabinose degradation IV
Rfer_3582	PWY-7425	2-chloroacrylate degradation I
Rfer_3605	PWY-5958	acridone alkaloid biosynthesis
Rfer_3605	PWY-6660	2-heptyl-3-hydroxy-4(1<i>H</i>)-quinolone biosynthesis
Rfer_3605	PWY-6661	4-hydroxy-2(1<i>H</i>)-quinolone biosynthesis
Rfer_3607	PWY-5958	acridone alkaloid biosynthesis
Rfer_3607	PWY-6660	2-heptyl-3-hydroxy-4(1<i>H</i>)-quinolone biosynthesis
Rfer_3607	PWY-6661	4-hydroxy-2(1<i>H</i>)-quinolone biosynthesis
Rfer_3611	PWY-181	photorespiration
Rfer_3612	PWY-5743	3-hydroxypropanoate cycle
Rfer_3612	PWY-5789	3-hydroxypropanoate/4-hydroxybutanate cycle
Rfer_3612	PWY-6728	methylaspartate cycle
Rfer_3612	PWY-7384	anaerobic energy metabolism (invertebrates, mitochondrial)
Rfer_3614	PWY-3961	phosphopantothenate biosynthesis II
Rfer_3631	PWY-5350	thiosulfate disproportionation III (rhodanese)
Rfer_3635	PWY-5674	nitrate reduction IV (dissimilatory)
Rfer_3650	PWY-6891	thiazole biosynthesis II (Bacillus)
Rfer_3650	PWY-6892	thiazole biosynthesis I (E. coli)
Rfer_3650	PWY-7560	methylerythritol phosphate pathway II
Rfer_3664	PWY-4621	arsenate detoxification II (glutaredoxin)
Rfer_3670	PWY-4261	glycerol degradation I
Rfer_3670	PWY-6118	glycerol-3-phosphate shuttle
Rfer_3670	PWY-6952	glycerophosphodiester degradation
Rfer_3678	PWY-4261	glycerol degradation I
Rfer_3679	PWY-3341	L-proline biosynthesis III
Rfer_3679	PWY-4981	L-proline biosynthesis II (from arginine)
Rfer_3679	PWY-6344	L-ornithine degradation II (Stickland reaction)
Rfer_3690	PWY-1042	glycolysis IV (plant cytosol)
Rfer_3690	PWY-5484	glycolysis II (from fructose 6-phosphate)
Rfer_3690	PWY-6886	1-butanol autotrophic biosynthesis
Rfer_3690	PWY-6901	superpathway of glucose and xylose degradation
Rfer_3690	PWY-7003	glycerol degradation to butanol
Rfer_3691	PWY-6832	2-aminoethylphosphonate degradation II
Rfer_3727	PWY-6386	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis II (lysine-containing)
Rfer_3727	PWY-6387	UDP-<i>N</i>-acetylmuramoyl-pentapeptide biosynthesis I (<i>meso</i>-diaminopimelate containing)
Rfer_3746	PWY-6167	flavin biosynthesis II (archaea)
Rfer_3749	PWY-4361	<i>S</i>-methyl-5-thio-&alpha;-D-ribose 1-phosphate degradation
Rfer_3749	PWY-7174	<i>S</i>-methyl-5-thio-&alpha;-D-ribose 1-phosphate degradation II
Rfer_3776	PWY-5686	UMP biosynthesis
Rfer_3801	PWY-5265	peptidoglycan biosynthesis II (staphylococci)
Rfer_3801	PWY-6471	peptidoglycan biosynthesis IV (Enterococcus faecium)
Rfer_3805	PWY-5188	tetrapyrrole biosynthesis I (from glutamate)
Rfer_3805	PWY-5189	tetrapyrrole biosynthesis II (from glycine)
Rfer_3824	PWY-5074	mevalonate degradation
Rfer_3832	PWY-4381	fatty acid biosynthesis initiation I
Rfer_3832	PWY-5743	3-hydroxypropanoate cycle
Rfer_3832	PWY-5744	glyoxylate assimilation
Rfer_3832	PWY-5789	3-hydroxypropanoate/4-hydroxybutanate cycle
Rfer_3832	PWY-6679	jadomycin biosynthesis
Rfer_3832	PWY-7388	octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)
Rfer_3841	PWY-241	C4 photosynthetic carbon assimilation cycle, NADP-ME type
Rfer_3841	PWY-6142	gluconeogenesis II (<i>Methanobacterium thermoautotrophicum</i>)
Rfer_3841	PWY-7115	C4 photosynthetic carbon assimilation cycle, NAD-ME type
Rfer_3841	PWY-7117	C4 photosynthetic carbon assimilation cycle, PEPCK type
Rfer_3846	PWY-5392	reductive TCA cycle II
Rfer_3846	PWY-561	superpathway of glyoxylate cycle and fatty acid degradation
Rfer_3846	PWY-5690	TCA cycle II (plants and fungi)
Rfer_3846	PWY-5913	TCA cycle VI (obligate autotrophs)
Rfer_3846	PWY-6728	methylaspartate cycle
Rfer_3846	PWY-6969	TCA cycle V (2-oxoglutarate:ferredoxin oxidoreductase)
Rfer_3846	PWY-7254	TCA cycle VII (acetate-producers)
Rfer_3846	PWY-7384	anaerobic energy metabolism (invertebrates, mitochondrial)
Rfer_3857	PWY-5382	hydrogen oxidation II (aerobic, NAD)
Rfer_3857	PWY-6758	hydrogen production II
Rfer_3874	PWY-6478	GDP-D-<i>glycero</i>-&alpha;-D-<i>manno</i>-heptose biosynthesis
Rfer_3879	PWY-7383	anaerobic energy metabolism (invertebrates, cytosol)
Rfer_3880	PWY-5041	<i>S</i>-adenosyl-L-methionine cycle II
Rfer_3880	PWY-5912	2'-deoxymugineic acid phytosiderophore biosynthesis
Rfer_3884	PWY-31	canavanine degradation
Rfer_3884	PWY-4984	urea cycle
Rfer_3884	PWY-6305	putrescine biosynthesis IV
Rfer_3884	PWY-6922	L-<i>N<sup>&delta;</sup></i>-acetylornithine biosynthesis
Rfer_3895	PWY-5941	glycogen degradation II (eukaryotic)
Rfer_3895	PWY-622	starch biosynthesis
Rfer_3895	PWY-6731	starch degradation III
Rfer_3895	PWY-6737	starch degradation V
Rfer_3895	PWY-7238	sucrose biosynthesis II
Rfer_3899	PWY-4381	fatty acid biosynthesis initiation I
Rfer_3899	PWY-5743	3-hydroxypropanoate cycle
Rfer_3899	PWY-5744	glyoxylate assimilation
Rfer_3899	PWY-5789	3-hydroxypropanoate/4-hydroxybutanate cycle
Rfer_3899	PWY-6679	jadomycin biosynthesis
Rfer_3899	PWY-7388	octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)
Rfer_3918	PWY-3722	glycine betaine biosynthesis II (Gram-positive bacteria)
Rfer_3918	PWY-7494	choline degradation IV
Rfer_3925	PWY-5921	glutaminyl-tRNA<sup>gln</sup> biosynthesis via transamidation
Rfer_3928	PWY-5686	UMP biosynthesis
Rfer_3934	PWY-6987	lipoate biosynthesis and incorporation III (Bacillus)
Rfer_3934	PWY-7381	lipoate biosynthesis and incorporation (glycine cleavage system, yeast)
Rfer_3934	PWY-7382	lipoate biosynthesis and incorporation (pyruvate dehydrogenase and oxoglutarate dehydrogenase, yeast)
Rfer_3935	PWY-6987	lipoate biosynthesis and incorporation III (Bacillus)
Rfer_3935	PWY-7381	lipoate biosynthesis and incorporation (glycine cleavage system, yeast)
Rfer_3944	PWY-5392	reductive TCA cycle II
Rfer_3944	PWY-5537	pyruvate fermentation to acetate V
Rfer_3944	PWY-5538	pyruvate fermentation to acetate VI
Rfer_3944	PWY-5690	TCA cycle II (plants and fungi)
Rfer_3944	PWY-5913	TCA cycle VI (obligate autotrophs)
Rfer_3944	PWY-6728	methylaspartate cycle
Rfer_3944	PWY-6969	TCA cycle V (2-oxoglutarate:ferredoxin oxidoreductase)
Rfer_3944	PWY-7384	anaerobic energy metabolism (invertebrates, mitochondrial)
Rfer_3945	PWY-5392	reductive TCA cycle II
Rfer_3945	PWY-5537	pyruvate fermentation to acetate V
Rfer_3945	PWY-5538	pyruvate fermentation to acetate VI
Rfer_3945	PWY-5690	TCA cycle II (plants and fungi)
Rfer_3945	PWY-5913	TCA cycle VI (obligate autotrophs)
Rfer_3945	PWY-6728	methylaspartate cycle
Rfer_3945	PWY-6969	TCA cycle V (2-oxoglutarate:ferredoxin oxidoreductase)
Rfer_3945	PWY-7384	anaerobic energy metabolism (invertebrates, mitochondrial)
Rfer_3946	PWY-5154	L-arginine biosynthesis III (via <i>N</i>-acetyl-L-citrulline)
Rfer_3946	PWY-7400	L-arginine biosynthesis IV (archaebacteria)
Rfer_3953	PWY-6987	lipoate biosynthesis and incorporation III (Bacillus)
Rfer_3953	PWY-7381	lipoate biosynthesis and incorporation (glycine cleavage system, yeast)
Rfer_3954	PWY-6424	Rfer_3954|Rfer_3954|REF_jgi:Rfer_3954|GeneID:3961594
Rfer_3974	PWY-4381	fatty acid biosynthesis initiation I
Rfer_3988	PWY-5971	palmitate biosynthesis II (bacteria and plants)
Rfer_3988	PWY-5973	<i>cis</i>-vaccenate biosynthesis
Rfer_3988	PWY-5989	stearate biosynthesis II (bacteria and plants)
Rfer_3988	PWY-5994	palmitate biosynthesis I (animals and fungi)
Rfer_3988	PWY-6113	superpathway of mycolate biosynthesis
Rfer_3988	PWY-6282	palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate)
Rfer_3988	PWY-6519	8-amino-7-oxononanoate biosynthesis I
Rfer_3988	PWY-7388	octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)
Rfer_3988	PWYG-321	mycolate biosynthesis
Rfer_4002	PWY-5971	palmitate biosynthesis II (bacteria and plants)
Rfer_4002	PWY-5973	<i>cis</i>-vaccenate biosynthesis
Rfer_4002	PWY-5989	stearate biosynthesis II (bacteria and plants)
Rfer_4002	PWY-5994	palmitate biosynthesis I (animals and fungi)
Rfer_4002	PWY-6113	superpathway of mycolate biosynthesis
Rfer_4002	PWY-6282	palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate)
Rfer_4002	PWY-6519	8-amino-7-oxononanoate biosynthesis I
Rfer_4002	PWY-7388	octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)
Rfer_4002	PWYG-321	mycolate biosynthesis
Rfer_4034	PWY-7268	NAD/NADP-NADH/NADPH cytosolic interconversion (yeast)
Rfer_4047	PWY-5367	petroselinate biosynthesis
Rfer_4047	PWY-5971	palmitate biosynthesis II (bacteria and plants)
Rfer_4047	PWY-5973	<i>cis</i>-vaccenate biosynthesis
Rfer_4047	PWY-5989	stearate biosynthesis II (bacteria and plants)
Rfer_4047	PWY-5994	palmitate biosynthesis I (animals and fungi)
Rfer_4047	PWY-6113	superpathway of mycolate biosynthesis
Rfer_4047	PWY-6282	palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate)
Rfer_4047	PWY-6519	8-amino-7-oxononanoate biosynthesis I
Rfer_4047	PWY-6951	Rfer_4047|Rfer_4047|REF_jgi:Rfer_4047|GeneID:3961726
Rfer_4047	PWY-7053	docosahexaenoate biosynthesis I (lower eukaryotes)
Rfer_4047	PWY-7388	octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)
Rfer_4047	PWYG-321	mycolate biosynthesis
Rfer_4049	PWY-6123	inosine-5'-phosphate biosynthesis I
Rfer_4049	PWY-6124	inosine-5'-phosphate biosynthesis II
Rfer_4049	PWY-7219	adenosine ribonucleotides <i>de novo</i> biosynthesis
Rfer_4049	PWY-7234	inosine-5'-phosphate biosynthesis III
Rfer_4073	PWY-5674	nitrate reduction IV (dissimilatory)
Rfer_4082	PWY-5674	nitrate reduction IV (dissimilatory)
Rfer_4109	PWY-1801	formaldehyde oxidation II (glutathione-dependent)
Rfer_4111	PWY-1042	glycolysis IV (plant cytosol)
Rfer_4111	PWY-5484	glycolysis II (from fructose 6-phosphate)
Rfer_4111	PWY-6901	superpathway of glucose and xylose degradation
Rfer_4111	PWY-7003	glycerol degradation to butanol
Rfer_4112	PWY-1861	formaldehyde assimilation II (RuMP Cycle)
Rfer_4112	PWY-5723	Rubisco shunt
Rfer_4112	PWY-6891	thiazole biosynthesis II (Bacillus)
Rfer_4112	PWY-6892	thiazole biosynthesis I (E. coli)
Rfer_4112	PWY-6901	superpathway of glucose and xylose degradation
Rfer_4112	PWY-7560	methylerythritol phosphate pathway II
Rfer_4127	PWY-3781	aerobic respiration I (cytochrome c)
Rfer_4127	PWY-4521	arsenite oxidation I (respiratory)
Rfer_4127	PWY-6692	Fe(II) oxidation
Rfer_4127	PWY-7279	aerobic respiration II (cytochrome c) (yeast)
Rfer_4164	PWY-5155	&beta;-alanine biosynthesis III
Rfer_4236	PWY-1269	CMP-3-deoxy-D-<I>manno</I>-octulosonate biosynthesis I
Rfer_4236	PWY-5111	CMP-3-deoxy-D-<i>manno</i>-octulosonate biosynthesis II (from D-arabinose 5-phosphate)
Rfer_4239	PWY-6605	adenine and adenosine salvage II
Rfer_4239	PWY-6610	adenine and adenosine salvage IV