 1. Oxidoreductases
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2. Transferases
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 3. Hydrolases
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3.1 Acting on ester bonds
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3.2 Glycosylases
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3.3 Acting on ether bonds
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3.4 Acting on peptide bonds (peptidases)
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3.4.11 Aminopeptidases
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3.4.13 Dipeptidases
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3.4.14 Dipeptidyl-peptidases and tripeptidyl-peptidases
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3.4.15 Peptidyl-dipeptidases
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3.4.16 Serine-type carboxypeptidases
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3.4.17 Metallocarboxypeptidases
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3.4.18 Cysteine-type carboxypeptidases
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3.4.19 Omega peptidases
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3.4.19.1 acylaminoacyl-peptidase
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 3.4.19.2 peptidyl-glycinamidase
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3.4.19.3 pyroglutamyl-peptidase I
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3.4.19.5 beta-aspartyl-peptidase
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3.4.19.6 pyroglutamyl-peptidase II
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3.4.19.7 N-formylmethionyl-peptidase
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3.4.19.9 folate gamma-glutamyl hydrolase
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3.4.19.11 gamma-D-glutamyl-meso-diaminopimelate peptidase
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3.4.19.12 ubiquitinyl hydrolase 1
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K01309 MINDY1_2; ubiquitin carboxyl-terminal hydrolase MINDY-1/2 [EC:3.4.19.12]
K05609 UCHL3, YUH1; ubiquitin carboxyl-terminal hydrolase L3 [EC:3.4.19.12]
K05610 UCHL5, UCH37; ubiquitin carboxyl-terminal hydrolase L5 [EC:3.4.19.12]
K05611 UCHL1; ubiquitin carboxyl-terminal hydrolase L1 [EC:3.4.19.12]
K08588 BAP1, UCHL2; ubiquitin carboxyl-terminal hydrolase BAP1 [EC:3.4.19.12]
K08601 CYLD, USLP2; ubiquitin carboxyl-terminal hydrolase CYLD [EC:3.4.19.12]
K09602 OTUB1; ubiquitin thioesterase protein OTUB1 [EC:3.4.19.12]
K09603 OTUB2; ubiquitin thioesterase protein OTUB2 [EC:3.4.19.12]
K11366 USP22_27_51, UBP8; ubiquitin carboxyl-terminal hydrolase 22/27/51 [EC:3.4.19.12]
K11832 USP1; ubiquitin carboxyl-terminal hydrolase 1 [EC:3.4.19.12]
K11833 USP2; ubiquitin carboxyl-terminal hydrolase 2 [EC:3.4.19.12]
K11834 USP44_49; ubiquitin carboxyl-terminal hydrolase 44/49 [EC:3.4.19.12]
K11835 USP4_11, UBP12; ubiquitin carboxyl-terminal hydrolase 4/11 [EC:3.4.19.12]
K11836 USP5_13, UBP14; ubiquitin carboxyl-terminal hydrolase 5/13 [EC:3.4.19.12]
K11837 USP6_32; ubiquitin carboxyl-terminal hydrolase 6/32 [EC:3.4.19.12]
K11838 USP7, UBP15; ubiquitin carboxyl-terminal hydrolase 7 [EC:3.4.19.12]
K11839 USP8, UBP5; ubiquitin carboxyl-terminal hydrolase 8 [EC:3.4.19.12]
K11840 USP9_24; ubiquitin carboxyl-terminal hydrolase 9/24 [EC:3.4.19.12]
K11841 USP10, UBP3; ubiquitin carboxyl-terminal hydrolase 10 [EC:3.4.19.12]
K11842 USP12_46; ubiquitin carboxyl-terminal hydrolase 12/46 [EC:3.4.19.12]
K11843 USP14, UBP6; ubiquitin carboxyl-terminal hydrolase 14 [EC:3.4.19.12]
K11844 USP16_45; ubiquitin carboxyl-terminal hydrolase 16/45 [EC:3.4.19.12]
K11845 USP17, DUB3; ubiquitin carboxyl-terminal hydrolase 17 [EC:3.4.19.12]
K11846 USP18_41; ubiquitin carboxyl-terminal hydrolase 18/41 [EC:3.4.19.12]
K11847 USP19; ubiquitin carboxyl-terminal hydrolase 19 [EC:3.4.19.12]
K11848 USP20_33; ubiquitin carboxyl-terminal hydrolase 20/33 [EC:3.4.19.12]
K11849 USP25; ubiquitin carboxyl-terminal hydrolase 25 [EC:3.4.19.12]
K11850 USP26_29_37; ubiquitin carboxyl-terminal hydrolase 26/29/37 [EC:3.4.19.12]
K11851 USP30; ubiquitin carboxyl-terminal hydrolase 30 [EC:3.4.19.12]
K11852 USP31; ubiquitin carboxyl-terminal hydrolase 31 [EC:3.4.19.12]
K11853 USP34; ubiquitin carboxyl-terminal hydrolase 34 [EC:3.4.19.12]
K11854 USP35_38; ubiquitin carboxyl-terminal hydrolase 35/38 [EC:3.4.19.12]
K11855 USP36_42; ubiquitin carboxyl-terminal hydrolase 36/42 [EC:3.4.19.12]
K11856 USP43; ubiquitin carboxyl-terminal hydrolase 43 [EC:3.4.19.12]
K11857 USP47; ubiquitin carboxyl-terminal hydrolase 47 [EC:3.4.19.12]
K11858 USP48; ubiquitin carboxyl-terminal hydrolase 48 [EC:3.4.19.12]
K11859 TNFAIP3, A20, OTUD7C; tumor necrosis factor, alpha-induced protein 3 [EC:3.4.19.12]
K11860 OTUD7A_B; OTU domain-containing protein 7 [EC:3.4.19.12]
K11861 VCPIP1, VCIP135; deubiquitinating protein VCIP135 [EC:3.4.19.12]
K11862 ZRANB1, TRABID; ubiquitin thioesterase ZRANB1 [EC:3.4.19.12]
K11866 STAMBP, AMSH; STAM-binding protein [EC:3.4.19.12]
K11867 STAMBPL1; AMSH-like protease [EC:3.4.19.12]
K11869 USP40; ubiquitin carboxyl-terminal hydrolase 40 [EC:3.4.19.12]
K11870 UBP1; ubiquitin carboxyl-terminal hydrolase 1 [EC:3.4.19.12]
K11871 UBP7_11; ubiquitin carboxyl-terminal hydrolase 7/11 [EC:3.4.19.12]
K11872 UBP9_13; ubiquitin carboxyl-terminal hydrolase 9/13 [EC:3.4.19.12]
K11873 UBP10; ubiquitin carboxyl-terminal hydrolase 10 [EC:3.4.19.12]
K11874 UBP16; ubiquitin carboxyl-terminal hydrolase 16 [EC:3.4.19.12]
K11986 USP3; ubiquitin carboxyl-terminal hydrolase 3 [EC:3.4.19.12]
K12655 OTUD5, DUBA; OTU domain-containing protein 5 [EC:3.4.19.12]
K13716 OTUD1; OTU domain-containing protein 1 [EC:3.4.19.12]
K13717 OTUD3; OTU domain-containing protein 3 [EC:3.4.19.12]
K13718 OTUD4; OTU domain-containing protein 4 [EC:3.4.19.12]
K15235 JOSD; josephin [EC:3.4.19.12]
K18342 OTUD6; OTU domain-containing protein 6 [EC:3.4.19.12]
K18343 OTULIN; ubiquitin thioesterase otulin [EC:3.4.19.12]
K21075 UL36, UL48; Herpesviridae large tegument protein deneddylase [EC:3.4.19.12 3.4.22.-]
K21122 USP28; ubiquitin carboxyl-terminal hydrolase 28 [EC:3.4.19.12]
K21343 USP15; ubiquitin carboxyl-terminal hydrolase 15 [EC:3.4.19.12]
K21634 USP21; ubiquitin carboxyl-terminal hydrolase 21 [EC:3.4.19.12]
K22647 MINDY3_4; ubiquitin carboxyl-terminal hydrolase MINDY-3/4 [EC:3.4.19.12]
K22763 DESI2, PPPDE1; deubiquitinase DESI2 [EC:3.4.19.12]
K22972 BPLF1; Lymphocryptovirus large tegment protein deneddylase [EC:3.4.19.12]
K24134 ZUP1, ZUFSP; zinc finger-containing ubiquitin peptidase 1 [EC:3.4.19.12]
K25013 nsp3; SARS coronavirus non-structural protein 3 [EC:3.4.19.12]
K25347 L; Orthonairovirus RNA-dependent RNA polymerase L [EC:2.7.7.48 3.4.19.12]
K25924 nsP3; Alphacoronavirus papain-like proteinase 1/2 [EC:3.4.19.12 3.4.22.-]
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3.4.19.13 glutathione gamma-glutamate hydrolase
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3.4.19.14 leukotriene-C4 hydrolase
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3.4.19.15 desampylase
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3.4.19.16 glucosinolate gamma-glutamyl hydrolase
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3.4.21 Serine endopeptidases
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3.4.22 Cysteine endopeptidases
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3.4.23 Aspartic endopeptidases
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3.4.24 Metalloendopeptidases
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3.4.25 Threonine endopeptidases
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3.4.26 Glutamic endopeptidases
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3.5 Acting on carbon-nitrogen bonds, other than peptide bonds
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3.6 Acting on acid anhydrides
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3.7 Acting on carbon-carbon bonds
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3.8 Acting on halide bonds
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3.9 Acting on phosphorus-nitrogen bonds
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3.10 Acting on sulfur-nitrogen bonds
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3.11 Acting on carbon-phosphorus bonds
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3.12 Acting on sulfur-sulfur bonds
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3.13 Acting on carbon-sulfur bonds
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4. Lyases
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5. Isomerases
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6. Ligases
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7. Translocases
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Enzymes