US 20150240226A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2015/0240226A1 Mathur et al. (43) Pub. Date: Aug. 27, 2015

(54) NUCLEICACIDS AND PROTEINS AND CI2N 9/16 (2006.01) METHODS FOR MAKING AND USING THEMI CI2N 9/02 (2006.01) CI2N 9/78 (2006.01) (71) Applicant: BP Corporation North America Inc., CI2N 9/12 (2006.01) Naperville, IL (US) CI2N 9/24 (2006.01) CI2O 1/02 (2006.01) (72) Inventors: Eric J. Mathur, San Diego, CA (US); CI2N 9/42 (2006.01) Cathy Chang, San Marcos, CA (US) (52) U.S. Cl. CPC. CI2N 9/88 (2013.01); C12O 1/02 (2013.01); (21) Appl. No.: 14/630,006 CI2O I/04 (2013.01): CI2N 9/80 (2013.01); CI2N 9/241.1 (2013.01); C12N 9/0065 (22) Filed: Feb. 24, 2015 (2013.01); C12N 9/2437 (2013.01); C12N 9/14 Related U.S. Application Data (2013.01); C12N 9/16 (2013.01); C12N 9/0061 (2013.01); C12N 9/78 (2013.01); C12N 9/0071 (62) Division of application No. 13/400,365, filed on Feb. (2013.01); C12N 9/1241 (2013.01): CI2N 20, 2012, now Pat. No. 8,962,800, which is a division 9/2482 (2013.01); C07K 2/00 (2013.01); C12Y of application No. 1 1/817,403, filed on May 7, 2008, 305/01004 (2013.01); C12Y 1 1 1/01016 now Pat. No. 8,119,385, filed as application No. PCT/ (2013.01); C12Y302/01004 (2013.01); C12Y US2006/007642 on Mar. 3, 2006. 303/02009 (2013.01); C12Y402/02002 (60) Provisional application No. 60/658,984, filed on Mar. (2013.01); C12Y 401/02 (2013.01); C12Y 4, 2005. 301/03 (2013.01) Publication Classification (57) ABSTRACT The invention provides polypeptides, including enzymes, (51) Int. Cl. structural proteins and binding proteins, polynucleotides CI2N 9/88 (2006.01) encoding these polypeptides, and methods of making and CI2O I/04 (2006.01) using these polynucleotides and polypeptides. Polypeptides, CI2N 9/80 (2006.01) including enzymes and antibodies, and nucleic acids of the CI2N 9/26 (2006.01) invention can be used in industrial, experimental, food and CI2N 9/08 (2006.01) feed processing, nutritional and pharmaceutical applications, C07K 2/00 (2006.01) e.g., for food and feed Supplements, colorants, neutraceuti CI2N 9/14 (2006.01) cals, cosmetic and pharmaceutical needs. Patent Application Publication Aug. 27, 2015 Sheet 1 of 4 US 2015/0240226A1

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FIGURE Patent Application Publication Aug. 27, 2015 Sheet 2 of 4 US 2015/0240226A1

201 200 NY START

2O2 STORE NEW SEQUENCE TO A MEMORY - - 4. OPEN DATABASE OF SECRUENCES 206 READ FIRST SEQUENCE IN DATABASE

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FIGURE 2 Patent Application Publication Aug. 27, 2015 Sheet 3 of 4 US 2015/0240226A1

252 250 NY START 254 STORE A FIRST SEQUENCE TO A MEMORY

256 STORE ASECOND SEQUENCE TO A MEMORY 260 READ FIRST CHARACTER OF FIRST SEQUENCE 262 READ FIRST CHARACTER OF SECOND SEQUENCE

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302 300 Na STAR 304 STORE AFRS SEQUENCE TO MEMORY 306 OPEN DATABASE OF SEQUENCE FEATURES -/ 308 READ FIRST FEATURE FROM DATABASE

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FIGURE A US 2015/0240226 A1 Aug. 27, 2015

NUCLECACDS AND PROTEINS AND these polypeptides, having the activities described in Table 1, METHODS FOR MAKING AND USING THEMI Table 2 or Table 3, below. The enzymes and proteins of the invention have utility in a variety of applications. CROSS-REFERENCE TO RELATED APPLICATIONS SUMMARY OF THE INVENTION 0001. This application is a divisional application of U.S. 0007. The invention provides isolated or recombinant application Ser. No. 13/400,365 filed Feb. 20, 2012, now nucleic acids comprising a nucleic acid sequence having at issued as U.S. Pat. No. 8,962,800; which is a divisional appli least about 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, cation of U.S. application Ser. No. 1 1/817.403 filed May 7, 58%, 59%, 60%, 61%. 62%, 63%, 64%. 65%, 66%, 67%, 2008, now issued as U.S. Pat. No. 8,119,385; which is a 35 68%, 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, USC S371 National Stage application of International Appli 78%, 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, cation No. PCT/US2006/007642 filed Mar. 3, 2006; which 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, claims the benefit under 35 USC S 119(e) to U.S. Application 98%, 99%, or more, or complete (100%) sequence identity to Ser. No. 60/658,984 filed Mar. 4, 2005, now expired. The an exemplary nucleic acid of the invention, e.g., including disclosure of each of the prior applications is considered part SEQID NO:1, SEQID NO:3, SEQID NO:5, SEQID NO:7, of and is incorporated by reference in the disclosure of this SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, SEQ ID application. NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID NO:21, SEQ ID NO:23, SEQ ID NO:25, and all nucleic acids dis BACKGROUND OF THE INVENTION closed in the SEQID listing, which include all odd numbered SEQID NO:s from SEQ ID NO:1 through SEQ ID NO:26, 0002 1. Field of the Invention 897, over a region of at least about 10, 20, 25, 30, 35, 40, 45, 0003. This invention relates to molecular and cellular biol 50, 75, 100, 150, 200,250, 300,350, 400, 450, 500,550, 600, ogy and biochemistry. In one aspect, the invention provides 650, 700, 750, 800, 850, 900, 950, 1000, 1050, 1100, 1150, polypeptides, including enzymes, structural proteins and 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, 1600, 1650, binding proteins (e.g., ligands, receptors), polynucleotides 1700, 1750, 1800, 1850, 1900, 1950, 2000, 2050,2100, 2200, encoding these polypeptides, and methods of making and 2250, 2300, 2350, 2400, 2450, 2500, or more residues, using these polynucleotides and polypeptides. In one aspect, encodes at least one polypeptide having an enzyme, structural the invention is directed to polypeptides, e.g., enzymes, struc orbinding activity, and the sequence identities are determined tural proteins and binding proteins, including thermostable by analysis with a sequence comparison algorithm or by a and thermotolerant activity, and polynucleotides encoding visual inspection. In one aspect, the enzymes and proteins of these enzymes, structural proteins and binding proteins and the invention include, e.g., aldolases, alpha-galactosidases, making and using these polynucleotides and polypeptides. amidases, e.g., secondary amidases, amylases, catalases, The polypeptides of the invention can be used in a variety of carotenoid pathway enzymes, dehalogenases, endogluca pharmaceutical, agricultural and industrial contexts, includ nases, epoxide hydrolases, esterases, hydrolases, glucosi ing the manufacture of cosmetics and nutraceuticals. dases, glycosidases, inteins, isomerases, laccases, lipases, 0004 Additionally, the polypeptides of the invention can monooxygenases, nitroreductases, nitrilases, P450 enzymes, be used in food processing, brewing, bath additives, alcohol pectate lyases, phosphatases, phospholipases, phytases, poly production, peptide synthesis, enantioselectivity, hide prepa merases and Xylanases. In another aspect, the isolated and ration in the leather industry, waste management and animal recombinant polypeptides of the invention, including degradation, silver recovery in the photographic industry, enzymes, structural proteins and binding proteins, and poly medical treatment, silk degumming, biofilm degradation, nucleotides encoding these polypeptides, of the invention biomass conversion to ethanol, biodefense, antimicrobial have activity as described in Table 1, Table 2 or Table 3, agents and disinfectants, personal care and cosmetics, biotech below. reagents, in corn wet milling and pharmaceuticals such as 0008. In one aspect, the invention also provides isolated or digestive aids and anti-inflammatory (anti-phlogistic) agents. recombinant nucleic acids with a common novelty in that they 0005 2. Background Information are all derived from a common Source, e.g., an environmental 0006. The invention provides isolated and recombinant Source, mixed environmental sources or mixed cultures. The polypeptides, including enzymes, structural proteins and invention provides isolated or recombinant nucleic acids iso binding proteins, polynucleotides encoding these polypep lated from a common Source, e.g., an environmental source, tides, and methods of making and using these polynucleotides mixed environmental sources or mixed cultures comprising a and polypeptides. The polypeptides of the invention, and the polynucleotide of the invention, e.g., an exemplary sequence polynucleotides encoding the polypeptides of the invention, of the invention, including SEQ ID NO:1, SEQ ID NO:3, encompass many classes of enzymes, structural proteins and SEQID NO:5, SEQID NO:7, SEQIDNO:9, SEQID NO:11, binding proteins. In one aspect, the enzymes and proteins of SEQ ID NO:13, SEQ ID NO:15, SEQ ID NO:17, SEQ ID the invention include, e.g., aldolases, alpha-galactosidases, NO:19, SEQID NO:21, SEQID NO:23, SEQID NO:25, and amidases, e.g., secondary amidases, amylases, catalases, all nucleic acids disclosed in the SEQ ID listing, which carotenoid pathway enzymes, dehalogenases, endogluca include all odd numbered SEQID NO:s from SEQID NO:1 nases, epoxide hydrolases, esterases, hydrolases, glucosi through SEQID NO:26,897, over a region of at least about dases, glycosidases, inteins, isomerases, laccases, lipases, 10, 15, 20, 25, 30, 35, 40, 45,50, 75, 100, 150, 200, 250,300, monooxygenases, nitroreductases, nitrilases, P450 enzymes, 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, pectate lyases, phosphatases, phospholipases, phytases, poly 950, 1000, 1050, 1100, 1150, 1200, 1250, 1300, 1350, 1400, merases and Xylanases. The invention also provides isolated 1450, 1500, 1550, 1600, 1650, 1700, 1750, 1800, 1850, 1900, and recombinant polypeptides, including enzymes, structural 1950, 2000, 2050,2100, 2200,2250,2300, 2350,2400, 2450, proteins and binding proteins, polynucleotides encoding 2500, or more residues, encodes at least one polypeptide US 2015/0240226 A1 Aug. 27, 2015 having an enzyme, structural or binding activity, and the tein activity, an inorganic ion transport activity, a nucleotide sequence identities are determined by analysis with a transport activity, a nucleotide metabolism activity, an actin sequence comparison algorithm or by a visual inspection. In or myosin activity, a lipase activity or a lipid acyl hydrolase one aspect, the enzymes and proteins of the invention include, (LAH) activity, a cell envelop biogenesis activity, an outer e.g., aldolases, alpha-galactosidases, amidases, e.g., second membrane synthesis activity, a ribosomal structure synthesis ary amidases, amylases, catalases, carotenoid pathway activity, a translational processing activity, a transcriptional enzymes, dehalogenases, endoglucanases, epoxide hydro initiation activity, a TATA-binding activity, a signal transduc lases, esterases, hydrolases, glucosidases, glycosidases, tion activity, an energy metabolism activity, an ATPase activ inteins, isomerases, laccases, lipases, monooxygenases, ity, an information storage and/or processing activity, and/or nitroreductases, nitrilases, P450 enzymes, pectate lyases, any of the polypeptides activities as set forth in Table 1, Table phosphatases, phospholipases, phytases, polymerases and 2 or Table 3, below. Xylanases. In another aspect, the isolated and recombinant 0011. In one aspect, the sequence comparison algorithm is polypeptides of the invention, including enzymes, structural a BLAST version 2.2.2 algorithm where a filtering setting is proteins and binding proteins, and polynucleotides encoding set to blastall-p blastp-d'nr pataa’-FF, and all other options these polypeptides, of the invention have activity as described are set to default. in Table 1, Table 2 or Table 3, below. 0012 Another aspect of the invention is an isolated or 0009. In alternative aspects, the isolated or recombinant recombinant nucleic acid including at least 10, 15, 20, 25.30, nucleic acid encodes a polypeptide comprising an exemplary 35, 40, 45,50, 75, 100, 150,200,250,300,350,400,450,500, sequence of the invention, e.g., including sequences as set 550, 600, 650, 700, 750, 800, 850, 900, 950, 1000, 1050, forth in SEQID NO:2, SEQID NO:4, SEQID NO:6, SEQID 1100, 1150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, NO:8, SEQID NO:10, SEQID NO:12, SEQID NO:14, SEQ 1600, 1650, 1700, 1750, 1800, 1850, 1900, 1950, 2000, 2050, ID NO:16, SEQID NO:18, SEQID NO:20, SEQID NO:22, 2100, 2200, 2250, 2300, 2350, 2400, 2450, 2500, or more SEQID NO:24, and all polypeptides disclosed in the SEQID consecutive bases of a nucleic acid sequence of the invention, listing, which include all even numbered SEQID NO:s from sequences substantially identical thereto, and the sequences SEQ ID NO:2 through SEQ ID NO:26,898. In one aspect complementary thereto. these polypeptides have an enzyme, structural or binding 0013. In one aspect, the isolated or recombinant nucleic activity. In one aspect, the enzymes and proteins of the inven acid encodes a polypeptide having a enzyme, structural or tion include, e.g., aldolases, alpha-galactosidases, amidases, binding activity, that is thermostable. The polypeptide can e.g., secondary amidases, amylases, catalases, carotenoid retain activity under conditions comprising a temperature pathway enzymes, dehalogenases, endoglucanases, epoxide range of between about 37° C. to about 95°C.; between about hydrolases, esterases, hydrolases, glucosidases, glycosi 55° C. to about 85°C., between about 70° C. to about 95°C., dases, inteins, isomerases, laccases, lipases, monooxygena or, between about 90° C. to about 95°C. ses, nitroreductases, nitrilases, P450 enzymes, pectate lyases, 0014. In another aspect, the isolated or recombinant phosphatases, phospholipases, phytases, polymerases and nucleic acid encodes a polypeptide having an enzyme, struc Xylanases. In another aspect, the isolated and recombinant tural or binding activity, which is thermotolerant. The polypeptides of the invention, including enzymes, structural polypeptide can retain activity after exposure to a temperature proteins and binding proteins, and polynucleotides encoding in the range from greater than 37° C. to about 95° C. or these polypeptides, of the invention have activity as described anywhere in the range from greater than 55°C. to about 85°C. in Table 1, Table 2 or Table 3, below. The polypeptide can retain activity after exposure to a tem 0010. In alternative aspects, the enzyme, structural or perature in the range between about 1° C. to about 5° C. binding activity comprises a recombinase activity, a helicase between about 5° C. to about 15°C., between about 15° C. to activity, a DNA replication activity, a DNA recombination about 25°C., between about 25°C. to about 37°C., between activity, an isomerase, a trans-isomerase activity or topoi about 37° C. to about 95°C., between about 55° C. to about Somerase activity, a methyl transferase activity, an ami 85°C., between about 70° C. to about 75° C., or between notransferase activity, auracil-5-methyltransferase activity, a about 90° C. to about 95°C., or more. In one aspect, the cysteinyl tRNA synthetase activity, a hydrolase, an esterase polypeptide retains activity after exposure to a temperature in activity, a phosphoesterase activity, an acetylmuramyl pen the range from greater than 90° C. to about 95°C. at about pH tapeptide phosphotransferase activity, a glycosyltransferase 4.5. activity, an acetyltransferase activity, an acetylglucosamine 0015 The invention provides isolated or recombinant phosphate transferase activity, a centromere binding activity, nucleic acids comprising a sequence that hybridizes under a telomerase activity or a transcriptional regulatory activity, a stringent conditions to a nucleic acid comprising a sequence heat shock protein activity, a protease activity, a proteinase of the invention, e.g., an exemplary sequence of the invention, activity, a peptidase activity, a carboxypeptidase activity, an including SEQID NO:1, SEQID NO:3, SEQID NO:5, SEQ endonuclease activity, an exonuclease activity, a RecB family ID NO:7, SEQ ID NO:9, SEQ ID NO:11, SEQ ID NO:13, exonuclease activity, a polymerase activity, a carbamoyl SEQ ID NO:15, SEQ ID NO:17, SEQ ID NO:19, SEQ ID phosphate synthetase activity, a methyl-thioadenine Syn NO:21, SEQID NO:23, SEQID NO:25, and all nucleic acids thetase activity, an oxidoreductase activity, an Fe—S oxi disclosed in the SEQID listing, which include all odd num doreductase activity, a flavodoxin reductase activity, a per bered SEQ ID NO:s from SEQ ID NO:1 through SEQ ID mease activity, a thymidylate activity, a dehydrogenase NO:26,897, or fragments or subsequences thereof. In one activity, a pyrophosphorylase activity, a coenzyme metabo aspect, the nucleic acid encodes a polypeptide having a lism activity, a dinucleotide-utilizing enzyme activity, a enzyme, structural or binding activity. The nucleic acid can be molybdopterin or thiamine biosynthesis activity, a beta-1 at least about 10, 15, 20, 25, 30, 35, 40, 45, 50, 75, 100, 150, actamase activity, a ligand binding activity, an ion transport 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, 750, activity, an ion metabolism activity, a tellurite resistance pro 800, 850, 900, 950, 1000, 1050, 1100, 1150, 1200 or more US 2015/0240226 A1 Aug. 27, 2015 residues in length or the full length of the gene or transcript. erated by amplification, e.g., polymerase chain reaction In one aspect, the stringent conditions include a wash step (PCR), using an amplification primer pair of the invention. comprising a wash in 0.2xSSC at a temperature of about 65° The invention provides methods of making a polypeptide, C. for about 15 minutes. enzyme, protein, e.g., structural or binding protein, by ampli 0016. The invention provides a nucleic acid probe for fication, e.g., polymerase chain reaction (PCR), using an identifying a nucleic acid encoding a polypeptide having a amplification primer pair of the invention. In one aspect, the enzyme, structural or binding activity, wherein the probe amplification primer pair amplifies a nucleic acid from a comprises at least about 10, 15, 20, 25, 30, 35, 40, 45, 50,55, library, e.g., a gene library, such as an environmental library. 60, 65, 70, 75, 80, 85,90, 95, 100, 150, 200, 250, 300, 350, 0021. The invention provides methods of amplifying a 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, 950, nucleic acid encoding a polypeptide having an enzyme, struc 1000 or more, consecutive bases of a sequence comprising a tural or binding activity, comprising amplification of a tem sequence of the invention, or fragments or Subsequences plate nucleic acid with an amplification primer sequence pair thereof, wherein the probe identifies the nucleic acid by bind capable of amplifying a nucleic acid sequence of the inven ing or hybridization. The probe can comprise an oligonucle tion, or fragments or Subsequences thereof. otide comprising at least about 10 to 50, about 20 to 60, about 0022. The invention provides expression cassettes com 30 to 70, about 40 to 80, or about 60 to 100 consecutive bases prising a nucleic acid of the invention or a Subsequence of a sequence comprising a sequence of the invention, or thereof. In one aspect, the expression cassette can comprise fragments or Subsequences thereof. the nucleic acid that is operably linked to a promoter. The 0017. The invention provides a nucleic acid probe for promoter can be a viral, bacterial, mammalian or plant pro identifying a nucleic acid encoding a polypeptide having a moter. In one aspect, the plant promoter can be a potato, rice, enzyme, structural or binding activity, wherein the probe corn, wheat, tobacco or barley promoter. The promoter can be comprises a nucleic acid comprising a sequence at least about a constitutive promoter. The constitutive promoter can com 10, 15, 20, 30, 40, 50, 60, 70, 80,90, 100, 150, 200, 250, 300, prise CaMV35S. In another aspect, the promoter can be an 350, 400, 450, 500, 550, 600, 650, 700, 750, 800, 850, 900, inducible promoter. In one aspect, the promoter can be a 950, 1000 or more residues having at least about 50%, 51%, tissue-specific promoter or an environmentally regulated or a 52%. 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, developmentally regulated promoter. Thus, the promoter can 62%, 63%, 64%. 65%, 66%, 67%, 68%, 69%, 70%, 71%, be, e.g., a seed-specific, a leaf-specific, a root-specific, a 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, stem-specific or an abscission-induced promoter. In one 82%, 83%, 84%, 85%. 86%, 87%, 88%. 89%, 90%, 91%, aspect, the expression cassette can further comprise a plant or 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more, or plant virus expression vector. complete (100%) sequence identity to a nucleic acid of the 0023 The invention provides cloning vehicles comprising invention. In one aspect, the sequence identities are deter an expression cassette (e.g., a vector) of the invention or a mined by analysis with a sequence comparison algorithm or nucleic acid of the invention. The cloning vehicle can be a by visual inspection. In alternative aspects, the probe can viral vector, a plasmid, a phage, a phagemid, a cosmid, a comprise an oligonucleotide comprising at least about 10 to fosmid, a bacteriophage or an artificial chromosome. The 50, about 20 to 60, about 30 to 70, about 40 to 80, or about 60 viral vector can comprise an adenovirus vector, a retroviral to 100 consecutive bases of a nucleic acid sequence of the vector or an adeno-associated viral vector. The cloning invention, or a Subsequence thereof. vehicle can comprise a bacterial artificial chromosome 0018. The invention provides an amplification primer pair (BAC), a plasmid, a bacteriophage P1-derived vector (PAC), for amplifying a nucleic acid encoding a polypeptide having a yeast artificial chromosome (YAC), or a mammalian artifi a enzyme, structural or binding activity, wherein the primer cial chromosome (MAC). pair is capable of amplifying a nucleic acid comprising a 0024. The invention provides transformed cell comprising sequence of the invention, or fragments or Subsequences a nucleic acid of the invention or an expression cassette (e.g., thereof. One or each member of the amplification primer a vector) of the invention, or a cloning vehicle of the inven sequence pair can comprise an oligonucleotide comprising at tion. In one aspect, the transformed cell can be a bacterial cell, least about 10 to 50, or more, consecutive bases of the a mammalian cell, a fungal cell, a yeast cell, an insect cell or sequence, or about 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22. a plant cell. In one aspect, the plant cell can be a cereal, a 23, 24, 25, 26, 27, 28, 29, 30 or more consecutive bases of the potato, wheat, rice, corn, tobacco or barley cell. Sequence. 0025. The invention provides transgenic non-human ani 0019. The invention provides amplification primer pairs, mals comprising a nucleic acid of the invention or an expres wherein the primer pair comprises a first member having a sion cassette (e.g., a vector) of the invention. In one aspect, the sequence as set forth by about the first (the 5') 12, 13, 14, 15, animal is a mouse, a rat, a pig, a goat or a sheep. 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,33, 0026. The invention provides transgenic plants compris 34, 35, 36 or more residues of a nucleic acid of the invention, ing a nucleic acid of the invention or an expression cassette and a second member having a sequence as set forth by about (e.g., a vector) of the invention. The transgenic plant can be a the first (the 5') 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, cereal plant, a corn plant, a potato plant, a tomato plant, a 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36 or more wheat plant, an oilseed plant, a rapeseed plant, a Soybean residues of the complementary strand of the first member. plant, a rice plant, a barley plant or a tobacco plant. 0020. The invention provides polypeptide-, enzyme-, pro 0027. The invention provides transgenic seeds comprising tein-, e.g., structural or binding protein-encoding nucleic a nucleic acid of the invention or an expression cassette (e.g., acids generated by amplification, e.g., polymerase chain reac a vector) of the invention. The transgenic seed can be a cereal tion (PCR), using an amplification primer pair of the inven plant, a corn seed, a wheat kernel, an oilseed, a rapeseed, a tion. The invention provides polypeptide-, enzyme-, protein-, Soybean seed, a palm kernel, a Sunflower seed, a sesame seed, e.g., structural or binding protein-encoding nucleic acids gen a peanut or a tobacco plant seed. US 2015/0240226 A1 Aug. 27, 2015

0028. The invention provides an antisense oligonucleotide phosphate synthetase activity, a methyl-thioadenine Syn comprising a nucleic acid sequence complementary to or thetase activity, an oxidoreductase activity, an Fe—S oxi capable of hybridizing understringent conditions to a nucleic doreductase activity, a flavodoxin reductase activity, a per acid of the invention. The invention provides methods of mease activity, a thymidylate activity, a dehydrogenase inhibiting the translation of a polypeptide, enzyme, protein, activity, a pyrophosphorylase activity, a coenzyme metabo e.g., structural or binding protein message in a cell compris lism activity, a dinucleotide-utilizing enzyme activity, a ing administering to the cell or expressing in the cell an molybdopterin or thiamine biosynthesis activity, a beta-lac antisense oligonucleotide comprising a nucleic acid sequence tamase activity, a ligand binding activity, an ion transport complementary to or capable of hybridizing under stringent activity, an ion metabolism activity, a tellurite resistance pro conditions to a nucleic acid of the invention. In one aspect, the tein activity, an inorganic ion transport activity, a nucleotide antisense oligonucleotide is between about 10 to 50, about 20 transport activity, a nucleotide metabolism activity, an actin to 60, about 30 to 70, about 40 to 80, or about 60 to 100 bases or myosin activity, a lipase activity or a lipid acyl hydrolase in length, e.g., 10, 15, 20, 25, 30,35, 40, 45,50, 55,60, 65,70, (LAH) activity, a cell envelop biogenesis activity, an outer 75, 80, 85,90, 95, 100 or more bases in length. membrane synthesis activity, a ribosomal structure synthesis 0029. The invention provides methods of inhibiting the activity, a translational processing activity, a transcriptional translation of a polypeptide, enzyme, protein, e.g., structural initiation activity, a TATA-binding activity, a signal transduc orbinding protein message in a cell comprising administering tion activity, an energy metabolism activity, an ATPase activ to the cell or expressing in the cell an antisense oligonucle ity, an information storage and/or processing activity, and/or otide comprising a nucleic acid sequence complementary to any of the polypeptides activities as set forth in Table 1, Table or capable of hybridizing under Stringent conditions to a 2 or Table 3, below. nucleic acid of the invention. The invention provides double 0032 Exemplary polypeptide or peptide sequences of the stranded inhibitory RNA (RNAi, or RNA interference) mol invention include SEQ ID NO:2, SEQ ID NO:4, SEQ ID ecules (including small interfering RNA, or siRNAs, for NO:6, SEQID NO:8, SEQID NO:10, etc., and all polypep inhibiting transcription, and microRNAs, or miRNAs, for tides disclosed in the SEQID listing, which include all even inhibiting translation) comprising a Subsequence of a numbered SEQID NO:s from SEQID NO:2 through SEQID sequence of the invention. In one aspect, the RNAi is about NO:26,898, and subsequences thereof and variants thereof. 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, Exemplary polypeptides also include fragments of at least 33, 34,35, 40, 45, 50, 55, 60, 65,70, 75, 80, 85,90, 95, 100 about 10, 15, 20, 25, 30, 35, 40, 45, 50, 75,80, 85,90, 95, 100, or more duplex nucleotides in length. The invention provides 150, 200, 250, 300, 350, 400, 450, 500, 550, 600 or more methods of inhibiting the expression of a polypeptide, residues in length, or over the full length of an enzyme. enzyme, protein, peptide, e.g., structural or binding protein in Exemplary polypeptide or peptide sequences of the invention a cell comprising administering to the cellor expressing in the include sequence encoded by a nucleic acid of the invention. cell a double-stranded inhibitory RNA (iRNA, including Exemplary polypeptide or peptide sequences of the invention small interfering RNA, or siRNAs, for inhibiting transcrip include polypeptides or peptides specifically bound by an tion, and microRNAs, or miRNAs, for inhibiting translation), wherein the RNA comprises a Subsequence of a sequence of antibody of the invention. the invention. 0033. In one aspect, the polypeptide, enzyme, protein, 0030 The invention provides isolated or recombinant e.g., structural or binding protein, is thermostable. The polypeptides encoded by a nucleic acid of the invention. In polypeptide, enzyme, protein, e.g., structural or binding pro alternative aspects, the polypeptide can have a sequence as set tein can retain activity under conditions comprising a tem forth in SEQID NO:2, SEQID NO:4, SEQID NO:6, SEQID perature range of between about 1°C. to about 5°C., between NO:8, SEQID NO:10, etc., and all polypeptides disclosed in about 5°C. to about 15°C., between about 15° C. to about 25° the SEQID listing, which include all even numbered SEQID C., between about 25°C. to about 37°C., between about 37° NO:s from SEQ ID NO:2 through SEQ ID NO:26,898 (the C. to about 95°C., between about 55° C. to about 85°C., exemplary sequences of the invention), or Subsequences between about 70° C. to about 75°C., or between about 90° C. thereof, including fragments having enzymatic and/or Sub to about 95°C., or more. In another aspect, the polypeptide, strate binding activity. The polypeptide can have an enzyme, enzyme, protein, e.g., structural or binding protein can be structural or binding activity. thermotolerant. The polypeptide, enzyme, protein, e.g., struc 0031. In alternative aspects, the enzyme, structural or tural or binding protein can retain activity after exposure to a binding activity comprises a recombinase activity, a helicase temperature in the range from greater than 37°C. to about 95° activity, a DNA replication activity, a DNA recombination C., or in the range from greater than 55° C. to about 85°C. In activity, an isomerase, a trans-isomerase activity or topoi one aspect, the polypeptide, enzyme, protein, e.g., structural Somerase activity, a methyl transferase activity, an ami or binding protein can retain activity after exposure to a notransferase activity, auracil-5-methyltransferase activity, a temperature in the range from greater than 90° C. to about 95° cysteinyl tRNA synthetase activity, a hydrolase, an esterase C. at pH 4.5. activity, a phosphoesterase activity, an acetylmuramyl pen 0034. Another aspect of the invention provides an isolated tapeptide phosphotransferase activity, a glycosyltransferase or recombinant polypeptide or peptide including at least 10, activity, an acetyltransferase activity, an acetylglucosamine 15, 20, 25, 30,35, 40, 45, 50,55, 60, 65,70, 75,80, 85,90,95 phosphate transferase activity, a centromere binding activity, or 100 or more consecutive bases of a polypeptide or peptide a telomerase activity or a transcriptional regulatory activity, a sequence of the invention, sequences Substantially identical heat shock protein activity, a protease activity, a proteinase thereto, and the sequences complementary thereto. The pep activity, a peptidase activity, a carboxypeptidase activity, an tide can be, e.g., an immunogenic fragment, a motif (e.g., a endonuclease activity, an exonuclease activity, a RecB family binding site), a signal sequence, a prepro sequence or an exonuclease activity, a polymerase activity, a carbamoyl active site. US 2015/0240226 A1 Aug. 27, 2015

0035. The invention provides isolated or recombinant 0040. In one aspect, the enzyme, structural or binding nucleic acids comprising a sequence encoding a polypeptide, activity comprises a specific activity at about 37° C. in the enzyme, protein, e.g., structural orbinding protein having any range from about 1 to about 1200 units per milligram of of the activities as set forth in Tables 1, 2 or 3, and a signal protein, or, about 100 to about 1000 units per milligram of sequence, wherein the nucleic acid comprises a sequence of protein. In another aspect, the polypeptide, enzyme, protein, the invention. In one aspect, the isolated or recombinant e.g., structural or binding proteinactivity comprises a specific polypeptide can comprise the polypeptide of the invention activity from about 100 to about 1000 units per milligram of comprising a heterologous signal sequence or a heterologous protein, or, from about 500 to about 750 units per milligram of preprosequence, Such as a heterologous enzyme or non-en protein. Alternatively, the enzyme, structural orbinding activ Zyme signal sequence. The invention provides isolated or ity comprises a specific activity at 37° C. in the range from recombinant nucleic acids comprising a sequence encoding a about 1 to about 750 units per milligram of protein, or, from polypeptide, enzyme, protein, e.g., structural or binding pro about 500 to about 1200 units per milligram of protein. In one tein having any of the activities as set forth in Tables 1, 2 or 3, aspect, the enzyme, structural or binding activity comprises a wherein the sequence does not contain a signal sequence and specific activity at 37°C. in the range from about 1 to about the nucleic acid comprises a sequence of the invention. In one 500 units per milligram of protein, or, from about 750 to about aspect, the invention provides an isolated or recombinant 1000 units per milligram of protein. In another aspect, the polypeptide comprising a polypeptide of the invention lack enzyme, structural or binding activity comprises a specific ing all or part of a signal sequence. activity at 37°C. in the range from about 1 to about 250 units 0036. In one aspect, the invention provides chimeric pro per milligram of protein. Alternatively, the enzyme, structural teins comprising a first domain comprising a signal sequence or binding activity comprises a specific activity at 37°C. in of the invention and at least a second domain. The protein can the range from about 1 to about 100 units per milligram of be a fusion protein. The second domain can comprise an protein. enzyme. The enzyme can be a non-enzyme. 0041. In another aspect, thermotolerance comprises reten tion of at least half of the specific activity of the enzyme, 0037. The invention provides chimeric polypeptides com structural or binding protein at 37°C. after being heated to the prising at least a first domain comprising signal peptide (SP), elevated temperature. Alternatively, thermotolerance can a prepro sequence and/or a catalytic domain (CD) of the comprise retention of specific activity at 37°C. in the range invention and at least a second domain comprising a heter from about 1 to about 1200 units per milligram of protein, or, ologous polypeptide or peptide, wherein the heterologous from about 500 to about 1000 units per milligram of protein, polypeptide or peptide is not naturally associated with the after being heated to the elevated temperature. In another signal peptide (SP), prepro sequence and/or catalytic domain aspect, thermotolerance can comprise retention of specific (CD). In one aspect, the heterologous polypeptide or peptide activity at 37°C. in the range from about 1 to about 500 units is not an enzyme. The heterologous polypeptide or peptide per milligram of protein after being heated to the elevated can be amino terminal to, carboxy terminal to or on both ends temperature. of the signal peptide (SP), prepro sequence and/or catalytic 0042. The invention provides the isolated or recombinant domain (CD). polypeptide of the invention, wherein the polypeptide com 0038. The invention provides isolated or recombinant prises at least one glycosylation site. In one aspect, glycosy nucleic acids encoding a chimeric polypeptide, wherein the lation can be an N-linked glycosylation. In one aspect, the chimeric polypeptide comprises at least a first domain com polypeptide can be glycosylated after being expressed in a P prising signal peptide (SP), a prepro domain and/or a catalytic pastoris or a S. pombe. domain (CD) of the invention and at least a second domain 0043. In one aspect, the polypeptide, enzyme, protein, comprising a heterologous polypeptide or peptide, wherein e.g., structural or binding protein can retain activity under the heterologous polypeptide or peptide is not naturally asso conditions comprising about pH 6.5, pH 6, pH 5.5, pH 5, pH ciated with the signal peptide (SP), prepro domain and/or 4.5 or pH 4. In another aspect, the polypeptide, enzyme, catalytic domain (CD). protein, e.g., structural or binding protein can retain activity 0039. The invention provides isolated or recombinant sig under conditions comprising about pH 7, pH 7.5 pH 8.0, pH nal sequences (e.g., signal peptides) consisting of or compris 8.5, pH 9, pH 9.5, pH 10, pH 10.5 or pH 11. In one aspect, the ing a sequence as set forth in residues 1 to 14, 1 to 15, 1 to 16, polypeptide can retain an enzyme, structural or binding activ 1 to 17, 1 to 18, 1 to 19, 1 to 20, 1 to 21, 1 to 22, 1 to 23, 1 to ity after exposure to conditions comprising about pH 6.5, pH 24, 1 to 25, 1 to 26, 1 to 27, 1 to 28, 1 to 28, 1 to 30, 1 to 31, 6, pH 5.5, pH 5, pH 4.5 or pH 4. In another aspect, the 1 to 32, 1 to 33, 1 to 34, 1 to 35, 1 to 36, 1 to 37, 1 to 38, 1 to polypeptide can retain enzyme, structural or binding activity 40, 1 to 41, 1 to 42, 1 to 43, 1 to 44, 1 to 45, 1 to 46 or 1 to 47, after exposure to conditions comprising about pH 7, pH 7.5 of a polypeptide of the invention, including the exemplary pH 8.0, pH 8.5, pH 9, pH 9.5, pH 10, pH 10.5 or pH 11. polypeptides of the invention (including SEQID NO:2, SEQ 0044. In one aspect, the polypeptide, enzyme, protein, ID NO:4, SEQID NO:6, SEQID NO:8, SEQID NO:10, etc., e.g., structural or binding protein of the invention has activity and all polypeptides disclosed in the SEQ ID listing, which at under alkaline conditions, e.g., the alkaline conditions of include all even numbered SEQID NO:s from SEQID NO:2 the gut, e.g., the Small intestine. In one aspect, the polypep through SEQ ID NO:26,898). In one aspect, the invention tide, enzyme, protein, e.g., structural or binding protein can provides signal sequences comprising the first 14, 15, 16, 17. retain activity after exposure to the acidic pH of the stomach. 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,33, 34, 0045. The invention provides protein preparations com 35,36, 37,38, 39, 40, 41,42, 43,44, 45,46, 47, 48,49, 50, 51, prising a polypeptide of the invention, wherein the protein 52,53,54, 55,56, 57,58, 59, 60, 61, 62,63, 64, 65, 66, 67,68, preparation comprises a liquid, a Solid or a gel. 69, 70 or more amino terminal residues of a polypeptide of the 0046. The invention provides heterodimers comprising a invention. polypeptide of the invention and a second protein or domain. US 2015/0240226 A1 Aug. 27, 2015

The second member of the heterodimer can be a different of the invention; or a polypeptide encoded by a nucleic acid of enzyme, a different enzyme or another protein. In one aspect, the invention; (b) providing an enzyme, structural or binding the second domain can be a polypeptide and the heterodimer activity Substrate; and (c) contacting the polypeptide or a can be a fusion protein. In one aspect, the second domain can fragment or variant thereof of step (a) with the substrate of be an epitope or a tag. In one aspect, the invention provides step (b) and detecting a decrease in the amount of substrate or homodimers comprising a polypeptide of the invention. an increase in the amount of a reaction product, wherein a 0047. The invention provides immobilized polypeptides decrease in the amount of the Substrate or an increase in the having enzyme, structural or binding activity, wherein the amount of the reaction product detects a polypeptide having a polypeptide comprises a polypeptide of the invention, a enzyme, structural or binding activity. polypeptide encoded by a nucleic acid of the invention, or a 0054 The invention provides methods for identifying a polypeptide comprising a polypeptide of the invention and a polypeptide, enzyme, protein, e.g., structural or binding pro second domain. In one aspect, the polypeptide can be immo tein, Substrate comprising the following steps: (a) providing a bilized on a cell, a metal, a resin, a polymer, a ceramic, a glass, polypeptide of the invention; or a polypeptide encoded by a a microelectrode, a graphitic particle, a bead, a gel, a plate, an nucleic acid of the invention; (b) providing a test Substrate; array or a capillary tube. and (c) contacting the polypeptide of step (a) with the test 0048. The invention provides arrays comprising an immo Substrate of step (b) and detecting a decrease in the amount of bilized nucleic acid of the invention. The invention provides Substrate or an increase in the amount of reaction product, arrays comprising an antibody of the invention. wherein a decrease in the amount of the Substrate or an 0049. The invention provides isolated or recombinant increase in the amount of a reaction product identifies the test antibodies that specifically bind to a polypeptide of the inven Substrate as a polypeptide, enzyme, protein, e.g., structural or tion or to a polypeptide encoded by a nucleic acid of the binding protein, Substrate. invention. These antibodies of the invention can be a mono 0055. The invention provides methods of determining clonal or a polyclonal antibody. The invention provides hybri whether a test compound specifically binds to a polypeptide domas comprising an antibody of the invention, e.g., an anti comprising the following steps: (a) expressing a nucleic acid body that specifically binds to a polypeptide of the invention or a vector comprising the nucleic acid under conditions or to a polypeptide encoded by a nucleic acid of the invention. permissive for translation of the nucleic acid to a polypeptide, The invention provides nucleic acids encoding these antibod wherein the nucleic acid comprises a nucleic acid of the 1S invention, or, providing a polypeptide of the invention; (b) 0050. The invention provides method of isolating or iden providing a test compound; (c) contacting the polypeptide tifying a polypeptide having enzyme, structural or binding with the test compound; and (d) determining whether the test activity comprising the steps of: (a) providing an antibody of compound of step specifically binds to the polypeptide. the invention; (b) providing a sample comprising polypep 0056. The invention provides methods for identifying a tides; and (c) contacting the sample of step (b) with the modulator of a enzyme, structural or binding activity com antibody of step (a) under conditions wherein the antibody prising the following steps: (a) providing a polypeptide of the can specifically bind to the polypeptide, thereby isolating or invention or a polypeptide encoded by a nucleic acid of the identifying a polypeptide having an enzyme, structural or invention; (b) providing a test compound; contacting the binding activity. polypeptide of step (a) with the test compound of step (b) and 0051. The invention provides methods of making an anti measuring an activity of the polypeptide, enzyme, protein, polypeptide, anti-enzyme, oranti-protein, e.g., anti-structural e.g., structural or binding protein, wherein a change in the oranti-binding protein, antibody comprising administering to enzyme, structural or binding activity measured in the pres a non-human animal a nucleic acid of the invention or a ence of the test compound compared to the activity in the polypeptide of the invention or Subsequences thereof in an absence of the test compound provides a determination that amount Sufficient to generate a humoral immune response, the test compound modulates the enzyme, structural or bind thereby making an anti-polypeptide, anti-enzyme, or anti ing activity. In one aspect, the enzyme, structural or binding protein, e.g., anti-structural oranti-binding protein, antibody. activity can be measured by providing a polypeptide, enzyme, The invention provides methods of making an anti-polypep protein, e.g., structural or binding protein, Substrate and tide, anti-enzyme, or anti-protein, e.g., anti-structural oranti detecting a decrease in the amount of the Substrate or an binding protein, immune comprising administering to a non increase in the amount of a reaction product, or, an increase in human animal a nucleic acid of the invention or a polypeptide the amount of the Substrate or a decrease in the amount of a of the invention or Subsequences thereof in an amount Suffi reaction product. A decrease in the amount of the Substrate or cient to generate an immune response. an increase in the amount of the reaction product with the test 0052. The invention provides methods of producing a compound as compared to the amount of substrate or reaction recombinant polypeptide comprising the steps of: (a) provid product without the test compound identifies the test com ing a nucleic acid of the invention operably linked to a pro pound as an activator of enzyme, structural or binding activ moter, and (b) expressing the nucleic acid of step (a) under ity. An increase in the amount of the Substrate or a decrease in conditions that allow expression of the polypeptide, thereby the amount of the reaction product with the test compound as producing a recombinant polypeptide. In one aspect, the compared to the amount of Substrate or reaction product method can further comprise transforming a host cell with the without the test compound identifies the test compound as an nucleic acid of step (a) followed by expressing the nucleic inhibitor of enzyme, structural or binding activity. acid of step (a), thereby producing a recombinant polypeptide 0057 The invention provides computer systems compris in a transformed cell. ing a processor and a data storage device wherein said data 0053. The invention provides methods for identifying a storage device has stored thereon a polypeptide sequence or a polypeptide having enzyme, structural or binding activity nucleic acid sequence of the invention (e.g., a polypeptide comprising the following steps: (a) providing a polypeptide encoded by a nucleic acid of the invention). In one aspect, the US 2015/0240226 A1 Aug. 27, 2015 computer system can further comprise a sequence compari ering a nucleic acid encoding a polypeptide, enzyme, protein, son algorithm and a data storage device having at least one e.g., structural or binding protein from an environmental reference sequence stored thereon. In another aspect, the sample. The environmental sample can comprise a water sequence comparison algorithm comprises a computer pro sample, a liquid sample, a Soil sample, an air sample or a gram that indicates polymorphisms. In one aspect, the com biological sample. In one aspect, the biological sample can be puter system can further comprise an identifier that identifies derived from a bacterial cell, a protozoan cell, an insect cell, one or more features in said sequence. The invention provides a yeast cell, a plant cell, a fungal cell or a mammalian cell. computer readable media having stored thereona polypeptide 0060. The invention provides methods of generating a sequence or a nucleic acid sequence of the invention. The variant of a nucleic acid encoding a polypeptide having an invention provides methods for identifying a feature in a enzyme, structural or binding activity comprising the steps sequence comprising the steps of: (a) reading the sequence of: (a) providing a template nucleic acid comprising a nucleic using a computer program which identifies one or more fea acid of the invention; and (b) modifying, deleting or adding tures in a sequence, wherein the sequence comprises a one or more nucleotides in the template sequence, or a com polypeptide sequence or a nucleic acid sequence of the inven bination thereof, to generate a variant of the template nucleic tion; and (b) identifying one or more features in the sequence acid. In one aspect, the method can further comprise express with the computer program. The invention provides methods ing the variant nucleic acid to generate a variant the polypep for comparing a first sequence to a second sequence compris tide, enzyme, protein, e.g., structural or binding protein. The ing the steps of: (a) reading the first sequence and the second modifications, additions or deletions can be introduced by a sequence through use of a computer program which com method comprising error-prone PCR, shuffling, oligonucle pares sequences, wherein the first sequence comprises a otide-directed mutagenesis, assembly PCR, sexual PCR polypeptide sequence or a nucleic acid sequence of the inven mutagenesis, in Vivo mutagenesis, cassette mutagenesis, tion; and (b) determining differences between the first recursive ensemble mutagenesis, exponential ensemble sequence and the second sequence with the computer pro mutagenesis, site-specific mutagenesis, gene reassembly, gram. The step of determining differences between the first Gene Site Saturation Mutagenesis (GSSM), synthetic liga sequence and the second sequence can further comprise the tion reassembly (SLR) or a combination thereof. In another step of identifying polymorphisms. In one aspect, the method aspect, the modifications, additions or deletions are intro can further comprise an identifier that identifies one or more duced by a method comprising recombination, recursive features in a sequence. In another aspect, the method can sequence recombination, phosphothioate-modified DNA comprise reading the first sequence using a computer pro mutagenesis, uracil-containing template mutagenesis, gram and identifying one or more features in the sequence. gapped duplex mutagenesis, point mismatch repair mutagen 0058. The invention provides methods for isolating or esis, repair-deficient host strain mutagenesis, chemical recovering a nucleic acid encoding a polypeptide, enzyme, mutagenesis, radiogenic mutagenesis, deletion mutagenesis, protein, e.g., structural or binding protein, from an environ restriction-selection mutagenesis, restriction-purification mental sample comprising the steps of: (a) providing an mutagenesis, artificial gene synthesis, ensemble mutagen amplification primer sequence pair for amplifying a nucleic esis, chimeric nucleic acid multimer creation and a combina acid encoding a polypeptide, enzyme, protein, e.g., structural tion thereof. or binding protein, wherein the primer pair is capable of 0061. In one aspect, the method can be iteratively repeated amplifying a nucleic acid of the invention; (b) isolating a until a polypeptide, enzyme, protein, e.g., structural or bind nucleic acid from the environmental sample or treating the ing protein having an altered or different activity oran altered environmental sample Such that nucleic acid in the sample is or different stability from that of a polypeptide encoded by the accessible for hybridization to the amplification primer pair; template nucleic acid is produced. In one aspect, the variant and, (c) combining the nucleic acid of step (b) with the ampli the polypeptide, enzyme, protein, e.g., structural or binding fication primer pair of step (a) and amplifying nucleic acid protein is thermotolerant, and retains some activity after from the environmental sample, thereby isolating or recover being exposed to an elevated temperature. In another aspect, ing a nucleic acid encoding a polypeptide, enzyme, protein, the variant the polypeptide, enzyme, protein, e.g., structural e.g., structural or binding protein from an environmental orbinding protein has increased glycosylation as compared to sample. One or each member of the amplification primer the polypeptide, enzyme, protein, e.g., structural or binding sequence pair can comprise an oligonucleotide comprising an protein encoded by a template nucleic acid. Alternatively, the amplification primer sequence pair of the invention, e.g., variant the polypeptide, enzyme, protein, e.g., structural or having at least about 10 to 50 consecutive bases of a sequence binding protein has an enzyme, structural or binding activity of the invention. under a high temperature, wherein the polypeptide, enzyme, 0059. The invention provides methods for isolating or protein, e.g., structural or binding protein encoded by the recovering a nucleic acid encoding a polypeptide, enzyme, template nucleic acid is not active under the high temperature. protein, e.g., structural or binding protein from an environ In one aspect, the method can be iteratively repeated until a mental sample comprising the steps of: (a) providing a poly polypeptide, enzyme, protein, e.g., structural or binding pro nucleotide probe comprising a nucleic acid of the invention or tein coding sequence having an altered codon usage from that a Subsequence thereof; (b) isolating a nucleic acid from the of the template nucleic acid is produced. In another aspect, the environmental sample or treating the environmental sample method can be iteratively repeated until a polypeptide, such that nucleic acid in the sample is accessible for hybrid enzyme, protein, e.g., structural or binding protein gene hav ization to a polynucleotide probe of step (a); (c) combining ing higher or lower level of message expression or stability the isolated nucleic acid or the treated environmental sample from that of the template nucleic acid is produced. of step (b) with the polynucleotide probe of step (a); and (d) 0062. The invention provides methods for modifying isolating a nucleic acid that specifically hybridizes with the codons in a nucleic acid encoding a polypeptide having an polynucleotide probe of step (a), thereby isolating or recov enzyme, structural or binding activity to increase its expres US 2015/0240226 A1 Aug. 27, 2015 sion in a host cell, the method comprising the following steps: or a polypeptide, enzyme, protein, e.g., structural or binding (a) providing a nucleic acid of the invention encoding a protein, Substrate binding site; (b) providing a set of polypeptide having an enzyme, structural orbinding activity; mutagenic oligonucleotides that encode naturally-occurring and, (b) identifying a non-preferred or a less preferred codon amino acid variants at a plurality of targeted codons in the first in the nucleic acid of step (a) and replacing it with a preferred nucleic acid; and, (c) using the set of mutagenic oligonucle or neutrally used codon encoding the same amino acid as the otides to generate a set of active site-encoding or substrate replaced codon, wherein a preferred codon is a codon over binding site-encoding variant nucleic acids encoding a range represented in coding sequences in genes in the host cell and of amino acid variations at each amino acid codon that was a non-preferred or less preferred codon is a codon under mutagenized, thereby producing a library of nucleic acids represented in coding sequences in genes in the host cell, encoding a plurality of modified the polypeptide, enzyme, thereby modifying the nucleic acid to increase its expression protein, e.g., structural or binding protein, active sites or in a host cell. Substrate binding sites. In one aspect, the method comprises 0063. The invention provides methods for modifying mutagenizing the first nucleic acid of step (a) by a method codons in a nucleic acid encoding a polypeptide having an comprising an optimized directed evolution system, Gene enzyme, structural or binding activity; the method compris Site Saturation Mutagenesis (GSSM), synthetic ligation reas ing the following steps: (a) providing a nucleic acid of the sembly (SLR), error-prone PCR, shuffling, oligonucleotide invention; and, (b) identifying a codon in the nucleic acid of directed mutagenesis, assembly PCR, sexual PCR mutagen step (a) and replacing it with a different codon encoding the esis, in Vivo mutagenesis, cassette mutagenesis, recursive same amino acid as the replaced codon, thereby modifying ensemble mutagenesis, exponential ensemble mutagenesis, codons in a nucleic acid encoding a polypeptide, enzyme, site-specific mutagenesis, gene reassembly, and a combina protein, e.g., structural or binding protein. tion thereof. In another aspect, the method comprises 0064. The invention provides methods for modifying mutagenizing the first nucleic acid of step (a) or variants by a codons in a nucleic acid encoding a polypeptide having an method comprising recombination, recursive sequence enzyme, structural or binding activity to increase its expres recombination, phosphothioate-modified DNA mutagenesis, sion in a host cell, the method comprising the following steps: uracil-containing template mutagenesis, gapped duplex (a) providing a nucleic acid of the invention encoding a mutagenesis, point mismatch repair mutagenesis, repair-de polypeptide, enzyme, protein, e.g., structural or binding pro ficient host strain mutagenesis, chemical mutagenesis, radio tein, polypeptide; and, (b) identifying a non-preferred or a genic mutagenesis, deletion mutagenesis, restriction-selec less preferred codon in the nucleic acid of step (a) and replac tion mutagenesis, restriction-purification mutagenesis, ing it with a preferred or neutrally used codon encoding the artificial gene synthesis, ensemble mutagenesis, chimeric same amino acid as the replaced codon, wherein a preferred nucleic acid multimer creation and a combination thereof. codon is a codon over-represented in coding sequences in 0067. The invention provides methods for making a small genes in the host cell and a non-preferred or less preferred molecule comprising the steps of: (a) providing a plurality of codon is a codon under-represented in coding sequences in biosynthetic enzymes capable of synthesizing or modifying a genes in the host cell, thereby modifying the nucleic acid to Small molecule, wherein one of the enzymes comprises an increase its expression in a host cell. enzyme encoded by a nucleic acid of the invention; (b) pro 0065. The invention provides methods for modifying a viding a substrate for at least one of the enzymes of step (a): codon in a nucleic acid encoding a polypeptide having an and, (c) reacting the Substrate of step (b) with the enzymes enzyme, structural or binding activity to decrease its expres under conditions that facilitate a plurality of biocatalytic reac sion in a host cell, the method comprising the following steps: tions to generate a small molecule by a series of biocatalytic (a) providing a nucleic acid of the invention; and (b) identi reactions. fying at least one preferred codon in the nucleic acid of step 0068. The invention provides methods for modifying a (a) and replacing it with a non-preferred or less preferred Small molecule comprising the steps: (a) providing a enzyme codon encoding the same amino acid as the replaced codon, encoded by a nucleic acid of the invention; (b) providing a wherein a preferred codon is a codon over-represented in Small molecule; and, (c) reacting the enzyme of step (a) with coding sequences in genes in a host cell and a non-preferred the small molecule of step (b) under conditions that facilitate or less preferred codon is a codon under-represented in cod an enzymatic reaction catalyzed by the enzyme, thereby ing sequences in genes in the host cell, thereby modifying the modifying a small molecule by an enzymatic reaction. In one nucleic acid to decrease its expression in a host cell. In one aspect, the method comprises providing a plurality of Small aspect, the host cell can be a bacterial cell, a fungal cell, an molecule Substrates for the enzyme of step (a), thereby gen insect cell, a yeast cell, a plant cell or a mammalian cell. erating a library of modified small molecules produced by at 0066. The invention provides methods for producing a least one enzymatic reaction catalyzed by the enzyme. In one library of nucleic acids encoding a plurality of modified aspect, the method further comprises a plurality of additional polypeptides, enzymes, proteins, e.g., structural or binding enzymes under conditions that facilitate a plurality of bio proteins, active sites or Substrate binding sites, wherein the catalytic reactions by the enzymes to form a library of modi modified active sites or substrate binding sites are derived fied small molecules produced by the plurality of enzymatic from a first nucleic acid comprising a sequence encoding a reactions. In one aspect, the method further comprises the first active site or a first substrate binding site the method step of testing the library to determine ifa particular modified comprising the following steps: (a) providing a first nucleic small molecule that exhibits a desired activity is present acid encoding a first active site or first Substrate binding site, within the library. The step of testing the library can further wherein the first nucleic acid sequence comprises a sequence comprises the steps of systematically eliminating all but one that hybridizes under Stringent conditions to a nucleic acid of of the biocatalytic reactions used to produce a portion of the the invention, and the nucleic acid encodes a polypeptide, plurality of the modified small molecules within the library enzyme, protein, e.g., structural or binding protein, active site by testing the portion of the modified small molecule for the US 2015/0240226 A1 Aug. 27, 2015

presence or absence of the particular modified Small molecule sequence comparison algorithm or by visual inspection, with a desired activity, and identifying at least one specific wherein overexpression is effected by use of a high activity biocatalytic reaction that produces the particular modified promoter, a dicistronic vector or by gene amplification of the small molecule of desired activity. Vector. 0069. The invention provides methods for determining a 0073. The invention provides methods of making a trans functional fragment of a polypeptide, enzyme, protein, e.g., genic plant comprising the following steps: (a) introducing a structural or binding protein, comprising the steps of: (a) heterologous nucleic acid sequence into the cell, wherein the providing a polypeptide, enzyme, protein, e.g., structural or heterologous nucleic sequence comprises a nucleic acid binding protein, wherein the enzyme comprises a polypeptide sequence of the invention, thereby producing a transformed of the invention, or a polypeptide encoded by a nucleic acid of plant cell; and (b) producing a transgenic plant from the the invention, or a Subsequence thereof, and (b) deleting a transformed cell. In one aspect, the step (a) can further com plurality of amino acid residues from the sequence of step (a) prise introducing the heterologous nucleic acid sequence by and testing the remaining Subsequence for an enzyme, struc electroporation or microinjection of plant cell protoplasts. In tural or binding activity, thereby determining a functional another aspect, the step (a) can further comprise introducing fragment of a polypeptide, enzyme, protein, e.g., structural or the heterologous nucleic acid sequence directly to plant tissue binding protein. In one aspect, the polypeptide, enzyme, pro by DNA particle bombardment. Alternatively, the step (a) can tein, e.g., structural or binding protein activity is measured by further comprise introducing the heterologous nucleic acid providing a polypeptide, enzyme, protein, e.g., structural or sequence into the plant cell DNA using an Agrobacterium binding protein, Substrate and detecting a decrease in the tumefaciens host. In one aspect, the plant cell can be a potato, amount of the Substrate or an increase in the amount of a corn, rice, wheat, tobacco, or barley cell. reaction product. 0074 The invention provides methods of expressing a het 0070 The invention provides methods for whole cellengi erologous nucleic acid sequence in a plant cell comprising the neering of new or modified phenotypes by using real-time following steps: (a) transforming the plant cell with a heter metabolic flux analysis, the method comprising the following ologous nucleic acid sequence operably linked to a promoter, steps: (a) making a modified cell by modifying the genetic wherein the heterologous nucleic sequence comprises a composition of a cell, wherein the genetic composition is nucleic acid of the invention; (b) growing the plant under modified by addition to the cell of a nucleic acid of the conditions wherein the heterologous nucleic acids sequence invention; (b) culturing the modified cell to generate a plural is expressed in the plant cell. The invention provides methods ity of modified cells; (c) measuring at least one metabolic of expressing a heterologous nucleic acid sequence in a plant parameter of the cell by monitoring the cell culture of step (b) cell comprising the following steps: (a) transforming the plant in real time; and, (d) analyzing the data of step (c) to deter cell with a heterologous nucleic acid sequence operably mine if the measured parameter differs from a comparable linked to a promoter, wherein the heterologous nucleic measurement in an unmodified cell under similar conditions, sequence comprises a sequence of the invention; (b) growing thereby identifying an engineered phenotype in the cell using the plant under conditions wherein the heterologous nucleic real-time metabolic flux analysis. In one aspect, the genetic acids sequence is expressed in the plant cell. composition of the cell can be modified by a method com 0075. The invention provides feeds or foods comprising a prising deletion of a sequence or modification of a sequence polypeptide of the invention, or a polypeptide encoded by a in the cell, or, knocking out the expression of a gene. In one nucleic acid of the invention. In one aspect, the invention aspect, the method can further comprise selecting a cell com provides a food, feed, a liquid, e.g., a beverage (such as a fruit prising a newly engineered phenotype. In another aspect, the juice or a beer), a bread or a dough or a bread product, or a method can comprise culturing the selected cell, thereby gen beverage precursor (e.g., a wort), comprising a polypeptide of erating a new cell strain comprising a newly engineered phe the invention. The invention provides food or nutritional notype. Supplements for an animal comprising a polypeptide of the 0071. The invention provides methods of increasing ther invention, e.g., a polypeptide encoded by the nucleic acid of motolerance or thermostability of a polypeptide, enzyme, the invention. protein, e.g., structural or binding protein, polypeptide, the 0076. In one aspect, the polypeptide in the food or nutri method comprising glycosylating a polypeptide, enzyme, tional Supplement can be glycosylated. The invention pro protein, e.g., structural or binding protein, wherein the vides edible enzyme delivery matrices comprising a polypep polypeptide, enzyme, protein, e.g., structural or binding pro tide of the invention, e.g., a polypeptide encoded by the tein comprises at least thirty contiguous amino acids of a nucleic acid of the invention. In one aspect, the delivery polypeptide of the invention; or a polypeptide encoded by a matrix comprises a pellet. In one aspect, the polypeptide can nucleic acid sequence of the invention, thereby increasing be glycosylated. In one aspect, the polypeptide, enzyme, pro thermotolerance or thermostability of the polypeptide, tein, e.g., structural or binding protein activity is thermotol enzyme, protein, e.g., structural or binding protein. In one erant. In another aspect, the polypeptide, enzyme, protein, aspect, the polypeptide, enzyme, protein, e.g., structural or e.g., structural or binding protein activity is thermostable. binding protein specific activity can be thermostable or ther 0077. The invention provides a food, a feed or a nutritional motolerant at a temperature in the range from greater than Supplement comprising a polypeptide of the invention. The about 37° C. to about 95° C. invention provides methods for utilizing a polypeptide, 0072 The invention provides methods for overexpressing enzyme, protein, e.g., structural or binding protein, as a nutri a recombinant polypeptide, enzyme, protein, e.g., structural tional Supplement in an animal diet, the method comprising: or binding protein, in a cell comprising expressing a vector preparing a nutritional Supplement containing a polypeptide, comprising a nucleic acid comprising a nucleic acid of the enzyme, protein, e.g., structural or binding protein, compris invention or a nucleic acid sequence of the invention, wherein ing at least thirty contiguous amino acids of a polypeptide of the sequence identities are determined by analysis with a the invention; and administering the nutritional Supplement to US 2015/0240226 A1 Aug. 27, 2015

an animal. The animal can be a human, a ruminant or a I0086 FIG. 4 is a flow diagram illustrating one aspect of an monogastric animal. The polypeptide, enzyme, protein, e.g., identifier process 300 for detecting the presence of a feature in structural or binding protein can be prepared by expression of a Sequence. a polynucleotide encoding the polypeptide, enzyme, protein, I0087. Like reference symbols in the various drawings e.g., structural or binding protein in an organism selected indicate like elements. from the group consisting of a bacterium, a yeast, a plant, an insect, a fungus and an animal. The organism can be selected from the group consisting of an S. pombe, S. cerevisiae, DETAILED DESCRIPTION OF THE INVENTION Pichia pastoris, E. coli, Streptomyces sp., Bacillus sp. and I0088. The invention provides isolated and recombinant Lactobacillus sp. polypeptides, including enzymes, structural proteins and 0078. The invention provides edible enzyme delivery binding proteins, polynucleotides encoding these polypep matrix comprising thermostable recombinant polypeptide, tides, and methods of making and using these polynucleotides enzyme, protein, e.g., structural or binding protein of the and polypeptides. The polypeptides of the invention, and the invention. The invention provides methods for delivering a polynucleotides encoding the polypeptides of the invention, polypeptide, enzyme, protein, e.g., structural or binding pro encompass many classes of enzymes, structural proteins and tein, Supplement to an animal, the method comprising: pre binding proteins. In one aspect, the enzymes and proteins of paring an edible enzyme delivery matrix in the form of pellets the invention comprise, e.g., aldolases, alpha-galactosidases, comprising a granulate edible carrier and thermostable amidases, e.g., secondary amidases, amylases, catalases, recombinant polypeptide, enzyme, protein, e.g., structural or carotenoid pathway enzymes, dehalogenases, endogluca binding protein, wherein the pellets readily disperse the nases, epoxide hydrolases, esterases, hydrolases, glucosi polypeptide, enzyme, protein, e.g., structural or binding pro dases, glycosidases, inteins, isomerases, laccases, lipases, tein contained therein into aqueous media, and administering monooxygenases, nitroreductases, nitrilases, P450 enzymes, the edible enzyme delivery matrix to the animal. The recom pectate lyases, phosphatases, phospholipases, phytases, poly binant polypeptide, enzyme, protein, e.g., structural or bind merases and Xylanases, which are more specifically described ing protein can comprise a polypeptide of the invention. The below. The invention also provides isolated and recombinant polypeptide, enzyme, protein, e.g., structural or binding pro polypeptides, including enzymes, structural proteins and tein can be glycosylated to provide thermostability at pellet binding proteins, polynucleotides encoding these polypep izing conditions. The delivery matrix can be formed by pel tides, having the activities described in Table 1, Table 2 or letizing a mixture comprising a grain germ and a polypeptide, Table 3, below. enzyme, protein, e.g., structural or binding protein. The pel letizing conditions can include application of steam. The pelletizing conditions can comprise application of a tempera Aldolases ture in excess of about 80° C. for about 5 minutes and the I0089. In one aspect, the invention provides aldolases, enzyme retains a specific activity of at least 350 to about 900 polynucleotides encoding them, and methods of making and units per milligram of enzyme. using these polynucleotides and polypeptides. In one aspect, 0079. In one aspect, invention provides a pharmaceutical the invention is directed to polypeptides, e.g., enzymes, hav composition comprising a polypeptide, enzyme, protein, e.g., ing an aldolase activity, including thermostable and thermo structural or binding protein, of the invention, or a polypep tolerant aldolase activity, and polynucleotides encoding these tide encoded by a nucleic acid of the invention. In one aspect, enzymes, and making and using these polynucleotides and the pharmaceutical composition acts as a digestive aid. polypeptides. In one aspect, the aldolase activity comprises 0080. The details of one or more aspects of the invention catalysis of the formation of a carbon-carbon bond. In one are set forth in the accompanying drawings and the descrip aspect, the aldolase activity comprises an aldol condensation. tion below. Other features, objects, and advantages of the The aldol condensation can have an aldol donor Substrate invention will be apparent from the description and drawings, comprising an acetaldehyde and an aldol acceptor Substrate and from the claims. comprising an aldehyde. The aldol condensation can yield a 0081 All publications, patents, patent applications, Gen product of a single chirality. In one aspect, the aldolase activ Bank sequences and ATCC deposits, cited herein are hereby ity is enantioselective. The aldolase activity can comprise a expressly incorporated by reference for all purposes. 2-deoxyribose-5-phosphate aldolase (DERA) activity. The aldolase activity can comprise catalysis of the condensation of acetaldehyde as donor and a 2CR)-hydroxy-3-(hydroxy or BRIEF DESCRIPTION OF THE DRAWINGS mercapto)-propionaldehyde derivative to form a 2-deox 0082. The following drawings are illustrative of aspects of ySugar. The aldolase activity can comprise catalysis of the the invention and are not meant to limit the scope of the condensation of acetaldehyde as donor and a 2-substituted invention as encompassed by the claims. acetaldehyde acceptor to form a 2,4,6-trideoxyhexose via a 4-substituted-3-hydroxybutanal intermediate. The aldolase 0083 FIG. 1 is a block diagram of a computer system. activity can comprise catalysis of the generation of chiral 0084 FIG. 2 is a flow diagram illustrating one aspect of a aldehydes using two acetaldehydes as Substrates. The aldo process for comparing a new nucleotide or protein sequence lase activity can comprises enantioselective assembling of with a database of sequences in order to determine the homol chiral 0.6-dihydroxyheptanoic acid side chains. The aldolase ogy levels between the new sequence and the sequences in the activity can comprise enantioselective assembling of the core database. of R—(R*,R)-2-(4-fluorophenyl)-b.d-dihydroxy-5-(1- 0085 FIG. 3 is a flow diagram illustrating one aspect of a methylethyl)-3-phenyl-4-(phenylamino)-carbonyl)-1H-pyr processina computer for determining whether two sequences role-1-heptanoic acid (Atorvastatin, or LIPITORTM), rosuv are homologous. astatin (CRESTORTM) and/or fluvastatin (LESCOLTM). The US 2015/0240226 A1 Aug. 27, 2015 aldolase activity can comprise, with an oxidation step. Syn the invention is directed to polypeptides, e.g., enzymes, hav thesis of a 3R,5S-6-chloro-2,4,6-trideoxy-erythro-hexono ing an amylase activity, including thermostable and thermo lactone. tolerant amylase activity, and polynucleotides encoding these 0090 Alpha-Galactosidases enzymes, and making and using these polynucleotides and 0091. In one aspect, the invention provides alpha-galac polypeptides. tosidases, polynucleotides encoding them, and methods of 0100. In one aspect, the polypeptides of the invention can making and using these polynucleotides and polypeptides. In be used as amylases, for example, alpha amylases or glu one aspect, the invention is directed to polypeptides, e.g., coamylases, to catalyze the hydrolysis of starch into Sugars. enzymes, having an alpha-galactosidase activity, including In one aspect, the invention is directed to polypeptides having thermostable and thermotolerant alpha-galactosidase activ thermostable amylase activity, such as alpha amylases or ity, and polynucleotides encoding these enzymes, and making glucoamylase activity, e.g., a 1,4-alpha-D-glucan glucohy and using these polynucleotides and polypeptides. drolase activity. In one aspect, the polypeptides of the inven 0092 An alpha galactosidase hydrolyses the non-reduc tion can be used as amylases, for example, alpha amylases or ing terminal alpha 1-3,4,6 linked galactose from poly- and glucoamylases, to catalyze the hydrolysis of starch into Sug oligosaccharides. These saccharides are commonly found in ars, such as glucose. The invention is also directed to nucleic legumes and are difficult to digest. As such, alpha-galactosi acid constructs, vectors, and host cells comprising the nucleic dases can be used as a digestive aid to break down raffinose, acid sequences of the invention as well as recombinant meth stachyose, and Verbascose, found in Such foods as beans and ods for producing the polypeptides of the invention. The other gassy foods. invention is also directed to the use of amylases of the inven 0093. Amidases tion in starch conversion processes, including production of 0094. In one aspect, the invention provides amidases, high fructose corn syrup (HFCS), ethanol, dextrose, and dex polynucleotides encoding them, and methods of making and trose syrups. using these polynucleotides and polypeptides. In one aspect, 0101 Commercially, glucoamylases are used to further the invention is directed to polypeptides, e.g., enzymes, hav hydrolyze cornstarch, which has already been partially ing an amidase activity, including thermostable and thermo hydrolyzed with an alpha-amylase. The glucose produced in tolerant amidase activity, and polynucleotides encoding these this reaction may then be converted to a mixture of glucose enzymes, and making and using these polynucleotides and and fructose by a glucose isomerase enzyme. This mixture, or polypeptides. In one aspect, the amidases of the invention are one enriched with fructose, is the high fructose corn syrup used in the removal of arginine, phenylalanine or methionine commercialized throughout the world. In general, starch to from the N-terminal end of peptides in peptide or peptidomi fructose processing consists of four steps: liquefaction of metic synthesis. In one aspect, the enzyme of the invention, granular starch, Saccharification of the liquefied Starch into e.g., an amidase, is selective for the L, or “natural enanti dextrose, purification, and isomerization to fructose. The omer of the amino acid derivatives and is therefore useful for object of a starch liquefaction process is to convert a concen the production of optically active compounds. These reac trated Suspension of starch polymer granules into a solution tions can be performed in the presence of the chemically more of soluble shorter chain length dextrins of low viscosity. reactive ester functionality, a step which is very difficult to 0102 The amylases of the invention can be used in auto achieve with nonenzymatic methods. The enzyme is also able matic dish wash (ADW) products and laundry detergent. In to tolerate high temperatures (at least 70° C.), and high con ADW products, the amylase will function at pH 10-11 and at centrations of organic solvents (>40% DMSO), both of which 45-60°C. in the presence of calcium chelators and oxidative cause a disruption of secondary structure in peptides, which conditions. For laundry, activity at pH 9-10 and 40°C. in the enables cleavage of otherwise resistant bonds. appropriate detergent matrix will be required. Amylases are 0095 Secondary Amidases also useful in textile desizing, brewing processes, starch 0096. In one aspect, the invention provides secondary ami modification in the paper and pulp industry and other pro dases, polynucleotides encoding them, and methods of mak cesses described in the art. ing and using these polynucleotides and polypeptides. In one 0103) Amylases can be used commercially in the initial aspect, the invention is directed to polypeptides, e.g., stages (liquefaction) of Starch processing; in wet corn mill enzymes, having a secondary amidase activity, including ing; in alcohol production; as cleaning agents in detergent thermostable and thermotolerant secondary amidase activity, matrices; in the textile industry for starch desizing; in baking and polynucleotides encoding these enzymes, and making applications; in the beverage industry; in oilfields in drilling and using these polynucleotides and polypeptides. processes; in inking of recycled paper and in animal feed. 0097. Secondary amidases include a variety of useful Amylases are also useful in textile desizing, brewing pro enzymes including peptidases, proteases, and hydantoinases. cesses, starch modification in the paper and pulp industry and This class of enzymes can be used in a range of commercial other processes. applications. For example, secondary amidases can be used 0104 Carotenoid Pathway Enzymes to: 1) increase flavor in food, in particular cheese (known as 0105. The invention provides novel enzymes, and the enzyme ripened cheese); 2) promote bacterial and fungal polynucleotides encoding them, involved in carotenoid (Such killing; 3) modify and de-protect fine chemical intermediates as lycopenes and luteins), astaxanthin and/or isoprenoid syn 4) synthesize peptide bonds; 5) and carry out chiral resolu thesis. The invention also provides novel genes in the caro tions. Particularly, there is a need in the art for an enzyme tenoid, astaxanthin and isoprenoid biosynthetic pathways capable of hydrolyzing Cephalosporin C. comprising at least one enzyme of the invention. For example, 0098. Amylases alternative aspects, the invention provides one or more 0099. In one aspect, the invention provides amylases, nucleic acid coding sequences (CDSs, or ORFs) encoding all, polynucleotides encoding them, and methods of making and or at least one, enzyme(s) involved in a desired biosynthetic using these polynucleotides and polypeptides. In one aspect, pathway for carotenoids, astaxanthins and/or isoprenoids. US 2015/0240226 A1 Aug. 27, 2015

The nucleic acid coding sequence(s) can be expressed ate polluted environments via microbial and related enzy through an expression plasmid, vector, engineered virus or matic processes. Unfortunately, many chemical pollutants are any episomal expression system, or, can be integrated into the either resistant to microbial degradation or are toxic to poten genome of the host cell. In one aspect, the enzyme(s) involved tial microbial-degraders when present in high concentrations in the biosynthetic pathway system comprise a novel combi and certain combinations. nation of enzymes. In another aspect, the enzyme(s) involved 0113 Dehalogenases, e.g., haloalkane dehalogenases, of in the biosynthetic pathway system comprise at least one the invention can cleave carbon-halogen bonds in haloal novel enzyme of the invention where nucleic acids used in the kanes and halocarboxylic acids by hydrolysis, thus convert system encode a novel enzyme of the invention. ing them to their corresponding alcohols. This reaction can be 0106 Carotenoids are natural pigments which have anti used for detoxification involving haloalkanes, such as ethyl oxidant and anti-carcinogenic activity. They are free radical chloride, methylchloride, and 1,2-dichloroethane (e.g., Scavengers, and as such, strong antioxidants. Carotenoids detoxification of toxic composition, e.g., pesticides, poisons, have a conjugated backbone structure and are very rigid mol chemical warfare agents and the like comprising haloal ecules, having a backbone consisting of 9 to 11 alternating kanes). single/double bonds and have very similar electro-optical 0114. The present invention provides a number of dehalo properties as polyacetylene. Astaxanthins are abundant natu genase enzymes useful in bioremediation having improved rally occurring carotenoids. They contain an internal unit enzymatic characteristics. The polynucleotides and poly similar to beta-carotene but have two terminal carbonyl and nucleotide products of the invention are useful in, for hydroxyl functionalities. These compounds are useful for example, groundwater treatment involving transformed host food and feed Supplements, colorants, neutraceuticals, cos cells containing a polynucleotide or polypeptide of the inven metic and pharmaceutical needs. Isoprenoids are compounds tion (e.g., the bacteria Xanthobacter autotrophicus) and the biosynthesized from or containing isoprene (unsaturated haloalkane 1,2-dichlorethane as well as removal of polychlo branched chain five-carbon hydrocarbon) units, includingter rinated biphenyls (PCBs) from soil sediment. penes, carotenoids, fat soluble vitamins, ubiquinone, rubber, 0115 The haloalkane dehalogenase of the invention are and some steroids. Biosynthetic pathways for carotenoids, useful in carbon-halide reduction efforts. The enzymes of the astaxanthins and isoprenoids are known; most of these pub invention initiate the degradation of haloalkanes. Alterna lished pathways are derived from one organism or a combi tively, host cells containing a dehalogenase polynucleotide or nation of genes from a few species. polypeptide of the invention can feed on the haloalkanes and 0107 Catalases produce the detoxifying enzyme. 0108. In one aspect, the invention provides catalases, 0116 Endoglucanases polynucleotides encoding them, and methods of making and 0117. In one aspect, the invention provides endogluca using these polynucleotides and polypeptides. In one aspect, nases, polynucleotides encoding them, and methods of mak the invention is directed to polypeptides, e.g., enzymes, hav ing and using these polynucleotides and polypeptides. In one ing a catalase activity, including thermostable and thermotol aspect, the invention is directed to polypeptides, e.g., erant catalase activity, and polynucleotides encoding these enzymes, having an endoglucanase activity, including ther enzymes, and making and using these polynucleotides and mostable and thermotolerant endoglucanase activity, and polypeptides. polynucleotides encoding these enzymes, and making and 0109. In processes where hydrogen peroxide is a by-prod using these polynucleotides and polypeptides. uct, catalases of the invention can be used to destroy or detect 0118. In one aspect, the enzymes of the invention have a hydrogen peroxide, e.g., in production of glyoxylic acid and glucanase, e.g., an endoglucanase, activity, e.g., catalyzing in glucose sensors. Also, in processes where hydrogen per hydrolysis of internal endo-B-1,4- and/or B-1,3-glucanase oxide is used as a bleaching orantibacterial agent, catalases of linkages. In one aspect, the endoglucanase activity (e.g., the invention can be used to destroy residual hydrogen per endo-1,4-beta-D-glucan 4-glucano hydrolase activity) com oxide, e.g., in contact lens cleaning, in bleaching steps in pulp prises hydrolysis of 1,4- and/or B-1,3-beta-D-glycosidic link and paper production, and in the pasteurization of dairy prod ages in cellulose, cellulose derivatives (e.g., carboxy methyl ucts. Further, Such catalases of the invention can be used as cellulose and hydroxy ethyl cellulose) lichenin, beta-1,4 catalysts for oxidation reactions, e.g., epoxidation and bonds in mixed beta-1,3 glucans, such as cereal beta-D-glu hydroxylation. cans or Xyloglucans and other plant material containing cel 0110 Dehalogenases lulosic parts. 0111. In one aspect, the invention provides dehalogenases, 0119 Endoglucanases of the invention (e.g., endo-beta-1, polynucleotides encoding them, and methods of making and 4-glucanases, EC 3.2.1.4, endo-beta-1,3(1)-glucanases, EC using these polynucleotides and polypeptides. In one aspect, 3.2.1.6; endo-beta-1,3-glucanases, EC 3.2.1.39) can hydro the invention is directed to polypeptides, e.g., enzymes, hav lyze internal B-1,4- and/or B-1,3-glucosidic linkages in cel ing a dehalogenase activity, including thermostable and ther lulose and glucan to produce Smaller molecular weight glu motolerant dehalogenase activity, and polynucleotides cose and glucose oligomers. Glucans are polysaccharides encoding these enzymes, and making and using these poly formed from 1,4-B- and/or 1.3-glycoside-linked D-glucopy nucleotides and polypeptides. ranose. Endoglucanases of the invention can be used in the 0112 Environmental pollutants consist of a large quantity food industry, for baking and fruit and vegetable processing, and variety of chemicals; many of these are toxic, environ breakdown of agricultural waste, in the manufacture of ani mental hazards that were designated in 1979 as priority pol mal feed, in pulp and paper production, textile manufacture lutants by the U.S. Environmental Protection Agency. Micro and household and industrial cleaning agents. Endogluca bial and enzymatic biodegradation is one method for the nases are produced by fungi and bacteria. elimination of these pollutants. Accordingly, methods have 0120 Beta-glucans are major non-starch polysaccharides been designed to treat commercial wastes and to bioremedi of cereals. The glucan content can vary significantly depend US 2015/0240226 A1 Aug. 27, 2015 ing on variety and growth conditions. The physicochemical cally enriched-epoxides (the unreacted enantiomer) and/or to properties of this polysaccharide are such that it gives rise to the corresponding vicinal diols. Viscous solutions or evengels under oxidative conditions. In O127 Esterases addition glucans have high water-binding capacity. All of I0128. In one aspect, the invention provides esterases, these characteristics present problems for several industries polynucleotides encoding them, and methods of making and including brewing, baking, animal nutrition. In brewing using these polynucleotides and polypeptides. In one aspect, applications, the presence of glucan results in wort filterabil the invention is directed to polypeptides, e.g., enzymes, hav ity and haze formation issues. In baking applications (espe ing an esterase activity, including thermostable and thermo cially for cookies and crackers), glucans can create sticky tolerantesterase activity, and polynucleotides encoding these doughs that are difficult to machine and reduce biscuit size. In enzymes, and making and using these polynucleotides and addition, this carbohydrate is implicated in rapid rehydration polypeptides. of the baked product resulting in loss of crispiness and reduced shelf-life. For monogastric animal feed applications I0129. Many esterases are known and have been discovered with cereal diets, beta-glucan is a contributing factor to vis in a broad variety of organisms, including bacteria, yeast and cosity of gut contents and thereby adversely affects the higher animals and plants. A principal example of esterases digestibility of the feed and animal growth rate. For ruminant are the lipases, which are used in the hydrolysis of lipids, animals, these beta-glucans represent Substantial components acidolysis (replacement of an esterified fatty acid with a free fatty acid) reactions, transesterification (exchange of fatty offiber intake and more complete digestion of glucans would acids between triglycerides) reactions, and in ester synthesis. facilitate higher feed conversion efficiencies. It is desirable The major industrial applications for lipases include: the for animal feed endoglucanases to be active in the animal detergent industry, where they are employed to decompose stomach. fatty materials in laundry stains into easily removable hydro 0121 Endoglucanases of the invention can be used in the philic substances; the food and beverage industry where they digestion of cellulose, a beta-1,4-linked glucan found in all are used in the manufacture of cheese, the ripening and fla plant material. Cellulose is the most abundant polysaccharide Voring of cheese, as antistaling agents for bakery products, in nature. Enzymes of the invention that digest cellulose have and in the production of margarine and other spreads with utility in the pulp and paper industry, in textile manufacture natural butter flavors; in waste systems; and in the pharma and in household and industrial cleaning agents. ceutical industry where they are used as digestive aids. 0122) Epoxide Hydrolases 0.130. Alternatively, esterases of the invention can be used 0123. In one aspect, the invention provides epoxide hydro in detergent compositions. In one aspect, the esterase can be lases, polynucleotides encoding them, and methods of mak a nonsurface-active esterase. In another aspect, the esterase ing and using these polynucleotides and polypeptides. In one can be a surface-active esterase. The esterase can be formu aspect, the invention is directed to polypeptides, e.g., lated in a non-aqueous liquid composition, a cast Solid, a enzymes, having an epoxide hydrolase activity, including granular form, a particulate form, a compressed tablet, a gel thermostable and thermotolerant epoxide hydrolase activity, form, a paste or a slurry form. and polynucleotides encoding these enzymes, and making I0131. In another aspect, the invention provides fabrics or and using these polynucleotides and polypeptides. The clothing comprising an esterase of the invention. In another polypeptides of the invention can be used as epoxide hydro aspect, esterases of the invention are used to treat a lipid lases to catalyze the hydrolysis of epoxides and arene oxides containing fabric. to their corresponding diols. 0.132. In another aspect, the invention provides foods and 0.124 Epoxide hydrolases catalyze the hydrolysis of drinks comprising an esterase of the invention. The invention epoxides and arene oxides to their corresponding diols. also provides cheeses comprising an esterase of the invention. Epoxide hydrolases from microbial sources are highly versa Additionally, the invention provides methods for the manu tile biocatalysts for the asymmetric hydrolysis of epoxides on facture of cheese comprising the following steps: (a) provid a preparative scale. Besides kinetic resolution, which fur ing a polypeptide having an esterase activity, wherein the nishes the corresponding vicinal diol and remaining non polypeptide comprises a polypeptide of the invention, or, a hydrolyzed epoxide in nonracemic form, enantioconvergent polypeptide encoded by a nucleic acid of the invention; (b) processes are possible. These are highly attractive as they lead providing a cheese precursor, and (c) contacting the polypep to the formation of a single enantiomeric diol from a racemic tide of step (a) with the precursor of step (b) under condition oxirane. wherein the esterase can catalyze cheese manufacturing pro 0.125 Microsomal epoxide hydrolases are biotransforma cesses. In one aspect, the method can comprise the process of tion enzymes that catalyze the conversion of a broad array of ripening and flavoring of cheese. xenobiotic epoxide substrates to more polar diol metabolites, I0133. In another aspect, the invention provides margarines see, e.g., Omiecinski (2000) Toxicol. Lett. 112-113:365-370. and spreads comprising an enzyme of the invention. The Microsomal epoxide hydrolases catalyze the addition of invention provides methods for production of margarine or water to epoxides in a two-step reaction involving initial other spreads with natural butter flavors comprising the fol attack of an active site carboxylate on the oxirane to give an lowing steps: (a) providing a polypeptide having an esterase ester intermediate followed by hydrolysis of the ester. Soluble activity, wherein the polypeptide comprises a polypeptide of epoxide hydrolase play a role in the biosynthesis of inflam the invention, or, a polypeptide encoded by a nucleic acid of mation mediators. the invention; (b) providing a margarine or a spread precur 0126 Epoxide hydrolases of the invention can be used in Sor, and (c) contacting the polypeptide of step (a) with the the detoxification of epoxides or in the biosynthesis of hor precursor of step (b) under condition wherein the esterase can mones. Additionally, epoxide hydrolases of the invention can catalyze processes involved in margarine or spread produc efficiently process several Substrates, leading to enantiomeri tion. US 2015/0240226 A1 Aug. 27, 2015

0134. The invention provides methods for treating solidor activity, lipase activity (hydrolysis of lipids), acidolysis reac liquid waste products comprising the following steps: (a) tions (to replace an esterified fatty acid with a free fatty acid), providing a polypeptide having an esterase activity, wherein transesterification reactions (exchange offatty acids between the polypeptide comprises a polypeptide of the invention, or, triglycerides), ester synthesis, ester interchange reactions, a polypeptide encoded by a nucleic acid of the invention; (b) phospholipase activity (e.g., phospholipase A, B, C and D providing a solid or a liquid waste; and (c) contacting the activity, patatin activity, lipid acyl hydrolase (LAH) activity) polypeptide of step (a) and the waste of step (b) under con and protease activity (hydrolysis of peptide bonds). The ditions wherein the polypeptide can treat the waste. The polypeptides of the invention can be used in a variety of invention provides solid or liquid waste products comprising pharmaceutical, agricultural and industrial contexts, includ a polypeptide of the invention. ing the manufacture of cosmetics and nutraceuticals. 0135 The invention provides methods for aiding digestion 0142. In one aspect, the polypeptides of the invention are in a mammal comprising (a) providing a polypeptide having used in the biocatalytic synthesis of structured lipids (lipids an esterase activity, wherein the polypeptide comprises a that contain a defined set offatty acids distributed in a defined polypeptide of the invention, or, a polypeptide encoded by a manner on the glycerol backbone), including cocoa butter nucleic acid of the invention; (b) providing a composition alternatives (CBA), lipids containing poly-unsaturated fatty comprising a Substrate for the polypeptide of step (a); (c) acids (PUFAs), diacylglycerides, e.g., 1,3-diacyl glycerides feeding or administering to the mammal the polypeptide of (DAGs), monoglycerides, e.g., 2-monoglycerides (MAGs) step (a) with a feed or food comprising a substrate for the and triacylglycerides (TAGs). In one aspect, the polypeptides polypeptide of step (a), thereby helping digestion in the mam of the invention are used to modify oils, such as fish, animal mal. In one aspect, the mammal is a human. and vegetable oils, and lipids, Such as poly-unsaturated fatty 0136. The invention provides pharmaceutical composi acids. The hydrolases of the invention having lipase activity tions comprising a polypeptide and/or a nucleic acid of the can modify oils by hydrolysis, alcoholysis, esterification, invention, e.g., a pharmaceutical composition for use as a transesterification and/or interesterification. The methods of digestive aid in a mammal comprising a polypeptide having the invention can use lipases with defined regio-specificity or an esterase activity, wherein the polypeptide comprises a defined chemoselectivity in biocatalytic synthetic reactions. polypeptide of the invention, or, a polypeptide encoded by a In another aspect, the polypeptides of the invention are used nucleic acid of the invention. In one aspect, the mammal to synthesize enantiomerically pure chiral products. comprises a human. The enzymes of the invention are used in 0.143 Additionally, the polypeptides of the invention can the manufacture of medicaments. be used in food processing, brewing, bath additives, alcohol 0.137 The invention provides bakery products comprising production, peptide synthesis, enantioselectivity, hide prepa a polypeptide of the invention. The invention provides anti ration in the leather industry, waste management and animal Staling agents for bakery products comprising a polypeptide degradation, silver recovery in the photographic industry, having an esterase activity, wherein the polypeptide com medical treatment, silk degumming, biofilm degradation, prises a polypeptide of the invention, or, a polypeptide biomass conversion to ethanol, biodefense, antimicrobial encoded by a nucleic acid of the invention. agents and disinfectants, personal care and cosmetics, biotech 0.138. The invention provides methods for hydrolyzing, reagents, in increasing starch yield from corn wet milling and breaking up or disrupting a ester-comprising composition pharmaceuticals such as digestive aids and anti-inflammatory comprising the following steps: (a) providing a polypeptide (anti-phlogistic) agents. of the invention having an esterase activity, or a polypeptide 0144. The major industrial applications for hydrolases, encoded by a nucleic acid of the invention; (b) providing a e.g., esterases, lipases, phospholipases and proteases, include composition comprising a protein; and (c) contacting the the detergent industry, where they are employed to decom polypeptide of step (a) with the composition of step (b) under pose fatty materials in laundry stains into easily removable conditions wherein the esterase hydrolyzes, breaks up or dis hydrophilic substances; the food and beverage industry where rupts the ester-comprising composition. they are used in the manufacture of cheese, the ripening and 0.139. Alternatively, the invention provides methods for flavoring of cheese, as antistaling agents for bakery products, liquefying or removing ester-comprising compositions com and in the production of margarine and other spreads with prising the following steps: (a) providing a polypeptide of the natural butter flavors; in waste systems; and in the pharma invention having an esterase activity, or a polypeptide ceutical industry where they are used as digestive aids. encoded by a nucleic acid of the invention; (b) providing a 0145. Oils and fats an important renewable raw material composition comprising a protein; and (c) contacting the for the chemical industry. They are available in large quanti polypeptide of step (a) with the composition of step (b) under ties from the processing of oilseeds from plants like rice bran conditions wherein esterase removes or liquefies the ester oil, rapeseed (canola), Sunflower, olive, palm or soy. Other comprising compositions. Sources of valuable oils and fats include fish, restaurant waste, 0140 Hydrolases and rendered animal fats. These fats and oils are a mixture of 0141. In one aspect, the invention provides hydrolases, triglycerides or lipids, i.e., fatty acids (FAS) esterified on a polynucleotides encoding them, and methods of making and glycerol scaffold. Each oil or fat contains a wide variety of using these polynucleotides and polypeptides. In one aspect, different lipid structures, defined by the FA content and their the invention is directed to polypeptides, e.g., enzymes, hav regiochemical distribution on the glycerol backbone. These ing a hydrolase activity, e.g., an esterase, acylase, lipase, properties of the individual lipids determine the physical phospholipase or protease activity, including thermostable properties of the pure triglyceride. Hence, the triglyceride and thermotolerant hydrolase activity, and polynucleotides content of a fator oil to a large extent determines the physical, encoding these enzymes, and making and using these poly chemical and biological properties of the oil. The value of nucleotides and polypeptides. The hydrolase activities of the lipids increases greatly as a function of their purity. High polypeptides and peptides of the invention include esterase purity can be achieved by fractional chromatography or dis US 2015/0240226 A1 Aug. 27, 2015 tillation, separating the desired triglyceride from the mixed can hydrolyze terminal non-reducing 1.4 or 1.6 linked C-D- background of the fat or oil source. However, this is costly and glucose residues in starch, with release of C-D-glucose. yields are often limited by the low levels at which the triglyc 0152 Alpha-glucosidases of the invention can be used eride occurs naturally. In addition, the purity of the product is commercially in the stages liquefaction and saccharification often compromised by the presence of many structurally and of starch processing; in wet corn milling; in alcohol produc physically or chemically similar triglycerides in the oil. tion; as cleaning agents in detergent matrices; in the textile 014.6 An alternative to purifying triglycerides or other industry for starch desizing; in baking applications; in the lipids from a natural source is to synthesize the lipids. The beverage industry; in oilfields in drilling processes; in inking products of Such processes are called structured lipids of recycled paper and in animal feed. Alpha-glucosidases of because they contain a defined set offatty acids distributed in the invention are also useful in textile desizing, brewing pro a defined manner on the glycerol backbone. The value of cesses, starch modification in the paper and pulp industry and lipids also increases greatly by controlling the fatty acid con other processes. tent and distribution within the lipid. Lipases can be used to 0153. Glycosidases affect such control. 0154 In one aspect, the invention provides glycosidases, 0147 Phospholipases are enzymes that hydrolyze the polynucleotides encoding them, and methods of making and ester bonds of phospholipids. Corresponding to their impor using these polynucleotides and polypeptides. In one aspect, tance in the metabolism of phospholipids, these enzymes are the invention is directed to polypeptides, e.g., enzymes, hav widespread among prokaryotes and eukaryotes. The phos ing a glycosidase activity, including thermostable and ther pholipases affect the metabolism, construction and reorgani motolerant glycosidase activity, and polynucleotides encod Zation of biological membranes and are involved in signal ing these enzymes, and making and using these cascades. Several types of phospholipases are known which polynucleotides and polypeptides. Glycosidase enzymes of differ in their specificity according to the position of the bond the invention can have more specific activity as glucosidases, attacked in the phospholipid molecule. Phospholipase A1 O-galactosidases, B-galactosidases, B-mannosidases, B-man (PLA1) removes the 1-position fatty acid to produce free fatty nanases, endoglucanases, and pullulanases. acid and 1-lyso-2-acylphospholipid. Phospholipase A2 0155 C.-galactosidases of the invention can catalyze the (PLA2) removes the 2-position fatty acid to produce free fatty hydrolysis of galactose groups on a polysaccharide backbone acid and 1-acyl-2-lysophospholipid. PLA1 and PLA2 or hydrolyze the cleavage of di- or oligosaccharides compris enzymes can be intra- or extra-cellular, membrane-bound or ing galactose. B-mannanases of the invention can catalyze the soluble. Intracellular PLA2 is found in almost every mamma hydrolysis of mannose groups internally on a polysaccharide liancell. Phospholipase C (PLC) removes the phosphate moi backbone or hydrolyze the cleavage of di- or oligosaccharides ety to produce 1.2 diacylglycerol and phospho base. Phos comprising mannose groups. B-mannosidases of the inven pholipase D (PLD) produces 1,2-diacylglycerophosphate and tion can hydrolyze non-reducing, terminal mannose residues base group. PLC and PLD are important in cell function and on a mannose-containing polysaccharide and the cleavage of signaling. Patatins are another type of phospholipase thought di- or oligosaccaharides comprising mannose groups. to work as a PLA. 0156 Guargum is a branched galactomannan polysaccha 0148. In general, enzymes, including hydrolases such as ride composed off3-1, 4 linked mannose backbone with C-1, esterases, lipases and proteases, are active over a narrow 6 linked galactose sidechains. The enzymes required for the range of environmental conditions (temperature, pH, etc.), degradation of guar are B-mannanase, B-mannosidase and and many are highly specific for particular Substrates. The O-galactosidase. B-mannanase hydrolyses the mannose back narrow range of activity for a given enzyme limits its appli bone internally and B-mannosidase hydrolyses non-reducing, cability and creates a need for a selection of enzymes that (a) terminal mannose residues. C-galactosidase hydrolyses have similar activities but are active under different condi O-linked galactose groups. tions or (b) have different substrates. For instance, an enzyme 0157 Galactomannan polysaccharides and the enzymes capable of catalyzing a reaction at 50° C. may be so inefficient of the invention that degrade them have a variety of applica at 35° C., that its use at the lower temperature will not be tions. Guar is commonly used as a thickening agent in food feasible. For this reason, laundry detergents generally contain and is utilized in hydraulic fracturing in oil and gas recovery. a selection of proteolytic enzymes (e.g., polypeptides of the Consequently, galactomannanases are industrially relevant invention), allowing the detergent to be used over a broad for the degradation and modification of guar. Furthermore, a range of wash temperature and pH. In view of the specificity need exists for thermostable galactomannases that are active of enzymes and the growing use of hydrolases in industry, in extreme conditions associated with oil drilling and well research, and medicine, there is an ongoing need in the art for stimulation. new enzymes and new enzyme inhibitors. 0158. There are other applications for these enzymes in various industries, such as in the beet sugar industry. 20-30% 0149 Glucosidases of the domestic U.S. Sucrose consumption is sucrose from 0150. In one aspect, the invention provides glucosidases, Sugar beets. Raw beet Sugar can contain a small amount of polynucleotides encoding them, and methods of making and raffinose when the Sugar beets are stored before processing using these polynucleotides and polypeptides. In one aspect, and rotting begins to set in. Raffinose inhibits the crystalliza the invention is directed to polypeptides, e.g., enzymes, hav tion of Sucrose and also constitutes a hidden quantity of ing a glucosidase activity, including thermostable and ther Sucrose. Thus, there is merit to eliminating raffinose from raw motolerant glucosidase activity, and polynucleotides encod beet Sugar. C-Galactosidase has also been used as a digestive ing these enzymes, and making and using these aid to break down raffinose, stachyose, and Verbascose in polynucleotides and polypeptides. Such foods as beans and other gassy foods. 0151. Alpha-glucosidases of the invention can catalyze 0159 B-Galactosidases of the invention can be used for the hydrolysis of starches into Sugars. Alpha-glucosidases the production of lactose-free dietary milk products. Addi US 2015/0240226 A1 Aug. 27, 2015

tionally, B-galactosidases of the invention can be used for the 0.167 Isomerases enzymatic synthesis of oligosaccharides via transglycosyla 0.168. In one aspect, the invention provides isomerases, tion reactions. e.g., Xylose isomerases, polynucleotides encoding them, and 0160 Pullulanase is well known as a debranching enzyme methods of making and using these polynucleotides and of pullulan and starch. The enzyme of the invention can polypeptides. In one aspect, the invention is directed to hydrolyze C-1,6-glucosidic linkages on these polymers. polypeptides, e.g., enzymes, having an isomerase activity, Starch degradation for the production or Sweeteners (glucose e.g., Xylose isomerase activity, including thermostable and or maltose) is a very important industrial application of this thermotolerant isomerase activity, e.g., Xylose isomerase enzyme. The degradation of starch is developed in two stages. activity, and polynucleotides encoding these enzymes, and The first stage involves the liquefaction of the substrate with making and using these polynucleotides and polypeptides. a-amylase, and the second stage, or Saccharification stage, is 0169. In one aspect, the invention provides xylose performed by B-amylase with pullalanase added as a isomerase enzymes, polynucleotides encoding the enzymes, debranching enzyme, to obtain better yields. methods of making and using these polynucleotides and 0161 Endoglucanases of the invention can be used in a polypeptides. The polypeptides of the invention can be used variety of industrial applications. For instance, the endoglu in a variety of agricultural and industrial contexts. For canases of the invention can hydrolyze the internal B-1,4- example, the polypeptides of the invention can be used for glycosidic bonds in cellulose, which may be used for the converting glucose to fructose or for manufacturing high conversion of plant biomass into fuels and chemicals. Endo content fructose syrups in large quantities. Other examples glucanases of the invention also have applications in deter include use of the polypeptides of the invention in confec gent formulations, the textile industry, in animal feed, in tionary, brewing, alcohol and soft drinks production, and in waste treatment, oil drilling and well stimulation, and in the diabetic foods and Sweeteners. fruit juice and brewing industry for the clarification and (0170 Laccases extraction of juices. 0171 In one aspect, the invention provides laccases, poly (0162 Inteins nucleotides encoding them, and methods of making and using 0163. In one aspect, the invention provides inteins, poly these polynucleotides and polypeptides. In one aspect, the nucleotides encoding them, and methods of making and using invention is directed to polypeptides, e.g., enzymes, having a these polynucleotides and polypeptides. In another aspect, laccase activity, including thermostable and thermotolerant the invention provides a chimeric protein comprising at least laccase activity, and polynucleotides encoding these three domains, wherein the first domain comprises at least enzymes, and making and using these polynucleotides and one enzyme domain or a binding protein domain, the second polypeptides. domain comprises at least one intein domain and a third 0172. In one aspect, the invention provides methods of domain comprising a detectable moiety domain, at least one depolymerizing lignin, e.g., in a pulp or paper manufacturing intein domain is positioned between at least one enzyme or process, using a polypeptide of the invention. In another binding protein and at least one detectable moiety domain, aspect, the invention provides methods for oxidizing products and the intein domain has at least one cleavage or splicing that can be mediators of laccase-catalyzed oxidation reac activity. tions, e.g., 2.2-azinobis-(3-ethylbenzthiazoline-6-sulfonate) 0164. In one aspect, the detectable moiety domain com (ABTS), 1-hydroxybenzotriazole (HBT), 2.2.6,6-tetrameth prises a detectable peptide or polypeptide. The detectable ylpiperidin-1-yloxy (TEMPO), dimethoxyphenol, dihy peptide or a polypeptide can be a fluorescent peptide or droxyfumaric acid (DHF) and the like. polypeptide. The detectable peptide or a polypeptide can be a 0173 Laccases are a subclass of the multicopper oxidase bioluminescent or a chemiluminescent peptide or polypep Super family of enzymes, which includes ascorbate oxidases tide. In one aspect, the bioluminescent or chemiluminescent and the mammalian protein, ceruloplasmin. Laccases are one polypeptide comprises a green fluorescent protein (GFP), an of the oldest known enzymes and were first implicated in the aequorin, an obelin, a mnemiopsin or aberovin. In one aspect, oxidation of urushiol and laccol. In one aspect, reactions the detectable moiety domain comprises an enzyme that gen catalyzed by laccases of the invention comprises the oxida erates a detectable signal. The enzyme that generates a detect tion of phenolic Substrates. The major target application has able signal can comprise an alpha-galactosidase, an antibiotic been in the delignification of wood fibers during the prepara (e.g., chloramphenicol acetyltransferase) or a kinase. The tion of pulp. detectable moiety domain can comprise a radioactive isotope. (0174 Lipases 0.165. In one aspect, the chimeric protein is a recombinant 0.175. In one aspect, the invention provides lipases, poly fusion protein. In one aspect, the intein domain splicing activ nucleotides encoding them, and methods of making and using ity results in cleavage of the enzyme domain from the intein these polynucleotides and polypeptides. In one aspect, the domain and detectable domain. The intein domain splicing invention is directed to polypeptides, e.g., enzymes, having a activity can result in cleavage of the enzyme domain from the lipase activity, including thermostable and thermotolerant intein domain and detectable domain and cleavage of the lipase activity, and polynucleotides encoding these enzymes, detectable domain from the intein domain. In one aspect, the and making and using these polynucleotides and polypep intein domain splicing activity results in cleavage of the tides. detectable domain from the intein domain. In one aspect, the 0176). In one aspect, the lipases of the invention can be intein domain has only splicing activity. The intein domain used in a variety of pharmaceutical, agricultural and indus can have only cleaving activity. trial contexts, including the manufacture of cosmetics and 0166 In one aspect, at least one domain is separated from nutraceuticals. In one aspect, the lipases of the invention are another domain by a linker. The linker can be a flexible linker. used in the biocatalytic synthesis of structured lipids (lipids The intein domain can be separated from the detectable moi that contain a defined set offatty acids distributed in a defined ety domain and the enzyme domain by a linker. manner on the glycerol backbone), including cocoa butter US 2015/0240226 A1 Aug. 27, 2015 alternatives (CBA), lipids containing poly-unsaturated fatty tured lipids, and the production of nutraceuticals (e.g., poly acids (PUFAs), diacylglycerides, e.g., 1,3-diacyl glycerides unsaturated fatty acids and oils), various foods and food addi (DAGs), monoglycerides, e.g., 2-monoglycerides (MAGs) tives (e.g., emulsifiers, fat replacers, margarines and spreads), and triacylglycerides (TAGs). In one aspect, the polypeptides cosmetics (e.g., emulsifiers, creams), pharmaceuticals and of the invention are used to modify oils, such as fish, animal drug delivery agents (e.g., liposomes, tablets, formulations), and vegetable oils, and lipids, Such as poly-unsaturated fatty and animal feed additives (e.g., polyunsaturated fatty acids, acids. The lipases of the invention can modify oils by hydroly Such as linoleic acids) comprising lipids made by the struc sis, alcoholysis, esterification, transesterification and/or tured synthesis methods of the invention or processed by the interesterification. The methods of the invention use lipases methods of the invention with defined regio-specificity or defined chemoselectivity in 0181. In one aspect, lipases of the invention can act on biocatalytic synthetic reactions. In another aspect, the fluorogenic fatty acid (FA) esters, e.g., umbelliferyl FA polypeptides of the invention are used to synthesize enantio esters. In one aspect, profiles of FA specificities of lipases merically pure chiral products. made or modified by the methods of the invention can be 0177. The invention provides lipase enzymes, polynucle obtained by measuring their relative activities on a series of otides encoding the enzymes, methods of making and using umbelliferyl FA esters, such as palmitate, Stearate, oleate, these polynucleotides and polypeptides. The polypeptides of laurate, PUFA, butyrate. the invention can be used in a variety of pharmaceutical, 0182. The methods and compositions (lipases) of the agricultural and industrial contexts, including the manufac invention can be used to synthesize enantiomerically pure ture of cosmetics and nutraceuticals. In one aspect, the chiral products. In one aspect, the methods and compositions polypeptides of the invention are used in the biocatalytic (lipases) of the invention can be used to prepare a D-amino synthesis of structured lipids (lipids that contain a defined set acid and corresponding esters from a racemic mix. For offatty acids distributed in a defined manner on the glycerol example, D-aspartic acid can be prepared from racemic backbone), including cocoa butter alternatives, poly-unsatur aspartic acid. In one aspect, optically active D-homopheny ated fatty acids (PUFAs), 1,3-diacyl glycerides (DAGs), lalanine and/or its esters are prepared. The enantioselectively 2-monoglycerides (MAGs) and triacylglycerides (TAGS), synthesized D-homophenylalanine can be starting material such as 1,3-dipalmitoyl-2-oleoylglycerol (POP), 1,3-dis for many drugs, such as Enalapril, Lisinopril, and Quinapril, tearoyl-2-oleoylglycerol (SOS), 1-palmitoyl-2-oleoyl-3- used in the treatment of hypertension and congestive heart stearoylglycerol (POS) or 1-oleoyl-2,3-dimyristoylglycerol failure. The D-aspartic acid and its derivatives made by the (OMM), long chain polyunsaturated fatty acids such as methods and compositions of the invention can be used in arachidonic acid, docosahexaenoic acid (DHA) and eicosap pharmaceuticals, e.g., for the inhibition of arginioSuccinate entaenoic acid (EPA). synthetase to prevent or treat sepsis or cytokine-induced sys 0178. In one aspect, the invention provides synthesis (us temic hypotension or as immunosuppressive agents. The ing lipases of the invention) of a triglyceride mixture com D-aspartic acid and its derivatives made by the methods and posed of POS (Palmitic-Oleic-Stearic), POP (Palmitic-Oleic compositions of the invention can be used as taste modifying Palmitic) and SOS (Stearic-Oleic-Stearic) from glycerol. compositions for foods, e.g., as Sweeteners (e.g., ALI This synthesis uses free fatty acids versus fatty acid esters. In TAMETM). For example, the methods and compositions (li one aspect, this reaction can be performed in one pot with pases) of the invention can be used to synthesize an optical sequential addition of fatty acids using crude glycerol and isomer S(+) of 2-(6-methoxy-2-naphthyl) propionic acid free fatty acids and fatty acid esters. In one aspect, Stearate from a racemic (R.S) ester of 2-(6-methoxy-2-naphthyl) pro and palmitate are mixed together to generate mixtures of pionic acid. DAGs. In one aspect, the diacylglycerides are Subsequently 0183 In one aspect, the methods and compositions (li acylated with oleate to give components of cocoa butter pases) of the invention can be used to for stereoselectively equivalents. In alternative aspects, the proportions of POS, hydrolyzing racemic mixtures of esters of 2-substituted acids, POP and SOS can be varied according to: Stearate to palmitate e.g., 2-aryloxy Substituted acids, such as R-2-(4-hydroxyphe ratio; selectivity of enzyme for palmitate versus Stearate; or noxyl)propionic acid, 2-arylpropionic acid, ketoprofen to enzyme enantioselectivity (could alter levels of POS/SOP). synthesize enantiomerically pure chiral products. One-pot synthesis of cocoa butter equivalents or other cocoa 0.184 The methods and compositions (lipases) of the butter alternatives is possible using this aspect of the inven invention can be used to hydrolyze oils, such as fish, animal tion. and vegetable oils, and lipids, Such as poly-unsaturated fatty 0179. In one aspect, lipases that exhibit regioselectivity acids. In one aspect, the polypeptides of the invention are used and/or chemoselectivity are used in the structure synthesis of process fatty acids (such as poly-unsaturated fatty acids), e.g., lipids or in the processing of lipids. Thus, the methods of the fish oil fatty acids, for use in or as a feed additive. Addition of invention use lipases with defined regio-specificity or defined poly-unsaturated fatty acids PUFAs to feed for dairy cattle chemoselectivity (e.g., a fatty acid specificity) in a biocata has been demonstrated to result in improved fertility and milk lytic synthetic reaction. For example, the methods of the yields. Fish oil contains a high level of PUFAs and therefore invention can use lipases with SN1, SN2 and/or SN3 regio is a potentially inexpensive source for PUFAS as a starting specificity, or combinations thereof. In one aspect, the meth material for the methods of the invention. The biocatalytic ods of the invention use lipases that exhibit regioselectivity methods of the invention can process fish oil under mild for the 2-position of a triacylglyceride (TAG). This SN2 regi conditions, thus avoiding harsh conditions utilized in some oselectivity can be used in the synthesis of a variety of struc processes. Harsh conditions may promote unwanted isomer tured lipids, e.g., triacylglycerides (TAGS), including 1,3- ization, polymerization and oxidation of the PUFAs. In one DAGs and components of cocoa butter. aspect, the methods of the invention comprise lipase-cata 0180. The methods and compositions (lipases) of the lyzed total hydrolysis of fish-oil or selective hydrolysis of invention can be used in the biocatalytic synthesis of struc PUFAs from fish oil to provide a mild alternative that would US 2015/0240226 A1 Aug. 27, 2015

leave the high-value PUFAs intact. In one aspect, the methods tion. The monooxygenase activity can be enantiospecific. In further comprise hydrolysis of lipids by chemical or physical one aspect, it can generate a substantially chiral product. splitting of the fat. 0193 In one aspect, the monooxygenase activity com 0185. In one aspect, the lipases and methods of the inven prises generation of an ester or a lactonehaving at least one of tion are used for the total hydrolysis of fish oil. Lipases can be the following structures: screened for their ability to catalyze the total hydrolysis of fish oil under different conditions using. In alternative aspects, a single or multiple lipases are used to catalyze the R total splitting of the fish oil. Several lipases of the invention may need to be used, owing to the presence of the PUFAs. In "x" s R one aspect, a PUFA-specific lipase of the invention is com RS R 5 -R bined with a general lipase to achieve the desired effect. O 0186 The methods and compositions (lipases) of the invention can be used to catalyze the partial or total hydrolysis 0194 wherein: of other oils, e.g., olive oils, that do not contain PUFAs. R. R. R. and Ra are each independently selected from —H. 0187. The methods and compositions (lipases) of the Substituted or unsubstituted alkyl, alkenyl, alkynyl, aryl, het invention can be used to catalyze the hydrolysis of PUFA eroaryl, cycloalkyl, and heterocyclic; wherein the substituted glycerol esters. These methods can be used to make feed groups are substituted with one or more of lower alkyl, additives. In one aspect, lipases of the invention catalyze the hydroxy, alkoxy, mercapto, cycloalkyl, heterocyclic, aryl, release of PUFAs from simple esters and fish oil. Standard heteroaryl, aryloxy, and halogen, or two or more of R. R. R. assays and analytical methods can be utilized. and R may together form cyclic moieties, and, R is selected 0188 The methods and compositions (lipases) of the from substituted or unsubstituted alkylene, alkenylene, alky invention can be used to selectively hydrolyze saturated esters nylene, arylene, heteroarylene, cycloalkylene, and heterocy over unsaturated esters into acids or alcohols. The methods clic; wherein the substitutions are substituted with one or and compositions (lipases) of the invention can be used to more of lower alkyl, hydroxy, alkoxy, mercapto, cycloalkyl, treat latexes for a variety of purposes, e.g., to treat latexes used heterocyclic, aryl, heteroaryl, aryloxy, and halogen. in hair fixative compositions to remove unpleasant odors. The 0.195. In one aspect, the monooxygenase activity com methods and compositions (lipases) of the invention can be prises oxidation of a cycloalkanone to produce a chiral lac used in the treatment of a lipase deficiency in an animal, e.g., tone. The cycloalkanone can comprise a cyclobutanone, a a mammal. Such as a human. The methods and compositions cyclopentanone, a cyclohexanone, a 2-methylcyclopen (lipases) of the invention can be used to prepare lubricants, tanone, a 2-methylcyclohexanone, a cyclohex-2-ene-1-one, a Such as hydraulic oils. The methods and compositions (li 2-(cyclohex-1-enyl)cyclohexanone, a 12-cyclohexanedione, pases) of the invention can be used in making and using a 1.3-cyclohexanedione or a 14-cyclohexanedione. detergents. The methods and compositions (lipases) of the 0196. In one aspect, the monooxygenase activity com invention can be used in processes for the chemical finishing prises a chlorophenol 4-monooxygenase activity or a Xylene of fabrics, fibers or yarns. In one aspect, the methods and monooxygenase activity. compositions (lipases) of the invention can be used for 0197) The invention provides a pharmaceutical composi obtaining flame retardancy in a fabric using, e.g., a halogen tion comprising a polypeptide of the invention. substituted carboxylic acid or an ester thereof, i.e., a fluori 0198 The invention provides a method for converting a nated, chlorinated or bromated carboxylic acid or an ester ketone to its corresponding ester comprising contacting the thereof. ketone with a polypeptide of the invention under conditions 0189 Monooxygenases wherein the polypeptide catalyzes the conversion of the 0190. In one aspect, the invention provides monooxyge ketone to its corresponding ester. In one aspect, the polypep nases, polynucleotides encoding them, and methods of mak tide has an monooxygenase activity that is enantiospecific to ing and using these polynucleotides and polypeptides. In one generate a Substantially chiral product. In one aspect, the ester aspect, the invention is directed to polypeptides, e.g., is an aromatic or an aliphatic ester. enzymes, having a monooxygenase activity, including ther 0199 The invention provides a method for converting a mostable and thermotolerant monooxygenase activity, and cycloaliphatic ketone to its corresponding lactone comprising polynucleotides encoding these enzymes, and making and contacting the cycloaliphatic ketone with a polypeptide of the using these polynucleotides and polypeptides. invention under conditions wherein the polypeptide catalyzes 0191 In one aspect, the monooxygenases of the invention the conversion of the cycloaliphatic ketone to its correspond have commercial utility as biocatalysts for use in the synthe ing lactone. In one aspect, the polypeptide has an monooxy sis of aromatic and aliphatic esters and their derivatives. Such genase activity that is enantiospecific to generate a substan as acids and alcohols. In one aspect, the monooxygenases of tially chiral product. In one aspect, the ester or lactone has at the invention are used in the catalysis of Sulfoxidation reac least one of the following structures: tions. In one aspect, the invention provides Baeyer-Villiger monooxygenases, polynucleotides encoding the Baeyer-Vil liger monooxygenases, and methods of using these Baeyer R Villiger monooxygenases and polynucleotides. In one aspect, the invention provides methods of producing chiral synthetic R3 Xr R4 R2 - R intermediates using Baeyer-Villiger monooxygenases. RS R O – 0192 In one aspect, the monooxygenase activity com prises catalysis of Sulfoxidation reactions. The monooxyge nase activity can comprise an asymmetric Sulfoxidation reac US 2015/0240226 A1 Aug. 27, 2015

wherein: R. R. R. and Ra are each independently selected 0207. In one aspect, nitrilases of the invention can be used from —H, substituted or unsubstituted alkyl, alkenyl, alky for making a composition oran intermediate thereof, wherein nyl, aryl, heteroaryl, cycloalkyl, and heterocyclic; wherein the nitrilase of the invention hydrolyzes a cyanohydrin or a the substituted groups are substituted with one or more of aminonitrile moiety. In one embodiment, the composition or lower alkyl, hydroxy, alkoxy, mercapto, cycloalkyl, hetero intermediate thereof comprises (S)-2-amino-4-phenyl cyclic, aryl, heteroaryl, aryloxy, and halogen, or two or more butanoic acid. In a further embodiment, the composition or of R. R. R. and R may together form cyclic moieties, and, intermediate thereof comprises an L-amino acid. In a further R" is selected from substituted or unsubstituted alkylene, alk embodiment, the composition comprises a food additive or a enylene, alkynylene, arylene, heteroarylene, cycloalkylene, pharmaceutical drug. and heterocyclic; wherein the substitutions are substituted 0208. In another aspect, nitrilases of the invention can be with one or more of lower alkyl, hydroxy, alkoxy, mercapto, used for making an (R)-ethyl 4-cyano-3-hydroxybutyric acid, cycloalkyl, heterocyclic, aryl, heteroaryl, aryloxy, and halo wherein the nitrilase of the invention acts upon a hydroxyglu gen. taryl nitrile and selectively produces an (R)-enantiomer, so as 0200 Nitroreductases to make (R)-ethyl 4-cyano-3-hydroxybutyric acid. In one 0201 In one aspect, the invention provides nitroreduc embodiment, the ee is at least 95% or at least 99%. In another tases, polynucleotides encoding them, and methods of mak embodiment, the hydroxyglutaryl nitrile comprises 1,3-di ing and using these polynucleotides and polypeptides. In one cyano-2-hydroxy-propane or 3-hydroxyglutaronitrile. aspect, the invention is directed to polypeptides, e.g., 0209. In another aspect, nitrilases of the invention can be enzymes, having a nitroreductase activity, including thermo used for making an (S)-ethyl 4-cyano-3-hydroxybutyric acid, stable and thermotolerant nitroreductase activity, and poly wherein the nitrilase of the invention acts upon a hydroxyglu nucleotides encoding these enzymes, and making and using taryl nitrile and selectively produces an (S)-enantiomer, so as these polynucleotides and polypeptides. to make (S)-ethyl 4-cyano-3-hydroxybutyric acid. 0202 Nitroreductases can catalyze the six-electron reduc 0210. In another aspect, the nitrilases of the invention can tion of nitro compounds to the corresponding amines. Amines be used for making a (R)-mandelic acid, wherein the nitrilase have a variety of applications as synthons and advanced phar of the invention acts upon a mandelonitrile to produce a maceutical intermediates. There are markets for both aro (R)-mandelic acid. In one embodiment, the (R)-mandelic matic amines and chiral aliphatic amines. acid comprises (R)-2-chloromandelic acid. In another 0203 Nitroreductases of the invention fall in to two main embodiment, the (R)-mandelic acid comprises an aromatic classes. These are the oxygen-sensitive and oxygen-insensi ring substitution in the ortho-, meta-, or para-positions; a tive nitroreductases. The oxygen-sensitive enzyme can cata 1-naphthyl derivative of (R)-mandelic acid, a pyridyl deriva lyze nitroreduction only under anaerobic conditions. A nitro tive of (R)-mandelic acid or a thienyl derivative of (R)-man anion radical is formed by a one-electron transfer and is delic acid or a combination thereof. immediately reoxidized in the presence of oxygen thus gen 0211. In another aspect, the nitrilases of the invention can erating a futile cycle whereby reducing equivalents are con be used for making a (S)-mandelic acid, wherein the nitrilase sumed without nitroreduction. On the other hand the oxygen of the invention acts upon a mandelonitrile to produce a insensitive nitroreductases catalyze nitroreduction in a series (S)-mandelic acid. In one embodiment, the (S)-mandelic acid of two electron transfers, first via the nitro so and then the comprises (S)-methylbenzyl cyanide and the mandelonitrile hydroxylamine intermediates before forming the amine. comprises (S)-methoxy-bonzyl cyanide. In one embodiment, 0204 Nitrilases the (S)-mandelic acid comprises an aromatic ring Substitution 0205. In one aspect, the invention provides nitrilases, in the ortho-, meta-, or para-positions; a 1-naphthyl derivative polynucleotides encoding them, and methods of making and of (S)-mandelic acid, a pyridyl derivative of (5-mandelic using these polynucleotides and polypeptides. In one aspect, acid or a thienyl derivative of (S)-mandelic acid or a combi the invention is directed to polypeptides, e.g., enzymes, hav nation thereof. ing a nitrilase activity, including thermostable and thermotol 0212. In yet another aspect, the nitrilases of the invention erant nitrilase activity, and polynucleotides encoding these can be used for making a (S)-phenyl lactic acid derivative or enzymes, and making and using these polynucleotides and a (R)-phenyl lactic acid derivative, wherein the nitrilase of the polypeptides. invention acts upon a phenylactonitrile and selectively pro 0206 Nitrilases of the invention can be used for hydrolyz duces an (S)-enantiomer oran (R)-enantiomer, thereby pro ing a nitrile to a carboxylic acid. In one embodiment, the ducing an (S)-phenyl lactic acid derivative oran (R)-phenyl conditions of the reaction comprise aqueous conditions. In lactic acid derivative. another embodiment, the conditions comprise a pH of about 0213 P450 Enzymes 8.0 and/or a temperature from about 37° C. to about 45° C. 0214. In one aspect, the invention provides P450 enzymes, Nitrilases of the invention can also be used for hydrolyzing a polynucleotides encoding them, and methods of making and cyanohydrin moiety or an aminonitrile moiety of a molecule. using these polynucleotides and polypeptides. In one aspect, Alternatively, the nitrilases of the invention can be used for the invention is directed to polypeptides, e.g., enzymes, hav making a chiral C-hydroxy acid molecule, a chiralamino acid ing a P450 enzymatic activity, including thermostable and molecule, a chiral B-hydroxy acid molecule, or a chiral thermotolerant P450 enzymatic activity, and polynucleotides gamma-hydroxy acid molecule. In one embodiment, the encoding these enzymes, and making and using these poly chiral molecule is an (R)-enantiomer. In another embodi nucleotides and polypeptides. ment, the chiral molecule is an (S)-enantiomer. In one 0215 P450s are oxidative enzymes that are widespread in embodiment of the invention, one particular enzyme can have nature and polypeptides of the invention having P450 activity R-specificity for one particular Substrate and the same can be used in processes such as detoxifying Xenobiotics, enzyme can have S-specificity for a different particular sub catabolism of unusual carbon sources and biosynthesis of Strate. secondary metabolites (e.g., detoxification of toxic composi US 2015/0240226 A1 Aug. 27, 2015 20 tion, e.g., pesticides, poisons, chemical warfare agents and prise beta-elimination (trans-elimination) or hydrolysis of a the like). These oxygenases activate molecular oxygen using plant fiber. The plant fiber can comprise cotton fiber, hemp an iron-heme center and utilize a redox electron shuttle to fiber or flax fiber. Support the epoxidation reaction. 0222. The pectate lyases, e.g., pectinases, of the invention 0216. In one aspect, the P450 activity comprises a mono can be used for hydrolyzing, breaking up or disrupting a oxygenation reaction. In one aspect, the P450 activity com pectin- or pectate (polygalacturonic acid)-comprising com prises catalysis of incorporation of oxygen into a substrate. In position, for liquefying or removing a pectin or pectate (po one aspect, the P450 activity can further comprise hydroxy lygalacturonic acid) from a composition. Alternatively, the lation of aliphatic or aromatic carbons. In another aspect, the pectate lyases, e.g., pectinases, of the invention can be used in P450 activity can comprise epoxidation. Alternatively, the detergent compositions. In one aspect, the pectate lyase is a P450 activity can comprise N—, O—, or S-dealkylation. In nonsurface-active pectate lyase or a surface-active pectate one aspect, the P450 activity can comprise dehalogenation. In lyase. The pectate lyase can be formulated in a non-aqueous another aspect the P450 activity can comprise oxidative liquid composition, a cast Solid, a granular form, a particulate deamination. Alternatively, the P450 activity can comprise form, a compressed tablet, a gel form, a paste or a slurry form. N-oxidation or N-hydroxylation. In one aspect, the P450 0223. In one aspect, the pectate lyases, e.g., pectinases, of activity can comprise Sulphoxide formation. the invention can be used for washing an object. In another 0217. In one aspect, the epoxidase activity further com aspect, textiles or fabrics comprise a polypeptide of the inven prises an alkene Substrate. The epoxidase activity can further tion, or a polypeptide encoded by a nucleic acid of the inven comprise production of a chiral product. In one aspect, the tion, wherein the polypeptide has pectate lyase, e.g., pecti epoxidase activity can be enantioselective. nase activity. Additionally, the pectate lyases, e.g., pectinases, 0218 Pectate Lyases of the invention can be used for fiber, thread, textile or fabric 0219. In one aspect, the invention providespectate lyases, scouring. In one aspect, the pectate lyase is an alkaline active e.g., pectinases, polynucleotides encoding them, and meth and thermostable pectate lyase. The desizing and scouring ods of making and using these polynucleotides and polypep treatments can be combined in a single bath. The method can tides. In one aspect, the invention is directed to polypeptides, further comprise addition of an alkaline and thermostable e.g., enzymes, having a pectate lyase, e.g., a pectinase activ amylase. The desizing or scouring treatments can comprise ity, including thermostable and thermotolerant pectate lyase, conditions of between about pH 8.5 to pH 10.0 and tempera e.g., a pectinase activity, and polynucleotides encoding these tures of at about 40° C. The method can further comprise enzymes, and making and using these polynucleotides and addition of a bleaching step. The desizing, scouring and polypeptides. bleaching treatments can be done simultaneously or sequen 0220. The pectate lyases, e.g., pectinases, of the invention tially in a single-bath container. The bleaching treatment can can be used to catalyze the beta-elimination or hydrolysis of comprise hydrogen peroxide or at least one peroxy compound pectin and/or polygalacturonic acid, such as 1.4-linked alpha that can generate hydrogen peroxide when dissolved in water, D-galacturonic acid. They can be used in variety of industrial or combinations thereof, and at leastonebleach activator. The applications, e.g., to treat plant cell walls, such as those in fiber, thread, textile or fabric can comprise a cellulosic mate cotton or other natural fibers. In another exemplary industrial rial. The cellulosic material can comprise a crude fiber, a yarn, application, the polypeptides of the invention can be used in a woven or knit textile, a cotton, a linen, a flax, a ramie, a textile Scouring. rayon, a hemp, a jute or a blend of natural or synthetic fibers. 0221. In one aspect, pectate lyase activity comprises 0224. Alternatively, the pectate lyases, e.g., pectinases, of catalysis of beta-elimination (trans-elimination) or hydroly the invention can be used in feeds or foods. For example, the sis of pectin or polygalacturonic acid (pectate). The pectate pectate lyases, e.g., pectinases, of the invention can be used to lyase activity can comprise the breakup or dissolution of plant improve the extraction of oil from an oil-rich plant material. cell walls. The pectate lyase activity can comprise beta-elimi In one aspect, the oil-rich plant material comprises an oil-rich nation (trans-elimination) or hydrolysis of 1.4-linked alpha seed. The oil can be a soybean oil, an olive oil, a rapeseed D-galacturonic acid. The pectate lyase activity can comprise (canola) oil or a Sunflower oil. catalysis of beta-elimination (trans-elimination) or hydroly 0225. In another aspect, the pectate lyases, e.g., pecti sis of methyl-esterified galacturonic acid. The pectate lyase nases, of the invention can be used for preparing a fruit or activity can be exo-acting or endo-acting. In one aspect, the Vegetablejuice, syrup, puree or extract. In yet another aspect, pectate lyase activity is endo-acting and acts at random sites the pectate lyases, e.g., pectinases, of the invention can used within a polymer chain to give a mixture of oligomers. In one for treating a paper or a paper or wood pulp. Alternatively, the aspect, the pectate lyase activity is exo-acting and acts from invention provides papers or paper products or paper pulps one end of a polymer chain and produces monomers or comprising a pectate lyase of the invention, or a polypeptide dimers. The pectate lyase activity can catalyze the random encoded by a nucleic acid of the invention. cleavage of alpha-1,4-glycosidic linkages in pectic acid (po 0226. In yet another aspect, the invention provides phar lygalacturonic acid) by trans-elimination or hydrolysis. The maceutical compositions comprising a polypeptide of the pectate lyase activity can comprise activity the same or simi invention, or a polypeptide encoded by a nucleic acid of the lar to pectate lyase (EC 4.2.2.2), poly(1,4-alpha-D-galactur invention, wherein the polypeptide has pectate lyase, e.g., onide) lyase, polygalacturonate lyase (EC 4.2.2.2), pectin pectinase activity. The pharmaceutical composition can act as lyase (EC 4.2.2.10), polygalacturonase (EC 3.2.1.15), exo a digestive aid. polygalacturonase (EC 3.2.1.67), exo-polygalacturonate 0227. Alternatively, the invention provides oral care prod lyase (EC 4.2.2.9) or exo-poly-alpha-galacturonosidase (EC ucts comprising a polypeptide of the invention, or a polypep 3.2.1.82). The pectate lyase activity can comprise beta-elimi tide encoded by a nucleic acid of the invention, wherein the nation (trans-elimination) or hydrolysis of galactan to galac polypeptide has pectate lyase, e.g., pectinase activity. The tose orgalactooligomers. The pectate lyase activity can com oral care product can comprise a toothpaste, a dental cream, a US 2015/0240226 A1 Aug. 27, 2015 gel or a tooth powder, anodontic, a mouth wash, a pre- or post ing and using these polynucleotides and polypeptides. In one brushing rinse formulation, a chewing gum, a lozenge or a aspect, the invention is directed to polypeptides, e.g., candy. enzymes, having a phospholipase activity, including thermo 0228 Phosphatases stable and thermotolerant phospholipase activity, and poly 0229. In one aspect, the invention provides phosphatases, nucleotides encoding these enzymes, and making and using polynucleotides encoding them, and methods of making and these polynucleotides and polypeptides. using these polynucleotides and polypeptides. In one aspect, 0237 Phospholipases are enzymes that hydrolyze the the invention is directed to polypeptides, e.g., enzymes, hav ester bonds of phospholipids. Corresponding to their impor ing a phosphatase activity, including thermostable and ther tance in the metabolism of phospholipids, these enzymes are motolerant phosphatase activity, and polynucleotides encod widespread among prokaryotes and eukaryotes. The phos ing these enzymes, and making and using these pholipases affect the metabolism, construction and reorgani polynucleotides and polypeptides. Zation of biological membranes and are involved in signal 0230 Phosphatases are a group of enzymes that remove cascades. Several types of phospholipases are known which phosphate groups from organophosphate ester compounds. differ in their specificity according to the position of the bond There are numerous phosphatases, including alkaline phos attacked in the phospholipid molecule. Phospholipase A1 phatases, phosphodiesterases and phytases. (PLA1) removes the 1-position fatty acid to produce free fatty 0231. Alkaline phosphatases are widely distributed acid and 1-lyso-2-acylphospholipid. Phospholipase A2 enzymes and are composed of a group of enzymes which (PLA2) removes the 2-position fatty acid to produce free fatty hydrolyze organic phosphate ester bonds at alkaline pH. acid and 1-acyl-2-lysophospholipid. PLAT and PLA2 0232 Phosphodiesterases are capable of hydrolyzing enzymes can be intra- or extra-cellular, membrane-bound or nucleic acids by hydrolyzing the phosphodiester bridges of soluble. Intracellular PLA2 is found in almost every mamma DNA and RNA. The classification of phosphodiesterases lian cell. Phospholipase C (PLC) removes the phosphate moi depends upon which side of the phosphodiester bridge is ety to produce 1.2 diacylglycerol and phospho base. Phos attacked. The 3' enzymes specifically hydrolyze the ester pholipase D (PLD) produces 1,2-diacylglycerophosphate and linkage between the 3' carbon and the phosphoric group base group. PLC and PLD are important in cell function and whereas the 5' enzymes hydrolyze the ester linkage between signaling. PLD had been the dominant phospholipase in bio the phosphoric group and the 5' carbon of the phosphodiester catalysis. Patatins are another type of phospholipase, thought bridge. The best known of the class 3' enzymes is a phos to work as aPLA. phodiesterase from the Venom of the rattlesnake or from a 0238. The invention provides methods for cleaving a glyc rustle's viper, which hydrolyses all the 3' bonds in either RNA erolphosphate ester linkage comprising the following steps: or DNA liberating nearly all the nucleotide units as nucleotide (a) providing a polypeptide having a phospholipase activity, 5' phosphates. This enzyme requires a free 3' hydroxyl group wherein the polypeptide comprises an amino acid sequence on the terminal nucleotide residue and proceeds stepwise of the invention, or the polypeptide is encoded by a nucleic from that end of the polynucleotide chain. This enzyme and acid of the invention; (b) providing a composition comprising all other nucleases which attack only at the ends of the poly a glycerolphosphate ester linkage; and, (c) contacting the nucleotide chains are called exonucleases. The 5' enzymes are polypeptide of step (a) with the composition of step (b) under represented by a phosphodiesterase from bovine spleen, also conditions wherein the polypeptide cleaves the glycerolphos an exonuclease, which hydrolyses all the 5' linkages of both phate ester linkage. In one aspect, the conditions comprise DNA and RNA and thus liberates only nucleoside 3' phos between about pH 5 to about 5.5, or, between about pH 4.5 to phates. It begins its attack at the end of the chain having a free about 5.0. In one aspect, the conditions comprise a tempera 3' hydroxyl group. ture of between about 40°C. and about 70°C. In one aspect, 0233 Phytase enzymes remove phosphate from phytic the composition comprises a vegetable oil. In one aspect, the acid (inositol hexaphosphoric acid), a compound found in composition comprises an oilseed phospholipid. In one plants such as corn, wheat and rice. The enzyme has commer aspect, the cleavage reaction can generate a water extractable cial use for the treatment of animal feed, making the inositol phosphorylated base and a diglyceride. of the phytic acid available for animal nutrition. Phytases are 0239 Phospholipases of the invention can be used in oil used to improve the utilization of natural phosphorus in ani degumming, wherein the phospholipase is used under condi mal feed. Use of phytase as a feed additive enables the animal tions wherein the phospholipase can cleave ester linkages in to metabolize a larger degree of its cereal feeds natural min an oil, thereby degumming the oil. In one aspect, the oil is a eral content thereby reducing or altogether eliminating the Vegetable oil. In another aspect, the vegetable oil comprises need for synthetic phosphorus additives. More important than oilseed. The vegetable oil can comprise palm oil, rapeseed oil, the reduced need for phosphorus additives is the correspond corn oil, soybean oil, canola oil, Sesame oil, peanut oil or ing reduction of phosphorus in pig and chicken waste. Many Sunflower oil. In one aspect, the method further comprises European countries severely limit the amount of manure that addition of a phospholipase of the invention, another phos can be spread per acre due to concerns regarding phosphorus pholipase, another enzyme, or a combination thereof. contamination of ground water. 0240. In another aspect of the invention, phospholipases 0234 Alkaline phosphatases hydrolyze monophosphate of the invention can be used for converting a non-hydratable esters, releasing an organic phosphate and the cognate alco phospholipid to a hydratable form or for caustic refining of a hol compound. It is non-specific with respect to the alcohol phospholipid-containing composition. In the latter use, the moiety and it is this feature which accounts for the many uses polypeptide of the invention can be added before caustic of this enzyme. refining and the composition comprising the phospholipid 0235. Phospholipases can comprise a plant and the polypeptide can be expressed 0236. In one aspect, the invention provides phospholi transgenically in the plant, the polypeptide having a phospho pases, polynucleotides encoding them, and methods of mak lipase activity can be added during crushing of a seed or other US 2015/0240226 A1 Aug. 27, 2015 22 plant part, or, the polypeptide having a phospholipase activity example, #EC 3.1.3.2 enzymes catalyze the hydrolysis of is added following crushing or prior to refining. The polypep orthophosphoric monoesters to orthophosphate products. tide can be added during caustic refining and varying levels of 0246 Phytases of the invention can be used in producing acid and caustic can be added depending on levels of phos phytase as a feed additive, e.g., for monogastric animals, fish, phorous and levels of free fatty acids. The polypeptide can be poultry, ruminants and other non-ruminants. Phytases of the added after caustic refining: in an intense mixer or retention invention can also be used for producing animal feed from mixer prior to separation; following a heating step; in a cen certain industrial processes, e.g., wheat and corn waste prod trifuge; in a Soapstock; in a washwater; or, during bleaching ucts. In one aspect, the wet milling process of corn produces or deodorizing steps. glutens sold as animal feeds. The addition of phytase 0241. In yet another aspect, the phospholipases of the improves the nutritional value of the feed product. invention can be used for purification of a phytosterol or a 0247 Phytases of the invention may also be used in dietary triterpene. The phytosterol or a triterpene can comprise a aids or in pharmaceutical compositions, for reducing pollu plant sterol. The plant sterol can be derived from a vegetable tion and increasing nutrient availability in an environment or oil. The vegetable oil can comprise a coconut oil, canola oil, environmental sample by degrading environmental phytic cocoa butter oil, corn oil, cottonseed oil, linseed oil, olive oil, acid, for liberating minerals from phytates in plant materials palm oil, peanut oil, oil derived from a rice bran, safflower oil, either in vitro, i.e., in feed treatment processes, or in vivo, i.e., sesame oil, soybean oil or a Sunflower oil. The method can by administering the enzymes to animals. comprise use of nonpolar solvents to quantitatively extract free phytosterols and phytosteryl fatty-acid esters. The phy 0248 Polymerases tosterol or a triterpene can comprise a P-sitosterol, a campes 0249. In one aspect, the invention provides polymerases, terol, a stigmasterol, a Stigmastanol, a P-sitostanol, a sito polynucleotides encoding them, and methods of making and stanol, a desmoSterol, a chalinasterol, a poriferasterol, a using these polynucleotides and polypeptides. In one aspect, clionasterol or a brassicasterol. the invention is directed to polypeptides, e.g., enzymes, hav 0242. In one embodiment, the phospholipases of the ing a polymerase activity, including thermostable and ther invention can be used for refining a crude oil. The polypeptide motolerant polymerase activity, and polynucleotides encod can have a phospholipase activity is in a water Solution that is ing these enzymes, and making and using these added to the composition. The water level can be between polynucleotides and polypeptides. about 0.5 to 5%. The process time can be less than about 2 0250. The polymerase enzymes of the invention can have hours, less than about 60 minutes, less than about 30 minutes, different polymerase activities at various high temperatures. less than 15 minutes, or less than 5 minutes. The hydrolysis In one aspect, the polymerase activity comprises addition of conditions can comprise a temperature of between about 25° deoxynucleotides at the 3' hydroxyl end of a polynucleotide. C.-70° C. The hydrolysis conditions can comprise use of The invention also provides kits, e.g., diagnostic kits, and caustics. The hydrolysis conditions can comprise a pH of methods for performing various amplification reactions, e.g., between about pH3 and pH 10, between about pH 4 and pH polymerase chain reactions, transcription amplifications, 9, or between about pH 5 and pH 8. The hydrolysis conditions ligase chain reactions, self-sustained sequence replication or can comprise addition of emulsifiers and/or mixing after the Q Beta replicase amplifications. contacting of step (c). The methods can comprise addition of 0251. In one aspect, the polymerase activity comprises an emulsion-breaker and/or heat to promote separation of an addition of nucleotides at the 3' hydroxyl end of a nucleic aqueous phase. The methods can comprise degumming acid. The polymerase activity can comprise a 5'-->3' poly before the contacting step to collect lecithin by centrifugation merase activity, a 3'->5' exonuclease activity or a 5'-->3' exo and then adding a PLC, a PLC and/or a PLA to remove nuclease activity or all or a combination thereof. In one non-hydratable phospholipids. The methods can comprise aspect, the polymerase activity comprises only a 5'-->3' poly water degumming of crude oil to less than 10 ppm for edible merase activity, but not a 3'->5' exonuclease activity or a oils and Subsequent physical refining to less than about 50 5'->3' exonuclease activity. In another aspect, the polymerase ppm for biodiesel oils. The methods can comprise addition of activity can comprise a 5'-->3' polymerase activity and a 3'->5' acid to promote hydration of non-hydratable phospholipids. exonuclease activity, but not a 5'-->3' exonuclease activity. 0243 Phytases Alternatively, the polymerase activity can comprise a 5'-->3' 0244. In one aspect, the invention provides phytases, poly polymerase activity and a 5'-->3' exonuclease activity, but not nucleotides encoding them, and methods of making and using a 3'->5' exonuclease activity. The polymerase activity can these polynucleotides and polypeptides. In one aspect, the comprise addition ofdUTP or dITP. The polymerase activity invention is directed to polypeptides, e.g., enzymes, having a can comprise addition of a modified or a non-natural nucle phytase activity, including thermostable and thermotolerant otide to a polynucleotide. Such as an analog of guanine, phytase activity, and polynucleotides encoding these cytosine, thymine, adenine or uracil, e.g., a 2-aminopurine, an enzymes, and making and using these polynucleotides and inosine or a 5-methylcytosine. polypeptides. 0252. In one aspect, the polymerase activity can comprise Strand displacement properties. In one aspect, the polymerase 0245 Conversion of phytate to inositol and inorganic phosphorous can be catalyzed by phytase enzymes. Phytases activity comprises reverse transcriptase activity. such as phytase #EC 3.1.3.8 are capable of catalyzing the 0253 Proteases hydrolysis of myo-inositol hexaphosphate to D-myo-inositol 0254. In one aspect, the invention provides proteases, 1,2,4,5,6-pentaphosphate and orthophosphate. Other polynucleotides encoding them, and methods of making and phytases hydrolyze inositol pentaphosphate to tetra-, tri-, and using these polynucleotides and polypeptides. In one aspect, lower phosphates. Acid phosphatases are enzymes that cata the invention is directed to polypeptides, e.g., enzymes, hav lytically hydrolyze a wide variety of phosphate esters. For ing a protease activity, including thermostable and thermo US 2015/0240226 A1 Aug. 27, 2015 tolerant protease activity, and polynucleotides encoding these tolerant Xylanase activity, and polynucleotides encoding enzymes, and making and using these polynucleotides and these enzymes, and making and using these polynucleotides polypeptides. and polypeptides. 0255 Proteases of the invention can be carbonyl hydro 0260 Xylanases (e.g., endo-1,4-beta-xylanase, EC 3.2.1. lases which act to cleave peptide bonds of proteins or pep 8) of the invention can hydrolyze internal B-1,4-xylosidic tides. Proteolytic enzymes are ubiquitous in occurrence, linkages in Xylan to produce Smaller molecular weight xylose found in all living organisms, and are essential for cell growth and Xylo-oligomers. Xylans are polysaccharides formed from and differentiation. The extracellular proteases are of com 1,4-B-glycoside-linked D-Xylopyranoses. Xylanases of the mercial value and find multiple applications in various indus invention are of considerable commercial value, being used in trial sectors. Industrial applications of proteases include food the food industry, for baking and fruit and vegetable process processing, brewing, alcohol production, peptide synthesis, ing, breakdown of agricultural waste, in the manufacture of enantioselectivity, hide preparation in the leather industry, animal feed and in pulp and paper production. waste management and animal degradation, silver recovery in 0261 Arabinoxylanase are major non-starch polysaccha the photographic industry, medical treatment, silk degum rides of cereals representing 2.5-7.1% w/w depending on ming, biofilm degradation, biomass conversion to ethanol, variety and growth conditions. The physicochemical proper biodefense, antimicrobial agents and disinfectants, personal ties of this polysaccharide are such that it gives rise to viscous care and cosmetics, biotech reagents and in increasing starch Solutions or evengels under oxidative conditions. In addition, yield from corn wet milling. Additionally, proteases are arabinoxylans have high water-binding capacity and may important components of laundry detergents and other prod have a role in protein foam stability. All of these characteris ucts. Within biological research, proteases are used in purifi tics present problems for several industries including brew cation processes to degrade unwanted proteins. It is often ing, baking, animal nutrition and paper manufacturing. In desirable to employ proteases of low specificity or mixtures brewing applications, the presence of Xylan results in wort of more specific proteases to obtain the necessary degree of filterability and haze formation issues. In baking applications degradation. (especially for cookies and crackers), these arabinoxylans 0256 Proteases are classified according to their catalytic create Sticky doughs that are difficult to machine and reduce mechanisms. The International Union of Biochemistry and biscuit size. In addition, this carbohydrate is implicated in Molecular Biology (IUBMB) recognizes four mechanistic rapid rehydration of the baked product resulting in loss of classes: (1) the serine proteases; (2) the cysteine proteases; (3) crispiness and reduced shelf-life. For monogastric animal the aspartic proteases; and (4) the metalloproteases. In addi feed applications with cereal diets, arabinoxylan is a major tion, the IUBMB recognizes a class of endopeptidases (oli contributing factor to viscosity of gut contents and thereby gopeptidases) of unknown catalytic mechanism. The serine adversely affects the digestibility of the feed and animal proteases have alkaline pH optima, the metalloproteases are growth rate. For ruminant animals, these polysaccharides optimally active around neutrality, and the cysteine and aspar represent Substantial components of fiber intake and more tic enzymes have acidic pH optima. Serine proteases class complete digestion of arabinoxylans would facilitate higher comprises two distinct families: the chymotrypsin family, feed conversion efficiencies. which includes the mammalian enzymes such as chymot 0262 Xylanases are currently used as additives (dough rypsin, trypsin, elastase, or kallikrein, and the Subtilisin fam conditioners) in dough processing for the hydrolysis of water ily, which include the bacterial enzymes such as subtilisin. soluble arabinoxylan. In baking applications (especially for Serine proteases are used for a variety of industrial purposes, cookies and crackers), arabinoxylan creates sticky doughs Such as laundry detergents to aid in the removal of proteina that are difficult to machine and reduce biscuit size. In addi ceous stains. In the food processing industry, serine proteases tion, this carbohydrate is implicated in rapid rehydration of are used to produce protein-rich concentrates from fish and the baked product resulting in loss of crispiness and reduced livestock, and in the preparation of dairy products. shelf-life. 0257 The proteases of the invention can be used in a 0263. The enhancement of xylan digestion in animal feed variety of diagnostic, therapeutic, and industrial contexts. may improve the availability and digestibility of valuable The proteases of the invention can be used as, e.g., an additive carbohydrate and protein feed nutrients. For monogastric ani for a detergent, for processing foods and for chemical Syn mal feed applications with cereal diets, arabinoxylan is a thesis utilizing a reverse reaction. Additionally, the proteases major contributing factor to viscosity of gut contents and of the invention can be used in food processing, brewing, bath thereby adversely affects the digestibility of the feed and additives, alcohol production, peptide synthesis, enantiose animal growth rate. For ruminant animals, these polysaccha lectivity, hide preparation in the leather industry, waste man rides represent Substantial components of fiber intake and agement and animal degradation, silver recovery in the pho more complete digestion would facilitate higher feed conver tographic industry, medical treatment, silk degumming, sion efficiencies. It is desirable for animal feed xylanases to biofilm degradation, biomass conversion to ethanol, biode be active in the animal stomach. This requires a feed enzyme fense, antimicrobial agents and disinfectants, personal care to have high activity at 37°C. and at low pH for monogastrics and cosmetics, biotech reagents, in increasing starch yield (pH 2-4) and near neutral pH for ruminants (pH 6.5-7). The from corn wet milling and pharmaceuticals such as digestive enzyme should also possess resistance to animal gut Xyla aids and anti-inflammatory (anti-phlogistic) agents. nases and stability at the higher temperatures involved in feed 0258 Xylanases pelleting. As such, there is a need in the art for Xylanase feed 0259. In one aspect, the invention provides xylanases, additives for monogastric feed with high specific activity, polynucleotides encoding them, and methods of making and activity at 35-40° C. and pH 2-4, half life greater than 30 using these polynucleotides and polypeptides. In one aspect, minutes in SGF and a half-life-5 minutes at 85°C. in formu the invention is directed to polypeptides, e.g., enzymes, hav lated state. For ruminant feed, there is a need for xylanase ing a Xylanase activity, including thermostable and thermo feed additives that have a high specific activity, activity at US 2015/0240226 A1 Aug. 27, 2015 24

35-40°C. and pH 6.5-7.0, halflife greater than 30 minutes in polypeptides of the invention, based on sequence identity SRF and stability as a concentrated dry powder. (homology). In one embodiment a sequence of the invention 0264. In one aspect, the Xylanases of the invention are also comprises an enzyme with at least 50%, 51%, 52%. 53%, used in improving the quality and quantity of milk protein 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, production in lactating cows, increasing the amount of 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, soluble saccharides in the stomach and Small intestine of pigs, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, improving late egg production efficiency and egg yields in 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, hens. Additionally, Xylanases of the inventions can be used in 94%. 95%, 96%, 97%, 98%, 99%, or more sequence identity biobleaching and treatment of chemical pulps, biobleaching (homology) to an enzyme as listed in Table 3. and treatment of wood or paper pulps, in reducing lignin in wood and modifying wood, as feed additives and/or Supple TABLE 1 ments or in manufacturing cellulose solutions. Detergent compositions comprising Xylanases of the invention are used EC (Enzyme Commission) Numbers with the corresponding mode of for fruit, vegetables and/or mud and clay compounds. action for each enzyme class, Subclass and Sub-Subclass 0265. In another aspect, Xylanases of the invention can be .——.— Oxidoreductases. used in compositions for the treatments and/or prophylaxis of .1.—— Acting on the CH-OH group of donors. .1.1.— With NAD(+) or NADP(+) as acceptor. coccidiosis. In yet another aspect, Xylanases of the invention .1.2.— With a cytochrome as acceptor. can be used in the production of water soluble dietary fiber, in .1.3.— With oxygen as acceptor. improving the filterability, separation and production of .1.4.— With a disulfide as acceptor. starch, the beverage industry in improving filterability of wort .1.5.— With a quinone or similar compound as acceptor. or beer, in reducing viscosity of plant material, or in increas .1.99.— With other acceptors. ing viscosity or gel strength of food products Such as jam, .2.—— Acting on the aldehyde or oxo group of marmalade, jelly, juice, paste, Soup, Salsa, etc. Xylanases of donors. the invention may also be used in hydrolysis of hemicellulose .2.1.— With NAD(+) or NADP(+) as acceptor. .2.2.— With a cytochrome as acceptor. for which it is selective, particularly in the presence of cellu .2.3.— With oxygen as acceptor. lose. In addition, Xylanases of the invention can also be used .2.4.— With a disulfide as acceptor. in the production of ethanol, in transformation of a microbe .2.7.— With an iron-sulfur protein as acceptor. that produces ethanol, in production of oenological tannins 2.99.— With other acceptors. .3.—— Acting on the CH-CH group of donors. and enzymatic composition, in stimulating the natural .3.1.— With NAD(+) or NADP(+) as acceptor. defenses of plants, in production of Sugars from hemicellu .3.2.— With a cytochrome as acceptor. lose Substrates, in the cleaning of fruit, vegetables, mud or .3.3.— With oxygen as acceptor. clay containing soils, in cleaning beer filtration membranes, .3.5.— With a quinone or related compound as acceptor. and in killing or inhibiting microbial cells. .3.7.— With an iron-sulfur protein as acceptor. 0266 Table 1, below, lists the various EC (Enzyme Com 3.99.— With other acceptors. mission) Numbers along with the corresponding mode of 4.- ...— Acting on the CH-NH(2) group of donors. action for each enzyme class, Subclass and Sub-Subclass. 4.1.— With NAD(+) or NADP(+) as acceptor. Enzyme nomenclature is based upon the recommendations of 4.2.— With a cytochrome as acceptor. the Nomenclature Committee of the International Union of 4.3.— With oxygen as acceptor. Biochemistry and Molecular Biology (IUBMB). Table 2, .4.4.— With a disulfide as acceptor. 4.7.— With an iron-sulfur protein as acceptor. below, lists the various EC Numbers along with the corre 4.99.— With other acceptors. sponding name given to each enzyme class, Subclass and .5.—— Acting on the CH-NH group of donors. Sub-Subclass. Tables 1 and 2 list exemplary enzymatic activi .5.1.— With NAD(+) or NADP(+) as acceptor. ties of polypeptides of the invention, as can be determined by .5.3.— With oxygen as acceptor. .5.4.— With a disulfide as acceptor. sequence identity (e.g., homology); and in one embodiment a .5.5.— With a quinone or similar compound as sequence of the invention comprises an enzyme having at acceptor. least 50%, 51%, 52%, 53%, 54%, 55%, 56%, 57%, 58%, .5.8.— With a flavin as acceptor. 59%, 60%, 61%, 62%, 63%, 64%. 65%, 66%, 67%, 68%, 5.99. With other acceptors. .6.—— Acting on NADH or NADPH. 69%, 70%, 71%, 72%, 73%, 74%, 75%, 76%, 77%, 78%, .6.1.— With NAD(+) or NADP(+) as acceptor. 79%, 80%, 81%, 82%, 83%, 84%, 85%, 86%, 87%, 88%, .6.2.— With a heme protein as acceptor. 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, .6.3.— With a oxygen as acceptor. 99%, or more sequence identity (homology) to an enzyme .6.4.— With a disulfide as acceptor. .6.5.— With a quinone or similar compound as encoded by an exemplary sequence of the invention, includ acceptor. ing all odd numbered SEQID NO:1 to SEQID NO:26,897, or .6.6.— With a nitrogenous group as acceptor. an exemplary polypeptide of the invention, including all even .6.8.— With a flavin as acceptor. numbered SEQID NO:2 to SEQID NO:26,898, and with an .6.99.— With other acceptors. .7.—— Acting on other nitrogenous compounds exemplary function as listed in Table 1 or Table 2. as donors. 0267 Table 3, below, contains the exemplary SEQ ID .7.1.— With NAD(+) or NADP(+) as acceptor. NO:s of the invention, and the closest hit (BLAST) informa .7.2.— With a cytochrome as acceptor. tion for the polynucleotides and polypeptides of the inven .7.3.— With oxygen as acceptor. .7.7.— With an iron-sulfur protein as acceptor. tion. This information includes the closest hit organism, 7.99. With other acceptors. accession number, definition of the closest hit, EC number, .8.—— Acting on a Sulfur group of donors. percentage amino acid identity and the percent nucleotide .8.1.— With NAD(+) or NADP(+) as acceptor. identity, along with the Evalue for the closest hits. The infor .8.2.— With a cytochrome as acceptor. mation contained in Table 3 identifies exemplary activities of US 2015/0240226 A1 Aug. 27, 2015 25

TABLE 1-continued TABLE 1-continued EC (Enzyme Commission) Numbers with the corresponding mode of EC (Enzyme Commission) Numbers with the corresponding mode of action for each enzyme class, Subclass and Sub-Subclass action for each enzyme class, Subclass and Sub-Subclass h oxygen as acceptor. .18.1.- With NAD(+) or NADP(+) as acceptor. h a disulfide as acceptor. .18.6.- With dinitrogen as acceptor. h a quinone or similar compound as .18.96.— With other, known, acceptors. acceptor. .18.99.— With H(+) as acceptor. W h an iron-sulfur protein as acceptor. .19.- ...— Acting on reduced flavodoxin as donor. 8.98.— W h other, known, acceptors. .19.6.— With dinitrogen as acceptor. .8.99.— W h other acceptors. .20.—.— Acting on phosphorus or arsenic in .9.- ...— Ac ing on a heme group of donors. donors. W h oxygen as acceptor. .20.1.— Acting on phosphorus or arsenic in W h a nitrogenous group as acceptor. donors, with NAD(P)(+) as acceptor W h other acceptors. .20.4.— Acting on phosphorus or arsenic in Ac ing on diphenols and related donors, with disulfide as acceptor Substances as donors. .20.98.— Acting on phosphorus or arsenic in h NAD(+) or NADP(+) as acceptor. donors, with other, known acceptors h a cytochrome as acceptor. .20.99.— Acting on phosphorus or arsenic in h oxygen as acceptor. donors, with other acceptors h other acceptors. Acting on X-H andy-H to form an X-y ing on a peroxide as acceptor bond. roxidases). With oxygen aSacceptor. ing on hydrogen as donor. With a disulfide as acceptor. h NAD(+) or NADP(+) as acceptor. With other acc eptors. h a cytochrome as acceptor. Other oxidoreductases. h a quinone or similar compound as Transferases. acceptor. Transferring one-carbon groups. W h an iron-sulfur protein as acceptor. Methyltransferases. W h other known acceptors. Hydroxymethyl-, formyl- and related W h other acceptors. transferases. Ac ing on single donors with Carboxyl- and carbamoyltransferases. incorporation of molecular oxygen. Amidinotransferases. h incorporation of two atoms of Transferring aldehyde or ketone Oxygen. residues. h incorporation of one atom of 2.2.1.— Transketolases and transaldolases. OXygen. 2.3.—— Acyltransferases. Ac ing on paired donors, with 2.3.1.— Transferring groups other than amino incorporation or reduction of molecular oxygen acyl groups. h 2-oxoglutarate as one donor, and 2.3.2.— Aminoacyltransferases. incorporation of one atom each of oxygen into both 2.3.3.— Acyl groups converted into alkyl on donors transfer. h NADH or NADPH as one donor, 2.4.—— Glycosyltrans (8Se.S. incorporation of two atoms of oxygen into one 2.4.1.— Hexosyltransferases. donor 2.4.2.— Pentosyltransferases. h NADH or NADPH as one donor, 2.4.99.— Transferringo her glycosyl groups. incorporation of one atom of oxygen 2.5.—— Transferring a kyl or aryl groups, other h reduced flavin or flavoprotein as than methyl groups. one donor, and incorporation of one atom of oxygen 2.6.—— Transferring nitrogenous groups. h a reduced iron-sulfur protein as one 2.6.1.— Transaminases (aminotransferases). donor, and incorporation of one atom of oxygen 2.6.3.— Oximinotrans (8Se.S. h reduced pteridine as one donor, and 2.6.99.— Transferringo her nitrogenous groups. incorporation of one atom of oxygen 2.7.- ...— Transferring phosphorous-containing h reduced ascorbate as one donor, groups. incorporation of one atom of oxygen 2.7.1.— Phosphotransferases with an alcohol h another compound as one donor, group as acceptor. incorporation of one incorporation of one atom 2.7.2.— Phosphotransferases with a carboxyl of oxygen group as acceptor. h oxidation of a pair of donors 2.7.3.— Phosphotransferases with a nitrogenous resulting in the reduction of molecular oxygen to group as accep O. two molecules of water 2.7.4.— Phosphotransferases with a phosphate W h 2-oxoglutarate as one donor, and group as accep O. the other dehydrogenated. 2.7.6.— Diphosphotransferases. W h NADH or NADPH as one donor, 2.7.7.— Nucleotidyltransferases. 8 the other dehydrogenated. 2.7.8.— Transferases or other substituted Ac ing on Superoxide as acceptor. phosphate groups. Oxidizing metal ions. 2.7.9.— Phosphotransferases with paired h NAD(+) or NADP(+) as acceptor. acceptors. h oxygen as acceptor. Transferring Sulfur-containing groups. h flavin as acceptor. Sulfurtransferases. ing on CH or CH(2) groups. Sulfotransferases. h NAD(+) or NADP(+) as acceptor. CoA-transferases. h oxygen as acceptor. Transferring allkylthio groups. h a disulfide as acceptor. Transferring selenium-containing h a quinone or similar compound as groups. acceptor Selenotransferases. h other acceptors. Hydrolases. Ac ing on iron-sulfur proteins as donors. Acting on ester bonds. US 2015/0240226 A1 Aug. 27, 2015 26

TABLE 1-continued TABLE 1-continued EC (Enzyme Commission) Numbers with the corresponding mode of EC (Enzyme Commission) Numbers with the corresponding mode of action for each enzyme class, Subclass and Sub-Subclass action for each enzyme class, Subclass and Sub-Subclass Carboxylic ester hydrolases. 3.6.3.— Acting on acid anhydrides; catalyzing hiolester hydrolases. transmembrane movement of Substances hosphoric monoester hydrolases. 3.6.4.— Acting on acid anhydrides; involved in hosphoric diester hydrolases. cellular and Subcellular movement 5 :riphosphoric monoester hydrolases. 3.6.5.— Acting on GTP; involved in cellular and S ric ester hydrolases. Subcellular movement. S. osphoric monoester hydrolases. 3.7.—— Acting on carbon-carbon bonds. hosphoric triester hydrolases. In ketonic Substances. eoxyribonucleases producing 5'- Acting on halide bonds. OSOOOCSES. In C-halide compounds. Xoribonucleases producing 5'- Acting on phosphorus-nitrogen bonds. OSOOOCSES. Acting on Sulfur-nitrogen bonds. .1.1 Xoribonucleases producing 3'- Acting on carbon-phosphorus bonds. OSOOOCSES. Acting on Sulfur-Sulfur bonds. 3 .1 5. xonucleases active with either ribo- or Acting on carbon-sulfur bonds. ribonucleic acid and producing 5'- Lyases. OSOOO(SCS Carbon-carbon lyases. 3 .1 6. xonucleases active with either ribo- or Carboxy-lyases. ribonucleic acid producing 3'- Aldehyde-lyases. OSOOO(SCS Oxo-acid-lyases. 3.1.21.— E.indodeoxyribonucleases producing 5'- Other carbon-carbon lyases. OOO(SciS. Carbon-oxygen lyases. 3.1.22.— Endodeoxyribonucleases producing other Hydro-lyases. han 5'-phosphomonoesters. Acting on polysaccharides. 3.1.25.— Site-specific endodeoxyribonucleases Acting on phosphates. specific for altered bases. Other carbon-oxygen lyases. 3.1.26.— Endoribonucleases producing 5'- Carbon-nitrogen lyases. phosphomonoesters. Ammonia-lyases. 3.1.27.— Endoribonucleases producing other than 5'-phosphomonoesters. Lyases acting on amides, amidines, etc. 3.1.30.— Endoribonucleases active with either Amine-lyases. ribo- or deoxyribonucleic and producing 5'- Other carbon-nitrogen-lyases. phosphomonoesters Carbon-sulfur lyases. Endoribonucleases active with either Carbon-halide lyases. ribo- or deoxyribonucleic and producing 3'- Phosphorus-oxygen lyases. phosphomonoesters Other lyases. 3.2.—— Glycosylases. Isomerases. 3.2.1.— Glycosidases, i.e., enzymes hydrolyzing Racemases and epimerases. O- and S-glycosyl compounds Acting on amino acids and derivatives. 3.2.2.— Hydrolyzing N-glycosyl compounds. Acting on hydroxy acids and derivatives. 3.3.- ...— Acting on ether bonds. Acting on carbohydrates and derivatives. 3.3.1.— Thioether and trialkylsulfonium Acting on other compounds. hydrolases. Cis-trans-isomerases. 3.3.2.— Ether hydrolases. intramolecular oxidoreductases. 3.4.—— Acting on peptide bonds (peptide hydrolases). interconverting aldoses and ketoses. 3.4.11.— Aminopeptidases. interconverting keto- and enol-groups. 3.4.13.— Dipeptidases. Transposing C=C bonds. 3.4.14.— Dipeptidyl-peptidases and tripeptidyl Transposing S-S bonds. peptidases. Other intramolecular oxidoreductases. 3.4.15.— Peptidyl-dipeptidases. intramolecular transferases (mutases). 3.4.16.— Serine-type carboxypeptidases. Transferring acyl groups. 3.4.17.— Metallocarboxypeptidases. Phosphotransferases (phosphomutases). 3.4.18.— Cysteine-type carboxypeptidases. Transferring amino groups. 3.4.19.— Omega peptidases. Transferring hydroxy groups. 3.4.21.— Serine endopeptidases. Transferring other groups. 3.4.22.— Cysteine endopeptidases. intramolecular lyases. 3.4.23.— Aspartic endopeptidases. Other isomerases. 3.4.24.— Metalloendopeptidases. Ligases. 3.4.25.— Threonine endopeptidases. Forming carbon-oxygen bonds. 3.4.99.— Endopeptidases of unknown catalytic Ligases forming aminoacyl-tRNA and mechanism. related compounds. 3.5.—— Acting on carbon-nitrogen bonds, other Forming carbon-sulfur bonds. than peptide bonds. Acid-thiol ligases. 3.5.1.— In linear amides. Forming carbon-nitrogen bonds. 3.5.2.— In cyclic amides. 6.3.1.— Acid-ammonia (or amide) ligases 3.5.3.— In linear amidines. (amide synthases). 3.5.4.— In cyclic amidines. 6.3.2.— Acid--D-amino-acid ligases (peptide 3.55. In nitriles. synthases). 3.5.99. In other compounds. 6.3.3.— Cyclo-ligases. 3.6.- ...— Acting on acid anhydrides. 6.3.4.— Other carbon-nitrogen ligases. 3.6.1.- In phosphorous-containing anhydrides. 6.3.5.— Carbon-nitrogen ligases with glutamine 3.6.2.— In Sulfonyl-containing anhydrides. as amido-N-donor. US 2015/0240226 A1 Aug. 27, 2015 27

TABLE 1-continued TABLE 1-continued

EC (Enzyme Commission) Numbers with the corresponding mode of EC (Enzyme Commission) Numbers with the corresponding mode of action for each enzyme class, Subclass and Sub-Subclass action for each enzyme class, Subclass and Sub-Subclass 6.6.—— Forming nitrogen-metal bonds. 6.4.—— Forming carbon-carbon bonds. 6.6.1.— Forming nitrogen-metal bonds. 6.5.—— Forming phosphoric ester bonds.

TABLE 2 EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. ENZYME: 1. . . . .1.1 Alcohol dehydrogenase. .1.2 Alcohol dehydrogenase (NADP+). .1.3 Homoserine dehydrogenase. .1.4 (R,R)-butanediol dehydrogenase. 1.5 Acetoin dehydrogenase. .1.6 Glycerol dehydrogenase. 1.7 Propanediol-phosphate dehydrogenase. .1.8 Glycerol-3-phosphate dehydrogenase (NAD+). 9 D-xylulose reductase. .1.10 L-xylulose reductase. .11 D-arabinitol 4-dehydrogenase. .12 L-arabinitol 4-dehydrogenase. 1.13 L-arabinitol 2-dehydrogenase. .1.14 L-iditol 2-dehydrogenase. 1.15 D-iditol 2-dehydrogenase. .1.16 Galactitol 2-dehydrogenase. 1.17 Mannitol-1-phosphate 5-dehydrogenase. .18 nositol 2-dehydrogenase. 19 L-glucuronate reductase. 1.2O Glucuronolactone reductase. .1.21 Aldehyde reductase. .1.22 UDP-glucose 6-dehydrogenase. 1.23 Histidinol dehydrogenase. .1.24 Quinate dehydrogenase. 25 Shikimate dehydrogenase. .1.26 Glyoxylate reductase. 1.27 L-lactate dehydrogenase. 1.28 D-lactate dehydrogenase. 1.29 Glycerate dehydrogenase. 1.30 3-hydroxybutyrate dehydrogenase. 1.31 3-hydroxyisobutyrate dehydrogenase. 1.32 Mevalidate reductase. 1.33 Mevaldate reductase (NADPH). 34 Hydroxymethylglutaryl-CoA reductase (NADPH). 1.35 3-hydroxyacyl-CoA dehydrogenase. 1.36 Acetoacetyl-CoA reductase. 37 Malate dehydrogenase. 38 Malate dehydrogenase (oxaloacetate decarboxylating). 39 Malate dehydrogenase (decarboxylating). .1.40 Malate dehydrogenase (oxaloacetate decarboxylating) (NADP+). .1.1.41 Isocitrate dehydrogenase (NAD+). .1.1.42 Isocitrate dehydrogenase (NADP+). .1.1.43 Phosphogluconate 2-dehydrogenase. .1.44 Phosphogluconate dehydrogenase (decarboxylating). 1.45 L-gulonate 3-dehydrogenase. .1.46 L-arabinose 1-dehydrogenase. 1.47 Glucose 1-dehydrogenase. .1.48 Galactose 1-dehydrogenase. 1.49 Glucose-6-phosphate 1-dehydrogenase. SO 3-alpha-hydroxysteroid dehydrogenase (B-specific). S1 3(or 17)beta-hydroxysteroid dehydrogenase. 52 3-alpha-hydroxycholanate dehydrogenase. US 2015/0240226 A1 Aug. 27, 2015 28

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 53 3-alpha(or 20-beta)-hydroxysteroid dehydrogenase. 1.54 Allyl-alcohol dehydrogenase. 1.55 L-acetaldehyde reductase (NADPH). 1.56 Ribitol 2-dehydrogenase. 1.57 Fructuronate reductase. 1.58 Tagaturonate reductase. 1.59 3-hydroxypropionate dehydrogenase. 1.60 2-hydroxy-3-oxopropionate reductase. 1.61 4-hydroxybutyrate dehydrogenase. .1.62 Estradiol 17-beta-dehydropenase. 1.63 Testosterone 17-beta-dehydrogenase. .64 Testosterone 17-beta-dehydrogenase (NADP+). 1.65 Pyridoxine 4-dehydrogenase. 66 Omega-hydroxy decanoate dehydrogenase. 1.67 Mannitol 2-dehydrogenase. 1.69 Gluconate 5-dehydrogenase. 1.71 Alcohol dehydrogenase (NAD(P)+). 1.72 Glycerol dehydrogenase (NADP+). 1.73 Octanol dehydrogenase. 1.75 (R)-aminopropanol dehydrogenase. 1.76 (S,S)-butanediol dehydrogenase. 1.77 Lactaldehyde reductase. 1.78 D-lactaldehyde dehydrogenase. 1.79 Glyoxylate reductase (NADP+). 18O Isopropanol dehydrogenase (NADP+). 1.81 Hydroxypyruvate reductase. 1.82 Malate dehydrogenase (NADP+). .83 D-malate dehydrogenase (decarboxylating). 1.84 Dimethylmalate dehydrogenase. 1.85 3-isopropylmalate dehydrogenase. 186 Ketol-acid reductoisomerase. 1.87 Homoisocitrate dehydrogenase. 1.88 Hydroxymethylglutaryl-CoA reductase. 1.90 Aryl-alcohol dehydrogenase. 1.91 Aryl-alcohol dehydrogenase (NADP+). 92 Oxaloglycolate reductase (decarboxylating). 1.93 Tartrate dehydrogenase. .94 Glycerol-3-phosphate dehydrogenase (NAD(P)+). 1.9S Phosphoglycerate dehydrogenase. 1.96 Diiodophenylpyruvate reductase. 1.97 3-hydroxybenzyl-alcohol dehydrogenase. 1.98 (R)-2-hydroxy-fatty-acid dehydrogenase. 1.99 (S)-2-hydroxy-fatty-acid dehydrogenase. 3-oxoacyl-acyl-carrier-protein reductase. .1.101 Acylglycerone-phosphate reductase. 1.102 3-dehydrosphinganine reductase. 1.103 L-threonine 3-dehydrogenase. .1.104 4-oxoproline reductase. 1105 Retinol dehydrogenase. 1106 Pantoate 4-dehydrogenase. 1.107 Pyridoxal 4-dehydrogenase. 1.108 Carnitine 3-dehydrogenase. .1.110 Indolelactate dehydrogenase. .1.111 3-(imidazol-5-yl)lactate dehydrogenase. .1.112 Indanol dehydrogenase. 1113 L-xylose 1-dehydrogenase. .1.114 Apiose 1-reductase. 1.115 Ribose 1-dehydrogenase (NADP+). .1.116 D-arabinose 1-dehydrogenase. 117 D-arabinose 1-dehydrogenase (NAD(P)+). 1118 Glucose 1-dehydrogenase (NAD+). 1119 Glucose 1-dehydrogenase (NADP+). 1.120 Galactose 1-dehydrogenase (NADP+). .1.121 Aldose 1-dehydrogenase. .1.122 D-threo-aldose 1-dehydrogenase. 123 Sorbose 5-dehydrogenase (NADP+). US 2015/0240226 A1 Aug. 27, 2015 29

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. .1.124 Fructose 5-dehydrogenase (NADP+). 1.125 2-deoxy-D-gluconate 3-dehydrogenase. 126 2-dehydro-3-deoxy-D-gluconate 6 dehydrogenase. 127 2-dehydro-3-deoxy-D-gluconate 5 dehydrogenase. 1.128 L-idonate 2-dehydrogenase. 1129 L-threonate 3-dehydrogenase. 1130 3-dehydro-L-gulonate 2-dehydrogenase. 1.131 Mannuronate reductase. 1.132 GDP-mannose 6-dehydrogenase. 1133 dTDP-4-dehydrorhamnose reductase. 134 dTDP-6-deoxy-L-talose 4 dehydrogenase. 13S GDP-6-deoxy-D-talose 4 dehydrogenase. 136 UDP-N-acetylglucosamine 6 dehydrogenase. 1.137 Ribitol-5-phosphate 2-dehydrogenase. 1.138 Mannitol 2-dehydrogenase (NADP+). .1.140 Sorbitol-6-phosphate 2-dehydrogenase. .141 15-hydroxyprostaglandin dehydrogenase (NAD+). .1.142 D-pinitol dehydrogenase. .1.143 Sequoyitol dehydrogenase. .1.144 Perillyl-alcohol dehydrogenase. 145 3-beta-hydroxy-delta(5)-steroid dehydrogenase. .1.146 11-beta-hydroxysteroid dehydrogenase. 1.147 16-alpha-hydroxysteroid dehydrogenase. .1.148 Estradiol 17-alpha-dehydrogenase. 1.149 20-alpha-hydroxysteroid dehydrogenase. 21-hydroxysteroid dehydrogenase (NAD+). 152 3-alpha-hydroxy-5-beta-androstane-17 one 3-alpha-dehydrogenase. 1.153 Sepiapterin reductase. 1.154 Ureidoglycolate dehydrogenase. 1.15S Homoisocitrate dehydrogenase. 1.156 Glycerol 2-dehydrogenase (NADP+). 1.157 3-hydroxybutyryl-CoA dehydrogenase. 1.158 UDP-N-acetylmuramate dehydrogenase. 1159 7-alpha-hydroxysteroid dehydrogenase. 1160 Dihydrobunolol dehydrogenase. .1.161 Cholestanetetraol 26-dehydrogenase. .1.162 Erythrulose reductase. 1.163 Cyclopentanol dehydrogenase. .1.164 Hexadecanol dehydrogenase. 1165 2-alkyn-1-oldehydrogenase. 166 Hydroxycyclohexanecarboxylate dehydrogenase. 1.167 Hydroxymalonate dehydrogenase. 168 2-dehydropantolactone reductase (A- specific). 1.169 2-dehydropantoate 2-reductase. 170 Sterol-4-alpha-carboxylate 3 dehydrogenase (decarboxylating). 1172 2-oxoadipate reductase. 1.173 L-rhamnose 1-dehydrogenase. 1.174 Cyclohexane-1,2-diol dehydrogenase. 1.175 D-xylose 1-dehydrogenase. 1176 12-alpha-hydroxysteroid dehydrogenase. 177 Glycerol-3-phosphate 1-dehydrogenase (NADP+). 178 3-hydroxy-2-methylbutyryl-CoA dehydrogenase. 1179 D-xylose 1-dehydrogenase (NADP+). 181 Cholest-5-ene-3-beta,7-alpha-diol 3 beta-dehydrogenase. 1.183 Geraniol dehydrogenase. .1.184 Carbonyl reductase (NADPH). .185 L-glycol dehydrogenase. 1186 dTDP-galactose 6-dehydrogenase. 187 GDP-4-dehydro-D-rhamnose reductase. US 2015/0240226 A1 Aug. 27, 2015 30

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 1.188 Prostaglandin-F synthase. 1.1.89 Prostaglandin-E(2) 9-reductase. 190 Indole-3-acetaldehyde reductase (NADH). 191 Indole-3-acetaldehyde reductase (NADPH). 1.192 Long-chain-alcohol dehydrogenase. 193 5-amino-6-(5- phosphoribosylamino)uracil reductase. 1.194 Coniferyl-alcohol dehydrogenase. 1.195 Cinnamyl-alcohol dehydrogenase. 196 15-hydroxyprostaglandin-D dehydrogenase (NADP+). 197 15-hydroxyprostaglandin dehydrogenase (NADP+). 198 (+)-borneol dehydrogenase. 1.199 (S)-uSnate reductase. 2OO Aldose-6-phosphate reductase (NADPH). 7-beta-hydroxysteroid dehydrogenase (NADP+). 1.2O2 1,3-propanediol dehydrogenase. 1.2O3 Uronate dehydrogenase. 1.205 IMP dehydrogenase. 12O6 Tropine dehydrogenase. 1.2O7 (-)-menthol dehydrogenase. 1208 (+)-neomenthol dehydrogenase. 209 3(or 17)-alpha-hydroxysteroid dehydrogenase. 3-beta(or 20-alpha)-hydroxysteroid dehydrogenase. Long-chain-3-hydroxyacyl-CoA dehydrogenase. 3-oxoacyl-acyl-carrier-protein reductase (NADH). 3-alpha-hydroxysteroid dehydrogenase (A-specific). 2-dehydropantolactone reductase (B- specific). Gluconate 2-dehydrogenase. g Famesol dehydrogenase. Benzyl-2-methyl-hydroxybutyrate dehydrogenase. Morphine 6-dehydrogenase. Dihydrokaempferol 4-reductase. 6-pyruvoyltetrahydropterin 2'-reductase. Vomifoliol 4'-dehydrogenase. (R)-4-hydroxyphenylactate dehydrogenase. 1.223 Isopiperitenol dehydrogenase. .1.224 Mannose-6-phosphate 6-reductase. 1.225 Chlordecome reductase. 226 4-hydroxycyclohexanecarboxylate dehydrogenase. 1.227 (-)-borneol dehydrogenase. 1228 (+)-Sabinol dehydrogenase. 229 Diethyl 2-methyl-3-oxoSuccinate reductase. 230 3-alpha-hydroxyglycyrrhetinate dehydrogenase. 231 15-hydroxyprostaglandin-I dehydrogenase (NADP+). 232 15-hydroxylicosatetraenoate dehydrogenase. 1.233 N-acylmannosamine 1-dehydrogenase. 1234 Flavanone 4-reductase. 1.235 8-oxocoformycin reductase. 1.236 Tropinone reductase. 1.237 Hydroxyphenylpyruvate reductase. 1.238 12-beta-hydroxysteroid dehydrogenase. 239 3-alpha-(17-beta)-hydroxysteroid dehydrogenase (NAD+). .1.240 N-acetylhexosamine 1-dehydrogenase. .241 6-endo-hydroxycineole dehydrogenase. US 2015/0240226 A1 Aug. 27, 2015 31

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 1243 Carveol dehydrogenase. .1.244 Methanol dehydrogenase. 1.245 Cyclohexanol dehydrogenase. .1.246 Pterocarpin synthase. 1.247 Codeinone reductase (NADPH). 1.248 Salutaridine reductase (NADPH). 1.2SO D-arabinitol 2-dehydrogenase. 1.251 Galactitol-1-phosphate 5-dehydrogenase. 1.252 Tetrahydroxynaphthalene reductase. 1.254 (S)-carnitine 3-dehydrogenase. 1.255 Mannitol dehydrogenase. 1.256 Fluoren-9-oldehydrogenase. 257 4-(hydroxymethyl)benzenesulfonate dehydrogenase. 1.258 6-hydroxyhexanoate dehydrogenase. 1.259 3-hydroxypimeloyl-CoA dehydrogenase. 1.260 Sulcatone reductase. 261 Glycerol-1-phosphate dehydrogenase (NAD(P)+). 262 4-hydroxythreonine-4-phosphate dehydrogenase. 1.263 1,5-anhydro-D-fructose reductase. .1.264 L-idonate 5-dehydrogenase. 1.265 3-methylbutanal reductase. 266 dTDP-4-dehydro-6-deoxyglucose reductase. .267 1-deoxy-D-xylulose-5-phosphate reductoisomerase. 268 2-(R)-hydroxypropyl-CoM dehydrogenase. 269 2-(S)-hydroxypropyl-CoM dehydrogenase. 1.270 3-keto-steroid reductase. 1.271 GDP-L-fucose synthase. 1.272 (R)-2-hydroxyacid dehydrogenase. 1.273 VelloSimine dehydrogenase. 1.274 2,5-didehydrogluconate reductase. 1275 (+)-trans-carveol dehydrogenase. 1.276 Serine 3-dehydrogenase. 277 3-beta-hydroxy-5-beta-steroid dehydrogenase. 278 3-beta-hydroxy-5-alpha-steroid dehydrogenase. 279 (R)-3-hydroxyacid-ester dehydrogenase. 1.28O (S)-3-hydroxyacid-ester dehydrogenase. 281 GDP-4-dehydro-6-deoxy-D-mannose reductase. 1.1.282 Quinateishikimate dehydrogenase. .1.2.2 Mannitol dehydrogenase (cytochrome). .1.2.3 L-lactate dehydrogenase (cytochrome). .1.2.4 D-lactate dehydrogenase (cytochrome). 2.5 D-lactate dehydrogenase (cytochrome c 553). 1.3.3 Malate oxidase. .1.3.4 Glucose oxidase. 13.5 Hexose oxidase. .1.3.6 Cholesterol oxidase. 1.3.7 Aryl-alcohol oxidase. 1.38 L-gulonolactone oxidase. 13.9 Galactose oxidase. 1.3.10 Pyranose oxidase. .1.3.11 L-Sorbose oxidase. .1.3.12 Pyridoxine 4-oxidase. 1.3.13 Alcohol oxidase. .1.3.14 Catechol oxidase (dimerizing). 1.3.15 (S)-2-hydroxy-acid oxidase. .1.3.16 Ecclysone oxidase. 1.3.17 Choline oxidase. 1.3.18 Secondary-alcohol oxidase. 1.3.19 4-hydroxymandelate oxidase. 1.3.20 Long-chain-alcohol oxidase. .1.3.21 Glycerol-3-phosphate oxidase. 13.23 Thiamine oxidase. 3.24 L-galactonolactone oxidase. US 2015/0240226 A1 Aug. 27, 2015 32

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 1.3.25 Cellobiose oxidase. 1.3.27 Hydroxyphytanate oxidase. 1.328 Nucleoside oxidase. 1.329 N-acylhexosamine oxidase. 13.30 Polyvinyl-alcohol oxidase. 1.3.37 D-arabinono-1,4-lactone oxidase. 13.38 Vanillyl-alcohol oxidase. 13.39 Nucleoside oxidase (H(2)0(2)-forming). .1.3.40 D-mannitol oxidase. .1.3.41 Xylitol oxidase. .1.4.1 Vitamin-K-epoxide reductase (warfarin sensitive). .1.4.2 Vitamin-K-epoxide reductase (warfarin insensitive). 15.2 Quinoprotein glucose dehydrogenase. 1.99.1 Choline dehydrogenase. 1992 2-hydroxyglutarate dehydrogenase. 1.99.3 luconate 2-dehydrogenase (acceptor). 1994 ehydrogluconate dehydrogenase. 1.99.5 ycerol-3-phosphate dehydrogenase. 1.99.6 -2-hydroxy-acid dehydrogenase. 1.99.7 actate-malate transhydrogenase. 1998 cohol dehydrogenase (acceptor). 1.99.9 Pyridoxine 5-dehydrogenase. 1.99.10 lucose dehydrogenase (acceptor). 1.99.11 Fructose 5-dehydrogenase. 1.99.12 Sorbose dehydrogenase. 1.99.13 lucoside 3-dehydrogenase. 1.99.14 ycolate dehydrogenase. 1.99.16 alate dehydrogenase (acceptor). 1.99.18 ellobiose dehydrogenase (acceptor). 1.99.19 racil dehydrogenase. 1.99.2O lcan-1-oldehydrogenase (acceptor). 1.99.21 -Sorbitol dehydrogenase (acceptor). 1.99.22 ycerol dehydrogenase (acceptor). 99.23 Polyvinyl-alcohol dehydrogenase (acceptor). 1.99.24 Hydroxyacid-oxoacid transhydrogenase. 99.25 Quinate dehydrogenase (pyrroloquinoline-quinone). 99.26 3-hydroxycyclohexanone dehydrogenase. 1.99.27 (R)-pantolactone dehydrogenase (flavin). 1.99.28 Glucose-fructose oxidoreductase. 1.99.29 Pyranose dehydrogenase (acceptor). 99.30 2-oxo-acid reductase. Formaldehyde dehydrogenase (glutathione). Formate dehydrogenase. Aldehyde dehydrogenase (NAD+). Aldehyde dehydrogenase (NADP+). Aldehyde dehydrogenase (NAD(P)+). Benzaldehyde dehydrogenase (NADP+). Betaine-aldehyde dehydrogenase. Glyceraldehyde-3-phosphate dehydrogenase (NADP+). 10 Acetaldehyde dehydrogenase (acetylating). 2. .11 Aspartate-semialdehyde dehydrogenase. .12 Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating). 13 Glyceraldehyde-3-phosphate dehydrogenase (NADP(+)) (phosphorylating). 1S Malonate-semialdehyde dehydrogenase. 16 Succinate-semialdehyde dehydrogenase (NAD(P)+). 17 Glyoxylate dehydrogenase (acylating). 18 Malonate-semialdehyde dehydrogenase (acetylating). 19 Aminobutyraldehyde dehydrogenase. 20 Glutarate-semialdehyde dehydrogenase. .21 Glycolaldehyde dehydrogenase. 22 Lactaldehyde dehydrogenase. 23 2-oxoaldehyde dehydrogenase (NAD+). US 2015/0240226 A1 Aug. 27, 2015 33

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. .2.1.24 Succinate-semialdehyde dehydrogenase. 2.1.25 2-oxoisovalerate dehydrogenase (acylating). .2.1.26 2,5-dioxovalerate dehydrogenase. 2.1.27 Methylmalonate-semialdehyde dehydrogenase (acylating). .2.1.28 Benzaldehyde dehydrogenase (NAD+). 2.1.29 Aryl-aldehyde dehydrogenase. 2.1.30 Aryl-aldehyde dehydrogenase (NADP+). .2.1.31 L-aminoadipate-semialdehyde dehydrogenase. .2.1.32 Aminomuconate-semialdehyde dehydrogenase. 2.1.33 (R)-dehydropantoate dehydrogenase. 2.1.36 Retinal dehydrogenase. 2.1.38 N-acetyl-gamma-glutamyl-phosphate reductase. 2.1.39 Phenylacetaldehyde dehydrogenase. .2.1.40 3-alpha,7-alpha,12-alpha trihydroxycholestan-26-all 26-oxidoreductase. .2.1.41 Glutamate-5-semialdehyde dehydrogenase. .2.1.42 Hexadecanal dehydrogenase (acylating). .2.1.43 Formate dehydrogenase (NADP+). .2.1.44 Cinnamoyl-CoA reductase. 2.1.45 4-carboxy-2-hydroxymuconate-6- semialdehyde dehydrogenase. .2.1.46 Formaldehyde dehydrogenase. 2.1.47 4-trimethylammoniobutyraldehyde dehydrogenase. .2.1.48 Long-chain-aldehyde dehydrogenase. .2.1.49 2-oxoaldehyde dehydrogenase (NADP+). 2.1.50 Long-chain-fatty-acyl-CoA reductase. 2.1.51 Pyruvate dehydrogenase (NADP+). 2.1.52 Oxoglutarate dehydrogenase (NADP+). 2.1.53 4-hydroxyphenylacetaldehyde dehydrogenase. 2.1.54 Gamma-guanidinobutyraldehyde dehydrogenase. 2.1.57 Butanal dehydrogenase. 2.1.58 Phenylglyoxylate dehydrogenase (acylating). 2.1.59 Glyceraldehyde-3-phosphate dehydrogenase (NAD(P)(+)) (phosphorylating). .2.1.60 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase. .2.1.61 4-hydroxymuconic-semialdehyde dehydrogenase. .2.1.62 4-formylbenzenesulfonate dehydrogenase. 2.1.63 6-oxohexanoate dehydrogenase. .2.1.64 4-hydroxybenzaldehyde dehydrogenase. 2.1.65 Salicylaldehyde dehydrogenase. .2.1.66 Mycothiol-dependent formaldehyde dehydrogenase. 2.1.67 Vanillin dehydrogenase. 2.1.68 Coniferyl-aldehyde dehydrogenase. 21.69 Fluoroacetaldehyde dehydrogenase. .2.2.1 Formate dehydrogenase (cytochrome). .2.2.2 Pyruvate dehydrogenase (cytochrome). .2.2.3 Formate dehydrogenase (cytochrome c 553). .2.2.4 Carbon-monoxide dehydrogenase (cytochrome b-561). .2.3.1 Aldehyde oxidase. 2.3.3 Pyruvate oxidase. .2.3.4 Oxalate oxidase. 2.3.5 Glyoxylate oxidase. 23.6 Pyruvate oxidase (CoA-acetylating). 2.3.7 Indole-3-acetaldehyde oxidase. 23.8 Pyridoxal oxidase. 23.9 Aryl-aldehyde oxidase. .2.3.11 Retinal oxidase. US 2015/0240226 A1 Aug. 27, 2015 34

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 2.3.13 4-hydroxyphenylpyruvate oxidase. .2.4.1 Pyruvate dehydrogenase (acetyl transferring). .2.4.2 Oxoglutarate dehydrogenase (Succinyl transferring). .2.4.4 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring). 2.7.1 Pyruvate synthase. 27.2 2-oxobutyrate synthase. 2.7.3 2-oxoglutarate synthase. 2.74 Carbon-monoxide dehydrogenase (ferredoxin). 2.7.5 Aldehyde ferredoxin oxidoreductase. 27.6 Glyceraldehyde-3-phosphate dehydrogenase (ferredoxin). 2.7.7 3-methyl-2-oxobutanoate dehydrogenase (ferredoxin). 2.78 Indolepyruvate ferredoxin oxidoreductase. 2.7.9 2-oxoglutarate ferredoxin oxidoreductase. 2.99.2 Carbon-monoxide dehydrogenase (acceptor). 2.99.3 Aldehyde dehydrogenase (pyrroloquinoline-quinone). 2.99.4 Formaldehyde dismutase. 2.99.5 Formylmethanofuran dehydrogenase. 2.99.6 Carboxylate reductase. 2.99.7 Aldehyde dehydrogenase (FAD independent). .3.1.1 Dihydrouracil dehydrogenase (NAD+). 3.1.2 Dihydropyrimidine dehydrogenase (NADP+). 3.13 Cortisone beta-reductase. 3.1.4 Cortisone alpha-reductase. 3.1.5 Cucurbitacin delta(23)-reductase. 3.1.6 Fumarate reductase (NADH). 3.1.7 Meso-tartrate dehydrogenase. 3.1.8 Acyl-CoA dehydrogenase (NADP+). 3.19 Enoyl-acyl-carrier-protein reductase (NADH). 3.1.10 Enoyl-acyl-carrier-protein reductase (NADPH, B-specific). .3.1.11 2-coumarate reductase. .3.1.12 Prephenate dehydrogenase. 3.1.13 Prephenate dehydrogenase (NADP+). .3.1.14 Orotate reductase (NADH). 3.1.15 Orotate reductase (NADPH). .3.1.16 Beta-nitroacrylate reductase. 3.1.17 3-methyleneoxindole reductase. 3.1.18 Kynurenate-7,8-dihydrodiol dehydrogenase. 3.1.19 Cis-1,2-dihydrobenzene-1,2-diol dehydrogenase. 3.1.2O Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase. .3.1.21 7-dehydrocholesterol reductase. .3.1.22 Cholestenone 5-alpha-reductase. 3.1.23 Cholestenone 5-beta-reductase. .3.1.24 Billiverdin reductase. 3.1.25 1,6-dihydroxycyclohexa-2,4-diene-1- carboxylate dehydrogenase. 3.1.26 Dihydrodipicolinate reductase. 3.1.27 2-hexadecenal reductase. 3.1.28 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase. 3.1.29 Cis-1,2-dihydro-1,2- dihydroxynaphthalene dehydrogenase. 3.1.30 Progesterone 5-alpha-reductase. 3.1.31 2-enoate reductase. 3.1.32 Maleylacetate reductase. 3.1.33 Protochlorophyllide reductase. 3.1.34 2,4-dienoyl-CoA reductase (NADPH). 3.1.35 Phosphatidylcholine desaturase. US 2015/0240226 A1 Aug. 27, 2015 35

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 3.1.36 Geissoschizine dehydrogenase. 3.1.37 Cis-2-enoyl-CoA reductase (NADPH). 3.1.38 Trans-2-enoyl-CoA reductase (NADPH). 3.139 Enoyl-acyl-carrier-protein reductase (NADPH, A-specific). .3.1.40 2-hydroxy-6-oxo-6-phenylhexa-2,4- ienoate reductase. .3.1.41 Xanthommatin reductase. .3.1.42 12-oxophytodienoate reductase. 3.143 Cyclohexadienyl dehydrogenase. .3.1.44 Trans-2-enoyl-CoA reductase (NAD+). 3.145 2'-hydroxyisoflavone reductase. .3.1.46 Biochanin-A reductase. 3.147 Alpha-Santonin 12-reductase. 3.148 5-oxoprostaglandin 13-oxidase. 3.149 Cis-3,4-dihydrophenanthrene-3,4-diol dehydrogenase. 31.51 2'-hydroxydaidzein reductase. 3.1.52 2-methyl-branched-chain-enoyl-CoA reductase. 3.1.53 (3S,4R)-3,4-dihydroxycyclohexa-1,5- iene-1,4-dicarboxylate dehydrogenase. 3.154 Precorrin-6A reductase. 3.156 Cis-2,3-dihydrobiphenyl-2,3-diol ehydrogenase. 3.1.57 Phloroglucinol reductase. 3.1.58 2,3-dihydroxy-2,3-dihydro-p-cumate ehydrogenase. 3.1.59 ,6-dihydroxy-5-methylcyclohexa-2,4- ienecarboxylate dehydrogenase. 3.1.60 Dibenzothiophene dihydrodiol ehydrogenase. .3.1.61 Terephthalate 12-cis-dihydrodiol ehydrogenase. 3.162 Pimeloyl-CoA dehydrogenase. 3.1.63 2,4-dichlorobenzoyl-CoA reductase. .3.1.64 Phthalate 4.5-cis-dihydrodiol ehydrogenase. 3.1.65 5,6-dihydroxy-3-methyl-2-oxo-1,2,5,6- etrahydroquinoline dehydrogenase. 3.1.66 Cis-dihydroethylcatechol dehydrogenase. 3.1.67 Cis-1,2-dihydroxy-4-methylcyclohexa 3,5-diene-1-carboxylate dehydrogenase. 3.1.68 ,2-dihydroxy-6-methylcyclohexa-3,5- dienecarboxylate dehydrogenase. 3.1.69 Zeatin reductase. 3.1.70 Delta (14)-sterol reductase. 3.171 Delta(24(24(1)))-sterol reductase. 3.1.72 Delta(24)-sterol reductase. 3.1.73 2-dihydrovomilenine reductase. 3.174 2-alkenal reductase. 3.1.75 Divinyl chlorophyllide a 8-vinyl reductase. 31.76 Precorrin-2 dehydrogenase. 3.23 Galactonolactone dehydrogenase. 3.31 Dihydroorotate oxidase. 3.32 Lathosterol oxidase. 3.3.3 Coproporphyrinogen oxidase. .3.3.4 Protoporphyrinogen oxidase. 3.35 Bilirubin oxidase. 33.6 Acyl-CoA oxidase. 3.3.7 Dihydrouracil oxidase. 3.38 Tetrahydroberberine oxidase. 33.9 Secologanin synthase. 3.3.10 Tryptophan alphabeta-oxidase. 35.1 Succinate dehydrogenase (ubiquinone). 3.7.1 6-hydroxynicotinate reductase. 3.7.2 15, 16-dihydrobiliverdin:ferredoxin oxidoreductase. 3.7.3 Phycoerythrobilin:ferredoxin oxidoreductase. 3.74 Phytochromobilin:ferredoxin oxidoreductase. US 2015/0240226 A1 Aug. 27, 2015 36

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 3.7.5 Phycocyanobilin:ferredoxin oxidoreductase. 3.99.1 Succinate dehydrogenase. 3.99.2 Butyryl-CoA dehydrogenase. 3.99.3 Acyl-CoA dehydrogenase. 3.99.4 3-oxosteroid 1-dehydrogenase. 3.99.5 3-oxo-5-alpha-steroid 4-dehydrogenase. 3.99.6 3-oxo-5-beta-steroid 4-dehydrogenase. 3.99.7 Glutaryl-CoA dehydrogenase. 3.99.8 2-furoyl-CoA dehydrogenase. 3.99.10 ISOValeryl-CoA dehydrogenase. 3.99.11 Dihydroorotate dehydrogenase. 3.99.12 2-methylacyl-CoA dehydrogenase. 3.99.13 Long-chain-acyl-CoA dehydrogenase. 3.99.14 Cyclohexanone dehydrogenase. 3.99.15 Benzoyl-CoA reductase. 3.99.16 Isoquinoline 1-oxidoreductase. 3.99.17 Quinoline 2-oxidoreductase. 3.99.18 Quinaldate 4-oxidoreductase. 3.99.19 Quinoline-4-carboxylate 2 oxidoreductase. 3.99.2O 4-hydroxybenzoyl-CoA reductase. 3.99.21 (R)-benzylsuccinyl-CoA dehydrogenase. Alanine dehydrogenase. Glutamate dehydrogenase. Glutamate dehydrogenase (NAD(P)+). Glutamate dehydrogenase (NADP+). L-amino-acid dehydrogenase. Serine 2-dehydrogenase. Valine dehydrogenase (NADP+). Leucine dehydrogenase. Glycine dehydrogenase. L-erythro-3,5-diaminohexanoate dehydrogenase. 2,4-diaminopentanoate dehydrogenase. Glutamate synthase (NADPH). Glutamate synthase (NADH). Lysine dehydrogenase. 1 6 Diaminopimelate dehydrogenase. N-methylalanine dehydrogenase. Lysine 6-dehydrogenase. Tryptophan dehydrogenase. Phenylalanine dehydrogenase. Glycine dehydrogenase (cytochrome). D-aspartate oxidase. L-amino-acid oxidase. D-amino-acid oxidase. Amine oxidase (flavin-containing). Pyridoxamine-phosphate oxidase. Amine oxidase (copper-containing). D-glutamate oxidase. Ethanolamine oxidase. Putrescine oxidase. L-glutamate oxidase. Cyclohexylamine oxidase. Protein-lysine 6-oxidase. L-lysine oxidase. D-glutamate(D-aspartate) oxidase. L-aspartate oxidase. Glycine oxidase. Glycine dehydrogenase (decarboxylating). Glutamate synthase (ferredoxin). D-amino-acid dehydrogenase. Taurine dehydrogenase. Amine dehydrogenase. Aralkylamine dehydrogenase. Glycine dehydrogenase (cyanide forming). Pyrroline-2-carboxylate reductase. Pyrroline-5-carboxylate reductase. Dihydrofolate reductase. Methylenetetrahydrofolate dehydrogenase (NADP+). US 2015/0240226 A1 Aug. 27, 2015 37

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. Formyltetrahydrofolate dehydrogenase. Saccharopine dehydrogenase (NAD+, L ysine-forming). Saccharopine dehydrogenase (NADP+, L-lysine-forming). Saccharopine dehydrogenase (NAD+, L glutamate-forming). 5.1.10 Saccharopine dehydrogenase (NADP+, L-glutamate-forming). 5.1.11 D-Octopine dehydrogenase. -pyrroline-5-carboxylate dehydrogenase. Methylenetetrahydrofolate dehydrogenase (NAD+). 16 D-lysopine dehydrogenase. 17 Alanopine dehydrogenase. 18 Ephedrine dehydrogenase. 19 D-nopaline dehydrogenase. 20 Methylenetetrahydrofolate reductase (NADPH). .5 .21 Delta(1)-piperideine-2-carboxylate reductase. 22 Strombine dehydrogenase. 23 Tauropine dehydrogenase. .24 N(5)-(carboxyethyl)ornithine synthase. 25 Thiomorpholine-carboxylate dehydrogenase. .5 26 Beta-alanopine dehydrogenase. .5 27 1,2-dehydroreticulinium reductase (NADPH). 28 Opine dehydrogenase. 29 FMN reductase. 30 Flavin reductase. 31 Berberine reductase. 32 Vomillenine reductase. .33 Pteridine reductase. 6,7-dihydropteridine reductase. 53.1 Sarcosine oxidase. S.3.2 N-methyl-L-amino-acid oxidase. 53.4 N(6)-methyl-lysine oxidase. S3.5 (S)-6-hydroxynicotine oxidase. 53.6 (R)-6-hydroxynicotine oxidase. 53.7 L-pipecolate oxidase. S.3.10 Dimethylglycine oxidase. 5.3.11 Polyamine oxidase. 5.312 Dihydrobenzophenanthridine oxidase. .5.4.1 Pyrimidodiazepine synthase. S.S.1 Electron-transferring-flavoprotein dehydrogenase. 5.8.1 Dimethylamine dehydrogenase. 5.8.2 Trimethylamine dehydrogenase. 5.99.1 Sarcosine dehydrogenase. S.99.2 Dimethylglycine dehydrogenase. S.99.3 L-pipecolate dehydrogenase. 5.99.4 Nicotine dehydrogenase. S.99.5 Methylglutamate dehydrogenase. 5.99.6 Spermidine dehydrogenase. S.99.8 Proline dehydrogenase. S.99.9 Methylenetetrahydromethanopterin dehydrogenase. 5.99.11 5,10-methylenetetrahydromethanopterin reductase. S.99.12 Cytokinin dehydrogenase. .6.1.1 NAD(P)(+) transhydrogenase (B- specific). .6.1.2 NAD(P)(+) transhydrogenase (AB specific). .6.2.2 Cytochrome-b5 reductase. .6.2.4 NADPH--hemoprotein reductase. 6.25 NADPH--cytochrome-c2 reductase. .6.2.6 Leghemoglobin reductase. 6.3.1 NAD(P)H oxidase. 6.53 NADH dehydrogenase (ubiquinone). US 2015/0240226 A1 Aug. 27, 2015 38

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 6.54 Monodehydroascorbate reductase (NADH). 6.S.S NADPH:duinone reductase. 65.6 p-benzoquinone reductase (NADPH). 6.5.7 2-hydroxy-1,4-benzoquinone reductase. 6.6.9 Trimethylamine-N-oxide reductase. 6.99.1 NADPH dehydrogenase. 6.99.2 NAD(P)H dehydrogenase (quinone). 6.99.3 NADH dehydrogenase. 6.99.5 NADH dehydrogenase (quinone). 6.99.6 NADPH dehydrogenase (quinone). .7.1.1 Nitrate reductase (NADH). .7.1.2 Nitrate reductase (NAD(P)H). .7.1.3 Nitrate reductase (NADPH). .7.1.4 Nitrite reductase (NAD(P)H). .7.1.5 Hyponitrite reductase. 71.6 Azobenzene reductase. .7.1.7 GMP reductase. .7.1.9 Nitroquinoline-N-oxide reductase. .7.1.10 Hydroxylamine reductase (NADH). .7.1.11 4-(dimethylamino)phenylazoxybenzene reductase. .7.1.12 N-hydroxy-2-acetamidofluorene reductase. 7.2.1 Nitrite reductase (NO-forming). 7.2.2 Nitrite reductase (cytochrome; ammonia forming). 7.2.3 Trimethylamine-N-oxide reductase (cytochrome c). 7.3.1 Nitroethane oxidase. 7.3.2 Acetylindoxyl oxidase. 7.3.3 Urate oxidase. 7.34 Hydroxylamine oxidase. 7.3.5 3-aci-nitropropanoate oxidase. 7.7.1 Ferredoxin-nitrite reductase. 7.7.2 Ferredoxin-nitrate reductase. 7.99.1 Hydroxylamine reductase. 7.99.4 Nitrate reductase. 7.99.5 5,10-methylenetetrahydrofolate reductase (FADH(2)). 7.99.6 Nitrous-oxide reductase. 7.99.7 Nitric-oxide reductase. 7.99.8 Hydroxylamine oxidoreductase. .8.1.2 Sulfite reductase (NADPH). 8.13 Hypotaurine dehydrogenase. .8.1.4 Dihydrolipoyl dehydrogenase. 8.15 2-oxopropyl-CoM reductase (carboxylating). .8.1.6 Cystine reductase. 8.17 Glutathione-disulfide reductase. 81.8 Protein-disulfide reductase. .8.19 Thioredoxin-disulfide reductase. 8.1.10 CoA-glutathione reductase. .8.1.11 Asparagusate reductase. .8.1.12 Trypanothione-disulfide reductase. 8.1.13 Bis-gamma-glutamylcystine reductase. .8.1.14 CoA-disulfide reductase. 8.1.15 Mycothione reductase. .8.2.1 Sulfite dehydrogenase. .8.2.2 Thiosulfate dehydrogenase. 8.31 Sulfite oxidase. 8.32 Thiol oxidase. 8.33 Glutathione oxidase. .8.3.4 Methanethiol oxidase. 8.3.5 Prenylcysteine oxidase. .8.4.1 Glutathione-homocystine transhydrogenase. .8.4.2 Protein-disulfide reductase (glutathione). .84.3 Glutathione--CoA-glutathione transhydrogenase. .8.44 Glutathione-cystine transhydrogenase. 84.5 Methionine-S-oxide reductase. .8.4.6 Protein-methionine-S-oxide reductase. US 2015/0240226 A1 Aug. 27, 2015 39

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 8.4.7 Enzyme-thiol transhydrogenase (glutathione-disulfide). .84.8 Phosphoadenylyl-sulfate reductase (thioredoxin). 84.9 Adenylyl-sulfate reductase (glutathione). .8.4.10 Adenylyl-sulfate reductase (thioredoxin). 85.1 Glutathione dehydrogenase (ascorbate). 8.7.1 Sulfite reductase (ferredoxin). 8.98.1 CoB-CoM heterodisulfide reductase. 8.99.1 Sulfite reductase. 8.99.2 Adenylyl-sulfate reductase. 8.99.3 Hydrogensulfite reductase. 9.31 Cytochrome-c oxidase. 96.1 Nitrate reductase (cytochrome). 9.99.1 ron--cytochrome-c reductase. .10.1.1 Trans-acenaphthene-1,2-diol dehydrogenase. .10.2.1 L-ascorbate-cytochrome-b5 reductase. .10.2.2 Ubiquinol-cytochrome-c reductase. 10.3.1 Catechol oxidase. 10.3.2 80C8SC. 10.3.3 L-ascorbate oxidase. .10.3.4 O-aminophenol oxidase. 10.3.5 3-hydroxyanthranilate oxidase. 10.3.6 Rifamycin-B oxidase. 10.99. 1 Plastoquinol-plastocyanin reductase. .11. NADH peroxidase. NADPH peroxidase. Fatty-acid peroxidase. Cytochrome-c peroxidase. Catalase. Peroxidase. odide peroxidase. Glutathione peroxidase. Chloride peroxidase. L-ascorbate peroxidase. Phospholipid-hydroperoxide glutathione peroxidase. Manganese peroxidase. Diarylpropane peroxidase. Hydrogen dehydrogenase. Hydrogen dehydrogenase (NADP+). Cytochrome-c3 hydrogenase. Hydrogen:Quinone oxidoreductase. 12.7.2 Ferredoxin hydrogenase. 12.98. 1 Coenzyme F420 hydrogenase. 12.98. 2 5,10-methenyltetrahydromethanopterin hydrogenase. 12.98. 3 Methanosarcina-phenazine hydrogenase. Hydrogenase (acceptor). Catechol 1,2-dioxygenase. Catechol 2,3-dioxygenase. Protocatechuate 3,4-dioxygenase. Gentisate 1,2-dioxygenase. Homogentisate 1,2-dioxygenase. 3-hydroxyanthranilate 3,4- dioxygenase. Protocatechuate 4,5-dioxygenase. 3. 2,5-dihydroxypyridine 5,6- dioxygenase. 10 7,8-dihydroxykynurenate 8,8a dioxygenase. .11 Tryptophan 2,3-dioxygenase. .12 Lipoxygenase. 13 Ascorbate 2,3-dioxygenase. .14 2,3-dihydroxybenzoate 3,4- dioxygenase. 1S 3,4-dihydroxyphenylacetate 2,3- dioxygenase. 16 3-carboxyethylcatechol 2,3- dioxygenase. 17 Indole 2,3-dioxygenase. 18 Sulfur dioxygenase. US 2015/0240226 A1 Aug. 27, 2015 40

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 19 Cysteamine dioxygenase. 20 Cysteine dioxygenase. 22 Caffeate 3,4-dioxygenase. 23 2,3-dihydroxyindole 2,3-dioxygenase. .24 Quercetin 2,3-dioxygenase. 25 3,4-dihydroxy-9,10-secoandrosta 1,3,5(10)-triene-9,17-dione 4,5-dioxygenase. 26 Peptide-tryptophan 2,3-dioxygenase. 27 4-hydroxyphenylpyruvate dioxygenase. s 28 2,3-dihydroxybenzoate 2,3- dioxygenase. 29 Stizolobate synthase. 30 Stizolobinate synthase. 31 Arachidonate 12-lipoxygenase. 32 2-nitropropane dioxygenase. .33 Arachidonate 15-lipoxygenase. 34 Arachidonate 5-lipoxygenase. 35 Pyrogallol 1,2-oxygenase. 36 Chloridazon-catechol dioxygenase. 37 Hydroxyquinol 1,2-dioxygenase. 38 1-hydroxy-2-naphthoate 1,2- dioxygenase. 39 Biphenyl-2,3-diol 1,2-dioxygenase. 40 Arachidonate 8-lipoxygenase. s 41 2,4'-dihydroxyacetophenone dioxygenase. 42 Indoleamine-pyrrole 2,3-dioxygenase. 43 Lignostilbene alpha-beta-dioxygenase. .44 Linoleate diol synthase. 45 Linoleate 11-lipoxygenase. 46 4-hydroxymandelate synthase. 47 3-hydroxy-4-oxoquinoline 2,4- dioxygenase. 48 3-hydroxy-2-methylquinolin-4-one 2,4- dioxygenase. 49 Chlorite O(2)-lyase. SO Acetylacetone-cleaving enzyme. 2.1 Arginine 2-monooxygenase. 2.2 Lysine 2-monooxygenase. 2.3 Tryptophan 2-monooxygenase. 2.4 Lactate 2-monooxygenase. 2.5 Renilla-luciferin 2-monooxygenase. 2.6 Cypridina-luciferin 2-monooxygenase. 2.7 Photinus-luciferin 4-monooxygenase (ATP-hydrolyzing). 2.8 Watasenia-luciferin 2-monooxygenase. 2.9 Phenylalanine 2-monooxygenase. 2.11 Methylphenyltetrahydropyridine N monooxygenase. 2.12 Apo-beta-carotenoid-14'13'- dioxygenase. 3. 2.13 Oplophorus-luciferin 2 monooxygenase. Inositol oxygenase. Tryptophan 2'-dioxygenase. Gamma-butyrobetaine dioxygenase. Procollagen-proline dioxygenase. Pyrimidine-deoxynucleoside 2'- dioxygenase. Procollagen-lysine 5-dioxygenase. Thymine dioxygenase. Procollagen-proline 3-dioxygenase. Trimethyllysine dioxygenase. Naringenin 3-dioxygenase. Pyrimidine-deoxynucleoside 1'- dioxygenase. Hyoscyamine (6S)-dioxygenase. Gibberellin-44 dioxygenase. Gibberellin 2-beta-dioxygenase. 6-beta-hydroxyhyoscyamine epoxidase. 1S Gibberellin 3-beta-dioxygenase. 16 Peptide-aspartate beta-dioxygenase. 17 Taurine dioxygenase. US 2015/0240226 A1 Aug. 27, 2015 41

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 1.18 Phytanoyl-CoA dioxygenase. 1.19 Leucocyanidin oxygenase. 1.20 Desacetoxyvindoline 4-hydroxylase. 1.21 Clavaminate synthase. 2.1 Anthranilate 1,2-dioxygenase (deaminating, decarboxylating). 2.3 Benzene 1,2-dioxygenase. 2.4 3-hydroxy-2- methylpyridinecarboxylate dioxygenase. 2.5 5-pyridoxate dioxygenase. 2.7 Phthalate 4,5-dioxygenase. 2.8 4-Sulfobenzoate 3,4-dioxygenase. 2.9 4-chlorophenylacetate 3,4- dioxygenase. 2.10 Benzoate 1,2-dioxygenase. 2.11 Toluene dioxygenase. 2.12 Naphthalene 1,2-dioxygenase. 2.13 2-chlorobenzoate 1,2-dioxygenase. 2.14 2-aminobenzenesulfonate 2,3- dioxygenase. 2.15 Terephthalate 1,2-dioxygenase. 2.16 2-hydroxyquinoline 5,6-dioxygenase. 2.17 Nitric oxide dioxygenase. 2.18 Biphenyl 2,3-dioxygenase. 3.1 Salicylate 1-monooxygenase. 3.2 4-hydroxybenzoate 3-monooxygenase. 3.3 4-hydroxyphenylacetate 3 monooxygenase. 3.4 Melilotate 3-monooxygenase. 3.5 Imidazoleacetate 4-monooxygenase. 3.6 Orcinol 2-monooxygenase. 3.7 Phenol 2-monooxygenase. 3.8 Dimethylaniline monooxygenase (N- oxide-forming). 6.4 Tryptophan 5-monooxygenase. 6.5 Glyceryl-ether monooxygenase. 6.6 Mandelate 4-monooxygenase. 7.1 Dopamine beta-monooxygenase. 7.3 Peptidylglycine monooxygenase. 7.4 Aminocyclopropanecarboxylate oxidase. 8.1 Monophenol monooxygenase. 8.2 CMP-N-acetylneuraminate monooxygenase. .14.19.1 Stearoyl-CoA 9-desaturase. .14.19.2 Acyl-acyl-carrier-protein desaturase. 14.19.3 Linoleoyl-CoA desaturase. .14.20.1 Deacetoxycephalosporin-C synthase. .14.21.1 (S)-stylopine synthase. .14.21.2 (S)-cheilanthifoline synthase. .14.21.3 Berbamunine synthase. .14.21.4 Salutaridine synthase. 14:21.5 (S)-canadine synthase. 14.99.1 Prostaglandin-endoperoxide synthase. 14.99.2 Kynurenine 7,8-hydroxylase. 14.99.3 Heme oxygenase (decyclizing). 14.99.4 Progesterone monooxygenase. 14.99.7 Squalene monooxygenase. 14.99.9 Steroid 17-alpha-monooxygenase. 14.99.10 Steroid 21-monooxygenase. 14.99.11 Estradiol 6-beta-monooxygenase. 14.99.12 Androst-4-ene-3,17-dione monooxygenase. 14.99.14 Progesterone 11-alpha-monooxygenase. 14.99.15 4-methoxybenzoate monooxygenase (O- demethylating). 14.99.19 Plasmanylethanolamine desaturase. 14.99.20 Phylloquinone monooxygenase (2,3- epoxidizing). 14.99.21 Latia-luciferin monooxygenase (demethylating). 14.99.22 Ecclysone 20-monooxygenase. 14.99.23 3-hydroxybenzoate 2-monooxygenase. 14.99.24 Steroid 9-alpha-monooxygenase. US 2015/0240226 A1 Aug. 27, 2015 42

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 14.99.26 2-hydroxypyridine 5-monooxygenase. 14.99.27 Juglone 3-monooxygenase. 14.99.28 Linalool 8-monooxygenase. 14.99.29 Deoxyhypusine monooxygenase. 14.99.30 Caroteine 7,8-desaturase. 14.99.31 Myristoyl-CoA 11-(E) desaturase. 14.99.32 Myristoyl-CoA 11-(Z) desaturase. 14.99.33 Delta(12)-fatty acid dehydrogenase. 14.99.34 Monoprenyl isoflavone epoxidase. 14.99.35 Thiophene-2-carbonyl-CoA monooxygenase. 14.99.36 Beta-caroteine 15,15'-monooxygenase. 14.99.37 Taxadiene 5-alpha-hydroxylase. 15.1.1 Superoxide dismutase. Superoxide reductase. Mercury(II) reductase. Diferric-transferrin reductase. Aquacobalamin reductase. Cob(II)alamin reductase. Aquacobalamin reductase (NADPH). Cyanocobalamin reductase (cyanide eliminating). Ferric-chelate reductase. Methionine synthase reductase. Ferroxidase. Cob(II)yrinic acid a,c-diamide reductase. CDP-4-dehydro-6-deoxyglucose reductase. 4-hydroxy-3-methylbut-2-enyl diphosphate reductase. Leucoanthocyanidin reductase. Xanthine dehydrogenase. Nicotinate dehydrogenase. Pteridine oxidase. Xanthine oxidase. 6-hydroxynicotinate dehydrogenase. Ribonucleoside-diphosphate reductase. Ribonucleoside-triphosphate reductase. 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase. Phenylacetyl-CoA dehydrogenase. 4-cresol dehydrogenase (hydroxylating). 17.99.2 Ethylbenzene hydroxylase. .18.1. Rubredoxin--NAD(+) reductase. .18.1.2 Ferredoxin-NADP(+) reductase. Ferredoxin-NAD(+) reductase. .18.1.4 Rubredoxin--NAD(P)(+) reductase. .18.6. Nitrogenase. 19.6. Nitrogenase (flavodoxin). .20.1. Phosphonate dehydrogenase. .20.4. Arsenate reductase (glutaredoxin). .20.4.2 Methylarsonate reductase. 2O.98.1 Arsenate reductase (aZurin). 2O.99.1 Arsenate reductase (donor). .21.3. Sopenicillin-N Synthase. .21.3.2 Columbamine oxidase. 21.3.3 Reticuline oxidase. .21.3.4 Sulochrin oxidase ((+)- bisdechlorogeodin-forming). 21.3.5 Sulochrin oxidase ((-)- bisdechlorogeodin-forming). 213.6 Aureusidin synthase. .21.4.1 D-proline reductase (dithiol). .21.4.2 Glycine reductase. .21.4.3 Sarcosine reductase. .21.4.4 Betaine reductase. 21.99.1 Beta-cyclopiazonate dehydrogenase. 97.1.1 Chlorate reductase. 97.1.2 Pyrogallol hydroxytransferase. 97.1.3 Sulfur reductase. 97.14 Formate acetyltransferase activating enzyme. US 2015/0240226 A1 Aug. 27, 2015 43

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 1.97.1.8 Tetrachloroethene reductive dehalogenase. 1.97.1.9 Selenate reductase. 1.97.1.10 Thyroxine 5'-deiodinase. 1.97.1.11 Thyroxine 5-deiodinase. ENZYME:2 . . .

2.1.1.1 Nicotinamide N-methyltransferase. 2.1.1.2 Guanidinoacetate N-methyltransferase. 2.1.1.3 Thetin-homocysteine S methyltransferase. 2.1.1.4 Acetylserotonin O-methyltransferase. 2.1.1.5 Betaine-homocysteine S methyltransferase. 2.1.1.6 Catechol O-methyltransferase. 2.1.1.7 Nicotinate N-methyltransferase. 2.1.1.8 Histamine N-methyltransferase. 2.1.19 Thiol S-methyltransferase. 2.1.1.10 Homocysteine S-methyltransferase. 2.1.1.11 Magnesium protoporphyrin IX methyltransferase. 2.1.1.12 Methionine S-methyltransferase. 2.1.1.13 Methionine synthase. 2.1.1.14 5-methyltetrahydropteroyltriglutamate-- homocysteine S-methyltransferase. 2.1.1.15 Fatty-acid O-methyltransferase. 2.1.1.16 Methylene-fatty-acyl-phospholipid synthase. 2.1.1.17 Phosphatidylethanolamine N methyltransferase. 2.1.1.18 Polysaccharide O-methyltransferase. 2.1.1.19 Trimethylsulfonium--tetrahydrofolate N methyltransferase. 2.1.1.20 Glycine N-methyltransferase. 2.1.1.21 Methylamine--glutamate N methyltransferase. 2.1.1.22 Camosine N-methyltransferase. 2.1.1.25 Phenol O-methyltransferase. 2.1.1.26 odophenol O-methyltransferase. 2.1.1.27 Tyramine N-methyltransferase. 2.1.1.28 Phenylethanolamine N methyltransferase. 2.1.1.29 RNA (cytosine-5-)-methyltransferase. 2.1.1.31 RNA (guanine-N(1)-)- methyltransferase. 2.1.1.32 RNA (guanine-N(2)-)- methyltransferase. 2.1.1.33 RNA (guanine-N(7)-)- methyltransferase. 2.1.1.34 RNA (guanosine-2'-O-)- methyltransferase. 2.1.1.35 RNA (uracil-5-)-methyltransferase. 2.1.1.36 RNA (adenine-N(1)-)-methyltransferase. 2.1.1.37 DNA (cytosine-5-)-methyltransferase. 2.1.1.38 O-demethylpuromycin O methyltransferase. 2.1.1.39 nositol 3-methyltransferase. 2.1.1.40 nositol 1-methyltransferase. 2.1.1.41 Sterol 24-C-methyltransferase. 2.1.1.42 Luteolin O-methyltransferase. 2.1.1.43 Histone-lysine N-methyltransferase. 2.1.1.44 Dimethylhistidine N-methyltransferase. 2.1.1.45 Thymidylate synthase. 2.1.1.46 soflavone 4'-O-methyltransferase. 2.1.1.47 indolepyruvate C-methyltransferase. 2.1.1.48 rRNA (adenine-N(6)-)- methyltransferase. 2.1.1.49 Amine N-methyltransferase. 2.1.1.50 Loganate O-methyltransferase. 2.1.1.51 rRNA (guanine-N(1)-)- methyltransferase. 2.1.1.52 rRNA (guanine-N(2)-)- methyltransferase. 2.1.1.53 Putrescine N-methyltransferase. US 2015/0240226 A1 Aug. 27, 2015 44

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 1.54 Deoxycytidylate C-methyltransferase. 3. 1.55 tRNA (adenine-N(6)-)-methyltransferase. S6 mRNA (guanine-N(7)-)- methyltransferase. 57 mRNA (nucleoside-2'-O-)- methyltransferase. 59 Cytochrome c-lysine N methyltransferase. 1.60 Calmodulin-lysine N-methyltransferase. 61 tRNA (5-methylaminomethyl-2- thiouridylate)-methyltransferase. 62 mRNA (2'-O-methyladenosine-N(6)-)- methyltransferase. 63 Methylated-DNA-protein-cysteine S methyltransferase. .64 3-demethylubiquinone-9 3-O- methyltransferase. 1.65 Licodione 2'-O-methyltransferase. 66 rRNA (adenosine-2'-O-)- methyltransferase. 1.67 Thiopurine S-methyltransferase. 3. 1.68 Caffeate O-methyltransferase. 69 5-hydroxyfuranocoumarin 5-O- methyltransferase. 70 8-hydroxyfuranocoumarin 8-O- methyltransferase. .71 Phosphatidyl-N-methylethanolamine N methyltransferase. 72 Site-specific DNA-methyltransferase (adenine-specific). .74 Methylenetetrahydrofolate--tRNA (uracil-5-)-methyltransferase (FADH(2)-oxidizing). 1.75 Apigenin 4'-O-methyltransferase. 1.76 Quercetin 3-O-methyltransferase. 77 Protein-L-isoaspartate(D-aspartate) O methyltransferase. 1.78 Isoorientin 3'-O-methyltransferase. .79 Cyclopropane-fatty-acyl-phospholipid synthase. 18O Protein-glutamate O-methyltransferase. 3. 1.82 3-methylquercitin 7-O-methyltransferase. .83 3,7-dimethylguercitin 4-O- methyltransferase. 84 Methylguercetagetin 6-O- methyltransferase. 1.85 Protein-histidine N-methyltransferase. 86 Tetrahydromethanopterin S methyltransferase. 1.87 Pyridine N-methyltransferase. 88 8-hydroxyquercitin 8-O- methyltransferase. 89 Tetrahydrocolumbamine 2-O- methyltransferase. 90 Methanol-5- hydroxybenzimidazolylcobamide Co methyltransferase. 1.91 sobutyraldoxime O-methyltransferase. 1.92 Bergaptol O-methyltransferase. 1.93 Xanthotoxol O-methyltransferase. .94 1-O-demethyl-17-0-deacetylvindoline O-methyltransferase. 1.9S Tocopherol O-methyltransferase. 3. 1.96 Thioether S-methyltransferase. 97 3-hydroxyanthranilate 4-C- methyltransferase. 2. 1.98 Diphthine synthase. .99 6-methoxy-2,3-dihydro-3- hydroxytabersonine N-methyltransferase. 1OO Protein-S-isoprenylcysteine O methyltransferase. 101 Macrocin O-methyltransferase. 3. 1.102 Demethylmacrocin O-methyltransferase. 103 Phosphoethanolamine N methyltransferase. US 2015/0240226 A1 Aug. 27, 2015 45

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. .1.104 Caffeoyl-CoA O-methyltransferase. 3. 105 N-benzoyl-4-hydroxyanthranilate 4-O- methyltransferase. 106 Tryptophan 2-C-methyltransferase. 107 Uroporphyrin-III C-methyltransferase. 108 6-hydroxymellein O-methyltransferase. 109 Demethylsterigmatocystin 6-O- methyltransferase. .1.110 Sterigmatocystin 7-O-methyltransferase. ..111 Anthranilate N-methyltransferase. .1.112 Glucuronoxylan 4-O-methyltransferase. 113 Site-specific DNA-methyltransferase (cytosine-N(4)-specific). .114 Hexaprenyldihydroxybenzoate methyltransferase. 115 (RS)-1-benzyl-1,2,3,4- tetrahydroisoquinoline N-methyltransferase. 116 3'-hydroxy-N-methyl-(S)-coclaurine 4'- O-methyltransferase. 117 (S)-scoulerine 9-O-methyltransferase. 3. 118 Columbamine O-methyltransferase. 119 10-hydroxydihydrosanguinarine 10-O- methyltransferase. 12O 12-hydroxydihydrochelirubine 12-O- methyltransferase. 121 6-O-methylnorlaudanosoline 5'-O- methyltransferase. 122 (S)-tetrahydroprotoberberine N methyltransferase. 123 Cytochrome-c-methionine S metnyltransIerase. .124 Cytochrome-c-arginine N methyltransferase. 12S Histone-arginine N-methyltransferase. 126 Myelin basic protein-arginine N methyltransferase. 127 Ribulose-bisphosphate carboxylase ysine N-methyltransferase. 2. 128 (RS)-norcoclaurine 6-O- methyltransferase. 1129 nositol 4-methyltransferase. 130 Precorrin-2 C(20)-methyltransferase. 1.131 Precorrin-3B C(17)-methyltransferase. 132 Precorrin-6Y C(5,15)-methyltransferase (decarboxylating). 133 Precorrin-4 C(11)-methyltransferase. 136 Chlorophenol O-methyltransferase. 137 Arsenite methyltransferase. 139 3'-demethylstaurosporine O methyltransferase. 140 (S)-coclaurine-N-methyltransferase. .1.141 Jasmonate O-methyltransferase. .142 Cycloartenol 24-C-methyltransferase. 143 24-methylenesterol C-methyltransferase. .144 Trans-aconitate 2-methyltransferase. 145 Trans-aconitate 3-methyltransferase. .146 (Iso)eugenol O-methyltransferase. 1.147 Corydaline synthase. 148 Thymidylate synthase (FAD). 149 Myricetin O-methyltransferase. 1150 Isoflavone 7-O-methyltransferase. 151 Cobalt-factor II C(20)- methyltransferase. 1152 Precorrin-6A synthase (deacetylating). 2. Glycine hydroxymethyltransferase. .2.2 Phosphoribosylglycinamide formyltransferase. 2. 2.3 Phosphoribosylaminoimidazolecarboxamide formyltransferase. .2.4 Glycine formimidoyltransferase. 2.5 Glutamate formimidoyltransferase. 2.7 D-alanine 2-hydroxymethyltransferase. 2.8 Deoxycytidylate 5 hydroxymethyltransferase. US 2015/0240226 A1 Aug. 27, 2015 46

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 2.1.2.9 Methionyl-tRNA formyltransferase. 2.1.2.10 Aminomethyltransferase. 2.1.2.11 3-methyl-2-oxobutanoate hydroxymethyltransferase. 2.1.3.1 Methylmalonyl-CoA carboxytransferase. 2.1.3.2 Aspartate carbamoyltransferase. 2.1.3.3 Ornithine carbamoyltransferase. 2.1.3.5 Oxamate carbamoyltransferase. 2.1.3.6 Putrescine carbamoyltransferase. 2.1.3.7 3-hydroxymethylcephem carbamoyltransferase. 2.1.3.8 Lysine carbamoyltransferase. 2.1.4.1 Glycine amidinotransferase. 2.1.4.2 Scyllo-inosamine-4-phosphate amidinotransferase. 2.2.1.1 Transketolase. 2.2.1.2 Transaldolase. 2.2.1.3 Formaldehyde transketolase. 2.2.1.4 Acetoin-ribose-5-phosphate transaldolase. 2.2.1.5 2-hydroxy-3-oxoadipate synthase. 2.2.1.6 Acetolactate synthase. 2.2.1.7 1-deoxy-D-xylulose-5-phosphate synthase. 2.2.1.8 Fluorothreonine transaldolase. 2.3.1.1 Amino-acid N-acetyltransferase. 2.3.1.2 Imidazole N-acetyltransferase. 2.3.1.3 Glucosamine N-acetyltransferase. 2.3.1.4 Glucosamine 6-phosphate N acetyltransferase. 2.3.1.5 Arylamine N-acetyltransferase. 2.3.1.6 Choline O-acetyltransferase. 2.3.1.7 Carnitine O-acetyltransferase. 2.3.1.8 Phosphate acetyltransferase. 2.3.1.9 Acetyl-CoA C-acetyltransferase. 2.3.1.10 Hydrogen-sulfide S-acetyltransferase. 2.3.1.11 Thioethanolamine S-acetyltransferase. 2.3.1.12 Dihydrolipoyllysine-residue acetyltransferase. 2.3.1.13 Glycine N-acyltransferase. 2.3.1.14 Glutamine N-phenylacetyltransferase. 2.3.1.15 Glycerol-3-phosphate O-acyltransferase. 2.3.1.16 Acetyl-CoA C-acyltransferase. 2.3.1.17 Aspartate N-acetyltransferase. 2.3.1.18 Galactoside O-acetyltransferase. 2.3.1.19 Phosphate butyryltransferase. 2.3.1.20 Diacylglycerol O-acyltransferase. 2.3.1.21 Carnitine O-palmitoyltransferase. 2.3.1.22 2-acylglycerol O-acyltransferase. 2.3.1.23 1-acylglycerophosphocholine O acyltransferase. 2.3.1.24 Sphingosine N-acyltransferase. 2.3.1.25 Plasmalogen synthase. 2.3.1.26 Sterol O-acyltransferase. 2.3.1.27 Cortisol O-acetyltransferase. 2.3.1.28 Chloramphenicol O-acetyltransferase. 2.3.1.29 Glycine C-acetyltransferase. 2.3.1.30 Serine O-acetyltransferase. 2.3.1.31 Homoserine O-acetyltransferase. 2.3.1.32 Lysine N-acetyltransferase. 2.3.1.33 Histidine N-acetyltransferase. 2.3.1.34 D-tryptophan N-acetyltransferase. 2.3.1.35 Glutamate N-acetyltransferase. 2.3.1.36 D-amino-acid N-acetyltransferase. 2.3.1.37 5-aminolevulinate synthase. 2.3.1.38 Acyl-carrier-protein S acetyltransferase. 2.3.139 Acyl-carrier-protein S malonyltransferase. 23.140 Acyl-acyl-carrier-protein-- phospholipid O-acyltransferase. 2.3.1.41 3-oxoacyl-acyl-carrier-protein synthase. 2.3.1.42 Glycerone-phosphate O-acyltransferase. US 2015/0240226 A1 Aug. 27, 2015 47

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 23. 43 Phosphatidylcholine-sterol O acyltransferase. 23. .44 N-acetylneuraminate 4-O- acetyltransferase. 23. 45 N-acetylneuraminate 7-O(or 9-O)- acetyltransferase. 23. 46 Homoserine O-Succinyltransferase. 23. 47 8-amino-7-Oxononanoate synthase. 23. 48 Histone acetyltransferase. 23. 49 Deacetyl-citrate-(pro-3S)-lyase S acetyltransferase. 23. SO Serine C-palmitoyltransferase. 23. S1 1-acylglycerol-3-phosphate O acyltransferase. 23. 52 2-acylglycerol-3-phosphate O acyltransferase. 23. 53 Phenylalanine N-acetyltransferase. 23. 54 Formate C-acetyltransferase. 23. S6 Aromatic-hydroxylamine O acetyltransferase. 23. 57 Diamine N-acetyltransferase. 23. S8 2,3-diaminopropionate N oxalyltransferase. 23. 59 Gentamicin 2'-N-acetyltransferase. 23. 60 Gentamicin 3'-N-acetyltransferase. 23. 61 Dihydrolipoyllysine-residue Succinyltransferase. 23. 62 2-acylglycerophosphocholine O acyltransferase. 23. 63 1-alkylglycerophosphocholine O acyltransferase. 23. .64 Agmatine N(4)-coumaroyltransferase. 23. .65 Glycine N-choloyltransferase. 23. 66 Leucine N-acetyltransferase. 23. .67 1-alkylglycerophosphocholine O acetyltransferase. 23. 68 Glutamine N-acyltransferase. 23. 69 Monoterpenol O-acetyltransferase. 23. 70 CDP-acylglycerol O arachidonoyltransferase. 23. .71 Glycine N-benzoyltransferase. 23. 72 Indoleacetylglucose-inositol O acyltransferase. 23. 73 Diacylglycerol-sterol O-acyltransferase. 23. .74 Naringenin-chalcone synthase. 23. .75 Long-chain-alcohol O-fatty acyltransferase. 23. .76 Retinol O-fatty-acyltransferase. 23. 77 Triacylglycerol--sterol O-acyltransferase. 23. .78 Heparan-alpha-glucosaminide N acetyltransferase. 23. .79 Maltose O-acetyltransferase. 23. 80 Cysteine-S-conjugate N acetyltransferase. 23. 81 Aminoglycoside N(3)-acetyltransferase. 23. 82 Aminoglycoside N(6')-acetyltransferase. 23. .83 Phosphatidylcholine--dolichol O acyltransferase. 23. 84 Alcohol O-acetyltransferase. 23. .85 Fatty-acid synthase. 23. 86 Fatty-acyl-CoA synthase. 23. 87 Arallcylamine N-acetyltransferase. 23. 88 Peptide alpha-N-acetyltransferase. 23. 89 Tetrahydrodipicolinate N acetyltransferase. 23. 90 Beta-glucogallin O-galloyltransferase. 23. 91 Sinapoylglucose-choline O Sinapoyltransferase. 23. 92 Sinapoylglucose-malate O Sinapoyltransferase. 23. 13-hydroxylupinine O tigloyltransferase. 23. .94 Erythronolide synthase. 23. 95 Trihydroxystilbene synthase. US 2015/0240226 A1 Aug. 27, 2015 48

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 23. .96 Glycoprotein N-palmitoyltransferase. 23. 97 Glycylpeptide N etradecanoyltransferase. 23. .98 Chlorogenate-glucarate O hydroxycinnamoyltransferase. 23. .99 Quinate O hydroxycinnamoyltransferase. 2.3.1. OO Myelin-proteolipid O palmitoyltransferase. 2.3.1. Formylmethanofuran-- etrahydromethanopterin N-formyltransferase. 2.3.1. N(6)-hydroxylysine O-acetyltransferase. 2.3.1. Sinapoylglucose--Sinapoylglucose O Sinapoyltransferase. 2.3.1. O4 -alkenylglycerophosphocholine O acyltransferase. 2.3.1. 05 Allcylglycerophosphate 2-O- acetyltransferase. 2.3.1. O6 Tartronate O hydroxycinnamoyltransferase. 2.3.1. O7 7-O-deacetylvindoline O acetyltransferase. 2.3.1. O8 Tubulin N-acetyltransferase. 2.3.1. 09 Arginine N-Succinyltransferase. 2.3.1. 10 Tyramine N-feruloyltransferase. 2.3.1. 11 Mycocerosate synthase. 2.3.1. 12 D-tryptophan N-malonyltransferase. 2.3.1. 13 Anthranilate N-malonyltransferase. 2.3.1. 14 3,4-dichloroaniline N malonyltransferase. 2.3.1. 15 Isoflavone-7-O-beta-glucoside 6"-O- malonyltransferase. 2.3.1. 16 Flavonol-3-O-beta-glucoside O malonyltransferase. 2.3.1. 17 2,3,4,5-tetrahydropyridine-2,6- dicarboxylate N-Succinyltransferase. 2.3.1. 18 N-hydroxyarylamine O acetyltransferase. 2.3.1. 19 Icosanoyl-CoA synthase. 2.3.1. 21 1-alkenylglycerophosphoethanolamine O-acyltransferase. 2.3.1. 22 Trehalose O-mycolyltransferase. 2.3.1. 23 Dolichol O-acyltransferase. 2.3.1. 25 1-alkyl-2-acetylglycerol O acyltransferase. 2.3.1. 26 Isocitrate O dihydroxycinnamoyltransferase. 2.3.1. 27 Ornithine N-benzoyltransferase. 2.3.1. 28 Ribosomal-protein-alanine N acetyltransferase. 2.3.1. 29 Acyl-[acyl-carrier-protein--UDP-N- acetylglucosamine O-acyltransferase. 2.3.1. 30 Galactarate O hydroxycinnamoyltransferase. 2.3.1. 31 Glucarate O hydroxycinnamoyltransferase. 2.3.1. 32 Glucarolactone O hydroxycinnamoyltransferase. 2.3.1. 33 Shikimate O hydroxycinnamoyltransferase. 2.3.1. 34 Galactolipid O-acyltransferase. 2.3.1. 35 Phosphatidylcholine-retinol O acyltransferase. 2.3.1. 36 Polysialic-acid O-acetyltransferase. 2.3.1. 37 Carnitine O-octanoyltransferase. 2.3.1. 38 Putrescine N hydroxycinnamoyltransferase. 2.3.1. 39 Ecclysone O-acyltransferase. 23. 140 Rosmarinate synthase. 23. .141 Galactosylacylglycerol O acyltransferase. 23. .142 Glycoprotein O-fatty-acyltransferase. 23. 143 Beta-glucogallin-tetrakisgalloylglucose O-galloyltransferase. US 2015/0240226 A1 Aug. 27, 2015 49

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 23. .144 Anthranilate N-benzoyltransferase. 23. 145 Piperidine N-piperoyltransferase. 23. .146 Pinosylvin synthase. 23. 147 Glycerophospholipid arachidonoyl transferase (CoA-independent). 23. 148 Glycerophospholipid acyltransferase (CoA-dependent). 23. 149 Platelet-activating factor acetyltransferase. 2.3.1. 50 Salutaridinol 7-O-acetyltransferase. 2.3.1. 51 Benzophenone synthase. 2.3.1. 52 Alcohol O-cinnamoyltransferase. 2.3.1. 53 Anthocyanin 5-aromatic acyltransferase. 2.3.1. S4 Propionyl-CoA C(2)- trimethyltridecanoyltransferase. 2.3.1. 55 Acetyl-CoA C-myristoyltransferase. 2.3.1. 56 Phloroisovalerophenone synthase. 2.3.1. 57 Glucosamine-1-phosphate N acetyltransferase. 2.3.1. 58 Phospholipid:diacylglycerol

2.3.1. 59 2.3.1. 60 Vinorine synthase. 2.3.1. 61 Lovastatin nonaketide synthase. 2.3.1. 62 Taxadien-5-alpha-ol O acetyltransferase. 2.3.1. 63 O-hydroxytaxane O-acetyltransferase. 2.3.1. 64 sopenicillin-NN-acyltransferase. 2.3.1. 65 6-methylsalicylic acid synthase. 2.3.1. 66 2-alpha-hydroxytaxane 2-O- benzoyltransferase. 2.3.1. 67 0-deacetylbaccatin III 10-O- acetyltransferase. 2.3.1. 68 Dihydrolipoyllysine-residue (2- methylpropanoyl)transferase. 2.3.1. 69 CO-methylating acetyl-CoA synthase. 2.3.2. D-glutamyltransferase. 2.3.2.2 Gamma-glutamyltransferase. 23.23 Lysyltransferase. 2.3.2.4 Gamma-glutamylcyclotransferase. 2.3.2.5 Glutaminyl-peptide cyclotransferase. 2.3.2.6 Leucyltransferase. 2.3.2.7 Aspartyltransferase. 2.3.2.8 Arginyltransferase. 2.3.2.9 Agaritine gamma-glutamyltransferase. 2.3.2.1 O UDP-N-acetylmuramoylpentapeptide ysine N(6)-alanyltransferase. 2.3.2.1 1 Alanylphosphatidylglycerol synthase. 2.3.2.1 2 Peptidyltransferase. 2.3.2.1 3 Protein-glutamine gamma glutamyltransferase. 2.3.2.14 D-alanine gamma-glutamyltransferase. 2.3.2.1 5 Glutathione gamma glutamylcysteinyltransferase. 2.3.3.1 Citrate (Si)-synthase. 2.3.3.2 Decylcitrate synthase. 2.3.3.3 Citrate (Re)-synthase. 2334 Decylhomocitrate synthase. 2.3.3.5 2-methylcitrate synthase. 2.3.3.6 2-ethylmalate synthase. 2.3.3.7 3-ethylmalate synthase. 23.38 ATP citrate synthase. 233.9 Malate synthase. 2.3.3.1 O Hydroxymethylglutaryl-CoA synthase. 2.3.3.1 1 2-hydroxyglutarate synthase. 2.3.3.1 2 3-propylmalate synthase. 2.3.3.1 3 2-isopropylmalate synthase. 2.3.3.14 Homocitrate synthase. 2.3.3.1 5 Sulfoacetaldehyde acetyltransferase. 2.4.1.1 Phosphorylase. 2.4.1.2 Dextrin dextranase. 2.4.1.4 Amylosucrase. 24.15 Dextranslucrase. 24.17 Sucrose phosphorylase. US 2015/0240226 A1 Aug. 27, 2015 50

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 2.4.1. Maltose phosphorylase. 2.4.1. Inulosucrase. 2.4. 10 LevanSucrase. 2.4. .11 Glycogen (starch) synthase. 2.4. .12 Cellulose synthase (UDP-forming). 2.4. 13 Sucrose synthase. 2.4. .14 Sucrose-phosphate synthase. 2.4. 1S Alpha,alpha-trehalose-phosphate synthase (UDP-forming). 2.4. 16 Chitin synthase. 2.4. 17 Glucuronosyltransferase. 2.4. 18 4-alpha-glucan branching enzyme. 2.4. 19 Cyclomaltodextrin glucanotransferase. 2.4. 20 Cellobiose phosphorylase. 2.4. .21 Starch synthase. 2.4. 22 Lactose synthase. 2.4. 23 Sphingosine beta-galactosyltransferase. 2.4. .24 4-alpha-glucan 6-alpha glucosyltransferase. 2.4. 25 4-alpha-glucanotransferase. 2.4. 26 DNA alpha-glucosyltransferase. 2.4. 27 DNA beta-glucosyltransferase. 2.4. 28 Glucosyl-DNA beta-glucosyltransferase. 2.4. 29 Cellulose synthase (GDP-forming). 2.4. 30 ,3-beta-oligoglucan phosphorylase. 2.4. 31 Laminaribiose phosphorylase. 2.4. 32 Glucomannan 4-beta mannosyltransferase. 2.4. .33 Alginate synthase. 2.4. 34 ,3-beta-glucan synthase. 2.4. 35 Phenol beta-glucosyltransferase. 2.4. 36 Alpha,alpha-trehalose-phosphate synthase (GDP-forming). 2.4. 37 Fucosylgalactoside 3-alpha galactosyltransferase. 2.4. 38 Beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase. 2.4. 39 Steroid N acetylglucosaminyltransferase. 2.4. 40 Glycoprotein-fucosylgalactoside alpha N-acetylgalactosaminyltransferase. 2.4. 41 Polypeptide N acetylgalactosaminyltransferase. 2.4. 43 Polygalacturonate 4-alpha galacturonosyltransferase. 2.4.1. Lipopolysaccharide 3-alpha galactosyltransferase. 2.4. 45 2-hydroxyacylsphingosine 1-beta galactosyltransferase. 2.4. 46 2-diacylglycerol 3-beta galactosyltransferase. 2.4. 47 N-acylsphingosine galactosyltransferase. 2.4. 48 Heteroglycan alpha mannosyltransferase. 2.4. 49 Cellodextrin phosphorylase. 2.4. SO Procollagen galactosyltransferase. 2.4. 52 Poly(glycerol-phosphate) alpha glucosyltransferase. 2.4. 53 Poly(ribitol-phosphate) beta glucosyltransferase. 2.4. 54 Undecaprenyl-phosphate mannosyltransferase. 2.4. S6 Lipopolysaccharide N acetylglucosaminyltransferase. 2.4. 57 Phosphatidylinositol alpha mannosyltransferase. 2.4. S8 Lipopolysaccharide glucosyltransferase

2.4. 60 Abequosyltransferase. 2.4. 62 Ganglioside galactosyltransferase. 2.4. 63 Linamarin synthase. 2.4. .64 Alpha,alpha-trehalose phosphorylase. US 2015/0240226 A1 Aug. 27, 2015 51

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 2.4. .65 3-galactosyl-N-acetylglucosaminide 4 alpha-L-fucosyltransferase. 2.4. 66 Procollagen glucosyltransferase. 2.4. .67 Galactinol--raffinose galactosyltransferase. 2.4. 68 Glycoprotein 6-alpha-L- lucosyltransferase. 2.4. 69 Galactoside 2-alpha-L- lucosyltransferase. 2.4. 70 Poly(ribitol-phosphate) N acetylglucosaminyltransferase. 2.4. .71 Arylamine glucosyltransferase. 2.4. 73 Lipopolysaccharide glucosyltransferase I. 2.4. .74 Glycosaminoglycan galactosyltransferase. 2.4. .75 UDP-galacturonosyltransferase. 2.4. .78 Phosphopolyprenol glucosyltransferase. 2.4. .79 Galactosylgalactosylglucosylceramide beta-D-acetylgalactosaminyltransferase. 2.4. 80 Ceramide glucosyltransferase. 2.4. 81 Flavone 7-O-beta-glucosyltransferase. 2.4. 82 Galactinol--Sucrose galactosyltransferase. 2.4. .83 Dolichyl-phosphate beta-D- mannosyltransferase. 2.4. .85 Cyanohydrin beta-glucosyltransferase. 2.4. 86 Glucosaminylgalactosylglucosylceramide beta-galactosyltransferase. 2.4. 87 N-acetylactosaminide 3-alpha galactosyltransferase. 2.4. 88 Globoside alpha-N- acetylgalactosaminyltransferase. 2.4. 90 N-acetylactosamine synthase. 2.4. 91 Flavonol 3-O-glucosyltransferase. 2.4. 92 (N-acetylneuraminy ) galactosylglucosylceramide N acetylgalactosaminy transferase. 2.4. .94 Protein N-acetylgluc Osaminyltransferase. 2.4. 95 Bilirubin-glucuronoside glucuronosyltransferase. 2.4. Sn-glycerol-3-phosphate 1 galactosyltransferase. 2.4. 97 ,3-beta-D-glucan phosphorylase. 2.4. .99 Sucrose:Sucrose fructosyltransferase. 2.4.1. OO 2,1-fructan:2,1-fructan 1 ructosyltransferase. 2.4.1. Alpha-1,3-mannosyl-glycoprotein 2 beta-N-acetylglucosaminyltransferase. 2.4.1. O2 Beta-1,3-galactosyl-O-glycosyl glycoprotein beta-1,6-N- acetylglucosaminyltransferase. 2.4.1. Alizarin 2-beta-glucosyltransferase. 2.4.1. O-dihydroxycoumarin 7-O- glucosyltransferase. 2.4.1. 05 Vitexin beta-glucosyltransferase. 2.4.1. O6 Isovitexin beta-glucosyltransferase. 2.4.1. 09 Dolichyl-phosphate-mannose--protein mannosyltransferase. 2.4.1. 10 tRNA-queuosine beta mannosyltransferase. 2.4.1. 11 Coniferyl-alcohol glucosyltransferase. 2.4.1. 12 Alpha-1,4-glucan-protein synthase (UDP-forming). 2.4.1. 13 Alpha-1,4-glucan-protein synthase (ADP-forming). 2.4.1. 14 2-coumarate O-beta-glucosyltransferase. 2.4.1. 15 Anthocyanidin 3-O-glucosyltransferase. 2.4.1. 16 Cyanidin-3-rhamnosylglucoside 5-O- glucosyltransferase. 2.4.1. 17 Dolichyl-phosphate beta glucosyltransferase. 2.4.1. 18 Cytokinin 7-beta-glucosyltransferase. US 2015/0240226 A1 Aug. 27, 2015 52

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 2.4.1. 19 Dolichyl-diphosphooligosaccharide-- protein glycotransferase. 2.4.1. 2O Sinapate 1-glucosyltransferase. 2.4.1. 21 indole-3-acetate beta glucosyltransferase. 2.4.1. 22 Glycoprotein-N-acetylgalactosamine 3 beta-galactosyltransferase. 2.4.1. 23 nositol 3-alpha-galactosyltransferase. 2.4.1. 25 Sucrose-1,6-alpha-glucan 3(6)-alpha glucosyltransferase. 2.4.1. 26 Hydroxycinnamate 4-beta glucosyltransferase. 2.4.1. 27 Monoterpenol beta-glucosyltransferase. 2.4.1. 28 Scopoletin glucosyltransferase. 2.4.1. 29 Peptidoglycan glycosyltransferase. 2.4.1. 30 Dolichyl-phosphate-mannose-- glycolipid alpha-mannosyltransferase. 2.4.1. 31 Glycolipid 2-alpha-mannosyltransferase. 2.4.1. 32 Glycolipid 3-alpha-mannosyltransferase. 2.4.1. 33 Xylosylprotein 4-beta galactosyltransferase. 2.4.1. 34 Galactosylxylosylprotein 3-beta galactosyltransferase. 2.4.1. 35 Galactosylgalacto Sylxylosylprotein 3 beta-glucuronosyltransferase. 2.4.1. 36 Gallate 1-beta-glucosyltransferase. 2.4.1. 37 Sn-glycerol-3-phosphate 2-alpha galactosyltransferase. 2.4.1. 38 Mannotetraose 2-alpha-N- acetylglucosaminyltransferase. 2.4.1. 39 Maltose synthase. 2.4. 140 Altemanslucrase. 2.4. .141 N-acetylglucosaminyldiphosphodolichol N-acetylghicosaminyltransferase. 2.4. .142 Chitobiosyldiphosphodolichol beta mannosyltransferase. 2.4. 143 Alpha-1,6-mannosyl-glycoprotein 2 beta-N-acetylglucosaminyltransferase. 2.4. .144 Beta-1,4-mannosyl-glycoprotein 4-beta N-acetylghicosaminyltransferase. 2.4. 145 Alpha-1,3-mannosyl-glycoprotein 4 beta-N-acetylglucosaminyltransferase. 2.4. .146 Beta-1,3-galactosyl-O-glycosyl glycoprotein beta-1,3-N- acetylglucosaminyltransferase. 2.4. 147 Acetylgalactosaminyl-O-glycosyl glycoprotein beta-1,3-N- acetylglucosaminyltransferase. 2.4. 148 Acetylgalactosaminyl-O-glycosyl glycoprotein beta-1,6-N- acetylglucosaminyltransferase. 2.4. 149 N-acetylactosaminide beta-1,3-N- acetylglucosaminyltransferase. 2.4.1. 50 N-acetylactosaminide beta-1,6-N- acetylglucosaminyl-transferase. 2.4.1. 52 4-galactosyl-N-acetylglucosaminide 3 alpha-L-fucosyltransferase. 2.4.1. 53 Dolichyl-phosphate alpha-N- acetylglucosaminyl transferase. 2.4.1. Globotriosylceramide beta-1,6-N- acetylgalactosaminyl-transferase. 2.4.1. 55 Alpha-1,6-mannosyl-glycoprotein 6 beta-N-acetylglucosaminyltransferase. 2.4.1. 56 Indolylacetyl-myo inositolgalactosyltransferase. 2.4.1. 57 1,2-diacylglycerol 3-glucosyltransferase. 2.4.1. 58 13-hydroxydocosanoate 13-beta glucosyltransferase. 2.4.1. 59 Flavonol-3-O-glucoside L rhamnosyltransferase. 2.4.1. 60 Pyridoxine 5'-O-beta-D- glucosyltransferase. 2.4.1. 61 Oligosaccharide 4-alpha-D- glucosyltransferase. US 2015/0240226 A1 Aug. 27, 2015 53

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 2.4. 162 Aldose beta-D-fructosyltransferase. 2.4. 163 Beta-galactosyl-N- acetylglucosaminylgalactosylglucosyl-ceramide beta-1,3-acetylglucosaminyltransferase. 2.4. .164 Galactosyl-N- acetylglucosaminylgalactosylglucosyl-ceramide beta-1,6-N-acetylglucosaminyltransferase. 2.4.1. 65 N acetylneuraminylgalactosylglucosylceramide beta 1,4-N-acetylgalactosaminyltransferase. 2.4. 166 Raffinose-raffinose alpha galactosyltransferase. 2.4. 167 Sucrose 6 (F)-alpha galactosyltransferase. 2.4. 168 Xyloglucan 4-glucosyltransferase. 2.4. 170 Isoflavone 7-O-glucosyltransferase. 2.4. 171 Methyl-ONN-azoxymethanol beta-D- glucosyltransferase. 2.4. 172 Salicyl-alcohol beta-D- glucosyltransferase. 2.4. 173 Sterol 3-beta-glucosyltransferase. 2.4. 174 Glucuronylgalactosylproteoglycan 4 beta-N-acetylgalactosaminyltransferase. 2.4. 175 Glucuronosyl-N-acetylgalactosaminyl proteoglycan 4-beta-N- acetylgalactosaminyltransferase. 2.4. 176 Gibberellin beta-D-glucosyltransferase. 2.4. 177 Cinnamate beta-D-glucosyltransferase. 2.4. 178 Hydroxymandelonitrile glucosyltransferase. 2.4. 179 Lactosylceramide beta-1,3- galactosyltransferase. 2.4. 18O Lipopolysaccharide N acetylmannosaminouronosyltransferase. 2.4. 181 Hydroxyanthraquinone glucosyltransferase. 2.4. 182 Lipid-A-disaccharide synthase. 2.4. 183 Alpha-1,3-glucan synthase. 2.4. 184 Galactolipid galactosyltransferase. 2.4. .185 Flavanone 7-O-beta-glucosyltransferase. 2.4. 186 Glycogenin glucosyltransferase. 2.4.1. 87 N acetylglucosaminyldiphosphoundecaprenol N acetyl-beta-D-mannosaminyltransferase. 2.4.1. 88 N acetylglucosaminyldiphosphoundecaprenol glucosyltransferase. 2.4. 189 Luteolin 7-O-glucuronosyltransferase. 2.4. 190 Luteolin-7-O-glucuronide 7-O- glucuronosyltransferase. 2.4. 191 Luteolin-7-O-diglucuronide 4-O- glucuronosyltransferase. 2.4. 192 Nuatigenin 3-beta-glucosyltransferase. 2.4. 193 Sarsapogenin 3-beta-glucosyltransferase. 2.4. 194 4-hydroxybenzoate 4-O-beta-D- glucosyltransferase. 2.4. 195 Thiohydroximate beta-D- glucosyltransferase. 2.4. 196 Nicotinate glucosyltransferase. 2.4. 197 High-mannose-oligosaccharide beta-1,4- N-acetylglucosaminyltransferase. 2.4. 198 Phosphatidylinositol N acetylglucosaminyltransferase. 2.4. 199 Beta-mannosylphosphodecaprenol mannooligosaccharide 6-mannosyltransferase. 2.4. 2O1 Alpha-1,6-mannosyl-glycoprotein 4 beta-N-acetylglucosaminyltransferase. 2.4. 2O2 2,4-dihydroxy-7-methoxy-2H-1,4- benzoxazin-3 (4H)-one 2-D-glucosyltransferase. 2.4. 2O3 Trans-zeatin O-beta-D- glucosyltransferase. 2.4. 2OS Galactogen 6-beta-galactosyltransferase. 2.4. 2O6 Lactosylceramide 1,3-N-acetyl-beta-D- glucosaminyltransferase. US 2015/0240226 A1 Aug. 27, 2015 54

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 2.4. 2O7 Xyloglucan:Xyloglucosyltransferase. 2.4. 208 Diglucosyl diacylglycerol synthase. 2.4. 209 Cis-p-coumarate glucosyltransferase. 2.4. 210 Limonoid glucosyltransferase. 2.4. 211 ,3-beta-galactosyl-N-acetylhexosamine phosphorylase. 2.4. 212 Hyaluronan synthase. 2.4. 213 Glucosylglycerol-phosphate synthase. 2.4. .214 Glycoprotein 3-alpha-L- lucosyltransferase. 2.4. 215 Cis-zeatin O-beta-D-glucosyltransferase. 2.4. 216 Trehalose 6-phosphate phosphorylase. 2.4. 217 Mannosyl-3-phosphoglycerate synthase. 2.4. 218 Hydroquinone glucosyltransferase. 2.4. 219 Vomilenine glucosyltransferase. 2.4. 22O indoxyl-UDPG glucosyltransferase. 2.4. 221 Peptide-O-fucosyltransferase. 2.4. 222 O-fucosylpeptide 3-beta-N- acetylglucosaminyltransferase. 2.4. 223 Glucuronyl-galactosyl-proteoglycan 4 alpha-N-acetylglucosaminyltransferase. 2.4. .224 Glucuronosyl-N-acetylglucosaminyl proteoglycan 4-alpha-N- acetylglucosaminyltransferase. 2.4. 225 N-acetylglucosaminyl-proteoglycan 4 beta-glucuronosyltransferase. 2.4. 226 N-acetylgalactosaminyl-proteoglycan 3 beta-glucuronosyltransferase. 2.4. 227 Undecaprenyldiphospho muramoylpentapeptide beta-N- acetylglucosaminyltransferase. 2.4. 228 Lactosylceramide 4-alpha galactosyltransferase. 2.4. 229 Skp1-protein-hydroxyproline N acetylglucosaminyltransferase. 2.4. 230 Koibiose phosphorylase. 2.4. 231 Alpha,alpha-trehalose phosphorylase (configuration-retaining). 2.4. 232 initiation-specific alpha-1,6- mannosyltransferase. 2.4.2.1 Purine-nucleoside phosphorylase. 2.4.2.2 Pyrimidine-nucleoside phosphorylase. 2.4.2.3 Uridine phosphorylase. 2.4.2.4 Thymidine phosphorylase. 24.25 Nucleoside ribosyltransferase. 2.4.2.6 Nucleoside deoxyribosyltransferase. 24.2.7 Adenine phosphoribosyltransferase. 2.4.2.8 Hypoxanthine phosphoribosyltransferase. 2.4.2.9 Uracil phosphoribosyltransferase. 2.4.2.10 Orotate phosphoribosyltransferase. 2.4.2.11 Nicotinate phosphoribosyltransferase. 2.4.2.12 Nicotinamide phosphoribosyltransferase. 2.4.2.14 Amidophosphoribosyltransferase. 24.2.15 Guanosine phosphorylase. 2.4.2.16 Urate-ribonucleotide phosphorylase. 24.2.17 ATP phosphoribosyltransferase. 2.4.2.18 Anthranilate phosphoribosyltransferase. 24.2.19 Nicotinate-nucleotide diphosphorylase (carboxylating). 2.4.2.20 Dioxotetrahydropyrimidine phosphoribosyltransferase. 2.4.2.21 Nicotinate-nucleotide-- dimethylbenzimidazole phosphoribosyltransferase. 2.4.2.22 Xanthine phosphoribosyltransferase. 2.4.2.23 Deoxyuridine phosphorylase. 2.4.2.24 1,4-beta-D-xylan synthase. 24.2.25 Flavone apiosyltransferase. 2.4.2.26 Protein xylosyltransferase. 24.2.27 dTDP-dihydrostreptose--streptidine-6- phosphate dihydrostreptosyltransferase. 2.4.2.28 S-methyl-5-thioadenosine phosphorylase. 24.2.29 Queuine tRNA-ribosyltransferase. US 2015/0240226 A1 Aug. 27, 2015 55

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 24.2.30 NAD(+) ADP-ribosyltransferase. 2.4.2.31 NAD(P)(+)--arginine ADP ribosyltransferase. 2.4.2.32 Dolichyl-phosphate D xylosyltransferase. 24.233 Dolichyl-xylosyl-phosphate-protein xylosyltransferase. 2.4.2.34 Indolylacetylinositol arabinosyltransferase. 24.2.35 Flavonol-3-O-glycoside xylosyltransferase. 24.236 NAD(+)--diphthamide ADP ribosyltransferase. 24.237 NAD(+)--dinitrogen-reductase ADP-D- ribosyltransferase. 24.238 Glycoprotein 2-beta-D- xylosyltransferase. 24.239 Xyloglucan 6-Xylosyltransferase. 2.4.2.40 Zeatin O-beta-D-xylosyltransferase. 24.99.1 Beta-galactoside alpha-2,6- sialyltransferase. 24.99.2 MonoSialoganglioside sialyltransferase. 24.99.3 Alpha-N-acetylgalactosaminide alpha 2,6-sialyltransferase. 24.99.4 Beta-galactoside alpha-2,3- sialyltransferase. 24.99.5 Galactosyldiacylglycerol alpha-2,3- sialyltransferase. 24.99.6 N-acetylactosaminide alpha-2,3- sialyltransferase. 24.99.7 (Alpha-N-acetylneuraminyl-2,3-beta galactosyl-1,3)-N-acetyl-galactosaminide 6-alpha sialyltransferase. 24.99.8 Alpha-N-acetylneuraminate alpha-2,8- sialyltransferase. 24.99.9 Lactosylceramide alpha-2,3- sialyltransferase. 24.99.10 Neolactotetraosylceramide alpha-2,3- sialyltransferase. 24.99.11 Lactosylceramide alpha-2,6-N- sialyltransferase. 2.5.1.1 Dimethylallyltranstransferase. 2.5.1.2 Thiamine pyridinylase. 2.51.3 Thiamine-phosphate diphosphorylase. 2.5.1.4 Adenosylmethionine cyclotransferase. 2.5.1.5 Galactose-6-sulfurylase. 2.51.6 Methionine adenosyltransferase. 2.5.1.7 UDP-N-acetylglucosamine 1 carboxyvinyltransferase. 2.5.1.8 tRNA isopentenyltransferase. 2.5.19 Riboflavin Synthase. 2.5.1.10 Geranyltranstransferase. 2.5.1.11 Trans-octaprenyltranstransferase. 2.5.1.15 Dihydropteroate synthase. 2.5.1.16 Spermidine synthase. 2.5.1.17 Cob(I)yrinic acid a,c-diamide adenosyltransferase. 2.5.1.18 Glutathione transferase. 2.5.1.19 3-phosphoshikimate 1 carboxyvinyltransferase. 2.5.1.20 Rubber cis-polyprenylcistransferase. 2.5.1.21 Famesyl-diphosphate famesyltransferase. 2.5.1.22 Spermine synthase. 2.5.1.23 Sym-norspermidine synthase. 2.5.1.24 Discadenine synthase. 2.5.1.25 tRNA-uridine aminocarboxypropyltransferase. 2.5.126 Alkylglycerone-phosphate synthase. 2.5.1.27 Adenylate dimethylallyltransferase. 2.5.1.28 Dimethylallylcistransferase. 2.5.1.29 FameSyltranstransferase. 2.5.1.30 Trans-hexaprenyltranstransferase. US 2015/0240226 A1 Aug. 27, 2015 56

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 2.S. 31 Di-trans, poly-cis decaprenylcistransferase. 2.S. 32 Geranylgeranyl-diphosphate geranylgeranyltransferase. 2.S. .33 Trans-pentaprenyltranstransferase. 2.S. 34 Tryptophan dimethylallyltransferase. 2.S. 35 Aspulvinone dimethylallyltransferase. 2.S. 36 Trihydroxypterocarpan dimethylallyltransferase. 2.S. 38 Isonocardicin synthase. 2.S. 39 4-hydroxybenzoate nonaprenyltransferase. 2.S. 41 Phosphoglycerol geranylgeranyltransferase. 2.S. 42 Geranylgeranylglycerol-phosphate geranylgeranyltransferase. 2.S. 43 Nicotianamine synthase. 2.S. .44 Homospermidine synthase. 2.S. 45 Homospermidine synthase (spermidine specific). 2.S. 46 Deoxyhypusine synthase. 2.S. 47 Cysteine synthase. 2.S. 48 CyStathionine gamma-synthase. 2.S. 49 O-acetylhomoserine aminocarboxypropyltransferase. 2.S. SO Zeatin 9-aminocarboxyethyltransferase. 2.S. S1 Beta-pyrazolylalanine synthase. 2.S. 52 L-mimosine synthase. 2.S. 53 Uracilylalanine synthase. 2.S. 54 3-deoxy-7-phosphoheptulonate synthase. 2.S. 55 3-deoxy-8-phosphooctulonate synthase. 2.S. S6 N-acetylneuraminate synthase. 2.S. 57 N-acylneuraminate-9-phosphate synthase. 2.S. S8 Protein famesyltransferase. 2.S. 59 Protein geranylgeranyltransferase type I. 2.S. 60 Protein geranylgeranyltransferase type II. 2.S. 61 Hydroxymethylbilane synthase. 2.S. 62 Chlorophyll synthase. 2.S. 63 Adenosyl-fluoride synthase. 2.S. .64 2-succinyl-6-hydroxy-2,4- cyclohexadiene-1-carboxylate synthase. 2.6. Aspartate transaminase. 2.6. Alanine transaminase. 2.6. Cysteine transaminase. 2.6. Glycine transaminase. 2.6. Tyrosine transaminase. 2.6. Leucine transaminase. 2.6. Kynurenine-oxoglutarate transaminase. 2.6. 2,5-diaminovalerate transaminase. 2.6. Histidinol-phosphate transaminase. 2.6.1. 1 Acetylomithine transaminase. 2.6.1. Alanine-oxo-acid transaminase. 2.6.1. Ornithine-oxo-acid transaminase. 2.6.1. Asparagine-oxo-acid transaminase. 2.6.1. Glutamine-pyruvate transaminase. 2.6.1. Glutamine-fructose-6-phosphate transaminase (isomerizing). 2.6. 17 Succinyldiaminopimelate transaminase. 2.6. 18 Beta-alanine-pyruvate transaminase. 2.6. 19 4-aminobutyrate transaminase. 2.6. .21 D-alanine transaminase. 2.6. 22 (S)-3-amino-2-methylpropionate transaminase. 2.6. 23 4-hydroxyglutamate transaminase. 2.6. .24 Diiodotyrosine transaminase. 2.6. 26 Thyroid-hormone transaminase. 2.6. 27 Tryptophan transaminase. 2.6. 28 Tryptophan-phenylpyruvate transaminase. 2.6. 29 Diamine transaminase. 2.6. 30 Pyridoxamine-pyruvate transaminase. 2.6. 31 Pyridoxamine--Oxaloacetate transaminase. US 2015/0240226 A1 Aug. 27, 2015 57

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 2.6. 32 Valine-3-methyl-2-oxovalerate transaminase. 2.6. .33 dTDP-4-amino-4,6-dideoxy-D-glucose transaminase. 2.6. 34 UDP-2-acetamido-4-amino-2,4,6- trideoxyglucose transaminase. 2.6. 35 Glycine-oxaloacetate transaminase. 2.6. 36 L-lysine 6-transaminase. 2.6. 37 2-aminoethylphosphonate-pyruvate transaminase. 2.6. 38 Histidine transaminase. 2.6. 39 2-aminoadipate transaminase. 2.6. 40 (R)-3-amino-2-methylpropionate-- pyruvate transaminase. 2.6. 41 D-methionine-pyruvate transaminase. 2.6. 42 Branched-chain-amino-acid transaminase. 2.6. 43 Aminolevulinate transaminase. 2.6. .44 Alanine-glyoxylate transaminase. 2.6. 45 Serine-glyoxylate transaminase. 2.6. 46 Diaminobutyrate-pyruvate transaminase. 2.6. 47 Alanine-oxomalonate transaminase. 2.6. 48 5-aminovalerate transaminase. 2.6. 49 Dihydroxyphenylalanine transaminase. 2.6. SO Glutamine-Scyllo-inositol transaminase. 2.6. S1 Serine-pyruvate transaminase. 2.6. 52 Phosphoserine transaminase. 2.6. 54 Pyridoxamine-phosphate transaminase. 2.6. 55 Taurine-2-oxoglutarate transaminase. 2.6. S6 D-1-guanidino-3-amino-1,3-dideoxy Scyllo-inositol transaminase. 2.6. 57 Aromatic-amino-acid transaminase. 2.6. S8 Phenylalanine(histidine) transaminase. 2.6. 59 dTDP-4-amino-4,6-dideoxygalactose transaminase. 2.6. 60 Aromatic-amino-acid-glyoxylate transaminase. 2.6. 62 Adenosylmethionine-8-amino-7- Oxononanoate transaminase. 2.6. 63 Kynurenine-glyoxylate transaminase. 2.6. .64 Glutamine-phenylpyruvate transaminase. 2.6. .65 N(6)-acetyl-beta-lysine transaminase. 2.6. 66 Valine-pyruvate transaminase. 2.6. .67 2-aminohexanoate transaminase. 2.6. 68 Omithine(lysine) transaminase. 2.6. 70 Aspartate--phenylpyruvate transaminase. 2.6. .71 Lysine-pyruvate 6-transaminase. 2.6. 72 D-4-hydroxyphenylglycine transaminase. 2.6. 73 Methionine-glyoxylate transaminase. 2.6. .74 Cephalosporin-C transaminase. 2.6. .75 Cysteine-conjugate transaminase. 2.6. .76 Diaminobutyrate-2-oxoglutarate transaminase. 2.6. 77 Taurine-pyruvate aminotransferase. 2.6. 3.1 Oximinotransferase. 2.6. 99.1 dATP(dGTP)--DNA purinetransferase. 2.7. Hexokinase. 2.7. Glucokinase. 2.7. Ketohexokinase. 2.7. Fructokinase. 2.7. Rhamnulokinase. 2.7. Galactokinase. 2.7. Mannokinase. 2.7. Glucosamine kinase. 2.7. 10 Phosphoglucokinase. 2.7. .11 6-phosphofructokinase. 2.7. .12 Gluconokinase. 2.7. 13 Dehydrogluconokinase. 2.7. .14 Sedoheptulokinase. 2.7. 1S Ribokinase. 2.7. 16 Ribulokinase. 2.7. 17 Xylulokinase. US 2015/0240226 A1 Aug. 27, 2015 58

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 2.7. 18 Phosphoribokinase. 2.7. 19 Phosphoribulokinase. 2.7. 20 Adenosine kinase. 2.7. .21 Thymidine kinase. 2.7. 22 Ribosylnicotinamide kinase. 2.7. 23 NAD(+) kinase. 2.7. .24 Dephospho-CoA kinase. 2.7. 25 Adenylyl-sulfate kinase. 2.7. 26 Riboflavin kinase. 2.7. 27 Erythritol kinase. 2.7. 28 Triokinase. 2.7. 29 Glycerone kinase. 2.7. 30 Glycerol kinase. 2.7. 31 Glycerate kinase. 2.7. 32 Choline kinase. 2.7. .33 Pantothenate kinase. 2.7. 34 Pantetheline kinase. 2.7. 35 Pyridoxal kinase. 2.7. 36 Mevalonate kinase. 2.7. 37 Protein kinase. 2.7. 38 Phosphorylasekinase. 2.7. 39 Homoserine kinase. 2.7. 40 Pyruvate kinase. 2.7. 41 Glucose-1-phosphate phosphodismutase. 2.7. 42 Riboflavin phosphotransferase. 2.7. 43 Glucuronokinase. 2.7. .44 Galacturonokinase. 2.7. 45 2-dehydro-3-deoxygluconokinase. 2.7. 46 L-arabinokinase. 2.7. 47 D-ribulokinase. 2.7. 48 Uridine kinase. 2.7. 49 Hydroxymethylpyrimidine kinase. 2.7. SO Hydroxyethylthiazole kinase. 2.7. S1 L-fuculokinase. 2.7. 52 Fucokinase. 2.7. 53 L-xylulokinase. 2.7. 54 D-arabinokinase. 2.7. 55 Allose kinase. 2.7. S6 -phosphofructokinase. 2.7. S8 2-dehydro-3-deoxygalactonokinase. 2.7. 59 N-acetylglucosamine kinase. 2.7. 60 N-acylmannosamine kinase. 2.7. 61 Acyl-phosphate--hexose phosphotransferase. 2.7. 62 Phosphoramidate--hexose phosphotransferase. 2.7. 63 Polyphosphate--glucose phosphotransferase. 2.7. .64 nositol 3-kinase. 2.7. .65 Scyllo-inosamine 4-kinase. 2.7. 66 Undecaprenol kinase. 2.7. .67 -phosphatidylinositol 4-kinase. 2.7. 68 -phosphatidylinosito 1-4-phosphate 5 kinase. 2.7. 69 Protein-N(pi)-phosphohistidine--sugar phosphotransferase. 2.7. .71 Shikimate kinase. 2.7. 72 Streptomycin 6-kinase. 2.7. 73 nosine kinase. 2.7. .74 Deoxycytidine kinase. 2.7. .76 Deoxyadenosine kinase. 2.7. 77 Nucleoside phosphotransferase. 2.7. .78 Polynucleotide 5'-hydroxy-kinase. 2.7. .79 Diphosphate-glycerol phosphotransferase. 2.7. 80 Diphosphate--serine phosphotransferase. 2.7. 81 Hydroxylysine kinase. 2.7. 82 Ethanolamine kinase. 2.7. .83 Pseudouridine kinase. 2.7. 84 Alkylglycerone kinase. 2.7. .85 Beta-glucoside kinase. 2.7. 86 NADH kinase. 2.7. 87 Streptomycin 3"-kinase. US 2015/0240226 A1 Aug. 27, 2015 59

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 2.7. 88 Dihydrostreptomycin-6-phosphate 3'- alpha-kinase. 2.7. 89 Thiamine kinase. 2.7. 90 Diphosphate--fructose-6-phosphate 1 phosphotransferase. 2.7. 91 Sphinganine kinase. 2.7. 92 5-dehydro-2-deoxygluconokinase. 2.7. .93 Alkylglycerol kinase. 2.7. .94 Acylglycerol kinase. 2.7. 95 Kanamycin kinase. 2.7. .99 Pyruvate dehydrogenase (lipoamide) kinase. 2.7.1. S-methyl-5-thioribose kinase. 2.7.1. Tagatose kinase. 2.7.1. Hamamelose kinase. 2.7.1. Viomycin kinase. 2.7.1. Diphosphate--protein phosphotransferase. 2.7.1. 6-phosphofructo-2-kinase. 2.7.1. Glucose-1,6-bisphosphate synthase. 2.7.1. Diacylglycerol kinase. 2.7.1. Dolichol kinase. 2.7.1. Hydroxymethylglutaryl-CoA reductase (NADPH) kinase. 2.7.1. 10 Dephospho-reductase kinase kinase. 2.7.1. 12 Protein-tyrosine kinase. 2.7.1. 13 Deoxyguanosine kinase. 2.7.1. 14 AMP--thymidine kinase. 2.7.1. 15 3-methyl-2-oxobutanoate dehydrogenase (lipoamide) kinase. 2.7.1. 16 Isocitrate dehydrogenase (NADP+) kinase. 2.7.1. 17 Myosin light-chain kinase. 2.7.1. 18 ADP--thymidine kinase. 2.7.1. 19 Hygromycin-B kinase. 2.7.1. 2O Caldesmon kinase. 2.7.1. 21 Phosphoenolpyruvate-glycerone phosphotransferase. 2.7.1. 22 Xylitol kinase. 2.7.1. 23 Calcium calmodulin-dependent protein kinase. 2.7.1. 24 Tyrosine 3-monooxygenase kinase. 2.7.1. 25 Rhodopsin kinase. 2.7.1. 26 Beta-adrenergic-receptor kinase. 2.7.1. 27 nositol-trisphosphate 3-kinase. 2.7.1. 28 Acetyl-CoA carboxylase kinase. 2.7.1. 29 Myosin heavy-chain kinase. 2.7.1. 30 Tetraacyldisaccharide 4'-kinase. 2.7.1. 31 Low-density lipoprotein receptor

2.7.1. 32 Tropomyosin kinase. 2.7.1. nositol-tetrakisphosphate 1-kinase. 2.7.1. 35 Tau protein kinase. 2.7.1. 36 Macrollide 2'-kinase. 2.7.1. 37 Phosphatidylinositol 3-kinase. 2.7.1. 38 Ceramide kinase. 2.7. 140 nositol-tetrakisphosphate 5-kinase. 2.7. .141 RNA-polymerase-subunit kinase. 2.7. .142 Glycerol-3-phosphate-glucose phosphotransferase. 2.7. 143 Diphosphate-purine nucleoside kinase. 2.7. .144 Tagatose-6-phosphate kinase. 2.7. 145 Deoxynucleoside kinase. 2.7. .146 ADP-specific phosphofructokinase. 2.7. 147 ADP-specific glucokinase. 2.7. 148 4-(cytidine 5'-diphospho)-2-C-methyl D-erythritol kinase. 2.7. 149 -phosphatidylinositol-5-phosphate 4 kinase. 2.7.1. 50 -phosphatidylinositol-3-phosphate 5 kinase. 2.7.1. 51 nositol-polyphosphate multikinase. 2.7.1. 53 Phosphatidylinositol-4,5-bisphosphate 3-kinase. US 2015/0240226 A1 Aug. 27, 2015 60

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 2.7.1.154 Phosphatidylinositol-4-phosphate 3 kinase. 2.7.1.15S Diphosphoinositol-pentakisphosphate kinase. 2.7.1.156 Adenosylcobinamide kinase. 27.2.1 Acetate kinase. 27.2.2 Carbamate kinase. 2.7.2.3 Phosphoglycerate kinase. 27.24 Aspartate kinase. 27.26 Formate kinase. 2.72.7 Butyrate kinase. 27.2.8 Acetylglutamate kinase. 27.2.10 Phosphoglycerate kinase (GTP). 27.2.11 Glutamate 5-kinase. 2.7212 Acetate kinase (diphosphate). 2.7.2.13 Glutamate 1-kinase. 27.2.14 Branched-chain-fatty-acid kinase. 2.7.3.1 Guanidinoacetate kinase. 2.7.32 Creatine kinase. 2.7.3.3 Arginine kinase. 2.73.4 Taurocyamine kinase. 2.73.5 Lombricine kinase. 2.73.6 Hypotaurocyamine kinase. 2.7.3.1 Opheline kinase. 2.73.8 Ammonia kinase. 2.73.9 Phosphoenolpyruvate--protein phosphotransferase. 2.7.3.10 Agmatine kinase. 2.73.11 Protein-histidine pros-kinase. 2.7.3.12 Protein-histidine tele-kinase. 2.74.1 Polyphosphate kinase. 2.74.2 Phosphomevalonate kinase. 2.74.3 Adenylate kinase. 2.7.4.4 Nucleoside-phosphate kinase. 2.74.6 Nucleoside-diphosphate kinase. 2.74.7 Phosphomethylpyrimidine kinase. 2.74.8 Guanylate kinase. 2.74.9 dTMP kinase. 2.74.10 Nucleoside-triphosphate--adenylate kinase. 27.4.11 (Deoxy)adenylate kinase. 2.7412 T(2)-induced deoxynucleotide kinase. 2.74.13 (Deoxy) nucleoside-phosphate kinase. 2.74.14 Cytidylate kinase. 2.74.15 Thiamine-diphosphate kinase. 2.74.16 Thiamine-phosphate kinase. 2.74.17 3-phosphoglyceroyl-phosphate-- polyphosphate phosphotransferase. 2.74.18 Famesyl-diphosphate kinase. 27.4.19 5-methyldeoxycytidine-5'-phosphate kinase. 2.74.2O Dolichyl-diphosphate-polyphosphate phosphotransferase. 2.74.21 Inositol-hexakisphosphate kinase. 2.76.1 Ribose-phosphate diphosphokinase. 2.7.62 Thiamine diphosphokinase. 2.1.6.3 2-amino-4-hydroxy-6- hydroxymethyldihydropteridine diphosphokinase. 27.64 Nucleotide diphosphokinase. 2.76.5 GTP diphosphokinase. 2.77.1 Nicotinamide-nucleotide adenylyltransferase. 2.77.2 FMN adenylyltransferase. 2.7.7.3 Pantetheine-phosphate adenylyl transferase. 2.7.74 Sulfate adenylyltransferase. 2.7.75 Sulfate adenylyltransferase (ADP). 2.7.76 DNA-directed RNA polymerase. 2.77.7 DNA-directed DNA polymerase. 2.77.8 Polyribonucleotide nucleotidyltransferase. 2.7.7.9 UTP-glucose-1-phosphate uridylyltransferase. US 2015/0240226 A1 Aug. 27, 2015 61

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 2.77.10 UTP-hexose-1-phosphate uridylyltransferase. 2.7.7.11 UTP--xylose-1-phosphate uridylyltransferase. 2.77.1.2 UDP-glucose--hexose-1-phosphate uridylyltransferase. 2.77.13 Mannose-1-phosphate guanylyltransferase. 2.77.14 Ethanolamine-phosphate cytidylyltransferase. 2.7.7.15 Choline-phosphate cytidylyltransferase. 2.77.18 Nicotinate-nucleotide adenylyltransferase. 2.7.7.19 Polynucleotide adenylyltransferase. 2.7.7.21 RNA cytidylyltransferase. 2.7.7.22 Mannose-1-phosphate guanylyltransferase (GDP). 2.7.7.23 UDP-N-acetylglucosamine diphosphorylase. 2.7.7.24 Glucose-1-phosphate hymidylyltransferase. 2.7.7.25 RNA adenylyltransferase. 2.77.27 Glucose-1-phosphate adenylyltransferase. 2.7.7.28 Nucleoside-triphosphate-aldose 1 phosphate nucleotidyltransferase. 2.7.7.30 Fucose-1-phosphate guanylyltransferase. 2.7.7.31 DNA nucleotidylexotransferase. 2.7.7.32 Galactose-1-phosphate hymidylyltransferase. 2.7.7.33 Glucose-1-phosphate cytidylyltransferase. 2.7.7.34 Glucose-1-phosphate guanylyltransferase. 2.7.7.35 Ribose-5-phosphate adenylyltransferase. 2.7.7.36 Aldose-1-phosphate adenylyltransferase. 2.7.737 Aldose-1-phosphate nucleotidyltransferase. 2.7.738 3-deoxy-manno-octulosonate cytidylyltransferase. 2.7.7.39 Glycerol-3-phosphate cytidylyltransferase. 2.7740 D-ribitol-5-phosphate cytidylyltransferase. 2.77.41 Phosphatidate cytidylyltransferase. 2.7.742 Glutamate--ammonia-ligase adenylyltransferase. 2.77.43 N-acylneuraminate cytidylyltransferase. 2.77.44 Glucuronate-1-phosphate uridylyltransferase. 2.7.7:45 Guanosine-triphosphate guanylyltransferase. 2.77.46 Gentamicin 2"-nucleotidyltransferase. 2.7.747 Streptomycin 3'-adenylyltransferase. 2.7.748 RNA-directed RNA polymerase. 2.7.7.49 RNA-directed DNA polymerase. 2.77.50 mRNA guanylyltransferase. 2.7.7.51 Adenylylsulfate--ammonia adenylyltransferase. 2.7.7.52 RNA uridylyltransferase. 2.7.7.53 ATP adenylyltransferase. 2.77.54 Phenylalanine adenylyltransferase. 2.77.55 Anthranilate adenylyltransferase. 2.77.56 tRNA nucleotidyltransferase. 2.7.7.57 N-methylphosphoethanolamine cytidylyltransferase. 2.7.7.58 (2,3-dihydroxybenzoyl)adenylate synthase. 2.7.7.59 Protein-PII uridylyltransferase. 2.7.7.60 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase. 2.7.7.61 Holo-ACP synthase. 2.7.7.62 Adenosylcobinamide-phosphate guanylyltransferase. 2.78.1 Ethanolaminephosphotransferase. US 2015/0240226 A1 Aug. 27, 2015 62

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 2.78.2 Diacylglycerol cholinephosphotransferase. 2.783 Ceramide cholinephosphotransferase. 27.84 Serine-phosphoethanolamine synthase. 2.78.5 CDP-diacylglycerol-glycerol-3- phosphate 3-phosphatidyltransferase. 2.78.6 Undecaprenyl-phosphate galactose phosphotransferase. 2.78.7 Holo-acyl-carrier-protein synthase. 2.78.8 CDP-diacylglycerol--serine O phosphatidyltransferase. 2.78.9 Phosphomannan mannosephosphotransferase. 2.78.10 Sphingosine cholinephosphotransferase. 2.78.11 CDP-diacylglycerol--inositol 3 phosphatidyltransferase. 2.78.12 CDP-glycerol glycerophosphotransferase. 2.78.13 Phospho-N-acetylmuramoyl pentapeptide-transferase. 2.78.14 CDP-ribitol ribitolphosphotransferase. 2.78.15 UDP-N-acetylglucosamine--dolichyl phosphate N-acetylglucosaminephosphotransferase. 2.78.17 UDP-N-acetylglucosamine--lysosomal enzyme N-acetylglucosaminephosphotransferase. 2.78.18 UDP-galactose-UDP-N- acetylglucosamine galactose phosphotransferase. 2.7.8.19 UDP-glucose--glycoprotein glucose phosphotransferase. 2.78.20 Phosphatidylglycerol--membrane oligosaccharide glycerophosphotransferase. 2.78.21 Membrane-oligosaccharide glycerophosphotransferase. 2.78.22 -alkenyl-2-acylglycerol choline phosphotransferase. 2.78.23 Carboxyvinyl-carboxyphosphonate phosphorylmutase. 2.78.24 Phosphatidylcholine synthase. 2.78.25 Triphosphoribosyl-dephospho-CoA synthase. 2.78.26 Adenosylcobinamide-GDP ribazoletransferase. 27.91 Pyruvate, phosphate dikinase. 2.79.2 Pyruvate, water dikinase. 2.79.3 Selenide, water dikinase. 2.79.4 Alpha-glucan, water dikinase. 2.8.1.1 Thiosulfate sulfur-transferase. 2.8.1.2 3-mercaptopyruvate Sulfur-transferase. 2.8.1.3 Thiosulfate--thiol sulfur-transferase. 2.8.1.4 tRNA sulfur-transferase. 2.8.1.5 Thiosulfate--dithiol sulfur-transferase. 2.8.1.6 Biotin synthase. 2.8.1.7 Cysteine desulfurase. 2.8.2.1 Aryl Sulfotransferase. 2.8.2.2 Alcohol sulfotransferase. 2.8.23 Amine Sulfotransferase. 2.8.2.4 Estrone sulfotransferase. 2.8.25 Chondroitin 4-sulfotransferase. 2.8.2.6 Choline sulfotransferase. 2.8.2.7 UDP-N-acetylgalactosamine-4-sulfate Sulfotransferase. 2.8.2.8 Heparan sulfate-glucosamine N Sulfotransferase. 2.8.2.9 Tyrosine-ester sulfotransferase. 2.8.2.10 Renilla-luciferin sulfotransferase. 2.8.2.11 Galactosylceramide Sulfotransferase. 2.8.2.13 Psychosine sulfotransferase. 2.8.2.14 Bile-salt sulfotransferase. 2.8.2.15 Steroid sulfotransferase. 2.8.2.16 Thiol sulfotransferase. 2.8.2.17 Chondroitin 6-sulfotransferase. 2.8.2.18 Cortisol sulfotransferase. 2.8.2.19 Triglucosylalkylacylglycerol Sulfotransferase. 2.8.2.2O Protein-tyrosine Sulfotransferase. US 2015/0240226 A1 Aug. 27, 2015 63

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 2.8.2.21 Keratan Sulfotransferase. 2.8.222 Arylsulfate sulfotransferase. 2.8.2.23 Heparan sulfate-glucosamine 3 Sulfotransferase 1. 2.8.2.24 Desulfoglucosinolate Sulfotransferase. 2.8.2.25 Flavonol 3-sulfotransferase. 2.8.2.26 Quercetin-3-sulfate 3'-sulfotransferase. 2.8.2.27 Quercetin-3-sulfate 4'-sulfotransferase. 2.8.2.28 Quercetin-3,3'-bisSulfate 7 Sulfotransferase. 2.8.2.29 Heparan sulfate-glucosamine 3 Sulfotransferase 2. 2.8.2.30 Heparan sulfate-glucosamine 3 Sulfotransferase 3. 2.8.31 Propionate CoA-transferase. 2.8.32 Oxalate CoA-transferase. 2.83.3 Malonate CoA-transferase. 2.8.35 3-oxoacid CoA-transferase. 2.83.6 3-oxoadipate CoA-transferase. 2.8.3.7 Succinate-citramalate CoA-transferase. 2.83.8 Acetate CoA-transferase. 2.83.9 Butyrate--acetoacetate CoA-transferase. 2.83. Citrate CoA-transferase. 2.83. Citramalate CoA-transferase. 2.83. Glutaconate CoA-transferase. 2.83. Succinate--hydroxymethylglutarate CoA transferase. 2.83. 5-hydroxypentanoate CoA-transferase. 2.83. s Succinyl-CoA:(R)-benzylsuccinate CoA transferase. 2.83.16 Formyl-CoA transferase. 2.8.3.17 Cinnamoyl-CoA:phenylactate CoA transferase. 2.84. Coenzyme-B sulfoethylthiotransferase. 2.9.1. L-seryl-tRNA(Sec) selenium transferase. ENZYME: 3. . . . Carboxylesterase. Arylesterase. Triacylglycerol lipase. Phospholipase A(2). Lysophospholipase. Acetylesterase. Acetylcholinesterase. Cholinesterase. 10 Tropinesterase. Pectinesterase. 1.13 Sterol esterase. .1.14 Chlorophyllase. 1.15 L-arabinonolactonase. 1.17 Gluconolactonase. 1.19 Uronolactonase. 1.20 Tannase. .1.21 Retinyl-palmitate esterase. .1.22 Hydroxybutyrate-dimer hydrolase. 1.23 Acylglycerol lipase. .1.24 3-oxoadipate enol-lactonase. 1.25 1,4-lactonase. .1.26 Galactolipase. 1.27 4-pyridoxolactonase. 1.28 Acylcamitine hydrolase. 1.29 Aminoacyl-tRNA hydrolase. 1.30 D-arabinonolactonase. 1.31 6-phosphogluconolactonase. 1.32 Phospholipase A(l). 1.33 6-acetylglucose deacetylase. .1.34 Lipoprotein lipase. 1.35 Dihydrocoumarin hydrolase. 1.36 Limonin-D-ring-lactonase. 1.37 Steroid-lactonase. 1.38 Triacetate-lactonase. 1.39 Actinomycin lactonase. 1.40 Orsellinate-depside hydrolase. .1.41 Cephalosporin-C deacetylase. US 2015/0240226 A1 Aug. 27, 2015 64

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. .1.42 Chlorogenate hydrolase. 1.43 Alpha-amino-acid esterase. .1.44 4-methyloxaloacetate esterase. 1.45 Carboxymethylenebutenolidase. .1.46 Deoxylimonate A-ring-lactonase. 1.47 1-alkyl-2-acetylglycerophosphocholine esterase. .1.48 Fusarinine-Cornithinesterase. 1.49 Sinapine esterase. SO Wax-ester hydrolase. 1.51 Phorbol-diester hydrolase. 1.52 Phosphatidylinositol deacylase. 1.53 Sialate O-acetylesterase. 1.54 Acetoxybutynylbithiophene deacetylase. 1.55 Acetylsalicylate deacetylase. 1.56 Methylumbelliferyl-acetate deacetylase. 1.57 2-pyrone-4,6-dicarboxylate lactonase. N-acetylgalactosaminoglycan deacetylase. 59 Juvenile-hormone esterase. 1.60 Bis(2-ethylhexyl)phthalate esterase. 1.61 Protein-glutamate methylesterase. 1.63 11-cis-retinyl-palmitate hydrolase. 1.64 All-trans-retinyl-palmitate hydrolase. 1.65 L-rhamnono-1,4-lactonase. 66 5-(3,4-diacetoxybut-1-ynyl)-2,2'- bithiophene deacetylase. Fatty-acyl-ethyl-ester synthase. 1.68 Xylono-1,4-lactonase. 1.70 Cetraxate benzylesterase. 1.71 Acetylallcylglycerol acetylhydrolase. 1.72 Acetylxylan esterase. 1.73 Feruloyl esterase. 1.74 Cutinase. 1.75 Poly(3-hydroxybutyrate) depolymerase. 1.76 Poly(3-hydroxyoctanoate) depolymerase. 1.77 Acyloxyacylhydrolase. 1.78 Polyneuridine-aldehyde esterase. 1.79 Hormone-sensitive lipase. .2.1 Acetyl-CoA hydrolase. .2.2 Palmitoyl-CoA hydrolase. 2.3 Succinyl-CoA hydrolase. .2.4 3-hydroxyisobutyryl-CoA hydrolase. 2.5 Hydroxymethylglutaryl-CoA hydrolase. .2.6 Hydroxyacylglutathione hydrolase. 2.7 Glutathione thiolesterase. 2.10 Formyl-CoA hydrolase. .2.11 Acetoacetyl-CoA hydrolase. .2.12 S-formylglutathione hydrolase. 2.13 S-Succinylglutathione hydrolase. .2.14 Oleoyl-acyl-carrier-protein hydrolase. 2.15 Ubiquitin thiolesterase. .2.16 Citrate-(pro-3S)-lyase thiolesterase. 2.17 (S)-methylmalonyl-CoA hydrolase. 2.18 ADP-dependent short-chain-acyl-CoA hydrolase. 2.19 ADP-dependent medium-chain-acyl-CoA hydrolase. 2.2O Acyl-CoA hydrolase. .2.21 Dodecanoyl-acyl-carrier protein hydrolase. .2.22 Palmitoyl-protein hydrolase. 2.23 4-hydroxybenzoyl-CoA thioesterase. i .2.24 2-(2-hydroxyphenyl)benzenesulfinate hydrolase. 2.25 Phenylacetyl-CoA hydrolase. .3.1 Alkaline phosphatase. 3.2 Acid phosphatase. 3.3 Phosphoserine phosphatase. .3.4 Phosphatidate phosphatase. 3.5 5'-nucleotidase. 3.6 3'-nucleotidase. 3.7 3'(2),5'-bisphosphate nucleotidase. 3.8 3-phytase. US 2015/0240226 A1 Aug. 27, 2015 65

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 3.9 Glucose-6-phosphatase. 3.10 Glucose-1-phosphatase. 3.11 Fructose-bisphosphatase. 3.12 Trehalose-phosphatase. 3.13 Bisphosphoglycerate phosphatase. 3.14 Methylphosphothioglycerate phosphatase. 3.15 Histidinol-phosphatase. 3.16 Phosphoprotein phosphatase. 3.17 Phosphorylase phosphatase. 3.18 Phosphoglycolate phosphatase. 3.19 Glycerol-2-phosphatase. 3.2O Phosphoglycerate phosphatase. 3.21 Glycerol-1-phosphatase. 3.22 Mannitol-1-phosphatase. 3.23 Sugar-phosphatase. 3.24 Sucrose-phosphatase. 3.25 Inositol-1(or 4)-monophosphatase. 3.26 4-phytase. 3.27 Phosphatidylglycerophosphatase. 3.28 ADP-phosphoglycerate phosphatase. 3.29 N-acylneuraminate-9-phosphatase. 3.31 Nucleotidase. 3.32 Polynucleotide 3'-phosphatase. 3.33 Polynucleotide 5'-phosphatase. 3.34 Deoxynucleotide 3'-phosphatase. 3.35 Thymidylate 5'-phosphatase. 3.36 Phosphoinositide 5-phosphatase. 3.37 Sedoheptulose-bisphosphatase. 3.38 3-phosphoglycerate phosphatase. 3.39 Streptomycin-6-phosphatase. 340 Guanidinodeoxy-Scyllo-inositol-4- phosphatase. 3.41 4-nitrophenylphosphatase. 3.42 Glycogen-synthase-D] phosphatase. i 3.43 Pyruvate dehydrogenase (lipoamide)- phosphatase. 3.44 Acetyl-CoA carboxylase-phosphatase. 3.45 3-deoxy-manno-octulosonate-8- phosphatase. 3.46 Fructose-2,6-bisphosphate 2 phosphatase. 3.47 Hydroxymethylglutaryl-CoA reductase (NADPH)-phosphatase. 3.48 Protein-tyrosine-phosphatase. 3.49 Pyruvate kinase-phosphatase. 3.SO Sorbitol-6-phosphatase. 3.51 Dolichyl-phosphatase. 3.52 3-methyl-2-oxobutanoate dehydrogenase (lipoamide)-phosphatase. 3.53 Myosin light-chain-phosphatase. s 3.54 Fructose-2,6-bisphosphate 6 phosphatase. 3.55 Caldesmon-phosphatase. 3.56 nositol-polyphosphate 5-phosphatase. 3.57 nositol-1,4-bisphosphate 1-phosphatase. 3.58 Sugar-terminal-phosphatase. 3.59 Alkylacetylglycerophosphatase. 3.60 Phosphoenolpyruvate phosphatase. 3.62 Multiple inositol-polyphosphate phosphatase. 3.63 2-carboxy-D-arabinitol-1-phosphatase. s 3.64 Phosphatidylinositol-3-phosphatase. 3.66 Phosphatidylinositol-3,4-bisphosphate 4 phosphatase. 3.67 Phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase. 3.68 2-deoxyglucose-6-phosphatase. 3.69 Glucosylglycerol 3-phosphatase. 3.70 Mannosyl-3-phosphoglycerate phosphatase. 3.71 2-phosphosulfolactate phosphatase. 3.72 5-phytase. 3.73 Alpha-ribazole phosphatase. US 2015/0240226 A1 Aug. 27, 2015 66

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. .4.1 Phosphodiesterase I. s .4.2 Glycerophosphocholine phosphodiesterase. 4.3 Phospholipase C. .4.4 Phospholipase D. .4.11 Phosphoinositide phospholipase C. .4.12 Sphingomyelin phosphodiesterase. 4.13 Serine-ethanolaminephosphate phosphodiesterase. 4.14 Acyl-carrier-protein phosphodiesterase. 4.15 Adenylyl-glutamate-ammonia ligase hydrolase. 4.16 2',3'-cyclic-nucleotide 2'- phosphodiesterase. 4.17 3',5'-cyclic-nucleotide phosphodiesterase. 4.35 3',5'-cyclic-GMP phosphodiesterase. 4.37 2',3'-cyclic-nucleotide 3'- phosphodiesterase. 4.38 Glycerophosphocholine cholinephosphodiesterase. 4.39 Alkylglycerophosphoethanolamine phosphodiesterase. 4.40 CMP-N-acylneuraminate phosphodiesterase. 4.41 Sphingomyelin phosphodiesterase D. 4.42 Glycerol-1,2-cyclic-phosphate 2 phosphodiesterase. 4.43 Glycerophosphoinositol inositolphosphodiesterase. .4.44 Glycerophosphoinositol glycerophosphodiesterase. 4.45 N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase. 4.46 Glycerophosphodiester phosphodiesterase. 4.48 Dolichylphosphate-glucose phosphodiesterase. 4.49 Dolichylphosphate-mannose phosphodiesterase. 4.50 Glycosylphosphatidylinositol phospholipase D. 3 4.51 Glucose-1-phospho-D- mannosylglycoprotein phosphodiesterase. 5.1 dGTPase. .6.1 Arylsulfatase. .6.2 Steryl-sulfatase. 6.3 Glycosulfatase. .6.4 N-acetylgalactosamine-6-sulfatase. .6.6 Choline-sulfatase. 6.7 Cellulose-polysulfatase. 6.8 Cerebroside-sulfatase. 6.9 Chondro-4-sulfatase. 6.10 Chondro-6-sulfatase. .6.11 Disulfoglucosamine-6-sulfatase. .6.12 N-acetylgalactosamine-4-Sulfatase. 6.13 Iduronate-2-sulfatase. .6.14 N-acetylglucosamine-6-sulfatase. 6.15 N-sulfoglucosamine-3-sulfatase. 6.16 Monomethyl-sulfatase. 6.17 D-lactate-2-sulfatase. 6.18 Glucuronate-2-sulfatase. .7.1 Prenyl-diphosphatase. 7.2 Guanosine-3',5'-bis(diphosphate) 3'- diphosphatase. 7.3 Monoterpenyl-diphosphatase. .8.1 Aryldialkylphosphatase. 8.2 Diisopropyl-fluorophosphatase. .11.1 Exodeoxyribonuclease I. .11.2 Exodeoxyribonuclease III. 11.3 Exodeoxyribonuclease (lambda induced). .11.4 Exodeoxyribonuclease (phage Sp3 induced). US 2015/0240226 A1 Aug. 27, 2015 67

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 11.5 Exodeoxyribonuclease V. .11.6 Exodeoxyribonuclease VII. 13.1 Exoribonuclease II. 13.2 Exoribonuclease H. 13.3 Oligonucleotidase. .13.4 Poly(A)-specific ribonuclease. .14.1 Yeast ribonuclease. 15.1 Venom exonuclease. .16.1 Spleen exonuclease. .21.1 Deoxyribonuclease I. .21.2 Deoxyribonuclease IV (phage-T(4)- induced). 21.3 Type I site-specific deoxyribonuclease. .21.4 Type II site-specific deoxyribonuclease. 21.5 Type III site-specific deoxyribonuclease. .21.6 CC-preferring endodeoxyribonuclease. 21.7 Deoxyribonuclease V. .22.1 Deoxyribonuclease II. .22.2 Aspergillus deoxyribonuclease K(1). .22.4 Crossover junction endoribonuclease. 22.5 Deoxyribonuclease X. 25.1 Deoxyribonuclease (pyrimidine dimer). .26.1 Physarum polycephalum ribonuclease. 26.2 ibonuclease alpha. 26.3 bonuclease III. .26.4 bonuclease H. 26.5 bonuclease P. 26.6 bonuclease IV. 26.7 bonuclease P4. 26.8 bonuclease M5. 26.9 bonuclease (poly-(U)-specific). 26.10 bonuclease IX. .26.11 bonuclease Z. 27.1 bonuclease T(2). 27.2 cillus Subtilis ribonuclease. 27.3 bonuclease T(1). 27.4 bonuclease U(2). 27.5 ancreatic ribonuclease. 27.6 Enterobacter ribonuclease. 27.7 Ribonuclease F. 27.8 Ribonuclease V. 27.9 RNA-intron endonuclease. 27.10 rRNA endonuclease. 30.1 Aspergillus nuclease S(1). 30.2 Serratia marcescens nuclease. 31.1 Micrococcal nuclease. Alpha-amylase. Beta-amylase. Glucan 1,4-alpha-glucosidase. Cellulase. Endo-1,3(4)-beta-glucanase. nulinase. :8 Endo-1,4-beta-xylanase. 10 Oligo-1,6-glucosidase. Dextranase. .14 Chitinase. 1S Polygalacturonase. 17 Lysozyme. 18 Exo-alpha-Sialidase. 20 Alpha-glucosidase. .21 Beta-glucosidase. 22 Alpha-galactosidase. 23 Beta-galactosidase. .24 Alpha-mannosidase. 25 Beta-mannosidase. 26 Beta-fructofuranosidase. 28 Alpha,alpha-trehalase. 31 Beta-glucuronidase. 32 Xylan endo-1,3-beta-xylosidase. .33 Amylo-alpha-1,6-glucosidase. 35 Hyaluronoglucosaminidase. 36 Hyaluronoglucuronidase. 37 Xylan 1,4-beta-xylosidase. 38 Beta-D-fucosidase. US 2015/0240226 A1 Aug. 27, 2015 68

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 3.2. 39 Glucan endo-1,3-beta-D-glucosidase. 3.2. 40 Alpha-L-rhamnosidase. 3.2. 41 Pullulanase. 3.2. 42 GDP-glucosidase. 3.2. 43 Beta-L-rhamnosidase. 3.2. .44 Fucoidanase. 3.2. 45 Glucosylceramidase. 3.2. 46 Galactosylceramidase. 3.2. 47 Galactosylgalactosylglucosylceramidase. 3.2. 48 Sucrose alpha-glucosidase. 3.2. 49 Alpha-N-acetylgalactosaminidase. 3.2. SO Alpha-N-acetylglucosaminidase. 3.2. S1 Alpha-L-fucosidase. 3.2. 52 Beta-N-acetylhexosaminidase. 3.2. 53 Beta-N-acetylgalactosaminidase. 3.2. 54 Cyclomaltodextrinase. 3.2. 55 Alpha-N-arabinofuranosidase. 3.2. S6 Glucuronosyl-disulfoglucosamine glucuronidase. 3.2. 57 Isopullulanase. 3.2. S8 Glucan 1,3-beta-glucosidase. 3.2. 59 Glucan endo-1,3-alpha-glucosidase. 3.2. 60 Glucan 1,4-alpha-maltotetraohydrolase. 3.2. 61 Mycodextranase. 3.2. 62 Glycosylceramidase. 3.2. 63 2-alpha-L-fucosidase. 3.2. .64 2,6-beta-fructan 6-levanbiohydrolase. 3.2. .65 (W88Se. 3.2. 66 Quercitrinase. 3.2. .67 Galacturan 1,4-alpha-galacturonidase. 3.2. 68 Soamylase. 3.2. 70 Glucan 1,6-alpha-glucosidase. 3.2. .71 Glucan endo-1,2-beta-glucosidase. 3.2. 72 Xylan 1,3-beta-xylosidase. 3.2. 73 Licheninase. 3.2. .74 Glucan 1,4-beta-glucosidase. 3.2. .75 Glucan endo-1,6-beta-glucosidase. 3.2. .76 L-iduronidase. 3.2. 77 Mannan 1,2-(1,3)-alpha-mannosidase. 3.2. .78 Mannan endo-1,4-beta-mannosidase. 3.2. 80 Fructan beta-fructosidase. 3.2. 81 Agarase. 3.2. 82 Exo-poly-alpha-galacturonosidase. 3.2. .83 Kappa-carrageenase. 3.2. 84 Glucan 1,3-alpha-glucosidase. 3.2. .85 6-phospho-beta-galactosidase. 3.2. 86 6-phospho-beta-glucosidase. 3.2. 87 Capsular-polysaccharide endo-1,3- alpha-galactosidase. 3.2. 88 Beta-L-arabinosidase. 3.2. 89 Arabinogalactan endo-1,4-beta galactosidase. 3.2. 91 Cellulose 1,4-beta-cellobiosidase. 3.2. 92 Peptidoglycan beta-N- acetylmuramidase. 3.2. .93 Alpha,alpha-phosphotrehalase. 3.2. .94 Glucan 1,6-alpha-isomaltosidase. 3.2. 95 Dextran 1,6-alpha-isomaltotriosidase. 3.2. .96 Mannosyl-glycoprotein endo-beta-N- acetylglucosaminidase. 3.2. 97 Glycopeptide alpha-N- acetylgalactosaminidase. 3.2. .98 Glucan 1,4-alpha-maltohexaosidase. 3.2. .99 Arabinan endo-1,5-alpha-L- arabinosidase. 3.2. 1OO Mannan 1,4-mannobiosidase. 3.2. 101 Mannan endo-1,6-alpha-mannosidase. 3.2. 102 Blood-group-substance endo-1,4-beta galactosidase. 3.2. 103 Keratan-sulfate endo-1,4-beta galactosidase. 3.2. 104 Steryl-beta-glucosidase. 3.2. 105 Strictosidine beta-glucosidase. 3.2. 106 Mannosyl-oligosaccharide glucosidase. US 2015/0240226 A1 Aug. 27, 2015 69

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 3.2.1.107 Protein glucosylgalactosylhydroxylysine glucosidase. 3.2.1.108 Lactase. 3.2.1.109 Endogalactosaminidase. 3.2.1.110 Mucinaminylserine mucinaminidase. 3.2.1.111 1,3-alpha-L-fucosidase. 3.2.1.112 2-deoxyglucosidase. 3.2.1.113 Mannosyl-oligosaccharide 1,2-alpha mannosidase. 3.2.1.114 Mannosyl-oligosaccharide 1,3-1,6- alpha-mannosidase. 3.2.1.115 Branched-dextran exo-1,2-alpha glucosidase. 3.21116 Glucan 1,4-alpha-maltotriohydrolase. 3.2.1.117 Amygdalin beta-glucosidase. 3.2.1.118 Prunasin beta-glucosidase. 3.2.1.119 Vicianin beta-glucosidase. 3.2.1.12O Oligoxyloglucan beta-glycosidase. 3.2.1.121 Polymannuronate hydrolase. 3.2.1122 Maltose-6-phosphate glucosidase. 3.2.1.123 Endoglycosylceramidase. 3.2.1.124 3-deoxy-2-octulosonidase. 3.2.1.125 Raucaffricine beta-glucosidase. 3.21126 Coniferin beta-glucosidase. 3.2.1.127 ,6-alpha-L-fucosidase. 3.2.1.128 Glycyrrhizinate beta-glucuronidase. 3.2.1.129 Endo-alpha-Sialidase. 3.21.130 Glycoprotein endo-alpha-1,2- mannosidase. 3.21.131 Xylan alpha-1,2-glucuronosidase. 3.21.132 Chitosanase. 3.21.133 Glucan 1,4-alpha-maltohydrolase. 3.21.134 Difructose-anhydride synthase. 3.2.1.135 Neopululanase. 3.21.136 Glucuronoarabinoxylan endo-1,4-beta Xylanase. 3.2.1.1.37 Mannan exo-1,2-1,6-alpha mannosidase. 3.21.139 Alpha-glucuronidase. 3.2.1.140 Lacto-N-biosidase. 3.2.1.141 4-alpha-D-(1->4)-alpha-D-glucano trehalose trehalohydrolase. 3.2.1.142 Limit dextrinase. 3.2.1.143 Poly(ADP-ribose) glycohydrolase. 3.2.1.144 3-deoxyoctulosonase. 3.2.1.145 Galactan 1,3-beta-galactosidase. 3.2.1.146 Beta-galactofuranosidase. 3.2.1.147 Thioglucosidase. 3.2.1.148 Ribosylhomocysteinase. 3.2.1.149 Beta-primeverosidase. 3.2.1.150 Oligoxyloglucan reducing-end-specific cellobiohydrolase. 3.2.1.151 Xyloglucan-specific endo-beta-1,4- glucanase. 3.2.2. Purine nucleosidase. 3.2.2.2 Inosine nucleosidase. 3.223 Uridine nucleosidase. 3.2.2.4 AMP nucleosidase. 3.22.5 NAD(+) nucleosidase. 3.22.6 NAD(P)(+) nucleosidase. 3.22.7 Adenosine nucleosidase. 3.22.8 Ribosylpyrimidine nucleosidase. 3.22.9 Adenosylhomocysteine nucleosidase. 3.22.10 Pyrimidine-5'-nucleotide nucleosidase. 3.22.11 Beta-aspartyl-N-acetylglucosaminidase. 3.2.2.12 Inosinate nucleosidase. 3.22.13 1-methyladenosine nucleosidase. 3.2.2.14 NMN nucleosidase. 3.22.15 DNA-deoxyinosine glycosylase. 3.22.16 Methylthioadenosine nucleosidase. 3.2.2.17 Deoxyribodipyrimidine endonucleosidase. 3.22.19 Protein ADP-ribosylarginine hydrolase. 3.2220 DNA-3-methyladenine glycosylase I. US 2015/0240226 A1 Aug. 27, 2015 70

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 3.22.21 DNA-3-methyladenine glycosylase II. 3.22.22 rRNA N-glycosylase. 3.22.23 DNA-formamidopyrimidine glycosylase. 3.2.2.24 ADP-ribosyl-dinitrogen reductase hydrolase. 3.3.1.1 Adenosylhomocysteinase. 3.31.2 Adenosylmethionine hydrolase. 3.3.2.1 Sochorismatase. 3.3.2.2 Alkenylglycerophosphocholine hydrolase. 3.32.3 Epoxide hydrolase. 3.32.4 Trans-epoxysuccinate hydrolase. 3.3.2.5 Alkenylglycerophosphoethanolamine hydrolase. 3.32.6 Leukotriene-A(4) hydrolase. 3.32.7 Hepoxilin-epoxide hydrolase. 3.32.8 Limonene-1,2-epoxide hydrolase. 3.4. Leucyl aminopeptidase. 3.4. Membrane alanyl aminopeptidase. 3.4. Cystinyl aminopeptidase. 3.4. Tripeptide aminopeptidase. 3.4. Prolylaminopeptidase. 3.4. Aminopeptidase B. 3.4. Glutamylaminopeptidase. 3.4. Xaa-Pro aminopeptidase. 3.4. 1O Bacterial leucyl aminopeptidase. 3.4. 13 Clostridial aminopeptidase. 3.4. .14 Cytosol alanyl aminopeptidase. 3.4. 1S Aminopeptidase Y. 3.4. 16 Xaa-Trp aminopeptidase. 3.4. 17 Tryptophanyl aminopeptidase. 3.4. 18 Methionyl aminopeptidase. 3.4. 19 D-stereospecific aminopeptidase. 3.4. 2O Aminopeptidase Ey. 3.4. .21 Aspartyl aminopeptidase. 3.4. 22 Aminopeptidase I. 3.4. 23 PepBaminopeptidase. 3.4. 3.3 Xaa-His dipeptidase. 3.4. 3.4 Xaa-Arg dipeptidase. 3.4. 3.5 Xaa-methyl-His dipeptidase. 3.4. 3.7 Glu-Glu dipeptidase. 3.4. 3.9 Xaa-Pro dipeptidase. 3.4. 3.12 Met-Xaa dipeptidase. 3.4. 3.17 Non-stereospecific dipeptidase. 3.4. 3.19 Membrane dipeptidase. 3.4. 3.20 Beta-Ala-His dipeptidase. 3.4. 3.21 Dipeptidase E. 3.4. 4.1 Dipeptidyl-peptidase I. 3.4. 4.2 Dipeptidyl-peptidase II. 3.4. 4.4 Dipeptidyl-peptidase III. 3.4. 4.5 Dipeptidyl-peptidase IV. 3.4. 4.6 Dipeptidyl-dipeptidase. 3.4. 4.9 Tripeptidyl-peptidase I. 3.4. 4.10 Tripeptidyl-peptidase II. 3.4. 4.11 Xaa-Pro dipeptidyl-peptidase. 3.4. S.1 Peptidyl-dipeptidase A. 3.4. 5.4 Peptidyl-dipeptidase B. 3.4. 5.5 Peptidyl-dipeptidase Dcp. 3.4. 6.2 Lysosomal Pro-X carboxypeptidase. 3.4. 6.4 Serine-type D-Ala-D-Ala carboxypeptidase. 3.4. 6.5 Carboxypeptidase C. 3.4. 6.6 Carboxypeptidase D. 3.4. 7.1 Carboxypeptidase A. 3.4. 7.2 Carboxypeptidase B. 3.4. 7.3 Lysine carboxypeptidase. 3.4. 7.4 Gly-X carboxypeptidase. 3.4. 7.6 Alanine carboxypeptidase. 3.4. 7.8 Muramoylpentapeptide carboxypeptidase. 3.4. 7.10 Carboxypeptidase E. 3.4. 7.11 Glutamate carboxypeptidase. 3.4. 7.12 Carboxypeptidase M. 3.4. 7.13 Muramoyltetrapeptide carboxypeptidase. US 2015/0240226 A1 Aug. 27, 2015 71

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 3.4. 7.14 Zinc D-Ala-D-Ala carboxypeptidase. 3.4. 7.15 Carboxypeptidase A2. 3.4. 7.16 Membrane Pro-X carboxypeptidase. 3.4. 7.17 Tubulinyl-Tyr carboxypeptidase. 3.4. 7.18 Carboxypeptidase T. 3.4. 7.19 Carboxypeptidase Taq. 3.4. 7.20 Carboxypeptidase U. 3.4. 7.21 Glutamate carboxypeptidase II. 3.4. 7.22 Metallocarboxypeptidase D. 3.4. 8.1 CathepsinX. 3.4. 9.1 Acylaminoacyl-peptidase. 3.4. 9.2 Peptidyl-glycinamidase. 3.4. 9.3 Pyroglutamyl-peptidase I. 3.4. 9.5 Beta-aspartyl-peptidase. 3.4. 9.6 Pyroglutamyl-peptidase II. 3.4. 9.7 N-formylmethionyl-peptidase. 3.4. 9.9 Gamma-glutamyl hydrolase. 3.4. 9.11 Gamma-D-glutamyl-meso diaminopimelate peptidase. 3.4. 9. 2 Ubiquitinyl hydrolase 1. 3.4.2 Chymotrypsin. 3.4.2 Chymotrypsin C. 3.4.2 Metridin. 3.4.2 Trypsin. 3.4.2 Thrombin. 3.4.2 Coagulation factor Xa. 3.4.2 Plasmin. 3.4.2 Enteropeptidase. 3.4.21. Acrosin. 3.4.21. Alpha-lytic endopeptidase. 3.4.21. Glutamyl endopeptidase. 3.4.21. Cathepsin G. 3.4.21. Coagulation factor VIIa. 3.4.21. Coagulation factor IXa. 3.4.21. Cucumisin. 3.4.21. Prolyl oligopeptidase. 3.4.21. Coagulation factor XIa. 3.4.21. Brachyurin. 3.4.21. Plasma kallikrein. 3.4.21. Tissue kallikrein. 3.4.21. Pancreatic elastase. 3.4.21. Leukocyte elastase. 3.4.21. Coagulation factor XIIa. 3.4.21. Chymase. 3.4.21. Complement Subcomponent Clr. 3.4.21. Complement Subcomponent Cls. 3.4.21. Classical-complement-pathway C3/C5 convertase. 3.4.2 45 Complement factor I. 3.4.2 46 Complement factor D. 3.4.2 47 Altemative-complement-pathway C3/C5 convertase. 3.4.2 48 Cerevisin. 3.4.2 49 Hypodermin C. 3.4.2 SO Lysyl endopeptidase. 3.4.2 53 Endopeptidase La. 3.4.2 54 Gamma-renin. 3.4.2 55 VenombinaB. 3.4.2 57 Leucyl endopeptidase. 3.4.2 59 Tryptase. 3.4.2 60 Scutelarin. 3.4.2 61 Kexin. 3.4.2 62 Subtilisin. 3.4.2 63 Oryzin. 3.4.2 .64 Endopeptidase K. 3.4.2 .65 Thermomycolin. 3.4.2 66 Thermitase. 3.4.2 .67 Endopeptidase So. 3.4.2 68 T-plasminogen activator. 3.4.2 69 Protein C (activated). 3.4.2 70 Pancreatic endopeptidase E. 3.4.2 .71 Pancreatic elastase II. 3.4.2 72 gA-specific serine endopeptidase. 3.4.2 73 U-plasminogen activator. US 2015/0240226 A1 Aug. 27, 2015 72

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 3.4.2 .74 Venombina. 3.4.2 .75 Furin. 3.4.2 .76 Myeloblastin. 3.4.2 77 Semenogelase. 3.4.2 .78 Granzyme A. 3.4.2 .79 Granzyme B. 3.4.2 8O Streptogrisin A. 3.4.2 81 Streptogrisin B. 3.4.2 82 Glutamyl endopeptidase II. 3.4.2 .83 Oligopeptidase B. 3.4.2 84 Limulus clotting factor C. 3.4.2 .85 Limulus clotting factor B. 3.4.2 86 Limulus clotting enzyme. 3.4.2 87 Omptin. 3.4.2 88 Repressor lexA. 3.4.2 89 Signal peptidase I. 3.4.2 90 Togavirin. 3.4.2 91 Flavivirin. 3.4.2 92 Endopeptidase Clp. 3.4.2 .93 Proprotein convertase 1. 3.4.2 .94 Proprotein convertase 2. 3.4.2 95 Snake venom factor Vactivator. 3.4.2 .96 Lactocepin. 3.4.2 97 Assemblin. 3.4.2 .98 Hepacivirin. 3.4.2 .99 Spermosin. 3.4.2 1OO Pseudomonalisin. 3.4.2 101 Xanthomonalisin. 3.4.2 102 C-terminal processing peptidase. 3.4.2 103 Physarolisin. 3.4.22.1 Cathepsin B. 3.4.22.2 Papain. 3.4.22.3 Ficain. 3.4.22.6 Chymopapain. 3.4.22.7 Asclepain. 3.4.22.8 Clostripain. 3.4.22.10 Streptopain. 3.4.22.14 Actinidain. 3.4.22.15 Cathepsin L. 3.4.22.16 Cathepsin H. 3.4.22.24 Cathepsin T. 3.4.22.25 Glycyl endopeptidase. 3.4.22.26 Cancer procoagulant. 3.4.2227 Cathepsin S. 3.4.22.28 Picomain 3C. 3.4.22.29 Picomain 2A. 3.4.22.30 Caricain. 3.4.22.31 Ananain. 3.4.22.32 Stem bromelain. 3.4.22.33 Fruit bromelain. 3.4.22.34 Legumain. 3.4.22.35 Histolysain. 3.4.22.36 Caspase-1. 3.4.22.37 Gingipain R. 3.4.22.38 Cathepsin K. 3.4.22.39 Adenain. 3.4.22.40 Bleomycin hydrolase. 3.4.22.41 Cathepsin F. 3.4.22.42 Cathepsin O. 3.4.22.43 Cathepsin V. 3.4.22.44 Nuclear-inclusion-a endopeptidase. 3.4.22.45 Helper-component proteinase. 3.4.22.46 L-peptidase. 3.4.22.47 Gingipain K. 3.4.22.48 Staphopain. 3.4.22.49 Separase. 3.4.22.50 V-cath endopeptidase. 3.4.22.51 Cruzipain. 3.4.22.52 Calpain-1. 3.4.22.53 Calpain-2. 3.4.23.1 Pepsin A. 3.4.23.2 Pepsin B. 3.4.23.3 Gastricsin. 3.4.23.4 Chymosin. US 2015/0240226 A1 Aug. 27, 2015 73

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 3.4.23.5 Cathepsin D. 3.4.23.12 Nepenthesin. 3.4.23.15 Renin. 3.4.23.16 HIV-1 retropepsin. 3.4.23.17 Pro-opiomelanocortin converting enzyme. 3.4.23.18 Aspergillopepsin I. 3.4.23.19 Aspergillopepsin II. 3.4.23.2O Penicillopepsin. 3.4.23.21 Rhizopuspepsin. 3.4.23.22 Endothiapepsin. 3.4.23.23 Mucorpepsin. 3.4.23.24 Candidapepsin. 3.4.23.25 Saccharopepsin. 3.4.23.26 Rhodotorulapepsin. 3.4.23.28 Acrocylindropepsin. 3.4.23.29 Polyporopepsin. 3.4.23.30 Pycnoporopepsin. 3.4.23.31 Scytalidopepsin A. 3.4.23.32 Scytalidopepsin B. 3.4.23.34 Cathepsin E. 3.4.23.35 Barrierpepsin. 3.4.23.36 Signal peptidase II. 3.4.23.38 Plasmepsinl. 3.4.23.39 Plasmepsin II. 3.4.23.40 Phytepsin. 3.4.23.41 Yapsin 1. 3.4.23.42 Thermopsin. 3.4.23.43 Prepilin peptidase. 3.4.23.44 Noda virus endopeptidase. 3.4.23.45 Memapsin 1. 3.4.23.46 Memapsin 2. 3.4.23.47 HIV-2 retropepsin. 3.4.23.48 Plasminogen activator Pla. 3.4.24.1 Atrolysin.A. 3.424.3 Microbial collagenase. 3.4.24.6 Leucolysin. 3.424.7 interstitial collagenase. 3.4.24.11 Neprilysin. 3.4.24.12 Envelysin. 3.424.13 gA-specific metalloendopeptidase. 3.4.24.14 Procollagen N-endopeptidase. 3.424.15 Thimet oligopeptidase. 3.4.24.16 Neurolysin. 3.424.17 Stromelysin 1. 3.424.18 MeprinA. 3.424.19 Procollagen C-endopeptidase. 3.424.2O Peptidyl-Lys metalloendopeptidase. 3.4.24.21 Astacin. 3.4.24.22 Stromelysin 2. 3.424.23 Matrilysin. 3.4.24.24 Gelatinase A. 3.424.25 Vibriolysin. 3.4.24.26 Pseudolysin. 3.424.27 Thermolysin. 3.424.28 Bacillolysin. 3.424.29 Aureolysin. 3.424.30 Coccolysin. 3.4.2431 Mycolysin. 3.424.32 Beta-lytic metalloendopeptidase. 3.424.33 Peptidyl-Asp metalloendopeptidase. 3.4.24.34 Neutrophil collagenase. 3.424.35 Gelatinase B. 3.424.36 Leishmanolysin. 3.424.37 Saccharolysin. 3.424.38 Gametolysin. 3.424.39 Deuterolysin. 3.4.24.40 Serralysin. 3.4.24.41 Atrolysin B. 3.4.24.42 Atrolysin C. 3.4.24.43 AtroXase. 3.4.24.44 Atrolysin E. 3.4.24.45 Atrolysin F. 3.4.24.46 Adamalysin. US 2015/0240226 A1 Aug. 27, 2015 74

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 3.4.24.47 Horrilysin. 3.4.24.48 Ruberlysin. 3.4.24.49 Bothropasin. 3.424.50 Bothrolysin. 3.424.51 Ophiolysin. 3.424.52 Trimerelysin I. 3.424.53 Trimerelysin II. 3.424.54 Mucrolysin. 3.424.55 Pitrilysin. 3.4.2456 Insulysin. 3.424.57 O-Sialoglycoprotein endopeptidase. 3.424.58 Russellysin. 3.424.59 Mitochondrial intermediate peptidase. 3.424.60 Dactylysin. 3.4.24.61 Nardilysin. 3.4.24.62 Magnolysin. 3.424.63 MeprinB. 3.4.24.64 Mitochondrial processing peptidase. 3.424.65 Macrophage elastase. 3.424.66 Choriolysin L. 3.424.67 Choriolysin H. 3.424.68 Tentoxilysin. 3.424.69 Bontoxilysin. 3.424.70 Oligopeptidase A. 3.424.71 Endothelin-converting enzyme 1. 3.424.72 Fibrolase. 3.424.73 Jararhagin. 3.424.74 Fragilysin. 3.424.75 Lysostaphin. 3.424.76 Flavastacin. 3.424.77 Snapalysin. 3.424.78 GPR endopeptidase. 3.424.79 Pappalysin-1. 3.424.8O Membrane-type matrix metalloproteinase-1. 3.424.81 ADAM10 endopeptidase. 3.424.82 ADAMTS-4 endopeptidase. 3.424.83 Anthrax lethal factor endopeptidase. 3.4.24.84 Ste24 endopeptidase. 3.424.85 S2P endopeptidase. 3.424.86 ADAM17 endopeptidase. 3.425.1 Proteasome endopeptidase complex. 3.5.1.1 Asparaginase. 3.5.1.2 Glutaminase. 3.5.1.3 Omega-amidase. 3.5.1.4 Amidase. 3.5.1.5 Urease. 3.5.1.6 Beta-ureidopropionase. 3.5.1.7 Ureidosuccinase. 3.5.1.8 Formylaspartate deformylase. 3.5.1.9 Arylformamidase. 3.5.1.10 Formyltetrahydrofolate deformylase. 3.5.1.11 Penicillin amidase. 3.5.1.12 Biotinidase. 3.5.1.13 Aryl-acylamidase. 3.5.1.14 Aminoacylase. 3.5.1.15 Aspartoacylase. 3.5.1.16 Acetylomithine deacetylase. 3.5.1.17 Acyl-lysine deacylase. 3.5.1.18 Succinyl-diaminopimelate desuccinylase. 3.5.1.19 Nicotinamidase. 3.5.1.20 Citrullinase. 3.5.1.21 N-acetyl-beta-alanine deacetylase. 35122 Pantothenase. 3.S.123 Ceramidase. 3.5.1.24 Choloylglycine hydrolase. 3.5.1.25 N-acetylglucosamine-6-phosphate deacetylase. 3.5.126 N(4)-(beta-N-acetylglucosaminyl)-L- asparaginase. 3.5.1.27 N-formylmethionylaminoacyl-tRNA deformylase. 3.5.1.28 N-acetylmuramoyl-L-alanine amidase. US 2015/0240226 A1 Aug. 27, 2015 75

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 3.5.1.29 2-(acetamidomethylene)Succinate hydrolase. 3.5.1.30 5-aminopentanamidase. 3.5.1.31 Formylmethionine deformylase. 3.5.1.32 Hippurate hydrolase. 3.5.1.33 N-acetylglucosamine deacetylase. 3.5.1.35 D-glutaminase. 3.5.1.36 N-methyl-2-oxoglutaramate hydrolase. 3.5.1.38 Glutamin-(asparagin-)ase. 3.5.1.39 Alkylamidase. 3.5.140 Acylagmatine amidase. 3.5.141 Chitin deacetylase. 3.5.1.42 Nicotinamide-nucleotide amidase. 3.5.1.43 Peptidyl-glutaminase. 3.5.1.44 Protein-glutamine glutaminase. 3.5.146 6-aminohexanoate-dimer hydrolase. 3.S.147 N-acetyldiaminopimelate deacetylase. 3.5.148 Acetylspermidine deacetylase. 3.5.1.49 Formamidase. 3.5.1. SO Pentanamidase. 3.5.1.51 4-acetamidobutyryl-CoA deacetylase. 3.5.1.52 Peptide-N(4)-(N-acetyl-beta glucosaminyl)asparagine amidase. 3.5.1.53 N-carbamoylputrescine amidase. 3.5.1.54 Allophanate hydrolase. 3.5.1.55 Long-chain-fatty-acyl-glutamate deacylase. 3.5.1.56 N,N-dimethylformamidase. 3.5.1.57 Tryptophanamidase. 3.5.1.58 N-benzyloxycarbonylglycine hydrolase. 3.5.1.59 N-carbamoylsarcosine amidase. 3.5.1.60 N-(long-chain-acyl)ethanolamine deacylase. 3.5.1.61 Mimosinase. 3.5.1.62 Acetylputrescine deacetylase. 3.5.1.63 4-acetamidobutyrate deacetylase. 3.5.1.64 N(alpha)-benzyloxycarbonyleucine hydrolase. 3.5.1.65 Theanine hydrolase. 3.5.1.66 2-(hydroxymethyl)-3- (acetamidomethylene)Succinate hydrolase. 3.5.1.67 4-methyleneglutaminase. 3.5.1.68 N-formylglutamate deformylase. 3.5.1.69 Glycosphingolipid deacylase. 3.5.1.70 Aculeacin-A deacylase. 3.5.1.71 N-feruloylglycine deacylase. 3.5.1.72 D-benzoylarginine-4-nitroanilide amidase. 3.5.1.73 Camitinamidase. 3.S.174 Chenodeoxycholoyltaurine hydrolase. 3.5.1.75 Urethanase. 3.5.1.76 Arylalkyl acylamidase. 3.5.177 N-carbamoyl-D-amino acid hydrolase. 3.5.1.78 Glutathionylspermidine amidase. 3.5.1.79 Phthalyl amidase. 3.5.1.81 N-acyl-D-amino-acid deacylase. 3.5.1.82 N-acyl-D-glutamate deacylase. 3.5.1.83 N-acyl-D-aspartate deacylase. 3.5.1.84 Biuret amidohydrolase. 3.5.1.85 (S)-N-acetyl-1-phenylethylamine hydrolase. 3.5.1.86 Mandelamide amidase. 3.5.1.87 N-carbamoyl-L-amino-acid hydrolase. 3.S.188 Peptide deformylase. 3.5.1.89 N acetylglucosaminylphosphatidylinositol deacetylase. 3.5.1.90 Adenosylcobinamide hydrolase. 3.5.2.1 Barbiturase. 3.5.2.2 Dihydropyrimidinase. 3.5.23 Dihydroorotase. 3.5.2.4 Carboxymethylhydantoinase. 3.5.2.5 Allantoinase. 3.5.2.6 Beta-lactamase. 3.5.2.7 midazolonepropionase. US 2015/0240226 A1 Aug. 27, 2015 76

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 3.5.2.9 5-oxoprolinase (ATP-hydrolyzing). 3.5.2.10 Creatininase. 3.5.2.11 L-lysine-lactamase. 3.5.2.12 6-aminohexanoate-cyclic-dimer hydrolase. 3.5.2.13 2,5-dioxopiperazine hydrolase. 3.5.2.14 N-methylhydantoinase (ATP hydrolyzing). 3.5.2.15 Cyanuric acid amidohydrolase. 3.5.2.16 Maleimide hydrolase. 3.5.2.17 Hydroxyisourate hydrolase. 3.5.3.1 Arginase. 3.5.3.2 Guanidinoacetase. 3.5.3.3 Creatinase. 3.534 Allantoicase. 3.5.3.5 Formimidoylaspartate deiminase. 3.5.3.6 Arginine deiminase. 3.5.3.7 Guanidinobutyrase. 3.5.3.8 Formimidoylglutamase. 3.5.3.9 Allantoate deiminase. 3.5.3.10 D-arginase. 3.5.3.11 Agmatinase. 3.5.3.12 Agmatine deiminase. 3.5.3.13 Formimidoylglutamate deiminase. 3.5.3.14 Amidinoaspartase. 3.5.3.15 Protein-arginine deiminase. 3.5.3.16 Methylguanidinase. 3.5.3.17 Guanidinopropionase. 3.5.3.18 Dimethylargininase. 3.5.3.19 Ureidoglycolate hydrolase. 3.5.3.20 Diguanidinobutanase. 3.5.3.21 Methylenediurea deaminase. 3.5.3.22 Proclavaminate amidinohydrolase. 3.54.1 Cytosine deaminase. 3.54.2 Adenine deaminase. 3.543 Guanine deaminase. 3.54.4 Adenosine deaminase. 3.54.5 Cytidine deaminase. 3.54.6 AMP deaminase. 3.54.7 ADP deaminase. 3.54.8 Aminoimidazolase. 3.54.9 Methenyltetrahydrofolate cyclohydrolase. 3.54.10 IMP cyclohydrolase. 3.54.11 Pterin deaminase. 3.54.12 dCMP deaminase. 3.54.13 dCTP deaminase. 3.54.14 Deoxycytidine deaminase. 3.54.15 Guanosine deaminase. 3.54.16 GTP cyclohydrolase I. 3.54.17 Adenosine-phosphate deaminase. 3.54.18 ATP deaminase. 3.54.19 Phosphoribosyl-AMP cyclohydrolase. 3.54.20 Pyrithiamine deaminase. 3.54.21 Creatinine deaminase. 35.4.22 1-pyrroline-4-hydroxy-2-carboxylate deaminase. 3.54.23 Blasticidin-S deaminase. 3.54.24 Sepiapterin deaminase. 3.54.25 GTP cyclohydrolase II. 35.426 Diaminohydroxyphosphoribosylaminopyrimidine deaminase. 3.54.27 Methenyltetrahydromethanopterin cyclohydrolase. 3.54.28 S-adenosylhomocysteine deaminase. 3.54.29 GTP cyclohydrolase Ha. 3.54.30 dCTP deaminase (dUMP-forming). 3.S.S.1 Nitrilase. 3.S.S.2 Ricinine nitrilase. 3.S.S.4 Cyanoalanine nitrilase. 3.5.5.5 Arylacetonitrilase. 3.S.S.6 Bromoxynil nitrilase. 3.5.5.7 Aliphatic nitrilase. 3.S.S.8 Thiocyanate hydrolase. US 2015/0240226 A1 Aug. 27, 2015 77

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 3.S.99.1 Riboflavinase. 3.S.99.2 Thiaminase. 3.S.99.3 Hydroxydechloroatrazine ethylamino hydrolase. 3.5.99.4 N-isopropylammelide isopropylamino hydrolase. 3.S.99.5 2-aminomuconate deaminase. 3.S.99.6 Glucosamine-6-phosphate deaminase. 3.S.99.7 1-aminocyclopropane-1-carboxylate deaminase. 3.6. Inorganic diphosphatase. 3.6. Trimetaphosphatase. 3.6. Adenosinetiriphosphatase. 3.6. Apyrase. 3.6. Nucleoside-diphosphatase. 3.6. Acylphosphatase. 3.6. ATP diphosphatase. 3.6. Nucleotide diphosphatase. 3.6.1. Endopolyphosphatase. 3.6.1. Exopolyphosphatase. 3.6.1. dCTP diphosphatase. 3.6.1. ADP-ribose diphosphatase. 3.6.1. Adenosine-tetraphosphatase. 3.6.1. Nucleoside-triphosphatase. 3.6.1. CDP-glycerol diphosphatase. 3.6.1. Bis(5'-nucleosyl)-tetraphosphatase (asymmetrical). 3.6. 18 FAD diphosphatase. 3.6. 19 Nucleoside-triphosphate diphosphatase. 3.6. 20 5'-acylphosphoadenosine hydrolase. 3.6. .21 ADP-Sugar diphosphatase. 3.6. 22 NAD+-diphosphatase. 3.6. 23 dUTP diphosphatase. 3.6. .24 Nucleoside phosphoacylhydrolase. 3.6. 25 Triphosphatase. 3.6. 26 CDP-diacylglycerol diphosphatase. 3.6. 27 Undecaprenyl-diphosphatase. 3.6. 28 Thiamine-triphosphatase. 3.6. 29 Bis(5'-adenosyl)-triphosphatase. 3.6. 30 M(7)G(5')pppN diphosphatase. 3.6. 31 Phosphoribosyl-ATP diphosphatase. 3.6. 39 Thymidine-triphosphatase. 3.6. 40 Guanosine-5'-triphosphate,3'- diphosphate diphosphatase. 3.6. 41 Bis(5'-nucleosyl)-tetraphosphatase (symmetrical). 3.6. 42 Guanosine-diphosphatase. 3.6. 43 Dolichyldiphosphatase. 3.6.1. Oligosaccharide-diphosphodolichol diphosphatase. 3.6. 45 UDP-Sugar diphosphatase. 3.6. 52 Diphosphoinositol-polyphosphate diphosphatase. 3.6.2.1 Adenylylsulfatase. 3.6.2.2 Phosphoadenylylsulfatase. 36.31 Phospholipid-translocating ATPase. 3.6.32 Magnesium-importing ATPase. 3.6.3.3 Cadmium-exporting ATPase. 3.6.3.4 Copper-exporting ATPase. 3.6.3.5 Zinc-exporting ATPase. 36.36 Proton-exporting ATPase. 3.63.1 Sodium-exporting ATPase. 36.38 Calcium-transporting ATPase. 3.63.9 Sodium potassium-exchanging ATPase. 3.6.3.10 Hydrogenipotassium-exchanging ATPase. 3.6.3.11 Chloride-transporting ATPase. 36.312 Potassium-transporting ATPase. 3.6.3.14 H(+)-transporting two-sector ATPase. 3.6.3.15 Sodium-transporting two-sector ATPase. 36.316 Arsenite-transporting ATPase. 3.6.3.17 Monosaccharide-transporting ATPase. 3.6.3.18 Oligosaccharide-transporting ATPase. US 2015/0240226 A1 Aug. 27, 2015 78

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 3.6.3.19 Maltose-transporting ATPase. 3.6.32O Glycerol-3-phosphate-transporting ATPase. 3.6.321 Polar-amino-acid-transporting ATPase. 3.6.322 Nonpolar-amino-acid-transporting ATPase. 3.6.323 Oligopeptide-transporting ATPase. 3.6.324 Nickel-transporting ATPase. 3.6.3.25 Sulfate-transporting ATPase. 3.6.326 Nitrate-transporting ATPase. 3.6.327 Phosphate-transporting ATPase. 3.6.328 Phosphonate-transporting ATPase. 3.6.329 Molybdate-transporting ATPase. 3.6.3.30 Fe(3+)-transporting ATPase. 3.6.3.31 Polyamine-transporting ATPase. 3.6.3.32 Quatemary-amine-transporting ATPase. 3.6.3.33 Vitamin B 12-transporting ATPase. 3.6.3.34 Iron-chelate-transporting ATPase. 3.6.3.35 Manganese-transporting ATPase. 3.6.3.36 Taurine-transporting ATPase. 3.6.3.37 Guanine-transporting ATPase. 36.338 Capsular-polysaccharide-transporting ATPase. 3.6.3.39 Lipopolysaccharide-transporting ATPase. 3.6.340 Teichoic-acid-transporting ATPase. 3.6.3.41 Heme-transporting ATPase. 3.6.3.42 Beta-glucan-transporting ATPase. 3.6.3.43 Peptide-transporting ATPase. 3.6.3.44 Xenobiotic-transporting ATPase. 3.6.345 Steroid-transporting ATPase. 3.6.3.46 Cadmium-transporting ATPase. 3.6.3.47 Fatty-acyl-CoA-transporting ATPase. 3.6.3.48 Alpha-factor-transporting ATPase. 3.6.3.49 Channel-conductance-controlling ATPase. 3.6.3SO Protein-secreting ATPase. 3.6.351 Mitochondrial protein-transporting ATPase. 3.6.352 Chloroplast protein-transporting ATPase. 3.6.353 Ag(+)-exporting ATPase. 3.6.4.1 Myosin ATPase. 3.6.4.2 Dynein ATPase. 36.4.3 Microtubule-severing ATPase. 3.6.4.4 Plus-end-directed kinesin ATPase. 3.64.5 Minus-end-directed kinesin ATPase. 3.6.46 Vesicle-fusing ATPase. 36.4.7 Peroxisome-assembly ATPase. 36.4.8 Proteasome ATPase. 36.4.9 Chaperonin ATPase. 36.4.10 Non-chaperonin molecular chaperone ATPase. 3.6.4.11 Nucleoplasmin ATPase. 36.5.1 Heterotrimeric G-protein GTPase. 36.5.2 Small monomeric GTPase. 3.6.5.3 Protein-synthesizing GTPase. 3.654 Signal-recognition-particle GTPase. 3.6.S.S Dynamin GTPase. 3.65.6 Tubulin GTPase. 3.7.1.1 Oxaloacetase. 3.7.1.2 Fumarylacetoacetase. 3.7.1.3 Kynureninase. 3.71.4 Phloretin hydrolase. 3.7.1.5 Acylpyruvate hydrolase. 3.7.1.6 Acetylpyruvate hydrolase. 3.7.1.7 Beta-diketone hydrolase. 3.7.1.8 2,6-dioxo-6-phenylhexa-3-enoate hydrolase. 3.7.1.9 2-hydroxymuconate-semialdehyde hydrolase. 3.7.1.10 Cyclohexane-1,3-dione hydrolase. 3.81.1 Alkylhalidase. 3.8.1.2 (S)-2-haloacid dehalogenase. US 2015/0240226 A1 Aug. 27, 2015 79

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 3.813 Haloacetate dehalogenase. 3.81.5 Haloallcane dehalogenase. 3.8.1.6 4-chlorobenzoate dehalogenase. 3.8.1.7 4-chlorobenzoyl-CoA dehalogenase. 3.8.1.8 Atrazine chlorohydrolase. 3.8.19 (R)-2-haloacid dehalogenase. 3.81.10 2-haloacid dehalogenase (configuration inverting). 3.8.1.11 2-haloacid dehalogenase (configuration retaining). 3.9.1.1 Phosphoamidase. 0.1.1 N-sulfoglucosamine Sulfohydrolase. O.12 Cyclamate Sulfohydrolase. 1.1.1 Phosphonoacetaldehyde hydrolase. 1.1.2 Phosphonoacetate hydrolase. 2.1.1 Trithionate hydrolase. 3.11 UDP-Sulfoquinovose synthase. ENZYME: 4. . . . Pyruvate decarboxylase. Oxalate decarboxylase. Oxaloacetate decarboxylase. Acetoacetate decarboxylase. Acetolactate decarboxylase. Aconitate decarboxylase. Benzoylformate decarboxylase. Oxalyl-CoA decarboxylase. Malonyl-CoA decarboxylase. 1 Aspartate 1-decarboxylase. Aspartate 4-decarboxylase. Valine decarboxylase. Glutamate decarboxylase. Hydroxyglutamate decarboxylase. Ornithine decarboxylase. Lysine decarboxylase. Arginine decarboxylase. Diaminopimelate decarboxylase. 1 Phosphoribosylaminoimidazole carboxylase. .1.22 Histidine decarboxylase. 1.23 Orotidine-5'-phosphate decarboxylase. .1.24 Aminobenzoate decarboxylase. 1.25 Tyrosine decarboxylase. 1.28 Aromatic-L-amino-acid decarboxylase. 1.29 Sulfimoalanine decarboxylase. 1.30 Pantothenoylcysteine decarboxylase. 1.31 Phosphoenolpyruvate carboxylase. 32 Phosphoenolpyruvate carboxykinase (GTP). 1.33 Diphosphomevalonate decarboxylase. .1.34 Dehydro-L-gulonate decarboxylase. 1.35 UDP-glucuronate decarboxylase. : 36 Phosphopantothenoylcysteine decarboxylase. 1.37 Uroporphyrinogen decarboxylase. 38 Phosphoenolpyruvate carboxykinase (diphosphate). 1.39 Ribulose-bisphosphate carboxylase. 1.40 Hydroxypyruvate decarboxylase. .1.41 Methylmalonyl-CoA decarboxylase. .1.42 Carnitine decarboxylase. 1.43 Phenylpyruvate decarboxylase. 4-carboxymuconolactone decarboxylase. 4. 1.45 Aminocarboxymuconate-semialdehyde decarboxylase. .1.46 O-pyrocatechuate decarboxylase. 1.47 Tartronate-semialdehyde synthase. .1.48 Indole-3-glycerol-phosphate synthase. : 1.49 Phosphoenolpyruvate carboxykinase (ATP). 4. 1...SO Adenosylmethionine decarboxylase. 4. S1 3-hydroxy-2-methylpyridine-4,5- dicarboxylate 4-decarboxylase. US 2015/0240226 A1 Aug. 27, 2015 80

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 52 6-methylsalicylate decarboxylase. 1.53 Phenylalanine decarboxylase. 1.54 Dihydroxyfumarate decarboxylase. 1.55 4,5-dihydroxyphthalate decarboxylase. 1.56 3-oxolaurate decarboxylase. 1.57 Methionine decarboxylase. 1.58 Orsellinate decarboxylase. 1.59 Gallate decarboxylase. 1.60 Stipitatonate decarboxylase. 1.61 4-hydroxybenzoate decarboxylase. .1.62 Gentisate decarboxylase. 1.63 Protocatechuate decarboxylase. .64 2,2-dialkylglycine decarboxylase (pyruvate). .65 Phosphatidylserine decarboxylase. 1.66 Uracil-5-carboxylate decarboxylase. 1.67 UDP-galacturonate decarboxylase. 68 5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase. 69 3,4-dihydroxyphthalate decarboxylase. 1.70 Glutaconyl-CoA decarboxylase. 1.71 2-oxoglutarate decarboxylase. 72 Branched-chain-2-oxoacid decarboxylase. 4. 73 Tartrate decarboxylase. 1.74 Indolepyruvate decarboxylase. .75 5-guanidino-2-oxopentanoate decarboxylase. .76 Arylmalonate decarboxylase. 1.77 4-oxalocrotonate decarboxylase. 1.78 Acetylenedicarboxylate decarboxylase. 1.79 Sulfopyruvate decarboxylase. 80 4-hydroxyphenylpyruvate decarboxylase. 81 Threonine-phosphate decarboxylase. .2.2 Ketotetrose-phosphate aldolase. .2.4 Deoxyribose-phosphate aldolase. 2.5 Threonine aldolase. 2.9 Phosphoketolase. 2.10 Mandelonitrile lyase. .2.11 Hydroxymandelonitrile lyase. .2.12 2-dehydropantoate aldolase. 2.13 Fructose-bisphosphate aldolase. .2.14 2-dehydro-3-deoxy-phosphogluconate 808SC. 2.17 L-fuculose-phosphate aldolase. 2.18 2-dehydro-3-deoxy-L-pentonate 808SC. 4. 2.19 Rhamnulose-1-phosphate aldolase. 2.2O 2-dehydro-3-deoxyglucarate aldolase. .2.21 2-dehydro-3-deoxy-6- phosphogalactonate aldolase. .2.22 Fructose-6-phosphate phosphoketolase. 2.23 3 eoxy-D-manno-octuloSonate O8Se. .2.24 imethylaniline-N-oxide aldolase. 2.25 hydroneopterin aldolase. 2.26 enylserine aldolase. 2.27 hinganine-1-phosphate aldolase. 2.28 s ehydro-3-deoxy-D-pentonate olase. 4. 2.29 ehydro-2-deoxyphosphogluconate olase. 2.30 7-alpha-hydroxyprogesterone aldolase. 2.32 imethylamine-oxide aldolase. 2.33 lucosterol-epoxide lyase. : .2.34 -(2-carboxyphenyl)-2-oxobut-3-enoate aldolase. 2.35 Propioin synthase. 2.36 Lactate aldolase. 2.37 Acetone-cyanohydrin lyase. 2.38 Benzoin aldolase. 2.39 Hydroxynitrilase. .2.40 Tagatose-bisphosphate aldolase. US 2015/0240226 A1 Aug. 27, 2015 81

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. .2.41 Vanillin synthase. .3.1 Isocitrate lyase. 3.3 N-acetylneuraminate lyase. .3.4 Hydroxymethylglutaryl-CoA lyase. 3.6 Citrate (pro-3S)-lyase. 3.13 Oxalomalate lyase. 3.14 3-hydroxyaspartate aldolase. 3.16 4-hydroxy-2-oxoglutarate aldolase. 3.17 4-hydroxy-4-methyl-2-oxoglutarate aldolase. 3.22 Citramalate lyase. 3.24 Malyl-CoA lyase. 3.25 Citramalyl-CoA lyase. : 3.26 3-hydroxy-3-isohexenylglutaryl-CoA lyase. 3.27 Anthranilate synthase. 3.30 Methylisocitrate lyase. 3.32 2,3-dimethylmalate lyase. 3.34 Citryl-CoA lyase. 3.35 (1-hydroxycyclohexan-1-yl)acetyl-CoA lyase. 3.36 Naphthoate synthase. 3.38 Aminodeoxychorismate lyase. 99.1 Tryptophanase. 99.2 Tyrosinephenol-lyase. 99.3 Deoxyribodipyrimidine photo-lyase. 99.5 Octadecanal decarbonylase. 99.11 Benzylsuccinate synthase. Carbonate dehydratase. Fumarate hydratase. Aconitate hydratase. Citrate dehydratase. Arabinonate dehydratase. Galactonate dehydratase. Altronate dehydratase. Mannonate dehydratase. Dihydroxy-acid dehydratase. 3-dehydroquinate dehydratase. Phosphopyruvate hydratase. Phosphogluconate dehydratase. Enoyl-CoA hydratase. Methylglutaconyl-CoA hydratase. midazoleglycerol-phosphate dehydratase. 4.2. 20 Tryptophan synthase. 4.2. 22 CyStathionine beta-synthase. 4.2. .24 Porphobilinogen synthase. 4.2. 25 L-arabinonate dehydratase. 4.2. 27 Acetylenecarboxylate hydratase. 4.2. 28 Propanediol dehydratase. 4.2. 30 Glycerol dehydratase. 4.2. 31 Maleate hydratase. 4.2. 32 L(+)-tartrate dehydratase. 4.2. .33 3-isopropylmalate dehydratase. 4.2. 34 (S)-2-methylmalate dehydratase. 4.2. 35 (R)-2-methylmalate dehydratase. 4.2. 36 Homoaconitate hydratase. 4.2. 39 Gluconate dehydratase. 4.2. 40 Glucarate dehydratase. 4.2. 41 5-dehydro-4-deoxyglucarate dehydratase. 4.2. 42 Galactarate dehydratase. 4.2. 43 2-dehydro-3-deoxy-L-arabinonate dehydratase. 4.2.1. Myo-inosose-2 dehydratase. 4.2. 45 CDP-glucose 4,6-dehydratase. 4.2. 46 dTDP-glucose 4,6-dehydratase. 4.2. 47 GDP-mannose 4,6-dehydratase. 4.2. 48 D-glutamate cyclase. 4.2. 49 Urocanate hydratase. 4.2. SO Pyrazolylalanine synthase. 4.2. S1 Prephenate dehydratase. 4.2. 52 Dihydrodipicolinate synthase. 4.2. 53 Oleate hydratase. US 2015/0240226 A1 Aug. 27, 2015 82

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 4.2. 54 Lactoyl-CoA dehydratase. 4.2. 55 3-hydroxybutyryl-CoA dehydratase. 4.2. S6 taconyl-CoA hydratase. 4.2. 57 Sohexenylglutaconyl-CoA hydratase. 4.2. S8 Crotonoyl-acyl-carrier-protein hydratase. 4.2. 59 3-hydroxyoctanoyl-acyl-carrier protein dehydratase. 4.2. 60 3-hydroxy decanoyl-acyl-carrier protein dehydratase. 4.2. 61 3-hydroxypalmitoyl-acyl-carrier protein dehydratase. 4.2. 62 5-alpha-hydroxysteroid dehydratase. 4.2. .65 3-cyanoalanine hydratase. 4.2. 66 Cyanide hydratase. 4.2. .67 D-fuconate dehydratase. 4.2. 68 L-fuconate dehydratase. 4.2. 69 Cyanamide hydratase. 4.2. 70 Pseudouridylate synthase. 4.2. 73 Protoaphin-aglucone dehydratase (cyclizing). 4.2. .74 Long-chain-enoyl-CoA hydratase. 4.2. .75 Uroporphyrinogen-III synthase. 4.2. .76 UDP-glucose 4,6-dehydratase. 4.2. 77 Trans-L-3-hydroxyproline dehydratase. 4.2. .78 (S)-norcoclaurine synthase. 4.2. .79 2-methylcitrate dehydratase. 4.2. 80 2-oxopent-4-enoate hydratase. 4.2. 81 D(-)-tartrate dehydratase. 4.2. 82 Xylonate dehydratase. 4.2. .83 4-oxalmesaconate hydratase. 4.2. 84 Nitrile hydratase. 4.2. .85 Dimethylmaleate hydratase. 4.2. 86 6-dehydroprogesterone hydratase. 4.2. 87 Octopamine dehydratase. 4.2. 88 Synephrine dehydratase. 4.2. 89 Carnitine dehydratase. 4.2. 90 L-rhamnonate dehydratase. 4.2. 91 Carboxycyclohexadienyl dehydratase. 4.2. 92 Hydroperoxide dehydratase. 4.2. .93 ATP-dependent NAD(P)H-hydrate dehydratase. 4.2. .94 Scytalone dehydratase. 4.2. 95 Kievitone hydratase. 4.2. .96 4a-hydroxytetrahydrobiopterin dehydratase. 4.2. 97 Phaseollidin hydratase. 4.2. .98 6-alpha-hydroxyprogesterone dehydratase. 4.2. 2-methylisocitrate dehydratase. 4.2. Cyclohexa-1,5-dienecarbonyl-CoA hydratase. 4.2. 101 Trans-feruloyl-CoA hydratase. 4.2. 103 Cyclohexyl-isocyanide hydratase. 4.2. 104 Cyanate hydratase. 4.2.2.1 Hyaluronate lyase. 4.2.2.2 Pectate lyase. 4.2.2.3 Poly(beta-D-mannuronate) lyase. 4.2.2.4 Chondroitin ABC lyase. 4.2.2.5 Chondroitin AC lyase. 4.2.2.6 Oligogalacturonide lyase. 4.22.7 Heparin lyase. 4.2.2.8 Heparin-sulfate lyase. 4.2.2.9 Pectate disaccharide-lyase. 4.2.2.10 Pectin lyase. 4.2.2.11 Poly(alpha-L-guluronate) lyase. 4.2.2.12 Xanthan lyase. 4.2.2.13 EXO-(1->4)-alpha-D-glucan lyase. 4.2.2.14 Glucuronan lyase. 4.2.2.15 Anhydrosialidase. 4.2.2.16 Levan fructotransferase (DFA-IV orming). 4.2.2.17 nulin fructotransferase (DFA-I- orming). US 2015/0240226 A1 Aug. 27, 2015 83

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 4.2.2.18 Inulin fructotransferase (DFA-III forming). 4.2.3.1 Threonine synthase. 4.2.3.2 Ethanolamine-phosphate phospho-lyase. 4.2.3.3 Methylglyoxal synthase. 4.2.3.4 3-dehydroquinate synthase. 4.23.5 Chorismate synthase. 4.2.3.6 Trichodiene synthase. 4.23.7 Pentalenene synthase. 4.238 Casbene synthase. 4.23.9 Aristolochene synthase. 4.23.10 (–)-endo-fenchol synthase. 4.2.3.11 Sabinene-hydrate synthase. 4.2.3.12 6-pyruvoyltetrahydropterin synthase. 4.2.3.13 (+)-delta-cadinene synthase. 4.2.3.14 Pinene synthase. 4.23.15 Myrcene synthase. 4.2.3.16 (4S)-limonene synthase. 4.23.17 Taxadiene synthase. 4.2.3.18 Abietadiene synthase. 4.23.19 Ent-kaurene synthase. 4.23.2O (+)-limonene synthase. 4.2.3.21 Vetispiradiene synthase. 4.2.99.12 Carboxymethyloxysuccinate lyase. 4.2.99.18 DNA-(apurinic or apyrimidinic site) yase. 4.2.99.19 2-hydroxypropyl-CoM lyase. 4.3. Aspartate ammonia-lyase. 4.3. Methylaspartate ammonia-lyase. 4.3. Histidine ammonia-lyase. 4.3. Formimidoyltetrahydrofolate cyclodeaminase. 4.3. Phenylalanine ammonia-lyase. 4.3. Beta-alanyl-CoA ammonia-lyase. 4.3. Ethanolamine ammonia-lyase. 4.3. Glucosaminate ammonia-lyase. 4.3. O Serine-Sulfate ammonia-lyase. 4.3. 1 Dihydroxyphenylalanine ammonia yase. 4.3. .12 Ornithine cyclodeaminase. 4.3. 13 Carbamoyl-serine ammonia-lyase. 4.3. .14 3-aminobutyryl-CoA ammonia-lyase. 4.3. 1S Diaminopropionate ammonia-lyase. 4.3. 16 Threo-3-hydroxyaspartate ammonia yase. 4.3. 17 L-serine ammonia-lyase. 4.3. 18 D-Serine ammonia-lyase. 4.3. 19 Threonine ammonia-lyase. 4.3. 20 Erythro-3-hydroxyaspartate ammonia yase. 4.3.2.1 Argininosuccinate lyase. 4.3.2.2 AdenyloSuccinate lyase. 4.3.2.3 Ureidoglycolate lyase. 4.3.2.4 Purine imidazole-ring cyclase. 4.3.25 Peptidylamidoglycolate lyase. 4.3.3.1 3-ketovalidoxylamine C-N-lyase. 4.3.3.2 Strictosidine synthase. 4.3.3.3 Deacetylisoipecoside synthase. 4.3.3.4 Deacetylipecoside synthase. 4.4.1.1 CyStathionine gamma-lyase. 4.4.1.2 Homocysteine desulfhydrase. 4.4.1.3 Dimethylpropiothetin dethiomethylase. 4.4.1.4 Alliin lyase. 4.4.1.5 Lactoylglutathione lyase. 4.4.1.6 S-alkylcysteine lyase. 4.4.1.8 CyStathionine beta-lyase. 4.4.1.9 L-3-cyanoalanine synthase. 4.4.1.10 Cysteine lyase. 4.4.1.11 Methionine gamma-lyase. 4.4.1.13 Cysteine-S-conjugate beta-lyase. 4.4.1.14 -aminocyclopropane-1-carboxylate synthase. 4.4.1.15 D-cysteine desulfhydrase. 4.4.1.16 Selenocysteine lyase. US 2015/0240226 A1 Aug. 27, 2015 84

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 4.4.1.17 Holocytochrome-c synthase. 4.4.1.19 Phosphosulfolactate synthase. 4.4.1.20 Leukotriene-C(4) synthase. 4.5.1.1 DDT-dehydrochlorinase. 4.51.2 3-chloro-D-alanine dehydrochlorinase. 4.51.3 Dichloromethane dehalogenase. 4.5.1.4 L-2-amino-4-chloropent-4-enoate dehydrochlorinase. 4.51.5 S-carboxymethylcysteine synthase. 4.6.1.1 Adenylate cyclase. 4.6.1.2 Guanylate cyclase. 4.6.1.6 Cytidylate cyclase. 4.6.1.12 2-C-methyl-D-erythritol 2,4- cyclodiphosphate synthase. 4.6.1.13 Phosphatidylinositol diacylglycerol lyase. 4.6.1.14 Glycosylphosphatidylinositol diacylglycerol-lyase. 4.6.1.15 FAD-AMP lyase (cyclizing). 4.99.1.1 Ferrochelatase. 4.99.1.2 Alkylmercury lyase. 4.99.13 Sirohydrochlorin cobaltochelatase. 4.99.14 Sirohydrochlorin ferrochelatase. 4.99.15 Aliphatic aldoxime dehydratase. 4.99.1.6 Indoleacetaldoxime dehydratase. ENZYME: 5. . . .

5.1.1.1 Alanine racemase. 5.1.1.2 Methionine racemase. 5.1.1.3 Glutamate racemase. 5.1.1.4 Proline racemase. 5.1.1.5 Lysine racemase. 5.1.16 Threonine racemase. 5.1.1.7 Diaminopimelate epimerase. 5.1.1.8 4-hydroxyproline epimerase. 5.1.19 Arginine racemase. 5.1.1.10 Amino-acid racemase. 5.1.1.11 Phenylalanine racemase (ATP hydrolyzing). 5.1.1.12 Ornithine racemase. 5.1.1.13 Aspartate racemase. 5.1.1.14 Nocardicin-A epimerase. 5.1.1.15 2-aminohexano-6-lactam racemase. 5.1.1.16 Protein-serine epimerase. 5.1.1.17 Isopenicillin-N epimerase. 5.1.2.1 Lactate racemase. 5.1.2.2 Mandelate racemase. 5.1.2.3 3-hydroxybutyryl-CoA epimerase. 5.1.2.4 Acetoin racemase. S.12.5 Tartrate epimerase. 5.12.6 Isocitrate epimerase. 5.1.3.1 Ribulose-phosphate 3-epimerase. 5.1.3.2 UDP-glucose 4-epimerase. S.1.3.3 Aldose 1-epimerase. 5.1.3.4 L-ribulose-phosphate 4-epimerase. S.1.3.5 UDP-arabinose 4-epimerase. 5.13.6 UDP-glucuronate 4-epimerase. S.1.3.7 UDP-N-acetylglucosamine 4-epimerase. 5.1.3.8 N-acylglucosamine 2-epimerase. S.1.3.9 N-acylglucosamine-6-phosphate 2 epimerase. 3.10 CDP-abequose epimerase. 3.11 Cellobiose epimerase. 3.12 UDP-glucuronate 5'-epimerase. 3.13 dTDP-4-dehydrorhamnose 3,5- epimerase. 3.14 UDP-N-acetylglucosamine 2-epimerase. 3.15 Glucose-6-phosphate 1-epimerase. 3.16 UDP-glucosamine 4-epimerase. 3.17 Heparosan-N-Sulfate-glucuronate 5 epimerase. 5 3.18 GDP-mannose 3,5-epimerase. 3.19 Chondroitin-glucuronate 5-epimerase. US 2015/0240226 A1 Aug. 27, 2015 85

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. S.1.3.20 ADP-glyceromanno-heptose 6 epimerase. 5.1.3.21 Maltose epimerase. 5.1.99.1 Methylmalonyl-CoA epimerase. S.1.99.2 16-hydroxysteroid epimerase. S.1.99.3 Allantoin racemase. 5.1994 Alpha-methylacyl-CoA racemase. S.2. Maleate isomerase. S.2. Maleylacetoacetate isomerase. S.2. Retinal isomerase. S.2. Maleylpyruvate isomerase. S.2. Linoleate isomerase. S.2. Furylfuramide isomerase. S.2. Retinol isomerase. S.2. Peptidylprolyl isomerase. S.2. Famesol 2-isomerase. S.2. 2-chloro-4-carboxymethylenebut-2-en 1,4-olide isomerase. 5.2.1. 4-hydroxyphenylacetaldehyde-oxime isomerase. 5.3. Triose-phosphate isomerase. 5.3. Arabinose isomerase. 5.3. L-arabinose isomerase. 5.3. Xylose isomerase. 5.3. Ribose-5-phosphate isomerase. 5.3. Mannose isomerase. 5.3. Mannose-6-phosphate isomerase. 5.3. Glucose-6-phosphate isomerase. 5.3.1. Glucuronate isomerase. 5.3.1. Arabinose-5-phosphate isomerase. 5.3.1. L-rhamnose isomerase. 5.3.1. D-lyxose lcetol-isomerase. 5.3.1. -(5-phosphoribosyl)-5-((5- phosphoribosylamino)methylideneamino)imidazole 4-carboxamide isomerase. 5.3. 17 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase. 5.3. 20 Ribose isomerase. 5.3. .21 Corticosteroid side-chain-isomerase. 5.3. 22 Hydroxypyruvate isomerase. 5.3. 23 S-methyl-5-thioribose-1-phosphate isomerase. 5.3. .24 Phosphoribosylanthranilate isomerase. 5.3. 25 L-fucose isomerase. 5.3. 26 Galactose-6-phosphate isomerase. 5.3.2.1 Phenylpyruvate tautomerase. 5.3.2.2 Oxaloacetate tautomerase. 5.3.3.1 Steroid delta-isomerase. 5.3.3.2 Sopentenyl-diphosphate delta-isomerase. 5.3.3.3 Vinylacetyl-CoA delta-isomerase. 5.33.4 Muconolactone delta-isomerase. 5.33.5 Cholestenol delta-isomerase. 5.3.3.6 Methylitaconate delta-isomerase. 5.33.7 Aconitate delta-isomerase. 5.3.3.8 Dodecenoyl-CoA delta-isomerase. 5.33.9 Prostaglandin-A(1) delta-isomerase. 5.3.3.10 5-carboxymethyl-2-hydroxymuconate delta-isomerase. 5.3.3.11 Sopiperitenone delta-isomerase. 5.3.3.12 Dopachrome isomerase. 5.3.3.13 Polyenoic fatty acid isomerase. 53.4.1 Protein disulfide-isomerase. 5.3.99.2 Prostaglandin-D synthase. 5.3.99.3 Prostaglandin-E synthase. 5.3.99.4 Prostaglandin-I synthase. 5.3.99.5 Thromboxane-A Synthase. 5.3.99.6 Allene-oxide cyclase. 5.3.99.7 Styrene-oxide isomerase. 5.4.1.1 Lysolecithin acylmutase. 5.4.1.2 Precorrin-8X methylmutase. 54.2.1 Phosphoglycerate mutase. 54.2.2 Phosphoglucomutase. 54.23 Phosphoacetylglucosamine mutase. 5.4.2.4 Bisphosphoglycerate mutase. US 2015/0240226 A1 Aug. 27, 2015 86

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 54.25 Phosphoglucomutase (glucose-cofactor). 54.2.6 Beta-phosphoglucomutase. S.4.2.7 Phosphopentomutase. 542.8 Phosphomannomutase. 54.29 Phosphoenolpyruvate mutase. 54.210 Phosphoglucosamine mutase. 5.432 Lysine 2,3-aminomutase. 5.4.3.3 Beta-lysine 5,6-aminomutase. 5.434 D-lysine 5,6-aminomutase. 5.43.5 D-Omithine 4,5-aminomutase. 54.36 Tyrosine 2,3-aminomutase. 5.43.7 Leucine 2,3-aminomutase. 5.4.38 Glutamate-1-semialdehyde 2,1- aminomutase. 5.4.4.1 (Hydroxyamino)benzene mutase. 5.4.4.2 Sochorismate synthase. 5.44.3 3-(hydroxyamino)phenol mutase. 5.499.1 Methylaspartate mutase. 5.4.99.2 Methylmalonyl-CoA mutase. 5.499.3 2-acetolactate mutase. 5.499.4 2-methyleneglutarate mutase. 5.4.99.5 Chorismate mutase. 5.4.99.7 Lanosterol synthase. 5.4.99.8 Cycloartenol synthase. 5.4.99.9 UDP-galactopyranose mutase. 5.499.11 Isomalitulose synthase. 5.499.12 tRNA-pseudouridine synthase I. 5.499.13 Isobutyryl-CoA mutase. 5.499.14 4-carboxymethyl-4-methylbutenolide mutase. 5.4.99.15 (1->4)-alpha-D-glucan 1-alpha-D- glucosylmutase. 5.499.16 Maltose alpha-D-glucosyltransferase. 5.4.99.17 Squalene-hopene cyclase. S.S.1.1 Muconate cycloisomerase. S.S.1.2 3-carboxy-cis,cis-muconate cycloisomerase. S.S.1.3 Tetrahydroxypteridine cycloisomerase. 5.5.1.4 Inositol-3-phosphate synthase. 5.5.1.5 Carboxy-cis,cis-muconate cyclase. S.S.1.6 Chalcone isomerase. 5.5.1.7 Chloromuconate cycloisomerase. S.S.1.8 Geranyl-diphosphate cyclase. S.S.1.9 Cycloeucalenol cycloisomerase. S.S.1.10 Alpha-pinene-oxide decyclase. S.S.1.11 Dichloromuconate cycloisomerase. S.S.1.12 Copalyl diphosphate synthase. S.S.1.13 Ent-copalyl diphosphate synthase. 5.99.1.1 Thiocyanate isomerase. 5.99.1.2 DNA topoisomerase. 5.99.13 DNA topoisomerase (ATP-hydrolyzing). ENZYME: 6. . . . Tyrosine--tRNA ligase. Tryptophan-tRNA ligase. Threonine--tRNA ligase. Leucine-tRNA ligase. Isoleucine--tRNA ligase. Lysine--tRNA ligase. Alanine--tRNA ligase. Valine--tRNA ligase. 10 Methionine--tRNA ligase. Serine--tRNA ligase. .1.12 Aspartate--tRNA ligase. 1.13 D-alanine-poly(phosphoribitol) ligase. .1.14 Glycine--tRNA ligase. 1.15 Proline--tRNA ligase. .1.16 Cysteine--tRNA ligase. 1.17 Glutamate--tRNA ligase. 1.18 Glutamine--tRNA ligase. 1.19 Arginine--tRNA ligase. 1.20 Phenylalanine--tRNA ligase. .1.21 Histidine--tRNA ligase. 22 Asparagine--tRNA ligase. US 2015/0240226 A1 Aug. 27, 2015 87

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 6.1.1. Aspartate--tRNA(ASn) ligase. 6.1.1. : Glutamate--tRNA(Gln) ligase. 6.1. Lysine--tRNA(Pyl) ligase. 6.2. Acetate-CoA ligase. 6.2. Butyrate--CoA ligase. 6.2. Long-chain-fatty-acid-CoA ligase. 6.2. Succinate--CoA ligase (GDP-forming). 6.2. Succinate--CoA ligase (ADP-forming). 6.2. Glutarate--CoA ligase. 6.2. Cholate--CoA ligase. 6.2. Oxalate--CoA ligase. 6.2. Malate-CoA ligase. 6.2.1. Acid--CoA ligase (GDP-forming). 6.2.1. Biotin-CoA ligase. 6.2.1. 4-coumarate--CoA ligase. 6.2.1. Acetate-CoA ligase (ADP-forming). 6.2.1. 6-carboxylhexanoate--CoA ligase. 6.2.1. Arachidonate-CoA ligase. 6.2.1. Acetoacetate--CoA ligase. 6.2.1. Propionate--CoA ligase. 6.2.1. Citrate--CoA ligase. 6.2.1. Long-chain-fatty-acid-luciferin component ligase. 6.2. 20 Long-chain-fatty-acid--acyl-carrier protein ligase. 6.2. 22 Citrate (pro-3S)-lyase ligase. 6.2. 23 Dicarboxylate-CoA ligase. 6.2. .24 Phytanate-CoA ligase. 6.2. 25 Benzoate--CoA ligase. 6.2. 26 O-Succinylbenzoate-CoA ligase. 6.2. 27 4-hydroxybenzoate--CoA ligase. 6.2. 28 3-alpha,7-alpha-dihydroxy-5-beta cholestanate-CoA ligase. 6.2. 29 3-alpha,7-alpha,12-alpha-trihydroxy-5- beta-cholestanate--CoA ligase. 6.2. 30 Phenylacetate--CoA ligase. 6.2. 31 2-furoate-CoA ligase. 6.2. 32 Anthranilate--CoA ligase. 6.2. .33 4-chlorobenzoate--CoA ligase. 6.2. 34 Trans-feruloyl-CoA synthase. 6.3.1. Aspartate--ammonia ligase. 6.3.1. Glutamate--ammonia ligase. 6.3. Aspartate--ammonia ligase (ADP forming). 6.3. NAD(+) synthase. 6.3. Glutamate--ethylamine ligase. 6.3. 4-methyleneglutamate-ammonia ligase. 6.3. Glutathionylspermidine synthase. 6.3. Trypanothione synthase. 6.3. Adenosylcobinamide-phosphate synthase. 6.3.2.1 Pantoate--beta-alanine ligase. 6.3.2.2 Glutamate-cysteine ligase. 6.3.2.3 Glutathione synthase. 6.3.2.4 D-alanine--D-alanine ligase. 6.3.25 Phosphopantothenate-cysteine ligase. 6.3.2.6 PhosphoribosylaminoimidazoleSuccinocarboxamide synthase. 63.2.1 UDP-N-acetylmuramoyl-L-alanyl-D- glutamate--L-lysine ligase. 6.3.2.8 UDP-N-acetylmuramate--L-alanine igase. 6.3.2.9 UDP-N-acetylmuramoylalanine--D- glutamate ligase. 6.3.2.10 UDP-N-acetylmuramoyl-tripeptide-D- alanyl-D-alanine ligase. 6.3.2.11 Camosine synthase. 6.3.2.12 Dihydrofolate synthase. 6.3.2.13 UDP-N-acetylmuramoylalanyl-D- glutamate-2,6-diaminopimelate ligase. 6.3.2.14 2,3-dihydroxybenzoate--serine ligase. 6.3.2.16 D-alanine-alanyl poly(glycerolphosphate) ligase. 6.3.2.17 Tetrahydrofolylpolyglutamate synthase. US 2015/0240226 A1 Aug. 27, 2015 88

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 6.3.2.18 Gamma-glutamylhistamine synthase. 6.3.2.19 Ubiquitin-protein ligase. 6.3.2.2O Indoleacetate-lysine synthetase. 6.3.2.21 Ubiquitin--calmodulin ligase. 6.3.2.22 Diphthine--ammonia ligase. 6.3.2.23 Homoglutathione synthase. 6.3.2.24 Tyrosine-arginine ligase. 6.3.2.25 Tubulin--tyrosine ligase. 6.3.2.26 N-(5-amino-5-carboxypentanoyl)-L- cysteinyl-D-valine synthase. 6.3.2.27 Aerobactin synthase. 6.3.3.1 Phosphoribosylformylglycinamidine cyclo-ligase. 6.3.3.2 5-formyltetrahydrofolate cyclo-ligase. 6.3.3.3 Dethiobiotin synthase. 6.3.3.4 (Carboxyethyl)arginine beta-lactam synthase. 6.3.4.1 GMP synthase. 6.3.4.2 CTP synthase. 6.3.4.3 Formate--tetrahydrofolate ligase. 6.3.4.4 AdenyloSuccinate synthase. 6.3.4.5 Argininosuccinate synthase. 6.3.4.6 Urea carboxylase. 6.3.4.7 Ribose-5-phosphate-ammonia ligase. 6.3.4.8 midazoleacetate-- phosphoribosyldiphosphate ligase. 6.3.4.9 Biotin-methylmalonyl-CoA carboxytransferase ligase. 6.3.4.10 Biotin-propionyl-CoA-carboxylase (ATP-hydrolyzing) ligase. 6.3.4.11 Biotin-methylcrotonoyl-CoA carboxylase ligase. 6.3.4.12 Glutamate-methylamine ligase. 6.3.4.13 Phosphoribosylamine-glycine ligase. 6.3.4.14 Biotin carboxylase. 6.3.4.15 Biotin-acetyl-CoA-carboxylase ligase. 6.3.4.16 Carbamoyl-phosphate synthase (ammonia). 6.3.4.17 Formate-dihydrofolate ligase. 6.35.1 NAD(+) synthase (glutamine hydrolyzing). 6.35.2 GMP synthase (glutamine-hydrolyzing). 6.35.3 Phosphoribosylformylglycinamidine synthase. 6.35.4 Asparagine synthase (glutamine hydrolyzing). 6.3.S.S Carbamoyl-phosphate synthase (glutamine-hydrolyzing). 6.35.6 Asparaginyl-tRNA synthase (glutamine hydrolyzing). 63.5.1 Glutaminyl-tRNA synthase (glutamine hydrolyzing). 6.35.8 Aminodeoxychorismate synthase. 6.35.9 Hydrogenobyrinic acid a,c-diamide synthase (glutamine-hydrolyzing). 6.35.10 Adenosylcobyric acid synthase (glutamine-hydrolyzing). 6.4.1.1 Pyruvate carboxylase. 6.4.1.2 Acetyl-CoA carboxylase. 6.4.1.3 Propionyl-CoA carboxylase. 6.4.1.4 Methylcrotonoyl-CoA carboxylase. 6.4.15 Geranoyl-CoA carboxylase. 6.4.1.6 Acetone carboxylase. 6.5.1.1 DNA ligase (ATP). 6.5.1.2 DNA ligase (NAD+). 6.5.1.3 RNA ligase (ATP). 6.5.1.4 RNA-3'-phosphate cyclase. 6.6.1.1 Magnesium chelatase. 6.6.1.2 Cobaltochelatase. 6.3.4.17 Formate-dihydrofolate ligase. 6.35.1 NAD(+) synthase (glutamine hydrolyzing). US 2015/0240226 A1 Aug. 27, 2015 89

TABLE 2-continued EC Numbers with the corresponding name given to each enzyme class, Subclass and Sub-Subclass. 6.35.2 GMP synthase (glutamine-hydrolyzing). 6.35.3 Phosphoribosylformylglycinamidine synthase. 6.35.4 Asparagine synthase (glutamine hydrolyzing). 6.3.S.S Carbamoyl-phosphate synthase (glutamine-hydrolyzing). 6.35.6 Asparaginyl-tRNA synthase (glutamine hydrolyzing). 63.5.1 Glutaminyl-tRNA synthase (glutamine hydrolyzing). 6.35.8 Aminodeoxychorismate synthase. 6.35.9 Hydrogenobyrinic acid a,c-diamide synthase (glutamine-hydrolyzing). 6.35.10 Adenosylcobyric acid synthase (glutamine-hydrolyzing). 6.4.1.1 Pyruvate carboxylase. 6.4.1.2 Acetyl-CoA carboxylase. 6.4.1.3 Propionyl-CoA carboxylase. 6.4.1.4 Methylcrotonoyl-CoA carboxylase. 6.4.15 Geranoyl-CoA carboxylase. 6.4.1.6 Acetone carboxylase. 6.5.1.1 DNA ligase (ATP). 6.5.1.2 DNA ligase (NAD+). 6.5.1.3 RNA ligase (ATP). 6.5.1.4 RNA-3'-phosphate cyclase. 6.6.1.1 Magnesium chelatase. 6.6.1.2 Cobaltochelatase.

0268 Table 3 summarizes exemplary functions of exem which is transcribed and translated into a polypeptide or plary enzymes of the invention; these enzyme functions were protein when placed under the control of appropriate regula determined using sequence identity comparison analysis tory sequences. using closest BLAST hits to the exemplary polypeptides and polynucleotides of the invention. text missing or illeg 0272 A promoter sequence is “operably linked to a cod ible when filed ing sequence when RNA polymerase which initiates tran 0269. The invention also provides isolated and recombi Scription at the promoter will transcribe the coding sequence nant nucleic acids encoding polypeptides, e.g., SEQID NO:1, into mRNA. SEQID NO:3, SEQID NO:5, SEQID NO:7, SEQID NO:9, 0273. The phrase “substantially identical' in the context etc., and all additional nucleic acids disclosed in the SEQID of two nucleic acids or polypeptides, refers to two or more listing, which include all odd numbered SEQID NO:s from sequences that have, e.g., at least about 50%, 51%, 52%. 53%, SEQIDNO:1 through SEQID NO:26,897 (the exemplary 10 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61%, 62%, 63%, polynucleotides of the invention). The invention also pro 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71%, 72%, 73%, vides isolated and recombinant polypeptides, SEQID NO:2. 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81%, 82%, 83%, SEQID NO:4, SEQID NO:6, SEQID NO:8, SEQID NO:10, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, etc., and all polypeptides disclosed in the SEQ ID listing, 94%. 95%, 96%, 97%, 98%, 99%, or more nucleotide or which include all even numbered SEQID NO:s from SEQID NO:2 through SEQ ID NO:26,898 (the exemplary polypep amino acid residue (sequence) identity, when compared and tides of the invention). aligned for maximum correspondence, as measured using 0270. In another embodiment, the polypeptides of the one of the known sequence comparison algorithms or by invention can be expressed in any expression system, in vitro visual inspection. In alternative aspects, the Substantial iden or in vivo, e.g., any microorganism or other cell system (e.g., tity exists over a region of at least about 100 or more residues eukaryotic, such as yeast or mammalian cells) using proce and most commonly the sequences are Substantially identical dures known in the art. In other aspects, the polypeptides of over at least about 150 to 200 or more residues. In some the invention can be immobilized on a Solid Support prior to aspects, the sequences are substantially identical over the use in the methods of the invention. Methods for immobiliz entire length of the coding regions. ing enzymes on Solid Supports are 20 commonly known in the 0274. Additionally a “substantially identical amino acid art, for example J. Mol. Cat. B: Enzymatic 6 (1999) 29-39; sequence is a sequence that differs from a reference sequence Chivata et al. Biocatalysis: Immobilized cells and enzymes, J by one or more conservative or non-conservative amino acid Mol. Cat. 37 (1986) 1-24: Sharma et al., Immobilized Bio Substitutions, deletions, or insertions. In one aspect, the Sub materials Techniques and Applications, Angew. Chem. Int. stitution occurs at a site that is not the active site of the Ed. Engl. 21 (1982) 837-54: Laskin (Ed.), Enzymes and molecule, or, alternatively the Substitution occurs at a site that Immobilized Cells in Biotechnology. is the active site of the molecule, provided that the polypep tide essentially retains its functional (enzymatic) properties. DEFINITIONS A conservative amino acid Substitution, for example, Substi 0271. A "coding sequence of or a “sequence encodes' a tutes one amino acid for another of the same class (e.g., particular polypeptide or protein, is a nucleic acid sequence Substitution of one hydrophobic amino acid, Such as isoleu US 2015/0240226 A1 Aug. 27, 2015 90 cine, Valine, leucine, or methionine, for another, or Substitu invention. Also provided are methods for modifying the tion of one polar amino acid for another, such as Substitution nucleic acids of the invention by, e.g., synthetic ligation reas of arginine for lysine, glutamic acid for aspartic acid or sembly, optimized directed evolution system and/or satura glutamine for asparagine). One or more amino acids can be tion mutagenesis. deleted, for example, from a polypeptide, resulting in modi 0282. The nucleic acids of the invention can be made, fication of the structure of the polypeptide, without signifi isolated and/or manipulated by, e.g., cloning and expression cantly altering its biological activity. For example, amino- or of cDNA libraries, amplification of message or genomic carboxyl-terminal amino acids that are not required for a DNA by PCR, and the like. For example, exemplary polypeptide, enzyme, protein, e.g., structural or binding pro sequences of the invention were initially derived from envi tein, biological activity can be removed. Modified polypep ronmental sources. tide sequences of the invention can be assayed for enzyme, 0283. In one aspect, the invention provides nucleic acids, structural or binding activity by any number of methods, and the polypeptides encoded by them, with a common nov including contacting the modified polypeptide sequence with elty in that they are derived from a common source, e.g., an a Substrate and determining whether the modified polypep environmental or a bacterial Source. tide decreases the amount of specific Substrate in the assay or 0284. In practicing the methods of the invention, homolo increases the bioproducts of the reaction of a functional gous genes can be modified by manipulating a template polypeptide, enzyme, protein, e.g., structural or binding pro nucleic acid, as described herein. The invention can be prac tein, with the substrate. Assays for enzyme activity are well ticed in conjunction with any method or protocol or device known in the art. known in theart, which are well described in the scientific and 0275 "Fragments’ as used herein are a portion of a natu patent literature. rally occurring protein which can existinat least two different 0285. The phrases “nucleic acid' or “nucleic acid conformations. Fragments can have the same or Substantially sequence' as used herein refer to an oligonucleotide, nucle the same amino acid sequence as the naturally occurring otide, polynucleotide, or to a fragment of any of these, to protein. Fragments which have different three dimensional DNA or RNA of genomic or synthetic origin which may be structures as the naturally occurring protein are also included. single-stranded or double-stranded and may represent a sense An example of this, is a "pro-form molecule, such as a low or antisense (complementary) Strand, to peptide nucleic acid activity proprotein that can be modified by cleavage to pro (PNA), or to any DNA-like or RNA-like material, natural or duce a mature enzyme with significantly higher activity. synthetic in origin. The phrases “nucleic acid' or “nucleic 0276. The term “variant” refers to polynucleotides or acid sequence” includes oligonucleotide, nucleotide, poly polypeptides of the invention modified at one or more base nucleotide, or to a fragment of any of these, to DNA or RNA pairs, codons, introns, exons, or amino acid residues (respec (e.g., mRNA, rRNA, tRNA, iRNA) of genomic or synthetic tively) yet still retain the biological activity of a polypeptide, origin which may be single-stranded or double-stranded and enzyme, protein, e.g., structural or binding protein, of the may represent a sense or antisense strand, to peptide nucleic invention. Variants can be produced by any number of means acid (PNA), or to any DNA-like or RNA-like material, natural included methods such as, for example, error-prone PCR, or synthetic in origin, including, e.g., iRNA, ribonucleopro shuffling, oligonucleotide-directed mutagenesis, assembly teins (e.g., e.g., double stranded iRNAs, e.g., iRNPs). The PCR, sexual PCR mutagenesis, in vivo mutagenesis, cassette term encompasses nucleic acids, i.e., oligonucleotides, con mutagenesis, recursive ensemble mutagenesis, exponential taining known analogues of natural nucleotides. The term ensemble mutagenesis, site-specific mutagenesis, gene reas also encompasses nucleic-acid-like structures with synthetic sembly, GSSM and any combination thereof. backbones, see e.g., Mata (1997) Toxicol. Appl. Pharmacol. 0277. The term “saturation mutagenesis”. Gene Site Satu 144:189-197; Strauss-Soukup (1997) Biochemistry 36:8692 ration Mutagenesis, or “GSSM includes a method that uses 8698; Samstag (1996) Antisense Nucleic Acid Drug Dev degenerate oligonucleotide primers to introduce point muta 6:153-156. “Oligonucleotide' includes either a single tions into a polynucleotide, as described in detail, below. Stranded poly deoxynucleotide or two complementary 0278. The term “optimized directed evolution system” or polydeoxynucleotide strands which may be chemically syn “optimized directed evolution' includes a method for reas thesized. Such synthetic oligonucleotides have no 5' phos sembling fragments of related nucleic acid sequences, e.g., phate and thus will not ligate to another oligonucleotide with related genes, and explained in detail, below. out adding a phosphate with an ATP in the presence of a (0279. The term “synthetic ligation reassembly” or “SLR' kinase. A synthetic oligonucleotide can ligate to a fragment includes a method of ligating oligonucleotide fragments in a that has not been dephosphorylated. non-stochastic fashion, and explained in detail, below. 0286 A "coding sequence of or a “nucleotide sequence 0280 Nucleic Acids encoding a particular polypeptide or protein, is a nucleic 0281. The invention provides nucleic acids (e.g., the acid sequence which is transcribed and translated into a exemplary SEQID NO:1, SEQID NO:3, SEQID NO:5, SEQ polypeptide or protein when placed under the control of ID NO:7, SEQ ID NO:9, SEQ ID NO:11, etc., including all appropriate regulatory sequences. The term “gene' means the nucleic acids disclosed in the SEQID listing, which include segment of DNA involved in producing a polypeptide chain; all odd numbered SEQID NO:s from SEQID NO:1 through it includes regions preceding and following the coding region SEQID NO:26,897), including expression cassettes such as (leader and trailer) as well as, where applicable, intervening expression vectors, encoding polypeptides (e.g., enzymes) of sequences (introns) between individual coding segments (ex the invention. The invention also includes methods for dis ons). “Operably linked as used herein refers to a functional covering new polypeptide (e.g., enzyme) sequences using the relationship between two or more nucleic acid (e.g., DNA) nucleic acids of the invention. The invention also includes segments. Typically, it refers to the functional relationship of methods for inhibiting the expression of enzymes, genes, transcriptional regulatory sequence to a transcribed transcripts and polypeptides using the nucleic acids of the sequence. For example, a promoter is operably linked to a US 2015/0240226 A1 Aug. 27, 2015

coding sequence, such as a nucleic acid of the invention, if it non-coding (anti-sense) strand. Alternatively, the isolated stimulates or modulates the transcription of the coding nucleic acids may comprise RNA. sequence in an appropriate host cell or other expression sys 0291. The isolated nucleic acids of the invention may be tem. Generally, promoter transcriptional regulatory used to prepare one of the polypeptides of the invention, or sequences that are operably linked to a transcribed sequence fragments comprising at least 5, 10, 15, 20, 25, 30, 35, 40, 50. are physically contiguous to the transcribed sequence, i.e., 75, 100, or 150 or more consecutive amino acids of one of the they are cis-acting. However, Some transcriptional regulatory polypeptides of the invention. Accordingly, another aspect of sequences. Such as enhancers, need not be physically contigu the invention is an isolated nucleic acid which encodes one of ous or located in close proximity to the coding sequences the polypeptides of the invention, or fragments comprising at whose transcription they enhance. least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 or more 0287. As used herein, the term “promoter” includes all consecutive amino acids of one of the polypeptides of the sequences capable of driving transcription of a coding invention. The coding sequences of these nucleic acids may sequence in a cell, e.g., a plant cell. Thus, promoters used in be identical to one of the coding sequences of one of the the constructs of the invention include cis-acting transcrip nucleic acids of the invention or may be different coding tional control elements and regulatory sequences that are sequences which encode one of the of the invention having at involved in regulating or modulating the timing and/or rate of least 5, 10, 15, 20, 25, 30, 35, 40, 50, 75, 100, or 150 or more transcription of a gene. For example, a promoter can be a consecutive amino acids of one of the polypeptides of the cis-acting transcriptional control element, including an invention, as a result of the redundancy or degeneracy of the enhancer, a promoter, a transcription terminator, an origin of genetic code. The genetic code is well known to those of skill replication, a chromosomal integration sequence, 5' and 3' in the art and can be obtained, e.g., on page 214 of B. Lewin, untranslated regions, or an intronic sequence, which are Genes VI, Oxford University Press, 1997. involved in transcriptional regulation. These cis-acting 0292. The isolated nucleic acid which encodes one of the sequences typically interact with proteins or other biomol polypeptides of the invention, but is not limited to: only the ecules to carry out (turn on/off, regulate, modulate, etc.) tran coding sequence of a nucleic acid of the invention and addi scription. “Constitutive' promoters are those that drive tional coding sequences, such as leader sequences or propro expression continuously under most environmental condi tein sequences and non-coding sequences, such as introns or tions and states of development or cell differentiation. non-coding sequences 5' and/or 3' of the coding sequence. “Inducible' or “regulatable promoters direct expression of Thus, as used herein, the term “polynucleotide encoding a the nucleic acid of the invention under the influence of envi polypeptide' encompasses a polynucleotide which includes ronmental conditions or developmental conditions. only the coding sequence for the polypeptide as well as a Examples of environmental conditions that may affect tran polynucleotide which includes additional coding and/or non Scription by inducible promoters include anaerobic condi coding sequence. tions, elevated temperature, drought, or the presence of light. 0293 Alternatively, the nucleic acid sequences of the 0288 "Plasmids’ can be commercially available, publicly invention, may be mutagenized using conventional tech available on an unrestricted basis, or can be constructed from niques, such as site directed mutagenesis, or other techniques available plasmids in accord with published procedures. familiar to those skilled in the art, to introduce silent changes Equivalent plasmids to those described herein are known in into the polynucleotides o of the invention. As used herein, the art and will be apparent to the ordinarily skilled artisan. 'silent changes' include, for example, changes which do not 0289. In one aspect, the term “recombinant’ means that alter the amino acid sequence encoded by the polynucleotide. the nucleic acid is adjacent to a “backbone' nucleic acid to Such changes may be desirable in order to increase the level which it is not adjacent in its natural environment. Addition of the polypeptide produced by host cells containing a vector ally, to be “enriched the nucleic acids will represent 5% or encoding the polypeptide by introducing codons or codon more of the number of nucleic acid inserts in a population of pairs which occur frequently in the host organism. nucleic acid backbone molecules. Backbone molecules 0294 The invention also relates to polynucleotides which according to the invention include nucleic acids such as have nucleotide changes which result in amino acid substitu expression vectors, self-replicating nucleic acids, viruses, tions, additions, deletions, fusions and truncations in the integrating nucleic acids and other vectors or nucleic acids polypeptides of the invention. Such nucleotide changes may used to maintain or manipulate a nucleic acid insert of inter beintroduced using techniques such as site directed mutagen est. Typically, the enriched nucleic acids represent 15% or esis, random chemical mutagenesis, exonuclease III deletion more of the number of nucleic acid inserts in the population of and other recombinant DNA techniques. Alternatively, such recombinant backbone molecules. More typically, the nucleotide changes may be naturally occurring allelic Vari enriched nucleic acids represent 50% or more of the number ants which are isolated by identifying nucleic acids which of nucleic acid inserts in the population of recombinant back specifically hybridize to probes comprising at least 10, 15, 20, bone molecules. In a one aspect, the enriched nucleic acids 25, 30, 35, 40, 50, 75, 100, 150, 200, 300, 400, or 500 con represent 90% or more of the number of nucleic acid inserts in secutive bases of one of the sequences of the invention (or the the population of recombinant backbone molecules. sequences complementary thereto) under conditions of high, 0290. One aspect of the invention is an isolated nucleic moderate, or low Stringency as provided herein. acid comprising one of the sequences of the invention, or a 0295 General Techniques fragment comprising at least 10, 15, 20, 25, 30, 35, 40, 50, 75, 0296. The nucleic acids used to practice this invention, 100, 150, 200, 300, 400, or 500 or more consecutive bases of whether RNA, iRNA, antisense nucleic acid, cDNA, genomic a nucleic acid of the invention. The isolated, nucleic acids DNA, vectors, viruses or hybrids thereof, may be isolated may comprise DNA, including cDNA, genomic DNA and from a variety of sources, genetically engineered, amplified, synthetic DNA. The DNA may be double-stranded or single and/or expressed/generated recombinantly. Recombinant Stranded and if single stranded may be the coding Strand or polypeptides generated from these nucleic acids can be indi US 2015/0240226 A1 Aug. 27, 2015 92 vidually isolated or cloned and tested for a desired activity. purification domain and the motif-comprising peptide or Any recombinant expression system can be used, including polypeptide to facilitate purification. For example, an expres bacterial, mammalian, yeast, insect or plant cell expression sion vector can include an epitope-encoding nucleic acid systems. sequence linked to six histidine residues followed by a thiore 0297 Alternatively, these nucleic acids can be synthesized doxin and an enterokinase cleavage site (see e.g., Williams in vitro by well-known chemical synthesis techniques, as (1995) Biochemistry 34:1787-1797; Dobeli (1998) Protein described in, e.g., Adams (1983).J. Am. Chem. Soc. 105:661; Expr. Purif. 12:404-414). The histidine residues facilitate Belousov (1997) Nucleic Acids Res. 25:3440-3444; Frenkel detection and purification while the enterokinase cleavage (1995) Free Radic. Biol. Med. 19:373-380: Blommers (1994) site provides a means for purifying the epitope from the Biochemistry 33:7886-7896; Narang (1979) Meth. Enzymol. remainder of the fusion protein. Technology pertaining to 68:90; Brown (1979) Meth. Enzymol. 68:109; Beaucage vectors encoding fusion proteins and application of fusion (1981) Tetra. Lett. 22:1859; U.S. Pat. No. 4,458,066. proteins are well described in the scientific and patent litera 0298 Techniques for the manipulation of nucleic acids, ture, see e.g., Kroll (1993) DNA Cell. Biol. 12:441-53. Such as, e.g., Subcloning, labeling probes (e.g., random 0302 Transcriptional and Translational Control primer labeling using Klenow polymerase, nick translation, Sequences amplification), sequencing, hybridization and the like are 0303. The invention provides nucleic acid (e.g., DNA) well described in the Scientific and patent literature, see, e.g., sequences of the invention operatively linked to expression Sambrook, ed., MOLECULAR CLONING: A LABORA (e.g., transcriptional or translational) control sequence(s), TORY MANUAL (2NDED.), Vols. 1-3, Cold Spring Harbor e.g., promoters or enhancers, to direct or modulate RNA Laboratory, (1989); CURRENT PROTOCOLS IN synthesis/expression. The expression control sequence can be MOLECULARBIOLOGY, Ausubel, ed. John Wiley & Sons, in an expression vector. Exemplary bacterial promoters Inc., New York (1997); LABORATORY TECHNIQUES IN include lacI, lacZ, T3, T7, gpt, lambda PR, PL and trp. Exem BIOCHEMISTRY AND MOLECULAR BIOLOGY: plary eukaryotic promoters include CMV immediate early, HYBRIDIZATION WITH NUCLEIC ACID PROBES, Part HSV thymidine kinase, early and late SV40, LTRs from ret I. Theory and Nucleic Acid Preparation, Tijssen, ed. Elsevier, rovirus, and mouse metallothionein I. N.Y. (1993). 0304 Promoters suitable for expressing a polypeptide in 0299. Another useful means of obtaining and manipulat bacteria include the E. coli lac or trp promoters, the lacI ing nucleic acids used to practice the methods of the invention promoter, the lacZ promoter, the T3 promoter, the T7 pro is to clone from genomic samples, and, if desired, Screen and moter, the gpt promoter, the lambda PR promoter, the lambda re-clone inserts isolated or amplified from, e.g., genomic PL promoter, promoters from operons encoding glycolytic clones or cDNA clones. Sources of nucleic acid used in the enzymes Such as 3-phosphoglycerate kinase (PGK), and the methods of the invention include genomic or cDNA libraries acid phosphatase promoter. Eukaryotic promoters include the contained in, e.g., mammalian artificial chromosomes CMV immediate early promoter, the HSV thymidine kinase (MACs), see, e.g., U.S. Pat. Nos. 5,721,118; 6,025,155: promoter, heat shock promoters, the early and late SV40 human artificial chromosomes, see, e.g., Rosenfeld (1997) promoter, LTRs from retroviruses, and the mouse metal Nat. Genet. 15:333-335:yeast artificial chromosomes (YAC); lothionein-I promoter. Other promoters known to control bacterial artificial chromosomes (BAC); P1 artificial chromo expression of genes in prokaryotic or eukaryotic cells or their somes, see, e.g., Woon (1998) Genomics 50:306-316; P1-de viruses may also be used. Promoters suitable for expressing rived vectors (PACs), see, e.g., Kern (1997) Biotechniques the polypeptide or fragment thereof in bacteria include the E. 23:120-124; cosmids, recombinant viruses, phages or plas colilac ortrp promoters, the lacI promoter, the lacz promoter, mids. the T3 promoter, the T7 promoter, the gpt promoter, the 0300. In one aspect, a nucleic acid encoding a polypeptide lambda P. promoter, the lambda P, promoter, promoters of the invention is assembled in appropriate phase with a from operons encoding glycolytic enzymes Such as 3-phos leader sequence capable of directing secretion of the trans phoglycerate kinase (PGK) and the acid phosphatase pro lated polypeptide or fragment thereof. moter. Fungal promoters include the C-factor promoter. 0301 The invention provides fusion proteins and nucleic Eukaryotic promoters include the CMV immediate early pro acids encoding them. A polypeptide of the invention can be moter, the HSV thymidine kinase promoter, heat shock pro fused to a heterologous peptide or polypeptide. Such as N-ter moters, the early and late SV40 promoter, LTRs from retro minal identification peptides which impart desired character viruses and the mouse metallothionein-I promoter. Other istics, such as increased stability or simplified purification. promoters known to control expression of genes in prokary Peptides and polypeptides of the invention can also be Syn otic or eukaryotic cells or their viruses may also be used. thesized and expressed as fusion proteins with one or more (0305 Tissue-Specific Promoters additional domains linked thereto for, e.g., producing a more 0306 The invention provides expression cassettes that can immunogenic peptide, to more readily isolate a recombi be expressed in a tissue-specific manner, e.g., that can express nantly synthesized peptide, to identify and isolate antibodies a polypeptide, enzyme, protein, e.g., structural or binding and antibody-expressing B cells, and the like. Detection and protein, of the invention in a tissue-specific manner. The purification facilitating domains include, e.g., metal chelating invention also provides plants or seeds that express a polypep peptides such as polyhistidine tracts and histidine-tryptophan tide, enzyme, protein, e.g., structural or binding protein, of modules that allow purification on immobilized metals, pro the invention in a tissue-specific manner. The tissue-specific tein A domains that allow purification on immobilized immu ity can be seed specific, stem specific, leaf specific, root noglobulin, and the domain utilized in the FLAGS extension/ specific, fruit specific and the like. affinity purification system (Immunex Corp, Seattle Wash.). 0307 The term “expression cassette' as used herein refers The inclusion of a cleavable linker sequences such as Factor to a nucleotide sequence which is capable of affecting expres Xa or enterokinase (Invitrogen, San Diego Calif.) between a sion of a structural gene (i.e., a protein coding sequence. Such US 2015/0240226 A1 Aug. 27, 2015 as a polypeptide, enzyme, protein, e.g., structural or binding Arabidopsis (Huang (1996) Plant Mol. Biol. 33:125-139); protein, of the invention) in a host compatible with such Cat3 from Arabidopsis (GenBankNo. U43147, Zhong (1996) sequences. Expression cassettes include at least a promoter Mol. Gen. Genet. 251:196-203); the gene encoding stearoyl operably linked with the polypeptide coding sequence; and, acyl carrier protein desaturase from Brassica napus (Gen optionally, with other sequences, e.g., transcription termina bank No. X74782, Solocombe (1994) Plant Physiol. 104: tion signals. Additional factors necessary or helpful in effect 1167-1176); GPc1 from maize (GenBank No. XI5596: ing expression may also be used, e.g., enhancers, alpha-fac Martinez (1989).J. Mol. Biol. 208:551-565); the Gpc2 from tors. Thus, expression cassettes also include plasmids, maize (GenBank No. U45855, Manjunath (1997) Plant Mol. expression vectors, recombinant viruses, any form of recom Biol. 33:97-112); plant promoters described in U.S. Pat. Nos. binant “naked DNA vector, and the like. A “vector” com 4,962,028; 5,633,440. prises a nucleic acid which can infect, transfect, transiently or 0311. The invention uses tissue-specific or constitutive permanently transduce a cell. It will be recognized that a promoters derived from viruses which can include, e.g., the vector can be a naked nucleic acid, or a nucleic acid com tobamovirus subgenomic promoter (Kumagai (1995) Proc. plexed with protein or lipid. The vector optionally comprises Natl. Acad. Sci. USA 92:1679-1683; the rice tungro bacilli viral or bacterial nucleic acids and/or proteins, and/or mem form virus (RTBV), which replicates only in phloem cells in branes (e.g., a cell membrane, a viral lipid envelope, etc.). infected rice plants, with its promoter which drives strong Vectors include, but are not limited to replicons (e.g., RNA phloem-specific reporter gene expression; the cassava vein replicons, bacteriophages) to which fragments of DNA may mosaic virus (CVMV) promoter, with highest activity invas be attached and become replicated. Vectors thus include, but cular elements, in leaf mesophyll cells, and in root tips (Ver are not limited to RNA, autonomous self-replicating circular daguer (1996) Plant Mol. Biol. 31:1129-1139). or linear DNA or RNA (e.g., plasmids, viruses, and the like, 0312 Alternatively, the plant promoter may direct expres see, e.g., U.S. Pat. No. 5.217.879), and include both the sion of a polypeptide, enzyme, protein, e.g., structural or expression and non-expression plasmids. Where a recombi binding protein-expressing nucleic acid in a specific tissue, nant microorganism or cell culture is described as hosting an organ or cell type (i.e., tissue-specific promoters) or may be “expression vector' this includes both extra-chromosomal otherwise under more precise environmental or developmen circular and linear DNA and DNA that has been incorporated tal control or under the control of an inducible promoter. into the host chromosome(s). Where a vector is being main Examples of environmental conditions that may affect tran tained by a host cell, the vector may either bestably replicated Scription include anaerobic conditions, elevated temperature, by the cells during mitosis as an autonomous structure, or is the presence of light, or sprayed with chemicals/hormones. incorporated within the host’s genome. For example, the invention incorporates the drought-induc 0308 “Tissue-specific' promoters are transcriptional con ible promoter of maize (Busk (1997) supra); the cold, trol elements that are only active in particular cells or tissues drought, and high salt inducible promoter from potato (Kirch or organs, e.g., in plants oranimals. Tissue-specific regulation (1997) Plant Mol. Biol. 33:897-909). may beachieved by certain intrinsic factors which ensure that 0313 Tissue-specific promoters can promote transcrip genes encoding proteins specific to a given tissue are tion only within a certain time frame of developmental stage expressed. Such factors are known to exist in mammals and within that tissue. See, e.g., Blazquez (1998) Plant Cell plants so as to allow for specific tissues to develop. 10:791-800, characterizing the Arabidopsis LEAFY gene 0309 The term “plant” includes whole plants, plant parts promoter. See also Cardon (1997) Plant J 12:367-77, describ (e.g., leaves, stems, flowers, roots, etc.), plant protoplasts, ing the transcription factor SPL3, which recognizes a con seeds and plant cells and progeny of same. The class of plants served sequence motif in the promoter region of the A. which can be used in the method of the invention is generally thaliana floral meristem identity gene AP1; and Mandel as broad as the class of higher plants amenable to transfor (1995) Plant Molecular Biology, Vol. 29, pp. 995-1004, mation techniques, including angiosperms (monocotyledon describing the meristem promoter eIF4. Tissue specific pro ous and dicotyledonous plants), as well as gymnosperms. It moters which are active throughout the life cycle of a particu includes plants of a variety of ploidy levels, including poly lar tissue can be used. In one aspect, the nucleic acids of the ploid, diploid, haploid and hemizygous states. As used herein, invention are operably linked to a promoter active primarily the term “transgenic plant' includes plants or plant cells into only in cotton fiber cells. In one aspect, the nucleic acids of which a heterologous nucleic acid sequence has been the invention are operably linked to a promoteractive prima inserted, e.g., the nucleic acids and various recombinant con rily during the stages of cotton fiber cell elongation, e.g., as structs (e.g., expression cassettes) of the invention. described by Rinehart (1996) supra. The nucleic acids can be 0310. In one aspect, a constitutive promoter such as the operably linked to the Fbl2A gene promoter to be preferen CaMV 35S promoter can be used for expression in specific tially expressed in cotton fiber cells (Ibid). See also, John parts of the plant or seed orthroughout the plant. For example, (1997) Proc. Natl. Acad. Sci. USA89:5769-5773: John, et al., for overexpression, a plant promoter fragment can be U.S. Pat. Nos. 5,608,148 and 5,602,321, describing cotton employed which will direct expression of a nucleic acid in fiber-specific promoters and methods for the construction of Some or all tissues of a plant, e.g., a regenerated plant. Such transgenic cotton plants. Root-specific promoters may also be promoters are referred to herein as “constitutive' promoters used to express the nucleic acids of the invention. Examples and are active under most environmental conditions and states of root-specific promoters include the promoter from the of development or cell differentiation. Examples of constitu alcoholdehydrogenase gene (DeLisle (1990) Int. Rev. Cytol. tive promoters include the cauliflower mosaic virus (CaMV) 123:39-60). Other promoters that can be used to express the 35S transcription initiation region, the 1'- or 2'-promoter nucleic acids of the invention include, e.g., ovule-specific, derived from T-DNA of Agrobacterium tumefaciens, and embryo-specific, endosperm-specific, integument-specific, other transcription initiation regions from various plant genes seed coat-specific promoters, or some combination thereof a known to those of skill. Such genes include, e.g., ACT11 from leaf-specific promoter (see, e.g., Busk (1997) Plant J. 11:1285 US 2015/0240226 A1 Aug. 27, 2015 94

1295, describing a leaf-specific promoter in maize); the exposure to chemicals reagents. These reagents include, e.g., ORF13 promoter from Agrobacterium rhizogenes (which herbicides, synthetic auxins, or antibiotics which can be exhibits high activity in roots, see, e.g., Hansen (1997) Supra); applied, e.g., sprayed, onto transgenic plants. Inducible a maize pollen specific promoter (see, e.g., Guerrero (1990) expression of the polypeptide, enzyme, protein, e.g., struc Mol. Gen. Genet. 224:161 168); a tomato promoter active tural or binding protein-producing nucleic acids of the inven during fruit ripening, senescence and abscission of leaves tion will allow the grower to select plants with the optimal and, to a lesser extent, offlowers can be used (see, e.g., Blume polypeptide, enzyme, protein, e.g., structural or binding pro (1997) Plant J. 12:731 746); a pistil-specific promoter from tein, expression and/or activity. The development of plant the potato SK2 gene (see, e.g., Ficker (1997) Plant Mol. Biol. parts can thus controlled. In this way the invention provides 35:425 431); the Blec4 gene from pea, which is active in the means to facilitate the harvesting of plants and plant parts. epidermal tissue of vegetative and floral shoot apices of trans For example, in various embodiments, the maize In2-2 pro genic alfalfa making it a useful tool to target the expression of moter, activated by benzenesulfonamide herbicide safeners, foreign genes to the epidermal layer of actively growing is used (De Veylder (1997) Plant Cell Physiol. 38:568-577): shoots or fibers; the ovule-specific BELL gene (see, e.g., application of different herbicide safeners induces distinct Reiser (1995) Cell 83:735-742, GenBank No. U39944); and/ gene expression patterns, including expression in the root, or, the promoter in Klee, U.S. Pat. No. 5,589,583, describing hydathodes, and the shoot apical meristem. Coding a plant promoter region is capable of conferring high levels of sequences of the invention are also under the control of a transcription in meristematic tissue and/or rapidly dividing tetracycline-inducible promoter, e.g., as described with trans cells. genic tobacco plants containing the Avena sativa L. (oat) 0314. Alternatively, plant promoters which are inducible arginine decarboxylase gene (Masgrau (1997) Plant J. upon exposure to plant hormones, such as auxins, are used to 11:465-473); or, a salicylic acid-responsive element (Stange express the nucleic acids of the invention. For example, the (1997) Plant J. 11:1315-1324). invention can use the auxin-response elements E1 promoter 0318. In some aspects, proper polypeptide expression may fragment (AuXREs) in the Soybean (Glycine max L.) (Liu require polyadenylation region at the 3'-end of the coding (1997) Plant Physiol. 115:397–407); the auxin-responsive region. The polyadenylation region can be derived from the Arabidopsis GST6 promoter (also responsive to salicylic acid natural gene, from a variety of other plant (or animal or other) and hydrogen peroxide) (Chen (1996) Plant J. 10:955-966); genes, or from genes in the Agrobacterial T-DNA. the auxin-inducible parC promoter from tobacco (Sakai (1996) 37:906-913); a plant biotin response element (Streit 0319 Expression Vectors and Cloning Vehicles (1997) Mol. Plant Microbe Interact. 10:933-937); and, the 0320. The invention provides expression vectors and clon promoter responsive to the stress hormone abscisic acid ing vehicles comprising nucleic acids of the invention, e.g., (Sheen (1996) Science 274: 1900-1902). sequences encoding the polypeptide, enzyme, protein, e.g., 0315. The nucleic acids of the invention can also be oper structural or binding proteins of the invention. Expression ably linked to plant promoters which are inducible upon vectors and cloning vehicles of the invention can comprise exposure to chemicals reagents which can be applied to the viral particles, baculovirus, phage, plasmids, phagemids, plant, Such as herbicides or antibiotics. For example, the cosmids, fosmids, bacterial artificial chromosomes, viral maize In2-2 promoter, activated by benzenesulfonamide her DNA (e.g., vaccinia, adenovirus, foulpox virus, pseudorabies bicide safeners, can be used (De Veylder (1997) Plant Cell and derivatives of SV40), PI-based artificial chromosomes, Physiol. 38:568-577); application of different herbicide yeast plasmids, yeast artificial chromosomes, and any other safeners induces distinct gene expression patterns, including vectors specific for specific hosts of interest (such as bacillus, expression in the root, hydathodes, and the shoot apical mer Aspergillus and yeast). Vectors of the invention can include istem. Coding sequence can be under the control of, e.g., a chromosomal, non-chromosomal and synthetic DNA tetracycline-inducible promoter, e.g., as described with trans sequences. Large numbers of Suitable vectors are known to genic tobacco plants containing the Avena sativa L. (oat) those of skill in the art, and are commercially available. arginine decarboxylase gene (Masgrau (1997) Plant J. Exemplary vectors are include: bacterial: pCE vectors 11:465-473); or, a salicylic acid-responsive element (Stange (Qiagen), pBLUESCRIPT plasmids, pNH vectors, (lambda (1997) Plant J. 11:1315-1324). Using chemically- (e.g., hor ZAP vectors (Stratagene); ptrc99a, pKK223-3, plR540, mone- or pesticide-) induced promoters, i.e., promoter pRIT2T (Pharmacia); Eukaryotic: pXT1, pSG5 (Stratagene), responsive to a chemical which can be applied to the trans pSVK3, pBPV, pMSG, pSVLSV40 (Pharmacia). However, genic plant in the field, expression of a polypeptide of the any other plasmid or other vector may be used so long as they invention can be induced at a particular stage of development are replicable and viable in the host. Low copy number or of the plant. Thus, the invention also provides for transgenic high copy number vectors may be employed with the present plants containing an inducible gene encoding for polypep invention. tides of the invention whose host range is limited to target 0321. The expression vector can comprise a promoter, a plant species, such as corn, rice, barley, wheat, potato or other ribosome binding site for translation initiation and a tran crops, inducible at any stage of development of the crop. Scription terminator. The vector may also include appropriate 0316. One of skill will recognize that a tissue-specific sequences for amplifying expression. Mammalian expression plant promoter may drive expression of operably linked vectors can comprise an origin of replication, any necessary sequences in tissues other than the target tissue. Thus, a ribosome binding sites, a polyadenylation site, splice donor tissue-specific promoter is one that drives expression prefer and acceptor sites, transcriptional termination sequences, and entially in the target tissue or cell type, but may also lead to 5' flanking non-transcribed sequences. In some aspects, DNA Some expression in other tissues as well. sequences derived from the SV40 splice and polyadenylation 0317. The nucleic acids of the invention can also be oper sites may be used to provide the required non-transcribed ably linked to plant promoters which are inducible upon genetic elements. US 2015/0240226 A1 Aug. 27, 2015

0322. In one aspect, the expression vectors contain one or can comprise a marker gene that confers a selectable pheno more selectable marker genes to permit selection of host cells type on a plant cell or a seed. For example, the marker may containing the vector. Such selectable markers include genes encode biocide resistance, particularly antibiotic resistance, encoding dihydrofolate reductase or genes conferring neo Such as resistance to kanamycin, G418, bleomycin, hygro mycin resistance for eukaryotic cell culture, genes conferring mycin, or herbicide resistance, Such as resistance to chloro tetracycline or amplicillin resistance in E. coli, and the S. sulfuron or Basta. cerevisiae TRP1 gene. Promoter regions can be selected from 0328 Expression vectors capable of expressing nucleic any desired gene using chloramphenicol transferase (CAT) acids and proteins in plants are well known in the art, and can vectors or other vectors with selectable markers. include, e.g., vectors from Agrobacterium spp., potato virus 0323 Vectors for expressing the polypeptide or fragment X (see, e.g., Angell (1997) EMBO.J. 16:3675-3684), tobacco thereof in eukaryotic cells can also contain enhancers to mosaic virus (see, e.g., Casper (1996) Gene 173:69-73), increase expression levels. Enhancers are cis-acting elements tomato bushy stunt virus (see, e.g., Hillman (1989) Virology of DNA that can be from about 10 to about 300 bp in length. 169:42-50), tobacco etch virus (see, e.g., Dolja (1997) Virol They can act on a promoter to increase its transcription. ogy 234:243-252), bean golden mosaic virus (see, e.g., Mori Exemplary enhancers include the SV40 enhancer on the late naga (1993) Microbiol Immunol. 37:471-476), cauliflower side of the replication origin bp 100 to 270, the cytomega mosaic virus (see, e.g., Cecchini (1997) Mol. Plant Microbe lovirus early promoter enhancer, the polyoma enhancer on the Interact. 10:1094-1101), maize Ac/Ds transposable element late side of the replication origin, and the adenovirus enhanc (see, e.g., Rubin (1997) Mol. Cell. Biol. 17:6294-6302: CS Kunze (1996) Curr. Top. Microbiol. Immunol. 204:161-194), 0324. A nucleic acid sequence can be inserted into a vector and the maize Suppressor-mutator (Spm) transposable ele by a variety of procedures. In general, the sequence is ligated ment (see, e.g., Schlappi (1996) Plant Mol. Biol. 32:717 to the desired position in the vector following digestion of the 725); and derivatives thereof. insert and the vector with appropriate restriction endonu 0329. In one aspect, the expression vector can have two cleases. Alternatively, blunt ends in both the insert and the replication systems to allow it to be maintained in two organ vector may be ligated. A variety of cloning techniques are isms, for example in mammalian or insect cells for expression known in the art, e.g., as described in Ausubel and Sambrook. and in a prokaryotic host for cloning and amplification. Fur Such procedures and others are deemed to be within the scope thermore, for integrating expression vectors, the expression of those skilled in the art. vector can contain at least one sequence homologous to the 0325 The vector can be in the form of a plasmid, a viral host cell genome. It can contain two homologous sequences particle, or a phage. Other vectors include chromosomal, which flank the expression construct. The integrating vector non-chromosomal and synthetic DNA sequences, derivatives can be directed to a specific locus in the host cell by selecting of SV40; bacterial plasmids, phage DNA, baculovirus, yeast the appropriate homologous sequence for inclusion in the plasmids, vectors derived from combinations of plasmids and vector. Constructs for integrating vectors are well known in phage DNA, viral DNA such as vaccinia, adenovirus, fowl the art. pox virus, and pseudorabies. A variety of cloning and expres 0330 Expression vectors of the invention may also sion vectors for use with prokaryotic and eukaryotic hosts are include a selectable marker gene to allow for the selection of described by, e.g., Sambrook. bacterial strains that have been transformed, e.g., genes which 0326 Particular bacterial vectors which can be used render the bacteria resistant to drugs such as ampicillin, include the commercially available plasmids comprising chloramphenicol, erythromycin, kanamycin, neomycin and genetic elements of the well known cloning vector pBR322 tetracycline. Selectable markers can also include biosynthetic (ATCC 37017), pKK223-3 (Pharmacia Fine Chemicals, genes, such as those in the histidine, tryptophan and leucine Uppsala, Sweden), GEM1 (Promega Biotec, Madison, Wis., biosynthetic pathways. USA) pOE70, pGE60, pGE-9 (Qiagen), pIDIO, psiX174 0331. The DNA sequence in the expression vector is pBLUESCRIPT II KS, pNH8A, pNH16a, pNH18A, operatively linked to an appropriate expression control pNH46A (Stratagene), ptrc99a, pKK223-3, pKK233-3, sequence(s) (promoter) to direct RNA synthesis. Particular DR540, pRIT5 (Pharmacia), pKK232-8 and pCM7. Particu named bacterial promoters include lacI, lac7, T3, T7, gpt, lar eukaryotic vectors include pSV2CAT, pOG44, pXT1, lambda P, P, and trp. Eukaryotic promoters include CMV pSG (Stratagene) pSVK3, pBPV, pMSG, and pSVL (Phar immediate early, HSV thymidine kinase, early and late SV40. macia). However, any other vector may be used as long as it is LTRs from retrovirus and mouse metallothionein-I. Selection replicable and viable in the host cell. of the appropriate vector and promoter is well within the level 0327. The nucleic acids of the invention can be expressed ofordinary skill in the art. The expression vector also contains in expression cassettes, vectors or viruses and transiently or a ribosome binding site for translation initiation and a tran stably expressed in plant cells and seeds. One exemplary Scription terminator. The vector may also include appropriate transient expression system uses episomal expression sys sequences for amplifying expression. Promoter regions can tems, e.g., cauliflower mosaic virus (CaMV) viral RNA gen be selected from any desired gene using chloramphenicol erated in the nucleus by transcription of an episomal mini transferase (CAT) vectors or other vectors with selectable chromosome containing Supercoiled DNA, see, e.g., Covey markers. In addition, the expression vectors in one aspect (1990) Proc. Natl. Acad. Sci. USA 87: 1633-1637. Alterna contain one or more selectable marker genes to provide a tively, coding sequences, i.e., all or Sub-fragments of phenotypic trait for selection of transformed host cells Such as sequences of the invention can be inserted into a plant host dihydrofolate reductase or neomycin resistance for eukary cell genome becoming an integral part of the host chromo otic cell culture, or Such as tetracycline or amplicillin resis Somal DNA. Sense or antisense transcripts can be expressed tance in E. coli. in this manner. A vector comprising the sequences (e.g., pro 0332 Mammalian expression vectors may also comprise moters or coding regions) from nucleic acids of the invention an origin of replication, any necessary ribosome binding