1.3.99.1	succinate dehydrogenase	deleted, now included with EC 1.3.5.1, succinate dehydrogenase (quinone)	
1.3.99.10	isovaleryl-CoA dehydrogenase	transferred to EC 1.3.8.4	
1.3.99.11	dihydroorotate dehydrogenase	transferred to EC 1.3.5.2	
1.3.99.12	2-methylacyl-CoA dehydrogenase	deleted. Now classified as EC 1.3.8.5, 2-methyl-branched-chain-enoyl-CoA reductase	
1.3.99.13	long-chain-acyl-CoA dehydrogenase	transferred to EC 1.3.8.8, long-chain-acyl-CoA dehydrogenase	
1.3.99.14	cyclohexanone dehydrogenase	-	
1.3.99.15	benzoyl-CoA reductase	transferred to EC 1.3.7.8	
1.3.99.16	Isoquinoline 1-oxidoreductase	-	
1.3.99.17	quinoline 2-oxidoreductase	-	
1.3.99.18	quinaldate 4-oxidoreductase	-	
1.3.99.19	quinoline-4-carboxylate 2-oxidoreductase	-	
1.3.99.2	butyryl-CoA dehydrogenase	transferred to EC 1.3.8.1	
1.3.99.20	4-hydroxybenzoyl-CoA reductase	transferred to EC 1.3.7.9	
1.3.99.21	(R)-benzylsuccinyl-CoA dehydrogenase	transferred to EC 1.3.8.3	
1.3.99.22	coproporphyrinogen dehydrogenase	transferred to EC 1.3.98.3	
1.3.99.23	all-trans-retinol 13,14-reductase	-	
1.3.99.24	2-amino-4-deoxychorismate dehydrogenase	transferred to EC 1.3.8.16	
1.3.99.25	carvone reductase	-	
1.3.99.26	all-trans-zeta-carotene desaturase	-	
1.3.99.27	1-hydroxycarotenoid 3,4-desaturase	-	
1.3.99.28	phytoene desaturase (neurosporene-forming)	-	
1.3.99.29	phytoene desaturase (zeta-carotene-forming)	-	
1.3.99.3	acyl-CoA dehydrogenase	transferred to EC 1.3.8.7, medium-chain acyl-CoA dehydrogenase, EC 1.3.8.8, long-chain acyl-CoA dehydrogenase, EC 1.3.8.9, very-long-chain acyl-CoA dehydrogenase	
1.3.99.30	phytoene desaturase (3,4-didehydrolycopene-forming)	-	
1.3.99.31	phytoene desaturase (lycopene-forming)	-	
1.3.99.32	glutaryl-CoA dehydrogenase (acceptor)	-	
1.3.99.33	urocanate reductase	-	
1.3.99.34	2,3-bis-O-geranylgeranyl-sn-glycerol 1-phosphate reductase (donor)	transferred to EC 1.3.7.11	
1.3.99.35	chlorophyllide a reductase	transferred to EC 1.3.7.15	
1.3.99.36	cypemycin cysteine dehydrogenase (decarboxylating)	-	
1.3.99.37	1-hydroxy-2-isopentenylcarotenoid 3,4-desaturase	-	
1.3.99.38	menaquinone-9 beta-reductase	-	
1.3.99.39	carotenoid phi-ring synthase	-	
1.3.99.4	3-oxosteroid 1-dehydrogenase	-	
1.3.99.40	carotenoid chi-ring synthase	-	
1.3.99.41	3-(methylsulfanyl)propanoyl-CoA 2-dehydrogenase	-	
1.3.99.5	3-oxo-5alpha-steroid 4-dehydrogenase (acceptor)	-	
1.3.99.6	3-oxo-5beta-steroid 4-dehydrogenase	-	
1.3.99.7	glutaryl-CoA dehydrogenase	transferred to EC 1.3.8.6	
1.3.99.8	2-furoyl-CoA dehydrogenase	-	
1.3.99.9	beta-cyclopiazonate dehydrogenase	transferred to EC 1.21.99.1	
1.3.99.B12	menaquinone-7 reductase (acceptor)	preliminary BRENDA-supplied EC number	
1.3.99.B13	3-(methylthio)propionyl-CoA dehydrogenase	deleted, replaced by EC 1.3.99.41	
1.3.99.B15	dolichyl phosphate omega-isoprene reductase	preliminary BRENDA-supplied EC number	
1.3.99.B16	3-phenylpropionyl-CoA dehydrogenase	preliminary BRENDA-supplied EC number	
1.3.99.B2	citronellyl-CoA dehydrogenase	preliminary BRENDA-supplied EC number