3.4.99.1	acrocylindricum proteinase	transferred to EC 3.4.23.28	
3.4.99.2	agavain	deleted	
3.4.99.3	angiotensinase	deleted	
3.4.99.32	Armillaria mellea neutral proteinase	transferred to EC 3.4.24.20	
3.4.99.4	aspartylendopeptidase	transferred to EC 3.4.23.12	
3.4.99.13	beta-lytic proteinase (Mycobacterium sorangium)	transferred to EC 3.4.24.32	
3.4.99.33	cathepsin R	deleted	
3.4.99.5	Clostridium histolyticum collagenase 2	transferred to EC 3.4.24.3	
3.4.99.6	crayfish low-molecular-weight proteinase	transferred to EC 3.4.24.21	
3.4.99.B2	D-aspartyl endopeptidase	preliminary BRENDA-supplied EC number	
3.4.99.27	Echis carinatus prothrombin-activating proteinase	deleted	
3.4.99.7	euphorbain	deleted	
3.4.99.8	Gliocladium proteinase	deleted	
3.4.99.9	hurain	deleted	
3.4.99.10	insulinase	transferred to EC 3.4.24.56	
3.4.99.45	insulinase	transferred to EC 3.4.24.56	
3.4.99.36	leader peptidase	transferred to EC 3.4.21.89	
3.4.99.42	leucyllysine endopeptidase	deleted	
3.4.99.14	mexicanain	deleted	
3.4.99.41	mitochondrial processing peptidase	transferred to EC 3.4.24.64	
3.4.99.46	multicatalytic endopeptidase complex	transferred to EC 3.4.25.1	
3.4.99.34	mytilidase	deleted	
3.4.99.29	Myxobacter AL-1 proteinase I	deleted	
3.4.99.30	Myxobacter AL-1 proteinase II	transferred to EC 3.4.24.20	
3.4.99.28	Oxyuranus scutellatus prothrombin-activating proteinase	transferred to EC 3.4.21.60	
3.4.99.15	Paecilomyces proteinase	deleted	
3.4.99.16	Penicillium notatum extracellular proteinase	deleted	
3.4.99.17	peptidoglycan endopeptidase	deleted	
3.4.99.18	pinguinain	deleted	
3.4.99.44	pitrilysin	transferred to EC 3.4.24.55	
3.4.99.35	premurein-leader peptidase	transferred to EC 3.4.23.36	
3.4.99.40	pro-gonadoliberin proteinase	deleted	
3.4.99.38	pro-opiomelanotropin-converting proteinase	transferred to EC 3.4.23.17	
3.4.99.39	pseudomurein endopeptidase	deleted	
3.4.99.B1	RCE1	preliminary BRENDA-supplied EC number	
3.4.99.37	RecA peptidase	deleted	
3.4.99.19	renin	transferred to EC 3.4.23.15	
3.4.99.20	scopulariopsis proteinase	deleted	
3.4.99.21	solanain	deleted	
3.4.99.22	staphylokinase	transferred to EC 3.4.24.29	
3.4.99.11	Streptomyces alkalophilic keratinase	deleted	
3.4.99.23	tabernamontanain	deleted	
3.4.99.24	Tenebrio alpha-proteinase	deleted	
3.4.99.43	thermopsin	transferred to EC 3.4.23.42	
3.4.99.31	Tissue endopeptidase degrading collagenase synthetic substrate	transferred to EC 3.4.24.15	
3.4.99.25	trametes acid proteinase	transferred to EC 3.4.23.21	
3.4.99.12	Trichophyton mentagrophytes keratinase	deleted	
3.4.99.26	urokinase	transferred to EC 3.4.21.7, EC 3.4.21.68