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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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YPL191C MIY2; ubiquitinyl hydrolase 1
YGL082W uncharacterized protein
YJR099W YUH1; ubiquitin-specific protease YUH1
YMR223W UBP8; ubiquitin-specific protease UBP8
YJL197W UBP12; putative ubiquitin-specific protease UBP12
YBR058C UBP14; ubiquitin-specific protease UBP14
YMR304W UBP15; ubiquitin-specific protease UBP15
YDR069C DOA4; ubiquitin-specific protease DOA4
YER144C UBP5; putative ubiquitin-specific protease UBP5
YER151C UBP3; mRNA-binding ubiquitin-specific protease UBP3
YFR010W UBP6; ubiquitin-specific protease UBP6
YOR124C UBP2; ubiquitin-specific protease UBP2
YDL122W UBP1; ubiquitin-specific protease UBP1
YKR098C UBP11; ubiquitin-specific protease UBP11
YIL156W UBP7; ubiquitin-specific protease UBP7
YER098W UBP9; putative ubiquitin-specific protease UBP9
YBL067C UBP13; ubiquitin-specific protease UBP13
YNL186W UBP10; ubiquitin-specific protease UBP10
YPL072W UBP16; putative ubiquitin-specific protease UBP16
YHL013C OTU2; Otu2p
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K01309 MINDY1_2; ubiquitin carboxyl-terminal hydrolase MINDY-1/2 [EC:3.4.19.12]
K01309 MINDY1_2; ubiquitin carboxyl-terminal hydrolase MINDY-1/2 [EC:3.4.19.12]
K05609 UCHL3; ubiquitin carboxyl-terminal hydrolase L3 [EC:3.4.19.12]
K11366 USP22_27_51; ubiquitin carboxyl-terminal hydrolase 22/27/51 [EC:3.4.19.12]
K11835 USP4_11; ubiquitin carboxyl-terminal hydrolase 4/11 [EC:3.4.19.12]
K11836 USP5_13; ubiquitin carboxyl-terminal hydrolase 5/13 [EC:3.4.19.12]
K11838 USP7; ubiquitin carboxyl-terminal hydrolase 7 [EC:3.4.19.12]
K11839 USP8; ubiquitin carboxyl-terminal hydrolase 8 [EC:3.4.19.12]
K11839 USP8; ubiquitin carboxyl-terminal hydrolase 8 [EC:3.4.19.12]
K11841 USP10; ubiquitin carboxyl-terminal hydrolase 10 [EC:3.4.19.12]
K11843 USP14; ubiquitin carboxyl-terminal hydrolase 14 [EC:3.4.19.12]
K11849 USP25; ubiquitin carboxyl-terminal hydrolase 25 [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]
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]
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]
K18342 OTUD6; OTU domain-containing protein 6 [EC:3.4.19.12]
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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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