WO2012048334A2

WO2012048334A2 - Novel fungal proteases

Info

Publication number: WO2012048334A2
Application number: PCT/US2011/055703
Authority: WO
Inventors: Johannes Visser; Sandra Hinz; Jan Werij; Jacob Visser; Vivi Joosten; Martijn Koetsier; Mark Emalfarb
Original assignee: Dyadic International (Usa) Inc.
Priority date: 2010-10-08
Filing date: 2011-10-11
Publication date: 2012-04-12
Also published as: WO2012048334A3

Abstract

This invention relates to novel enzymes and novel methods for producing the same. More specifically this invention relates to a variety of fungal enzymes. Nucleic acid molecules encoding such enzymes, compositions, recombinant and genetically modified host cells, and methods of use are described. The invention also relates to a method to the degradation of protein and novel combinations of enzymes, including those that provide a synergistic release of amino acids or lower molecular weight proteins. The invention also relates to methods to use the novel enzymes and compositions of such enzymes in a variety of other processes, including washing or treating of clothing or fabrics, detergent processes, cleaning of carpets, leather treatment, animal feed, food processing, baking, increasing the protein yield of food, modification of food taste, processing of proteins in protein production, processing of beverages, medical treatment, and cosmetic treatment, and bio fuels.

Description

[001 ] Novel Fungal Proteases

[002] This application claims benefit of priority under 35. U.S.C. § 1 19(e) of United States Provisional Application number 61/391,565 filed on October 9, 2010.

[003] INCORPORATION BY REFERENCE

[004] The content of all patents, patent applications, publications, articles, or literature cited herein are expressly incorporated by reference.

[005] FIELD OF THE INVENTION

[006] This invention relates to novel enzymes and novel methods for producing the same.

More specifically this invention relates to enzymes produced by fungi. The invention also relates to novel proteases which represent a category of various enzymes, including endopeptidases and exopeptidases, that catalyze the processing of proteins or the hydrolytic breakdown of proteins into peptides and amino acids. The invention also relates to methods of using the novel enzymes and compositions of such enzymes in a variety of other processes, such as washing or treating of clothing or fabrics, detergent processes, cleaning of carpets, leather treatment, animal feed, food processing, baking, increasing the protein yield of food, modification of food taste, processing of proteins in protein production, processing of beverages, medical treatment, and cosmetic treatment, and bio fuels.

[007] BACKGROUND OF THE INVENTION

[008] Proteases are enzymes that cleave proteins and peptides at the peptide bond that forms the backbone of the protein or peptide chain. As a group they represent one of the largest classes of hydrolytic enzymes which posses a wide range of specificities towards amino acid sequences, different pH and temperature optima, and different amino acids at active sites with some requiring cations such as zinc or iron for optimal activity. Proteases have found a great number of uses in the industrial production of detergents, animal hide processing, clarifying beer, debittering protein hydrolysates, modifying gluten in bakery dough, enhancing the flavor of cheese, animal feed, modification (e.g, metabolizing) of larger proteins into lower molecular weight proteins like in soybean processing, meat tenderizing as well as in other food applications involving animal and plant materials.

[009] For example, animal feed is composed of cereals, plant material, and plant and animal proteins that are not easily digested or utilized by the animal. Proteases can be used to pre-digest (metabolize) the proteins found in the animal feed so that the animal can now more efficiently utilize the protein thus gaining greater nutrition. Thus, protease supplementation in animal feed aids in the overall health of animals. There, however, still exists a need to develop new proteases that unlock the nutritional value of a large variety of feed proteins by complementing the activity of digestive enzymes such as pepsin and pancreatic proteases.

[010] Certain proteases have been used in food processing for centuries. For example, rennet, which is obtained from the fourth stomach of unweaned calves has been traditionally used in the production of cheese. Calf rennet is a relatively expensive enzyme and various attempts have been made to find cheaper alternatives from microbial sources. Thus, there exists the need to develop cheaper more effective proteases to replace the classic more expensive proteases in the food industry.

[Oi l] Many stains on clothes are proteinaceous and wide-specificity proteases can substantially improve removal of such stains. Thus, proteases are widely used in cleaning materials, washing powders, and detergents. Despite the enormous efforts over the past 20 years to find improved detergent proteases, there exists the need to develop cheaper more effective proteases to replace the classic proteases used in detergents. There also exists a need for proteases that are suitable for use in more specific environments (e.g., low-temperature, specific pH ranges).

[012] Besides being the target of drugs, proteases have many uses in the medical field for the removal of parasites, debridement of wounds, determination of blood groups, stimulate anti-inflammatory effects, to treat sepsis, and in contact lens cleaning solutions. Proteases are also used in a research laboratory setting for the proteolysis of proteins, for example the removal of a prosequence or signal peptide. Proteases can also be used for generating the peptides used for protein sequencing, and the processing of recombinant fusion proteins by engineering portions of the target protein such that they are acted upon by a site-specific protease. There exists a continuing need to develop new and improved proteases to meet the demands of the medical and research areas.

[013] Enzymes useful for the hydrolysis of complex proteins are also highly useful in a variety of industrial textile applications. For example, the production of leather is a multistep process that utilizes enzymes in several of the steps. In particular, proteases can be utilized to remove some of the surface proteins such as hair. Proteases also find their use in preserving the animal hide from microbial attack while maintaining the natural collagen of the hide. Neutral and alkaline proteases may also be useful in the soaking process. The use of new and improved proteases in the leather industry can aid in lowering the use of caustic chemicals.

[014] Proteases can also be combined with other enzymes to create combinations useful in the food and animal feed industry. For example, esterases can be utilized to degum vegetable oils; improving the production of various food products as well as enhancing the flavor of food products. Esterases can be used in the feed to reduce the amount of phosphate in feed. Carbohydrases can be used to increase the yield of fruit juice and oils; stimulate fermentation in the brewing industry; produce gelling agents; and modify starches, to make a few. Carbohydrases in the feed industry include, but are not limited to, improving feed conversion, reducing the viscosity, and producing oligosaccharides.

[015] Regardless of the type of use, the cost and hydrolytic efficiency of enzymes are major factors that can inhibit the use of proteases. The production costs of microbially produced enzymes are tightly connected with the productivity of the enzyme-producing strain and the final activity yield in the fermentation broth. The hydrolytic efficiency of a multi-enzyme cocktail depends on properties of individual enzymes, the synergies between them, and their ratio in the multi-enzyme cocktail.

[016] Filamentous fungi such as Aspergillus sp.. are sources of proteases useful in the enzymatic hydrolysis of peptide bonds to break down proteins. In particular, strains of Aspergillus sp., such as A. oryzae, A. sojae, A. niger as well as Mucor and Penicillium sp., and enzymes derived from these strains, have previously been used for proteolysis. However, in some cases the costs associated with producing enzymes from these fungi, but foremost the narrow window of operating of these enzymes in terms of pH and temperature, remains a drawback. It is therefore desirable to produce inexpensive enzymes and enzyme mixtures that efficiently degrade or process proteins for use in a variety of agricultural and industrial applications.

[017] Other applications of proteases are in the use of these enzymes in biocatalysis, which is the use of a natural catalysts to perform transformations on organic compounds. Although proteases are mainly used as hydrolases they also catalyze the reverse reaction under certain conditions and are thus able to stereospecifically synthesize peptide bonds for example like in the synthesis of the artificial sweetener aspartame. [018] In spite of the continued research, it remains desirable to discover or to engineer new highly active proteases. It would also be highly desirable to construct highly efficient enzyme compositions capable of performing rapid and efficient biodegradation of materials.

[019] SUMMARY OF THE INVENTION

[020] In one embodiment, the present invention comprises an isolated nucleic acid sequence selected from the group consisting of:

a) a nucleic acid sequence encoding a protein comprising an amino acid sequence selected from a nucleic acid sequence encoding a protein comprising an amino acid sequence selected from the amino acid sequences of SEQ ID NO: 2, SEQ ID No: 4, SEQ ID No: 6, SEQ ID No: 8, SEQ ID No: 10, SEQ ID No: 12, SEQ ID No: 14, SEQ ID No: 16, SEQ ID No: 18, SEQ ID No: 20, SEQ ID No: 22, SEQ ID No: 24, SEQ ID No: 26, SEQ ID No: 28, SEQ ID No: 30, SEQ ID No: 32, SEQ ID No: 34, SEQ ID No: 36, SEQ ID No: 38, SEQ ID No: 40, SEQ ID No: 42, SEQ ID No: 44, SEQ ID No: 46, SEQ ID No: 48, SEQ ID No: 50, SEQ ID No: 52, SEQ ID No: 54, SEQ ID No: 56, SEQ ID No: 58, SEQ ID No: 60, SEQ ID No: 62, SEQ ID No: 64, SEQ ID No: 66, SEQ ID No: 68, SEQ ID No: 70, SEQ ID No: 72, SEQ ID No: 74, SEQ ID No: 76, SEQ ID No: 78, SEQ ID No: 80, SEQ ID No: 82, SEQ ID No: 84, SEQ ID No: 86, SEQ ID No: 88, SEQ ID No: 90, SEQ ID No: 92, SEQ ID No: 94, SEQ ID No: 96, SEQ ID No: 98, SEQ ID No: 100, SEQ ID No: 102, SEQ ID No: 104, SEQ ID No: 106, SEQ ID No: 108, SEQ ID No: 110, SEQ ID No: 112, SEQ ID No: 114, SEQ ID No: 116, SEQ ID No: 118, SEQ ID No: 120, SEQ ID No: 122, SEQ ED No: 124, SEQ ID No: 126, SEQ ID No: 128, SEQ ID No: 130, SEQ ID No: 132, SEQ ID No: 134, SEQ ID No: 136, SEQ ID No: 138, SEQ ID No: 140, SEQ ID No: 142, SEQ ID No: 144, SEQ ID No: 146, SEQ ID No: 148, SEQ ID No: 150, SEQ ID No: 152, SEQ ID No: 154, SEQ ID No: 156, SEQ ID No: 158, SEQ ID No: 160, SEQ ID No: 162, SEQ ID No: 164, SEQ ID No: 166, SEQ ID No: 168, SEQ ID No: 170, SEQ ID No: 172, SEQ ID No: 174, SEQ ID No: 176, SEQ ID No: 178, SEQ ID No: 180, SEQ ID No: 182, SEQ ID No: 184, SEQ ID No: 186, SEQ ID No: 188, SEQ ID No: 190, SEQ ID No: 192, SEQ ID No: 194, SEQ ID No: 196, SEQ ID No: 198, SEQ ID No: 200, SEQ ID No: 202, SEQ ID No: 204, SEQ ID No: 206, SEQ ID No: 208, SEQ ID No: 210, SEQ ED No: 212, SEQ ID No: 214, SEQ ID No: 216, SEQ ID No: 218, SEQ ID No: 220, SEQ ID No: 222, SEQ ID No: 224, SEQ ID No: 226, SEQ ID No: 228, SEQ ID No: 230, SEQ ID No: 232, SEQ ID No: 234, SEQ ID No: 236, SEQ ID No: 238, SEQ ED No: 240, SEQ ID No: 242, SEQ ED No: 244, SEQ ED No: 246, SEQ ED No: 248, SEQ ED No: 250, SEQ ED No: 252, SEQ ED No: 254, SEQ ED No: 256, SEQ ID No: 258, SEQ ED No: 260, SEQ ED No: 262, SEQ ED No: 264, SEQ ED No: 266, SEQ ED No: 268, SEQ ED No: 270, SEQ ED No: 272, SEQ ED No: 274, SEQ ED No: 276, SEQ ED No: 278, SEQ ED No: 280, SEQ ED No: 282, SEQ ED No: 284, SEQ ED No: 286, SEQ ED No: 288, SEQ ID No: 290, SEQ ED No: 292, SEQ ID No: 294, SEQ ED No: 296, SEQ ED No: 298, SEQ ED No:300, SEQ ID No: 302, SEQ ID No: 304, SEQ ED No: 306, SEQ ED No: 308, SEQ ID No: 310, SEQ ID No: 312, SEQ ID No: 314, SEQ ED No: 316, SEQ ED No: 318, SEQ ID No: 320, SEQ ED No: 322, SEQ ED No: 324, SEQ ID No: 326, SEQ ID No: 328, SEQ ID No: 330, SEQ ED No: 332, SEQ ED No: 334, SEQ ED No: 336, SEQ ED No: 338, SEQ ED No: 340, SEQ ED No: 342, SEQ ED No: 344, SEQ ID No: 346, SEQ ID No: 348, SEQ ED No: 350, SEQ ED No: 352, SEQ ED No: 354, SEQ ED No: 356, SEQ ED No: 358, SEQ ED No: 360, SEQ ED No: 362, SEQ ID No: 364, SEQ ID No: 366, SEQ ED No: 368, SEQ ED No: 370, SEQ ED No: 372, SEQ ED No: 374, SEQ ED No: 376, SEQ ID No: 378, SEQ ID No: 380, SEQ ID No: 382, SEQ ID No: 384, SEQ ED No: 386, SEQ ED No: 388, SEQ ED No: 390, SEQ ED No: 392, SEQ ED No: 394, SEQ ED No: 396, SEQ ID No: 398, 400, SEQ ED No: 402, SEQ ID No: 404, SEQ ED No: 406, SEQ ID No: 408, SEQ ED No: 410, SEQ ED No: 412, SEQ ED No: 414, SEQ ED No: 416, SEQ ED No: 418, SEQ ED No: 420, SEQ ED No: 422, SEQ ED No: 424, SEQ ED No: 426, SEQ ED No: 428, SEQ ED No: 430, SEQ ED No: 432, SEQ ED No: 434, SEQ ED No: 436, SEQ ED No: 438, SEQ ID No: 440, SEQ ID No: 442, SEQ ED No: 444, SEQ ED No: 446, SEQ ID No: 448, SEQ ED No: 450, SEQ ED No: 452, SEQ ED No: 454, SEQ ID No: 456, SEQ ID No: 458, SEQ ED No: 460, SEQ ED No: 462, SEQ ED No: 464, SEQ ED No: 466, SEQ ED No: 468, SEQ ED No: 470, SEQ ED No: 472, SEQ ED No: 474, SEQ ID No: 476, SEQ ED No: 478, SEQ ED No: 480, SEQ ED No: 482, SEQ ID No: 484, SEQ ED No: 486, SEQ ID No: 488, SEQ ED No: 490, SEQ ED No: 492, SEQ ID No: 494, SEQ ED No: 496, SEQ ED No: 498, SEQ ED No: 500, SEQ ED No: 502, SEQ ED No: 504, SEQ ED No: 506, SEQ ID No: 508, SEQ ID No: 510, SEQ ID No: 512, SEQ ID No: 514, SEQ ID No: 516, SEQ ID No: 518, SEQ ID No: 520, SEQ ID No: 522, SEQ ID No: 524, SEQ ID No: 526, SEQ ID No: 528, SEQ ID No: 530, SEQ ID No: 532, SEQ ID No: 534, SEQ ID No: 536, SEQ ID No: 538, SEQ ID No: 540, SEQ ID No: 542, SEQ ID No: 544, SEQ ID No: 546, SEQ ID No: 548, SEQ ID No: 550, SEQ ID No: 552, SEQ ID No: 554, SEQ ID No: 556, SEQ ID No: 558, SEQ ID No: 560, SEQ ID No: 562, SEQ ID No: 564, SEQ ID No: 566, SEQ ID No: 568, SEQ ID No: 570, SEQ ED No: 572, SEQ ID No: 574, SEQ ID No: 576, SEQ ID No: 578, SEQ ID No: 580, SEQ ID No: 582, SEQ ID No: 584, SEQ ID No: 586, SEQ ID No: 588, SEQ ID No: 590, SEQ ID No: 592, SEQ ID No: 594, SEQ ID No: 596, SEQ ID No: 598, SEQ ID No:600, SEQ ID No: 602, SEQ ID No: 604, SEQ ID No: 606, SEQ ED No: 608, SEQ ID No: 610, SEQ ID No: 612, SEQ ED No: 614, SEQ ID No: 616, SEQ ED No: 618, SEQ ID No: 620, SEQ ED No: 622, SEQ ED No: 624, SEQ ID No: 626, SEQ ID No: 628, SEQ ED No: 630, SEQ ED No: 632, SEQ DD No: 634, SEQ ID No: 636, SEQ ID No: 638, SEQ ED No: 640, SEQ DD No: 642, SEQ ED No: 644, SEQ DD No: 646, SEQ ED No: 648, SEQ ED No: 650, SEQ ED No: 652, SEQ ED No: 654, SEQ ID No: 656, SEQ DD No: 658, SEQ ID No: 660, SEQ ED No: 662, SEQ DD No: 664, SEQ DD No: 666, SEQ ED No: 668, SEQ ID No: 670, SEQ DD No: 672, SEQ ID No: 674, SEQ DD No: 676, SEQ DD No: 678, SEQ DD No: 680, SEQ DD No: 682, SEQ DD No: 684, SEQ ED No: 686, SEQ DD No: 688, SEQ DD No: 690, SEQ DD No: 692, SEQ DD No: 694, SEQ DD No: 696, SEQ ED No: 698, SEQ DD No: 700, SEQ DD No: 702, SEQ DD No: 704, SEQ DD No: 706, SEQ DD No: 708, SEQ ID No: 710, SEQ DD No: 712, SEQ ED No: 714, SEQ DD No: 716, SEQ DD No: 718, SEQ DD No: 720, SEQ ED No: 722, SEQ DD No: 724, SEQ DD No: 726, SEQ ID No: 728, SEQ ED No: 730, SEQ DD No: 732, SEQ ED No: 734, SEQ DD No: 736, SEQ DD No: 738, SEQ DD No: 740, SEQ DD No: 742, SEQ DD No: 744, SEQ ID No: 746, SEQ ED No: 748, SEQ ED No: 750, SEQ DD No: 752, SEQ ED No: 754, SEQ DD No: 756, SEQ ED No: 758, SEQ DD No: 760, SEQ DD No: 762, SEQ ID No: 764, SEQ DD No: 766, SEQ DD No: 768, SEQ DD No: 770, SEQ DD No: 772, SEQ DD No: 774, SEQ DD No: 776, SEQ DD No: 778, SEQ ED No: 780, SEQ DD No: 782, SEQ DD No: 784, SEQ ED No: 786, SEQ ID No: 788, SEQ ID No: 790, SEQ DD No: 792, SEQ ID No: 794, SEQ DD No: 796, SEQ DD No: 798, SEQ ID No: 800, SEQ DD No: 802, SEQ DD No: 804, SEQ DD No: 806, SEQ DD No: 808, SEQ ED No: 810, SEQ ED No: 812, SEQ ED No: 814, SEQ ID No: 816, SEQ ID No: 818, SEQ ED No: 820, SEQ ED No: 822, SEQ ED No: 824, SEQ ED No: 826, SEQ ED No: 828, SEQ ED No: 830, SEQ ED No: 832, SEQ ED No: 834, SEQ ED No: 836, SEQ ED No: 838, SEQ ED No: 840, SEQ ED No: 842, SEQ ED No: 844, SEQ ED No: 846, SEQ ED No: 848, SEQ ED No: 850, SEQ ID No: 852, SEQ ED No: 854, SEQ ED No: 856, SEQ ED No: 858, SEQ ED No: 860. .

b) a nucleic acid sequence encoding a fragment of the protein of (a), wherein the fragment has a biological activity of the protein of (a); and

c) a nucleic acid sequence encoding an amino acid sequence that is at least about 70% identical to an amino acid sequence of (a) and has a biological activity of the protein comprising the amino acid sequence.

[021] In some embodiments, the nucleic acid sequence encodes an amino acid sequence that is at least about 90%, at least about 95%, at least about 97% or at least about 99% identical to the amino acid sequence of (a) and has a biological activity of the protein comprising the amino acid sequence.

[022] In some embodiments, the nucleic acid sequence encodes a protein comprising an amino acid sequence selected from: SEQ ED NO: 2, SEQ ED No: 4, SEQ ED No: 6, SEQ ED No: 8, SEQ ID No: 10, SEQ ED No: 12, SEQ ID No: 14, SEQ ED No: 16, SEQ ED No: 18, SEQ ID No: 20, SEQ ID No: 22, SEQ ID No: 24, SEQ ED No: 26, SEQ ID No: 28, SEQ ID No: 30, SEQ ID No: 32, SEQ ID No: 34, SEQ ID No: 36, SEQ ID No: 38, SEQ ED No: 40, SEQ ED No: 42, SEQ ED No: 44, SEQ ED No: 46, SEQ ID No: 48, SEQ ED No: 50, SEQ ED No: 52, SEQ ED No: 54, SEQ ED No: 56, SEQ ED No: 58, SEQ ED No: 60, SEQ ED No: 62, SEQ ED No: 64, SEQ ID No: 66, SEQ ID No: 68, SEQ ED No: 70, SEQ ED No: 72, SEQ ED No: 74, SEQ ID No: 76, SEQ ID No: 78, SEQ ED No: 80, SEQ ED No: 82, SEQ ED No: 84, SEQ ID No: 86, SEQ ID No: 88, SEQ ED No: 90, SEQ ED No: 92, SEQ ED No: 94, SEQ ID No: 96, SEQ ID No: 98, SEQ ED No: 100, SEQ ID No: 102, SEQ ED No: 104, SEQ ID No: 106, SEQ ID No: 108, SEQ ED No: 1 10, SEQ ED No: 1 12, SEQ ED No: 114, SEQ ED No: 116, SEQ ID No: 118, SEQ ED No: 120, SEQ ED No: 122, SEQ ED No: 124, SEQ ED No: 126, SEQ ED No: 128, SEQ ED No: 130, SEQ ED No: 132, SEQ ED No: 134, SEQ ED No: 136, SEQ ED No: 138, SEQ ID No: 140, SEQ ED No: 142, SEQ ID No: 144, SEQ ED No: 146, SEQ ED No: 148, SEQ ID No: 150, SEQ ID No: 152, SEQ ED No: 154, SEQ ID No: 156, SEQ ED No: 158, SEQ ID No: 160, SEQ ED No: 162, SEQ ED No: 164, SEQ ID No: 166, SEQ ID No: 168, SEQ ID No: 170, SEQ ID No: 172, SEQ ID No: 174, SEQ ID No: 176, SEQ ID No: 178, SEQ ID No: 180, SEQ ID No: 182, SEQ ID No: 184, SEQ ID No: 186, SEQ ID No: 188, SEQ ID No: 190, SEQ ID No: 192, SEQ ID No: 194, SEQ ID No: 196, SEQ ID No: 198, SEQ ID No: 200, SEQ ID No: 202, SEQ ID No: 204, SEQ ID No: 206, SEQ ID No: 208, SEQ ID No: 210, SEQ ID No: 212, SEQ ID No: 214, SEQ ID No: 216, SEQ ID No: 218, SEQ ID No: 220, SEQ ID No: 222, SEQ ID No: 224, SEQ ID No: 226, SEQ ID No: 228, SEQ ID No: 230, SEQ ID No: 232, SEQ ID No: 234, SEQ ID No: 236, SEQ ID No: 238, SEQ ID No: 240, SEQ ID No: 242, SEQ ID No: 244, SEQ ID No: 246, SEQ ED No: 248, SEQ ID No: 250, SEQ ED No: 252, SEQ ID No: 254, SEQ ED No: 256, SEQ ID No: 258, SEQ ED No: 260, SEQ ID No: 262, SEQ ED No: 264, SEQ ID No: 266, SEQ ID No: 268, SEQ ID No: 270, SEQ ED No: 272, SEQ ID No: 274, SEQ ED No: 276, SEQ ID No: 278, SEQ ID No: 280, SEQ ID No: 282, SEQ ED No: 284, SEQ ED No: 286, SEQ ED No: 288, SEQ ED No: 290, SEQ ID No: 292, SEQ ED No: 294, SEQ ID No: 296, SEQ ID No: 298, SEQ ED No:300, SEQ ED No: 302, SEQ ED No: 304, SEQ ED No: 306, SEQ ID No: 308, SEQ ED No: 310, SEQ ED No: 312, SEQ ED No: 314, SEQ ED No: 316, SEQ ED No: 318, SEQ ED No: 320, SEQ ED No: 322, SEQ ED No: 324, SEQ ED No: 326, SEQ ED No: 328, SEQ ED No: 330, SEQ ED No: 332, SEQ ID No: 334, SEQ ED No: 336, SEQ ED No: 338, SEQ ED No: 340, SEQ ED No: 342, SEQ ED No: 344, SEQ ID No: 346, SEQ ED No: 348, SEQ ED No: 350, SEQ ED No: 352, SEQ ED No: 354, SEQ ED No: 356, SEQ ED No: 358, SEQ ED No: 360, SEQ ED No: 362, SEQ ED No: 364, SEQ ED No: 366, SEQ ID No: 368, SEQ ID No: 370, SEQ ED No: 372, SEQ ED No: 374, SEQ ED No: 376, SEQ ID No: 378, SEQ ED No: 380, SEQ ID No: 382, SEQ ID No: 384, SEQ ED No: 386, SEQ ID No: 388, SEQ ED No: 390, SEQ ED No: 392, SEQ ED No: 394, SEQ ED No: 396, SEQ ED No: 398, 400, SEQ ED No: 402, SEQ ID No: 404, SEQ ED No: 406, SEQ ED No: 408, SEQ ED No: 410, SEQ ED No: 412, SEQ ID No: 414, SEQ ED No: 416, SEQ ED No: 418, SEQ ED No: 420, SEQ ED No: 422, SEQ ED No: 424, SEQ ED No: 426, SEQ ED No: 428, SEQ ED No: 430, SEQ ED No: 432, SEQ ID No: 434, SEQ ID No: 436, SEQ ED No: 438, SEQ ID No: 440, SEQ ED No: 442, SEQ ED No: 444, SEQ ED No: 446, SEQ ED No: 448, SEQ ED No: 450, SEQ ID No: 452, SEQ ED No: 454, SEQ ID No: 456, SEQ ED No: 458, SEQ ED No: 460, SEQ ED No: 462, SEQ ID No: 464, SEQ ED No: 466, SEQ ED No: 468, SEQ ED No: 470, SEQ ED No: 472, SEQ ID No: 474, SEQ ED No: 476, SEQ ID No: 478, SEQ ID No: 480, SEQ ID No: 482, SEQ ID No: 484, SEQ ID No: 486, SEQ ED No: 488, SEQ ID No: 490, SEQ ED No: 492, SEQ ED No: 494, SEQ ID No: 496, SEQ ED No: 498, 500, SEQ DD No: 502, SEQ ID No: 504, SEQ ED No: 506, SEQ ID No: 508, SEQ ED No: 510, SEQ ED No: 512, SEQ ED No: 514, SEQ ED No: 516, SEQ ED No: 518, SEQ ID No: 520, SEQ ID No: 522, SEQ ID No: 524, SEQ ID No: 526, SEQ ED No: 528, SEQ ED No: 530, SEQ ED No: 532, SEQ ED No: 534, SEQ ED No: 536, SEQ ED No: 538, SEQ ED No: 540, SEQ ID No: 542, SEQ ED No: 544, SEQ ID No: 546, SEQ ED No: 548, SEQ ED No: 550, SEQ ED No: 552, SEQ ED No: 554, SEQ ED No: 556, SEQ ED No: 558, SEQ ED No: 560, SEQ ID No: 562, SEQ ED No: 564, SEQ ED No: 566, SEQ ED No: 568, SEQ ED No: 570, SEQ ID No: 572, SEQ ED No: 574, SEQ ID No: 576, SEQ ED No: 578, SEQ ID No: 580, SEQ ED No: 582, SEQ ID No: 584, SEQ ED No: 586, SEQ ID No: 588, SEQ ID No: 590, SEQ ED No: 592, SEQ ED No: 594, SEQ ID No: 596, SEQ ED No: 598, 600, SEQ ED No: 602, SEQ ED No: 604, SEQ ED No: 606, SEQ ED No: 608, SEQ ED No: 610, SEQ ED No: 612, SEQ ID No: 614, SEQ ED No: 616, SEQ ED No: 618, SEQ ED No: 620, SEQ ED No: 622, SEQ ED No: 624, SEQ ID No: 626, SEQ ED No: 628, SEQ ED No: 630, SEQ ED No: 632, SEQ ID No: 634, SEQ ED No: 636, SEQ ED No: 638, SEQ ED No: 640, SEQ ED No: 642, SEQ ED No: 644, SEQ ED No: 646, SEQ ID No: 648, SEQ ED No: 650, SEQ ID No: 652, SEQ ED No: 654, SEQ ED No: 656, SEQ ED No: 658, SEQ ID No: 660, SEQ ED No: 662, SEQ ID No: 664, SEQ ED No: 666, SEQ ED No: 668, SEQ ED No: 670, SEQ ID No: 672, SEQ ED No: 674, SEQ ED No: 676, SEQ ED No: 678, SEQ ED No: 680, SEQ ED No: 682, SEQ ED No: 684, SEQ ED No: 686, SEQ ED No: 688, SEQ ID No: 690, SEQ ED No: 692, SEQ ED No: 694, SEQ ID No: 696, SEQ ED No: 698, 700, SEQ ED No: 702, SEQ ED No: 704, SEQ ED No: 706, SEQ ED No: 708, SEQ ID No: 710, SEQ ED No: 712, SEQ ED No: 714, SEQ ID No: 716, SEQ ED No: 718, SEQ ID No: 720, SEQ ED No: 722, SEQ ED No: 724, SEQ ED No: 726, SEQ ID No: 728, SEQ ED No: 730, SEQ ID No: 732, SEQ ED No: 734, SEQ ID No: 736, SEQ ED No: 738, SEQ ED No: 740, SEQ ED No: 742, SEQ ED No: 744, SEQ ED No: 746, SEQ ED No: 748, SEQ ED No: 750, SEQ ED No: 752, SEQ DD No: 754, SEQ ED No: 756, SEQ ED No: 758, SEQ ED No: 760, SEQ ED No: 762, SEQ ED No: 764, SEQ ED No: 766, SEQ ED No: 768, SEQ ID No: 770, SEQ ED No: 772, SEQ ED No: 774, SEQ ED No: 776, SEQ ED No: 778, SEQ ED No: 780, SEQ ED No: 782, SEQ ED No: 784, SEQ ED No: 786, SEQ ED No: 788, SEQ ED No: 790, SEQ ID No: 792, SEQ ED No: 794, SEQ ID No: 796, SEQ ED No: 798, 800, SEQ ID No: 802, SEQ ID No: 804, SEQ ID No: 806, SEQ ID No: 808, SEQ ID No: 810, SEQ ID No: 812, SEQ ID No: 814, SEQ ID No: 816, SEQ ID No: 818, SEQ ID No: 820, SEQ ID No: 822, SEQ ID No: 824, SEQ ID No: 826, SEQ ID No: 828, SEQ ID No: 830, SEQ ID No: 832, SEQ ID No: 834, SEQ ED No: 836, SEQ ID No: 838, SEQ ID No: 840, SEQ ED No: 842, SEQ ED No: 844, SEQ ED No: 846, SEQ ED No: 848, SEQ ED No: 850, SEQ ED No: 852, SEQ ED No: 854, SEQ ED No: 856, SEQ ED No: 858, SEQ ED No: 860.

In some embodiments, the nucleic acid sequence comprises a nucleic acid sequence selected from : SEQ ID No: 1, SEQ ED No: 3, SEQ ED No: 5, SEQ ID No: 7, SEQ ID No: 9, SEQ ED No: 11, SEQ ID No: 13, SEQ ED No: 15, SEQ ID No: 17, SEQ ED No: 19, SEQ ED No: 21, SEQ ED No: 23, SEQ ED No: 25, SEQ ID No: 27, SEQ ED No: 29, SEQ ED No: 31, SEQ ED No: 33, SEQ ED No: 35, SEQ ID No: 37, SEQ ED No: 39, SEQ ED No: 41, SEQ ED No: 43, SEQ ED No: 45, SEQ ID No: 47, SEQ ID No: 49, SEQ ED No: 51, SEQ ED No: 53, SEQ ED No: 55, SEQ ID No: 56, SEQ ID No: 57, SEQ ED No: 59, SEQ ED No: 61, SEQ ED No: 63, SEQ ID No: 65, SEQ ID No: 67, SEQ ED No: 69, SEQ ED No: 71, SEQ ID No: 73, SEQ ID No: 75, SEQ ID No: 77, SEQ ED No: 79, SEQ ED No: 81, SEQ ED No: 83, SEQ ID No: 85, SEQ ID No: 87, SEQ ED No: 89, SEQ ED No: 91, SEQ ED No: 93, SEQ ID No: 95, SEQ ID No: 97, SEQ ED No: 99, SEQ ED No: 101, SEQ ED No: 103, SEQ ID No: 105, SEQ ED No: 107, SEQ ED No: 109, SEQ ED No: 1 11, SEQ ED No: 1 13, SEQ ED No: 115, SEQ ID No: 117, SEQ ED No: 119, SEQ ID No: 121 , SEQ ED No: 123, SEQ ED No: 125, SEQ ED No: 127, SEQ ED No: 129, SEQ ED No: 131, SEQ ED No: 133, SEQ ED No: 135, SEQ ED No: 137, SEQ ID No: 139, SEQ ED No: 141, SEQ ID No: 143, SEQ ID No: 145, SEQ ED No: 147, SEQ ED No: 149, SEQ ED No: 151, SEQ ED No: 153, SEQ ID No: 155, SEQ ED No: 157, SEQ ID No: 159, SEQ ED No: 161, SEQ ED No: 163, SEQ ED No: 165, SEQ ED No: 167, SEQ ED No: 169, SEQ ED No: 171, SEQ ED No: 173, SEQ ED No: 175, SEQ ED No: 177, SEQ ED No: 179, SEQ ED No: 181, SEQ ED No: 183, SEQ ED No: 185, SEQ ED No: 187, SEQ ED No: 189, SEQ ED No: 191, SEQ ID No: 193, SEQ ID No: 195, SEQ ID No: 197, SEQ ED No: 199, SEQ ED No: 201, SEQ ED No: 203, SEQ ID No: 205, SEQ ED No: 207, SEQ ID No: 209, SEQ ED No: 21 1, SEQ ID No: 213, SEQ ID No: 215, SEQ ID No: 217, SEQ ID No: 219, SEQ ED No: 221, SEQ ED No: 223, SEQ ED No: 225, SEQ ED No: 227, SEQ ED No: 229, SEQ ID No: 231, SEQ ED No: 233, SEQ ID No: 235. SEQ ED No: 237, SEQ ED No: 239, SEQ ID No: 241, SEQ ID No: 243, SEQ ID No: 245, SEQ ID No: 247, SEQ ID No: 249, SEQ ID No: 251, SEQ ID No: 253, SEQ ID No: 255, SEQ ID No: 257, SEQ ID No: 259, SEQ ID No: 261, SEQ ID No: 263, SEQ ID No: 265, SEQ ID No: 267, SEQ ID No: 269, SEQ ID No: 271, SEQ ID No: 273, SEQ ID No: 275, SEQ ID No: 277, SEQ ID No: 279, SEQ ID No: 281, SEQ ID No: 283, SEQ ID No: 285, SEQ ID No: 287, SEQ ID No: 289, SEQ ID No: 291, SEQ ID No: 293, SEQ ID No: 295, SEQ ID No: 297, SEQ ID No: 299, SEQ ID No: 301, SEQ ID No: 303, SEQ ID No: 305, SEQ ID No: 307, SEQ ID No: 309, SEQ ID No: 311, SEQ ED No: 313, SEQ ID No: 315, SEQ ID No: 317, SEQ ID No: 319, SEQ ID No: 321, SEQ ID No: 323, SEQ ID No: 325, SEQ ID No: 327, SEQ ID No: 329, SEQ ID No: 331, SEQ ED No: 333, SEQ ED No: 335, SEQ ED No: 337, SEQ ED No: 339, SEQ ED No: 341, SEQ ED No: 343, SEQ ID No: 345, SEQ ED No: 347, SEQ ID No: 349, SEQ D No: 351, SEQ ED No: 353, SEQ ED No: 355, SEQ ED No: 357, SEQ ED No: 359, SEQ ED No: 361, SEQ ED No: 363, SEQ ED No: 365, SEQ ID No: 367, SEQ ED No: 369, SEQ ID No: 371, SEQ ED No: 373, SEQ ED No: 375, SEQ ED No: 377, SEQ ED No: 379, SEQ ED No: 381, SEQ ID No: 383, SEQ ED No: 385, SEQ ED No: 387, SEQ ED No: 389, SEQ ED No: 391, SEQ ED No: 393, SEQ ED No: 395, SEQ ED No: 397, SEQ ED No: 399, SEQ ED No: 401, SEQ ED No: 403, SEQ ID No: 405, SEQ ED No: 407, SEQ ED No: 409, SEQ ED No: 411, SEQ ED No: 413, SEQ ED No: 415, SEQ ED No: 417, SEQ ED No: 419, SEQ ID No: 421, SEQ ED No: 423, SEQ ID No: 425, SEQ ED No: 427, SEQ ID No: 429, SEQ ED No: 431, SEQ ED No: 433, SEQ ED No: 435, SEQ ID No: 437, SEQ ED No: 439, SEQ ED No: 441, SEQ ID No: 443, SEQ ED No: 445, SEQ ID No: 447, SEQ ED No: 449, SEQ ED No: 451, SEQ ED No: 453, SEQ ED No: 455, SEQ ED No: 457, SEQ ED No: 459, SEQ ED No: 461, SEQ ID No: 463, SEQ ID No: 465, SEQ ED No: 467, SEQ ED No: 469, SEQ ED No: 471, SEQ ED No: 473, SEQ ED No: 475, SEQ ED No: 477, SEQ ID No: 479, SEQ ID No: 481, SEQ ED No: 483, SEQ ID No: 485, SEQ ED No: 487, SEQ ED No: 489, SEQ ED No: 491, SEQ ED No: 493, SEQ ID No: 495, SEQ ID No: 497, SEQ ED No: 499, SEQ ED No: 501, SEQ ED No: 503, SEQ ED No: 505, SEQ ED No: 507, SEQ ED No: 509, SEQ ED No: 511, SEQ ED No: 513, SEQ ED No: 515, SEQ ED No: 517, SEQ ID No: 519, SEQ ED No: 521, SEQ ID No: 523, SEQ ED No: 525, SEQ ED No: 527, SEQ ED No: 529, SEQ ED No: 531, SEQ ED No: 533, SEQ ID No: 535, SEQ ED No: 537, SEQ ID No: 539, SEQ ED No: 541, SEQ ED No: 543, SEQ ED No: 545, SEQ ED No: 547, SEQ ED No: 549, SEQ ID No: 551 , SEQ ED No: 553, SEQ ID No: 555, SEQ ID No: 557, SEQ ID No: 559, SEQ ID No: 561, SEQ ID No: 563, SEQ ED No: 565, SEQ ID No: 567, SEQ ED No: 569, SEQ ED No: 571, SEQ ID No: 573, SEQ D No: 575, SEQ ED No: 577, SEQ ED No: 579, SEQ ED No: 581, SEQ ED No: 583, SEQ ED No: 585, SEQ ED No: 587, SEQ ED No: 589, SEQ ED No: 591, SEQ ED No: 593, SEQ ID No: 595, SEQ ED No: 597, SEQ ID No: 599, SEQ ED No: 601, SEQ ED No: 603, SEQ ED No: 605, SEQ ED No: 607, SEQ ED No: 609, SEQ ID No: 611, SEQ ED No: 613, SEQ ID No: 615, SEQ ED No: 617, SEQ ED No: 619, SEQ ED No: 621, SEQ ED No: 623, SEQ ED No: 625, SEQ ED No: 627, SEQ ED No: 629, SEQ ED No: 631, SEQ ID No: 633, SEQ ED No: 635, SEQ ID No: 637, SEQ ED No: 639, SEQ ED No: 641, SEQ ED No: 643, SEQ ED No: 645, SEQ ED No: 647, SEQ ID No: 649, SEQ ID No: 651, SEQ ID No: 653, SEQ ED No: 655, SEQ ED No: 657, SEQ ED No: 659, SEQ ID No: 661, SEQ ED No: 663, SEQ ED No: 665, SEQ ED No: 667, SEQ ED No: 669, SEQ ED No: 671, SEQ ED No: 673, SEQ ID No: 675, SEQ ED No: 677, SEQ ED No: 679, SEQ ED No: 681, SEQ ED No: 683, SEQ ED No: 685, SEQ ID No: 687, SEQ ED No: 689, SEQ ID No: 691, SEQ ED No: 693, SEQ ID No: 695, SEQ ID No: 697, SEQ ED No: 699, SEQ ED No: 701, SEQ ID No: 703, SEQ ED No: 705, SEQ ED No: 707, SEQ ED No: 709, SEQ ED No: 71 1, SEQ ID No: 713, SEQ ID No: 715, SEQ ED No: 717, SEQ ED No: 719, SEQ ED No: 721, SEQ ID No: 723, SEQ ID No: 725, SEQ ED No: 727, SEQ ID No: 729, SEQ ED No: 731, SEQ ED No: 733, SEQ ED No: 735, SEQ ED No: 737, SEQ ED No: 739, SEQ ED No: 741, SEQ ED No: 743, SEQ ED No: 745, SEQ ID No: 747, SEQ ED No: 749, SEQ ID No: 751, SEQ ED No: 753, SEQ ED No: 755, SEQ ED No: 757, SEQ ED No: 759, SEQ ED No: 761, SEQ ID No: 763, SEQ ED No: 765, SEQ ID No: 767, SEQ ED No: 769, SEQ ED No: 771, SEQ ED No: 773, SEQ ED No: 775, SEQ ID No: 777, SEQ ED No: 779, SEQ ED No: 781 , SEQ ED No: 783, SEQ ID No: 785, SEQ ED No: 787, SEQ ED No: 789, SEQ ED No: 791, SEQ ED No: 793, SEQ ED No: 795, SEQ ID No: 797, SEQ ED No: 799, SEQ ID No: 801, SEQ ED No: 803, SEQ ID No: 805, SEQ ID No: 807, SEQ ED No: 809, SEQ ED No: 81 1, SEQ ED No: 813, SEQ ED No: 815, SEQ ED No: 817, SEQ ED No: 819, SEQ ID No: 821 , SEQ ID No: 823, SEQ ID No: 825, SEQ ID No: 827, SEQ ED No: 829, SEQ ED No: 831, SEQ ED No: 833, SEQ ED No: 835, SEQ ED No: 837, SEQ ID No: 839, SEQ ED No: 841, SEQ ED No: 843, SEQ ED No: 845, SEQ ED No: 847, SEQ ID No: 849, SEQ ED No: 851, SEQ ED No: 853, SEQ ID No: 855, SEQ ED No: 857, SEQ ED No: 859. [024] In some embodiments, the present invention comprises nucleic acid sequences that are folly complementary to any of the nucleic acid sequences described above.

[025] In some embodiments, the present invention comprises an isolated protein comprising an amino acid sequence encoded by any of the nucleic acid molecules described above.

[026] In some embodiments, the present invention comprises an isolated fusion protein comprising an isolated protein of the present invention fused to a protein comprising an amino acid sequence that is heterologous to the isolated protein.

[027] In some embodiments, the present invention comprises an isolated antibody or antigen binding fragment thereof that selectively binds to a protein of the present invention.

[028] In some embodiments, the present invention comprises a kit for processing animal hides comprising at least one isolated protein of the present invention.

[029] In some embodiments, the present invention comprises a detergent comprising at least one isolated protein of the present invention.

[030] In some embodiments, the present invention comprises a composition for the tenderizing of meat comprising at least one isolated protein of the present invention.

[031] In some embodiments, the present invention comprises a composition for the processing of cheese comprising at least one isolated protein of the present invention.

[032] In some embodiments, the present invention comprises a composition for increasing bread volume comprising at least one isolated protein of the present invention.

[033] In some embodiments, the present invention comprises a composition for increasing the protein yield in the production of rice bran protein comprising at least one isolated protein of the present invention.

[034] In some embodiments, the present invention comprises a composition for the reduction of acrylamide in food products comprising at least one isolated protein of the present invention.

[035] In some embodiments, the present invention comprises a composition for the processing of proteins comprising at least one isolated protein of the present invention.

[036] In some embodiments, the present invention comprises a pharmaceutical composition for the treatment of ischemic stroke comprising at least one isolated protein of the present invention.

[037] In some embodiments, the present invention comprises a pharmaceutical composition for the debridement of wounds comprising at least one isolated protein of the present invention. [038] In some embodiments, the present invention comprises a pharmaceutical composition for the treatment inflammation comprising at least one isolated protein of the present invention.

[039] In some embodiments, the present invention comprises a pharmaceutical composition for the treatment of sepsis comprising at least one isolated protein of the present invention.

[040] In some embodiments, the present invention comprises a pharmaceutical composition for the reduction of fine wrinkles of the skin comprising at least one isolated protein of the present invention.

[041] In some embodiments, the present invention comprises a detergent comprising at least one isolated protein of the present invention.

[042] In some embodiments, the present invention comprises a composition for the degradation of a lignocellulosic material comprising at least one isolated protein of the present invention.

[043] In some embodiments, the present invention comprises a recombinant nucleic acid molecule comprising an isolated nucleic acid molecule of the present invention, operatively linked to at least one expression control sequence. In some embodiments, the recombinant nucleic acid molecule comprises an expression vector. In some embodiments, the recombinant nucleic acid molecule comprises a targeting vector.

[044] In some embodiments, the present invention comprises an isolated host cell transfected with a nucleic acid molecule of the present invention. In some embodiments, the host cell is a fungus. In some embodiments, the host cell is a filamentous fungus. In some embodiments, the filamentous fungus is from a genus selected from the group consisting of: Cfaysosporium, Thielavia Thermomyces, Thermoascus, Neurospora, Aureobasidiiim, Filibasidium, Piromyces, Corynascus, Cryptococcus, Acremonium, Talaromyces, Tolypocladium, Scytalidium, Schizophyllum, Sporotrichum, Penicillium, Gibberella, Myceliophthora, Mucor, Aspergillus, Fusarium, Humicola, and Trichoderma, and anamorphs and teleomorphs thereof. In some embodiments, the host cell is a bacterium.

[045] In some embodiments, the present invention comprises an oligonucleotide consisting essentially of at least 12 consecutive nucleotides of a nucleic acid sequence selected from SEQ ID No: 1, SEQ ID No: 3, SEQ ID No: 5, SEQ ID No: 7, SEQ ID No: 9, SEQ ID No: 11, SEQ ID No: 13, SEQ ID No: 15, SEQ ID No: 17, SEQ ID No: 19, SEQ ED No: 21, SEQ ED No: 23, SEQ ED No: 25, SEQ ID No: 27, SEQ ID No: 29,

SEQ ED No: 31, SEQ ED No: 33, SEQ ED No: 35, SEQ ID No: 37, SEQ ID No: 39,

SEQ ID No: 41, SEQ ED No: 43, SEQ ED No: 45, SEQ ID No: 47, SEQ ID No: 49,

SEQ ED No: 51, SEQ ID No: 53, SEQ ED No: 55, SEQ ID No: 56, SEQ ID No: 57,

SEQ ED No: 59, SEQ ED No: 61, SEQ ED No: 63, SEQ ID No: 65, SEQ ID No: 67,

SEQ ED No: 69, SEQ ED No: 71, SEQ ED No: 73, SEQ ID No: 75, SEQ ID No: 77,

SEQ ED No: 79, SEQ ED No: 81, SEQ ED No: 83, SEQ ID No: 85, SEQ ID No: 87,

SEQ ED No: 89, SEQ ED No: 91, SEQ ED No: 93, SEQ ID No: 95, SEQ ID No: 97,

SEQ ED No: 99, SEQ ED No: 101, SEQ ED No: 103, SEQ ED No: 105, SEQ ED No:

107, SEQ ED No: 109, SEQ ED No: 11 1, SEQ ED No: 1 13, SEQ ED No: 115, SEQ ED

No: 117, SEQ ED No: 119, SEQ ID No: 121, SEQ ED No: 123, SEQ ID No: 125, SEQ ED No: 127, SEQ ID No: 129, SEQ ED No: 131, SEQ ED No: 133, SEQ ED No: 135, SEQ ED No: 137, SEQ ID No: 139, SEQ ED No: 141, SEQ ID No: 143, SEQ ED No: 145, SEQ ED No: 147, SEQ ED No: 149, SEQ ED No: 151, SEQ ED No: 153, SEQ ID No: 155, SEQ ED No: 157, SEQ ID No: 159, SEQ ED No: 161, SEQ ED No: 163, SEQ ED No: 165, SEQ ED No: 167, SEQ ED No: 169, SEQ ED No: 171, SEQ ED No: 173, SEQ ED No: 175, SEQ ED No: 177, SEQ ED No: 179, SEQ ID No: 181, SEQ ED No: 183, SEQ ED No: 185, SEQ ED No: 187, SEQ ED No: 189, SEQ ED No: 191, SEQ ID No: 193, SEQ ED No: 195, SEQ ID No: 197, SEQ ED No: 199, SEQ ID No: 201, SEQ ED No: 203, SEQ ED No: 205, SEQ ID No: 207, SEQ ID No: 209, SEQ ED No: 211, SEQ ED No: 213, SEQ ID No: 215, SEQ ED No: 217, SEQ ID No: 219, SEQ ED No: 221, SEQ ED No: 223, SEQ ED No: 225, SEQ ED No: 227, SEQ ED No: 229, SEQ ID No: 231, SEQ ED No: 233, SEQ ID No: 235. SEQ ED No: 237, SEQ ED No: 239, SEQ ED No: 241, SEQ ED No: 243, SEQ ED No: 245, SEQ ED No: 247, SEQ ED No: 249, SEQ ED No: 251, SEQ ED No: 253, SEQ ED No: 255, SEQ ED No: 257, SEQ ED No: 259, SEQ ED No: 261, SEQ ED No: 263, SEQ ED No: 265, SEQ ED No: 267, SEQ ID No: 269, SEQ ED No: 271, SEQ ID No: 273, SEQ ED No: 275, SEQ ED No: 277, SEQ ED No: 279, SEQ ED No: 281, SEQ ED No: 283, SEQ ED No: 285, SEQ ID No: 287, SEQ ED No: 289, SEQ ED No: 291, SEQ ED No: 293, SEQ ID No: 295, SEQ ED No: 297, SEQ ED No: 299, SEQ ED No: 301, SEQ ED No: 303, SEQ ED No: 305, SEQ ID No: 307, SEQ ED No: 309, SEQ ID No: 31 1, SEQ ED No: 313, SEQ ID No: 315, SEQ ED No: 317, SEQ ED No: 319, SEQ ED No: 321, SEQ ED No: 323, SEQ ED No: 325, SEQ ED No: 327, SEQ ID No: 329, SEQ ED No: 331, SEQ ID No: 333, SEQ ED No: 335, SEQ ID No: 337, SEQ ID No: 339, SEQ ID No: 341, SEQ ID No: 343, SEQ ID No: 345, SEQ ID No: 347, SEQ ID No: 349, SEQ ID No: 351, SEQ ID No: 353, SEQ ID No: 355, SEQ ID No: 357, SEQ ID No: 359, SEQ ED No: 361, SEQ ED No: 363, SEQ ED No: 365, SEQ ID No: 367, SEQ ED No: 369, SEQ ID No: 371, SEQ ED No: 373, SEQ ED No: 375, SEQ ED No: 377, SEQ ED No: 379, SEQ ED No: 381, SEQ ID No: 383, SEQ ED No: 385, SEQ ID No: 387, SEQ ED No: 389, SEQ ED No: 391, SEQ ED No: 393, SEQ ED No: 395, SEQ ED No: 397, SEQ ED No: 399, SEQ ED No: 401, SEQ ED No: 403, SEQ ID No: 405, SEQ ID No: 407, SEQ ED No: 409, SEQ ED No: 411, SEQ ED No: 413, SEQ ED No: 415, SEQ ED No: 417, SEQ ID No: 419, SEQ ID No: 421, SEQ ED No: 423, SEQ ID No: 425, SEQ ED No: 427, SEQ ID No: 429, SEQ ED No: 431, SEQ ED No: 433, SEQ ED No: 435, SEQ ED No: 437, SEQ ED No: 439, SEQ ED No: 441, SEQ ID No: 443, SEQ ED No: 445, SEQ ID No: 447, SEQ ED No: 449, SEQ ED No: 451, SEQ ED No: 453, SEQ ED No: 455, SEQ ED No: 457, SEQ ID No: 459, SEQ ED No: 461, SEQ ID No: 463, SEQ ED No: 465, SEQ ED No: 467, SEQ ID No: 469, SEQ ED No: 471, SEQ ED No: 473, SEQ ID No: 475, SEQ ED No: 477, SEQ ED No: 479, SEQ ID No: 481, SEQ ID No: 483, SEQ ID No: 485, SEQ ED No: 487, SEQ ED No: 489, SEQ ED No: 491, SEQ ED No: 493, SEQ ED No: 495, SEQ ID No: 497, SEQ ED No: 499, SEQ ED No: 501, SEQ ED No: 503, SEQ ED No: 505, SEQ ED No: 507, SEQ ED No: 509, SEQ ED No: 51 1, SEQ ED No: 513, SEQ ED No: 515, SEQ ED No: 517, SEQ ID No: 519, SEQ ED No: 521, SEQ ID No: 523, SEQ ED No: 525, SEQ ED No: 527, SEQ ED No: 529, SEQ ED No: 531, SEQ ED No: 533, SEQ ID No: 535, SEQ ED No: 537, SEQ ID No: 539, SEQ ID No: 541, SEQ ID No: 543, SEQ ED No: 545, SEQ ID No: 547, SEQ ED No: 549, SEQ ED No: 551 , SEQ ED No: 553, SEQ ED No: 555, SEQ ED No: 557, SEQ ED No: 559, SEQ ID No: 561, SEQ ED No: 563, SEQ ED No: 565, SEQ ED No: 567, SEQ ED No: 569, SEQ ED No: 571, SEQ ID No: 573, SEQ ED No: 575, SEQ ED No: 577, SEQ ED No: 579, SEQ ED No: 581, SEQ ED No: 583, SEQ ED No: 585, SEQ ED No: 587, SEQ ED No: 589, SEQ ED No: 591, SEQ ED No: 593, SEQ ED No: 595, SEQ ED No: 597, SEQ ED No: 599, SEQ ED No: 601, SEQ ED No: 603, SEQ ED No: 605, SEQ ED No: 607, SEQ ID No: 609, SEQ ID No: 611, SEQ ED No: 613, SEQ ID No: 615, SEQ ED No: 617, SEQ ED No: 619, SEQ ED No: 621, SEQ ED No: 623, SEQ ED No: 625, SEQ ED No: 627, SEQ ID No: 629, SEQ ED No: 631, SEQ ID No: 633, SEQ ED No: 635, SEQ ID No: 637, SEQ ED No: 639, SEQ ED No: 641, SEQ ED No: 643, SEQ ED No: 645, SEQ ED No: 647, SEQ ID No: 649, SEQ ID No: 651, SEQ ID No: 653, SEQ ID No: 655, SEQ ID No: 657, SEQ ID No: 659, SEQ ED No: 661, SEQ ID No: 663, SEQ ID No: 665, SEQ ID No: 667, SEQ ID No: 669, SEQ ID No: 671, SEQ ID No: 673, SEQ ID No: 675, SEQ ID No: 677, SEQ ID No: 679, SEQ ID No: 681, SEQ ID No: 683, SEQ ID No: 685, SEQ ID No: 687, SEQ ID No: 689, SEQ ID No: 691, SEQ ID No: 693, SEQ ID No: 695, SEQ ID No: 697, SEQ ID No: 699, SEQ ID No: 701 , SEQ ID No: 703, SEQ ID No: 705, SEQ ID No: 707, SEQ ID No: 709, SEQ ID No: 71 1, SEQ ID No: 713, SEQ ID No: 715, SEQ ID No: 717, SEQ ED No: 719, SEQ ED No: 721, SEQ ED No: 723, SEQ ID No: 725, SEQ ED No: 727, SEQ ED No: 729, SEQ ED No: 731, SEQ ED No: 733, SEQ ID No: 735, SEQ ED No: 737, SEQ ED No: 739, SEQ ED No: 741, SEQ ED No: 743, SEQ ED No: 745, SEQ ID No: 747, SEQ ID No: 749, SEQ ID No: 751, SEQ ED No: 753, SEQ ID No: 755, SEQ ID No: 757, SEQ ED No: 759, SEQ ED No: 761, SEQ ID No: 763, SEQ ED No: 765, SEQ ID No: 767, SEQ ED No: 769, SEQ ED No: 771, SEQ ED No: 773, SEQ ED No: 775, SEQ ED No: 777, SEQ ED No: 779, SEQ ED No: 781, SEQ ED No: 783, SEQ ED No: 785, SEQ ED No: 787, SEQ ED No: 789, SEQ ED No: 791, SEQ ED No: 793, SEQ ED No: 795, SEQ ED No: 797, SEQ ED No: 799, SEQ ID No: 801, SEQ ED No: 803, SEQ ED No: 805, SEQ ED No: 807, SEQ ED No: 809, SEQ ED No: 81 1, SEQ ED No: 813, SEQ ED No: 815, SEQ ED No: 817, SEQ ED No: 819, SEQ ED No: 821 , SEQ ID No: 823, SEQ ID No: 825, SEQ ID No: 827, SEQ ED No: 829, SEQ ED No: 831, SEQ ED No: 833, SEQ ED No: 835, SEQ ID No: 837, SEQ ID No: 839, SEQ ED No: 841, SEQ ID No: 843, SEQ ED No: 845, SEQ ED No: 847, SEQ ED No: 849, SEQ ED No: 851, SEQ ED No: 853, SEQ ED No: 855, SEQ ED No: 857, SEQ ED No: 859 or the complement thereof.

[046] In some embodiments, the present invention comprises a kit comprising at least one oligonucleotide of the present invention.

[047] In some embodiments, the present invention comprises methods for producing a protein of the present invention, comprising culturing a cell that has been transfected with a nucleic acid molecule comprising a nucleic acid sequence encoding the protein, and expressing the protein with the transfected cell. In some embodiments, the present invention further comprises recovering the protein from the cell or from a culture comprising the cell.

[048] In some embodiments, the present invention comprises a genetically modified organism comprising components suitable for degrading proteins, wherein the organism has been genetically modified to express at least one protein of the present invention.

[049] In some embodiments, the genetically modified organism is a plant, alga, fungus or bacterium. In some embodiments, the fungus is yeast, mushroom or filamentous fungus. In some embodiments, the filamentous fungus is from a genus selected from the group consisting of: Chrysosporium, Thielavia Thermomyces, Thermoascus Neurospora, Aureobasidium, Filibasidium, Piromyces, Corynascus, Cryptococcus, Acremonium, Tolypocladium, Scytalidium, Schizophyllum, Sporotrichum, Penicillhim, Talaromyces, Gibberella, Myceliophthora, Mucor, Aspergillus, Fusarium, Humicola, and Trichoderma. In some embodiments, the filamentous fungus is selected from the group consisting of: Trichoderma reesei, Trichoderma harzanium, Chrysosporium lucknowense, Aspergillus niger, Aspergillus oryzae, Aspergillus japonicus, Penicill im canescens, Penicillium solitum, Penicillium funiculosum, Talaromyces flavus, Talaromyces emersonii and Myceliophthora thermophila.

[050] In some embodiments, the genetically modified organism has been genetically modified to express at least one additional enzyme. In some embodiments, the additional enzyme is an enzyme selected from the group consisting of: cellulase, glucosidase, xylanase, xylosidase, ligninase, glucuronidase, arabinofuranosidase, arabinase, arabinogalactanase, ferulic acid esterase, lipase, pectinase, glucomannase, amylase, laminarinase, xyloglucanase, galactanase, galactosidase, glucoamylase, pectate and pectin lyase, chitosanases, exo-p-D-glucosaminidase, cellobiose dehydrogenase, glucuronyl esterase and acetylxylan esterase.

[051] In some embodiments, the genetically modified organism is a plant.

[052] In some embodiments, the present invention comprises a recombinant enzyme isolated from a genetically modified microorganism of the present invention. In some embodiments the recombinant enzyme has been subjected to a purification step.

[053] In some embodiments, the present invention comprises a crude fermentation product produced by culturing the cells from the genetically modified organism of the present invention, wherein the crude fermentation product contains at least one protein of the present invention.

[054] In some embodiments, the present invention comprises a multi-enzyme composition comprising enzymes produced by a genetically modified organism of the present invention, and recovered therefrom. [055] In some embodiments, the present invention comprises a multi-enzyme composition comprising at least one protein of the present inventions, and at least one additional protein for degrading a protein or a fragment thereof that has biological activity.

[056] In some embodiments, the multi-enzyme composition of the present invention is a crude fermentation product that has been subjected to a purification step.

[057] In some embodiments, the present invention comprises a method for degrading a protein into lower molecular proteins or amino acids, comprising contacting protein with at least one isolated protein of the present invention.

[058] In some embodiments, the present invention comprises a method for metabolizing a protein into lower molecular proteins or amino acids, comprising contacting protein with at least one isolated protein of the present invention.

[059] In some embodiments, the present invention comprises a method of further comprising contacting a protein with at least one additional isolated protein comprising an amino acid sequence that is at least about 95% identical to an amino acid sequence selected from the group consisting of the amino acid sequences : SEQ ED NO: 2, SEQ ID No: 4, SEQ ID No: 6, SEQ ID No: 8, SEQ ED No: 10, SEQ ED No: 12, SEQ ED No: 14, SEQ ED No: 16, SEQ ID No: 18, SEQ ED No: 20, SEQ ID No: 22, SEQ ED No: 24, SEQ ID No: 26, SEQ ID No: 28, SEQ ID No: 30, SEQ ID No: 32, SEQ ED No: 34, SEQ ED No: 36, SEQ ED No: 38, SEQ ED No: 40, SEQ ED No: 42, SEQ ED No: 44, SEQ ID No: 46, SEQ ID No: 48, SEQ ED No: 50, SEQ ED No: 52, SEQ ID No: 54, SEQ ID No: 56, SEQ ED No: 58, SEQ ED No: 60, SEQ ED No: 62, SEQ ED No: 64, SEQ ED No: 66, SEQ ED No: 68, SEQ ED No: 70, SEQ ED No: 72, SEQ ID No: 74, SEQ ID No: 76, SEQ ED No: 78, SEQ ED No: 80, SEQ ED No: 82, SEQ ED No: 84, SEQ ID No: 86, SEQ ED No: 88, SEQ ED No: 90, SEQ ED No: 92, SEQ ED No: 94, SEQ ID No: 96, SEQ ED No: 98, SEQ ED No: 100, SEQ ED No: 102, SEQ ID No: 104, SEQ ED No: 106, SEQ ED No: 108, SEQ ED No: 1 10, SEQ ED No: 1 12, SEQ ED No: 1 14, SEQ ID No: 116, SEQ ID No: 1 18, SEQ ID No: 120, SEQ ED No: 122, SEQ ED No: 124, SEQ ED No: 126, SEQ ED No: 128, SEQ ED No: 130, SEQ ED No: 132, SEQ ED No: 134, SEQ ED No: 136, SEQ ED No: 138, SEQ ED No: 140, SEQ ED No: 142, SEQ ED No: 144, SEQ ED No: 146, SEQ ED No: 148, SEQ ED No: 150, SEQ ED No: 152, SEQ ID No: 154, SEQ ED No: 156, SEQ ID No: 158, SEQ ED No: 160, SEQ ED No: 162, SEQ ED No: 164, SEQ ED No: 166, SEQ ED No: 168, SEQ ED No: 170, SEQ ED No: 172, SEQ ED No: 174, SEQ ID No: 176, SEQ ED No: 178, SEQ ID No: 180, SEQ ED No: 182, SEQ ID No: 184, SEQ ID No: 186, SEQ ED No: 188, SEQ ID No: 190, SEQ ID No: 192, SEQ ID No: 194, SEQ ID No: 196, SEQ ID No: 198, SEQ ID No: 200, SEQ ID No: 202, SEQ ID No: 204, SEQ ID No: 206, SEQ ID No: 208, SEQ ID No: 210, SEQ ID No: 212, SEQ ID No: 214, SEQ ID No: 216, SEQ ID No: 218, SEQ ID No: 220, SEQ ID No: 222, SEQ ID No: 224, SEQ ID No: 226, SEQ ID No: 228, SEQ ID No: 230, SEQ ID No: 232, SEQ ID No: 234, SEQ ID No: 236, SEQ ID No: 238, SEQ ID No: 240, SEQ ID No: 242, SEQ ID No: 244, SEQ ID No: 246, SEQ ID No: 248, SEQ ID No: 250, SEQ ID No: 252, SEQ ID No: 254, SEQ ID No: 256, SEQ ID No: 258, SEQ ID No: 260, SEQ ID No: 262, SEQ ID No: 264, SEQ ED No: 266, SEQ ID No: 268, SEQ ED No: 270, SEQ ID No: 272, SEQ ID No: 274, SEQ ID No: 276, SEQ ED No: 278, SEQ ID No: 280, SEQ ID No: 282, SEQ ID No: 284, SEQ ED No: 286, SEQ ED No: 288, SEQ ID No: 290, SEQ ED No: 292, SEQ ID No: 294, SEQ ID No: 296, SEQ ED No: 298, SEQ ED No:300, SEQ ED No: 302, SEQ ED No: 304, SEQ ID No: 306, SEQ ED No: 308, SEQ ID No: 310, SEQ ID No: 312, SEQ ED No: 314, SEQ ED No: 316, SEQ ED No: 318, SEQ ED No: 320, SEQ ED No: 322, SEQ ED No: 324, SEQ ED No: 326, SEQ ID No: 328, SEQ ED No: 330, SEQ ID No: 332, SEQ ED No: 334, SEQ ED No: 336, SEQ ED No: 338, SEQ ED No: 340, SEQ ED No: 342, SEQ ID No: 344, SEQ ED No: 346, SEQ ID No: 348, SEQ ID No: 350, SEQ ED No: 352, SEQ ED No: 354, SEQ ED No: 356, SEQ ED No: 358, SEQ ED No: 360, SEQ ED No: 362, SEQ ED No: 364, SEQ ED No: 366, SEQ ED No: 368, SEQ ED No: 370, SEQ ED No: 372, SEQ ED No: 374, SEQ ED No: 376, SEQ ED No: 378, SEQ ED No: 380, SEQ ID No: 382, SEQ ED No: 384, SEQ ID No: 386, SEQ ED No: 388, SEQ ED No: 390, SEQ ED No: 392, SEQ ED No: 394, SEQ ID No: 396, SEQ ED No: 398, 400, SEQ ED No: 402, SEQ ED No: 404, SEQ ED No: 406, SEQ ED No: 408, SEQ ED No: 410, SEQ ID No: 412, SEQ ED No: 414, SEQ ID No: 416, SEQ ED No: 418, SEQ ED No: 420, SEQ ED No: 422, SEQ ED No: 424, SEQ ED No: 426, SEQ ED No: 428, SEQ ED No: 430, SEQ ED No: 432, SEQ ED No: 434, SEQ ED No: 436, SEQ ID No: 438, SEQ ED No: 440, SEQ ID No: 442, SEQ ED No: 444, SEQ ED No: 446, SEQ ED No: 448, SEQ ID No: 450, SEQ ED No: 452, SEQ ID No: 454, SEQ ED No: 456, SEQ ED No: 458, SEQ ED No: 460, SEQ ED No: 462, SEQ ED No: 464, SEQ ED No: 466, SEQ ED No: 468, SEQ ED No: 470, SEQ ID No: 472, SEQ ED No: 474, SEQ ID No: 476, SEQ ED No: 478, SEQ ED No: 480, SEQ ID No: 482, SEQ ED No: 484, SEQ ED No: 486, SEQ ID No: 488, SEQ ED No: 490, SEQ ED No: 492, SEQ ED No: 494, SEQ ED No: 496, SEQ ID No: 498, 500, SEQ ID No: 502, SEQ ID No: 504, SEQ ID No: 506, SEQ ID No: 508, SEQ ID No: 510, SEQ ID No: 512, SEQ ID No: 514, SEQ ID No: 516, SEQ ID No: 518, SEQ ID No: 520, SEQ ID No: 522, SEQ ID No: 524, SEQ ID No: 526, SEQ ID No: 528, SEQ ID No: 530, SEQ ED No: 532, SEQ ID No: 534, SEQ ID No: 536, SEQ ID No: 538, SEQ ID No: 540, SEQ ID No: 542, SEQ ID No: 544, SEQ ID No: 546, SEQ ID No: 548, SEQ ID No: 550, SEQ ID No: 552, SEQ ID No: 554, SEQ ID No: 556, SEQ ID No: 558, SEQ ID No: 560, SEQ ID No: 562, SEQ ID No: 564, SEQ ID No: 566, SEQ ID No: 568, SEQ ID No: 570, SEQ ID No: 572, SEQ ID No: 574, SEQ ID No: 576, SEQ ID No: 578, SEQ ID No: 580, SEQ ID No: 582, SEQ ID No: 584, SEQ ID No: 586, SEQ ID No: 588, SEQ ID No: 590, SEQ ID No: 592, SEQ ID No: 594, SEQ ID No: 596, SEQ ID No: 598, 600, SEQ ID No: 602, SEQ ID No: 604, SEQ ID No: 606, SEQ ID No: 608, SEQ ID No: 610, SEQ ID No: 612, SEQ ID No: 614, SEQ ID No: 616, SEQ ID No: 618, SEQ ID No: 620, SEQ ID No: 622, SEQ ID No: 624, SEQ ID No: 626, SEQ ID No: 628, SEQ ID No: 630, SEQ ID No: 632, SEQ ID No: 634, SEQ ID No: 636, SEQ ID No: 638, SEQ ID No: 640, SEQ ID No: 642, SEQ ID No: 644, SEQ ID No: 646, SEQ ID No: 648, SEQ ID No: 650, SEQ ID No: 652, SEQ ID No: 654, SEQ ID No: 656, SEQ ID No: 658, SEQ ID No: 660, SEQ ID No: 662, SEQ ID No: 664, SEQ ID No: 666, SEQ ID No: 668, SEQ ID No: 670, SEQ ID No: 672, SEQ ID No: 674, SEQ ID No: 676, SEQ ID No: 678, SEQ ID No: 680, SEQ ID No: 682, SEQ ID No: 684, SEQ ID No: 686, SEQ ID No: 688, SEQ ID No: 690, SEQ ID No: 692, SEQ ID No: 694, SEQ ID No: 696, SEQ ID No: 698, 700, SEQ ID No: 702, SEQ ID No: 704, SEQ ID No: 706, SEQ ID No: 708, SEQ ID No: 710, SEQ ID No: 712, SEQ ID No: 714, SEQ ID No: 716, SEQ ID No: 718, SEQ ID No: 720, SEQ ED No: 722, SEQ ID No: 724, SEQ ED No: 726, SEQ ID No: 728, SEQ ID No: 730, SEQ ED No: 732, SEQ ID No: 734, SEQ ED No: 736, SEQ ED No: 738, SEQ ED No: 740, SEQ ED No: 742, SEQ ED No: 744, SEQ ED No: 746, SEQ ED No: 748, SEQ ID No: 750, SEQ ID No: 752, SEQ ID No: 754, SEQ ID No: 756, SEQ ID No: 758, SEQ ED No: 760, SEQ ED No: 762, SEQ ID No: 764, SEQ ED No: 766, SEQ ID No: 768, SEQ ED No: 770, SEQ ED No: 772, SEQ ED No: 774, SEQ ED No: 776, SEQ ED No: 778, SEQ ED No: 780, SEQ ED No: 782, SEQ ED No: 784, SEQ ED No: 786, SEQ ED No: 788, SEQ ID No: 790, SEQ ED No: 792, SEQ ID No: 794, SEQ ED No: 796, SEQ ID No: 798, 800, SEQ ID No: 802, SEQ ID No: 804, SEQ ED No: 806, SEQ ID No: 808, SEQ ED No: 810, SEQ ED No: 812, SEQ ED No: 814, SEQ ED No: 816, SEQ ID No: 818, SEQ ID No: 820, SEQ ID No: 822, SEQ ID No: 824, SEQ ID No: 826, SEQ ID No: 828, SEQ ID No: 830, SEQ ID No: 832, SEQ ID No: 834, SEQ ID No: 836, SEQ ID No: 838, SEQ ID No: 840, SEQ ID No: 842, SEQ ID No: 844, SEQ ID No: 846, SEQ ID No: 848, SEQ ID No: 850, SEQ ID No: 852, SEQ ID No: 854, SEQ ID No: 856, SEQ ID No: 858, SEQ ID No: 860.

In another embodiments, the present invention comprises a method of further comprising contacting a protein with at least one additional isolated protein comprising an amino acid sequence that is at least about 95% identical to an amino acid sequence selected from the group consisting of the amino acid sequences of SEQ ED NO: 2, SEQ ED No: 4, SEQ ID No: 6, SEQ ID No: 8, SEQ ID No: 10, SEQ ED No: 12, SEQ ED No: 14, SEQ ED No: 16, SEQ ED No: 18, SEQ ED No: 20, SEQ ED No: 22, SEQ ID No: 24, SEQ ID No: 26, SEQ ED No: 28, SEQ ED No: 30, SEQ ID No: 32, SEQ ID No: 34, SEQ ED No: 36, SEQ ED No: 38, SEQ ED No: 40, SEQ ED No: 42, SEQ ID No: 44, SEQ ED No: 46, SEQ ED No: 48, SEQ ED No: 50, SEQ ED No: 52, SEQ ED No: 54, SEQ ED No: 56, SEQ ED No: 58, SEQ ED No: 60, SEQ ED No: 62, SEQ ID No: 64, SEQ ID No: 66, SEQ ED No: 68, SEQ ID No: 70, SEQ ID No: 72, SEQ ID No: 74, SEQ ED No: 76, SEQ ED No: 78, SEQ ED No: 80, SEQ ED No: 82, SEQ ID No: 84, SEQ ED No: 86, SEQ ED No: 88, SEQ ID No: 90, SEQ ID No: 92, SEQ ID No: 94, SEQ ID No: 96, SEQ ID No: 98, SEQ ED No: 100, SEQ ID No: 102, SEQ ID No: 104, SEQ ED No: 106, SEQ ID No: 108, SEQ D No: 1 10, SEQ ID No: 1 12, SEQ ED No: 1 14, SEQ ED No: 116, SEQ ED No: 1 18, SEQ ED No: 120, SEQ ED No: 122, SEQ ED No: 124, SEQ ED No: 126, SEQ ID No: 128, SEQ ED No: 130, SEQ ED No: 132, SEQ ED No: 134, SEQ ED No: 136, SEQ ED No: 138, SEQ ED No: 140, SEQ ED No: 142, SEQ ED No: 144, SEQ ID No: 146, SEQ ED No: 148, SEQ ID No: 150, SEQ ED No: 152, SEQ ED No: 154, SEQ ED No: 156, SEQ ED No: 158, SEQ ED No: 160, SEQ ID No: 162, SEQ ID No: 164, SEQ ED No: 166, SEQ ED No: 168, SEQ ED No: 170, SEQ ED No: 172, SEQ ED No: 174, SEQ ED No: 176, SEQ ED No: 178, SEQ ED No: 180, SEQ ED No: 182, SEQ ID No: 184, SEQ ED No: 186, SEQ ED No: 188, SEQ ED No: 190, SEQ ED No: 192, SEQ ED No: 194, SEQ ED No: 196, SEQ ID No: 198, SEQ ID No: 200, SEQ ED No: 202, SEQ ID No: 204, SEQ ED No: 206, SEQ ED No: 208, SEQ ED No: 210, SEQ ED No: 212, SEQ ED No: 214, SEQ ID No: 216, SEQ ID No: 218, SEQ ED No: 220, SEQ ID No: 222, SEQ ID No: 224, SEQ ID No: 226, SEQ ED No: 228, SEQ ED No: 230, SEQ ED No: 232, SEQ ED No: 234, SEQ ID No: 236, SEQ ID No: 238, SEQ ID No: 240, SEQ ID No: 242, SEQ ID No: 244, SEQ ID No: 246, SEQ ID No: 248, SEQ ID No: 250, SEQ ID No: 252, SEQ ID No: 254, SEQ ID No: 256, SEQ ID No: 258, SEQ ID No: 260, SEQ ID No: 262, SEQ ID No: 264, SEQ ID No: 266, SEQ ID No: 268, SEQ ID No: 270, SEQ ID No: 272, SEQ ID No: 274, SEQ ID No: 276, SEQ ID No: 278, SEQ ID No: 280, SEQ ID No: 282, SEQ ID No: 284, SEQ ID No: 286, SEQ ID No: 288, SEQ ID No: 290, SEQ ID No: 292, SEQ ID No: 294, SEQ ID No: 296, SEQ ID No: 298, SEQ ID No:300, SEQ ID No: 302, SEQ ID No: 304, SEQ ID No: 306, SEQ ID No: 308, SEQ ID No: 310, SEQ ID No: 312, SEQ ID No: 314, SEQ ID No: 316, SEQ ID No: 318, SEQ ID No: 320, SEQ ID No: 322, SEQ ID No: 324, SEQ ID No: 326, SEQ ID No: 328, SEQ ID No: 330, SEQ ID No: 332, SEQ ID No: 334, SEQ ID No: 336, SEQ ID No: 338, SEQ ID No: 340, SEQ ID No: 342, SEQ ID No: 344, SEQ ID No: 346, SEQ ID No: 348, SEQ ID No: 350, SEQ ID No: 352, SEQ ID No: 354, SEQ ID No: 356, SEQ ID No: 358, SEQ ID No: 360, SEQ ID No: 362, SEQ ID No: 364, SEQ ID No: 366, SEQ ID No: 368, SEQ ID No: 370, SEQ ID No: 372, SEQ ID No: 374, SEQ ID No: 376, SEQ ID No: 378, SEQ ID No: 380, SEQ ID No: 382, SEQ ID No: 384, SEQ ID No: 386, SEQ ID No: 388, SEQ ID No: 390, SEQ ID No: 392, SEQ ID No: 394, SEQ ID No: 396, SEQ ID No: 398, 400, SEQ ED No: 402, SEQ ID No: 404, SEQ ID No: 406, SEQ ID No: 408, SEQ ID No: 410, SEQ ID No: 412, SEQ ID No: 414, SEQ ID No: 416, SEQ ID No: 418, SEQ ID No: 420, SEQ ID No: 422, SEQ ID No: 424, SEQ ID No: 426, SEQ ID No: 428, SEQ ID No: 430, SEQ ID No: 432, SEQ ID No: 434, SEQ ID No: 436, SEQ ID No: 438, SEQ ID No: 440, SEQ ID No: 442, SEQ ID No: 444, SEQ ID No: 446, SEQ ID No: 448, SEQ ID No: 450, SEQ ID No: 452, SEQ ID No: 454, SEQ ID No: 456, SEQ ID No: 458, SEQ ID No: 460, SEQ ID No: 462, SEQ ID No: 464, SEQ ID No: 466, SEQ ID No: 468, SEQ ID No: 470, SEQ ID No: 472, SEQ ID No: 474, SEQ ID No: 476, SEQ ID No: 478, SEQ ID No: 480, SEQ ID No: 482, SEQ ID No: 484, SEQ ID No: 486, SEQ ID No: 488, SEQ ID No: 490, SEQ ID No: 492, SEQ ID No: 494, SEQ ID No: 496, SEQ ID No: 498, 500, SEQ ID No: 502, SEQ ID No: 504, SEQ ID No: 506, SEQ ID No: 508, SEQ ID No: 510, SEQ ID No: 512, SEQ ID No: 514, SEQ ID No: 516, SEQ ID No: 518, SEQ ID No: 520, SEQ ED No: 522, SEQ ID No: 524, SEQ ID No: 526, SEQ ED No: 528, SEQ ID No: 530, SEQ ID No: 532, SEQ ED No: 534, SEQ ID No: 536, SEQ ID No: 538, SEQ ID No: 540, SEQ ID No: 542, SEQ ID No: 544, SEQ ED No: 546, SEQ ID No: 548, SEQ ID No: 550, SEQ ID No: 552, SEQ ID No: 554, SEQ ID No: 556, SEQ ID No: 558, SEQ ID No: 560, SEQ ID No: 562, SEQ ID No: 564, SEQ ID No: 566, SEQ ID No: 568, SEQ ID No: 570, SEQ ID No: 572, SEQ ID No: 574, SEQ ED No: 576, SEQ ID No: 578, SEQ ID No: 580, SEQ ID No: 582, SEQ ID No: 584, SEQ ID No: 586, SEQ ID No: 588, SEQ ID No: 590, SEQ ID No: 592, SEQ ID No: 594, SEQ ID No: 596, SEQ ID No: 598, 600, SEQ ID No: 602, SEQ ID No: 604, SEQ ID No: 606, SEQ ID No: 608, SEQ ID No: 610, SEQ ID No: 612, SEQ ID No: 614, SEQ ID No: 616, SEQ ID No: 618, SEQ ID No: 620, SEQ ID No: 622, SEQ ID No: 624, SEQ ID No: 626, SEQ ID No: 628, SEQ ID No: 630, SEQ ID No: 632, SEQ ID No: 634, SEQ ID No: 636, SEQ ID No: 638, SEQ ID No: 640, SEQ ID No: 642, SEQ ID No: 644, SEQ ID No: 646, SEQ ID No: 648, SEQ ID No: 650, SEQ ID No: 652, SEQ ID No: 654, SEQ ID No: 656, SEQ ID No: 658, SEQ ID No: 660, SEQ ID No: 662, SEQ ID No: 664, SEQ ID No: 666, SEQ ID No: 668, SEQ ID No: 670, SEQ ID No: 672, SEQ ID No: 674, SEQ ID No: 676, SEQ ID No: 678, SEQ ID No: 680, SEQ ID No: 682, SEQ ID No: 684, SEQ ID No: 686, SEQ ID No: 688, SEQ ID No: 690, SEQ ID No: 692, SEQ ID No: 694, SEQ ID No: 696, SEQ ID No: 698, 700, SEQ ID No: 702, SEQ ID No: 704, SEQ ID No: 706, SEQ ID No: 708, SEQ ID No: 710, SEQ ID No: 712, SEQ ID No: 714, SEQ ID No: 716, SEQ ID No: 718, SEQ ID No: 720, SEQ ID No: 722, SEQ ID No: 724, SEQ ID No: 726, SEQ ID No: 728, SEQ ID No: 730, SEQ ID No: 732, SEQ ID No: 734, SEQ ID No: 736, SEQ ID No: 738, SEQ ED No: 740, SEQ ID No: 742, SEQ ID No: 744, SEQ ID No: 746, SEQ ID No: 748, SEQ ID No: 750, SEQ ID No: 752, SEQ ED No: 754, SEQ ID No: 756, SEQ ID No: 758, SEQ ID No: 760, SEQ ID No: 762, SEQ ID No: 764, SEQ ID No: 766, SEQ DD No: 768, SEQ ID No: 770, SEQ ID No: 772, SEQ ID No: 774, SEQ ID No: 776, SEQ ID No: 778, SEQ ID No: 780, SEQ ID No: 782, SEQ ID No: 784, SEQ ID No: 786, SEQ ID No: 788, SEQ ID No: 790, SEQ ID No: 792, SEQ DD No: 794, SEQ ID No: 796, SEQ ID No: 798, 800, SEQ DD No: 802, SEQ DD No: 804, SEQ ID No: 806, SEQ DD No: 808, SEQ ID No: 810, SEQ DD No: 812, SEQ DD No: 814, SEQ ED No: 816, SEQ DD No: 818, SEQ ED No: 820, SEQ ED No: 822, SEQ DD No: 824, SEQ DD No: 826, SEQ ID No: 828, SEQ DD No: 830, SEQ ID No: 832, SEQ ED No: 834, SEQ DD No: 836, SEQ DD No: 838, SEQ DD No: 840, SEQ DD No: 842, SEQ ED No: 844, SEQ DD No: 846, SEQ ID No: 848, SEQ DD No: 850, SEQ ED No: 852, SEQ DD No: 854, SEQ DD No: 856, SEQ DD No: 858, SEQ DD No: 860., wherein the isolated protein is part of a multi-enzyme composition. [061] In some embodiments, the present invention comprises a method for degrading a protein into lower molecular weight proteins or amino acids, comprising contacting the protein with at least one multi-enzyme composition of the present invention.

[062] In some embodiments, the present invention comprises a method for metabolizing a protein into lower molecular weight proteins or amino acids, comprising contacting the protein with at least one multi-enzyme composition of the present invention.

[063] In some embodiments, the present invention comprises a feed additive comprising at least one protein of the present invention.

[064] In some embodiments, the present invention comprises a feed additive, wherein the utilizable protein content is higher than that of the feed material without the feed additive due to the enzymes of the present invention.

[065] In some embodiments, the present invention comprises a method of improving the performance of an animal which comprises administering to the animal the feed additive of the present invention.

[066] In some embodiments, the present invention comprises a method for improving the nutritional quality of an animal feed comprising adding the feed additive of the present invention to an animal feed.

[067] In some embodiments, the present invention comprises a method for removing stains from a fabric, comprising contacting the stained material with at least one isolated protein of the present invention. In some embodiments the fabric is carpet or clothing.

[068] In some embodiments, the present invention comprises a method for washing fabric, comprising contacting the fabric with at least one isolated protein of the present invention.

[069] In some embodiments, the present invention comprises a method for enhancing the cleaning ability of a detergent composition, comprising adding at least one isolated protein of the present invention to the detergent composition.

[070] In some embodiments, the present invention comprises a method for enhancing the cleaning ability of a detergent composition, comprising adding at least one multi- enzyme composition of the present invention to the detergent composition.

[071] In some embodiments, the present invention comprises a detergent composition, comprising at least one isolated protein of the present invention and at least one surfactant.

[072] In some embodiments, the present invention comprises a detergent composition, comprising at least one multi-enzyme composition of the present invention and at least one surfactant.

[073] In some embodiments, the present invention comprises a method for improving the nutritional quality of food comprising adding to the food at least one isolated protein of the present invention.

[074] In some embodiments, the present invention comprises a method for improving the nutritional quality of food comprising pretreating the food with at least one isolated protein of the present invention.

[075] In some embodiments, the present invention comprises a method for improving the nutritional quality of animal feed comprising adding to the animal feed at least one isolated protein of the present invention.

[076] In some embodiments, the present invention comprises a method for improving the nutritional quality of animal feed comprising pretreating the feed with at least one isolated protein of the present invention.

[077] In some embodiments, the present invention comprises a genetically modified organism comprising at least one nucleic acid sequence encoding al least one protein of the present invention, in which the activity of one or more of the proteins of the present invention is upregulated, the activity of one or more of the proteins of the present invention downregulated, or the activity of one or more of the proteins of the present invention is upregulated and the activity of one or more of the proteins of the present invention is downregulated.

[078] DETAILED DESCRIPTION OF THE INVENTION

[079] The present invention relates generally to proteins that play a role in the degradation of protein and nucleic acids encoding the same. In particular, the present invention relates to enzymes isolated from a filamentous fungal strain denoted herein as CI (Accession No. VKM F-3500-D), nucleic acids encoding the enzymes, and methods of producing and using the enzymes. The invention also provides compositions that include at least one of the enzymes described herein for uses including. The invention stems, in part, from the discovery of a variety of novel proteases produced by the CI fungus that exhibit high activity toward peptide bonds.

[080] The enzymes of the present invention may be used alone, or in combination with other enzymes, chemicals or biological materials. The enzymes of the present invention may be used for in vitro applications in which the enzymes or mixtures thereof are added to or mixed with the appropriate substrates to catalyze the desired reactions. Additionally, the enzymes of the present invention may be used for in vivo applications in which nucleic acid molecules encoding the enzymes are introduced into cells and are expressed therein to produce the enzymes and catalyze the desired reactions within the cells. Some embodiments may combine the in vitro applications with the in vivo applications.

In one aspect, the present invention includes proteins isolated from, or derived from the knowledge of enzymes from, a fungus such as Myceliophthora thermophila or a mutant or other derivative thereof, and more particularly, from the fungal strain denoted herein as CI (Accession No. VKM F-3500-D). M. thermophila has previously appeared in patent applications and in the literature as Chrysosporium lucknowense or Sporotrichum thermophile. Preferably, the proteins of the invention possess enzymatic activity. As described in U.S. Patent No. 6,015,707 or U.S. Patent No. 6,573,086 a strain called CI (Accession No. VKM F-3500-D), was isolated from samples of forest alkaline soil from Sola Lake, Far East of the Russian Federation. This strain was deposited at the All-Russian Collection of Microorganisms of Russian Academy of Sciences (VKM), Bakhurhina St. 8, Moscow, Russia, 113184, under the terms of the Budapest Treaty on the International Regulation of the Deposit of Microorganisms for the Purposes of Patent Procedure on August 29, 1996, as Chrysosporium lucknowense Garg 27K, VKM-F 3500 D. Various mutant strains of M. thermophila (C. lucknowense) CI have been constructed and these strains have also been deposited at the All-Russian Collection of Microorganisms of Russian Academy of Sciences (VKM), Bakhurhina St. 8, Moscow, Russia, 113184, under the terms of the Budapest Treaty on the International Regulation of the Deposit of Microorganisms for the Purposes of Patent Procedure on September 2, 1998 or at the Centraal Bureau voor Schimmelcultures (CBS), Uppsalalaan 8, 3584 CT Utrecht, The Netherlands for the purposes of Patent Procedure on December 5, 2007. For example, Strain CI was mutagenised by subjecting it to ultraviolet light to generate strain UV13-6 (Accession No. VKM F-3632 D). This strain was subsequently further mutated with N-methyl-N'- nitro-N-nitrosoguanidine to generate strain NG7C-19 (Accession No. VKM F-3633 D). This latter strain in turn was subjected to mutation by ultraviolet light, resulting in strain UV18-25 (Accession No. VKM F-3631 D). This strain in turn was again subjected to mutation by ultraviolet light, resulting in strain W1L (Accession No. CBS 122189), which was subsequently subjected to mutation by ultraviolet light, resulting in strain W1L#100L (Accession No. CBS122190). Strain CI was previously classified as a Chrysosporium lucknowense based on morphological and growth characteristics of the microorganism, as discussed in detail in U.S. Patent No. 6,015,707, U.S. Patent No. 6,573,086 and patent PCT NL2010/000045.

In certain embodiments of the present invention, a protein of the invention comprises, consists essentially of, or consists of an amino acid sequence selected from SEQ ID NO: 2, SEQ ID No: 4, SEQ ID No: 6, SEQ ID No: 8, SEQ ID No: 10, SEQ DD No: 12, SEQ ID No: 14, SEQ ID No: 16, SEQ ID No: 18, SEQ ID No: 20, SEQ ID No: 22, SEQ ID No: 24, SEQ ID No: 26, SEQ ID No: 28, SEQ ID No: 30, SEQ ID No: 32, SEQ ID No: 34, SEQ ID No: 36, SEQ ID No: 38, SEQ ID No: 40, SEQ ID No: 42, SEQ ID No: 44, SEQ ID No: 46, SEQ ID No: 48, SEQ ID No: 50, SEQ ID No: 52, SEQ ID No: 54, SEQ ID No: 56, SEQ ID No: 58, SEQ ID No: 60, SEQ ID No: 62, SEQ ID No: 64, SEQ ID No: 66, SEQ ID No: 68, SEQ ID No: 70, SEQ ID No: 72, SEQ ID No: 74, SEQ ID No: 76, SEQ ID No: 78, SEQ ID No: 80, SEQ ID No: 82, SEQ ID No: 84, SEQ ID No: 86, SEQ ID No: 88, SEQ ID No: 90, SEQ ID No: 92, SEQ ID No: 94, SEQ ID No: 96, SEQ ID No: 98, SEQ ID No: 100, SEQ ID No: 102, SEQ ID No: 104, SEQ ID No: 106, SEQ ID No: 108, SEQ ID No: 110, SEQ ID No: 112, SEQ ID No: 114, SEQ ID No: 116, SEQ ID No: 118, SEQ ID No: 120, SEQ ID No: 122, SEQ ID No: 124, SEQ ID No: 126, SEQ ID No: 128, SEQ ID No: 130, SEQ ID No: 132, SEQ ID No: 134, SEQ ID No: 136, SEQ ID No: 138, SEQ ID No: 140, SEQ ID No: 142, SEQ ID No: 144, SEQ ID No: 146, SEQ ID No: 148, SEQ ID No: 150, SEQ ID No: 152, SEQ ID No: 154, SEQ ID No: 156, SEQ ID No: 158, SEQ ID No: 160, SEQ ID No: 162, SEQ ID No: 164, SEQ ID No: 166, SEQ ID No: 168, SEQ ID No: 170, SEQ ID No: 172, SEQ ID No: 174, SEQ ID No: 176, SEQ ID No: 178, SEQ ID No: 180, SEQ ID No: 182, SEQ ID No: 184, SEQ ID No: 186, SEQ ID No: 188, SEQ ID No: 190, SEQ ID No: 192, SEQ ID No: 194, SEQ ID No: 196, SEQ ID No: 198, SEQ ID No: 200, SEQ ID No: 202, SEQ ID No: 204, SEQ ID No: 206, SEQ ID No: 208, SEQ ID No: 210, SEQ ID No: 212, SEQ ID No: 214, SEQ ID No: 216, SEQ ID No: 218, SEQ ID No: 220, SEQ ID No: 222, SEQ ID No: 224, SEQ ID No: 226, SEQ ID No: 228, SEQ ID No: 230, SEQ ID No: 232, SEQ ID No: 234, SEQ ID No: 236, SEQ ID No: 238, SEQ ID No: 240, SEQ ID No: 242, SEQ ID No: 244, SEQ ID No: 246, SEQ ID No: 248, SEQ ID No: 250, SEQ ID No: 252, SEQ ID No: 254, SEQ ID No: 256, SEQ ID No: 258, SEQ ID No: 260, SEQ ID No: 262, SEQ ID No: 264, SEQ ID No: 266, SEQ ID No: 268, SEQ ID No: 270, SEQ ID No: 272, SEQ ID No: 274, SEQ ID No: 276, SEQ ID No: 278, SEQ ID No: 280, SEQ ID No: 282, SEQ ID No: 284, SEQ ID No: 286, SEQ ID No: 288, SEQ ID No: 290, SEQ ID No: 292, SEQ ID No: 294, SEQ ID No: 296, SEQ ID No: 298, SEQ ID No:300, SEQ ID No: 302, SEQ ID No: 304, SEQ ID No: 306, SEQ ID No: 308, SEQ ID No: 310, SEQ ID No: 312, SEQ ID No: 314, SEQ ID No: 316, SEQ ID No: 318, SEQ ID No: 320, SEQ ID No: 322, SEQ ID No: 324, SEQ ID No: 326, SEQ ID No: 328, SEQ ID No: 330, SEQ ID No: 332, SEQ ID No: 334, SEQ ID No: 336, SEQ ID No: 338, SEQ ID No: 340, SEQ ID No: 342, SEQ ID No: 344, SEQ ID No: 346, SEQ ID No: 348, SEQ ID No: 350, SEQ ID No: 352, SEQ ID No: 354, SEQ ID No: 356, SEQ ID No: 358, SEQ ID No: 360, SEQ ID No: 362, SEQ ID No: 364, SEQ ID No: 366, SEQ ID No: 368, SEQ ID No: 370, SEQ ID No: 372, SEQ ID No: 374, SEQ ID No: 376, SEQ ID No: 378, SEQ ID No: 380, SEQ ID No: 382, SEQ ID No: 384, SEQ ID No: 386, SEQ ID No: 388, SEQ ID No: 390, SEQ ID No: 392, SEQ ID No: 394, SEQ ID No: 396, SEQ ID No: 398, 400, SEQ ID No: 402, SEQ ID No: 404, SEQ ID No: 406, SEQ ID No: 408, SEQ ID No: 410, SEQ ID No: 412, SEQ ID No: 414, SEQ ID No: 416, SEQ ID No: 418, SEQ ID No: 420, SEQ ID No: 422, SEQ ID No: 424, SEQ ID No: 426, SEQ ID No: 428, SEQ ID No: 430, SEQ ID No: 432, SEQ ID No: 434, SEQ ID No: 436, SEQ ID No: 438, SEQ ID No: 440, SEQ ID No: 442, SEQ ID No: 444, SEQ ID No: 446, SEQ ID No: 448, SEQ ID No: 450, SEQ ID No: 452, SEQ ID No: 454, SEQ ID No: 456, SEQ ID No: 458, SEQ ID No: 460, SEQ ID No: 462, SEQ ID No: 464, SEQ ID No: 466, SEQ ID No: 468, SEQ ID No: 470, SEQ ID No: 472, SEQ ID No: 474, SEQ ID No: 476, SEQ ID No: 478, SEQ ID No: 480, SEQ ID No: 482, SEQ ID No: 484, SEQ ID No: 486, SEQ ID No: 488, SEQ ID No: 490, SEQ ID No: 492, SEQ ID No: 494, SEQ ID No: 496, SEQ ID No: 498, 500, SEQ ID No: 502, SEQ ID No: 504, SEQ ID No: 506, SEQ ID No: 508, SEQ ID No: 510, SEQ ID No: 512, SEQ ID No: 514, SEQ ID No: 516, SEQ ID No: 518, SEQ ID No: 520, SEQ ID No: 522, SEQ ID No: 524, SEQ ID No: 526, SEQ ID No: 528, SEQ ID No: 530, SEQ ID No: 532, SEQ ID No: 534, SEQ ID No: 536, SEQ ID No: 538, SEQ ID No: 540, SEQ ID No: 542, SEQ ID No: 544, SEQ ID No: 546, SEQ ID No: 548, SEQ ID No: 550, SEQ ID No: 552, SEQ ID No: 554, SEQ ID No: 556, SEQ ID No: 558, SEQ ID No: 560, SEQ ID No: 562, SEQ ID No: 564, SEQ ID No: 566, SEQ ID No: 568, SEQ ID No: 570, SEQ ID No: 572, SEQ ID No: 574, SEQ ID No: 576, SEQ ID No: 578, SEQ ID No: 580, SEQ ID No: 582, SEQ ID No: 584, SEQ ID No: 586, SEQ ID No: 588, SEQ ID No: 590, SEQ ID No: 592, SEQ ID No: 594, SEQ ED No: 596, SEQ ID No: 598, 600, SEQ ID No: 602, SEQ ID No: 604, SEQ ED No: 606, SEQ ED No: 608, SEQ DD No: 610, SEQ ED No: 612, SEQ ID No: 614, SEQ ED No: 616, SEQ ID No: 618, SEQ ED No: 620, SEQ ED No: 622, SEQ ED No: 624, SEQ ED No: 626, SEQ ED No: 628, SEQ ID No: 630, SEQ ED No: 632, SEQ ID No: 634, SEQ ED No: 636, SEQ ED No: 638, SEQ ED No: 640, SEQ ED No: 642, SEQ ED No: 644, SEQ ID No: 646, SEQ ED No: 648, SEQ ED No: 650, SEQ ID No: 652, SEQ ED No: 654, SEQ ED No: 656, SEQ ED No: 658, SEQ ED No: 660, SEQ ED No: 662, SEQ ED No: 664, SEQ DD No: 666, SEQ ID No: 668, SEQ ED No: 670, SEQ ID No: 672, SEQ ED No: 674, SEQ ED No: 676, SEQ ED No: 678, SEQ ID No: 680, SEQ ED No: 682, SEQ ED No: 684, SEQ ED No: 686, SEQ ID No: 688, SEQ ID No: 690, SEQ ID No: 692, SEQ ID No: 694, SEQ ED No: 696, SEQ ED No: 698, 700, SEQ ED No: 702, SEQ ID No: 704, SEQ ED No: 706, SEQ ED No: 708, SEQ ED No: 710, SEQ ED No: 712, SEQ ID No: 714, SEQ ED No: 716, SEQ ED No: 718, SEQ ED No: 720, SEQ ED No: 722, SEQ ED No: 724, SEQ ID No: 726, SEQ ED No: 728, SEQ ED No: 730, SEQ ED No: 732, SEQ DD No: 734, SEQ ED No: 736, SEQ ED No: 738, SEQ ED No: 740, SEQ ED No: 742, SEQ ED No: 744, SEQ ED No: 746, SEQ ED No: 748, SEQ ED No: 750, SEQ ED No: 752, SEQ ED No: 754, SEQ ED No: 756, SEQ ID No: 758, SEQ ED No: 760, SEQ ED No: 762, SEQ ED No: 764, SEQ ED No: 766, SEQ ED No: 768, SEQ ED No: 770, SEQ ED No: 772, SEQ ID No: 774, SEQ ID No: 776, SEQ ID No: 778, SEQ ED No: 780, SEQ DD No: 782, SEQ DD No: 784, SEQ DD No: 786, SEQ ED No: 788, SEQ ED No: 790, SEQ ED No: 792, SEQ DD No: 794, SEQ DD No: 796, SEQ DD No: 798, 800, SEQ DD No: 802, SEQ ID No: 804, SEQ DD No: 806, SEQ DD No: 808, SEQ DD No: 810, SEQ DD No: 812, SEQ DD No: 814, SEQ ED No: 816, SEQ ED No: 818, SEQ DD No: 820, SEQ DD No: 822, SEQ DD No: 824, SEQ ID No: 826, SEQ DD No: 828, SEQ DD No: 830, SEQ ED No: 832, SEQ DD No: 834, SEQ DD No: 836, SEQ DD No: 838, SEQ DD No: 840, SEQ ID No: 842, SEQ ED No: 844, SEQ ID No: 846, SEQ ED No: 848, SEQ ED No: 850, SEQ ED No: 852, SEQ DD No: 854, SEQ DD No: 856, SEQ DD No: 858, SEQ ID No: 860.. The present invention also includes homologues or variants of any of the above sequences, including fragments and sequences having a given identity to any of the above sequences, wherein the homologue, variant, or fragment has at least one biological activity of the wild-type protein, as described herein.

[083] As used herein, "protease" refers to any protein that catalyzes the hydrolysis of proteins. They act to catalyze the processing of protein or the hydrolytic breakdown of proteins into peptides or amino acids. Proteases include endopeptidases and exopeptidases.

[084] "Endopeptidases" are proteolytic peptidases that break peptide bonds of nonterminal amino acids (i.e. within the molecule).

[085] "Exopeptidases" are proteolytic peptidases that break peptide bonds from their end- pieces.

[086] "Aspartic-type peptidases" are a family of protease enzymes that use an aspartate residue for catalysis of their peptide substrates.

[087] "Cysteine-type peptidases" are a family of protease enzymes that use a cysteine residue for catalysis of their peptide substrates.

[088] "Serine-type peptidases" are a family of protease enzymes that use a serine residue for catalysis of their peptide substrates.

[089] "Carboxypeptidases" are protease enzymes that hydrolyze (i.e. cleave) the peptide bond of an amino acid residue at the carboxy-terminal (C-terminal) end.

[090] "Aminopeptidases" are protease enzymes that hydrolyze (i.e. cleave) the peptide bond of an amino acid residue at the amino-terminal (N-terminal) end.

[091] "Metalloproteinases," or metalloproteases, are proteolytic enzymes whose catalytic mechanism require a divalent metal ion for their activity. The ion is usually coordinated by two to four side chains, and it is indispensable for the activity of the enzyme. The ion itself is also coordinated by a water molecule, which is also crucial for catalytical activity. There are two subgroups of metalloproteinases: metalloexopeptidases and metalloendopeptidases

[092] "Amidohydrolases" are a type of hydrolase that act upon amide bonds.

[093] "Asparaginases" are enzymes that catalyze the hydrolysis of asparagine to aspartic acid.

[094] "Signal-peptide peptidases" are a protease enzymes that catalyze the proteolysis of a specific peptide sequence (signal-peptide).

[095] Proteases may exhibit more than one activity described above.

[096] Proteases can also be combined with additional enzymes to create multi-enzyme compositions. Various types of enzymes such as carbohydrases, esterases, lipases or oxidoreductases can be combined with proteases.

[097] "Carbohydrase" refers to any protein that catalyzes the hydrolysis of carbohydrates.

"Glycoside hydrolase", "glycosyl hydrolase" or "glycosidase" refers to a protein that catalyzes the hydrolysis of the glycosidic bonds between carbohydrates or between a carbohydrate and a non-carbohydrate residue. Endoglucanases, cellobiohydrolases, β- glucosidases, a-glucosidases, xylanases, β-xylosidases, alpha- xylosidases, galactanases, a-galactosidases, β-galactosidases, a-amylases, glucoamylases, endo- arabinases, arabinofuranosidases, mannanases, β-mannosidases, pectinases, acetyl xylan esterases, acetyl mannan esterases, ferulic acid esterases, coumaric acid esterases, pectin methyl esterases, and chitosanases are examples of glycosidases.

[098] "Cellulase" refers to a protein that catalyzes the hydrolysis of l,4^-D-glycosidic linkages in cellulose (such as bacterial cellulose, cotton, filter paper, phosphoric acid swollen cellulose, Avicel^®); cellulose derivatives (such as carboxymethylcellulose and hydroxyethylcellulose); plant lignocellulosic materials, beta-D-glucans or xyloglucans. Cellulose is a linear beta-( 1-4) glucan consisting of anhydrocellobiose units. Endoglucanases, cellobiohydrolases, and β-glucosidases are examples of cellulases.

[099] "Endoglucanase" refers to a protein that catalyzes the hydrolysis of cellulose to oligosaccharide chains at random locations by means of an endoglucanase activity.

[0100] "Cellobiohydrolase" refers to a protein that catalyzes the hydrolysis of cellulose to cellobiose via an exoglucanase activity, sequentially releasing molecules of cellobiose from the reducing or non-reducing ends of cellulose or cello-oligosaccharides. " β - glucosidase" refers to an enzyme that catalyzes the conversion of cellobiose and oligosaccharides to glucose.

[0101] "Hemicellulase" refers to a protein that catalyzes the hydrolysis of hemicellulose, such as that found in lignocellulosic materials. Hemicelluloses are complex polymers, and their composition often varies widely from organism to organism, and from one tissue type to another. Hemicelluloses include a variety of compounds, such as xylans, arabinoxylans, xyloglucans, mannans, glucomannans, pectins, polygalacturonan, rhamnogalacturonan, xylogalacturonan and galacto(gluco)mannans. Hemicellulose can also contain glucan, which is a general term for beta-linked glucose residues. In general, a main component of hemicellulose is beta-l,4-linked xylose, a five carbon sugar. However, this xylose is often branched as beta- 1,3 linkages or beta- 1,2 linkages, and can be substituted with linkages to arabinose, galactose, mannose, glucuronic acid, or by esterification to acetic acid. The composition, nature of substitution, and degree of branching of hemicellulose is very different in dicotyledonous plants (dicots, i.e., plant whose seeds have two cotyledons or seed leaves such as lima beans, peanuts, almonds, peas, kidney beans) as compared to monocotyledonous plants (monocots; i.e., plants having a single cotyledon or seed leaf such as corn, wheat, rice, grasses, barley). In dicots, hemicellulose is comprised mainly of xyloglucans that are 1,4-beta-linked glucose chains with 1,6-alpha-linked xylosyl side chains. In monocots, including most grain crops, the principal components of hemicellulose are heteroxylans. These are primarily comprised of 1,4-beta-linked xylose backbone polymers with 1,2- or 1,3-alpha linkages to arabinose, linkage of galactose and mannose to arabinose or xylose in side chains, as well as xylose modified by ester-linked acetic acids. Also present are branched beta glucans comprised of 1,3- and 1,4-beta-linked glucosyl chains. In monocots, cellulose, heteroxylans and beta glucans are present in roughly equal amounts, each comprising about 15-25% of the dry matter of cell walls. Hemicellulolytic enzymes, i.e. hemicellulases, include both endo-acting and exo-acting enzymes, such as xylanases, β -xylosidases. alpha-xylosidases, galactanases, a-galactosidases, β-galactosidases, endo- arabinases, arabinofuranosidases, mannanases, β-mannosidases. Hemicellulases also include the accessory enzymes, such as acetylesterases, ferulic acid esterases, and coumaric acid esterases. Among these, xylanases and acetyl xylan esterases cleave the xylan and acetyl side chains of xylan and the remaining xylo-oligomers are unsubstituted and can thus be hydrolysed with β -xylosidase only. In addition, several less known side activities have been found in enzyme preparations which hydrolyze hemicellulose. Accordingly, xylanases, acetylesterases and β -xylosidases are examples of hemicellulases.

[0102] "Xylanase" specifically refers to an enzyme that hydrolyzes the β-1,4 bond in the xylan backbone, producing short xylooligosaccharides.

[0103] "D-Mannanase" or "endo-1,4- β -mannosidase" refers to a protein that hydrolyzes mannan-based hemicelluloses (mannan, glucomannan, galacto(gluco)mannan) and produces short β-l,4-mannooligosaccharides.

[0104] "Mannan endo-1,6- β -mannosidase" refers to a protein that hydrolyzes 1,6-D- mannosidic linkages in unbranched 1,6-mannans. [0105] "β-Mannosidase" (P-l,4-mannoside mannohydrolase; EC 3.2.1.25) refers to a protein that catalyzes the removal of β-D-mannose residues from the nonreducing ends of oligosaccharides.

[0106] "Galactanase", "endo- β -1,6-galactanse" or "arabinogalactan endo-1,4- β - galactosidase" refers to a protein that catalyzes the hydrolysis of endo-1,4- β -D- galactosidic linkages in arabinogalactans.

[0107] "Glucoamylase" refers to a protein that catalyzes the hydrolysis of terminal 1,4-linked -D-glucose residues successively from non-reducing ends of the glycosyl chains in starch with the release of β-D-glucose.

[0108] "β -hexosaminidase" or "β -N-acetylglucosaminidase" refers to a protein that catalyzes the hydrolysis of terminal N-acetyl-D-hexosamine residues in N-acetyl- β -D- hexosamines.

[0109] "a-L-arabinofuranosidase", "a-N-arabinofuranosidase", "a-arabinofuranosidase", "arabinosidase" or "arabinofuranosidase" refers to a protein that hydrolyzes arabinofuranosyl-containing hemicelluloses or pectins. Some of these enzymes remove arabinofuranoside residues from 0-2 or 0-3 single substituted xylose residues, as well as from 0-2 and/or 0-3 double substituted xylose residues. Some of these enzymes remove arabinose residues from arabinan oligomers.

[01 10] "Endo-arabinase" refers to a protein that catalyzes the hydrolysis of 1,5-a- arabinofuranosidic linkages in 1,5-arabinans.

[0111] "Exo-arabinase" refers to a protein that catalyzes the hydrolysis of 1,5-a-linkages in 1,5-arabinans or 1,5-a-L arabino-oligosaccharides, releasing mainly arabinobiose, although a small amount of arabinotriose can also be liberated.

[0112] "β -xylosidase" refers to a protein that hydrolyzes short l,4-p-D-xylooligomers into xylose.

[01 13] "Cellobiose dehydrogenase" refers to a protein that oxidizes cellobiose to cellobionolactone.

[01 14] "Chitosanase" refers to a protein that catalyzes the endohydrolysis of β -1,4-linkages between D-glucosamine residues in acetylated chitosan (i.e., deacetylated chitin).

[01 15] "Exo-polygalacturonase" refers to a protein that catalyzes the hydrolysis of terminal alpha 1,4-linked galacturonic acid residues from non-reducing ends thus converting polygalacturonides to galacturonic acid.

[0116] "Acetyl xylan esterase" refers to a protein that catalyzes the removal of the acetyl groups from xylose residues. "Acetyl mannan esterase" refers to a protein that catalyzes the removal of the acetyl groups from mannose residues, "ferulic esterase" or "ferulic acid esterase" refers to a protein that hydrolyzes the ester bond between the arabinose substituent group and ferulic acid. "Coumaric acid esterase" refers to a protein that hydrolyzes the ester bond between the arabinose substituent group and coumaric acid. Acetyl xylan esterases, ferulic acid esterases and pectin methyl esterases are examples of carbohydrate esterases.

[0117] "Pectate lyase" and "pectin lyases" refer to proteins that catalyze the cleavage of 1,4-cc- D-galacturonan by beta-elimination acting on polymeric and/or oligosaccharide substrates (pectates and pectins, respectively).

[0118] "Endo-1,3- β -glucanase" or "laminarinase" refers to a protein that catalyzes the cleavage of 1,3-linkages in β-D-glucans such as laminarin or lichenin. Laminarin is a linear polysaccharide made up of β -1 ,3-glucan with β -1 ,6-linkages.

[01 19] "Lichenase" refers to a protein that catalyzes the hydrolysis of lichenan, a linear, 1,3- 1,4-β-ϋ glucan.

[001] Rhamnogalacturonan is composed of alternating a -1,4-rhamnose and a-l,2-linked galacturonic acid, with side chains linked 1,4 to rhamnose. The side chains include Type I galactan, which is β-l,4-linked galactose with -1,3-Iinked arabinose substituents; Type Π galactan, which is P-l,3-l,6-linked galactoses (very branched) with arabinose substituents; and arabinan, which is β-l,5-linked arabinose with - 1,3-linked arabinose branches. The galacturonic acid substituents may be acetylated and/or methylated.

[0120] "Exo-rhamnogalacturonanase" refers to a protein that catalyzes the degradation of the rhamnogalacturonan backbone of pectin from the nonreducing end.

[0121] "Rhamnogalacturonan acetylesterase" refers to a protein that catalyzes the removal of the acetyl groups ester-linked to the highly branched rhamnogalacturonan (hairy) regions of pectin.

[0122] "Rhamnogalacturonan lyase" refers to a protein that catalyzes the degradation of the rhamnogalacturonan backbone of pectin via a β -elimination mechanism (see, e.g., Pages et al, J. Bacteriol. 185:4727-4733 (2003)).

[0123] "Alpha-rhamnosidase" refers to a protein that catalyzes the hydrolysis of terminal non- reducing oc-L-rhamnose residues in oc-L-rhamnosides.

[0124] Glycosidases (glycoside hydrolases; GH), a large family of enzymes that includes cellulases and hemicellulases, catalyze the hydrolysis of glycosidic linkages, predominantly in carbohydrates. Glycosidases such as the proteins of the present invention may be assigned to families on the basis of sequence similarities, and there are now over 100 different such families defined (see the CAZy (Carbohydrate Active EnZymes database) website, maintained by the Architecture of Fonction de Macromolecules Biologiques of the Centre National de la Recherche Scientifique, which describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds; Coutinho, P.M. & Henrissat, B. (1999) Carbohydrate-active enzymes: an integrated database approach. In "Recent Advances in Carbohydrate Bioengineering", H.J. Gilbert, G. Davies, B. Henrissat and B. Svensson eds., The Royal Society of Chemistry, Cambridge, pp. 3-12). Because there is a direct relationship between the amino acid sequence of a protein and its folding similarities, such a classification reflects the structural features of these enzymes and their substrate specificity. Such a classification system can help to reveal the evolutionary relationships between these enzymes and provide a convenient tool to determine information such as an enzyme's activity and function. Thus, enzymes assigned to a particular family based on sequence homology with other members of the family are expected to have similar enzymatic activities and related substrate specificities. CAZy family classifications also exist for glycosyltransferases (GT), polysaccharide lyases (PL), and carbohydrate esterases (CE). Likewise, sequence homology may be used to identify particular domains within proteins, such as carbohydrate binding modules (CBMs; also known as carbohydrate binding domains (CBDs), sometimes called cellulose binding domains).

[0125] In certain embodiments, the multi-enzyme products of the present invention may exhibit one or more of the enzyme activities belonging to the classes mentioned above.

[0126] Proteins of the present invention may also include homologues, variants, and fragments of the proteins disclosed herein. The protein fragments include, but are not limited to, fragments comprising a catalytic domain (CD). Protein fragments comprising a CD for each protein disclosed herein can be readily produced using standard techniques known in the art. In some embodiments, a protein fragment comprises a domain of a protein that has at least one biological activity of the full-length protein. Homologues or variants of proteins of the invention that have at least one biological activity of the full- length protein are described in detail below. [0127] As used herein, the phrase "biological activity" of a protein refers to any function(s) exhibited or performed by the protein that is ascribed to the naturally occurring form of the protein as measured or observed in vitro or in vivo. In certain embodiments, a protein fragment comprises a domain of a protein that has the catalytic activity of the full-length enzyme. Specific biological activities of the proteins of the invention, and structures within the proteins that are responsible for the activities, are described below.

[0128] Descriptions of the enzymes of the present invention are provided below, along with activities and homologies. Although each enzyme is expected to exhibit the activity exemplified below, enzymes of the present invention may also exhibit any of the enzyme activities or substrate specificities discussed throughout this disclosure.

[0129] Proteases of the Present Invention

[0130] Proteases represent a category of various enzymes, including the endopeptidases and exopeptidases, that catalyze the processing of proteins or the hydrolytic breakdown of proteins into peptides or amino acids.

[0131] Applications of proteases in the food industry include, but are not limited to, tenderizing meat; meat processing; clotting milk (e.g., cheese production); increasing bread volume; processing food; reducing acrylamide in various food (e.g., baked) products; releasing flavor in cheese production; producing rice bran protein (e.g., increase yield); modifying taste; and valorizing plant proteins.

[0132] Applications of proteases in the feed industry include, but are not limited to, the pre- digestion (e.g., metabolization) of proteins found in the animal feed and breaking larger proteins into lower molecular weight proteins.

[0133] Applications of proteases in the leather industry include, but are not limited to the dehairing of hides and skins.

[0134] Applications of proteases in the houshold products industry include, but are not limited to detergents for the removal of stains; dish washing powders; and detergents to cleaning carpets.

[0135] Applications of proteases in the medical industry include, but are not limited to treatment of ischemic stroke; debridement (the removal of dead or damaged tissue from wounds) in order to promote healing; stimulating anti-inflammatory effects; and treatment of severe sepsis.

[0136] Other applications that proteases can be used for include, but are not limited to, recovering silver from waste X-ray and photographic films; biocatalysis; hydrolyzing feathers (production of amino acids); removing fine wrinkles of the skin; and processing of proteins or fusion proteins in protein production.

7] The following is a listing of nucleic acid and amino acid sequences of the proteases of the present invention (Enzymes PR 1- PR 430) along with their expected activity.

[002] Enzyme PR 1 encodes the 1356 nucleotides in SEQ ID No: 1 which encodes the 404 amino acid sequence of SEQ ID NO: 2. This enzyme is believed to have aspartic-type endopeptidase activity.

[003] Enzyme PR 2 is encoded by the 2918 nucleotides in SEQ ID No: 3 which encodes the 600 amino acid sequence of SEQ ID No: 4. This enzyme is believed to have aspartic-type endopeptidase activity.

[004] Enzyme PR 3 is encoded by the 3802 nucleotides in SEQ ID No: 5 which encodes the 1175 amino acid sequence of SEQ ID No: 6. This enzyme is believed to have cysteine-type peptidase activity.

[005] Enzyme PR 4 is encoded by the 3551 nucleotides in SEQ ID No: 7 which encodes the 1032 amino acid sequence of SEQ ID No: 8. This enzyme is believed to have aspartic-type endopeptidase activity.

[006] Enzyme PR 5 is encoded by the 2428 nucleotides in SEQ ID No: 9 which encodes the 706 amino acid sequence of SEQ ID No: 10. This enzyme is believed to have cysteine-type endopeptidase activity.

[007] Enzyme PR 6 is encoded by the 2248 nucleotides in SEQ ID No: 11 which encodes the 680 amino acid sequence of SEQ ID No: 12. This enzyme is believed to have peptidase activity.

[008] Enzyme PR 7 is encoded by the 1715 nucleotides in SEQ ID No: 13 which encodes the 489 amino acid sequence of SEQ ID No: 14. This enzyme is believed to have endopeptidase activity.

[009] Enzyme PR 8 is encoded by the 422 nucleotides in SEQ ID No: 15 which encodes the 102 amino acid sequence of SEQ ID No: 16. This enzyme is believed to have peptidase activity.

[010] Enzyme PR 9 is encoded by the 294 nucleotides in SEQ ID No: 17 which encodes the 97 amino acid sequence of SEQ ID No: 18. This enzyme is believed to have carboxypeptidase activity.

[011] Enzyme PR 10 is encoded by the 21 15 nucleotides in SEQ ID No: 19 which encodes the 5* 95 amino acid sequence of SEQ ID No: 20. This enzyme is believed to have dipeptidyl-peptidase activity.

[012] Enzyme PR 11 is encoded by the 2404 nucleotides in SEQ ID No: 21 which

encodes the 547 amino acid sequence of SEQ ID No: 22. This enzyme is believed to have serine-type peptidase activity.

[013] Enzyme PR 12 is encoded by the 1074 nucleotides in SEQ ID No: 23 which

encodes the 286 amino acid sequence of SEQ ID No: 24. This enzyme is believed to have aspartic-type endopeptidase activity.

[014] Enzyme PR 13 is encoded by the 953 nucleotides in SEQ ID No: 25 which encodes the 237 amino acid sequence of SEQ ID No: 26. This enzyme is believed to have cysteine-type peptidase activity.

[015] Enzyme PR 14 is encoded by the 1493 nucleotides in SEQ ID No: 27 which

encodes the 475 amino acid sequence of SEQ ID No: 28. This enzyme is believed to have aminopeptidase activity.

[016] Enzyme PR 15 is encoded by the 3252 nucleotides in SEQ ID No: 29 which

encodes the 1083 amino acid sequence of SEQ ID No: 30. This enzyme is believed to have metalloendopeptidase activity.

[017] Enzyme PR 16 is encoded by the 2376 nucleotides in SEQ ID No: 31 which

encodes the 791 amino acid sequence of SEQ ID No: 32. This enzyme is believed to have metalloendopeptidase activity.

[018] Enzyme PR 17 is encoded by the 873 nucleotides in SEQ ID No: 33 which encodes the 237 amino acid sequence of SEQ ID No: 34. This enzyme is believed to have peptidase activity.

[019] Enzyme PR 18 is encoded by the 1952 nucleotides in SEQ ID No: 35 which

encodes the 560 amino acid sequence of SEQ ID No: 36. This enzyme is believed to have serine-type peptidase activity.

[020] Enzyme PR 19 is encoded by the 1776 nucleotides in SEQ ID No: 37 which

encodes the 569 amino acid sequence of SEQ ID No: 38. This enzyme is believed to have aspartic-type endopeptidase activity.

[021] Enzyme PR 20 is encoded by the 1 163 nucleotides in SEQ ID No: 39 which

encodes the 296 amino acid sequence of SEQ ID No: 40. This enzyme is believed to have serine-type endopeptidase activity.

[022] Enzyme PR 21 is encoded by the 2394 nucleotides in SEQ ID No: 41 which encodes the 662 amino acid sequence of SEQ ID No: 42. This enzyme is believed to have serine-type endopeptidase activity.

[023] Enzyme PR 22 is encoded by the 3108 nucleotides in SEQ ID No: 43 which

encodes the 928 amino acid sequence of SEQ ID No: 44. This enzyme is believed to have aspartic-type endopeptidase activity.

[024] Enzyme PR 23 is encoded by the 672 nucleotides in SEQ ID No: 45 which encodes the 174 amino acid sequence of SEQ ID No: 46. This enzyme is believed to have serine-type peptidase activity.

[025] Enzyme PR 24 is encoded by the 1732 nucleotides in SEQ ID No: 47 which

encodes the 482 amino acid sequence of SEQ ED No: 48. This enzyme is believed to have endopeptidase activity.

[026] Enzyme PR 25 is encoded by the 391 nucleotides in SEQ ID No: 49 which encodes the 72 amino acid sequence of SEQ ED No: 50. This enzyme is believed to have serine-type endopeptidase activity.

[027] Enzyme PR 26 is encoded by the 1358 nucleotides in SEQ ID No: 51 which

encodes the 41 1 amino acid sequence of SEQ ID No: 52. This enzyme is believed to have endopeptidase activity.

[028] Enzyme PR 27 is encoded by the 2076 nucleotides in SEQ ID No: 53 which

encodes the 617 amino acid sequence of SEQ ID No: 54. This enzyme is believed to have metalloexopeptidase activity.

[029] Enzyme PR 28 is encoded by the 1298 nucleotides in SEQ ID No: 55 which

encodes the 393 amino acid sequence of SEQ ED No: 56. This enzyme is believed to have peptidase activity.

[030] Enzyme PR 29 is encoded by the 1509 nucleotides in SEQ ED No: 57 which

encodes the 444 amino acid sequence of SEQ ID No: 58. This enzyme is believed to have aminopeptidase activity.

[031] Enzyme PR 30 is encoded by the 844 nucleotides in SEQ ID No: 59 which encodes the 223 amino acid sequence of SEQ ID No: 60. This enzyme is believed to have aspartic-type endopeptidase activity.

[032] Enzyme PR 31 is encoded by the 262 nucleotides in SEQ ID No: 61 which encodes the 75 amino acid sequence of SEQ DD No: 62. This enzyme is believed to have peptidase activity.

[033] Enzyme PR 32 is encoded by the 798 nucleotides in SEQ ID No: 63 which encodes the 245 amino acid sequence of SEQ ID No: 64. This enzyme is believed to have serine-type peptidase activity.

[034] Enzyme PR 33 is encoded by the 2485 nucleotides in SEQ ID No: 65 which

encodes the 598 amino acid sequence of SEQ ID No: 66. This enzyme is believed to have cysteine-type peptidase activity.

[035] Enzyme PR 34 is encoded by the 1013 nucleotides in SEQ ID No: 67 which

encodes the 292 amino acid sequence of SEQ ID No: 68. This enzyme is believed to have peptidase activity.

[036] Enzyme PR 35 is encoded by the 5189 nucleotides in SEQ ED No: 69 which

encodes the 1 160 amino acid sequence of SEQ ID No: 70. This enzyme is believed to have metalloendopeptidase activity.

[037] Enzyme PR 36 is encoded by the 1589 nucleotides in SEQ ID No: 71 which

encodes the 471 amino acid sequence of SEQ ID No: 72. This enzyme is believed to have metalloendopeptidase activity.

[038] Enzyme PR 37 is encoded by the 1339 nucleotides in SEQ ED No: 73 which

encodes the 288 amino acid sequence of SEQ ED No: 74. This enzyme is believed to have aspartic-type endopeptidase activity.

[039] Enzyme PR 38 is encoded by the 1898 nucleotides in SEQ ID No: 75 which

encodes the 544 amino acid sequence of SEQ ED No: 76. This enzyme is believed to have serine-type peptidase activity.

[040] Enzyme PR 39 is encoded by the 2830 nucleotides in SEQ ED No: 77 which

encodes the 897 amino acid sequence of SEQ ED No: 78. This enzyme is believed to have serine-type endopeptidase activity.

[041] Enzyme PR 40 is encoded by the 1968 nucleotides in SEQ ED No: 79 which

encodes the 655 amino acid sequence of SEQ ED No: 80. This enzyme is believed to have aspartic-type endopeptidase activity.

[042] Enzyme PR 41 is encoded by the 1587 nucleotides in SEQ ED No: 81 which

encodes the 502 amino acid sequence of SEQ ED No: 82. This enzyme is believed to have aminopeptidase activity.

[043] Enzyme PR 42 is encoded by the 675 nucleotides in SEQ ID No: 83 which encodes the 225 amino acid sequence of SEQ ED No: 84. This enzyme is believed to have peptidase activity.

[044] Enzyme PR 43 is encoded by the 983 nucleotides in SEQ ID No: 85 which encodes the 274 amino acid sequence of SEQ ID No: 86. This enzyme is believed to have peptidase activity.

[045] Enzyme PR 44 is encoded by the 1689 nucleotides in SEQ ID No: 87 which

encodes the 548 amino acid sequence of SEQ ID No: 88. This enzyme is believed to have aspartic-type endopeptidase activity.

[046] Enzyme PR 45 is encoded by the 2561 nucleotides in SEQ ID No: 89 which

encodes the 824 amino acid sequence of SEQ ID No: 90. This enzyme is believed to have metalloendopeptidase activity.

[047] Enzyme PR 46 is encoded by the 2818 nucleotides in SEQ ID No: 91 which

encodes the 868 amino acid sequence of SEQ ID No: 92. This enzyme is believed to have metalloprotease activity.

[048] Enzyme PR 47 is encoded by the 732 nucleotides in SEQ ID No: 93 which encodes the 243 amino acid sequence of SEQ ID No: 94. This enzyme is believed to have aspartic-type endopeptidase activity.

[049] Enzyme PR 48 is encoded by the 1523 nucleotides in SEQ ID No: 95 which

encodes the 424 amino acid sequence of SEQ ID No: 96. This enzyme is believed to have aspartic-type endopeptidase activity.

[050] Enzyme PR 49 is encoded by the 226 nucleotides in SEQ ID No: 97 which encodes the amino acid sequence of SEQ ID No: 98. This enzyme is believed to have metallopeptidase activity.

[051] Enzyme PR 50 is encoded by the 5409 nucleotides in SEQ ID No: 99 which

encodes the 1778 amino acid sequence of SEQ ED No: 100. This enzyme is believed to have cysteine-type peptidase activity.

[052] Enzyme PR 51 is encoded by the 918 nucleotides in SEQ ID No: 101 which

encodes the 305 amino acid sequence of SEQ ED No: 102. This enzyme is believed to have cysteine-type peptidase activity.

[053] Enzyme PR 52 is encoded by the 1740 nucleotides in SEQ ED No: 103 which

encodes the 471 amino acid sequence of SEQ ED No: 104. This enzyme is believed to have cysteine-type endopeptidase activity.

[054] Enzyme PR 53 is encoded by the 1623 nucleotides in SEQ ED No: 105 which

encodes the 540 amino acid sequence of SEQ ED No: 106. This enzyme is believed to have metalloendopeptidase activity.

[055] Enzyme PR 54 is encoded by the 1453 nucleotides in SEQ ED No: 107 which encodes the 406 amino acid sequence of SEQ ID No: 108. This enzyme is believed to have aminopeptidase activity.

[056] Enzyme PR 55 is encoded by the 3186 nucleotides in SEQ ID No: 109 which

encodes the 819 amino acid sequence of SEQ ID No: 1 10. This enzyme is believed to have metalloendopeptidase activity.

[057] Enzyme PR 56 is encoded by the 3512 nucleotides in SEQ ID No: 1 1 1 which

encodes the 1 1 18 amino acid sequence of SEQ ID No: 1 12. This enzyme is believed to have serine-type endopeptidase activity.

[058] Enzyme PR 57 is encoded by the 1328 nucleotides in SEQ ID No: 113 which

encodes the 417 amino acid sequence of SEQ ID No: 1 14. This enzyme is believed to have aspartic-type endopeptidase activity.

[059] Enzyme PR 58 is encoded by the 1439 nucleotides in SEQ ID No: 115 which

encodes the 419 amino acid sequence of SEQ Γΰ No: 1 16. This enzyme is believed to have cysteine-type endopeptidase activity.

[060] Enzyme PR 59 is encoded by the 1314 nucleotides in SEQ ID No: 117 which

encodes the 412 amino acid sequence of SEQ ID No: 1 18. This enzyme is believed to have serine-type endopeptidase activity.

[061] Enzyme PR 60 is encoded by the 1383 nucleotides in SEQ ID No: 119 which

encodes the 400 amino acid sequence of SEQ ID No: 120. This enzyme is believed to have metalloexopeptidase activity.

[062] Enzyme PR 61 is encoded by the 1305 nucleotides in SEQ ID No: 121 which

encodes the 457 amino acid sequence of SEQ ID No: 122. This enzyme is believed to have serine-type carboxypeptidase activity.

[063] Enzyme PR 62 is encoded by the 1320 nucleotides in SEQ ID No: 123 which

encodes the 397 amino acid sequence of SEQ ID No: 124. This enzyme is believed to have aspartic-type endopeptidase activity.

[064] Enzyme PR 63 is encoded by the 1447 nucleotides in SEQ ID No: 125 which

encodes the 443 amino acid sequence of SEQ ED No: 126. This enzyme is believed to have aspartic-type endopeptidase activity.

[065] Enzyme PR 64 is encoded by the 1514 nucleotides in SEQ ID No: 127 which

encodes the 445 amino acid sequence of SEQ ED No: 128. This enzyme is believed to have peptidase activity.

[066] Enzyme PR 65 is encoded by the 1538 nucleotides in SEQ DD No: 129 which encodes the 415 amino acid sequence of SEQ ID No: 130. This enzyme is believed to have serine-type endopeptidase activity.

[067] Enzyme PR 66 is encoded by the 798 nucleotides in SEQ ID No: 131 which

encodes the 223 amino acid sequence of SEQ ID No: 132. This enzyme is believed to have cysteine-type peptidase activity.

[068] Enzyme PR 67 is encoded by the 1713426 nucleotides in SEQ ID No: 133 which encodes the amino acid sequence of SEQ ID No: 134. This enzyme is- believed to have cysteine-type endopeptidase activity.

[069] Enzyme PR 68 is encoded by the 1691 nucleotides in SEQ ID No: 135 which

encodes the 525 amino acid sequence of SEQ ID No: 136. This enzyme is believed to have metallopeptidase activity.

[070] Enzyme PR 69 is encoded by the 1687 nucleotides in SEQ ID No: 137 which

encodes the 493 amino acid sequence of SEQ ED No: 138. This enzyme is believed to have metallopeptidase activity.

[071] Enzyme PR 70 is encoded by the 2780 nucleotides in SEQ ID No: 139 which

encodes the 893 amino acid sequence of SEQ ED No: 140. This enzyme is believed to have serine-type endopeptidase activity.

[072] Enzyme PR 71 is encoded by the 2474 nucleotides in SEQ ED No: 141 which

encodes the 685 amino acid sequence of SEQ ED No: 142. This enzyme is believed to have serine-type peptidase activity.

[073] Enzyme PR 72 is encoded by the 1732 nucleotides in SEQ ED No: 143 which

encodes the 475 amino acid sequence of SEQ ED No: 144. This enzyme is believed to have metalloendopeptidase activity.

[074] Enzyme PR 73 is encoded by the 2839 nucleotides in SEQ ED No: 145 which

encodes the 924 amino acid sequence of SEQ ED No: 146. This enzyme is believed to have aminopeptidase activity.

[075] Enzyme PR 74 is encoded by the 1553 nucleotides in SEQ ED No: 147 which

encodes the 454 amino acid sequence of SEQ ED No: 148. This enzyme is believed to have aspartic-type endopeptidase activity.

[076] Enzyme PR 75 is encoded by the 3022 nucleotides in SEQ ED No: 149 which

encodes the 886 amino acid sequence of SEQ D No: 150. This enzyme is believed to have metalloendopeptidase activity.

[077] Enzyme PR 76 is encoded by the 2758 nucleotides in SEQ ED No: 151 which encodes the 874 amino acid sequence of SEQ ID No: 152. This enzyme is believed to have aminopeptidase activity.

[078] Enzyme PR 77 is encoded by the 2733 nucleotides in SEQ ID No: 153 which

encodes the 812 amino acid sequence of SEQ ID No: 154. This enzyme is believed to have aminopeptidase activity.

[079] Enzyme PR 78 is encoded by the 2835 nucleotides in SEQ ID No: 155 which

encodes the 665 amino acid sequence of SEQ ID No: 156. This enzyme is believed to have aminopeptidase activity.

[080] Enzyme PR 79 is encoded by the 1701 nucleotides in SEQ ID No: 157 which

encodes the 566 amino acid sequence of SEQ ID No: 158. This enzyme is believed to have aspartic-type endopeptidase activity.

[081] Enzyme PR 80 is encoded by the 308 nucleotides in SEQ ID No: 159 which

encodes the 102 amino acid sequence of SEQ ID No: 160. This enzyme is believed to have serine-type endopeptidase activity.

[082] Enzyme PR 81 is encoded by the 1 197 nucleotides in SEQ ID No: 161 which

encodes the 398 amino acid sequence of SEQ ED No: 162. This enzyme is believed to have serine-type endopeptidase activity.

[083] Enzyme PR 82 is encoded by the 2777 nucleotides in SEQ ID No: 163 which

encodes the 573 amino acid sequence of SEQ ID No: 164. This enzyme is believed to have serine-type peptidase activity.

[084] Enzyme PR 83 is encoded by the 2904 nucleotides in SEQ ID No: 165 which

encodes the 922 amino acid sequence of SEQ Γΰ No: 166. This enzyme is believed to have metallopeptidase activity.

[085] Enzyme PR 84 is encoded by the 4796 nucleotides in SEQ ID No: 167 which

encodes the 1230 amino acid sequence of SEQ Γΰ No: 168. This enzyme is believed to have cysteine-type endopeptidase activity.

[086] Enzyme PR 85 is encoded by the 3376 nucleotides in SEQ ID No: 169 which

encodes the 1096 amino acid sequence of SEQ ID No: 170. This enzyme is believed to have serine-type endopeptidase activity.

[087] Enzyme PR 86 is encoded by the 2216 nucleotides in SEQ ID No: 171 which

encodes the 669 amino acid sequence of SEQ ID No: 172. This enzyme is believed to have serine-type carboxypeptidase activity.

[088] Enzyme PR 87 is encoded by the 1059 nucleotides in SEQ TD No: 173 which encodes the 334 amino acid sequence of SEQ ID No: 174. This enzyme is believed to have aspartic-type endopeptidase activity.

[089] Enzyme PR 88 is encoded by the 1296 nucleotides in SEQ ID No: 175 which

encodes the 432 amino acid sequence of SEQ ID No: 176. This enzyme is believed to have serine-type endopeptidase activity.

[090] Enzyme PR 89 is encoded by the 1737 nucleotides in SEQ ID No: 177 which

encodes the 578 amino acid sequence of SEQ ED No: 178. This enzyme is believed to have carboxypeptidase activity.

[091] Enzyme PR 90 is encoded by the 2445 nucleotides in SEQ ID No: 179 which

encodes the 814 amino acid sequence of SEQ ID No: 180. This enzyme is believed to have aminopeptidase activity.

[092] Enzyme PR 91 is encoded by the 947 nucleotides in SEQ ID No: 181 which

encodes the 289 amino acid sequence of SEQ ID No: 182. This enzyme is believed to have metallopeptidase activity.

[093] Enzyme PR 92 is encoded by the 1517 nucleotides in SEQ ID No: 183 which

encodes the 475 amino acid sequence of SEQ ID No: 184. This enzyme is believed to have aspartic-type endopeptidase activity.

[094] Enzyme PR 93 is encoded by the 2949 nucleotides in SEQ ID No: 185 which

encodes the 910 amino acid sequence of SEQ ID No: 186. This enzyme is believed to have metalloendopeptidase activity.

[095] Enzyme PR 94 is encoded by the 1720 nucleotides in SEQ ID No: 187 which

encodes the 554 amino acid sequence of SEQ ID No: 188. This enzyme is believed to have serine-type carboxypeptidase activity.

[096] Enzyme PR 95 is encoded by the 984 nucleotides in SEQ ID No: 189 which

encodes the 327 amino acid sequence of SEQ ID No: 190. This enzyme is believed to have aminopeptidase activity.

[097] Enzyme PR 96 is encoded by the 1547 nucleotides in SEQ ID No: 191 which

encodes the 392 amino acid sequence of SEQ JD No: 192. This enzyme is believed to have serine-type endopeptidase activity.

[098] Enzyme PR 97 is encoded by the 1428 nucleotides in SEQ ID No: 193 which

encodes the 475 amino acid sequence of SEQ ID No: 194. This enzyme is believed to have metallopeptidase activity.

[099] Enzyme PR 98 is encoded by the 2041 nucleotides in SEQ ID No: 195 which encodes the 639 amino acid sequence of SEQ ID No: 196. This enzyme is believed to have serine-type carboxypeptidase activity.

[0100] Enzyme PR 99 is encoded by the 1509 nucleotides in SEQ ID No: 197 which

encodes the 444 amino acid sequence of SEQ ID No: 198. This enzyme is believed to have aminopeptidase activity.

[0101] Enzyme PR 100 is encoded by the 1520 nucleotides in SEQ ID No: 199 which encodes the 466 amino acid sequence of SEQ ID No: 200. This enzyme is believed to have aspartic-type endopeptidase activity.

[0102] Enzyme PR 101 is encoded by the 2015 nucleotides in SEQ ID No: 201 which encodes the 613 amino acid sequence of SEQ ID No: 202. This enzyme is believed to have metallopeptidase activity.

[0103] Enzyme PR 102 is encoded by the 1933 nucleotides in SEQ ID No: 203 which encodes the 571 amino acid sequence of SEQ ID No: 204. This enzyme is believed to have serine-type carboxypeptidase activity.

[0104] Enzyme PR 103 is encoded by the 1083 nucleotides in SEQ ED No: 205 which encodes the 360 amino acid sequence of SEQ ED No: 206. This enzyme is believed to have metalloendopeptidase activity.

[0105] Enzyme PR 104 is encoded by the 3342 nucleotides in SEQ ED No: 207 which encodes the 1052 amino acid sequence of SEQ ED No: 208. This enzyme is believed to have metallopeptidase activity.

[0106] Enzyme PR 105 is encoded by the 926 nucleotides in SEQ ED No: 209 which encodes the 253 amino acid sequence of SEQ ED No: 210. This enzyme is believed to have serine-type endopeptidase activity.

[0107] Enzyme PR 106 is encoded by the 1640 nucleotides in SEQ ED No: 211 which encodes the 421 amino acid sequence of SEQ ED No: 212. This enzyme is believed to have metallocarboxypeptidase activity.

[0108] Enzyme PR 107 is encoded by the 2143 nucleotides in SEQ ED No: 213 which encodes the 621 amino acid sequence of SEQ ED No: 214. This enzyme is believed to have serine-type endopeptidase activity.

[0109] Enzyme PR 108 is encoded by the 1718 nucleotides in SEQ ID No: 215 which encodes the 535 amino acid sequence of SEQ ED No: 216. This enzyme is believed to have metallocarboxypeptidase activity.

[01 10] Enzyme PR 109 is encoded by the 2777 nucleotides in SEQ ED No: 217 which encodes the 902 amino acid sequence of SEQ ID No: 218. This enzyme is believed to have metalloendopeptidase activity.

[011 1] Enzyme PR 1 10 is encoded by the 1720 nucleotides in SEQ ID No: 219 which encodes the 475 amino acid sequence of SEQ ID No: 220. This enzyme is believed to have aminopeptidase activity.

[0112] Enzyme PR 11 1 is encoded by the 1716 nucleotides in SEQ ID No: 221 which encodes the 513 amino acid sequence of SEQ ID No: 222. This enzyme is believed to have metalloaminopeptidase activity.

[01 13] Enzyme PR 112 is encoded by the 1497 nucleotides in SEQ ID No: 223 which encodes the 461 amino acid sequence of SEQ ID No: 224. This enzyme is believed to have metalloendopeptidase activity.

[0114] Enzyme PR 1 13 is encoded by the 3101 nucleotides in SEQ ID No: 225 which encodes the 1010 amino acid sequence of SEQ ID No: 226. This enzyme is believed to have metalloendopeptidase activity.

[0115] Enzyme PR 1 14 is encoded by the 1661 nucleotides in SEQ ID No: 227 which encodes the 434 amino acid sequence of SEQ ID No: 228. This enzyme is believed to have metalloendopeptidase activity.

[01 16] Enzyme PR 115 is encoded by the 1355 nucleotides in SEQ ID No: 229 which encodes the 390 amino acid sequence of SEQ ID No: 230. This enzyme is believed to have aspartic-type endopeptidase activity.

[0117] Enzyme PR 116 is encoded by the 1635 nucleotides in SEQ ID No: 231 which encodes the 387 amino acid sequence of SEQ ED No: 232. This enzyme is believed to have serine-type endopeptidase activity.

[0118] Enzyme PR 1 17 is encoded by the 2769 nucleotides in SEQ ID No: 233 which encodes the 902 amino acid sequence of SEQ ID No: 234. This enzyme is believed to have metallopeptidase activity.

[0119] Enzyme PR 118 is encoded by the 1619 nucleotides in SEQ ID No: 235. which encodes the 510 amino acid sequence of SEQ ID No: 236. This enzyme is believed to have aspartic-type endopeptidase activity.

[0120] Enzyme PR 119 is encoded by the 2586 nucleotides in SEQ ID No: 237 which encodes the 783

[0121] amino acid sequence of SEQ ID No: 238. This enzyme is believed to have

metallopeptidase activity. [0122] Enzyme PR 120 is encoded by the 806 nucleotides in SEQ ID No: 239 which encodes the 185 amino acid sequence of SEQ ID No: 240. This enzyme is believed to have metallocarboxypeptidase activity.

[0123] Enzyme PR 121 is encoded by the 2885 nucleotides in SEQ ID No: 241 which encodes the 888 amino acid sequence of SEQ ID No: 242. This enzyme is believed to have aminopeptidase activity.

[0124] Enzyme PR 122 is encoded by the 2032 nucleotides in SEQ ID No: 243 which encodes the 519 amino acid sequence of SEQ JD No: 244. This enzyme is believed to have serine-type endopeptidase activity.

[0125] Enzyme PR 123 is encoded by the 470 nucleotides in SEQ ID No: 245 which encodes the 88 amino acid sequence of SEQ JD No: 246. This enzyme is believed to have serine-type endopeptidase activity.

[0126] Enzyme PR 124 is encoded by the 264 nucleotides in SEQ ID No: 247 which encodes the 102 amino acid sequence of SEQ ID No: 248. This enzyme is believed to have metalloexopeptidase activity.

[0127] Enzyme PR 125 is encoded by the 998 nucleotides in SEQ ID No: 249 which encodes the 341 amino acid sequence of SEQ ID No: 250. This enzyme is believed to have metalloexopeptidase activity.

[0128] Enzyme PR 126 is encoded by the 5496 nucleotides in SEQ ID No: 251 which encodes the 246 amino acid sequence of SEQ ID No: 252. This enzyme is believed to have aspartic-type endopeptidase activity.

[0129] Enzyme PR 127 is encoded by the 3097 nucleotides in SEQ ID No: 253 which encodes the 950 amino acid sequence of SEQ ID No: 254. This enzyme is believed to have aspartic-type endopeptidase activity.

[0130] Enzyme PR 128 is encoded by the 393 nucleotides in SEQ ID No: 255 which

encodes the 102 amino acid sequence of SEQ ID No: 256. This enzyme is believed to have serine-type endopeptidase activity.

[0131] Enzyme PR 129 is encoded by the 2428 nucleotides in SEQ ID No: 257 which encodes the 706 amino acid sequence of SEQ ID No: 258. This enzyme is believed to have cysteine-type endopeptidase activity.

[0132] Enzyme PR 130 is encoded by the 2251 nucleotides in SEQ ID No: 259 which encodes the 681 amino acid sequence of SEQ ID No: 260. This enzyme is believed to have cysteine-type peptidase activity. [0133] Enzyme PR 131 is encoded by the 1827 nucleotides in SEQ ID No: 261 which encodes the 546 amino acid sequence of SEQ ID No: 262. This enzyme is believed to have serine-type endopeptidase activity.

[0134] Enzyme PR 132 is encoded by the 723 nucleotides in SEQ ID No: 263 which encodes the 1 1 1 amino acid sequence of SEQ ED No: 264. This enzyme is believed to have peptidase activity.

[0135] Enzyme PR 133 is encoded by the 14322 nucleotides in SEQ ID No: 265 which encodes the 792 amino acid sequence of SEQ ID No: 266. This enzyme is believed to have aspartic-type endopeptidase activity.

[0136] Enzyme PR 134 is encoded by the 267 nucleotides in SEQ ID No: 267 which

encodes the 88 amino acid sequence of SEQ ID No: 268. This enzyme is believed to have serine-type carboxypeptidase activity GO .

[0137] Enzyme PR 135 is encoded by the 4720 nucleotides in SEQ ID No: 269 which encodes the 657 amino acid sequence of SEQ ED No: 270. This enzyme is believed to have dipeptidyl-peptidase activity.

[0138] Enzyme PR 136 is encoded by the 159 nucleotides in SEQ ED No: 271 which

encodes the 52 amino acid sequence of SEQ ED No: 272. This enzyme is believed to have peptidase activity.

[0139] Enzyme PR 137 is encoded by the 640 nucleotides in SEQ ED No: 273 which

encodes the 166 amino acid sequence of SEQ ED No: 274. This enzyme is believed to have serine-type peptidase activity.

[0140] Enzyme PR 138 is encoded by the 1493 nucleotides in SEQ ED No: 275 which encodes the 475 amino acid sequence of SEQ ED No: 276. This enzyme is believed to have aminopeptidase activity.

[0141] Enzyme PR 139 is encoded by the 3252 nucleotides in SEQ ED No: 277 which encodes the 1083 amino acid sequence of SEQ ED No: 278. This enzyme is believed to have metal loendopeptidase activity.

[0142] Enzyme PR 140 is encoded by the 4213 nucleotides in SEQ ED No: 279 which encodes the 197 amino acid sequence of SEQ ED No: 280. This enzyme is believed to have aspartic-type endopeptidase activity.

[0143] Enzyme PR 141 is encoded by the 1302 nucleotides in SEQ ED No: 281 which encodes the 265 amino acid sequence of SEQ ID No: 282. This enzyme is believed to have peptidase activity. [0144] Enzyme PR 142 is encoded by the 4624 nucleotides in SEQ ID No: 283 which encodes the 788 amino acid sequence of SEQ ID No: 284. This enzyme is believed to have serine-type peptidase activity.

[0145] Enzyme PR 143 is encoded by the 1976 nucleotides in SEQ ID No: 285 which encodes the 481 amino acid sequence of SEQ ID No: 286. This enzyme is believed to have serine-type endopeptidase activity.

[0146] Enzyme PR 144 is encoded by the 1 170 CHECK THIS ONE nucleotides in SEQ

ID No: 287 which encodes the 389 amino acid sequence of SEQ ID No: 288. This enzyme is believed to have serine-type endopeptidase activity.

[0147] Enzyme PR 145 is encoded by the 3018 nucleotides in SEQ ID No: 289 which encodes the 866 amino acid sequence of SEQ ID No: 290. This enzyme is believed to have aspartic-type endopeptidase activity.

[0148] Enzyme PR 146 is encoded by the 3323 nucleotides in SEQ ID No: 291 which encodes the 918 amino acid sequence of SEQ ID No: 292. This enzyme is believed to have serine-type endopeptidase activity.

[0149] Enzyme PR 147 is encoded by the 1279 nucleotides in SEQ ID No: 293 which encodes the 400 amino acid sequence of SEQ ED No: 294. This enzyme is believed to have aspartic-type endopeptidase activity.

[0150] Enzyme PR 148 is encoded by the 661 nucleotides in SEQ ID No: 295 which

encodes the 162 amino acid sequence of SEQ ED No: 296. This enzyme is believed to have serine-type endopeptidase activity.

[0151] Enzyme PR 149 is encoded by the 2969 nucleotides in SEQ ED No: 297 which encodes the 709 amino acid sequence of SEQ ED No: 298. This enzyme is believed to have metal loexopeptidase activity.

[0152] Enzyme PR 150 is encoded by the 891 nucleotides in SEQ ED No: 299 which

encodes the 276 amino acid sequence of SEQ ED No:300. This enzyme is believed to have aspartic-type endopeptidase activity.

[0153] Enzyme PR 151 is encoded by the 408 nucleotides in SEQ ED No: 301 which

encodes the 135 amino acid sequence of SEQ ED No: 302. This enzyme is believed to have aspartic-type endopeptidase activity.

[0154] Enzyme PR 152 is encoded by the 1894 nucleotides in SEQ ED No: 303 which encodes the 398 amino acid sequence of SEQ ID No: 304. This enzyme is believed to have peptidase activity. [0155] Enzyme PR 153 is encoded by the 765 nucleotides in SEQ ID No: 305 which encodes the 237 amino acid sequence of SEQ ID No: 306. This enzyme is believed to. have peptidase activity.

[0156] Enzyme PR 154 is encoded by the 3325 nucleotides in SEQ ID No: 307 which encodes the 1056 amino acid sequence of SEQ ID No: 308. This enzyme is believed to have metalloendopeptidase activity.

[0157] Enzyme PR 155 is encoded by the 1589 nucleotides in SEQ ID No: 309 which encodes the 471 amino acid sequence of SEQ ID No: 310. This enzyme is believed to have metalloendopeptidase activity.

[0158] Enzyme PR 156 is encoded by the 920 nucleotides in SEQ ID No: 311 which

encodes the 186 amino acid sequence of SEQ ID No: 312. This enzyme is believed to have aspartic-type endopeptidase activity.

[0159] Enzyme PR 157 is encoded by the 1898 nucleotides in SEQ ID No: 313 which encodes the 544 amino acid sequence of SEQ ID No: 314. This enzyme is believed to have serine-type peptidase activity.

[0160] Enzyme PR 158 is encoded by the 3426 nucleotides in SEQ ID No: 315 which encodes the 959 amino acid sequence of SEQ ID No: 316. This enzyme is believed to have serine-type endopeptidase activity.

[0161] Enzyme PR 159 is encoded by the 632 nucleotides in SEQ ID No: 317 which

encodes the 128 amino acid sequence of SEQ ID No: 318. This enzyme is believed to have aspartic-type endopeptidase activity.

[0162] Enzyme PR 160 is encoded by the 756 nucleotides in SEQ ID No: 319 which

encodes the 251 amino acid sequence of SEQ ID No: 320. This enzyme is believed to have metal loexopeptidase activity.

[0163] Enzyme PR 161 is encoded by the 1476 nucleotides in SEQ ID No: 321 which encodes the 444 amino acid sequence of SEQ ID No: 322. This enzyme is believed to have aspartic-type endopeptidase activity.

[0164] Enzyme PR 162 is encoded by the 1476

[0165] Same as 321 nucleotides in SEQ ID No: 323 which encodes the 585 amino acid sequence of SEQ ID No: 324. This enzyme is believed to have aspartic-type endopeptidase activity.

[0166] Enzyme PR 163 is encoded by the 221 1 nucleotides in SEQ ID No: 325 which encodes the 408 amino acid sequence of SEQ ID No: 326. This enzyme is believed to have metallopeptidase activity.

[0167] Enzyme PR 164 is encoded by the 3682 nucleotides in SEQ ID No: 327 which encodes the 284 amino acid sequence of SEQ ID No: 328. This enzyme is believed to have aspartyl protease activity.

[0168] Enzyme PR 165 is encoded by the 1689 nucleotides in SEQ ID No: 329 which encodes the 545 amino acid sequence of SEQ ED No: 330. This enzyme is believed to have aspartic-type endopeptidase activity.

[0169] Enzyme PR 166 is encoded by the 2561 nucleotides in SEQ ED No: 331 which encodes the 824 amino acid sequence of SEQ ED No: 332. This enzyme is believed to have metalloendopeptidase activity.

[0170] Enzyme PR 167 is encoded by the 2818 nucleotides in SEQ ED No: 333 which encodes the 868 amino acid sequence of SEQ ED No: 334. This enzyme is believed to have metalloendopeptidase activity.

[0171] Enzyme PR 168 is encoded by the 732 nucleotides in SEQ ED No: 335 which

encodes the 243 amino acid sequence of SEQ ED No: 336. This enzyme is believed to have aspartic-type endopeptidase activity.

[0172] Enzyme PR 169 is encoded by the 2406 nucleotides in SEQ ED No: 337 which encodes the 452 amino acid sequence of SEQ ED No: 338. This enzyme is believed to have aspartic-type endopeptidase activity.

[0173] Enzyme PR 170 is encoded by the 4555 nucleotides in SEQ ED No: 339 which encodes the 1442 amino acid sequence of SEQ ED No: 340. This enzyme is believed to have cysteine-type peptidase activity.

[0174] Enzyme PR 171 is encoded by the 1482 nucleotides in SEQ ED No: 341 which encodes the 319 amino acid sequence of SEQ ED No: 342. This enzyme is believed to have cysteine-type peptidase activity.

[0175] Enzyme PR 172 is encoded by the 2503 nucleotides in SEQ ED No: 343 which encodes the 519 amino acid sequence of SEQ ED No: 344. This enzyme is believed to have cysteine-type endopeptidase activity.

[0176] Enzyme PR 173 is encoded by the 1291 nucleotides in SEQ ED No: 345 which encodes the 387 amino acid sequence of SEQ ED No: 346. This enzyme is believed to have metallopeptidase activity .

[0177] Enzyme PR 174 is encoded by the 3321 nucleotides in SEQ ED No: 347 which encodes the 720 amino acid sequence of SEQ ED No: 348. This enzyme is believed to have metalloendopeptidase activity.

[0178] Enzyme PR 175 is encoded by the 1453 nucleotides in SEQ ID No: 349 which encodes the 406 amino acid sequence of SEQ ID No: 350. This enzyme is believed to have aminopeptidase activity.

[0179] Enzyme PR 176 is encoded by the 402 nucleotides in SEQ ID No: 351 which

encodes the 133 amino acid sequence of SEQ ID No: 352. This enzyme is believed to have peptidase activity.

[0180] Enzyme PR 177 is encoded by the 2416 nucleotides in SEQ ID No: 353 which encodes the 722 amino acid sequence of SEQ ID No: 354. This enzyme is believed to have metalloendopeptidase activity.

[0181] Enzyme PR 178 is encoded by the 597 nucleotides in SEQ ID No: 355 which

encodes the 198 amino acid sequence of SEQ ID No: 356. This enzyme is believed to have aspartic-type endopeptidase activity.

[0182] Enzyme PR 179 is encoded by the 576 nucleotides in SEQ ID No: 357 which

encodes the 191 amino acid sequence of SEQ ID No: 358. This enzyme is believed to have aspartic-type endopeptidase activity.

[0183] Enzyme PR 180 is encoded by the 4871 nucleotides in SEQ ID No: 359 which encodes the 491 amino acid sequence of SEQ ID No: 360. This enzyme is believed to have nucleotides in .

[0184] Enzyme PR 181 is encoded by the 644 nucleotides in SEQ ID No: 361 which

encodes the 133 amino acid sequence of SEQ ID No: 362. This enzyme is believed to have aspartic-type endopeptidase activity.

[0185] Enzyme PR 182 is encoded by the 5813 nucleotides in SEQ ID No: 363 which encodes the 382 amino acid sequence of SEQ ID No: 364. This enzyme is believed to have aspartic-type endopeptidase activity.

[0186] Enzyme PR 183 is encoded by the 2262 nucleotides in SEQ ID No: 365 which encodes the 514 amino acid sequence of SEQ ID No: 366. This enzyme is believed to have aspartic-type endopeptidase activity.

[0187] Enzyme PR 184 is encoded by the 3429 nucleotides in SEQ ID No: 367 which encodes the 1056 amino acid sequence of SEQ ID No: 368. This enzyme is believed to have serine-type endopeptidase activity.

[0188] Enzyme PR 185 is encoded by the 1328 nucleotides in SEQ ID No: 369 which encodes the 417 amino acid sequence of SEQ ID No: 370. This enzyme is believed to have aspartic-type endopeptidase activity.

[0189] Enzyme PR 186 is encoded by the 1971 nucleotides in SEQ ED No: 371 which encodes the 480 amino acid sequence of SEQ ID No: 372. This enzyme is believed to have cysteine-type endopeptidase activity.

[0190] Enzyme PR 187 is encoded by the 7770 nucleotides in SEQ ID No: 373 which encodes the 41 1 amino acid sequence of SEQ ID No: 374. This enzyme is believed to have aspartic-type endopeptidase activity.

[0191] Enzyme PR 188 is encoded by the 1314 nucleotides in SEQ ID o: 375 which encodes the 407 amino acid sequence of SEQ ID No: 376. This enzyme is believed to have serine-type endopeptidase activity.

[0192] Enzyme PR 189 is encoded by the 3319 nucleotides in SEQ ID No: 377 which encodes the 650 amino acid sequence of SEQ ID No: 378. This enzyme is believed to have metal lopeptidase activity.

[0193] Enzyme PR 190 is encoded by the 1383 nucleotides in SEQ ID No: 379 which encodes the 400 amino acid sequence of SEQ ID No: 380. This enzyme is believed to have metalloexopeptidase activity.

[0194] Enzyme PR 191 is encoded by the 1751 nucleotides in SEQ ID No: 381 which encodes the 398 amino acid sequence of SEQ ID No: 382. This enzyme is believed to have aspartic-type endopeptidase activity.

[0195] Enzyme PR 192 is encoded by the 1447 nucleotides in SEQ ID No: 383 which encodes the 443 amino acid sequence of SEQ ED No: 384. This enzyme is believed to have aspartic-type endopeptidase activity.

[0196] Enzyme PR 193 is encoded by the 1538 nucleotides in SEQ ED No: 385 which encodes the 420 amino acid sequence of SEQ ED No: 386. This enzyme is believed to have serine-type endopeptidase activity.

[0197] Enzyme PR 194 is encoded by the 1627 nucleotides in SEQ ED No: 387 which encodes the 461 amino acid sequence of SEQ ED No: 388. This enzyme is believed to have cysteine-type peptidase activity.

[0198] Enzyme PR 195 is encoded by the 1201 nucleotides in SEQ ED No: 389 which encodes the 353 amino acid sequence of SEQ ED No: 390. This enzyme is believed to have cysteine-type endopeptidase activity.

[0199] Enzyme PR 196 is encoded by the 2529 nucleotides in SEQ ED No: 391 which encodes the 781 amino acid sequence of SEQ ED No: 392. This enzyme is believed to have metallopeptidase activity.

[0200] Enzyme PR 197 is encoded by the 1 103 nucleotides in SEQ ED No: 393 which encodes the 273 amino acid sequence of SEQ ED No: 394. This enzyme is believed to have serine-type peptidase activity.

[0201] Enzyme PR 198 is encoded by the 3164 nucleotides in SEQ ED No: 395 which encodes the 623 amino acid sequence of SEQ ED No: 396. This enzyme is believed to have metallopeptidase activity.

[0202] Enzyme PR 199 is encoded by the 2780 nucleotides in SEQ ED No: 397 which encodes the 893 amino acid sequence of SEQ ID No: 398. This enzyme is believed to have serine-type endopeptidase activity.

[0203] Enzyme PR 200 is encoded by the 4735 nucleotides in SEQ ID No: 399 which encodes the 994 amino acid sequence of SEQ ED No: 400. This enzyme is believed to have aminopeptidase activity.

[0204] Enzyme PR 201 is encoded by the 2022 nucleotides in SEQ ED No: 401 which encodes the 485 amino acid sequence of SEQ ED No: 402. This enzyme is believed to have metalloendopeptidase activity.

* [0205] Enzyme PR 202 is encoded by the 1622 nucleotides in SEQ ED No: 403 which encodes the 501 amino acid sequence of SEQ D No: 404. This enzyme is believed to have aspartic-type endopeptidase activity.

[0206] Enzyme PR 203 is encoded by the 2150 nucleotides in SEQ ED No: 405 which encodes the 446 amino acid sequence of SEQ ED No: 406. This enzyme is believed to have aspartic-type endopeptidase activity.

[0207] Enzyme PR 204 is encoded by the 1 178 nucleotides in SEQ ED No: 407 which encodes the 172 amino acid sequence of SEQ ID No: 408. This enzyme is believed to have aspartic-type endopeptidase activity.

[0208] Enzyme PR 205 is encoded by the 953 nucleotides in SEQ ED No: 409 which

encodes the 232 amino acid sequence of SEQ ED No: 410. This enzyme is believed to have protease activity.

[0209] Enzyme PR 206 is encoded by the 2839 nucleotides in SEQ ED No: 41 1 which encodes the 924 amino acid sequence of SEQ ED No: 412. This enzyme is believed to have endopeptidase activity.

[0210] Enzyme PR 207 is encoded by the 1553 nucleotides in SEQ ED No: 413 which encodes the 454 amino acid sequence of SEQ ED No: 414. This enzyme is believed to have aspartic-type endopeptidase activity.

[0211] Enzyme PR 208 is encoded by the 2397 nucleotides in SEQ ID No: 415 which encodes the 798 amino acid sequence of SEQ ID No: 416. This enzyme is believed to have metalloendopeptidase activity.

[0212] Enzyme PR 209 is encoded by the 576 nucleotides in SEQ ID No: 417 which

encodes the 191 amino acid sequence of SEQ ID No: 418. This enzyme is believed to have aspartic-type endopeptidase activity.

[0213] Enzyme PR 210 is encoded by the 4938 nucleotides in SEQ ID No: 419 which encodes the 1200 amino acid sequence of SEQ ID No: 420. This enzyme is believed to have metalloaminopeptidase activity.

[0214] Enzyme PR 211 is encoded by the 4485 nucleotides in SEQ ID No: 421 which encodes the 980 amino acid sequence of SEQ ID No: 422. This enzyme is believed to have aminopeptidase activity.

[0215] Enzyme PR 212 is encoded by the 1707 nucleotides in SEQ ID No: 423 which encodes the 568 amino acid sequence of SEQ ID No: 424. This enzyme is believed to have serine-type peptidase activity.

[0216] Enzyme PR 213 is encoded by the 2619 nucleotides in SEQ ID No: 425 which encodes the 872 amino acid sequence of SEQ ED No: 426. This enzyme is believed to have metalloendopeptidase activity.

[0217] Enzyme PR 214 is encoded by the 2835 nucleotides in SEQ ID No: 427 which encodes the 654 amino acid sequence of SEQ ID No: 428. This enzyme is believed to have aminopeptidase activity.

[0218] Enzyme PR 215 is encoded by the 1959 nucleotides in SEQ ID No: 429 which encodes the 595 amino acid sequence of SEQ ID No: 430. This enzyme is believed to have aspartic-type endopeptidase activity.

[0219] Enzyme PR 216 is encoded by the 1701 nucleotides in SEQ ID No: 431 which encodes the 566 amino acid sequence of SEQ ED No: 432. This enzyme is believed to have aspartic-type endopeptidase activity.

[0220] Enzyme PR 217 is encoded by the 1 197 nucleotides in SEQ ED No: 433 which encodes the 398 amino acid sequence of SEQ ED No: 434. This enzyme is believed to have serine-type endopeptidase activity.

[0221] Enzyme PR 218 is encoded by the 1424 nucleotides in SEQ ED No: 435 which encodes the 284 amino acid sequence of SEQ ED No: 436. This enzyme is believed to have aspartic-type endopeptidase activity.

[0222] Enzyme PR 219 is encoded by the 3592 nucleotides in SEQ ID No: 437 which encodes the 1033 amino acid sequence of SEQ ID No: 438. This enzyme is believed to have metal lopeptidase activity.

[0223] Enzyme PR 220 is encoded by the 1187 nucleotides in SEQ ID No: 439 which encodes the 376 amino acid sequence of SEQ ID No: 440. This enzyme is believed to have cysteine-type endopeptidase activity.

[0224] Enzyme PR 221 is encoded by the 3323 nucleotides in SEQ ID No: 441 which encodes the 918 amino acid sequence of SEQ ID No: 442. This enzyme is believed to have serine-type endopeptidase activity.

[0225] Enzyme PR 222 is encoded by the 1094 nucleotides in SEQ ID No: 443 which encodes the 246 amino acid sequence of SEQ ID No: 444. This enzyme is believed to have serine-type peptidase activity.

[0226] Enzyme PR 223 is encoded by the 3376 nucleotides in SEQ ID No: 445 which encodes the 1096 amino acid sequence of SEQ ID No: 446. This enzyme is believed to have serine-type endopeptidase activity.

[0227] Enzyme PR 224 is encoded by the 2627 nucleotides in SEQ ID No: 447 which encodes the 698 amino acid sequence of SEQ ID No: 448. This enzyme is believed to have serine-type carboxypeptidase activity.

[0228] Enzyme PR 225 is encoded by the 5838 nucleotides in SEQ ID No: 449 which encodes the 667 amino acid sequence of SEQ ID No: 450. This enzyme is believed to have aspartic-type endopeptidase activity.

[0229] Enzyme PR 226 is encoded by the 2294 nucleotides in SEQ ID No: 451 which encodes the 423 amino acid sequence of SEQ ID No: 452. This enzyme is believed to have serine-type endopeptidase activity.

[0230] Enzyme PR 227 is encoded by the 1737 nucleotides in SEQ ID No: 453 which encodes the 578 amino acid sequence of SEQ ID No: 454. This enzyme is believed to have carboxypeptidase activity.

[0231] Enzyme PR 228 is encoded by the 4591 nucleotides in SEQ ID No: 455 which encodes the 1020 amino acid sequence of SEQ ID No: 456. This enzyme is believed to have aminopeptidase activity.

[0232] Enzyme PR 229 is encoded by the 947 nucleotides in SEQ Γΰ No: 457 which encodes the 289 amino acid sequence of SEQ ID No: 458. This enzyme is believed to have metallopeptidase activity.

[0233] Enzyme PR 230 is encoded by the 1517 nucleotides in SEQ ID No: 459 which encodes the 475 amino acid sequence of SEQ ID No: 460. This enzyme is believed to have aspartic-type endopeptidase activity.

[0234] Enzyme PR 231 is encoded by the 5358 nucleotides in SEQ ID No: 461 which encodes the 1080 amino acid sequence of SEQ ID No: 462. This enzyme is believed to have metal loendopeptidase activity.

[0235] Enzyme PR 232 is encoded by the 1720 nucleotides in SEQ ID No: 463 which encodes the 554 amino acid sequence of SEQ ID No: 464. This enzyme is believed to have serine-type carboxypeptidase activity.

[0236] Enzyme PR 233 is encoded by the 576 nucleotides in SEQ ID No: 465 which

encodes the 191 amino acid sequence of SEQ Γΰ No: 466. This enzyme is believed to have aspartic-type endopeptidase activity.

[0237] Enzyme PR 234 is encoded by the 1547 nucleotides in SEQ ID No: 467 which encodes the 330 amino acid sequence of SEQ ID No: 468. This enzyme is believed to have serine-type endopeptidase activity.

[0238] Enzyme PR 235 is encoded by the 1428 nucleotides^' in SEQ ID No: 469 which encodes the 475 amino acid sequence of SEQ ID No: 470. This enzyme is believed to have metallopeptidase activity.

[0239] Enzyme PR 236 is encoded by the 2041 nucleotides in SEQ ED No: 471 which encodes the 639 amino acid sequence of SEQ ID No: 472. This enzyme is believed to have serine-type carboxypeptidase activity.

[0240] Enzyme PR 237 is encoded by the 2543 nucleotides in SEQ ID No: 473 which encodes the 645 amino acid sequence of SEQ ED No: 474. This enzyme is believed to have metal loexopeptidase activity.

[0241] Enzyme PR 238 is encoded by the 1538 nucleotides in SEQ ID No: 475 which encodes the 290 amino acid sequence of SEQ ID No: 476. This enzyme is believed to have aspartic-type endopeptidase activity.

[0242] Enzyme PR 239 is encoded by the 2991 nucleotides in SEQ ID No: 477 which encodes the 745 amino acid sequence of SEQ ID No: 478. This enzyme is believed to have metallopeptidase activity.

[0243] Enzyme PR 240 is encoded by the 1933 nucleotides in SEQ ID No: 479 which encodes the 571 amino acid sequence of SEQ ID No: 480. This enzyme is believed to have serine-type carboxypeptidase activity.

[0244] Enzyme PR 241 is encoded by the 1083 nucleotides in SEQ ID No: 481 which encodes the 360 amino acid sequence of SEQ ID No: 482. This enzyme is believed to have metalloendopeptidase activity.

[0245] Enzyme PR 242 is encoded by the 3342 nucleotides in SEQ ID No: 483 which encodes the 1052 amino acid sequence of SEQ ID No: 484. This enzyme is believed to have metallopeptidase activity.

[0246] Enzyme PR 243 is encoded by the 926 nucleotides in SEQ ID No: 485 which encodes the 253 amino acid sequence of SEQ ID No: 486. This enzyme is believed to have serine-type endopeptidase activity.

[0247] Enzyme PR 244 is encoded by the 1282 nucleotides in SEQ ID No: 487 which encodes the 346 amino acid sequence of SEQ ID No: 488. This enzyme is believed to have metal locarboxypeptidase activity.

[0248] Enzyme PR 245 is encoded by the 2143 nucleotides in SEQ ID No: 489 which encodes the 621 amino acid sequence of SEQ ED No: 490. This enzyme is believed to have serine-type endopeptidase activity.

[0249] Enzyme PR 246 is encoded by the 1718 nucleotides in SEQ ID No: 491 which encodes the 535 amino acid sequence of SEQ ID No: 492. This enzyme is believed to have metallocarboxypeptidase activity.

[0250] Enzyme PR 247 is encoded by the 798 nucleotides in SEQ ID No: 493 which

encodes the 245 amino acid sequence of SEQ ID No: 494. This enzyme is believed to have serine-type peptidase activity.

[0251] Enzyme PR 248 is encoded by the 6946 nucleotides in SEQ ID No: 495 which encodes the 1650 amino acid sequence of SEQ ED No: 496. This enzyme is believed to have metalloendopeptidase activity.

[0252] Enzyme PR 249 is encoded by the 1898 nucleotides in SEQ ID No: 497 which encodes the 533 amino acid sequence of SEQ ID No: 498. This enzyme is believed to have metalloaminopeptidase activity.

[0253] Enzyme PR 250 is encoded by the 1645 nucleotides in SEQ ID No: 499 which encodes the 492 amino acid sequence of SEQ ID No: 500. This enzyme is believed to have metalloendopeptidase activity.

[0254] Enzyme PR 251 is encoded by the 3876 nucleotides in SEQ ID No: 501 which encodes the 1153 amino acid sequence of SEQ ID No: 502. This enzyme is believed to have metalloendopeptidase activity.

[0255] Enzyme PR 252 is encoded by the 925 nucleotides in SEQ ID No: 503 which

encodes the 221 amino acid sequence of SEQ ID No: 504. This enzyme is believed to have aspartic-type endopeptidase activity.

[0256] Enzyme PR 253 is encoded by the 1729 nucleotides in SEQ ID No: 505 which encodes the 375 amino acid sequence of SEQ ID No: 506. This enzyme is believed to have aminopeptidase activity .

[0257] Enzyme PR 254 is encoded by the 1635 nucleotides in SEQ ID No: 507 which encodes the 387 amino acid sequence of SEQ ID No: 508. This enzyme is believed to have serine-type endopeptidase activity.

[0258] Enzyme PR 255 is encoded by the 375 nucleotides in SEQ ID No: 509 which

encodes the 124 amino acid sequence of SEQ ID No: 510. This enzyme is believed to have aspartic-type endopeptidase activity.

[0259] Enzyme PR 256 is encoded by the 3751 nucleotides in SEQ ED No: 511 which encodes the 1033 amino acid sequence of SEQ ID No: 512. This enzyme is believed to have peptidase activity.

[0260] Enzyme PR 257 is encoded by the 2882 nucleotides in SEQ ID No: 513 which encodes the 640 amino acid sequence of SEQ ED No: 514. This enzyme is believed to have aspartic-type endopeptidase activity.

[0261] Enzyme PR 258 is encoded by the 2500 nucleotides in SEQ DD No: 515 which encodes the 775 amino acid sequence of SEQ DD No: 516. This enzyme is believed to have nucleotides in .

[0262] Enzyme PR 259 is encoded by the 3123 nucleotides in SEQ ED No: 517 which encodes the 248 amino acid sequence of SEQ ED No: 518. This enzyme is believed to have aspartic-type endopeptidase activity.

[0263] Enzyme PR 260 is encoded by the 564 nucleotides in SEQ ED No: 519 which

encodes the 148 amino acid sequence of SEQ ED No: 520. This enzyme is believed to have metallocarboxypeptidase activity.

[0264] Enzyme PR 261 is encoded by the 1968 nucleotides in SEQ ID No: 521 which encodes the 655 amino acid sequence of SEQ ED No: 522. This enzyme is believed to have aspartic-type endopeptidase activity.

[0265] Enzyme PR 262 is encoded by the 7157 nucleotides in SEQ DD No: 523 which encodes the 2033 amino acid sequence of SEQ ED No: 524. This enzyme is believed to have aminopeptidase activity.

[0266] Enzyme PR 263 is encoded by the 3436 nucleotides in SEQ ED No: 525 which encodes the 641 amino acid sequence of SEQ ID No: 526. This enzyme is believed to have serine-type endopeptidase activity.

[0267] Enzyme PR 264 is encoded by the 1578 nucleotides in SEQ ED No: 527 which encodes the 295 amino acid sequence of SEQ ED No: 528. This enzyme is believed to have aspartic-type endopeptidase activity.

[0268] Enzyme PR 265 is encoded by the 2325 nucleotides in SEQ ED No: 529 which encodes the 354 amino acid sequence of SEQ ED No: 530. This enzyme is believed to have aspartic-type endopeptidase activity.

[0269] Enzyme PR 266 is encoded by the 4135 nucleotides in SEQ ED No: 531 which encodes the 502 amino acid sequence of SEQ ED No: 532. This enzyme is believed to have metalloexopeptidase activity.

[0270] Enzyme PR 267 is encoded by the 7657 nucleotides in SEQ ED No: 533 which encodes the 1581 amino acid sequence of SEQ ID No: 534. This enzyme is believed to have aspartic-type endopeptidase activity.

[0271] Enzyme PR 268 is encoded by the 393 nucleotides in SEQ ID No: 535 which

encodes the 102 amino acid sequence of SEQ ED No: 536. This enzyme is believed to have serine-type endopeptidase activity.

[0272] Enzyme PR 269 is encoded by the 2379 nucleotides in SEQ ED No: 537 which encodes the 588 amino acid sequence of SEQ ED No: 538. This enzyme is believed to have cysteine-type endopeptidase activity.

[0273] Enzyme PR 270 is encoded by the 3711 nucleotides in SEQ ED No: 539 which encodes the 964 amino acid sequence of SEQ ID No: 540. This enzyme is believed to have cysteine-type peptidase activity.

[0274] Enzyme PR 271 is encoded by the 1715 nucleotides in SEQ ED No: 541 which encodes the 259 amino acid sequence of SEQ ED No: 542. This enzyme is believed to have serine-type endopeptidase activity.

[0275] Enzyme PR 272 is encoded by the 422 nucleotides in SEQ ED No: 543 which

encodes the 110 amino acid sequence of SEQ ED No: 544. This enzyme is believed to have peptidase activity.

[0276] Enzyme PR 273 is encoded by the 2671 nucleotides in SEQ ED No: 545 which encodes the 707 amino acid sequence of SEQ ED No: 546. This enzyme is believed to have metalloendopeptidase activity.

[0277] Enzyme PR 274 is encoded by the 867 nucleotides in SEQ ID No: 547 which

encodes the 181 amino acid sequence of SEQ ID No: 548. This enzyme is believed to have aspartic-type endopeptidase activity.

[0278] Enzyme PR 275 is encoded by the 1934 nucleotides in SEQ ID No: 549 which encodes the 499 amino acid sequence of SEQ ID No: 550. This enzyme is believed to have dipeptidyl-peptidase activity.

[0279] Enzyme PR 276 is encoded by the 2023 nucleotides in SEQ ID No: 551 which encodes the 412 amino acid sequence of SEQ ID No: 552. This enzyme is believed to have serine-type peptidase activity.

[0280] Enzyme PR 277 is encoded by the 1954 nucleotides in SEQ ID No: 553 which encodes the 554 amino acid sequence of SEQ ED No: 554. This enzyme is believed to have aminopeptidase activity.

[0281] Enzyme PR 278 is encoded by the 873 nucleotides in SEQ ID No: 555 which

encodes the 237 amino acid sequence of SEQ ED No: 556. This enzyme is believed to have peptidase activity.

[0282] Enzyme PR 279 is encoded by the 2202 nucleotides in SEQ ID No: 557 which encodes the 610 amino acid sequence of SEQ ID No: 558. This enzyme is believed to have serine-type peptidase activity.

[0283] Enzyme PR 280 is encoded by the 2275 nucleotides in SEQ ED No: 559 which encodes the 435 amino acid sequence of SEQ ED No: 560. This enzyme is believed to have serine-type endopeptidase activity.

[0284] Enzyme PR 281 is encoded by the 1 170 nucleotides in SEQ ED No: 561 which encodes the 389 amino acid sequence of SEQ ED No: 562. This enzyme is believed to have serine-type endopeptidase activity.

[0285] Enzyme PR 282 is encoded by the 3779 nucleotides in SEQ ED No: 563 which encodes the 932 amino acid sequence of SEQ ED No: 564. This enzyme is believed to have aspartic-type endopeptidase activity.

[0286] Enzyme PR 283 is encoded by the 1577 nucleotides in SEQ ID No: 565 which encodes the 455 amino acid sequence of SEQ ED No: 566. This enzyme is believed to have aspartic-type endopeptidase activity.

[0287] Enzyme PR 284 is encoded by the 2028 nucleotides in SEQ D No: 567 which encodes the 601 amino acid sequence of SEQ ED No: 568. This enzyme is believed to have metalloexopeptidase activity.

[0288] Enzyme PR 285 is encoded by the 2771 nucleotides in SEQ ID No: 569 which encodes the 476 amino acid sequence of SEQ ED No: 570. This enzyme is believed to have peptidase activity.

[0289] Enzyme PR 286 is encoded by the 3301 nucleotides in SEQ ID No: 571 which encodes the 1049 amino acid sequence of SEQ ED No: 572. This enzyme is believed to have metalloendopeptidase activity.

[0290] Enzyme PR 287 is encoded by the 1589 nucleotides in SEQ ED No: 573 which encodes the 471 amino acid sequence of SEQ ED No: 574. This enzyme is believed to have metalloendopeptidase activity.

[0291] Enzyme PR 288 is encoded by the 3071 nucleotides in SEQ ID No: 575 which encodes the 711 amino acid sequence of SEQ ID No: 576. This enzyme is believed to have serine-type peptidase activity.

[0292] Enzyme PR 289 is encoded by the 2830 nucleotides in SEQ ED No: 577 which encodes the 897 amino acid sequence of SEQ ED No: 578. This enzyme is believed to have serine-type endopeptidase. activity.

[0293] Enzyme PR 290 is encoded by the 1522 nucleotides in SEQ ED No: 579 which encodes the 482 amino acid sequence of SEQ ED No: 580. This enzyme is believed to have metalloexopeptidase activity.

[0294] Enzyme PR 291 is encoded by the 1737 nucleotides in SEQ ED No: 581 which encodes the 477 amino acid sequence of SEQ ED No: 582. This enzyme is believed to have aspartic-type endopeptidase activity.

[0295] Enzyme PR 292 is encoded by the 1986 nucleotides in SEQ ID No: 583 which encodes the 358 amino acid sequence of SEQ ID No: 584. This enzyme is believed to have aspartic-type endopeptidase activity.

[0296] Enzyme PR 293 is encoded by the 1651 nucleotides in SEQ ED No: 585 which encodes the 519 amino acid sequence of SEQ ED No: 586. This enzyme is believed to have aspartic-type endopeptidase activity.

[0297] Enzyme PR 294 is encoded by the 4365 nucleotides in SEQ ED No: 587 which encodes the 1 142 amino acid sequence of SEQ ED No: 588. This enzyme is believed to have metalloendopeptidase activity.

[0298] Enzyme PR 295 is encoded by the 2818 nucleotides in SEQ ED No: 589 which encodes the 846 amino acid sequence of SEQ ED No: 590. This enzyme is believed to have metalloendopeptidase activity.

[0299] Enzyme PR 296 is encoded by the 1412 nucleotides in SEQ ID No: 591 which encodes the 404 amino acid sequence of SEQ ID No: 592. This enzyme is believed to have aspartic-type endopeptidase activity.

[0300] Enzyme PR 297 is encoded by the 2671 nucleotides in SEQ ID No: 593 which encodes the 707 amino acid sequence of SEQ ED No: 594. This enzyme is believed to have metalloendopeptidase activity.

[0301] Enzyme PR 298 is encoded by the 1544 nucleotides in SEQ ED No: 595 which encodes the 408 amino acid sequence of SEQ ED No: 596. This enzyme is believed to have aminopeptidase activity.

[0302] Enzyme PR 299 is encoded by the 835 nucleotides in SEQ ED No: 597 which

encodes the 244 amino acid sequence of SEQ ED No: 598. This enzyme is believed to have peptidase activity.

[0303] Enzyme PR 300 is encoded by the 2416 nucleotides in SEQ ED No: 599 which encodes the 712 amino acid sequence of SEQ ED No: 600. This enzyme is believed to have metalloendopeptidase activity.

[0304] Enzyme PR 301 is encoded by the 1328 nucleotides in SEQ ED No: 601 which encodes the 431 amino acid sequence of SEQ 3D No: 602. This enzyme is believed to have aspartic-type endopeptidase activity.

[0305] Enzyme PR 302 is encoded by the 1393 nucleotides in SEQ ID No: 603 which encodes the 415 amino acid sequence of SEQ ED No: 604. This enzyme is believed to have cysteine-type endopeptidase activity.

[0306] Enzyme PR 303 is encoded by the 201 1 nucleotides in SEQ ID No: 605 which encodes the 523 amino acid sequence of SEQ ED No: 606. This enzyme is believed to have serine-type endopeptidase activity.

[0307] Enzyme PR 304 is encoded by the 2764 nucleotides in SEQ ID No: 607 which encodes the 517 amino acid sequence of SEQ ED No: 608. This enzyme is believed to have metalloexopeptidase activity.

[0308] Enzyme PR 305 is encoded by the 1751 nucleotides in SEQ ED No: 609 which encodes the 398 amino acid sequence of SEQ ED No: 610. This enzyme is believed to have aspartic-type endopeptidase activity.

[0309] Enzyme PR 306 is encoded by the 1447 nucleotides in SEQ ED No: 61 1 which encodes the 401 amino acid sequence of SEQ ED No: 612. This enzyme is believed to have aspartic-type endopeptidase activity.

[0310] Enzyme PR 307 is encoded by the 1538 nucleotides in SEQ ID No: 613 which encodes the 436 amino acid sequence of SEQ ID No: 614. This enzyme is believed to have serine-type endopeptidase activity.

[0311] Enzyme PR 308 is encoded by the 1627 nucleotides in SEQ ID No: 615 which encodes the 259 amino acid sequence of SEQ ID No: 616. This enzyme is believed to have cysteine-type peptidase activity.

[0312] Enzyme PR 309 is encoded by the 2273 nucleotides in SEQ ID No: 617 which encodes the 461 amino acid sequence of SEQ ID No: 618. This enzyme is believed to have cysteine-type endopeptidase activity.

[0313] Enzyme PR 310 is encoded by the 1743 nucleotides in SEQ ID No: 619 which encodes the 516 amino acid sequence of SEQ ID No: 620. This enzyme is believed to have metallopeptidase activity.

[0314] Enzyme PR 31 1 is encoded by the 1729 nucleotides in SEQ ID No: 621 which encodes the 487 amino acid sequence of SEQ ID No: 622. This enzyme is believed to have aminopeptidase activity.

[0315] Enzyme PR 312 is encoded by the 2780 nucleotides in SEQ ID No: 623 which encodes the 893 amino acid sequence of SEQ ID No: 624. This enzyme is believed to have serine-type endopeptidase activity.

[0316] Enzyme PR 313 is encoded by the 4427 nucleotides in SEQ ID No: 625 which encodes the 890 amino acid sequence of SEQ ID No: 626. This enzyme is believed to have serine-type peptidase activity.

[0317] Enzyme PR 314 is encoded by the 2095 nucleotides in SEQ ID No: 627 which encodes the 524 amino acid sequence of SEQ ID No: 628. This enzyme is believed to have metalloendopeptidase activity.

[0318] Enzyme PR 315 is encoded by the 1681 nucleotides in SEQ ID No: 629 which encodes the 451 amino acid sequence of SEQ ID No: 630. This enzyme is believed to have aspartic-type endopeptidase activity.

[0319] Enzyme PR 316 is encoded by the 4572 nucleotides in SEQ ID No: 631 which encodes the 1222 amino acid sequence of SEQ ID No: 632. This enzyme is believed to have endopeptidase activity.

[0320] Enzyme PR 317 is encoded by the 1553 nucleotides in SEQ ID No: 633 which encodes the 454 amino acid sequence of SEQ ID No: 634. This enzyme is believed to have aspartic-type endopeptidase activity.

[0321] Enzyme PR 318 is encoded by the 3545 nucleotides in SEQ ID No: 635 which encodes the 924 amino acid sequence of SEQ ID No: 636. This enzyme is believed to have metalloendopeptidase activity.

[0322] Enzyme PR 319 is encoded by the 2758 nucleotides in SEQ ID No: 637 which encodes the 893 amino acid sequence of SEQ ID No: 638. This enzyme is believed to have metallopeptidase activity.

[0323] Enzyme PR 320 is encoded by the 3684 nucleotides in SEQ ID No: 639 which encodes the 832 amino acid sequence of SEQ ID No: 640. This enzyme is believed to have aminopeptidase activity.

[0324] Enzyme PR 321 is encoded by the 5035 nucleotides in SEQ ID No: 641 which encodes the 958 amino acid sequence of SEQ ID No: 642. This enzyme is believed to have serine-type peptidase activity.

[0325] Enzyme PR 322 is encoded by the 6479 nucleotides in SEQ ID No: 643 which encodes the 1910 amino acid sequence of SEQ ID No: 644. This enzyme is believed to have endopeptidase activity.

[0326] Enzyme PR 323 is encoded by the 3913 nucleotides in SEQ ED No: 645 which encodes the 691 amino acid sequence of SEQ ID No: 646. This enzyme is believed to have aminopeptidase activity.

[0327] Enzyme PR 324 is encoded by the 573 nucleotides in SEQ ID No: 647 which

encodes the 173 amino acid sequence of SEQ ID No: 648. This enzyme is believed to have threonine-type endopeptidase activity.

[0328] Enzyme PR 325 is encoded by the 2191 nucleotides in SEQ ID No: 649 which encodes the 562 amino acid sequence of SEQ ID No: 650. This enzyme is believed to have aspartic-type endopeptidase activity.

[0329] Enzyme PR 326 is encoded by the 1790 nucleotides in SEQ ID No: 651 which encodes the 553 amino acid sequence of SEQ ID No: 652. This enzyme is believed to have aspartic-type endopeptidase activity.

[0330] Enzyme PR 327 is encoded by the 553 nucleotides in SEQ ID No: 653 which encodes the 129 amino acid sequence of SEQ ID No: 654. This enzyme is believed to have cysteine-type endopeptidase activity.

[0331] Enzyme PR 328 is encoded by the 1843 nucleotides in SEQ ID No: 655 which encodes the 505 amino acid sequence of SEQ ID No: 656. This enzyme is believed to have serine-type endopeptidase activity.

[0332] Enzyme PR 329 is encoded by the 308 nucleotides in SEQ ID No: 657 which

encodes the 75 amino acid sequence of SEQ ID No: 658. This enzyme is believed to have serine-type peptidase activity.

[0333] Enzyme PR 330 is encoded by the 2904 nucleotides in SEQ ID No: 659 which encodes the 916 amino acid sequence of SEQ ID No: 660. This enzyme is believed to have metallopeptidase activity.

[0334] Enzyme PR 331 is encoded by the 1387 nucleotides in SEQ ID No: 661 which encodes the 385 amino acid sequence of SEQ ED No: 662. This enzyme is believed to have cysteine-type endopeptidase activity.

[0335] Enzyme PR 332 is encoded by the 3323 nucleotides in SEQ ID No: 663 which encodes the 946 amino acid sequence of SEQ ED No: 664. This enzyme is believed to have serine-type endopeptidase activity.

[0336] Enzyme PR 333 is encoded by the 672 nucleotides in SEQ ED No: 665 which

encodes the 168 amino acid sequence of SEQ ED No: 666. This enzyme is believed to have serine-type peptidase activity.

[0337] Enzyme PR 334 is encoded by the 3983 nucleotides in SEQ ED No: 667 which encodes the 1099 amino acid sequence of SEQ ED No: 668. This enzyme is believed to have serine-type endopeptidase activity.

[0338] Enzyme PR 335 is encoded by the 2455 nucleotides in SEQ ED No: 669 which encodes the 659 amino acid sequence of SEQ ED No: 670. This enzyme is believed to have serine-type carboxypeptidase activity.

[0339] Enzyme PR 336 is encoded by the 1059 nucleotides in SEQ ED No: 671 which encodes the 352 amino acid sequence of SEQ ED No: 672. This enzyme is believed to have aspartic-type endopeptidase activity.

[0340] Enzyme PR 337 is encoded by the 1737 nucleotides in SEQ ED No: 673 which encodes the 578 amino acid sequence of SEQ ED No: 674. This enzyme is believed to have carboxypeptidase activity.

[0341] Enzyme PR 338 is encoded by the 3034 nucleotides in SEQ ED No: 675 which encodes the 879 amino acid sequence of SEQ ED No: 676. This enzyme is believed to have aminopeptidase activity.

[0342] Enzyme PR 339 is encoded by the 1006 nucleotides in SEQ ED No: 677 which encodes the 239 amino acid sequence of SEQ ED No: 678. This enzyme is believed to have metallopeptidase activity.

[0343] Enzyme PR 340 is encoded by the 2293 nucleotides in SEQ ID No: 679 which encodes the 507 amino acid sequence of SEQ ID No: 680. This enzyme is believed to have aspartic-type endopeptidase activity.

[0344] Enzyme PR 341 is encoded by the 1720 nucleotides in SEQ ID No: 681 which encodes the 554 amino acid sequence of SEQ ED No: 682. This enzyme is believed to have serine-type carboxypeptidase activity.

[0345] Enzyme PR 342 is encoded by the 1547 nucleotides in SEQ ID No: 683 which encodes the 392 amino acid sequence of SEQ ED No: 684. This enzyme is believed to have serine-type endopeptidase activity.

[0346] Enzyme PR 343 is encoded by the 1662 nucleotides in SEQ ED No: 685 which encodes the 553 amino acid sequence of SEQ ED No: 686. This enzyme is believed to have metallopeptidase activity.

[0347] Enzyme PR 344 is encoded by the 2041 nucleotides in SEQ ID No: 687 which encodes the 639 amino acid sequence of SEQ ED No: 688. This enzyme is believed to have serine-type carboxypeptidase activity.

[0348] Enzyme PR 345 is encoded by the 1884 nucleotides in SEQ ID No: 689 which encodes the 508 amino acid sequence of SEQ ED No: 690. This enzyme is believed to have aminopeptidase activity.

[0349] Enzyme PR 346 is encoded by the 3552 nucleotides in SEQ ID No: 691 which encodes the 789 amino acid sequence of SEQ ED No: 692. This enzyme is believed to have aspartic-type endopeptidase activity.

[0350] Enzyme PR 347 is encoded by the 2015 nucleotides in SEQ ED No: 693 which encodes the 613 amino acid sequence of SEQ ED No: 694. This enzyme is believed to have metallopeptidase activity.

[0351] Enzyme PR 348 is encoded by the 1810 nucleotides in SEQ ED No: 695 which encodes the 530 amino acid sequence of SEQ ED No: 696. This enzyme is believed to have serine-type carboxypeptidase activity.

[0352] Enzyme PR 349 is encoded by the 1640 nucleotides in SEQ ID No: 697 which encodes the 421 amino acid sequence of SEQ ID No: 698. This enzyme is believed to have metallocarboxypeptidase activity.

[0353] Enzyme PR 350 is encoded by the 2143 nucleotides in SEQ ED No: 699 which encodes the 621 amino acid sequence of SEQ ID No:700. This enzyme is believed to have serine-type endopeptidase activity.

[0354] Enzyme PR 351 is encoded by the 1576 nucleotides in SEQ ID No: 701 which encodes the 490 amino acid sequence of SEQ ID No: 702. This enzyme is believed to have metallocarboxypeptidase activity.

[0355] Enzyme PR 352 is encoded by the 7466 nucleotides in SEQ ID No: 703 which encodes the 1630 amino acid sequence of SEQ ID No: 704. This enzyme is believed to have metalloendopeptidase activity.

[0356] Enzyme PR 353 is encoded by the 4096 nucleotides in SEQ ID No: 705 which encodes the 936 amino acid sequence of SEQ ID No: 706. This enzyme is believed to have metalloaminopeptidase activity.

[0357] Enzyme PR 354 is encoded by the 5235 nucleotides in SEQ ID No: 707 which encodes the 1004 amino acid sequence of SEQ ID No: 708. This enzyme is believed to have metalloendopeptidase activity.

[0358] Enzyme PR 355 is encoded by the 3101 nucleotides in SEQ ID No: 709 which encodes the 1010 amino acid sequence of SEQ ID No: 710. This enzyme is believed to have metalloendopeptidase activity.

[0359] Enzyme PR 356 is encoded by the 1661 nucleotides in SEQ ID No: 71 1 which encodes the 348 amino acid sequence of SEQ ID No: 712. This enzyme is believed to have metalloendopeptidase activity.

[0360] Enzyme PR 357 is encoded by the 925 nucleotides in SEQ ID No: 713 which

encodes the 265 amino acid sequence of SEQ ID No: 714. This enzyme is believed to have aspartic-type endopeptidase activity.

[0361] Enzyme PR 358 is encoded by the 1339 nucleotides in SEQ ID No: 715 which encodes the 288 amino acid sequence of SEQ ID No: 716. This enzyme is believed to have aspartic-type endopeptidase activity.

[0362] Enzyme PR 359 is encoded by the 1635 nucleotides in SEQ ID No: 717 which encodes the 381 amino acid sequence of SEQ ID No: 718. This enzyme is believed to have serine-type endopeptidase activity.

[0363] Enzyme PR 360 is encoded by the 3751 nucleotides in SEQ ID No: 719 which encodes the 980 amino acid sequence of SEQ ID No: 720. This enzyme is believed to have metallopeptidase activity.

[0364] Enzyme PR 361 is encoded by the 2153 nucleotides in SEQ ID No: 721 which encodes the 528 amino acid sequence of SEQ ID No: 722. This enzyme is believed to have aspartic-type endopeptidase activity.

[0365] Enzyme PR 362 is encoded by the 2500 nucleotides in SEQ ID No: 723 which encodes the 774 amino acid sequence of SEQ ED No: 724. This enzyme is believed to have metallopeptidase activity.

[0366] Enzyme PR 363 is encoded by the 4020 nucleotides in SEQ ID No: 725 which encodes the 734 amino acid sequence of SEQ ED No: 726. This enzyme is believed to have metallocarboxypeptidase activity.

[0367] Enzyme PR 364 is encoded by the 2252 nucleotides in SEQ ID No: 727 which encodes the 648 amino acid sequence of SEQ ID No: 728. This enzyme is believed to have aspartic-type endopeptidase activity.

[0368] Enzyme PR 365 is encoded by the 3155 nucleotides in SEQ ID No: 729 which encodes the 978 amino acid sequence of SEQ ID No: 730. This enzyme is believed to have aminopeptidase activity.

[0369] Enzyme PR 366 is encoded by the 1582 nucleotides in SEQ ED No: 731 which encodes the 325 amino acid sequence of SEQ ID No: 732. This enzyme is believed to have metalloexopeptidase activity.

[0370] Enzyme PR 367 is encoded by the 1657 nucleotides in SEQ ID No: 733 which encodes the 404 amino acid sequence of SEQ ID No: 734. This enzyme is believed to have peptidase activity.

[0371] Enzyme PR 368 is encoded by the 423 nucleotides in SEQ ID No: 735 which

encodes the 140 amino acid sequence of SEQ ID No: 736. This enzyme is believed to have protease activity.

[0372] Enzyme PR 369 is encoded by the 537 nucleotides in SEQ ED No: 737 which

encodes the 178 amino acid sequence of SEQ ID No: 738. This enzyme is believed to have metallopeptidase activity.

[0373] Enzyme PR 370 is encoded by the 2883 nucleotides in SEQ ID No: 739 which encodes the 158 amino acid sequence of SEQ ID No: 740. This enzyme is believed to have peptidase activity.

[0374] Enzyme PR 371 is encoded by the 546 nucleotides in SEQ ID No: 741 which

encodes the 182 amino acid sequence of SEQ ID No: 742. This enzyme is believed to have peptidase activity.

[0375] Enzyme PR 372 is encoded by the 435 nucleotides in SEQ ID No: 743 which

encodes the 145 amino acid sequence of SEQ ED No: 744. This enzyme is believed to have peptidase activity.

[0376] Enzyme PR 373 is encoded by the 9337 nucleotides in SEQ ID No: 745 which encodes the 105 amino acid sequence of SEQ ID No: 746. This enzyme is believed to have metalloprotease activity.

[0377] Enzyme PR 374 is encoded by the 5785 nucleotides in SEQ ID No: 747 which encodes the 157 amino acid sequence of SEQ ED No: 748. This enzyme is believed to have dipeptidyl peptidase activity.

[0378] Enzyme PR 375 is encoded by the 309 nucleotides in SEQ ID No: 749 which

encodes the 50 amino acid sequence of SEQ ID No: 750. This enzyme is believed to have peptidase activity.

[0379] Enzyme PR 376 is encoded by the 631 nucleotides in SEQ ID No: 751 which

encodes the 187 amino acid sequence of SEQ ID No: 752. This enzyme is believed to have peptidase activity.

[0380] Enzyme PR 377 is encoded by the 301 nucleotides in SEQ ID No: 753 which

encodes the 55 amino acid sequence of SEQ DD No: 754. This enzyme is believed to have peptidase activity.

[0381] Enzyme PR 378 is encoded by the 426 nucleotides in SEQ DD No: 755 which

encodes the 141 amino acid sequence of SEQ DD No: 756. This enzyme is believed to have peptidase activity.

[0382] Enzyme PR 379 is encoded by the 177 nucleotides in SEQ DD No: 757 which

encodes the 50 amino acid sequence of SEQ DD No: 758. This enzyme is believed to have aspartyl protease activity.

[0383] Enzyme PR 380 is encoded by the 564 nucleotides in SEQ DD No: 759 which

encodes the 147 amino acid sequence of SEQ DD No: 760. This enzyme is believed to have protease activity.

[0384] Enzyme PR 381 is encoded by the 1753 nucleotides in SEQ DD No: 761 which encodes the 139 amino acid sequence of SEQ DD No: 762. This enzyme is believed to have aspartyl protease activity.

[0385] Enzyme PR 382 is encoded by the 776 nucleotides in SEQ DD No: 763 which

encodes the 165 amino acid sequence of SEQ DD No: 764. This enzyme is believed to have peptidase activity.

[0386] Enzyme PR 383 is encoded by the 678 nucleotides in SEQ DD No: 765 which

encodes the 92 amino acid sequence of SEQ DD No: 766. This enzyme is believed to have peptidase .

[0387] Enzyme PR 384 is encoded by the 557 nucleotides in SEQ ID No: 767 which encodes the 63 amino acid sequence of SEQ ID No: 768. This enzyme is believed to have peptidase activity.

[0388] Enzyme PR 385 is encoded by the 3198 nucleotides in SEQ ID No: 769 which encodes the 92 amino acid sequence of SEQ ID No: 770. This enzyme is believed to have endopeptidase activity.

[0389] Enzyme PR 386 is encoded by the 189 nucleotides in SEQ ID No: 771 which encodes the 62 amino acid sequence of SEQ ID No: 772. This enzyme is believed to have peptidase activity.

[0390] Enzyme PR 387 is encoded by the 642 nucleotides in SEQ ID No: 773 which encodes the 57 amino acid sequence of SEQ ID No: 774. This enzyme is believed to have protease activity.

[0391] Enzyme PR 388 is encoded by the 450 nucleotides in SEQ ID No: 775 which encodes the 99 amino acid sequence of SEQ ID No: 776. This enzyme is believed to have peptidase activity.

[0392] Enzyme PR 389 is encoded by the 375 nucleotides in SEQ ID No: 777 which encodes the 124 amino acid sequence of SEQ ID No: 778. This enzyme is believed to have metallopeptidase activity.

[0393] Enzyme PR 390 is encoded by the 505 nucleotides in SEQ ΰ No: 779 which

encodes the 72 amino acid sequence of SEQ ID No: 780. This enzyme is believed to have peptidase activity.

[0394] Enzyme PR 391 is encoded by the 564 nucleotides in SEQ ID No: 781 which

encodes the 147 amino acid sequence of SEQ ID No: 782. This enzyme is believed to have protease activity.

[0395] Enzyme PR 392 is encoded by the 348 nucleotides in SEQ ID No: 783 which encodes the 76 amino acid sequence of SEQ ID No: 784. This enzyme is believed to have peptidase activity.

[0396] Enzyme PR 393 is encoded by the 171 nucleotides in SEQ ID No: 785 which encodes the 56 amino acid sequence of SEQ ID No: 786. This enzyme is believed to have peptidase activity.

[0397] Enzyme PR 394 is encoded by the 347 nucleotides in SEQ ID No: 787 which

encodes the 100 amino acid sequence of SEQ ID No: 788. This enzyme is believed to have peptidase activity.

[0398] Enzyme PR 395 is encoded by the 251 nucleotides in SEQ ID No: 789 which encodes the 47 amino acid sequence of SEQ ID No: 790. This enzyme is believed to have peptidase activity.

[0399] Enzyme PR 396 is encoded by the 1144 nucleotides in SEQ ID No: 791 which encodes the 188 amino acid sequence of SEQ ID No: 792. This enzyme is believed to have metallopeptidase activity.

[0400] Enzyme PR 397 is encoded by the 777 nucleotides in SEQ ID No: 793 which

encodes the 129 amino acid sequence of SEQ ID No: 794. This enzyme is believed to have peptidase activity.

[0401] Enzyme PR 398 is encoded by the 2896 nucleotides in SEQ ID No: 795 which encodes the 171 amino acid sequence of SEQ ID No: 796. This enzyme is believed to have peptidase activity.

[0402] Enzyme PR 399 is encoded by the 1923 nucleotides in SEQ ID No: 797 which encodes the 91 amino acid sequence of SEQ ID No: 798. This enzyme is believed to have peptidase activity.

[0403] Enzyme PR 400 is encoded by the 926 nucleotides in SEQ ID No: 799 which

encodes the 260 amino acid sequence of SEQ ID No: 800. This enzyme is believed to have enzyme .

[0404] Enzyme PR 401 is encoded by the 4230 nucleotides in SEQ ID No: 801 which encodes the 955 amino acid sequence of SEQ ID No: 802. This enzyme is believed to have protease activity.

[0405] Enzyme PR 402 is encoded by the 1731 nucleotides in SEQ ID No: 803 which encodes the 441 amino acid sequence of SEQ ID No: 804. This enzyme is believed to have protease activity.

[0406] Enzyme PR 403 is encoded by the 2211 nucleotides in SEQ ID No: 805 which encodes the 695 amino acid sequence of SEQ ID No: 806. This enzyme is believed to have peptidase activity.

[0407] Enzyme PR 404 is encoded by the 2232 nucleotides in SEQ ED No: 807 which encodes the *632 amino acid sequence of SEQ ID No: 808. This enzyme is believed to have metallopeptidase activity.

[0408] Enzyme PR 405 is encoded by the 6960 nucleotides in SEQ ID No: 809 which encodes the 2272 amino acid sequence of SEQ ED No: 810. This enzyme is believed to have peptidase activity.

[0409] Enzyme PR 406 is encoded by the 4230 nucleotides in SEQ ED No: 811 which encodes the 955 amino acid sequence of SEQ ED No: 812. This enzyme is believed to have protease activity.

[0410] Enzyme PR 407 is encoded by the 435 nucleotides in SEQ ED No: 813 which

encodes the 66 amino acid sequence of SEQ ED No: 814. This enzyme is believed to have peptidase activity.

[0411] Enzyme PR 408 is encoded by the 538 nucleotides in SEQ ID No: 815 which encodes the 55 amino acid sequence of SEQ ED No: 816. This enzyme is believed to have peptidase activity.

[0412] Enzyme PR 409 is encoded by the 984 nucleotides in SEQ ED No: 817 which

encodes the 159 amino acid sequence of SEQ ED No: 818. This enzyme is believed to have peptidase activity.

[0413] Enzyme PR 410 is encoded by the 1731 nucleotides in SEQ ED No: 819 which encodes the 441 amino acid sequence of SEQ ED No: 820. This enzyme is believed to have aminopeptidase activity.

[0414] Enzyme PR 41 1 is encoded by the 891 nucleotides in SEQ ED No: 821 which

encodes the 157 amino acid sequence of SEQ ED No: 822. This enzyme is believed to have metallopeptidase activity.

[0415] Enzyme PR 412 is encoded by the 4361 nucleotides in SEQ ED No: 823 which encodes the 1232 amino acid sequence of SEQ ED No: 824. This enzyme is believed to have peptidase activity.

[0416] Enzyme PR 413 is encoded by the 744 nucleotides in SEQ ED No: 825 which

encodes the 136 amino acid sequence of SEQ ED No: 826. This enzyme is believed to have peptidase activity.

[0417] Enzyme PR 414 is encoded by the 2457 nucleotides in SEQ ED No: 827 which encodes the 419 amino acid sequence of SEQ ED No: 828. This enzyme is believed to have peptidase activity.

[0418] Enzyme PR 415 is encoded by the 1906 nucleotides in SEQ ED No: 829 which encodes the 334 amino acid sequence of SEQ ED No: 830. This enzyme is believed to have metallopeptidase activity.

[0419] Enzyme PR 416 is encoded by the 3453 nucleotides in SEQ ED No: 831 which encodes the 861 amino acid sequence of SEQ ED No: 832. This enzyme is believed to have protease activity.

[0420] Enzyme PR 417 is encoded by the 2038 nucleotides in SEQ ID No: 833 which encodes the 657 amino acid sequence of SEQ ID No: 834. This enzyme is believed to have protease activity.

[0421] Enzyme PR 418 is encoded by the 950 nucleotides in SEQ ID No: 835 which

encodes the 296 amino acid sequence of SEQ ID No: 836. This enzyme is believed to have protease activity.

[0422] Enzyme PR 419 is encoded by the 1521 nucleotides in SEQ ID No: 837 which encodes the 422 amino acid sequence of SEQ ID No: 838. This enzyme is believed to have protease activity.

[0423] Enzyme PR 420 is encoded by the 671 nucleotides in SEQ ID No: 839 which

encodes the 90 amino acid sequence of SEQ ID No: 840. This enzyme is believed to have protease activity.

[0424] Enzyme PR 421 is encoded by the 1464 nucleotides in SEQ ID No: 841 which encodes the 487 amino acid sequence of SEQ ID No: 842. This enzyme is believed to have asparaginase activity.

■ [0425] Enzyme PR 422 is encoded by the 600 nucleotides in SEQ ID No: 843 which

encodes the 199 amino acid sequence of SEQ ID No: 844. This enzyme is believed to have peptidase activity.

[0426] Enzyme PR 423 is encoded by the 600 nucleotides in SEQ ID No: 845 which

encodes the 200 amino acid sequence of SEQ ID No: 846. This enzyme is believed to have peptidase activity.

[0427] Enzyme PR 424 is encoded by the 1 176 nucleotides in SEQ ID No: 847 which encodes the 391 amino acid sequence of SEQ ID No: 848. This enzyme is believed to have asparaginase activity.

[0428] Enzyme PR 425 is encoded by the 1854 nucleotides in SEQ ID No: 849 which encodes the 617 amino acid sequence of SEQ ID No: 850. This enzyme is believed to have amidohydrolase activity.

[0429] Enzyme PR 426 is encoded by the 1233 nucleotides in SEQ ID No: 851 which encodes the 410 amino acid sequence of SEQ ID No: 852. This enzyme is believed to have amidohydrolase activity.

[0430] Enzyme PR 427 is encoded by the 1044 nucleotides in SEQ ID No: 853 which encodes the 347 amino acid sequence of SEQ ID No: 854. This enzyme is believed to have amidohydrolase activity.

[0431] Enzyme PR 428 is encoded by the 2898 nucleotides in SEQ ID No: 855 which encodes the 965 amino acid sequence of SEQ ID No: 856. This enzyme is believed to have amidohydrolase activity.

[0432] Enzyme PR 429 is encoded by the 1398 nucleotides in SEQ ID No: 857 which encodes the 465 amino acid sequence of SEQ ID No: 858. This enzyme is believed to have amidohydrolase activity.

8] Enzyme PR 430 is encoded by the 174 nucleotides in SEQ ID No: 859 which encodes the 57 amino acid sequence of SEQ ID No: 860. This enzyme is believed to have protease activity.

[0139] As used herein, reference to an isolated protein or polypeptide in the present invention, including any of the enzymes disclosed herein, includes full-length proteins and their glycosylated or otherwise modified forms forms, fusion proteins, or any fragment or homologue or variant of such a protein. More specifically, an isolated protein, such as an enzyme according to the present invention, is a protein (including a polypeptide or peptide) that has been removed from its natural milieu (i.e., that has been subject to human manipulation) and can include purified proteins, partially purified proteins, recombinantly produced proteins, synthetically produced proteins, proteins complexed with lipids, soluble proteins, and isolated proteins associated with other proteins, for example. As such, "isolated" does not reflect the extent to which the protein has been purified. Preferably, an isolated protein of the present invention is produced recombinantly. In addition, and by way of example, a "Myceliophthora thermophila or M. thermophila protein" or "Myceliophthora thermophila or M. thermophila enzyme" refers to a protein (generally including a homologue or variant of a naturally occurring protein) from Myceliophthora thermophila or to a protein that has been otherwise produced from the knowledge of the structure (e.g., sequence) and perhaps the function of a naturally occurring protein from Myceliophthora thermophila. In other words, a M. thermophila protein includes any protein that has substantially similar structure and function of a naturally occurring M. thermophila protein or that is a biologically active (i.e., has biological activity) homologue or variant of a naturally occurring protein from M. thermophila as described in detail herein. As such, a M. thermophila protein can include purified, partially purified, recombinant, mutated/modified and synthetic proteins. According to the present invention, the terms "modification," "mutation," and "variant" can be used interchangeably, particularly with regard to the modifications/mutations to the amino acid sequence of a M. thermophila protein (or nucleic acid sequences) described herein. An isolated protein according to the present invention can be isolated from its natural source, produced recombinantly or produced synthetically.

[0140] According to the present invention, the terms "modification" and "mutation" can be used interchangeably, particularly with regard to the modifications/mutations to the primary amino acid sequences of a protein or peptide (or nucleic acid sequences) described herein. The term "modification" can also be used to describe post- translational modifications to a protein or peptide including, but not limited to, rnethylation, farnesylation, carboxymethylation, geranyl geranylation, glycosylation, phosphorylation, acetylation, myristoylation, prenylation, palmitation, and/or amidation. Modification can also include the cleavage of a signal peptide, or methionine, or other portions of the peptide that require cleavage to generate the mature peptide. Modifications can also include, for example, complexing a protein or peptide with another compound. Such modifications can be considered to be mutations, for example, if the modification is different than the post-translational modification that occurs in the natural, wild-type protein or peptide.

[0141] As used herein, the terms "homologue" or "variants" are used to refer to a protein or peptide which differs from a naturally occurring protein or peptide (i.e., the "prototype" or "wild-type" protein) by minor modifications to the naturally occurring protein or peptide, but which maintains the basic protein and side chain structure of the naturally occurring form. Such changes include, but are not limited to: changes in one or a few amino acid side chains; changes one or a few amino acids, including deletions (e.g., a truncated version of the protein or peptide), insertions and/or substitutions; changes in stereochemistry of one or a few atoms; and/or minor derivatizations, including but not limited to: rnethylation, glycosylation, phosphorylation. A homologue or variant can have either enhanced, decreased, or substantially similar properties as compared to the naturally occurring protein or peptide.

[0142] Homologues or variants can be the result of natural allelic variation or natural mutation. A naturally occurring allelic variant of a nucleic acid encoding a protein is a gene that occurs at essentially the same locus (or loci) in the genome as the gene which encodes such protein, but which, due to natural variations caused by, for example, mutation or recombination, has a similar but not identical sequence. Homologous can also be the result of a gene duplication and rearrangement, resulting in a different location. Allelic variants typically encode proteins having similar activity to that of the protein encoded by the gene to which they are being compared. One class of allelic variants can encode the same protein but have different nucleic acid sequences due to the degeneracy of the genetic code. Allelic variants can also comprise alterations in the 5' or 3' untranslated regions of the gene (e.g., in regulatory control regions). Allelic variants are well known to those skilled in the art.Homologues or variants can be produced using techniques known in the art for the production of proteins including, but not limited to, direct modifications to the isolated, naturally occurring protein, direct protein synthesis, or modifications to the nucleic acid sequence encoding the protein using, for example, classic or recombinant DNA techniques to effect random or targeted mutagenesis.

[0143] Modifications of a protein, such as in a homologue or variant, may result in proteins having the same biological activity as the naturally occurring protein, or in proteins having decreased or increased biological activity as compared to the naturally occurring protein. Modifications which result in a decrease in protein expression or a decrease in the activity of the protein, can be referred to as inactivation (complete or partial), down-regulation, or decreased action of a protein. Similarly, modifications which result in an increase in protein expression or an increase in the activity of the protein, can be referred to as amplification, overproduction, activation, enhancement, up-regulation or increased action of a protein.

[0144] According to the present invention, an isolated protein, including a biologically active homologue, variant, or fragment thereof, has at least one characteristic of biological activity of a wild-type, or naturally occurring, protein. As discussed above, in general, the biological activity or biological action of a protein refers to any function(s) exhibited or performed by the protein that is ascribed to the naturally occurring form of the protein as measured or observed in vivo (i.e., in the natural physiological environment of the protein) or in vitro (i.e., under laboratory conditions). The biological activity of a protein of the present invention can include an enzyme activity (catalytic activity and/or substrate binding activity), endopeptidase, exopeptidase, metallopeptidase, amino peptidase, carboxy peptidase, amino acid-specific peptidase or any other activity disclosed herein. Specific biological activities of the proteins disclosed herein are described in detail above and in the Examples. Methods of detecting and measuring the biological activity of a protein of the invention include, but are not limited to, the assays described in the Examples section below. Such assays include, but are not limited to, measurement of enzyme activity (e.g., catalytic activity), measurement of substrate binding, and the like. It is noted that an isolated protein of the present invention (including homologues or variants) is not required to have a biological activity such as catalytic activity. A protein can be a truncated, mutated or inactive protein, or lack at least one activity of the wild-type enzyme, for example. Inactive proteins may be useful in some screening assays, for example, or for other purposes such as antibody production.Methods to measure protein expression levels of a protein according to the invention include, but are not limited to: western blotting, immunocytochemistry, flow cytometry or other immunologic-based assays; assays based on a property of the protein including but not limited to, ligand binding or interaction with other protein partners. Binding assays are also well known in the art. For example, a BIAcore machine can be used to determine the binding constant of a complex between two proteins. The dissociation constant for the complex can be determined by monitoring changes in the refractive index with respect to time as buffer is passed over the chip (O'Shannessy et al. Anal. Biochem. 212:457-468 (1993); Schuster et al., Nature 365:343-347 (1993)). Other suitable assays for measuring the binding of one protein to another include, for example, immunoassays such as enzyme linked immunoabsorbent assays (ELISA) and radioimmunoassays (RIA), or determination of binding by monitoring the change in the spectroscopic or optical properties of the proteins through fluorescence, UV absorption, circular dichroism, or nuclear magnetic resonance (NMR).

Many of the enzymes and proteins of the present invention may be desirable targets for modification and use in the processes described herein. These proteins have been described in terms of function and amino acid sequence (and nucleic acid sequence encoding the same) of representative wild-type proteins. In one embodiment of the invention, homologues or variants of a given protein (which can include related proteins from other organisms or modified forms of the given protein) are encompassed for use in the invention. Homologues or variants of a protein encompassed by the present invention can comprise, consist essentially of, or consist of, in one embodiment, an amino acid sequence that is at least about 35% identical, and more preferably at least about 40% identical, and more preferably at least about 45% identical, and more preferably at least about 50% identical, and more preferably at least about 55% identical, and more preferably at least about 60% identical, and more preferably at least about 65% identical, and more preferably at least about 70% identical, and more preferably at least about 75% identical, and more preferably at least about 80%) identical, and more preferably at least about 85%) identical, and more preferably at least about 90%> identical, and more preferably at least about 95% identical, and more preferably at least about 96% identical, and more preferably at least about 97%> identical, and more preferably at least about 98% identical, and more preferably at least about 99% identical, or any percent identity between 35%> and 99%), in whole integers (i.e., 36%>, 37%>, etc.), to an amino acid sequence disclosed herein that represents the amino acid sequence of an enzyme or protein according to the invention (including a biologically active domain of a full-length protein). Preferably, the amino acid sequence of the homologue or variant has a biological activity of the wild-type or reference protein or of a biologically active domain thereof (e.g., a catalytic domain). When denoting mutation positions, the amino acid position of the wild-type is typically used. The wild-type can also be referred to as the "parent." Additionally, any generation before the variant at issue can be a parent.

In one embodiment, a protein of the present invention comprises, consists essentially of, or consists of an amino acid sequence that, alone or in combination with other characteristics of such proteins disclosed herein, is less than 100% identical to an amino acid sequence selected from SEQ ID NO: 2, SEQ ID No: 4, SEQ ID No: 6, SEQ ID No: 8, SEQ ID No: 10, SEQ ID No: 12, SEQ ID No: 14, SEQ ID No: 16, SEQ ID No: 18, SEQ ID No: 20, SEQ ID No: 22, SEQ ID No: 24, SEQ ID No: 26, SEQ ID No: 28, SEQ ID No: 30, SEQ ID No: 32, SEQ ID No: 34, SEQ ID No: 36, SEQ ID No: 38, SEQ ID No: 40, SEQ ID No: 42, SEQ ID No: 44, SEQ ID No: 46, SEQ ID No: 48, SEQ ID No: 50, SEQ ID No: 52, SEQ ID No: 54, SEQ ID No: 56, SEQ ID No: 58, SEQ ID No: 60, SEQ ID No: 62, SEQ ID No: 64, SEQ ID No: 66, SEQ ID No: 68, SEQ ID No: 70, SEQ ID No: 72, SEQ ID No: 74, SEQ ID No: 76, SEQ ID No: 78, SEQ ID No: 80, SEQ ID No: 82, SEQ ID No: 84, SEQ ID No: 86, SEQ ID No: 88, SEQ ID No: 90, SEQ ID No: 92, SEQ ID No: 94, SEQ ID No: 96, SEQ ID No: 98, SEQ ID No: 100, SEQ ID No: 102, SEQ ID No: 104, SEQ ID No: 106, SEQ ID No: 108, SEQ ID No: 1 10, SEQ ID No: 112, SEQ ID No: 1 14, SEQ ID No: 116, SEQ ID No: 118, SEQ ID No: 120, SEQ ID No: 122, SEQ ID No: 124, SEQ ID No: 126, SEQ ID No: 128, SEQ ID No: 130, SEQ ED No: 132, SEQ ID No: 134, SEQ ED No: 136, SEQ ED No: 138, SEQ ID No: 140, SEQ ED No: 142, SEQ ID No: 144, SEQ ID No: 146, SEQ ED No: 148, SEQ ED No: 150, SEQ ED No: 152, SEQ ID No: 154, SEQ ID No: 156, SEQ DD No: 158, SEQ ID No: 160, SEQ ED No: 162, SEQ ED No: 164, SEQ ID No: 166, SEQ ED No: 168, SEQ ED No: 170, SEQ ED No: 172, SEQ ED No: 174, SEQ ED No: 176, SEQ ID No: 178, SEQ ED No: 180, SEQ ID No: 182, SEQ ED No: 184, SEQ ED No: 186, SEQ ED No: 188, SEQ ED No: 190, SEQ ED No: 192, SEQ ED No: 194, SEQ ED No: 196, SEQ ID No: 198, SEQ ED No: 200, SEQ ED No: 202, SEQ ED No: 204, SEQ ED No: 206, SEQ ED No: 208, SEQ ED No: 210, SEQ ED No: 212, SEQ ED No: 214, SEQ ID No: 216, SEQ ED No: 218, SEQ ID No: 220, SEQ ID No: 222, SEQ ID No: 224, SEQ ED No: 226, SEQ ED No: 228, SEQ ED No: 230, SEQ ID No: 232, SEQ ED No: 234, SEQ ID No: 236, SEQ ED No: 238, SEQ ED No: 240, SEQ ED No: 242, SEQ ED No: 244, SEQ ED No: 246, SEQ ED No: 248, SEQ ED No: 250, SEQ ED No: 252, SEQ ID No: 254, SEQ ED No: 256, SEQ ID No: 258, SEQ ED No: 260, SEQ ED No: 262, SEQ ED No: 264, SEQ ED No: 266, SEQ ED No: 268, SEQ ID No: 270, SEQ ED No: 272, SEQ ID No: 274, SEQ ID No: 276, SEQ ED No: 278, SEQ ED No: 280, SEQ ID No: 282, SEQ ED No: 284, SEQ ED No: 286, SEQ ED No: 288, SEQ ED No: 290, SEQ ED No: 292, SEQ ED No: 294, SEQ ID No: 296, SEQ ED No: 298, SEQ ED No:300, SEQ ED No: 302, SEQ ED No: 304, SEQ ED No: 306, SEQ ED No: 308, SEQ ED No: 310, SEQ ID No: 312, SEQ ED No: 314, SEQ ED No: 316, SEQ ED No: 318, SEQ ED No: 320, SEQ ED No: 322, SEQ ED No: 324, SEQ ED No: 326, SEQ ED No: 328, SEQ ID No: 330, SEQ ID No: 332, SEQ ID No: 334, SEQ ED No: 336, SEQ ED No: 338, SEQ ED No: 340, SEQ ED No: 342, SEQ ED No: 344, SEQ ID No: 346, SEQ ED No: 348, SEQ ID No: 350, SEQ ED No: 352, SEQ ED No: 354, SEQ ED No: 356, SEQ ED No: 358, SEQ ED No: 360, SEQ ED No: 362, SEQ ED No: 364, SEQ ED No: 366, SEQ ED No: 368, SEQ ED No: 370, SEQ ID No: 372, SEQ ED No: 374, SEQ ED No: 376, SEQ ED No: 378, SEQ ED No: 380, SEQ ED No: 382, SEQ ID No: 384, SEQ ED No: 386, SEQ ED No: 388, SEQ ED No: 390, SEQ ED No: 392, SEQ ID No: 394, SEQ ED No: 396, SEQ ED No: 398, 400, SEQ ID No: 402, SEQ ED No: 404, SEQ ED No: 406, SEQ ED No: 408, SEQ ID No: 410, SEQ ID No: 412, SEQ ID No: 414, SEQ ED No: 416, SEQ ID No: 418, SEQ ID No: 420, SEQ ED No: 422, SEQ ED No: 424, SEQ ED No: 426, SEQ ED No: 428, SEQ ED No: 430, SEQ ED No: 432, SEQ ID No: 434, SEQ ID No: 436, SEQ ID No: 438, SEQ ID No: 440, SEQ ID No: 442, SEQ ID No: 444, SEQ ID No: 446, SEQ ID No: 448, SEQ ID No: 450, SEQ ID No: 452, SEQ ID No: 454, SEQ ID No: 456, SEQ ID No: 458, SEQ 3D No: 460, SEQ ID No: 462, SEQ ED No: 464, SEQ ID No: 466, SEQ ID No: 468, SEQ ID No: 470, SEQ ID No: 472, SEQ ID No: 474, SEQ ID No: 476, SEQ ID No: 478, SEQ ID No: 480, SEQ ID No: 482, SEQ ID No: 484, SEQ ID No: 486, SEQ ID No: 488, SEQ ID No: 490, SEQ ID No: 492, SEQ ID No: 494, SEQ ID No: 496, SEQ ID No: 498, SEQ ID No: 500, SEQ ID No: 502, SEQ ID No: 504, SEQ ID No: 506, SEQ ID No: 508, SEQ ID No: 510, SEQ ID No: 512, SEQ ID No: 514, SEQ ID No: 516, SEQ ID No: 518, SEQ ED No: 520, SEQ ED No: 522, SEQ ID No: 524, SEQ ID No: 526, SEQ ID No: 528, SEQ DD No: 530, SEQ ED No: 532, SEQ ED No: 534, SEQ ED No: 536, SEQ ED No: 538, SEQ DD No: 540, SEQ DD No: 542, SEQ DD No: 544, SEQ DD No: 546, SEQ ID No: 548, SEQ ID No: 550, SEQ DD No: 552, SEQ ID No: 554, SEQ ID No: 556, SEQ ED No: 558, SEQ ED No: 560, SEQ ID No: 562, SEQ DD No: 564, SEQ DD No: 566, SEQ DD No: 568, SEQ ID No: 570, SEQ DD No: 572, SEQ DD No: 574, SEQ ED No: 576, SEQ DD No: 578, SEQ DD No: 580, SEQ DD No: 582, SEQ DD No: 584, SEQ ED No: 586, SEQ ED No: 588, SEQ ED No: 590, SEQ ED No: 592, SEQ DD No: 594, SEQ ED No: 596, SEQ ID No: 598, SEQ ED No:600, SEQ DD No: 602, SEQ ID No: 604, SEQ ED No: 606, SEQ ID No: 608, SEQ DD No: 610, SEQ ID No: 612, SEQ DD No: 614, SEQ ID No: 616, SEQ ID No: 618, SEQ DD No: 620, SEQ ED No: 622, SEQ DD No: 624, SEQ ID No: 626, SEQ DD No: 628, SEQ ID No: 630, SEQ ED No: 632, SEQ DD No: 634, SEQ DD No: 636, SEQ ED No: 638, SEQ DD No: 640, SEQ ID No: 642, SEQ ED No: 644, SEQ ID No: 646, SEQ DD No: 648, SEQ ID No: 650, SEQ DD No: 652, SEQ ED No: 654, SEQ ED No: 656, SEQ ED No: 658, SEQ ED No: 660, SEQ ED No: 662, SEQ ED No: 664, SEQ ED No: 666, SEQ ID No: 668, SEQ ID No: 670, SEQ ED No: 672, SEQ ED No: 674, SEQ DD No: 676, SEQ DD No: 678, SEQ ID No: 680, SEQ ED No: 682, SEQ ID No: 684, SEQ D No: 686, SEQ ED No: 688, SEQ DD No: 690, SEQ DD No: 692, SEQ ID No: 694, SEQ DD No: 696, SEQ ED No: 698, SEQ ED No: 700, SEQ ED No: 702, SEQ ED No: 704, SEQ ID No: 706, SEQ ED No: 708, SEQ ED No: 710, SEQ ED No: 712, SEQ ED No: 714, SEQ ED No: 716, SEQ ID No: 718, SEQ ED No: 720, SEQ ID No: 722, SEQ DD No: 724, SEQ DD No: 726, SEQ DD No: 728, SEQ DD No: 730, SEQ ED No: 732, SEQ ED No: 734, SEQ ED No: 736, SEQ DD No: 738, SEQ ED No: 740, SEQ ED No: 742, SEQ ID No: 744, SEQ ED No: 746, SEQ ID No: 748, SEQ ID No: 750, SEQ ID No: 752, SEQ ID No: 754, SEQ ID No: 756, SEQ ID No: 758, SEQ ID No: 760, SEQ ID No: 762, SEQ ID No: 764, SEQ ID No: 766, SEQ ID No: 768, SEQ ID No: 770, SEQ ID No: 772, SEQ ID No: 774, SEQ ID No: 776, SEQ ID No: 778, SEQ ID No: 780, SEQ ID No: 782, SEQ ID No: 784, SEQ ID No: 786, SEQ ID No: 788, SEQ ID No: 790, SEQ ID No: 792, SEQ ID No: 794, SEQ ID No: 796, SEQ ID No: 798, SEQ ID No: 800, SEQ ID No: 802, SEQ ID No: 804, SEQ ID No: 806, SEQ ID No: 808, SEQ ID No: 810, SEQ ED No: 812, SEQ ED No: 814, SEQ ID No: 816, SEQ ID No: 818, SEQ ID No: 820, SEQ ID No: 822, SEQ ID No: 824, SEQ ID No: 826, SEQ DD No: 828, SEQ ED No: 830, SEQ ID No: 832, SEQ ED No: 834, SEQ ID No: 836, SEQ ED No: 838, SEQ DD No: 840, SEQ ED No: 842, SEQ ID No: 844, SEQ ED No: 846, SEQ ID No: 848, SEQ DD No: 850, SEQ ID No: 852, SEQ ID No: 854, SEQ ED No: 856, SEQ ID No: 858, SEQ ID No: 860. (i.e., a homologue or variant). For example, a protein of the present invention can be less than 100% identical, in combination with being at least about 35% identical, to a given disclosed sequence. In another aspect of the invention, a homologue or variant according to the present invention has an amino acid sequence that is less than about 99% identical to any of such amino acid sequences, and in another embodiment, is less than about 98% identical to any of such amino acid sequences, and in another embodiment, is less than about 97% identical to any of such amino acid sequences, and in another embodiment, is less than about 96% identical to any of such amino acid sequences, and in another embodiment, is less than about 95% identical to any of such amino acid sequences, and in another embodiment, is less than about 94% identical to any of such amino acid sequences, and in another embodiment, is less than about 93% identical to any of such amino acid sequences, and in another embodiment, is less than about 92% identical to any of such amino acid sequences, and in another embodiment, is less than about 91% identical to any of such amino acid sequences, and in another embodiment, is less than about 90% identical to any of such amino acid sequences, and so on, in increments of whole integers.

As used herein, unless otherwise specified, reference to a percent (%) identity refers to an evaluation of homology which is performed using: (1) a BLAST 2.0 Basic BLAST homology search using blastp for amino acid searches and blastn for nucleic acid searches with standard default parameters, wherein the query sequence is filtered for low complexity regions by default (described in Altschul, S.F., Madden, T.L., Schaaffer, A.A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D.J. (1997) "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs." Nucleic Acids Res. 25:3389-3402); (2) a BLAST 2 alignment (using the parameters described below); (3) PSI-BLAST with the standard default parameters (Position- Specific Iterated BLAST; and/or (4) CAZy homology determined using standard default parameters from the Carbohydrate Active EnZymes database (Coutinho, P.M. & Henrissat, B. (1999) Carbohydrate-active enzymes: an integrated database approach. In "Recent Advances in Carbohydrate Bioengineering", H.J. Gilbert, G. Davies, B. Henrissat and B. Svensson eds., The Royal Society of Chemistry, Cambridge, pp. 3- 12).

[0148] It is noted that due to some differences in the standard parameters between BLAST 2.0 Basic BLAST and BLAST 2, two specific sequences might be recognized as having significant homology using the BLAST 2 program, whereas a search performed in BLAST 2.0 Basic BLAST using one of the sequences as the query sequence may not identify the second sequence in the top matches. In addition, PSI-BLAST provides an automated, easy-to-use version of a "profile" search, which is a sensitive way to look for sequence homologues or variants. The program first performs a gapped BLAST database search. The PSI-BLAST program uses the information from any significant alignments returned to construct a position-specific score matrix, which replaces the query sequence for the next round of database searching. Therefore, it is to be understood that percent identity can be determined by using any one of these programs.

[0149] Two specific sequences can be aligned to one another using BLAST 2 sequence as described in Tatusova and Madden, (1999), "Blast 2 sequences - a new tool for comparing protein and nucleotide sequences", FEMS Microbiol Lett. 174:247-250. BLAST 2 sequence alignment is performed in blastp or blastn using the BLAST 2.0 algorithm to perform a Gapped BLAST search (BLAST 2.0) between the two sequences allowing for the introduction of gaps (deletions and insertions) in the resulting alignment. For purposes of clarity herein, a BLAST 2 sequence alignment is performed using the standard default parameters as follows.

[0150] For blastn, using 0 BLOSUM62 matrix:

Reward for match = 1

Penalty for mismatch = -2 Open gap (5) and extension gap (2) penalties gap x_dropoff (50) expect (10) word size (11) filter (on)

[0151] For blastp, using 0 BLOSUM62 matrix:

Open gap (11) and extension gap (1) penaltiesgap x_dropoff (50) expect (10) word size (3) filter (on).

[0152] A protein of the present invention can also include proteins having an amino acid sequence comprising at least 10 contiguous amino acid residues of any of the sequences described herein (i.e., 10 contiguous amino acid residues having 100% identity with 10 contiguous amino acids of the amino acid sequences of SEQ ID NO: 2, SEQ ID No: 4, SEQ ID No: 6, SEQ ID No: 8, SEQ ID No: 10, SEQ ID No: 12, SEQ ID No: 14, SEQ ID No: 16, SEQ ID No: 18, SEQ ID No: 20, SEQ ID No: 22, SEQ ID No: 24, SEQ ID No: 26, SEQ ID No: 28, SEQ ID No: 30, SEQ ID No: 32, SEQ ID No: 34, SEQ ID No: 36, SEQ ID No: 38, SEQ ID No: 40, SEQ ID No: 42, SEQ ID No: 44, SEQ ID No: 46, SEQ ID No: 48, SEQ ID No: 50, SEQ ID No: 52, SEQ ID No: 54, SEQ ID No: 56, SEQ ID No: 58, SEQ ID No: 60, SEQ ID No: 62, SEQ ID No: 64, SEQ ID No: 66, SEQ ID No: 68, SEQ ID No: 70, SEQ ID No: 72, SEQ ID No: 74, SEQ ID No: 76, SEQ ID No: 78, SEQ ID No: 80, SEQ ID No: 82, SEQ ID No: 84, SEQ ID No: 86, SEQ ID No: 88, SEQ ID No: 90, SEQ ID No: 92, SEQ ID No: 94, SEQ ID No: 96, SEQ ID No: 98, SEQ ID No: 100, SEQ ID No: 102, SEQ ID No: 104, SEQ ID No: 106, SEQ ID No: 108, SEQ ID No: 110, SEQ ID No: 112, SEQ ID No: 114, SEQ ID No: 116, SEQ ED No: 118, SEQ ED No: 120, SEQ ID No: 122, SEQ ID No: 124, SEQ ID No: 126, SEQ ID No: 128, SEQ ID No: 130, SEQ ED No: 132, SEQ ED No: 134, SEQ ED No: 136, SEQ ED No: 138, SEQ ED No: 140, SEQ ED No: 142, SEQ ED No: 144, SEQ ED No: 146, SEQ ED No: 148, SEQ ID No: 150, SEQ ID No: 152, SEQ ED No: 154, SEQ ED No: 156, SEQ ED No: 158, SEQ ED No: 160, SEQ ID No: 162, SEQ ED No: 164, SEQ ID No: 166, SEQ ED No: 168, SEQ ED No: 170, SEQ ED No: 172, SEQ ED No: 174, SEQ ED No: 176, SEQ ED No: 178, SEQ ID No: 180, SEQ ED No: 182, SEQ ID No: 184, SEQ ED No: 186, SEQ ID No: 188, SEQ ID No: 190, SEQ ED No: 192, SEQ ED No: 194, SEQ ED No: 196, SEQ ED No: 198, SEQ ID No: 200, SEQ ED No: 202, SEQ ID No: 204, SEQ ED No: 206, SEQ ID No: 208, SEQ ED No: 210, SEQ ED No: 212, SEQ ED No: 214, SEQ ID No: 216, SEQ ID No: 218, SEQ ID No: 220, SEQ ID No: 222, SEQ ED No: 224, SEQ ID No: 226, SEQ ED No: 228, SEQ ID No: 230, SEQ ID No: 232, SEQ ID No: 234, SEQ ID No: 236, SEQ ID No: 238, SEQ ID No: 240, SEQ ID No: 242, SEQ ID No: 244, SEQ ID No: 246, SEQ ID No: 248, SEQ ID No: 250, SEQ ID No: 252, SEQ ID No: 254, SEQ ID No: 256, SEQ ID No: 258, SEQ ID No: 260, SEQ ID No: 262, SEQ ID No: 264, SEQ ID No: 266, SEQ ID No: 268, SEQ ID No: 270, SEQ ID No: 272, SEQ ID No: 274, SEQ ID No: 276, SEQ ID No: 278, SEQ ID No: 280, SEQ ID No: 282, SEQ ID No: 284, SEQ ID No: 286, SEQ ID No: 288, SEQ ID No: 290, SEQ ID No: 292, SEQ ID No: 294, SEQ ID No: 296, SEQ ID No: 298, SEQ ID No:300, SEQ ID No: 302, SEQ ID No: 304, SEQ ID No: 306, SEQ ID No: 308, SEQ ID No: 310, SEQ ID No: 312, SEQ ID No: 314, SEQ ID No: 316, SEQ ID No: 318, SEQ ID No: 320, SEQ ID No: 322, SEQ ID No: 324, SEQ ID No: 326, SEQ ID No: 328, SEQ ID No: 330, SEQ ID No: 332, SEQ ID No: 334, SEQ ID No: 336, SEQ ID No: 338, SEQ ID No: 340, SEQ ID No: 342, SEQ ID No: 344, SEQ ID No: 346, SEQ ID No: 348, SEQ ED No: 350, SEQ ID No: 352, SEQ ID No: 354, SEQ ID No: 356, SEQ ED No: 358, SEQ ID No: 360, SEQ ID No: 362, SEQ ED No: 364, SEQ ID No: 366, SEQ ID No: 368, SEQ ID No: 370, SEQ ID No: 372, SEQ ID No: 374, SEQ ID No: 376, SEQ ID No: 378, SEQ ID No: 380, SEQ ID No: 382, SEQ ED No: 384, SEQ ID No: 386, SEQ ID No: 388, SEQ ID No: 390, SEQ ID No: 392, SEQ ID No: 394, SEQ ID No: 396, SEQ ID No: 398, 400, SEQ ID No: 402, SEQ ID No: 404, SEQ ID No: 406, SEQ ED No: 408, SEQ ID No: 410, SEQ ID No: 412, SEQ ED No: 414, SEQ ID No: 416, SEQ ID No: 418, SEQ ID No: 420, SEQ ED No: 422, SEQ ID No: 424, SEQ ID No: 426, SEQ ID No: 428, SEQ ED No: 430, SEQ ID No: 432, SEQ ID No: 434, SEQ ID No: 436, SEQ ED No: 438, SEQ ED No: 440, SEQ ID No: 442, SEQ ED No: 444, SEQ ID No: 446, SEQ ID No: 448, SEQ ID No: 450, SEQ ED No: 452, SEQ ID No: 454, SEQ ED No: 456, SEQ ID No: 458, SEQ ED No: 460, SEQ ID No: 462, SEQ ED No: 464, SEQ ID No: 466, SEQ ED No: 468, SEQ ED No: 470, SEQ ID No: 472, SEQ ID No: 474, SEQ ID No: 476, SEQ ID No: 478, SEQ ID No: 480, SEQ ID No: 482, SEQ ID No: 484, SEQ ED No: 486, SEQ ED No: 488, SEQ ID No: 490, SEQ ID No: 492, SEQ ID No: 494, SEQ ID No: 496, SEQ ID No: 498, SEQ ID No: 500, SEQ ID No: 502, SEQ ID No: 504, SEQ ID No: 506, SEQ ID No: 508, SEQ ID No: 510, SEQ ID No: 512, SEQ ID No: 514, SEQ ID No: 516, SEQ ED No: 518, SEQ ED No: 520, SEQ ID No: 522, SEQ ID No: 524, SEQ ID No: 526, SEQ ED No: 528, SEQ ID No: 530, SEQ ID No: 532, SEQ ID No: 534, SEQ ID No: 536, SEQ ID No: 538, SEQ ID No: 540, SEQ ID No: 542, SEQ ED No: 544, SEQ ED No: 546, SEQ ED No: 548, SEQ ED No: 550, SEQ ED No: 552, SEQ ED No: 554, SEQ ID No: 556, SEQ ED No: 558, SEQ ED No: 560, SEQ ED No: 562, SEQ ID No: 564, SEQ ED No: 566, SEQ ED No: 568, SEQ ED No: 570, SEQ ID No: 572, SEQ ED No: 574, SEQ ED No: 576, SEQ ID No: 578, SEQ ED No: 580, SEQ ED No: 582, SEQ ED No: 584, SEQ ED No: 586, SEQ ED No: 588, SEQ ED No: 590, SEQ ED No: 592, SEQ ED No: 594, SEQ ED No: 596, SEQ ID No: 598, SEQ ID No:600, SEQ ED No: 602, SEQ ED No: 604, SEQ ED No: 606, SEQ ED No: 608, SEQ ED No: 610, SEQ ED No: 612, SEQ ED No: 614, SEQ ED No: 616, SEQ ED No: 618, SEQ ED No: 620, SEQ ID No: 622, SEQ ID No: 624, SEQ ID No: 626, SEQ ED No: 628, SEQ ED No: 630, SEQ ED No: 632, SEQ ED No: 634, SEQ ED No: 636, SEQ ID No: 638, SEQ ID No: 640, SEQ ID No: 642, SEQ ED No: 644, SEQ ID No: 646, SEQ ID No: 648, SEQ ED No: 650, SEQ ED No: 652, SEQ ED No: 654, SEQ ID No: 656, SEQ ED No: 658, SEQ ED No: 660, SEQ ED No: 662, SEQ ID No: 664, SEQ ED No: 666, SEQ ED No: 668, SEQ ID No: 670, SEQ ED No: 672, SEQ ED No: 674, SEQ ID No: 676, SEQ ED No: 678, SEQ ID No: 680, SEQ ED No: 682, SEQ ED No: 684, SEQ ED No: 686, SEQ ED No: 688, SEQ ED No: 690, SEQ ED No: 692, SEQ ID No: 694, SEQ ED No: 696, SEQ ID No: 698, SEQ ED No: 700, SEQ ED No: 702, SEQ ID No: 704, SEQ ED No: 706, SEQ ED No: 708, SEQ ED No: 710, SEQ ED No: 712, SEQ ID No: 714, SEQ ED No: 716, SEQ ID No: 718, SEQ ED No: 720, SEQ ED No: 722, SEQ ED No: 724, SEQ ED No: 726, SEQ ED No: 728, SEQ ED No: 730, SEQ ED No: 732, SEQ ED No: 734, SEQ ED No: 736, SEQ ED No: 738, SEQ ED No: 740, SEQ ID No: 742, SEQ ED No: 744, SEQ ED No: 746, SEQ ED No: 748, SEQ ED No: 750, SEQ ID No: 752, SEQ ED No: 754, SEQ ID No: 756, SEQ ED No: 758, SEQ ED No: 760, SEQ ED No: 762, SEQ ID No: 764, SEQ ED No: 766, SEQ ED No: 768, SEQ ED No: 770, SEQ ED No: 772, SEQ ID No: 774, SEQ ED No: 776, SEQ ID No: 778, SEQ ED No: 780, SEQ ED No: 782, SEQ ED No: 784, SEQ ED No: 786, SEQ ED No: 788, SEQ ID No: 790, SEQ ID No: 792, SEQ ED No: 794, SEQ ED No: 796, SEQ ED No: 798, SEQ ED No: 800, SEQ ID No: 802, SEQ ED No: 804, SEQ ED No: 806, SEQ ED No: 808, SEQ ED No: 810, SEQ ID No: 812, SEQ ED No: 814, SEQ ID No: 816, SEQ ID No: 818, SEQ ID No: 820, SEQ ED No: 822, SEQ ED No: 824, SEQ ED No: 826, SEQ ID No: 828, SEQ ED No: 830, SEQ ID No: 832, SEQ ED No: 834, SEQ ID No: 836, SEQ ED No: 838, SEQ ED No: 840, SEQ ED No: 842, SEQ ED No: 844, SEQ ED No: 846, SEQ ED No: 848, SEQ ID No: 850, SEQ ED No: 852, SEQ ID No: 854, SEQ ED No: 856, SEQ ID No: 858, SEQ ID No: 860.)· In other embodiments, a homologue or variant of a protein amino acid sequence includes amino acid sequences comprising at least 20, or at least 30, or at least 40, or at least 50, or at least 75, or at least 100, or at least 125, or at least 150, or at least 175, or at least 150, or at least 200, or at least 250, or at least 300, or at least 350 contiguous amino acid residues of any of the amino acid sequence represented disclosed herein. Even small fragments of proteins without biological activity are useful in the present invention, for example, in the preparation of antibodies against the full-length protein or in a screening assay (e.g., a binding assay). Fragments can also be used to construct fusion proteins, for example, where the fusion protein comprises functional domains from two or more different proteins (e.g., a CBM from one protein linked to a CD from another protein). In one embodiment, a homologue or variant has a measurable or detectable biological activity associated with the wild-type protein (e.g., enzymatic activity).

[0153] According to the present invention, the term "contiguous" or "consecutive", with regard to nucleic acid or amino acid sequences described herein, means to be connected in an unbroken sequence. For example, for a first sequence to comprise 30 contiguous (or consecutive) amino acids of a second sequence, means that the first sequence includes an unbroken sequence of 30 amino acid residues that is 100% identical to an unbroken sequence of 30 amino acid residues in the second sequence. Similarly, for a first sequence to have "100% identity" with a second sequence means that the first sequence exactly matches the second sequence with no gaps between nucleotides or amino acids.

[0154] In another embodiment, a protein of the present invention, including a homologue or variant, includes a protein having an amino acid sequence that is sufficiently similar to a natural amino acid sequence that a nucleic acid sequence encoding the homologue or variant is capable of hybridizing under moderate, high or very high stringency conditions (described below) to (i.e., with) a nucleic acid molecule encoding the natural protein (i.e., to the complement of the nucleic acid strand encoding the natural amino acid sequence). Preferably, a homologue or variant of a protein of the present invention is encoded by a nucleic acid molecule comprising a nucleic acid sequence that hybridizes under low, moderate, or high stringency conditions to the complement of a nucleic acid sequence that encodes a protein comprising, consisting essentially of, or consisting of, an amino acid, sequence represented by any of SEQ ID NO: 2, SEQ ID No: 4, SEQ ID No: 6, SEQ ID No: 8, SEQ ID No: 10, SEQ ID No: 12, SEQ ID No: 14, SEQ ID No: 16, SEQ ID No: 18, SEQ ID No: 20, SEQ ID No: 22, SEQ ID No: 24, SEQ ID No: 26, SEQ ID No: 28, SEQ ID No: 30, SEQ ID No: 32, SEQ ID No: 34, SEQ ID No: 36, SEQ ID No: 38, SEQ ID No: 40, SEQ ID No: 42, SEQ ID No: 44, SEQ ID No: 46, SEQ ID No: 48, SEQ ID No: 50, SEQ ID No: 52, SEQ ID No: 54, SEQ ID No: 56, SEQ ID No: 58, SEQ ID No: 60, SEQ ID No: 62, SEQ ID No: 64, SEQ ID No: 66, SEQ ID No: 68, SEQ ID No: 70, SEQ ID No: 72, SEQ ID No: 74, SEQ ID No: 76, SEQ ID No: 78, SEQ ID No: 80, SEQ ID No: 82, SEQ ID No: 84, SEQ ID No: 86, SEQ ID No: 88, SEQ ID No: 90, SEQ ID No: 92, SEQ ID No: 94, SEQ ID No: 96, SEQ ID No: 98, SEQ ID No: 100, SEQ ID No: 102, SEQ ID No: 104, SEQ ID No: 106, SEQ ID No: 108, SEQ ID No: 110, SEQ ID No: 112, SEQ ID No: 114, SEQ ID No: 1 16, SEQ ID No: 118, SEQ ID No: 120, SEQ ID No: 122, SEQ ID No: 124, SEQ ID No: 126, SEQ ID No: 128, SEQ ID No: 130, SEQ ID No: 132, SEQ ID No: 134, SEQ ID No: 136, SEQ ID No: 138, SEQ ID No: 140, SEQ ID No: 142, SEQ ID No: 144, SEQ ID No: 146, SEQ ID No: 148, SEQ ID No: 150, SEQ ID No: 152, SEQ ID No: 154, SEQ ID No: 156, SEQ ID No: 158, SEQ ID No: 160, SEQ ID No: 162, SEQ ID No: 164, SEQ ID No: 166, SEQ ID No: 168, SEQ ID No: 170, SEQ ID No: 172, SEQ ID No: 174, SEQ ID No: 176, SEQ ID No: 178, SEQ ID No: 180, SEQ ID No: 182, SEQ ID No: 184, SEQ ID No: 186, SEQ ID No: 188, SEQ ID No: 190, SEQ ID No: 192, SEQ ID No: 194, SEQ ID No: 196, SEQ ID No: 198, SEQ ID No: 200, SEQ ID No: 202, SEQ ID No: 204, SEQ ID No: 206, SEQ ID No: 208, SEQ ID No: 210, SEQ ID No: 212, SEQ ID No: 214, SEQ ID No: 216, SEQ ID No: 218, SEQ ID No: 220, SEQ ID No: 222, SEQ ID No: 224, SEQ ID No: 226, SEQ ID No: 228, SEQ ID No: 230, SEQ ID No: 232, SEQ ID No: 234, SEQ ID No: 236, SEQ ID No: 238, SEQ ID No: 240, SEQ ID No: 242, SEQ ID No: 244, SEQ ID No: 246, SEQ ID No: 248, SEQ ID No: 250, SEQ ID No: 252, SEQ ID No: 254, SEQ ID No: 256, SEQ ID No: 258, SEQ ID No: 260, SEQ ID No: 262, SEQ ID No: 264, SEQ ID No: 266, SEQ ID No: 268, SEQ ID No: 270, SEQ ID No: 272, SEQ ID No: 274, SEQ ID No: 276, SEQ ID No: 278, SEQ ID No: 280, SEQ ID No: 282, SEQ ID No: 284, SEQ ID No: 286, SEQ ID No: 288, SEQ ID No: 290, SEQ ID No: 292, SEQ ID No: 294, SEQ ID No: 296, SEQ ID No: 298, SEQ ID No:300, SEQ ID No: 302, SEQ ID No: 304, SEQ ID No: 306, SEQ ID No: 308, SEQ ID No: 310, SEQ ID No: 312, SEQ ID No: 314, SEQ ID No: 316, SEQ ID No: 318, SEQ ID No: 320, SEQ ID No: 322, SEQ ID No: 324, SEQ ID No: 326, SEQ ID No: 328, SEQ ID No: 330, SEQ ID No: 332, SEQ ID No: 334, SEQ ID No: 336, SEQ ID No: 338, SEQ ID No: 340, SEQ ID No: 342, SEQ ID No: 344, SEQ ID No: 346, SEQ ID No: 348, SEQ ID No: 350, SEQ ID No: 352, SEQ ID No: 354, SEQ ID No: 356, SEQ ID No: 358, SEQ ID No: 360, SEQ ID No: 362, SEQ ID No: 364, SEQ ID No: 366, SEQ ID No: 368, SEQ ID No: 370, SEQ ID No: 372, SEQ ID No: 374, SEQ ID No: 376, SEQ ID No: 378, SEQ ID No: 380, SEQ ID No: 382, SEQ ED No: 384, SEQ ID No: 386, SEQ ID No: 388, SEQ ID No: 390, SEQ ID No: 392, SEQ ID No: 394, SEQ ID No: 396, SEQ ID No: 398, 400, SEQ ID No: 402, SEQ ED No: 404, SEQ ED No: 406, SEQ ID No: 408, SEQ ED No: 410, SEQ ED No: 412, SEQ ED No: 414, SEQ ED No: 416, SEQ ED No: 418, SEQ ED No: 420, SEQ ED No: 422, SEQ ID No: 424, SEQ ED No: 426, SEQ ED No: 428, SEQ ED No: 430, SEQ ED No: 432, SEQ ID No: 434, SEQ ED No: 436, SEQ ED No: 438, SEQ ED No: 440, SEQ ID No: 442, SEQ ED No: 444, SEQ ID No: 446, SEQ ED No: 448, SEQ ID No: 450, SEQ ED No: 452, SEQ ID No: 454, SEQ ID No: 456, SEQ ID No: 458, SEQ ED No: 460, SEQ ID No: 462, SEQ ED No: 464, SEQ ED No: 466, SEQ ED No: 468, SEQ ED No: 470, SEQ ED No: 472, SEQ ED No: 474, SEQ ED No: 476, SEQ ED No: 478, SEQ ED No: 480, SEQ ED No: 482, SEQ ID No: 484, SEQ ED No: 486, SEQ ED No: 488, SEQ ED No: 490, SEQ ED No: 492, SEQ ED No: 494, SEQ ID No: 496, SEQ ED No: 498, SEQ ID No: 500, SEQ ID No: 502, SEQ ID No: 504, SEQ ED No: 506, SEQ ED No: 508, SEQ ED No: 510, SEQ ED No: 512, SEQ ED No: 514, SEQ ED No: 516, SEQ ID No: 518, SEQ ED No: 520, SEQ ID No: 522, SEQ ED No: 524, SEQ ED No: 526, SEQ ID No: 528, SEQ ID No: 530, SEQ ED No: 532, SEQ ID No: 534, SEQ ED No: 536, SEQ ID No: 538, SEQ ED No: 540, SEQ ED No: 542, SEQ ED No: 544, SEQ ED No: 546, SEQ ED No: 548, SEQ ED No: 550, SEQ ED No: 552, SEQ ED No: 554, SEQ ID No: 556, SEQ ED No: 558, SEQ ID No: 560, SEQ ED No: 562, SEQ ED No: 564, SEQ ED No: 566, SEQ ED No: 568, SEQ ED No: 570, SEQ ID No: 572, SEQ ED No: 574, SEQ ID No: 576, SEQ ED No: 578, SEQ ED No: 580, SEQ ED No: 582, SEQ ED No: 584, SEQ ED No: 586, SEQ ED No: 588, SEQ ED No: 590, SEQ ED No: 592, SEQ ID No: 594, SEQ ID No: 596, SEQ ID No: 598, SEQ ID No:600, SEQ ED No: 602, SEQ ED No: 604, SEQ ED No: 606, SEQ ED No: 608, SEQ ED No: 610, SEQ ED No: 612, SEQ ID No: 614, SEQ ED No: 616, SEQ ID No: 618, SEQ ED No: 620, SEQ ID No: 622, SEQ ED No: 624, SEQ ID No: 626, SEQ ED No: 628, SEQ ED No: 630, SEQ ED No: 632, SEQ ID No: 634, SEQ ED No: 636, SEQ ID No: 638, SEQ ID No: 640, SEQ ID No: 642, SEQ ID No: 644, SEQ ID No: 646, SEQ ID No: 648, SEQ ID No: 650, SEQ ID No: 652, SEQ ID No: 654, SEQ ID No: 656, SEQ ID No: 658, SEQ ID No: 660, SEQ ID No: 662, SEQ ID No: 664, SEQ ID No: 666, SEQ ID No: 668, SEQ ID No: 670, SEQ ID No: 672, SEQ ID No: 674, SEQ ID No: 676, SEQ ID No: 678, SEQ ID No: 680, SEQ ID No: 682, SEQ ID No: 684, SEQ ID No: 686, SEQ ID No: 688, SEQ ID No: 690, SEQ ED No: 692, SEQ ID No: 694, SEQ ID No: 696, SEQ ID No: 698, SEQ ID No: 700, SEQ ID No: 702, SEQ ID No: 704, SEQ ID No: 706, SEQ ID No: 708, SEQ ID No: 710, SEQ ID No: 712, SEQ ID No: 714, SEQ ID No: 716, SEQ ID No: 718, SEQ ID No: 720, SEQ ID No: 722, SEQ ID No: 724, SEQ ID No: 726, SEQ ID No: 728, SEQ ID No: 730, SEQ ID No: 732, SEQ ID No: 734, SEQ ID No: 736, SEQ ID No: 738, SEQ ID No: 740, SEQ ID No: 742, SEQ ID No: 744, SEQ ID No: 746, SEQ ID No: 748, SEQ ID No: 750, SEQ ID No: 752, SEQ ID No: 754, SEQ ED No: 756, SEQ ED No: 758, SEQ ED No: 760, SEQ ID No: 762, SEQ ED No: 764, SEQ ED No: 766, SEQ ED No: 768, SEQ ED No: 770, SEQ ED No: 772, SEQ ID No: 774, SEQ ED No: 776, SEQ ED No: 778, SEQ ED No: 780, SEQ ED No: 782, SEQ ED No: 784, SEQ ED No: 786, SEQ ED No: 788, SEQ ED No: 790, SEQ ED No: 792, SEQ ID No: 794, SEQ ED No: 796, SEQ ED No: 798, SEQ ED No: 800, SEQ ID No: 802, SEQ ED No: 804, SEQ ID No: 806, SEQ ED No: 808, SEQ ED No: 810, SEQ ID No: 812, SEQ ED No: 814, SEQ ID No: 816, SEQ ED No: 818, SEQ ED No: 820, SEQ ED No: 822, SEQ ED No: 824, SEQ ED No: 826, SEQ ED No: 828, SEQ ED No: 830, SEQ ID No: 832, SEQ ED No: 834, SEQ ED No: 836, SEQ ED No: 838, SEQ ED No: 840, SEQ ED No: 842, SEQ ED No: 844, SEQ ED No: 846, SEQ ID No: 848, SEQ ED No: 850, SEQ ID No: 852, SEQ ID No: 854, SEQ ED No: 856, SEQ ID No: 858, SEQ ED No: 860.. Such hybridization conditions are described in detail below.

A nucleic acid sequence complement of nucleic acid sequence encoding a protein of the present invention refers to the nucleic acid sequence of the nucleic acid strand that is complementary to the strand which encodes the protein. It will be appreciated that a double stranded DNA which encodes a given amino acid sequence comprises a single strand DNA and its complementary strand having a sequence that is a complement to the single strand DNA. As such, nucleic acid molecules of the present invention can be either double-stranded or single-stranded, and include those nucleic acid molecules that form stable hybrids under stringent hybridization conditions with a nucleic acid sequence that encodes an amino acid sequence such as the amino acid sequences of SEQ ID NO: 2, SEQ ID No: 4, SEQ ID No: 6, SEQ ID No: 8, SEQ ID No: 10, SEQ ID No: 12, SEQ ID No: 14, SEQ ID No: 16, SEQ ID No: 18, SEQ ID No: 20, SEQ ID No: 22, SEQ ID No: 24, SEQ ID No: 26, SEQ ID No: 28, SEQ ID No: 30, SEQ ID No: 32, SEQ ID No: 34, SEQ ID No: 36, SEQ ID No: 38, SEQ ID No: 40, SEQ ID No: 42, SEQ ID No: 44, SEQ ID No: 46, SEQ ID No: 48, SEQ ID No: 50, SEQ ID No: 52, SEQ ID No: 54, SEQ ID No: 56, SEQ ID No: 58, SEQ ID No: 60, SEQ ID No: 62, SEQ ID No: 64, SEQ ID No: 66, SEQ ID No: 68, SEQ ID No: 70, SEQ ID No: 72, SEQ ID No: 74, SEQ ID No: 76, SEQ ID No: 78, SEQ ID No: 80, SEQ ID No: 82, SEQ ID No: 84, SEQ ID No: 86, SEQ ID No: 88, SEQ ID No: 90, SEQ ID No: 92, SEQ ID No: 94, SEQ ID No: 96, SEQ ID No: 98, SEQ ID No: 100, SEQ ID No: 102, SEQ ID No: 104, SEQ ID No: 106, SEQ ID No: 108, SEQ ID No: 110, SEQ ID No: 112, SEQ ID No: 114, SEQ ID No: 116, SEQ ID No: 1 18, SEQ ID No: 120, SEQ ID No: 122, SEQ ID No: 124, SEQ ID No: 126, SEQ ID No: 128, SEQ ID No: 130, SEQ ID No: 132, SEQ ID No: 134, SEQ ID No: 136, SEQ ID No: 138, SEQ ID No: 140, SEQ ID No: 142, SEQ ID No: 144, SEQ ID No: 146, SEQ ID No: 148, SEQ ID No: 150, SEQ ID No: 152, SEQ ID No: 154, SEQ ID No: 156, SEQ ID No: 158, SEQ ID No: 160, SEQ ID No: 162, SEQ ID No: 164, SEQ ID No: 166, SEQ ID No: 168, SEQ ID No: 170, SEQ ID No: 172, SEQ ID No: 174, SEQ ID No: 176, SEQ ID No: 178, SEQ ID No: 180, SEQ ID No: 182, SEQ ID No: 184, SEQ ID No: 186, SEQ ID No: 188, SEQ ID No: 190, SEQ ID No: 192, SEQ ID No: 194, SEQ ED No: 196, SEQ ID No: 198, SEQ ED No: 200, SEQ ID No: 202, SEQ ID No: 204, SEQ ID No: 206, SEQ ED No: 208, SEQ ED No: 210, SEQ ED No: 212, SEQ ED No: 214, SEQ ED No: 216, SEQ ED No: 218, SEQ ED No: 220, SEQ ED No: 222, SEQ ID No: 224, SEQ ED No: 226, SEQ ED No: 228, SEQ ED No: 230, SEQ ED No: 232, SEQ ED No: 234, SEQ ID No: 236, SEQ ED No: 238, SEQ ED No: 240, SEQ ED No: 242, SEQ ED No: 244, SEQ ED No: 246, SEQ ED No: 248, SEQ ED No: 250, SEQ ED No: 252, SEQ ED No: 254, SEQ ED No: 256, SEQ ID No: 258, SEQ ID No: 260, SEQ ID No: 262, SEQ ED No: 264, SEQ ED No: 266, SEQ ID No: 268, SEQ ED No: 270, SEQ ID No: 272, SEQ ID No: 274, SEQ ED No: 276, SEQ ED No: 278, SEQ ED No: 280, SEQ ED No: 282, SEQ ED No: 284, SEQ ED No: 286, SEQ ED No: 288, SEQ ED No: 290, SEQ ED No: 292, SEQ ED No: 294, SEQ ED No: 296, SEQ ED No: 298, SEQ ED No:300, SEQ ED No: 302, SEQ ED No: 304, SEQ ED No: 306, SEQ ED No: 308, SEQ ED No: 310, SEQ ID No: 312, SEQ ED No: 314, SEQ ED No: 316, SEQ ED No: 318, SEQ ED No: 320, SEQ ED No: 322, SEQ ED No: 324, SEQ ED No: 326, SEQ ED No: 328, SEQ ED No: 330, SEQ ED No: 332, SEQ ID No: 334, SEQ ED No: 336, SEQ ED No: 338, SEQ ID No: 340, SEQ ED No: 342, SEQ ID No: 344, SEQ ED No: 346, SEQ ED No: 348, SEQ ID No: 350, SEQ ED No: 352, SEQ ID No: 354, SEQ ED No: 356, SEQ ED No: 358, SEQ ED No: 360, SEQ ED No: 362, SEQ ED No: 364, SEQ ED No: 366, SEQ ED No: 368, SEQ ED No: 370, SEQ ID No: 372, SEQ ED No: 374, SEQ ID No: 376, SEQ ED No: 378, SEQ ED No: 380, SEQ ED No: 382, SEQ ED No: 384, SEQ ED No: 386, SEQ ED No: 388, SEQ ED No: 390, SEQ ID No: 392, SEQ ED No: 394, SEQ ED No: 396, SEQ ED No: 398, 400, SEQ ID No: 402, SEQ ID No: 404, SEQ ID No: 406, SEQ ED No: 408, SEQ ED No: 410, SEQ ED No: 412, SEQ ED No: 414, SEQ ED No: 416, SEQ ID No: 418, SEQ ED No: 420, SEQ ID No: 422, SEQ ED No: 424, SEQ ED No: 426, SEQ ID No: 428, SEQ ED No: 430, SEQ ID No: 432, SEQ ED No: 434, SEQ ID No: 436, SEQ ED No: 438, SEQ ED No: 440, SEQ ED No: 442, SEQ ID No: 444, SEQ ED No: 446, SEQ ED No: 448, SEQ ED No: 450, SEQ ED No: 452, SEQ ED No: 454, SEQ ID No: 456, SEQ ED No: 458, SEQ ED No: 460, SEQ ED No: 462, SEQ ED No: 464, SEQ ED No: 466, SEQ ED No: 468, SEQ ED No: 470, SEQ ED No: 472, SEQ ID No: 474, SEQ ED No: 476, SEQ ID No: 478, SEQ ED No: 480, SEQ ID No: 482, SEQ ED No: 484, SEQ ED No: 486, SEQ ED No: 488, SEQ ED No: 490, SEQ ED No: 492, SEQ ID No: 494, SEQ ED No: 496, SEQ ED No: 498, SEQ ED No: 500, SEQ ED No: 502, SEQ ED No: 504, SEQ ED No: 506, SEQ ED No: 508, SEQ ED No: 510, SEQ ED No: 512, SEQ ED No: 514, SEQ ID No: 516, SEQ ED No: 518, SEQ ED No: 520, SEQ ED No: 522, SEQ ED No: 524, SEQ ED No: 526, SEQ ED No: 528, SEQ ED No: 530, SEQ ED No: 532, SEQ ED No: 534, SEQ ID No: 536, SEQ ED No: 538, SEQ ED No: 540, SEQ ID No: 542, SEQ ED No: 544, SEQ ED No: 546, SEQ ED No: 548, SEQ ED No: 550, SEQ ED No: 552, SEQ ID No: 554, SEQ ED No: 556, SEQ ID No: 558, SEQ ID No: 560, SEQ ED No: 562, SEQ ED No: 564, SEQ ID No: 566, SEQ ID No: 568, SEQ ID No: 570, SEQ ED No: 572, SEQ ID No: 574, SEQ ED No: 576, SEQ ED No: 578, SEQ ED No: 580, SEQ ED No: 582, SEQ ED No: 584, SEQ ED No: 586, SEQ ED No: 588, SEQ ED No: 590, SEQ ID No: 592, SEQ ED No: 594, SEQ ID No: 596, SEQ ID No: 598, SEQ ID No:600, SEQ ED No: 602, SEQ ED No: 604, SEQ ED No: 606, SEQ ID No: 608, SEQ ID No: 610, SEQ ID No: 612, SEQ ED No: 614, SEQ ED No: 616, SEQ ED No: 618, SEQ ED No: 620, SEQ ED No: 622, SEQ ED No: 624, SEQ ED No: 626, SEQ ID No: 628, SEQ ID No: 630, SEQ ID No: 632, SEQ ID No: 634, SEQ ID No: 636, SEQ ID No: 638, SEQ ID No: 640, SEQ ID No: 642, SEQ ID No: 644, SEQ ID No: 646, SEQ ID No: 648, SEQ ID No: 650, SEQ ID No: 652, SEQ ID No: 654, SEQ ID No: 656, SEQ ID No: 658, SEQ ID No: 660, SEQ ID No: 662, SEQ ID No: 664, SEQ ID No: 666, SEQ ID No: 668, SEQ ID No: 670, SEQ ID No: 672, SEQ ID No: 674, SEQ ID No: 676, SEQ ID No: 678, SEQ ID No: 680, SEQ ID No: 682, SEQ ID No: 684, SEQ ID No: 686, SEQ ID No: 688, SEQ ID No: 690, SEQ ID No: 692, SEQ ID No: 694, SEQ ID No: 696, SEQ ID No: 698, SEQ ID No: 700, SEQ ID No: 702, SEQ ID No: 704, SEQ ID No: 706, SEQ ID No: 708, SEQ ID No: 710, SEQ ED No: 712, SEQ ED No: 714, SEQ ED No: 716, SEQ ED No: 718, SEQ ED No: 720, SEQ ID No: 722, SEQ ID No: 724, SEQ ID No: 726, SEQ ED No: 728, SEQ ID No: 730, SEQ ED No: 732, SEQ ID No: 734, SEQ ED No: 736, SEQ ED No: 738, SEQ ED No: 740, SEQ ED No: 742, SEQ ID No: 744, SEQ ED No: 746, SEQ ED No: 748, SEQ ID No: 750, SEQ ED No: 752, SEQ ED No: 754, SEQ ED No: 756, SEQ ED No: 758, SEQ ID No: 760, SEQ ED No: 762, SEQ ID No: 764, SEQ ED No: 766, SEQ ED No: 768, SEQ ED No: 770, SEQ ED No: 772, SEQ ED No: 774, SEQ ED No: 776, SEQ ED No: 778, SEQ ED No: 780, SEQ ID No: 782, SEQ ED No: 784, SEQ ED No: 786, SEQ ED No: 788, SEQ ED No: 790, SEQ ID No: 792, SEQ ED No: 794, SEQ ED No: 796, SEQ ID No: 798, SEQ ED No: 800, SEQ ID No: 802, SEQ ED No: 804, SEQ ED No: 806, SEQ ED No: 808, SEQ ED No: 810, SEQ ED No: 812, SEQ ED No: 814, SEQ ED No: 816, SEQ ED No: 818, SEQ ID No: 820, SEQ ED No: 822, SEQ ID No: 824, SEQ ID No: 826, SEQ ID No: 828, SEQ ED No: 830, SEQ ED No: 832, SEQ ID No: 834, SEQ ID No: 836, SEQ ED No: 838, SEQ ID No: 840, SEQ ED No: 842, SEQ ED No: 844, SEQ ED No: 846, SEQ ED No: 848, SEQ ED No: 850, SEQ ED No: 852, SEQ ED No: 854, SEQ ED No: 856, SEQ ID No: 858, SEQ ED No: 860., and/or with the complement of the nucleic acid sequence that encodes an amino acid sequence such as the amino acid sequences of SEQ ID NO: 2, SEQ ED No: 4, SEQ ED No: 6, SEQ ED No: 8, SEQ ID No: 10, SEQ ID No: 12, SEQ ID No: 14, SEQ ID No: 16, SEQ ED No: 18, SEQ ED No: 20, SEQ ED No: 22, SEQ ID No: 24, SEQ ED No: 26, SEQ ID No: 28, SEQ ID No: 30, SEQ ED No: 32, SEQ ED No: 34, SEQ ED No: 36, SEQ ID No: 38, SEQ ID No: 40, SEQ ED No: 42, SEQ ED No: 44, SEQ ED No: 46, SEQ ID No: 48, SEQ ID No: 50, SEQ ED No: 52, SEQ ED No: 54, SEQ ED No: 56, SEQ ED No: 58, SEQ ID No: 60, SEQ ED No: 62, SEQ ED No: 64, SEQ ED No: 66, SEQ ID No: 68, SEQ ID No: 70, SEQ ED No: 72, SEQ ED No: 74, SEQ ID No: 76, SEQ ID No: 78, SEQ ID No: 80, SEQ ED No: 82, SEQ ED No: 84, SEQ ED No: 86, SEQ ID No: 88, SEQ ID No: 90, SEQ ED No: 92, SEQ ED No: 94, SEQ ED No: 96, SEQ ED No: 98, SEQ ID No: 100, SEQ ID No: 102, SEQ ID No: 104, SEQ ED No: 106, SEQ ID No: 108, SEQ ED No: 1 10, SEQ ED No: 1 12, SEQ ED No: 1 14, SEQ ED No: 1 16, SEQ ED No: 1 18, SEQ ID No: 120, SEQ ED No: 122, SEQ ED No: 124, SEQ ED No: 126, SEQ ED No: 128, SEQ ED No: 130, SEQ ED No: 132, SEQ ED No: 134, SEQ ED No: 136, SEQ ED No: 138, SEQ ED No: 140, SEQ ID No: 142, SEQ ED No: 144, SEQ ED No: 146, SEQ ID No: 148, SEQ ED No: 150, SEQ ED No: 152, SEQ ID No: 154, SEQ ED No: 156, SEQ ID No: 158, SEQ ED No: 160, SEQ ID No: 162, SEQ ID No: 164, SEQ ED No: 166, SEQ ED No: 168, SEQ ED No: 170, SEQ ED No: 172, SEQ ED No: 174, SEQ ID No: 176, SEQ ID No: 178, SEQ ID No: 180, SEQ ID No: 182, SEQ ID No: 184, SEQ ED No: 186, SEQ ED No: 188, SEQ ED No: 190, SEQ ID No: 192, SEQ ED No: 194, SEQ ID No: 196, SEQ ED No: 198, SEQ ID No: 200, SEQ ID No: 202, SEQ ED No: 204, SEQ ED No: 206, SEQ ED No: 208, SEQ ED No: 210, SEQ ED No: 212, SEQ ED No: 214, SEQ ED No: 216, SEQ ED No: 218, SEQ ED No: 220, SEQ ID No: 222, SEQ ED No: 224, SEQ ID No: 226, SEQ ED No: 228, SEQ ED No: 230, SEQ ED No: 232, SEQ ED No: 234, SEQ ED No: 236, SEQ ID No: 238, SEQ ED No: 240, SEQ ED No: 242, SEQ ED No: 244, SEQ ED No: 246, SEQ ID No: 248, SEQ ED No: 250, SEQ ED No: 252, SEQ ED No: 254, SEQ ID No: 256, SEQ ED No: 258, SEQ ED No: 260, SEQ ED No: 262, SEQ ED No: 264, SEQ ED No: 266, SEQ ED No: 268, SEQ ED No: 270, SEQ ID No: 272, SEQ ED No: 274, SEQ ID No: 276, SEQ ED No: 278, SEQ ED No: 280, SEQ ED No: 282, SEQ ID No: 284, SEQ ED No: 286, SEQ ED No: 288, SEQ ED No: 290, SEQ ID No: 292, SEQ ID No: 294, SEQ ID No: 296, SEQ ID No: 298, SEQ ID No:300, SEQ ID No: 302, SEQ ED No: 304, SEQ ED No: 306, SEQ ID No: 308, SEQ ID No: 310, SEQ ED No: 312, SEQ ID No: 314, SEQ ED No: 316, SEQ ED No: 318, SEQ ED No: 320, SEQ ID No: 322, SEQ ED No: 324, SEQ ID No: 326, SEQ ID No: 328, SEQ ED No: 330, SEQ ED No: 332, SEQ ED No: 334, SEQ ED No: 336, SEQ ID No: 338, SEQ ED No: 340, SEQ ID No: 342, SEQ ED No: 344, SEQ ED No: 346, SEQ ED No: 348, SEQ ED No: 350, SEQ ED No: 352, SEQ ED No: 354, SEQ ED No: 356, SEQ ED No: 358, SEQ ID No: 360, SEQ ED No: 362, SEQ ID No: 364, SEQ ED No: 366, SEQ ID No: 368, SEQ ED No: 370, SEQ ID No: 372, SEQ ED No: 374, SEQ ID No: 376, SEQ ID No: 378, SEQ ID No: 380, SEQ ED No: 382, SEQ ED No: 384, SEQ ID No: 386, SEQ ID No: 388, SEQ ID No: 390, SEQ ID No: 392, SEQ ID No: 394, SEQ ID No: 396, SEQ ID No: 398, 400, SEQ ID No: 402, SEQ ID No: 404, SEQ ID No: 406, SEQ ID No: 408, SEQ ID No: 410, SEQ ID No: 412, SEQ ID No: 414, SEQ ED No: 416, SEQ ID No: 418, SEQ ED No: 420, SEQ ID No: 422, SEQ ID No: 424, SEQ ID No: 426, SEQ ID No: 428, SEQ ID No: 430, SEQ ID No: 432, SEQ ID No: 434, SEQ ID No: 436, SEQ ID No: 438, SEQ ED No: 440, SEQ ID No: 442, SEQ ID No: 444, SEQ ID No: 446, SEQ ID No: 448, SEQ ID No: 450, SEQ ID No: 452, SEQ ID No: 454, SEQ ID No: 456, SEQ ID No: 458, SEQ ID No: 460, SEQ ED No: 462, SEQ ID No: 464, SEQ ID No: 466, SEQ ED No: 468, SEQ ID No: 470, SEQ ED No: 472, SEQ ID No: 474, SEQ ID No: 476, SEQ ID No: 478, SEQ ID No: 480, SEQ ID No: 482, SEQ ED No: 484, SEQ ID No: 486, SEQ ID No: 488, SEQ ID No: 490, SEQ ED No: 492, SEQ ID No: 494, SEQ ED No: 496, SEQ ID No: 498, SEQ ID No: 500, SEQ ID No: 502, SEQ ID No: 504, SEQ ID No: 506, SEQ ID No: 508, SEQ ED No: 510, SEQ ED No: 512, SEQ ID No: 514, SEQ ED No: 516, SEQ ID No: 518, SEQ ID No: 520, SEQ ID No: 522, SEQ ID No: 524, SEQ ID No: 526, SEQ ID No: 528, SEQ ID No: 530, SEQ ED No: 532, SEQ ID No: 534, SEQ ID No: 536, SEQ ID No: 538, SEQ ID No: 540, SEQ ID No: 542, SEQ ID No: 544, SEQ ID No: 546, SEQ ID No: 548, SEQ ED No: 550, SEQ ID No: 552, SEQ ED No: 554, SEQ ID No: 556, SEQ ID No: 558, SEQ ID No: 560, SEQ ID No: 562, SEQ ID No: 564, SEQ ED No: 566, SEQ ED No: 568, SEQ ED No: 570, SEQ ED No: 572, SEQ ID No: 574, SEQ ED No: 576, SEQ ID No: 578, SEQ ID No: 580, SEQ ID No: 582, SEQ ID No: 584, SEQ ID No: 586, SEQ ID No: 588, SEQ ED No: 590, SEQ ED No: 592, SEQ ID No: 594, SEQ ID No: 596, SEQ ID No: 598, SEQ ID No:600, SEQ ID No: 602, SEQ ED No: 604, SEQ ID No: 606, SEQ ID No: 608, SEQ ID No: 610, SEQ ID No: 612, SEQ ID No: 614, SEQ ID No: 616, SEQ ID No: 618, SEQ ID No: 620, SEQ ID No: 622, SEQ ID No: 624, SEQ ID No: 626, SEQ ID No: 628, SEQ ID No: 630, SEQ ID No: 632, SEQ ID No: 634, SEQ ED No: 636, SEQ ID No: 638, SEQ ID No: 640, SEQ ID No: 642, SEQ ID No: 644, SEQ ID No: 646, SEQ ID No: 648, SEQ ID No: 650, SEQ ID No: 652, SEQ ID No: 654, SEQ ID No: 656, SEQ ED No: 658, SEQ ID No: 660, SEQ ED No: 662, SEQ ID No: 664, SEQ ID No: 666, SEQ ED No: 668, SEQ ID No: 670, SEQ ID No: 672, SEQ ID No: 674, SEQ ID No: 676, SEQ ED No: 678, SEQ ID No: 680, SEQ ID No: 682, SEQ ID No: 684, SEQ ID No: 686, SEQ ID No: 688, SEQ ID No: 690, SEQ ID No: 692, SEQ ED No: 694, SEQ ED No: 696, SEQ ID No: 698, SEQ ED No: 700, SEQ ID No: 702, SEQ ID No: 704, SEQ ID No: 706, SEQ ID No: 708, SEQ ID No: 710, SEQ ID No: 712, SEQ ID No: 714, SEQ ED No: 716, SEQ ID No: 718, SEQ ID No: 720, SEQ ID No: 722, SEQ ID No: 724, SEQ ID No: 726, SEQ ID No: 728, SEQ ID No: 730, SEQ ID No: 732, SEQ ID No: 734, SEQ ID No: 736, SEQ ID No: 738, SEQ ID No: 740, SEQ ID No: 742, SEQ ID No: 744, SEQ ID No: 746, SEQ ID No: 748, SEQ ID No: 750, SEQ ID No: 752, SEQ ID No: 754, SEQ ID No: 756, SEQ ID No: 758, SEQ ID No: 760, SEQ ID No: 762, SEQ ID No: 764, SEQ ID No: 766, SEQ ID No: 768, SEQ ID No: 770, SEQ ID No: 772, SEQ ID No: 774, SEQ ID No: 776, SEQ ID No: 778, SEQ ID No: 780, SEQ ID No: 782, SEQ ID No: 784, SEQ ID No: 786, SEQ ID No: 788, SEQ ID No: 790, SEQ ID No: 792, SEQ ID No: 794, SEQ ID No: 796, SEQ ID No: 798, SEQ ID No: 800, SEQ ID No: 802, SEQ ID No: 804, SEQ ID No: 806, SEQ ID No: 808, SEQ ID No: 810, SEQ ID No: 812, SEQ ID No: 814, SEQ ID No: 816, SEQ ID No: 818, SEQ ID No: 820, SEQ ID No: 822, SEQ ID No: 824, SEQ ID No: 826, SEQ ID No: 828, SEQ ID No: 830, SEQ ID No: 832, SEQ ID No: 834, SEQ ID No: 836, SEQ ID No: 838, SEQ ID No: 840, SEQ ID No: 842, SEQ ID No: 844, SEQ ID No: 846, SEQ ID No: 848, SEQ ID No: 850, SEQ ID No: 852, SEQ ID No: 854, SEQ ID No: 856, SEQ ID No: 858, SEQ ID No: 860.. Methods to deduce a complementary sequence are known to those skilled in the art. It should be noted that since nucleic acid sequencing technologies are not entirely error-free, the sequences presented herein, at best, represent apparent sequences of the proteins of the present invention.

[0156] As used herein, reference to hybridization conditions refers to standard hybridization conditions under which nucleic acid molecules are used to identify similar nucleic acid molecules. Such standard conditions are disclosed, for example, in Sambrook et al., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Labs Press, 1989. Sambrook et al., ibid., (see specifically, pages 9.31-9.62). In addition, formulae to calculate the appropriate hybridization and wash conditions to achieve hybridization permitting varying degrees of mismatch of nucleotides are disclosed, for example, in Meinkoth et al., 1984, Anal. Biochem. 138, 267-284; Meinkoth et al., ibid.

[0157] More particularly, moderate stringency hybridization and washing conditions, as referred to herein, refer to conditions which permit isolation of nucleic acid molecules having at least about 70% nucleic acid sequence identity with the nucleic acid molecule being used to probe in the hybridization reaction (i.e., conditions permitting about 30% or less mismatch of nucleotides). High stringency hybridization and washing conditions, as referred to herein, refer to conditions which permit isolation of nucleic acid molecules having at least about 80% nucleic acid sequence identity with the nucleic acid molecule being used to probe in the hybridization reaction (i.e., conditions permitting about 20% or less mismatch of nucleotides). Very high stringency hybridization and washing conditions, as referred to herein, refer to conditions which permit isolation of nucleic acid molecules having at least about 90% nucleic acid sequence identity with the nucleic acid molecule being used to probe in the hybridization reaction (i.e., conditions permitting about 10% or less mismatch of nucleotides). As discussed above, one of skill in the art can use the formulae in Meinkoth et al., ibid, to calculate the appropriate hybridization and wash conditions to achieve these particular levels of nucleotide mismatch. Such conditions will vary, depending on whether DNA:K A or DNA:DNA hybrids are being formed. Calculated melting temperatures for DNA:DNA hybrids are 10°C less than for DNA:RNA hybrids. In particular embodiments, stringent hybridization conditions for DNA:DNA hybrids include hybridization at an ionic strength of 6X SSC (0.9 M Na^1") at a temperature of between about 20°C and about 35°C (lower stringency), more preferably, between about 28°C and about 40°C (more stringent), and even more preferably, between about 35°C and about 45°C (even more stringent), with appropriate wash conditions. In particular embodiments, stringent hybridization conditions for DNA:RNA hybrids include hybridization at an ionic strength of 6X SSC (0.9 M Na⁺) at a temperature of between about 30°C and about 45°C, more preferably, between about 38°C and about 50°C, and even more preferably, between about 45°C and about 55°C, with similarly stringent wash conditions. These values are based on calculations of a melting temperature for molecules larger than about 100 nucleotides, 0% formamide and a G + C content of about 40%. Alternatively, T_m can be calculated empirically as set forth in Sambrook et al, supra, pages 9.31 to 9.62. In general, the wash conditions should be as stringent as possible, and should be appropriate for the chosen hybridization conditions. For example, hybridization conditions can include a combination of salt and temperature conditions that are approximately 20-25°C below the calculated T_m of a particular hybrid, and wash conditions typically include a combination of salt and temperature conditions that are approximately 12-20°C below the calculated T_m of the particular hybrid. One example of hybridization conditions suitable for use with DNA:DNA hybrids includes a 2-24 hour hybridization in 6X SSC (50% formamide) at about 42°C, followed by washing steps that include one or more washes at room temperature in about 2X SSC, followed by additional washes at higher temperatures and lower ionic strength (e.g., at least one wash as about 37°C in about 0.1X-0.5X SSC, followed by at least one wash at about 68°C in about 0.1X-0.5X SSC).

[0158] The minimum size of a protein and/or homologue or variant of the present invention is a size sufficient to have biological activity or, when the protein is not required to have such activity, sufficient to be useful for another purpose associated with a protein of the present invention, such as for the production of antibodies that bind to a naturally occurring protein. In one embodiment, the protein of the present invention is at least 20 amino acids in length, or at least about 25 amino acids in length, or at least about 30 amino acids in length, or at least about 40 amino acids in length, or at least about 50 amino acids in length, or at least about 60 amino acids in length, or at least about 70 amino acids in length, or at least about 80 amino acids in length, or at least about 90 amino acids in length, or at least about 100 amino acids in length, or at least about 125 amino acids in length, or at least about 150 amino acids in length, or at least about 175 amino acids in length, or at least about 200 amino acids in length, or at least about 250 amino acids in length, and so on up to a full length of each protein, and including any size in between in increments of one whole integer (one amino acid). There is no limit, other than a practical limit, on the maximum size of such a protein in that the protein can include a portion of a protein or a full-length protein, plus additional sequence (e.g., a fusion protein sequence), if desired.

[0159] The present invention also includes a fusion protein that includes a domain of a protein of the present invention (including a homologue or variant) attached to one or more fusion segments, which are typically heterologous in sequence to the protein sequence (i.e., different than protein sequence). Suitable fusion segments for use with the present invention include, but are not limited to, segments that can: enhance a protein's stability; provide other desirable biological activity; and/or assist with the purification of the protein (e.g., by affinity chromatography). A suitable fusion segment can be a domain of any size that has the desired function (e.g., imparts increased stability, solubility, action or biological activity; and/or simplifies purification of a protein). Fusion segments can be joined to amino and/or carboxyl termini of the domain of a protein of the present invention and can be susceptible to cleavage in order to enable straight-forward recovery of the protein. Fusion proteins are preferably produced by culturing a recombinant cell transfected with a fusion nucleic acid molecule that encodes a protein including the fusion segment attached to either the carboxyl and/or amino terminal end of a domain of a protein of the present invention. Accordingly, proteins of the present invention also include expression products of gene fusions (for example, used to overexpress soluble, active forms of the recombinant protein), of mutagenized genes (such as genes having codon modifications to enhance gene transcription and translation), and of truncated genes (such as genes having membrane binding modules removed to generate soluble forms of a membrane protein, or genes having signal sequences removed which are poorly tolerated in a particular recombinant host).

[0160] In one embodiment of the present invention, any of the amino acid sequences described herein can be produced with from at least one, and up to about 20, additional heterologous amino acids flanking each of the C- and/or N-terminal ends of the specified amino acid sequence. The resulting protein or polypeptide can be referred to as "consisting essentially of the specified amino acid sequence. According to the present invention, the heterologous amino acids are a sequence of amino acids that are not naturally found (i.e., not found in nature, in vivo) flanking the specified amino acid sequence, or that are not related to the function of the specified amino acid sequence, or that would not be encoded by the nucleotides that flank the naturally occurring nucleic acid sequence encoding the specified amino acid sequence as it occurs in the gene, if such nucleotides in the naturally occurring sequence were translated using standard codon usage for the organism from which the given amino acid sequence is derived.

[0161] The present invention also provides enzyme combinations that can be used to break down lignocellulose material. Such enzyme combinations or mixtures can include a multi-enzyme composition that contains at least one protein of the present invention in combination with one or more additional proteins of the present invention or one or more enzymes or other proteins from other microorganisms, plants, or similar organisms. Synergistic enzyme combinations and related methods are contemplated. In particular, the enzymes of the present invention act in the multi-enzyme composition to aid in the delignify of the lignocellulose material by degrading the proteins present in the material. The invention includes methods to identify the optimum ratios and compositions of enzymes with which to degrade each lignocellulosic material. These methods entail tests to identify the optimum enzyme composition and ratios for efficient conversion of any lignocellulosic substrate to its constituent sugars. The Examples below include assays that may be used to identify optimum ratios and compositions of enzymes with which to degrade lignocellulosic materials.

[0162] Any combination of the proteins disclosed herein is suitable for use in the multi- enzyme compositions of the present invention. Due to the complex nature of most biomass sources, which can contain cellulose, hemicellulose, pectin, lignin, protein, and ash, among other components, preferred enzyme combinations may contain enzymes with a range of substrate specificities that work together to degrade biomass in the most efficient manner. One example of a multi-enzyme complex for lignocellulose saccharification is a mixture of cellobiohydrolase(s), xylanase(s), endoglucanase(s), p-glucosidase(s), P-xylosidase(s), peptidase(s), and accessory enzymes. However, it is to be understood that any of the enzymes described specifically herein can be combined with any one or more of the enzymes described herein or with any other available and suitable enzymes, to produce a multi-enzyme composition. The invention is not restricted or limited to the specific exemplary combinations listed below.

[0163] The enzymes of the multi-enzyme composition can be provided by a variety of sources.

In one embodiment, the enzymes can be produced by growing organisms such as bacteria, algae, fungi, and plants which produce the enzymes naturally or by virtue of being genetically modified to express the enzyme or enzymes. In another embodiment, at least one enzyme of the multi-enzyme composition is a commercially available enzyme.

[0164] In some embodiments, the multi-enzyme compositions comprise an accessory enzyme.

An accessory enzyme can have the same or similar function or a different function as an enzyme or enzymes in the core set of enzymes. These enzymes have been described elsewhere herein, and can generally include peptidases, cellulases, xylanases, ligninases, amylases, lipidases, or glucuronidases, for example. An accessory enzyme or enzyme mix may be composed of enzymes from (1) commercial suppliers; (2) cloned genes expressing enzymes; (3) complex broth (such as that resulting from growth of a microbial strain in media, wherein the strains secrete proteins and enzymes into the media); (4) cell lysates of strains grown as in (3); and, (5) plant material expressing enzymes.

[0165] The multi-enzyme compositions, in some embodiments, comprise a biomass comprising microorganisms or a crude fermentation product of microorganisms. A crude fermentation product refers to the fermentation broth which has been separated from the microorganism biomass (by filtration, for example). In general, the microorganisms are grown in fermentors, optionally centrifuged or filtered to remove biomass, and optionally concentrated, formulated, and dried to produce an enzyme(s) or a multi-enzyme composition that is a crude fermentation product. In other embodiments, enzyme(s) or multi-enzyme compositions produced by the microorganism (including a genetically modified microorganism as described below) are subjected to one or more purification steps, such as ammonium sulfate precipitation, chromatography, and/or ultrafiltration, which result in a partially purified or purified enzyme(s). If the microorganism has been genetically modified to express the enzyme(s), the enzyme(s) will include recombinant enzymes. If the genetically modified microorganism also naturally expresses the enzyme(s) or other enzymes useful for the degradation of protein, the enzyme(s) may include both naturally occurring and recombinant enzymes.

[0166] Another embodiment of the present invention relates to a composition comprising at least about 500 ng, and preferably at least about 1 ^ig, and more preferably at least about 5 ^ig, and more preferably at least about 10 ^ig, and more preferably at least about 25 ^ig, and more preferably at least about 50 μg, and more preferably at least about 75 Hg, and more preferably at least about 100 μg, and more preferably at least about 250 μ¾ and more preferably at least about 500 μ¾ and more preferably at least about 750 μg, and more preferably at least about 1 mg, and more preferably at least about 5 mg, of an isolated protein comprising any of the proteins or homologues, variants, or fragments thereof discussed herein. Such a composition of the present invention may include any carrier with which the protein is associated by virtue of the protein preparation method, a protein purification method, or a preparation of the protein for use in any method according to the present invention. For example, such a carrier can include any suitable buffer, extract, or medium that is suitable for combining with the protein of the present invention so that the protein can be used in any method described herein according to the present invention. [0167] In one embodiment of the invention, one or more enzymes of the invention is bound to a solid support, i.e., an immobilized enzyme. As used herein, an immobilized enzyme includes immobilized isolated enzymes, immobilized microbial cells which contain one or more enzymes of the invention, other stabilized intact cells that produce one or more enzymes of the invention, and stabilized cell/membrane homogenates. Stabilized intact cells and stabilized cell/membrane homogenates include cells and homogenates from naturally occurring microorganisms expressing the enzymes of the invention and preferably, from genetically modified microorganisms as disclosed elsewhere herein. Thus, although methods for immobilizing enzymes are discussed below, it will be appreciated that such methods are equally applicable to immobilizing microbial cells and in such an embodiment, the cells can be lysed, if desired.

[0168] A variety of methods for immobilizing an enzyme are disclosed in Industrial Enzymology 2nd Ed., Godfrey, T. and West, S. Eds., Stockton Press, New York, N.Y.. 1996, pp. 267-272; Immobilized Enzymes, Chibata, I. Ed., Halsted Press, New York, N.Y., 1978; Enzymes and Immobilized Cells in Biotechnology, Laskin, A. Ed., Benjamin/Cummings Publishing Co., Inc., Menlo Park, California, 1985; and Applied Biochemistry and Bioengineering, Vol. 4, Chibata, I. and Wingard, Jr., L. Eds, Academic Press, New York, N.Y., 1983.

[0169] Briefly, a solid support refers to any solid organic, biopolymer or inorganic supports that can form a bond with an enzyme without significantly effecting the activity of the enzyme. Exemplary organic solid supports include polymers such as polystyrene, nylon, phenol-formaldehyde resins, acrylic copolymers (e.g., polyacrylamide), stabilized intact whole cells, and stabilized crude whole cell/membrane homogenates. Exemplary biopolymer supports include cellulose, polydextrans (e.g., Sephadex®), agarose, collagen and chitin. Exemplary inorganic supports include glass beads (porous and nonporous), stainless steel, metal oxides (e.g., porous ceramics such as ZrC>2, Ti0₂, AI2O3, and NiO) and sand. In one embodiment, the solid support is selected from the group consisting of stabilized intact cells and/or crude cell homogenates (e.g., produced from the microbial host cells expressing recombinant enzymes, alone or in combination with natural enzymes). Preparation of such supports requires a minimum of handling and cost. Additionally, such supports provide excellent stability of the enzyme.

[0170] Stabilized intact cells and/or cell/membrane homogenates can be produced, for example, by using bifunctional crosslinkers (e.g., glutaraldehyde) to stabilize cells and cell homogenates. In both the intact cells and the cell membranes, the cell wall and membranes act as immobilizing supports. In such a system, integral membrane proteins are in the "best" lipid membrane environment. Whether starting with intact pells or homogenates, in this_, system the cells are either no longer "alive" or "metabolizing", or alternatively, are "resting" (i.e., the cells maintain metabolic potential and active enzyme, but under the culture conditions are not growing); in either case, the immobilized cells or membranes serve as biocatalysts.

[0171] An enzyme of the invention can be bound to a solid support by a variety of methods including adsorption, cross-linking (including covalent bonding), and entrapment. Adsorption can be through van del Waal's forces, hydrogen bonding, ionic bonding, or hydrophobic binding. Exemplary solid supports for adsorption immobilization include polymeric adsorbents and ion-exchange resins. Solid supports in a bead form are particularly well-suited. The particle size of an adsorption solid support can be selected such that the immobilized enzyme is retained in the reactor by a mesh filter while the substrate is allowed to flow through the reactor at a desired rate. With porous particulate- supports it is possible to control the adsorption process to allow enzymes or cells to be embedded within the cavity of the particle, thus providing protection without an unacceptable loss of activity.

[0172] Cross-linking of an enzyme to a solid support involves forming a chemical bond between a solid support and the enzyme. It will be appreciated that although cross- linking generally involves linking the enzyme to a solid support using an intermediary compound, it is also possible to achieve a covalent bonding between the enzyme and the solid support directly without the use of an intermediary compound. Cross-linking commonly uses a bifunctional or multifunctional reagent to activate and attach a carboxyl group, amino group, sulfur group, hydroxy group or other functional group of the enzyme to the solid support. The term "activate" refers to a chemical transformation of a functional group which allows a formation of a bond at the functional group. Exemplary amino group activating reagents include water-soluble carbodiimides, glutaraldehyde, cyanogen bromide, N-hydroxysuccinimide esters, triazines, cyanuric chloride, and carbonyl diimidazole. Exemplary carboxyl group activating reagents include water-soluble carbodiimides, and N-ethyl-5- phenylisoxazolium-3-sulfonate. Exemplary tyrosyl group activating reagents include diazonium compounds. And exemplary sulfhydryl group activating reagents include dithiobis-5,5'-(2-nitrobenzoic acid), and glutathione-2-pyridyl disulfide. Systems for covalently linking an enzyme directly to a solid support include Eupergit®, a polymethacrylate bead support available from Rohm Pharma (Darmstadt, Germany), kieselguh] (Macrosorbs), available from Sterling Organics, kaolinite available from English China Clay as "Biofix" supports, silica gels which can be activated by silanization, available from W.R. Grace, and high-density alumina, available from UOP (Des Plains, IL).

[0173] Entrapment can also be used to immobilize an enzyme. Entrapment of an enzyme involves formation of, inter alia, gels (using organic or biological polymers), vesicles (including microencapsulation), semipermeable membranes or other matrices. Exemplary materials used for entrapment of an enzyme include collagen, gelatin, agar, cellulose triacetate, alginate, polyacrylamide, polystyrene, polyurethane, epoxy resins, carrageenan, and egg albumin. Some of the polymers, in particular cellulose triacetate, can be used to entrap the enzyme as they are spun into a fiber. Other materials such as polyacrylamide gels can be polymerized in solution to entrap the enzyme. Still other materials such as polyglycol oligomers that are functionalized with polymerizable vinyl end groups can entrap enzymes by forming a cross-linked polymer with UV light illumination in the presence of a photosensitizer.

[0174] Further embodiments of the present invention include nucleic acid molecules that encode a protein of the present invention, as well as homologues, variants, or fragments of such nucleic acid molecules. A nucleic acid molecule of the present invention includes a nucleic acid molecule comprising, consisting essentially of, or consisting of, a nucleic acid sequence encoding any of the isolated proteins disclosed herein, including a fragment or a homologue or variant of such proteins, described above. Nucleic acid molecules can include a nucleic acid sequence that encodes a fragment of a protein that does not have biological activity, and can also include portions of a gene or polynucleotide encoding the protein that are not part of the coding region for the protein {e.g., introns or regulatory regions of a gene encoding the protein). Nucleic acid molecules can include a nucleic acid sequence that is useful as a probe or primer (oligonucleotide sequences).

[0175] In one embodiment, a nucleic acid molecule of the present invention includes a nucleic acid molecule comprising, consisting essentially of, or consisting of, a nucleic acid sequence represented in Sequences PR 1- PR 430 or fragments or homologues or variants thereof. Preferably, the nucleic acid sequence encodes a protein (including fragments and homologues or variants thereof) useful in the invention, or encompasses useful oligonucleotides or complementary nucleic acid sequences.

In one embodiment, a nucleic molecule of the present invention includes a nucleic acid molecule comprising, consisting essentially of, or consisting of, a nucleic acid sequence encoding an amino acid sequence represented in SEQ ED NO: 2, SEQ ED No:

4, SEQ ID No: 6, SEQ ID No: 8, SEQ ID No: 10, SEQ ID No: 12, SEQ ID No: 14,

SEQ ID No: 16, SEQ ID No: 18, SEQ ID No: 20, SEQ ID No: 22, SEQ ID No: 24,

SEQ ID No: 26, SEQ ED No: 28, SEQ ID No: 30, SEQ ID No: 32, SEQ ID No: 34,

SEQ ED No: 36, SEQ ED No: 38, SEQ ED No: 40, SEQ ID No: 42, SEQ ID No: 44,

SEQ ID No: 46, SEQ ED No: 48, SEQ ED No: 50, SEQ ED No: 52, SEQ ID No: 54,

SEQ ID No: 56, SEQ ID No: 58, SEQ ED No: 60, SEQ ID No: 62, SEQ ED No: 64,

SEQ ID No: 66, SEQ ED No: 68, SEQ ED No: 70, SEQ ID No: 72, SEQ ID No: 74,

SEQ ED No: 76, SEQ ED No: 78, SEQ ED No: 80, SEQ ID No: 82, SEQ ID No: 84,

SEQ ED No: 86, SEQ ED No: 88, SEQ ID No: 90, SEQ ID No: 92, SEQ ED No: 94,

SEQ ID No: 96, SEQ ED No: 98, SEQ ED No: 100, SEQ ID No: 102, SEQ ID No: 104, SEQ ID No: 106, SEQ ID No: 108, SEQ ED No: 1 10, SEQ ED No: 112, SEQ ED No: 114, SEQ ED No: 116, SEQ ED No: 1 18, SEQ ED No: 120, SEQ ED No: 122, SEQ ID No: 124, SEQ ED No: 126, SEQ ID No: 128, SEQ ED No: 130, SEQ ED No: 132, SEQ ED No: 134, SEQ ED No: 136, SEQ ED No: 138, SEQ ED No: 140, SEQ ED No: 142, SEQ ED No: 144, SEQ ID No: 146, SEQ ED No: 148, SEQ ID No: 150, SEQ ID No: 152, SEQ ED No: 154, SEQ ED No: 156, SEQ ED No: 158, SEQ ED No: 160, SEQ ID No: 162, SEQ ED No: 164, SEQ ID No: 166, SEQ ED No: 168, SEQ ID No: 170, SEQ ID No: 172, SEQ ED No: 174, SEQ ED No: 176, SEQ ED No: 178, SEQ ED No: 180, SEQ ED No: 182, SEQ ID No: 184, SEQ ED No: 186, SEQ ED No: 188, SEQ ED No: 190, SEQ ^'ED NO: 192, SEQ ED No: 194, SEQ ED No: 196, SEQ ED No: 198, SEQ ID No: 200, SEQ ED No: 202, SEQ ID No: 204, SEQ ED No: 206, SEQ ED No: 208, SEQ ED No: 210, SEQ ED No: 212, SEQ ED No: 214, SEQ ED No: 216, SEQ ED No: 218, SEQ ED No: 220, SEQ ID No: 222, SEQ ED No: 224, SEQ ID No: 226, SEQ ED No: 228, SEQ ED No: 230, SEQ ED No: 232, SEQ ED No: 234, SEQ ED No: 236, SEQ ID No: 238, SEQ ED No: 240, SEQ ED No: 242, SEQ ED No: 244, SEQ ED No: 246, SEQ ED No: 248, SEQ ED No: 250, SEQ ED No: 252, SEQ ED No: 254, SEQ ID No: 256, SEQ ID No: 258, SEQ ID No: 260, SEQ ID No: 262, SEQ ID No: 264, SEQ ID No: 266, SEQ ID No: 268, SEQ ID No: 270, SEQ ID No: 272, SEQ ID No: 274, SEQ ID No: 276, SEQ ID No: 278, SEQ ID No: 280, SEQ ID No: 282, SEQ ID No: 284, SEQ ID No: 286, SEQ ED No: 288, SEQ ED No: 290, SEQ ID No: 292, SEQ ED No: 294, SEQ ID No: 296, SEQ ED No: 298, SEQ ED No:300, SEQ ED No: 302, SEQ ED No: 304, SEQ ED No: 306, SEQ ED No: 308, SEQ ED No: 310, SEQ ED No: 312, SEQ ID No: 314, SEQ ED No: 316, SEQ ED No: 318, SEQ ED No: 320, SEQ ED No: 322, SEQ ED No: 324, SEQ ED No: 326, SEQ ED No: 328, SEQ ED No: 330, SEQ ED No: 332, SEQ ED No: 334, SEQ ED No: 336, SEQ ED No: 338, SEQ ID No: 340, SEQ ID No: 342, SEQ ED No: 344, SEQ ED No: 346, SEQ ED No: 348, SEQ ID No: 350, SEQ ID No: 352, SEQ ID No: 354, SEQ ID No: 356, SEQ ID No: 358, SEQ ID No: 360, SEQ ID No: 362, SEQ ID No: 364, SEQ ED No: 366, SEQ D No: 368, SEQ ED No: 370, SEQ ID No: 372, SEQ ID No: 374, SEQ ED No: 376, SEQ ED No: 378, SEQ ED No: 380, SEQ ED No: 382, SEQ ED No: 384, SEQ ED No: 386, SEQ ED No: 388, SEQ ID No: 390, SEQ ED No: 392, SEQ ED No: 394, SEQ ID No: 396, SEQ ED No: 398, 400, SEQ ED No: 402, SEQ ID No: 404, SEQ ED No: 406, SEQ ID No: 408, SEQ ED No: 410, SEQ ED No: 412, SEQ ED No: 414, SEQ ED No: 416, SEQ ED No: 418, SEQ ID No: 420, SEQ ED No: 422, SEQ ED No: 424, SEQ ED No: 426, SEQ ED No: 428, SEQ ID No: 430, SEQ ED No: 432, SEQ ED No: 434, SEQ ED No: 436, SEQ ID No: 438, SEQ ED No: 440, SEQ ID No: 442, SEQ ID No: 444, SEQ ID No: 446, SEQ ED No: 448, SEQ ED No: 450, SEQ ED No: 452, SEQ ED No: 454, SEQ ED No: 456, SEQ ID No: 458, SEQ ED No: 460, SEQ ID No: 462, SEQ ED No: 464, SEQ ED No: 466, SEQ ED No: 468, SEQ ED No: 470, SEQ ID No: 472, SEQ ED No: 474, SEQ ID No: 476, SEQ ED No: 478, SEQ ID No: 480, SEQ ED No: 482, SEQ ID No: 484, SEQ ED No: 486, SEQ ED No: 488, SEQ ID No: 490, SEQ ID No: 492, SEQ ED No: 494, SEQ ID No: 496, SEQ ED No: 498, SEQ ID No: 500, SEQ ID No: 502, SEQ ED No: 504, SEQ ED No: 506, SEQ ED No: 508, SEQ ED No: 510, SEQ ED No: 512, SEQ ED No: 514, SEQ ED No: 516, SEQ ED No: 518, SEQ ID No: 520, SEQ ID No: 522, SEQ ED No: 524, SEQ ID No: 526, SEQ ED No: 528, SEQ ED No: 530, SEQ ID No: 532, SEQ ID No: 534, SEQ ED No: 536, SEQ ID No: 538, SEQ ID No: 540, SEQ ED No: 542, SEQ ID No: 544, SEQ ED No: 546, SEQ ID No: 548, SEQ ID No: 550, SEQ ID No: 552, SEQ ED No: 554, SEQ ID No: 556, SEQ ED No: 558, SEQ ED No: 560, SEQ ED No: 562, SEQ ID No: 564, SEQ ED No: 566, SEQ ED No: 568, SEQ ED No: 570, SEQ ID No: 572, SEQ ID No: 574, SEQ ID No: 576, SEQ ID No: 578, SEQ ID No: 580, SEQ ID No: 582, SEQ ID No: 584, SEQ ID No: 586, SEQ ID No: 588, SEQ ID No: 590, SEQ ED No: 592, SEQ ED No: 594, SEQ ID No: 596, SEQ ID No: 598, SEQ. ID No:600, SEQ ED No: 602, SEQ ED No: 604, SEQ ID No: 606, SEQ ED No: 608, SEQ ED No: 610, SEQ ED No: 612, SEQ ED No: 614, SEQ ED No: 616, SEQ ED No: 618, SEQ ID No: 620, SEQ ID No: 622, SEQ ED No: 624, SEQ ID No: 626, SEQ ID No: 628, SEQ ED No: 630, SEQ ID No: 632, SEQ ED No: 634, SEQ ED No: 636, SEQ ID No: 638, SEQ ED No: 640, SEQ ID No: 642, SEQ ED No: 644, SEQ ED No: 646, SEQ ED No: 648, SEQ ED No: 650, SEQ ED No: 652, SEQ ED No: 654, SEQ ED No: 656, SEQ ID No: 658, SEQ ED No: 660, SEQ ED No: 662, SEQ ID No: 664, SEQ ED No: 666, SEQ ED- No: 668, SEQ ED No: 670, SEQ ID No: 672, SEQ ED No: 674, SEQ ID No: 676, SEQ ED No: 678, SEQ ID No: 680, SEQ ED No: 682, SEQ ED No: 684, SEQ ED No: 685, SEQ ID No: 688, SEQ ED No: 690, SEQ ED No: 692, SEQ ID No: 694, SEQ ED No: 696, SEQ ID No: 698, SEQ ED No: 700, SEQ ID No: 702, SEQ ID No: 704, SEQ ED No: 706, SEQ ID No: 708, SEQ ED No: 710, SEQ ED No: 712, SEQ ID No: 714, SEQ ID No: 716, SEQ ID No: 718, SEQ ID No: 720, SEQ ID No: 722, SEQ ID No: 724, SEQ ED No: 726, SEQ ID No: 728, SEQ ED No: 730, SEQ ED No: 732, SEQ ED No: 734, SEQ ED No: 736, SEQ ED No: 738, SEQ ED No: 740, SEQ ED No: 742, SEQ ED No: 744, SEQ ED No: 746, SEQ ED No: 748, SEQ ED No: 750, SEQ ID No: 752, SEQ ED No: 754, SEQ^' ID No: 756, SEQ ED No: 758, SEQ ED No: 760, SEQ ED No: 162, SEQ ED No: 764, SEQ ID No: 766, SEQ ED No: 768, SEQ ED No: 770, SEQ ED No: 772, SEQ ID No: 774, SEQ ED No: 776, SEQ ID No: 778, SEQ ED No: 780, SEQ ED No: 782, SEQ ID No: 784, SEQ ED No: 786, SEQ ED No: 788, SEQ ID No: 790, SEQ ID No: 792, SEQ ED No: 794, SEQ ED No: 796, SEQ ED No: 798, SEQ ID No: 800, SEQ ID No: 802, SEQ ID No: 804, SEQ ED No: 806, SEQ ED No: 808, SEQ ED No: 810, SEQ ID No: 812, SEQ ID No: 814, SEQ ID No: 816, SEQ ID No: 818, SEQ No: 820, SEQ ED No: 822, SEQ ID No: 824, SEQ ID No: 826, SEQ ID No: 828, SEQ ED No: 830, SEQ ID No: 832, SEQ ED No: 834, SEQ ED No: 836, SEQ ID No: 838, SEQ ED No: 840, SEQ ED No: 842, SEQ ED No: 844, SEQ ED No: 846, SEQ ED No: 848, SEQ ID No: 850, SEQ ED No: 852, SEQ ID No: 854, SEQ ED No: 856, SEQ ED No: 858, SEQ ED No: 860 or fragments or homologues or variants thereof. Preferably, the nucleic acid sequence encodes a protein (including fragments and homologues or variants thereof) useful in the invention, or encompasses useful oligonucleotides or complementary nucleic acid sequences.

In one embodiment, such nucleic acid molecules include isolated nucleic acid molecules that nybrldize under moderate stringency conditions, and more preferably under high stringency conditions, and even more preferably under very high stringency conditions, as described above, with the complement of a nucleic acid sequence encoding a protein of the present invention (i.e., including naturally occurring allelic variants encoding a protein of the present invention). Preferably, an isolated nucleic acid molecule encoding a protein of the present invention comprises a nucleic acid sequence that hybridizes under moderate, high, or very high stringency conditions to the complement of a nucleic acid sequence that encodes a protein comprising an amino acid sequence represented in SEQ ID NO: 2, SEQ ID No: 4, SEQ ID No: 6, SEQ ID No: 8, SEQ ID No: 10, SEQ ID No: 12, SEQ ID No: 14, SEQ ID No: 16, SEQ ID No: 18, SEQ ID No: 20, SEQ ID No: 22, SEQ ED No: 24, SEQ ID No: 26, SEQ ID No: 28, SEQ ID No: 30, SEQ ID No: 32, SEQ ID No: 34, SEQ ID No: 36, SEQ ID No: 38, SEQ ID No: 40, SEQ ID No: 42, SEQ ID No: 44, SEQ ID No: 46, SEQ ID No: 48, SEQ ID No: 50, SEQ ED No: 52, SEQ ED No: 54, SEQ ID No: 56, SEQ ID No: 58, SEQ ED No: 60, SEQ ED No: 62, SEQ ED No: 64, SEQ ID No: 66, SEQ ID No: 68, SEQ D No: 70, SEQ ED No: 72, SEQ ED No: 74, SEQ ED No: 76, SEQ ID No: 78, SEQ ED No: 80, SEQ ED No: 82, SEQ ED No: 84, SEQ ID No: 86, SEQ ID No: 88, SEQ ED No: 90, SEQ ID No: 92, SEQ ED No: 94, SEQ ED No: 96, SEQ ID No: 98, SEQ ED No: 100, SEQ ED No: 102, SEQ DD No: 104, SEQ ID No: 106, SEQ ED No: 108, SEQ ED No: 110, SEQ ED No: 1 12, SEQ ED No: 114, SEQ ED No: 116, SEQ ID No: 1 18, SEQ ED No: 120, SEQ ID No: 122, SEQ ED No: 124, SEQ ED No: 126, SEQ DD No: 128, SEQ ED No: 130, SEQ ED No: 132, SEQ ED No: 134, SEQ ID No: 136, SEQ ED No: 138, SEQ ID No: 140, SEQ ED No: 142, SEQ ID No: 144, SEQ ID No: 146, SEQ ED No: 148, SEQ ID No: 150, SEQ ED No: 152, SEQ ED No: 154, SEQ ED No: 156, SEQ ID No: 158, SEQ ID No: 160, SEQ ED No: 162, SEQ ED No: 164, SEQ ED No: 166, SEQ DD No: 168, SEQ D No: 170, SEQ DD No: 172, SEQ ED No: 174, SEQ DD No: 176, SEQ ID No: 178, SEQ DD No: 180, SEQ ED No: 182, SEQ ID No: 184, SEQ DD No: 186, SEQ DD No: 188, SEQ ED No: 190, SEQ DD No: 192, SEQ ID No: 194, SEQ DD No: 196, SEQ ID No: 198, SEQ ID No: 200, SEQ DD No: 202, SEQ ED No: 204, SEQ DD No: 206, SEQ DD No: 208, SEQ DD No: 210, SEQ DD No: 212, SEQ DD No: 214, SEQ ID No: 216, SEQ DD No: 218, SEQ ID No: 220, SEQ DD No: 222, SEQ ID No: 224, SEQ ID No: 226, SEQ ID No: 228, SEQ ID No: 230, SEQ ID No: 232, SEQ ID No: 234, SEQ ID No: 236, SEQ ID No: 238, SEQ ED No: 240, SEQ ID No: 242, SEQ ID No: 244, SEQ ID No: 246, SEQ ID No: 248, SEQ ID No: 250, SEQ ID No: 252, SEQ ID No: 254, SEQ ID No: 256, SEQ ID No: 258, SEQ ID No: 260, SEQ ID No: 262, SEQ ID No: 264, SEQ ID No: 266, SEQ ID No: 268, SEQ ID No: 270, SEQ ID No: 272, SEQ ID No: 274, SEQ ID No: 276, SEQ ID No: 278, SEQ ID No: 280, SEQ ID No: 282, SEQ ID No: 284, SEQ ID No: 286, SEQ ID No: 288, SEQ ID No: 290, SEQ ID No: 292, SEQ ED No: 294, SEQ ID No: 296, SEQ ID No: 298, SEQ ID No:300, SEQ ED No: 302, SEQ ED No: 304, SEQ ED No: 306, SEQ ID No: 308, SEQ ED No: 310, SEQ ID No: 312, SEQ ED No: 314, SEQ ED No: 316, SEQ ED No: 318, SEQ ED No: 320, SEQ ED No: 322, SEQ ID No: 324, SEQ ED No: 326, SEQ ED No: 328, SEQ ID No: 330, SEQ ID No: 332, SEQ ID No: 334, SEQ ED No: 336, SEQ ID No: 338, SEQ ID No: 340, SEQ ED No: 342, SEQ ID No: 344, SEQ ID No: 346, SEQ ED No: 348, SEQ ID No: 350, SEQ ED No: 352, SEQ ED No: 354, SEQ ED No: 356, SEQ ED No: 358, SEQ ED No: 360, SEQ ID No: 362, SEQ ED No: 364, SEQ ED No: 366, SEQ ED No: 368, SEQ ED No: 370, SEQ ED No: 372, SEQ ED No: 374, SEQ ED No: 376, SEQ ED No: 378, SEQ ED No: 380, SEQ ED No: 382, SEQ ID No: 384, SEQ ED No: 386, SEQ ED No: 388, SEQ ED No: 390, SEQ ED No: 392, SEQ ED No: 394, SEQ ED No: 396, SEQ ED No: 398, 400, SEQ ED No: 402, SEQ ED No: 404, SEQ ID No: 406, SEQ ED No: 408, SEQ ED No: 410, SEQ ED No: 412, SEQ ID No: 414, SEQ ED No: 416, SEQ ID No: 418, SEQ ED No: 420, SEQ ED No: 422, SEQ ED No: 424, SEQ ID No: 426, SEQ ID No: 428, SEQ ED No: 430, SEQ ED No: 432, SEQ ED No: 434, SEQ ID No: 436, SEQ ED No: 438, SEQ ED No: 440, SEQ ED No: 442, SEQ ED No: 444, SEQ ID No: 446, SEQ ED No: 448, SEQ ED No: 450, SEQ ID No: 452, SEQ ED No: 454, SEQ ID No: 456, SEQ ED No: 458, SEQ ED No: 460, SEQ ED No: 462, SEQ ED No: 464, SEQ ED No: 466, SEQ ID No: 468, SEQ ED No: 470, SEQ ED No: 472, SEQ ED No: 474, SEQ ED No: 476, SEQ ID No: 478, SEQ ED No: 480, SEQ ED No: 482, SEQ ED No: 484, SEQ ED No: 486, SEQ ED No: 488, SEQ ID No: 490, SEQ ID No: 492, SEQ ID No: 494, SEQ ED No: 496, SEQ ED No: 498, SEQ ED No: 500, SEQ ID No: 502, SEQ ID No: 504, SEQ ED No: 506, SEQ ED No: 508, SEQ ED No: 510, SEQ ID No: 512, SEQ ED No: 514, SEQ ID No: 516, SEQ ED No: 518, SEQ ED No: 520, SEQ ED No: 522, SEQ ED No: 524, SEQ ED No: 526, SEQ ID No: 528, SEQ ID No: 530, SEQ ID No: 532, SEQ ED No: 534, SEQ ED No: 536, SEQ ID No: 538, SEQ ID No: 540, SEQ ID No: 542, SEQ ID No: 544, SEQ ID No: 546, SEQ ID No: 548, SEQ ID No: 550, SEQ ID No: 552, SEQ ID No: 554, SEQ ID No: 556, SEQ ID No: 558, SEQ ID No: 560, SEQ ID No: 562, SEQ ID No: 564, SEQ ID No: 566, SEQ ID No: 568, SEQ ID No: 570, SEQ ID No: 572, SEQ ID No: 574, SEQ ID No: 576, SEQ ID No: 578, SEQ ID No: 580, SEQ ID No: 582, SEQ ID No: 584, SEQ ID No: 586, SEQ ID No: 588, SEQ ID No: 590, SEQ ID No: 592, SEQ ID No: 594, SEQ ID No: 596, SEQ ID No: 598, SEQ ID No:600, SEQ ID No: 602, SEQ ID No: 604, SEQ ID No: 606, SEQ ID No: 608, SEQ ID No: 610, SEQ ID No: 612, SEQ ID No: 614, SEQ ID No: 616, SEQ ID No: 618, SEQ ED No: 620, SEQ ID No: 622, SEQ ID No: 624, SEQ ID No: 626, SEQ ID No: 628, SEQ ID No: 630, SEQ ID No: 632, SEQ ID No: 634, SEQ ID No: 636, SEQ ID No: 638, SEQ ID No: 640, SEQ ID No: 642, SEQ ID No: 644, SEQ ID No: 646, SEQ ID No: 648, SEQ ID No: 650, SEQ ID No: 652, SEQ ID No: 654, SEQ ID No: 656, SEQ ID No: 658, SEQ ID No: 660, SEQ ID No: 662, SEQ ID No: 664, SEQ ID No: 666, SEQ ID No: 668, SEQ 3D No: 670, SEQ ID No: 672, SEQ ID No: 674, SEQ ID No: 676, SEQ ID No: 678, SEQ ID No: 680, SEQ ID No: 682, SEQ ID No: 684, SEQ ID No: 686, SEQ ID No: 688, SEQ ID No: 690, SEQ ID No: 692, SEQ ID No: 694, SEQ ID No: 696, SEQ ID No: 698, SEQ ID No: 700, SEQ ID No: 702, SEQ ID No: 704, SEQ ID No: 706, SEQ ID No: 708, SEQ ED No: 710, SEQ ED No: 712, SEQ ID No: 714, SEQ ED No: 716, SEQ ID No: 718, SEQ ED No: 720, SEQ ED No: 722, SEQ ED No: 724, SEQ ID No: 726, SEQ ED No: 728, SEQ ED No: 730, SEQ ED No: 732, SEQ ED No: 734, SEQ ED No: 736, SEQ ED No: 738, SEQ ID No: 740, SEQ ED No: 742, SEQ ID No: 744, SEQ ED No: 746, SEQ ED No: 748, SEQ ED No: 750, SEQ ED No: 752, SEQ ED No: 754, SEQ ID No: 756, SEQ ID No: 758, SEQ ED No: 760, SEQ ED No: 762, SEQ ED No: 764, SEQ ED No: 766, SEQ ED No: 768, SEQ ED No: 770, SEQ ED No: 772, SEQ ID No: 774, SEQ ED No: 776, SEQ ID No: 778, SEQ ID No: 780, SEQ ID No: 782, SEQ ED No: 784, SEQ ED No: 786, SEQ ED No: 788, SEQ ED No: 790, SEQ ED No: 792, SEQ ID No: 794, SEQ ED No: 796, SEQ ID No: 798, SEQ ED No: 800, SEQ ED No: 802, SEQ ED No: 804, SEQ ED No: 806, SEQ ED No: 808, SEQ ED No: 810, SEQ ED No: 812, SEQ ED No: 814, SEQ ED No: 816, SEQ ED No: 818, SEQ ED No: 820, SEQ ED No: 822, SEQ ED No: 824, SEQ ID No: 826, SEQ ED No: 828, SEQ ED No: 830, SEQ ID No: 832, SEQ ID No: 834, SEQ ID No: 836, SEQ ED No: 838, SEQ ED No: 840, SEQ ED No: 842, SEQ ED No: 844, SEQ ID No: 846, SEQ ED No: 848, SEQ ED No: 850, SEQ ID No: 852, SEQ ID No: 854, SEQ ID No: 856, SEQ ID No: 858, SEQ ID No: 860..

[0178] In accordance with the present invention, an isolated nucleic acid molecule is a nucleic acid molecule (polynucleotide) that has been removed from its natural milieu (i.e., that has been subject to human manipulation) and can include DNA, RNA, or derivatives of either DNA or RNA, including cDNA. As such, "isolated" does not reflect the extent to which the nucleic acid molecule has been purified. Although the phrase "nucleic acid molecule" primarily refers to the physical nucleic acid molecule, and the phrase "nucleic acid sequence" primarily refers to the sequence of nucleotides on the nucleic acid molecule, the two phrases can be used interchangeably, especially with respect to a nucleic acid molecule, or a nucleic acid sequence, being capable of encoding a protein. An isolated nucleic acid molecule of the present invention can be isolated from its natural source or produced using recombinant DNA technology (e.g., polymerase chain reaction (PCR) amplification, cloning) or chemical synthesis. Isolated nucleic acid molecules can include, for example, genes, natural allelic variants of genes, coding regions or portions thereof, and coding and/or regulatory regions modified by nucleotide insertions, deletions, substitutions, and/or inversions in a manner such that the modifications do not substantially interfere with the nucleic acid molecule's ability to encode a protein of the present invention or to form stable hybrids under stringent conditions with natural gene isolates. An isolated nucleic acid molecule can include degeneracies. As used herein, nucleotide degeneracy refers to the phenomenon that one amino acid can be encoded by different nucleotide codons. Thus, the nucleic acid sequence of a nucleic acid molecule that encodes a protein of the present invention can vary due to degeneracies. It is noted that a nucleic acid molecule of the present invention is not required to encode a protein having protein activity. A nucleic acid molecule can encode a truncated, mutated or inactive protein, for example. In addition, nucleic acid molecules of the invention are useful as probes and primers for the identification, isolation and/or purification of other nucleic acid molecules. If the nucleic acid molecule is an oligonucleotide, such as a probe or primer, the oligonucleotide preferably ranges from about 5 to about 50 or about 500 nucleotides, more preferably from about 10 to about 40 nucleotides, and most preferably from about 15 to about 40 nucleotides in length.

[0179] According to the present invention, reference to a gene includes all nucleic acid sequences related to a natural (i.e. wild-type) gene, such as regulatory regions that control production of the protein encoded by that gene (such as, but not limited to, transcription, translation or post-translation control regions) as well as the coding region itself. In another embodiment, a gene can be a naturally occurring allelic variant that includes a similar but not identical sequence to the nucleic acid sequence encoding a given protein. Allelic variants have been previously described above. Genes can include or exclude one or more introns or any portions thereof or any other sequences or which are not included in the cDNA for that protein. The phrases "nucleic acid molecule" and "gene" can be used interchangeably when the nucleic acid molecule comprises a gene as described above.

[0180] Preferably, an isolated nucleic acid molecule of the present invention is produced using recombinant DNA technology (e.g., polymerase chain reaction (PC ) amplification, cloning, etc.) or chemical synthesis. Isolated nucleic acid molecules include any nucleic acid molecules and homologues or variants thereof that are part of a gene described herein and/or that encode a protein described herein, including, but not limited to, natural allelic variants and modified nucleic acid molecules (homologues or variants) in which nucleotides have been inserted, deleted, substituted, and/or inverted in such a manner that such modifications provide the desired effect on protein biological activity or on the activity of the nucleic acid molecule. Allelic variants and protein homologues or variants (e.g., proteins encoded by nucleic acid homologues or variants) have been discussed in detail above.

[0181] A nucleic acid molecule homologue or variant (i.e., encoding a homologue or variant of a protein of the present invention) can be produced using a number of methods known to those skilled in the art (see, for example, Sambrook et al). For example, nucleic acid molecules can be modified using a variety of techniques including,^' but not limited to, by classic mutagenesis and recombinant DNA techniques (e.g., site-directed mutagenesis, chemical treatment, restriction enzyme cleavage, ligation of nucleic acid fragments and/or PCR amplification), or synthesis of oligonucleotide mixtures and ligation of mixture groups to "build" a mixture of nucleic acid molecules and combinations thereof. Another method for modifying a recombinant nucleic acid molecule encoding a protein is gene shuffling (i.e., molecular breeding) (See, for example, U.S. Patent No. 5,605,793 to Stemmer; Minshull and Stemmer; 1999, Curr. Opin. Chem. Biol. 3:284-290; Stemmer, 1994, P.N.A.S. USA 91 : 10747-10751) This technique can be used to efficiently introduce multiple simultaneous changes in the protein. Nucleic acid molecule homologues or variants can be selected by hybridization with a gene or polynucleotide, or by screening for the function of a protein encoded by a nucleic acid molecule (i.e., biological activity).

[0182] The minimum size of a nucleic acid molecule of the present invention is a size sufficient to encode a protein (including a fragment, homologue, or variant of a full- length protein) having biological activity, sufficient to encode a protein comprising at least one epitope which binds to an antibody, or sufficient to form a probe or oligonucleotide primer that is capable of forming a stable hybrid with the complementary sequence of a nucleic acid molecule encoding a natural protein (e.g., under moderate, high, or high stringency conditions). As such, the size of the nucleic acid molecule encoding such a protein can be dependent on nucleic acid composition and percent homology r or identity between the nucleic acid molecule and complementary sequence as well as upon hybridization conditions per se (e.g., temperature, salt concentration, and formamide concentration). The minimal size of a nucleic acid molecule that is used as an oligonucleotide primer or as a probe is typically at least about 12 to about 15 nucleotides in length if the nucleic acid molecules are GC-rich and at least about 15 to about 18 bases in length if they are AT- rich. There is no limit, other than a practical limit, on the maximal size of a nucleic acid molecule of the present invention, in that the nucleic acid molecule can include a portion of a protein encoding sequence, a nucleic acid sequence encoding a full-length protein (including a gene), including any length fragment between about 20 nucleotides and the number of nucleotides that make up the full length cDNA encoding a protein, in whole integers (e.g., 20, 21, 22, 23, 24, 25 nucleotides), or multiple genes, or portions thereof.

[0183] The phrase "consisting essentially of, when used with reference to a nucleic acid sequence herein, refers to a nucleic acid sequence encoding a specified amino acid sequence that can be flanked by from at least one, and up to as many as about 60, additional heterologous nucleotides at each of the 5' and/or the 3' end of the nucleic acid sequence encoding the specified amino acid sequence. The heterologous nucleotides are not naturally found (i.e., not found in nature, in vivo) flanking the nucleic acid sequence encoding the specified amino acid sequence as it occurs in the natural gene or do not encode a protein that imparts any additional function to the protein or changes the function of the protein having the specified amino acid sequence.

[0184] In one embodiment, the polynucleotide probes or primers of the invention are conjugated to detectable markers. Detectable labels suitable for use in the present invention include any composition detectable by spectroscopic, photochemical, biochemical, immunochemical, electrical, optical or chemical means. Useful labels in the present invention include biotin for staining with labeled streptavidin conjugate, magnetic beads (e.g., Dynabeads™), fluorescent dyes (e.g., fluorescein, texas red, rhodamine, green fluorescent protein, and the like), radiolabels (e.g., ³H, ¹²⁵1, ³⁵S, ¹⁴C, or ³²P), enzymes (e.g., horse radish peroxidase, alkaline phosphatase and others commonly used in an ELISA), and colorimetric labels such as colloidal gold or colored glass or plastic (e.g., polystyrene, polypropylene, latex, etc.) beads. Preferably, the polynucleotide probes are immobilized on a substrate such as: artificial membranes, organic supports, biopolymer supports and inorganic supports.

[0185] One embodiment of the present invention relates to a recombinant nucleic acid molecule which comprises the isolated nucleic acid molecule described above which is operatively linked to at least one expression control sequence. More particularly, according to the present invention, a recombinant nucleic acid molecule typically comprises a recombinant vector and any one or more of the isolated nucleic acid molecules as described herein. According to the present invention, a recombinant vector is an engineered (i.e., artificially produced) nucleic acid molecule that is used as a tool for manipulating a nucleic acid sequence of choice and/or for introducing such a nucleic acid sequence into a host cell. The recombinant vector is therefore suitable for use in cloning, sequencing, and/or otherwise manipulating the nucleic acid sequence of choice, such as by expressing and/or delivering the nucleic acid sequence of choice into a host cell to form a recombinant cell. Such a vector typically contains nucleic acid sequences that are not naturally found adjacent to nucleic acid sequence to be cloned or delivered, although the vector can also contain regulatory nucleic acid sequences (e.g., promoters, untranslated regions) which are naturally found adjacent to nucleic acid sequences of the present invention or which are useful for expression of the nucleic acid molecules of the present invention (discussed in detail below). The vector can be either RNA or DNA, either prokaryotic or eukaryotic, and typically is a plasmid. The vector can be maintained as an extrachromosomal element (e.g., a plasmid) or it can be integrated into the chromosome of a recombinant host cell, although it is preferred if the vector remains separate from the genome for most applications of the invention. The entire vector can remain in place within a host cell, or under certain conditions, the plasmid DNA can be deleted, leaving behind the nucleic acid molecule of the present invention. An integrated nucleic acid molecule can be under chromosomal promoter control, under native or plasmid promoter control, or under a combination of several promoter controls. Single or multiple copies of the nucleic acid molecule can be integrated into the chromosome. A recombinant vector of the present invention can contain at least one selectable marker.

[0186] In one embodiment, a recombinant vector used in a recombinant nucleic acid molecule of the present invention is an expression vector. As used herein, the phrase "expression vector" is used to refer to a vector that is suitable for production of an encoded product (e.g., a protein of interest, such as an enzyme of the present invention). In this embodiment, a nucleic acid sequence encoding the product to be produced (e.g., the protein or homologue or variant thereof) is inserted into the recombinant vector to produce a recombinant nucleic acid molecule. The nucleic acid sequence encoding the protein to be produced is inserted into the vector in a manner that operatively links the nucleic acid sequence to regulatory sequences in the vector which enable the transcription and translation of the nucleic acid sequence within the recombinant host cell.

[0187] Typically, a recombinant nucleic acid molecule includes at least one nucleic acid molecule of the present invention operatively linked to one or more expression control sequences (e.g., transcription control sequences or translation control sequences). As used herein, the phrase "recombinant molecule" or "recombinant nucleic acid molecule" primarily refers to a nucleic acid molecule or nucleic acid sequence operatively linked to a transcription control sequence, but can be used interchangeably with the phrase "nucleic acid molecule", when such nucleic acid molecule is a recombinant molecule as discussed herein. According to the present invention, the phrase "operatively linked" refers to linking a nucleic acid molecule to an expression control sequence in a manner such that the molecule is able to be expressed when transfected (i.e., transformed, transduced, transfected, conjugated or conduced) into a host cell. Transcription control sequences are sequences which control the initiation, elongation, or termination of transcription. Particularly important transcription control sequences are those which control transcription initiation, such as promoter, enhancer, operator and repressor sequences. Suitable transcription control sequences include any transcription control sequence that can function in a host cell or organism into which the recombinant nucleic acid molecule is to be introduced. Transcription control sequences may also include any combination of one or more of any of the foregoing.

[0188] Recombinant nucleic acid molecules of the present invention can also contain additional regulatory sequences, such as translation regulatory sequences, origins of replication, and other regulatory, sequences that are compatible with the recombinant cell. In one embodiment, a recombinant molecule of the present invention, including those which are integrated into the host cell chromosome, , also contains secretory signals (i.e., signal segment nucleic acid sequences) to enable an expressed protein to be secreted^from the cell that produces the protein. Suitable signal segments include a signal segment that is naturally associated with the protein to be expressed or any heterologous signal segment capable of directing the secretion of the protein according to the present invention. In another embodiment, a recombinant molecule of the present invention comprises a leader sequence to enable an expressed protein to be delivered to and inserted into the membrane of a host cell. Suitable leader sequences include a leader sequence that is naturally associated with the protein, or any heterologous leader sequence capable of directing the delivery and insertion of the protein to the membrane of a cell.

[0189] According to the present invention, the term "transfection" is generally used to refer to any method by which an exogenous nucleic acid molecule (i.e., a recombinant nucleic acid molecule) can be inserted into a cell. The term "transformation" can be used interchangeably with the term "transfection" when such term is used to refer to the introduction of nucleic acid molecules into microbial cells or plants and describes an inherited change due to the acquisition of exogenous nucleic acids by the microorganism that is essentially synonymous with the term "transfection." Transfection techniques include, but are not limited to, transformation, particle bombardment, electroporation, microinjection, lipofection, adsorption, infection and protoplast fusion.

[0190] One or more recombinant molecules of the present invention can be used to produce an encoded product (e.g., a protein) of the present invention. In one embodiment, an encoded product is produced by expressing a nucleic acid molecule as described herein under conditions effective to produce the protein. A preferred method to produce an encoded protein is by transfecting a host cell with one or more recombinant molecules to form a recombinant cell. Suitable host cells to transfect include, but are not limited to, any bacterial, fungal (e.g., filamentous fungi or yeast or mushrooms), algal, plant, insect, or animal cell that can be transfected. Host cells can be either untransfected cells or cells that are already transfected with at least one other recombinant nucleic acid molecule.

[0191] Suitable cells (e.g., a host cell or production organism) may include any microorganism (e.g., a bacterium, a protist, an alga, a fungus, or other microbe), and is preferably a bacterium, a yeast or a filamentous fungus. Suitable bacterial genera include, but are not limited to, Escherichia, Bacillus, Lactobacillus, Pseudomonas and Streptomyces. Suitable bacterial species include, but are not limited to, Escherichia coli, Bacillus subtilis, Bacillus licheniformis, Bacillus stearothermophilus, Lactobacillus brevis, Pseudomonas aeruginosa and Streptomyces lividans. Suitable genera of yeast include, but are not limited to, Saccharomyces, Schizosaccharomyces, Candida, Hansenula, Pichia, Kluyveromyces, and Phaffia. Suitable yeast species include, but are not . limited to, Saccharomyces cerevisiae, Schizosaccharomyce pombe, Candida albicans, Hansenula polymorpha, Pichia pastoris, P. canadensis, Kluyveromyces marxianus and Phaffia rhodozyma.

[0192] Suitable fungal genera include, but are not limited to, Chrysosporium, Thielavia, Thermomyces, Thermoascus, Neurospora, Aureobasidium, Filibasidium, Piromyces, Corynascus, Cryptococcus, Acremonium, Tolypocladium, Scytalidium, Schizophyllum, Sporotrichum, Penicillium, Gibberella, Myceliophthora, Mucor, Aspergillus, Fusarium, Humicola, Talaromyces and Trichoderma, and anamorphs and teleomorphs thereof Suitable fungal species include, but are not limited to, Aspergillus niger, Aspergillus or >zae, Aspergillus nidulans, Aspergillus japonicus, Absidia coerulea, Rhizopus oryzae, Chrysosporium lucknowense, Neurospora crassa, Neurospora intermedia, Trichoderma reesei, Penicillium canescens, Penicillium solitum, Penicillium funiculo sum, and Talaromyces fiavus. hi one embodiment, the host cell is a fungal cell of the species Chrysosporium lucknowense. In another embodiment, a while (low cellulose) strain is sued. In one embodiment, the host cell is a fungal cell of Strain CI (VKM F-3500-D) or a mutant strain derived therefrom (e.g., UV13-6 (Accession No. VKM F-3632 D); NG7C-19 (Accession No. VKM F-3633 D); UV18- 25 (VKM F-3631D), W1L (CBS122189), or WIUIOOL (CBS.122190)). Host cells can be either untransfected cells or cells that are already transfected with at least one other recombinant nucleic acid molecule. Additional embodiments of the present invention include any of the genetically modified cells described herein.

[0193] In another embodiment, suitable host cells include insect cells (most particularly Drosophila melanogaster cells, Spodoptera frugiperda Sf9 and Sf21 cells and Trichoplusa High-Five cells), nematode cells (particularly C. elegans cells), avian cells, amphibian cells (particularly Xenopus laeyis cells), reptilian cells, and mammalian cells (most particularly human, simian, canine, rodent, bovine, or sheep cells, e.g. NIH3T3, CHO (Chinese hamster ovary cell), COS, VERO, BHK, HEK, and other rodent or human cells).

[0194] In one embodiment, one or more protein(s) expressed by an isolated nucleic acid molecule of the present invention are produced by culturing a cell that expresses the protein {i.e., a recombinant cell or recombinant host cell) under conditions effective to produce the protein. In some instances, the protein may be recovered, and in others, the cell may be harvested in whole, either of which can be used in a composition.

[0195] Microorganisms used in the present invention (including recombinant host cells or genetically modified microorganisms) are cultured in an appropriate fermentation medium. An appropriate, or effective, fermentation medium refers to any medium in which a cell of the present invention, including a genetically modified microorganism (described below), when cultured, is capable of expressing enzymes useful in the present invention and/or of catalyzing the production of amino acids or lower molecular weight proteins. Such a medium is typically an aqueous medium comprising assimilable carbon, nitrogen and phosphate sources. Such a medium can also include appropriate salts, minerals, metals and other nutrients. Microorganisms and other cells of the present invention can be cultured in conventional fermentation bioreactors. The microorganisms can be cultured by any fermentation process which includes, but is not limited to, batch, fed-batch, cell recycle, and continuous fermentation. The fermentation of microorganisms such as fungi may be carried out in any appropriate reactor, using methods known to those skilled in the art. For example, the fermentation may be carried out for a period of 1 to 14 days, or more preferably between about 3 and 10 days. The temperature of the medium is typically maintained between about 25 and 50°C, and more preferably between 28 and 40°C. The pH of the fermentation medium is regulated to a pH suitable for growth and protein production of the particular organism. The fermentor can be aerated in order to supply the oxygen necessary for fermentation and to avoid the excessive accumulation of carbon dioxide produced by fermentation. In addition, the aeration helps to control the temperature and the moisture of the culture medium. In general the fungal strains are grown in fermentors, optionally centrifuged or filtered to remove biomass, and optionally concentrated, formulated, and dried to produce an enzyme(s) or a multi-enzyme composition that is a crude fermentation product. Particularly suitable conditions for culturing filamentous fungi are described, for example, in U.S. Patent No. 6,015,707 and U.S. Patent No. 6,573,086, supra.

[0196] Depending on the vector and host system used for production, resultant proteins of the present invention may either remain within the recombinant cell; be secreted into the culture medium; be secreted into a space between two cellular membranes; or be retained on the outer surface of a cell membrane. The phrase "recovering the protein" refers to collecting the whole culture medium containing the protein and need not imply additional steps of separation or purification. Proteins produced according to the present invention can be purified using a variety of standard protein purification techniques, such as, but not limited to, affinity chromatography, ion exchange chromatography, filtration, electrophoresis, hydrophobic interaction chromatography, gel filtration chromatography, reverse phase chromatography, concanavalin A chromatography, chromatofocusing and differential precipitation or solubilization.

[0197] Proteins of the present invention are preferably retrieved, obtained, and/or used in "substantially pure" form. As used herein, "substantially pure" refers to a purity that allows for the effective use of the protein in any method according to the present invention. For a protein to be useful in any of the methods described herein or in any method utilizing enzymes of the types described herein according to the present invention, it is substantially free of contaminants, other proteins and/or chemicals that might interfere or that would interfere with its use in a method disclosed by the present invention (e.g., that might interfere with enzyme activity), or that at least would be undesirable for inclusion with a protein of the present invention (including homologues and variants) when it is used in a method disclosed by the present invention (described in detail below). Preferably, a "substantially pure" protein, as referenced herein, is a protein that can be produced by any method (i.e., by direct purification from a natural source, recombinantly, or synthetically), and that has been purified from other protein components such that the protein comprises at least about 80% weight/weight of the total protein in a given composition (e.g., the protein of interest is about 80% of the protein in a solution/composition/buffer), and more preferably, at least about 85%, and more preferably at least about 90%, and more preferably at least about 91%, and more preferably at least about 92%, and more preferably at least about 93%, and more preferably at least about 94%, and more preferably at least about 95%, and more preferably at least about 96%, and more preferably at least about 97%, and more preferably at least about 98%, and more preferably at least about 99%, weight/weight of the total protein in a given composition.

[0198] It will be appreciated by one skilled in the art that use of recombinant DNA technologies can improve control of expression of transfected nucleic acid molecules by manipulating, for example, the number of copies of the nucleic acid molecules within the host cell, the efficiency with which those nucleic acid molecules are transcribed, the efficiency with which the resultant transcripts are translated, and the efficiency of post-translational modifications. Additionally, the promoter sequence might be genetically engineered to improve the level of expression as compared to the native promoter. Recombinant techniques useful for controlling the expression of nucleic acid molecules include, but are not limited to, integration of the nucleic acid molecules into one or more host cell chromosomes, addition of vector stability sequences to plasmids, substitutions or modifications of transcription control signals (e.g., promoters, operators, enhancers), substitutions or modifications of translational control signals (e.g., ribosome binding sites), modification of nucleic acid molecules to correspond to the codon usage of the host cell, and deletion of sequences that destabilize transcripts.

[0199] Another aspect of the present invention relates to a genetically modified microorganism that has been transfected with one or more nucleic acid molecules of the present invention. As used herein, a genetically modified microorganism can include a genetically modified bacterium, alga, yeast, filamentous fungus, or other microbe. Such a genetically modified microorganism has a genome which is modified (i.e., mutated or changed) from its normal (i.e., wild-type or naturally occurring) form such that the desired result is achieved (i.e., increased or modified activity and/or production of at least one enzyme or a multi-enzyme composition for the degradation of proteins). Genetic modification of a microorganism can be accomplished using classical strain development and/or molecular genetic techniques. Such techniques known in the art and are generally disclosed for microorganisms, for example, in Sambrook et al., 1989, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Labs Press or Molecular Cloning: A Laboratory Manual, third edition (Sambrook and Russel, 2001), (jointly referred to herein as "Sambrook"). A genetically modified microorganism can include a microorganism in which nucleic acid molecules have been inserted, deleted or modified (i.e., mutated; e.g., by insertion, deletion, substitution, and/or inversion of nucleotides), in such a manner that such modifications provide the desired effect within the microorganism.

[0200] In one embodiment, a genetically modified microorganism can endogenously contain and express an enzyme or a multi-enzyme composition for the degradation of protein, and the genetic modification can be a genetic modification of one or more of such endogenous enzymes, whereby the modification has some effect on the ability of the microorganism to degrade protein {e.g., increased expression of the protein by introduction of promoters or other expression control sequences, or modification of the coding region by homologous recombination to increase the activity of the encoded protein).

[0201] In another embodiment, a genetically modified microorganism can endogenously contain and express an enzyme for the degradation of protein, and the genetic modification can be an introduction of at least one exogenous nucleic acid sequence (e.g., a recombinant nucleic acid molecule), wherein the exogenous nucleic acid sequence encodes at least one additional enzyme useful for the degradation of protein and/or a protein that improves the efficiency of the enzyme for the degradation of protein. In this aspect of the invention, the microorganism can also have at least one modification to a gene or genes comprising its endogenous enzyme(s) for the conversion of degradation of protein.

[0202] In yet another embodiment, the genetically modified microorganism does not necessarily endogenously (naturally) contain an enzyme for the degradation of protein, but is genetically modified to introduce at least one recombinant nucleic acid molecule encoding at least one enzyme or a multiplicity of enzymes for the degradation of protein. Such a microorganism can be used in a method of the invention, or as a production microorganism for crude fermentation products, partially purified recombinant enzymes, and/or purified recombinant enzymes, any of which can then be used in a method of the present invention.

[0203] Once the proteins (enzymes) are expressed in a host cell, a cell extract that contains the activity to test can be generated. For example, a lysate from the host cell is produced, and the supernatant containing the activity is harvested and/or the activity can be isolated from the lysate. In the case of cells that secrete enzymes into the culture medium, the culture medium containing them can be harvested, and/or the activity can be purified from the culture medium. The extracts/activities prepared in this way can be tested using assays known in the art. Accordingly, methods to identify multi- enzyme compositions capable of degrading protein are provided.

[0204] The present invention is not limited to fungi and also contemplates genetically modified organisms such as algae, bacteria, and plants transformed with one or more nucleic acid molecules of the invention. The plants may be used for production of the enzymes. Methods to generate recombinant plants are known in the art. For instance, numerous methods for plant transformation have been developed, including biological and physical transformation protocols. See, for example, Miki et al., "Procedures for Introducing Foreign DNA into Plants" in Methods in Plant Molecular Biology and Biotechnology, Glid , B.R. and Thompson, J.E. Eds. (CRC Press, Inc., Boca Raton, 1993) pp. 67-88. In addition, vectors and in vitro culture methods for plant cell or tissue^' transformation and regeneration of plants are available. See, for example, Gruber et al., "Vectors for Plant Transformation" in Methods in Plant Molecular Biology and Biotechnology, G ick, B.R. and Thompson, J.E. Eds. (CRC Press, Inc., Boca Raton, 1993) pp. 89-119.

[0205] The most widely utilized method for introducing an expression vector into plants is based on the natural transformation system of Agrobacterium. See, for example, Horsch et al., Science 227:1229 (1985). A. tumefaciens and A. rhizogenes are plant pathogenic soil bacteria which genetically transform plant cells. The Ti and Ri plasmids of A. tumefaciens and A. rhizogenes, respectively, cany genes responsible for genetic transformation of the plant. See, for example, Kado, C.I., Crit. Rev. Plant. Sci. 10: 1 (1991). Descriptions of Agrobacterium vector systems and methods for Agrobacterium-medi&ted gene transfer are provided by numerous references, including Gruber et al., supra, Miki et al., supra, Moloney et al., Plant Cell Reports 8:238 (1989), and U.S. Patents Nos. 4,940,838 and 5,464,763. [0206] Another generally applicable method of plant transformation is microprojectile- mediated transformation wherein DNA is carried on the surface of microprojectiles. The expression vector is introduced into plant tissues with a Holistic device that accelerates the microprojectiles to speeds sufficient to penetrate plant cell walls and membranes. Sanford et al., Part. Set Technol. 5:27 (1987), Sanford, J.C., Trends Biotech. 6:299 (1988), Sanford, J.C., Physiol. Plant 79:206 (1990), Klein et al., Biotechnology 10:268 (1992).

[0207] Another method for physical delivery of DNA to plants is sonication of target cells.

Zhang et al., Bio/Technology 9:996 (1991). Alternatively, liposome or spheroplast fusion have been used to introduce expression vectors into plants. Deshayes et al., EMBO J., 4:2731 (1985), Christou et al, Proc Natl. Acad. Sci. USA 84:3962 (1987). Direct uptake of DNA into protoplasts using CaCl₂ precipitation, polyvinyl alcohol or poly-L-ornithine have also been reported. Hain et al., Mol. Gen. Genet. 199: 161 (1985) and Draper et al., Plant Cell Physiol. 23:451 (1982). Electroporation of protoplasts and whole cells and tissues have also been described. Donn et al., In Abstracts of Vllth International Congress on Plant Cell and Tissue Culture IAPTC, A2-38, p. 53 (1990); D'Halluin et al., Plant Cell 4: 1495-1505 (1992) and Spencer et al. Plant Mol. Biol. 24:51-61 (1994).

[0208] Some embodiments of the present invention include genetically modified organisms comprising at least one nucleic acid molecule encoding at least one enzyme of the present invention, in which the activity of the enzyme is downregulated. The downregulation may be achieved, for example, by introduction of inhibitors (chemical or biological) of the enzyme activity, by manipulating the efficiency with which those nucleic acid molecules are transcribed, the efficiency with which the resultant transcripts are translated, and the efficiency of post-translational modifications, or by "knocking out" the endogenous copy of the gene. A "knock out" of a gene refers to a molecular biological technique by which the gene in the organism is made inoperative, so that the expression of the gene is substantially reduced or eliminated. Alternatively, in some embodiments the activity of the enzyme may be upregulated. The present invention also contemplates downregulating activity of one or more enzymes while simultaneously upregulating activity of one or more enzymes to achieve the desired outcome.

[0209] Another embodiment of the present invention relates to an isolated binding agent capable of selectively binding to a protein of the present invention. Suitable binding agents may be selected from an antibody, an antigen binding fragment, or a binding partner. The binding agent selectively binds to an amino acid sequence selected from SEQ ID NO: 2, SEQ ID No: 4, SEQ ID No: 6, SEQ ID No: 8, SEQ ID No: 10, SEQ ID No: 12, SEQ ID No: 14, SEQ ID No: 16, SEQ ID No: 18, SEQ ID No: 20, SEQ ID No: 22, SEQ ID No: 24, SEQ ID No: 26, SEQ ID No: 28, SEQ ID No: 30, SEQ ID No: 32, SEQ ID No: 34, SEQ ID No: 36, SEQ ID No: 38, SEQ ID No: 40, SEQ ID No: 42, SEQ ID No: 44, SEQ ID No: 46, SEQ ID No: 48, SEQ ID No: 50, SEQ ID No: 52, SEQ ID No: 54, SEQ ID No: 56, SEQ ID No: 58, SEQ ID No: 60, SEQ ID No: 62, SEQ ID No: 64, SEQ ID No: 66, SEQ ID No: 68, SEQ ID No: 70, SEQ ID No: 72, SEQ ID No: 74, SEQ ID No: 76, SEQ ID No: 78, SEQ ID No: 80, SEQ ID No: 82, SEQ ID No: 84, SEQ ID No: 86, SEQ ID No: 88, SEQ ID No: 90, SEQ ID No: 92, SEQ ID No: 94, SEQ ID No: 96, SEQ ID No: 98, SEQ ID No: 100, SEQ ID No: 102, SEQ ID No: 104, SEQ ID No: 106, SEQ ID No: 108, SEQ ID No: 110, SEQ ID No: 1 12, SEQ ED No: 1 14, SEQ ID No: 1 16, SEQ ID No: 1 18, SEQ ID No: 120, SEQ ID No: 122, SEQ ID No: 124, SEQ ID No: 126, SEQ ID No: 128, SEQ ID No: 130, SEQ Γΰ No: 132, SEQ ID No: 134, SEQ ID No: 136, SEQ ID No: 138, SEQ ID No: 140, SEQ ID No: 142, SEQ ID No: 144, SEQ ID No: 146, SEQ ID No: 148, SEQ ID No: 150, SEQ ID No: 152, SEQ ID No: 154, SEQ ID No: 156, SEQ ID No: 158, SEQ ID No: 160, SEQ ED No: 162, SEQ ED No: 164, SEQ ID No: 166, SEQ ED No: 168, SEQ ED No: 170, SEQ ED No: 172, SEQ ED No: 174, SEQ ED No: 176, SEQ ED No: 178, SEQ ED No: 180, SEQ ED No: 182, SEQ ED No: 184, SEQ ID No: 186, SEQ ID No: 188, SEQ ED No: 190, SEQ ED No: 192, SEQ ED No: 194, SEQ ED No: 196, SEQ ID No: 198, SEQ ED No: 200, SEQ ED No: 202, SEQ ED No: 204, SEQ ED No: 206, SEQ ED No: 208, SEQ ED No: 210, SEQ ID No: 212, SEQ ID No: 214, SEQ ED No: 216, SEQ ED No: 218, SEQ ID No: 220, SEQ ID No: 222, SEQ ID No: 224, SEQ ED No: 226, SEQ ID No: 228, SEQ ED No: 230, SEQ ED No: 232, SEQ ED No: 234, SEQ ID No: 236, SEQ ED No: 238, SEQ ID No: 240, SEQ ED No: 242, SEQ ED No: 244, SEQ ED No: 246, SEQ ED No: 248, SEQ ID No: 250, SEQ ED No: 252, SEQ ED No: 254, SEQ ED No: 256, SEQ ID No: 258, SEQ ID No: 260, SEQ ID No: 262, SEQ ED No: 264, SEQ ED No: 266, SEQ ED No: 268, SEQ ED No: 270, SEQ ED No: 272, SEQ ID No: 274, SEQ ID No: 276, SEQ ID No: 278, SEQ ED No: 280, SEQ ED No: 282, SEQ ED No: 284, SEQ ID No: 286, SEQ ED No: 288, SEQ ED No: 290, SEQ ID No: 292, SEQ ID No: 294; SEQ ID No: 296, SEQ ID No: 298, SEQ ID No:300, SEQ ID No: 302, SEQ ID No: 304, SEQ ID No: 306, SEQ ID No: 308, SEQ ID No: 310, SEQ ID No: 312, SEQ ID No: 314, SEQ ID No: 316, SEQ ID No: 318, SEQ ID No: 320, SEQ ID No: 322, SEQ ID No: 324, SEQ ID No: 326, SEQ ID No: 328, SEQ ID No: 330, SEQ ID No: 332, SEQ ID No: 334, SEQ ID No: 336, SEQ ID No: 338, SEQ ID No: 340, SEQ ID No: 342, SEQ ID No: 344, SEQ ID No: 346, SEQ ID No: 348, SEQ ID No: 350, SEQ ID No: 352, SEQ ID No: 354, SEQ ID No: 356, SEQ ID No: 358, SEQ ID No: 360, SEQ ID No: 362, SEQ ID No: 364, SEQ ID No: 366, SEQ ID No: 368, SEQ ID No: 370, SEQ ID No: 372, SEQ ID No: 374, SEQ ID No: 376, SEQ ID No: 378, SEQ ID No: 380, SEQ ID No: 382, SEQ ID No: 384, SEQ ID No: 386, SEQ ID No: 388, SEQ ID No: 390, SEQ ID No: 392, SEQ ID No: 394, SEQ ID No: 396, SEQ ID No: 398, 400, SEQ ID No: 402, SEQ ID No: 404, SEQ ID No: 406, SEQ ID No: 408, SEQ ID No: 410, SEQ ID No: 412, SEQ ID No: 414, SEQ ID No: 416, SEQ ID No: 418, SEQ ID No: 420, SEQ ID No: 422, SEQ ID No: 424, SEQ ID No: 426, SEQ ID No: 428, SEQ ID No: 430, SEQ ID No: 432, SEQ ID No: 434, SEQ ID No: 436, SEQ ID No: 438, SEQ ID No: 440, SEQ ID No: 442, SEQ ID No: 444, SEQ ID No: 446, SEQ ID No: 448, SEQ ID No: 450, SEQ ID No: 452, SEQ ID No: 454, SEQ ID No: 456, SEQ ID No: 458, SEQ ID No: 460, SEQ ID No: 462, SEQ ID No: 464, SEQ ID No: 466, SEQ ID No: 468, SEQ ID No: 470, SEQ ID No: 472, SEQ ID No: 474, SEQ ID No: 476, SEQ ID No: 478, SEQ ID No: 480, SEQ ID No: 482, SEQ ID No: 484, SEQ ID No: 486, SEQ ID No: 488, SEQ ID No: 490, SEQ ED No: 492, SEQ ID No: 494, SEQ ID No: 496, SEQ ID No: 498, 500, SEQ ID No: 502, SEQ ID No: 504, SEQ ID No: 506, SEQ ID No: 508, SEQ ID No: 510, SEQ ID No: 512, SEQ ID No: 514, SEQ ID No: 516, SEQ ID No: 518, SEQ ID No: 520, SEQ ID No: 522, SEQ ID No: 524, SEQ ID No: 526, SEQ ID No: 528, SEQ ID No: 530, SEQ ID No: 532, SEQ ID No: 534, SEQ ID No: 536, SEQ ID No: 538, SEQ ID No: 540, SEQ ID No: 542, SEQ ID No: 544, SEQ ID No: 546, SEQ ID No: 548, SEQ ID No: 550, SEQ ID No: 552, SEQ ID No: 554, SEQ ID No: 556, SEQ ID No: 558, SEQ ID No: 560, SEQ ID No: 562, SEQ ID No: 564, SEQ ID No: 566, SEQ ID No: 568, SEQ ED No: 570, SEQ ED No: 572, SEQ ED No: 574, SEQ ED No: 576, SEQ ED No: 578, SEQ ED No: 580, SEQ ED No: 582, SEQ ID No: 584, SEQ ED No: 586, SEQ ID No: 588, SEQ ED No: 590, SEQ ED No: 592, SEQ ID No: 594, SEQ ED No: 596, SEQ ED No: 598, 600, SEQ ED No: 602, SEQ ID No: 604, SEQ ED No: 606, SEQ ED No: 608, SEQ ED No: 610, SEQ ID No: 612, SEQ ID No: 614, SEQ ID No: 616, SEQ ID No: 618, SEQ ID No: 620, SEQ ID No: 622, SEQ ID No: 624, SEQ ID No: 626, SEQ ID No: 628, SEQ ID No: 630, SEQ ED No: 632, SEQ ID No: 634, SEQ ID No: 636, SEQ ID No: 638, SEQ ID No: 640, SEQ ID No: 642, SEQ ID No: 644, SEQ ID No: 646, SEQ ID No: 648, SEQ ID No: 650, SEQ ID No: 652, SEQ ID No: 654, SEQ ID No: 656, SEQ ID No: 658, SEQ ID No: 660, SEQ ID No: 662, SEQ ID No: 664, SEQ ED No: 666, SEQ ID No: 668, SEQ ID No: 670, SEQ ID No: 672, SEQ ID No: 674, SEQ ID No: 676, SEQ ID No: 678, SEQ ID No: 680, SEQ ID No: 682, SEQ ID No: 684, SEQ ID No: 686, SEQ ID No: 688, SEQ ID No: 690, SEQ ID No: 692, SEQ ID No: 694, SEQ ID No: 696, SEQ ID No: 698, 700, SEQ ID No: 702, SEQ ID No: 704, SEQ ID No: 706, SEQ ID No: 708_;:SEQ .ID No: 710, SEQ ID No: 712, SEQ ID No: 714, SEQ ID No: 716, SEQ ID No: 718, SEQ ID No: 720, SEQ ID No: 722, SEQ ID No: 724, SEQ ID No: 726, SEQ ID No: 728, SEQ ID No: 730, SEQ ID No: 732, SEQ ID No: 734, SEQ ID No: 736, SEQ ID No: 738, SEQ ID No: 740, SEQ ID No: 742, SEQ ID No: 744, SEQ ID No: 746, SEQ ID No: 748, SEQ ID No: 750, SEQ ID No: 752, SEQ ID No: 754, SEQ ID No: 756, SEQ ID No: 758, SEQ ID No: 760, SEQ ID No: 762, SEQ ID No: 764, SEQ ID No: 766, SEQ ID No: 768, SEQ ID No: 770, SEQ ID No: 772, SEQ ID No: 774, SEQ ID No: 776, SEQ ID No: 778, SEQ ID No: 780, SEQ ID No: 782, SEQ ID No: 784, SEQ ID No: 786, SEQ ID No: 788, SEQ ID No: 790, SEQ ED No: 792, SEQ ID No: 794, SEQ ID No: 796, SEQ ID No: 798, 800, SEQ ID No: 802, SEQ ED No: 804, SEQ ED No: 806, SEQ ID No: 808, SEQ ED No: 810, SEQ ED No: 812, SEQ ED No: 814, SEQ ED No: 816, SEQ ED No: 818, SEQ ED No: 820, SEQ ED No: 822, SEQ ED No: 824, SEQ ED No: 826, SEQ ED No: 828, SEQ ID No: 830, SEQ ED No: 832, SEQ ED No: 834, SEQ ED No: 836, SEQ ED No: 838, SEQ ED No: 840, SEQ ID No: 842, SEQ ID No: 844, SEQ ID No: 846, SEQ ED No: 848, SEQ ED No: 850, SEQ ID No: 852, SEQ ID No: 854, SEQ ID No: 856, SEQ ED No: 858, SEQ ED No: 860.., including to any fragment of any of the above sequences comprising at least one antibody binding epitope.

According to the present invention, the phrase "selectively binds to" refers to the ability of an antibody, antigen binding fragment or binding partner of the present invention to preferentially bind to specified proteins. More specifically, the phrase "selectively binds" refers to the specific binding of one protein to another (e.g., an antibody, fragment thereof, or binding partner to an antigen), wherein the level of binding, as measured by any standard assay (e.g., an immunoassay), is statistically significantly higher than the background control for the assay. For example, when performing an immunoassay, controls typically include a reaction well/tube that contain antibody or antigen binding fragment alone (i.e., in the absence of antigen), wherein an amount of reactivity (e.g., non-specific binding to the well) by the antibody or antigen binding fragment thereof in the absence of the antigen is considered to be background. Binding can be measured using a variety of methods standard in the art including enzyme immunoassays (e.g., ELISA), immunoblot assays, etc.).

[021 1] Antibodies are characterized in that they comprise immunoglobulin domains and as such, they are members of the immunoglobulin superfamily of proteins. An antibody of the invention includes polyclonal and monoclonal antibodies, divalent and monovalent antibodies, bi- or multi-specific antibodies, serum containing such antibodies, antibodies that have been purified to varying degrees, and any functional equivalents of whole antibodies. Isolated antibodies of the present invention can include serum containing such antibodies, or antibodies that have been purified to varying degrees. Whole antibodies of the present invention can be polyclonal or monoclonal. Alternatively, functional equivalents of whole antibodies, such as antigen binding fragments in which one or more antibody domains are truncated or absent (e.g., Fv, Fab, Fab', or F(ab)₂ fragments), as well as genetically-engineered antibodies or antigen binding fragments thereof, including single chain antibodies or antibodies that can bind to more than one epitope (e.g., bi-specific antibodies), or antibodies that can bind to one or more different antigens (e.g., bi- or multi-specific antibodies), may also be employed in the invention. Methods for the generation and production of antibodies are well known in the art.

[0212] Monoclonal antibodies may be produced according to the methodology of Kohler and Milstein (Nature 256:495-497, 1975). Non-antibody polypeptides, sometimes referred to as binding partners, are designed to bind specifically to a protein of the invention. Examples of the design of such polypeptides, which possess a prescribed ligand specificity are given in Beste et al. (Proc. Natl. Acad. Sci. 96: 1898-1903, 1999). In one embodiment, a binding agent of the invention is immobilized on a substrate such as: artificial membranes, organic supports, biopolymer supports and inorganic supports such as for use in a screening assay.

[0213] Proteins of the present invention, at least one protein of the present invention, compositions comprising such protein(s) of the present invention, and multi-enzyme compositions (examples of which are described above) may be used in any method where it is desirable to degrade protein, or any other method wherein enzymes of the same or similar function are useful.

[0214] In one embodiment, the present invention includes the use of at least one protein of the present invention, compositions comprising at least one protein of the present invention, or multi-enzyme compositions in methods for hydrolyzing protein therefrom. In one embodiment, the method comprises contacting the protein with an effective amount of one or more proteins of the present invention, composition comprising at least one protein of the present invention, or a multi-enzyme composition, whereby at least one amino acid is liberated.

[0215] Typically, the amount of enzyme or enzyme composition contacted with the protein will depend upon the amount of the protein, order of the sequence, or environmental conditions. In some embodiments, the amount of enzyme or enzyme composition contacted with the protein may be from about 0.1 to about 200 mg enzyme or enzyme . composition per gram of protein; in other embodiments, from about 3 to about 20 mg enzyme or enzyme composition per gram of protein. The invention encompasses the use of any suitable or sufficient amount of enzyme or enzyme composition between about 0.1 mg and about 200 mg enzyme per gram protein, in increments of 0.05 mg (i.e., 0.1 mg, 0.15 mg, 0.2 mg... 199.9 mg, 199.95 mg, 200 mg).

[0216] In some embodiments, the present invention provides methods for improving the nutritional quality of food (or animal feed) comprising adding to the food (or the animal feed) at least one protein of the present invention. In some embodiments, the present invention provides methods for improving the nutritional quality of the food (or animal feed) comprising pretreating the food (or the animal feed) with at least one isolated protein of the present invention. In some embodiments, the proteins of the present invention may be used as part of nutritional supplements. In some embodiments, the proteins of the present invention may be used as part of digestive aids, and may help in providing relief from digestive disorders such as acid reflux and celiac disease.

[0217] The proteins or compositions of the subject invention can be used in detergent compositions. In one embodiment, the detergent composition may comprise at least one protein or composition of the present invention and one or more surfactants. The detergent compositions may also include any additional detergent ingredient known in the art. Detergent ingredients contemplated for use with the detergent compositions of the subject invention include, but are not limited to, detergents, buffers, surfactants, bleaching agents, softeners, solvents, solid forming agents, abrasives, alkalis, inorganic electrolytes, cellulase activators, antioxidants, builders, silicates, preservatives, and stabilizers. The detergent compositions of this invention preferably employ a surface active agent, i.e., surfactant, including anionic, non-ionic, and ampholytic surfactants well known for their use in detergent compositions. In addition to the at least one protein or composition of the present invention and the surface active agent, the detergent compositions of this invention can additionally contain one or more of the following components: the enzymes amylases, cellulases, proteinase, lipases, oxido- reductases, peroxidases and other enzymes; cationic surfactants and long-chain fatty acids; builders; antiredeposition agents; bleaching agents; bluing agents and fluorescent dyes; caking inhibitors; masking agents for factors inhibiting the cellulase activity; cellulase activators; antioxidants; and solubilizers. In addition, perfumes, preservatives, dyes, and the like can be used, if desired, with the detergent compositions of this invention. Examples of detergent compositions employing cellulases are exemplified in U.S. Pat . Nos. 4,435,307; 4,443,355; 4,661,289; 4,479,881 ; 5,120,463.

[0218] When a detergent base used in the present invention is in the form of a powder, it may be one which is prepared by any known preparation method including a spray-drying method and/or a granulation method. The granulation method are the most preferred because of the non-dusting nature of granules compared to spray dry products. The detergent base obtained by the spray-drying method is hollow granules which are obtained by spraying an aqueous slurry of heat-resistant ingredients, such as surface active agents and builders, into a hot space. The granules have a size of from about 50 to about 2000 micrometers. After the spray-drying, perfumes, enzymes, bleaching agents, and/or inorganic alkaline builders may be added. With a highly dense, granular detergent base obtained by such as the spray-drying-granulation method, various ingredients may also be added after the preparation of the base. When the detergent base is a liquid, it may be either a homogenous solution or an inhomogeneous solution.

[0219] Exemplary methods according to the invention are presented below. Examples of the methods described above may also be found in the following references: Trichoderma & Gliocladium, Volume 2, Enzymes, biological control and commercial applications, Editors: Gary E. Harman, Christian P. Kubicek, Taylor & Francis Ltd. 1998, 393 (in particular, chapters 14, 15 and 16); Helmut Uhlig, Industrial enzymes and their applications, Translated and updated by Elfriede M. Linsmaier-Bednar, John Wiley & Sons, Inc 1998, p. 454 (in particular, chapters 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.7, 5.9, 5.10, 5.11, and 5.13). For saccharification applications: Hahn-Hagerdal, B., Galbe, M., Gorwa-Grauslund, M.F. Liden, Zacchi, G. Bio-ethanol - the fuel of tomorrow from the residues of today, Trends in Biotechnology, 2006, 24 (12), 549-556; Mielenz, J.R. Ethanol production from biomass: technology and commercialization status, Current Opinion in Microbiology, 2001, 4, 324-329; Himmel, M.E., Ruth, M.F., Wyman, C.E., Cellulase for commodity products from cellulosic biomass, Current Opinion in Biotechnology, 1999, 10, 358-364; Sheehan, J., Himmel, M. Enzymes, energy, and the environment: a strategic perspective on the U.S. Department of Energy's Research and Development Activities for Bioethanol, Biotechnology Progress. 1999, 15, 817-827. For textile processing applications: Galante, Y.M., Formantici, C, Enzyme applications in detergency and in manufacturing industries, Current Organic Chemistry, 2003, 7, 1399-1422. For pulp and paper applications: Bajpai, P., Bajpai, P.K Deinking with enzymes: a review. TAP PI Journal, 1998, 81(12), 1 1 1-1 17; Viikari, L., Pere, J., Suurnakki, A., Oksanen, T., Buchert, J. Use of cellulases in pulp and paper applications. In: "Carbohydrates from Trichoderma reesei and other microorganisms. Structure, Biochemistry, Genetics and Applications." Editors: Mark Claessens, Wim Nerinckx, and Kathleen Piens, The Royal Society of Chemistry 1998, 245-254. For food and beverage applications: Roller, S., Dea, I.C.M. Biotechnology in the production and modification of biopolymers for foods, Critical Reviews in Biotechnology, 1992, 12(3), 261-277.

[0220] Additional assays and methods for examining the activity of the enzymes are found in U.S. Patent Applications 60/806,876, 60/970,876, 1 1/487,547, 1 1/775,777, 1 1/833,133, and 12/205,694 and incorporated herein by reference.

[0221] One reference that reviews microbial proteases and their application is: Rao, M.B., Tanksale, A.M., Ghatge, M.S., Deshpnade, V.V. 1998. Molecular and biotechnological aspects of microbial proteases. Microbiology and Molecular Biology Reviews, 62: 597-635.

[0222] One reference that reviews the use of proteases in peptide synthesis is: Lombard, C, Saulnier, J., Wallach, J.M. 2005. Recent trends in protease-catalyzed peptide synthesis. Protein Pept Lett. 12: page 621-629

[0223] The following examples are provided for the purpose of illustration and are not intended to limit the scope of the present invention.

[0224] EXAMPLES

[0225] Example 1

[0226] Exemplary protease activity assay:

[0227] Activity of some proteases can be determined by measurement of degradation of protease substrates in solution, such as bovine serum albumin (BSA), as described by van den Hombergh et al. (Curr Genet 28, 299-308, 1995). As the protease enzymes • digest the protein in suspension, the mixture becomes more transparent and the <^■ absorbance changes in the reaction mixture can be followed spectophotometrically.

[02281 Example ¹! ^'

[0229] Exemplary protease activity assay:

[0230] Activity of some proteases can be determined by measurement of degi'adation of AZCL-casein in solution as described by the manufacturer (Megazyme, Ireland). As the protease enzymes digest the AZCL-casein in suspension, the mixture becomes blue and the absorbance changes in the reaction mixture can, be followed spectophotometrically.

[0231] Assays for peptidase activity are extremely well known in the art. One of skill will be able to choose the appropriate assay for the desired enzyme activity. U.S. patent 6, 184,020 teaches aminopeptidase assays. U.S. Patent 6,518,054 teaches metallo endopeptidase assays.

[0232] While the compositions here in are primarly useful for their enzymatic activity, one of skill in the art will readily appreciate that constructs can be designed having reduced activity for one or more of the enzymes present. Through recombinant techniques enzyirfes of the present invention can be inactivated such as through mutation or antisense techniques which are well known in the art. Such techniques are taught in U.S. patent 6,184,020.

[0233] While various embodiments of the present invention have been described in detai l, it is apparent that modifications and adaptations of those embodiments will occur to those skilled in the art. It is to be expressly understood, however, that such modifications and. adaptations are within the scope of the present invention, as set forth in the following exemplary claims.

Claims

We Claim:

1. An isolated nucleic acid sequence selected from the group consisting of: a) a nucleic acid sequence encoding a protein comprising an amino acid sequence selected from the amino acid sequences of SEQ ID NC: 2, SEQ ID No: 4, SEQ ID No: 6, SEQ ID No: 8, SEQ ID No: 10, SEQ ID No: 12, SEQ ID No: 14, SEQ ID No: 16, SEQ ID No: 18, SEQ ID No: 20, SEQ ID No: 22, SEQ ID No: 24, SEQ ID No: 26, SEQ ID No: 28, SEQ ID No: 30, SEQ ID No: 32, SEQ ID No: 34, SEQ ID No: 36, SEQ ID No: 38, SEQ ID No: 40, SEQ ID No: 42, SEQ ID No: 44, SEQ ID No: 46, SEQ ID No: 48, SEQ ID No: 50, SEQ ID No: 52, SEQ ID No: 54, SEQ ID No: 56, SEQ ID No: 58, SEQ ID No: 60, SEQ ID No: 62, SEQ ID No: 64, SEQ ID No: 66, SEQ ID No: 68, SEQ ID No: 70, SEQ ID No: 72, SEQ ID No: 74, SEQ ID No: 76, SEQ ID No: 78, SEQ ID No: 80, SEQ ID No: 82, SEQ ID No: 84, SEQ ID No: 86, SEQ ID No: 88, SEQ ID No: 90, SEQ ID No: 92,

SEQ ID No: 94, SEQ ID No: 96, SEQ ED No: 98 , SEQ ID No: 100, SEQ ED No: 102, SEQ

ID No: 104, SEQ ID No: 106, SEQ ED No: 108, SEQ ED No: 1 10, SEQ ID No: 1 12, SEQ

ID No: 114, SEQ ID No: 116, SEQ ED No: 1 18, SEQ ED No: 120, SEQ ID No: 122, SEQ

ID No: 124, SEQ ID No: 126, SEQ ED No: 128, SEQ ED No: 130, SEQ ED No: 132, SEQ

ID No: 134, SEQ ID No: 136, SEQ ED No: 138, SEQ ID No: 140, SEQ ED No: 142, SEQ

ID No: 144, SEQ ID No: 146, SEQ ED No: 148, SEQ ID No: 150, SEQ ED No: 152, SEQ

ID No: 154, SEQ ED No: 156, SEQ ED No: 158, SEQ ED No: 160, SEQ ID No: 162, SEQ

ID No: 164, SEQ ID No: 166, SEQ ED No: 168, SEQ ID No: 170, SEQ ID No: 172, SEQ

ID No: 174, SEQ ID No: 176, SEQ ED No: 178, SEQ ED No: 180, SEQ ID No: 182, SEQ

ID No: 184, SEQ ID No: 186, SEQ ED No: 188, SEQ ED No: 190, SEQ ID No: 192, SEQ

ID No: 194, SEQ ED No: 196, SEQ ED No: 198, SEQ ED No: 200, SEQ ED No: 202, SEQ

ID No: 204, SEQ ID No: 206, SEQ ED No: 208, SEQ ED No: 210, SEQ ID No: 212, SEQ

ID No: 214, SEQ ID No: 216, SEQ ED No: 218, SEQ ED No: 220, SEQ ID No: 222, SEQ

ID No: 224, SEQ ED No: 226, SEQ ED No: 228, SEQ ED No: 230, SEQ ID No: 232, SEQ

ID No: 234, SEQ ED No: 236, SEQ ED No: 238, SEQ ID No: 240, SEQ ID No: 242, SEQ

ID No: 244, SEQ ED No: 246, SEQ ED No: 248, SEQ ED No: 250, SEQ ID No: 252, SEQ

ID No: 254, SEQ ID No: 256, SEQ ED No: 258, SEQ ED No: 260, SEQ ID No: 262, SEQ

ID No: 264, SEQ ID No: 266, SEQ ED No: 268, SEQ ED No: 270, SEQ ID No: 272, SEQ

ID No: 274, SEQ ED No: 276, SEQ ED No: 278, SEQ ED No: 280, SEQ ID No: 282, SEQ

ID No: 284, SEQ ED No: 286, SEQ ED No: 288, SEQ ED No: 290, SEQ ID No: 292, SEQ ID No: 294, SEQ ED No: 296, SEQ ID No: 298, SEQ ED No:300, SEQ ED No: 302, SEQ ED No: 304, SEQ ED No: 306, SEQ ID No: 308, SEQ ED No: 310, SEQ ID No: 312, SEQ ID No: 314, SEQ ED No: 316, SEQ ED No: 318, SEQ ED No: 320, SEQ ED No: 322, SEQ ID No: 324, SEQ ID No: 326, SEQ ED No: 328, SEQ ED No: 330, SEQ ID No: 332, SEQ ED No: 334, SEQ ED No: 336, SEQ ED No: 338, SEQ ED No: 340, SEQ ID No: 342, SEQ ED No: 344, SEQ ID No: 346, SEQ ED No: 348, SEQ ED No: 350, SEQ ID No: 352, SEQ ED No: 354, SEQ ID No: 356, SEQ ED No: 358, SEQ ED No: 360, SEQ ID No: 362, SEQ ED No: 364, SEQ ED No: 366, SEQ ED No: 368, SEQ ED No: 370, SEQ ID No: 372, SEQ ED No: 374, SEQ ED No: 376, SEQ ED No: 378, SEQ ID No: 380, SEQ ID No: 382, SEQ ED No: 384, SEQ ED No: 386, SEQ ED No: 388, SEQ ED No: 390, SEQ ID No: 392, SEQ ID No: 394, SEQ ED No: 396, SEQ ED No: 398, 400, SEQ ID No: 402, SEQ ID No: 404, SEQ ED No: 406, SEQ ED No: 408, SEQ ED No: 410, SEQ ED No: 412, SEQ ED No: 414, SEQ ED No: 416, SEQ ED No: 418, SEQ ED No: 420, SEQ ED No: 422, SEQ ED No: 424, SEQ ED No: 426, SEQ ED No: 428, SEQ ED No: 430, SEQ ED No: 432, SEQ ED No: 434, SEQ ED No: 436, SEQ ED No: 438, SEQ ED No: 440, SEQ ED No: 442, SEQ ED No: 444, SEQ ED No: 446, SEQ ED No: 448, SEQ ED No: 450, SEQ ED No: 452, SEQ ED No: 454, SEQ ED No: 456, SEQ ED No: 458, SEQ ED No: 460, SEQ ED No: 462, SEQ ED No: 464, SEQ ED No: 466, SEQ ED No: 468, SEQ ID No: 470, SEQ ID No: 472, SEQ ED No: 474, SEQ ED No: 476, SEQ ED No: 478, SEQ ED No: 480, SEQ ED No: 482, SEQ ED No: 484, SEQ ED No: 486, SEQ ED No: 488, SEQ ED No: 490, SEQ ED No: 492, SEQ ED No: 494, SEQ ED No: 496, SEQ ED No: 498, SEQ ED No: 500, SEQ ED No: 502, SEQ ED No: 504, SEQ ED No: 506, SEQ ED No: 508, SEQ ED No: 510, SEQ ED No: 512, SEQ ED No: 514, SEQ ED No: 516, SEQ ED No: 518, SEQ ED No: 520, SEQ ED No: 522, SEQ ED No: 524, SEQ ED No: 526, SEQ ID No: 528, SEQ ED No: 530, SEQ ED No: 532, SEQ ED No: 534, SEQ ED No: 536, SEQ ED No: 538, SEQ ED No: 540, SEQ ED No: 542, SEQ ID No: 544, SEQ ED No: 546, SEQ ID No: 548, SEQ ED No: 550, SEQ ED No: 552, SEQ ID No: 554, SEQ ID No: 556, SEQ ED No: 558, SEQ ED No: 560, SEQ ED No: 562, SEQ ED No: 564, SEQ ED No: 566, SEQ ED No: 568, SEQ ED No: 570, SEQ ED No: 572, SEQ ED No: 574, SEQ ED No: 576, SEQ ID No: 578, SEQ ED No: 580, SEQ ED No: 582, SEQ ED No: 584, SEQ ED No: 586, SEQ ED No: 588, SEQ ID No: 590, SEQ ED No: 592, SEQ ED No: 594, SEQ ED No: 596, SEQ ED No: 598, SEQ ED No: 600, SEQ ED No: 602, SEQ ED No: 604, SEQ ID No: 606, SEQ ED No: 608, SEQ ED No: 610, SEQ ID No: 612, SEQ ED No: 614, SEQ ID No: 616, SEQ ID No: 618, SEQ ID No: 620, SEQ ID No: 622, SEQ ID No: 624,

SEQ ID No: 626, SEQ ID No: 628, SEQ ID No: 630, SEQ ID No: 632, SEQ ID No: 634,

SEQ ID No: 636, SEQ ID No: 638, SEQ ID No: 640, SEQ ID No: 642, SEQ ID No: 644,

SEQ ID No: 646, SEQ ID No: 648, SEQ ID No: 650, SEQ ID No: 652, SEQ ID No: 654,

SEQ ID No: 656, SEQ ID No: 658, SEQ ID No: 660, SEQ ID No: 662, SEQ ID No: 664,

SEQ ID No: 666, SEQ ID No: 668, SEQ ID No: 670, SEQ ID No: 672, SEQ ID No: 674,

SEQ ID No: 676, SEQ ID No: 678, SEQ ID No: 680, SEQ ID No: 682, SEQ ID No: 684,

SEQ ID No: 686, SEQ ID No: 688, SEQ ID No: 690, SEQ ID No: 692, SEQ ID No: 694,

SEQ ID No: 696, SEQ ID No: 698, SEQ ID No: 700, SEQ ID No: 702, SEQ ID No: 704,

SEQ ID No: 706, SEQ ID No: 708, SEQ ID No: 710, SEQ ID No: 712, SEQ ID No: 714,

SEQ ID No: 716, SEQ ID No: 718, SEQ ID No: 720, SEQ ID No: 722, SEQ ID No: 724,

SEQ ID No: 726, SEQ ID No: 728, SEQ ID No: 730, SEQ ID No: 732, SEQ ID No: 734,

SEQ ID No: 736, SEQ ID No: 738, SEQ ID No: 740, SEQ ID No: 742, SEQ ID No: 744,

SEQ ID No: 746, SEQ ID No: 748, SEQ ID No: 750, SEQ ID No: 752, SEQ ID No: 754,

SEQ ID No: 756, SEQ ID No: 758, SEQ ID No: 760, SEQ ID No: 762, SEQ ID No: 764,

SEQ ID No: 766, SEQ ID No: 768, SEQ ID No: 770, SEQ ID No: 772, SEQ ID No: 774,

SEQ ID No: 776, SEQ ID No: 778, SEQ ID No: 780, SEQ ID No: 782, SEQ ID No: 784,

SEQ ID No: 786, SEQ ID No: 788, SEQ ID No: 790, SEQ ID No: 792, SEQ ID No: 794,

SEQ ID No: 796, SEQ ID No: 798, SEQ ID No: 800, SEQ ID No: 802, SEQ ID No: 804,

SEQ ID No: 806, SEQ ID No: 808, SEQ ID No: 810, SEQ ID No: 812, SEQ ID No: 814,

SEQ ID No: 816, SEQ ID No: 818, SEQ ID No: 820, SEQ ID No: 822, SEQ ID No: 824,

SEQ ID No: 826, SEQ ID No: 828, SEQ ID No: 830, SEQ ID No: 832, SEQ ID No: 834,

SEQ ID No: 836, SEQ ID No: 838, SEQ ID No: 840, SEQ ID No: 842, SEQ ID No: 844,

SEQ ID No: 846, SEQ ID No: 848, SEQ ID No: 850, SEQ ID No: 852, SEQ ID No: 854,

SEQ ID No: 856, SEQ ID No: 858, SEQ ID No: 860.

b) a nucleic acid sequence encoding a fragment of the protein of (a), wherein the fragment has a biological activity of the protein of (a); and c) a nucleic acid sequence encoding an amino acid sequence that is at least about 70% identical to an amino acid sequence of (a) and has a biological activity of the protein comprising the amino acid sequence.

2. The isolated nucleic acid sequence of claim 1, wherein said nucleic acid sequence encodes an amino acid sequence that is at least about 80% identical to the amino acid sequence of (a) and has a biological activity of the protein comprising the amino acid sequence.

3. The isolated nucleic acid sequence of claim 1, wherein said nucleic acid sequence encodes an amino acid sequence that is at least about 90% identical to the amino acid sequence of (a) and has a biological activity of the protein comprising the amino acid sequence,

4. The isolated nucleic acid sequence of claim 1, wherein said nucleic acid sequence encodes an amino acid sequence that is at least about 95% identical to the amino acid sequence of (a) and has a biological activity of the protein comprising the amino acid sequence.

5. The isolated nucleic acid sequence of claim 1, wherein said nucleic acid sequence encodes an amino acid sequence that is at least about 97% identical to the amino acid sequence of (a) and has a biological activity of the protein comprising the amino acid sequence.

6. The isolated nucleic acid sequence of claim 1, wherein said nucleic acid sequence encodes an amino acid sequence that is at least about 99% identical to the amino acid sequence of (a) arid has a biological activity of the protein comprising the amino acid sequence.

7. The isolated nucleic acid sequence of claim 1, wherein said nucleic acid sequence encodes a protein comprising an amino acid sequence selected from the group consisting of: the amino acid sequences of Sequences PR1- PR 430.

4. The isolated nucleic acid sequence of claim 1, wherein said nucleic acid sequence comprises a nucleic acid sequence selected from the group consisting of: the nucleic acid sequences of SEQ ID No: 1, SEQ ID No: 3, SEQ ID No: 5, SEQ ID No: 7, SEQ ID No: 9, SEQ ED No: 11, SEQ ID No: 13, SEQ ID No: 15, SEQ ID No: 17, SEQ ID No: 19, SEQ ID No: 21, SEQ ID No: 23, SEQ ID No: 25, SEQ ID No: 27, SEQ ID No: 29, SEQ ID No: 31, SEQ ID No: 33, SEQ ID No: 35, SEQ ID No: 37, SEQ ED No: 39, SEQ ID No: 41, SEQ ID No: 43, SEQ ID No: 45, SEQ ED No: 47, SEQ ID No: 49, SEQ ID No: 51, SEQ ID No: 53, SEQ ID No: 55, SEQ ID No: 56, SEQ ID No: 57, SEQ ID No: 59, SEQ ID No: 61, SEQ ID No: 63, SEQ ID No: 65, SEQ ED No: 67, SEQ ED No: 69, SEQ ID No: 71, SEQ' ID No: 73, SEQ ID No: 75, SEQ ED No: 77, SEQ ED No: 79, SEQ ED No: 81, SEQ ED No: 83, SEQ ED No: 85, SEQ ED No: 87, SEQ ED No: 89, SEQ ED No: 91, SEQ ED No: 93, SEQ ED No: 95, SEQ ED No: 97, SEQ ED No: 99, SEQ ED No: 101, SEQ ED No: 103, SEQ ID No: 105, SEQ ED No: 107, SEQ ED No: 109, SEQ ID No: 111, SEQ ED No: 113, SEQ ID No: 115, SEQEDNo: 117, SEQ EDNo: 119, SEQ ED No: 121, SEQ ED No: 123, SEQ ID No: 125, SEQEDNo: 127, SEQ ED No: 129, SEQ DNo: 131, SEQ ED No: 133, SEQEDNo: 135, SEQ ED No: 137,. SEQ EDNo: 139, SEQEDNo: 141, SEQ ED No: 143, SEQ ID No: 145, SEQEDNo: 147, SEQEDNo: 149, SEQ ED No: 151, SEQ ED No: 153, SEQ ID No: 155, SEQ ED No: 157, SEQ ED No: 159, SEQ ED No: 161, SEQ ID No: 163, SEQEDNo: ί 65, SEQ ED No: 167, SEQEDNo: 169, SEQEDNo: 171, SEQEDNo: 173, SEQED o: 175, SEQ ED No: 177, SEQ EDNo: 179, SEQEDNo: 181, SEQ EDNo; 183, SEQEDNo: 185, SEQED o: 187, SEQEDNo: 189, SEQEDNo: 191, SEQEDNo: 193, SEQ ID No: 195, SEQ ED No: 197, SEQ ED No: 199, SEQ ED No: 201, SEQ ED No: 203, SEQ ID No: 205, SEQ ED No: 207, SEQ ED No: 209, SEQ ED No: 211, SEQ ED No: 213, SEQ ED No: 215, SEQ ED No: 217, SEQ ED No: 219, SEQ ED No: 221, SEQ ED No: 223, SE^ ID No: 225, SEQ ID No: 227, SEQ ID No: 229, SEQ ID No: 231 SEQ ID No: 233, SEQ ID No: 235. SEQ ID No: 237, SEQ ID No: 239, SEQ ID No: 241 SEQ ID No: 243, SEQ ID No: 245, SEQ ID No: 247, SEQ ID No: 249, SEQ ED No: 251 SEQ ID No: 253, SEQ ID No: 255, SEQ ID No: 257, SEQ ID No: 259, SEQ ID No: 261 SEQ ED No: 263, SEQ ID No: 265, SEQ ID No: 267, SEQ ID No: 269, SEQ ID No: 271 SEQ ED No: 273, SEQ ID No: 275, SEQ ID No: 277, SEQ ID No: 279, SEQ ID No: 281 SEQ ID No: 283, SEQ ID No: 285, SEQ ID No: 287, SEQ ID No: 289, SEQ ED No: 291 SEQ ID No: 293, SEQ ID No: 295, SEQ ID No: 297, SEQ ID No: 299, SEQ ED No: 301 SEQ ED No: 303, SEQ ID No: 305, SEQ ID No: 307, SEQ ID No: 309, SEQ ED No: 31 1 SEQ ED No: 313, SEQ ID No: 315, SEQ ID No: 317, SEQ ID No: 319, SEQ ED No: 321 SEQ ED No: 323, SEQ ID No: 325, SEQ ID No: 327, SEQ ID No: 329, SEQ ED No: 331 SEQ ID No: 333, SEQ ID No: 335, SEQ ID No: 337, SEQ ID No: 339, SEQ ID No: 341 SEQ ID No: 343, SEQ ID No: 345, SEQ ID No: 347, SEQ ED No: 349, SEQ ID No: 351 SEQ ID No: 353, SEQ ID No: 355, SEQ ID No: 357, SEQ ED No: 359, SEQ ED No: 361 SEQ ID No: 363, SEQ ID No: 365, SEQ ID No: 367, SEQ ID No: 369, SEQ ED No: 371 SEQ ID No: 373, SEQ ID No: 375, SEQ ID No: 377, SEQ ID No: 379, SEQ ED No: 38L SEQ ED No: 383, SEQ ID No: 385, SEQ ID No: 387, SEQ ED No: 389, SEQ ID No: 391_; SEQ ED No: 393, SEQ ID No: 395, SEQ ID No: 397, SEQ ED No: 399, SEQ ED No: 40L SEQ ED No: 403, SEQ ID No: 405, SEQ ID No: 407, SEQ ID No: 409, SEQ ID No: 41 1. SEQ ID No: 413, SEQ ID No: 41 , SEQ ID No: 417, SEQ ED No: 419, SEQ ED No: 42L SEQ ID No: 423, SEQ ID No: 425, SEQ ID No: 427, SEQ ED No: 429, SEQ ID No: 431. SEQ ID No: 433, SEQ ID No: 435, SEQ ID No: 437, SEQ ED No: 439, SEQ ID No: 441, SEQ ID No: 443, SEQ ID No: 445, SEQ ID No: 447, SEQ ID No: 449, SEQ ID No: 45 L SEQ ID No: 453, SEQ ID No: 455, SEQ ID No: 457, SEQ ID No: 459, SEQ ID No: 461. SEQ ID No: 463, SEQ ID No: 465, SEQ IDNo: 467, SEQ ID No: 469, SEQ ID No: 471 SEQ ID No: 473,

SEQ IDNo: 475, SEQ IDNo: 477, SEQ ED No: 479, SEQ ID No: 481 SEQ ID No: 483,

SEQ ID No: 485, SEQ IDNo: 487, SEQ IDNo: 489, SEQ ID No: 491 SEQ ID No: 493,

SEQ IDNo: 495, SEQ IDNo: 497, SEQ IDNo: 499, SEQ ID No: 501 SEQ ID No: 503,

SEQ IDNo: 505, SEQ IDNo: 507, SEQ IDNo: 509, SEQ ID No: 511 SEQ ID No: 513,

SEQ ID No: 515, SEQ IDNo: 517, SEQ IDNo: 519, SEQ ID No: 521 SEQ ID No: 523,

SEQ IDNo: 525, SEQ IDNo: 527, SEQ IDNo: 529, SEQ ID No: 531 SEQ ID No: 533,

SEQ IDNo: 535, SEQ IDNo: 537, SEQ IDNo: 539, SEQ ED No: 541 SEQ ID No: 543,

SEQ ID No: 545, SEQ IDNo: 547, SEQ IDNo: 549, SEQ ID No: 551 SEQ ID No: 553,

SEQ IDNo: 555, SEQ IDNo: 557, SEQ ID o: 559, SEQ ID No: 561 SEQ ID No: 563,

SEQ IDNo: 565, SEQ IDNo: 567, SEQ IDNo: 569, SEQ ID No: 571 SEQ ID No: 573,

SEQ ID No: 575, SEQ IDNo: 577, SEQ IDNo: 579, SEQ ID No: 581 SEQ ID No: 583,

SEQ IDNo: 585, SEQ IDNo: 587, SEQ IDNo: 589, SEQ ID No: 591 SEQ ED No: 593,

SEQ IDNo: 595, SEQ IDNo: 597, SEQ IDNo: 599, SEQ ID No: 601 SEQ ID No: 603,

SEQ IDNo: 605, SEQ IDNo: 607, SEQ IDNo: 609, SEQ ID No: 611 SEQ ED No: 613,

SEQ IDNo: 615, SEQ IDNo: 617, SEQ IDNo: 619, SEQ ID No: 621 SEQ ED No: 623,

SEQ ID o: 625, SEQ IDNo: 627, SEQ IDNo: 629, SEQ ID No: 631 SEQ ID No: 633,

SEQ ID No: 635, SEQ IDNo: 637, SEQ IDNo: 639, SEQ ID No: 641 SEQ ED No: 643,

SEQ IDNo: 645, SEQ IDNo: 647, SEQ IDNo: 649, SEQ ID No: 651. SEQ ED No: 653,

SEQ IDNo: 655, SEQ IDNo: 657, SEQ IDNo: 659, SEQ ID No: 661 SEQ ED No: 663,

SEQ ID No: 665, SEQ IDNo: 667, SEQ IDNo: 669, SEQ ID No: 671 SEQ ED No: 673,

SEQ IDNo: 675, SEQ IDNo: 677, SEQ IDNo: 679, SEQ ID No: 681. SEQ ID No: 683,

SEQ IDNo: 685, SEQ IDNo: 687, SEQ IDNo: 689, SEQ ID No: 691. SEQ ID No: 693,

SEQ IDNo: 695, SEQ IDNo: 697, SEQ IDNo: 699, SEQ ID No: 701. SEQ ED No: 703, SEQ ID No: 705, SEQ ID No: 707, SEQ ID No: 709, SEQ ID No: 711, SEQ ED No: 713,

SEQ ID No: 715, SEQ ID No: 717, SEQ ID No: 719, SEQ ID No: 721, SEQ ED No: 723,

SEQ ID No: 725, SEQ ID No: 727, SEQ ID No: 729, SEQ ID No: 731, SEQ ED No: 733,

SEQ ID No: 735, SEQ ID No: 737, SEQ ID No: 739, SEQ ID No: 741, SEQ ID No: 743,

SEQ ID No: 745, SEQ ED No: 747, SEQ ID No: 749, SEQ ID No: 751, SEQ ED No: 753,

SEQ ID No: 755, SEQ ID No: 757, SEQ ID No: 759, SEQ ID No: 761, SEQ ED No: 763,

SEQ ID No: 765, SEQ ID No: 767, SEQ ID No: 769, SEQ ID No: 771, SEQ ED No: 773,

SEQ ID No: 775, SEQ ID No: 777, SEQ ID No: 779, SEQ ID No: 781, SEQ ED No: 783,

SEQ ID No: 735, SEQ ID No: 787, SEQ ID No: 789, SEQ ID No: 791, SEQ ED No: 793,

SEQ ID No: 795, SEQ ID No: 797, SEQ ID No: 799, SEQ ID No: 801, SEQ ED No: 803,

SEQ ID No: 805, SEQ ID No: 807, SEQ ID No: 809, SEQ ID No: 811, SEQ ED No: 813,

SEQ ID No: 815, SEQ ID No: 817, SEQ ID No: 819, SEQ ID No: 821, SEQ ED No: 823,

SEQ ID No: 825, SEQ ID No: 827, SEQ ID No: 829, SEQ ID No: 831, SEQ ED No: 833,

SEQ ID No: 835, SEQ ID No: 837, SEQ ID No: 839, SEQ ID No: 841, SEQ ED No: 843,

SEQ ID No: 845, SEQ ID No: 847, SEQ ID No: 849, SEQ ID No: 851, SEQ ED No: 853,

SEQ ID No: 855, SEQ ID No: 857, SEQ ID No: 859.

9. An isolated nucleic acid sequence comprising a nucleic acid sequence that is iiilly complementary to the nucleic acid sequence of the nucleic acid sequence of any one of Claims 1 to 8.^;

10. An isolated protein comprising an amino acid sequence encoded by the nucleic acid sequence of any one of Claims 1 to 8.

11. An isolated fusion protein comprising the isolated protein of Claim 10 fused to a protein comprising an amino acid sequence that is heterologous to the isolated protein of Claim 1 0. ^{' '}

12. An isolated antibody or antigen binding fragment thereof that selectively binds to the protein of Claim 10.

13. A kit for processing animal hides comprising at least one isolated protein of Claim 10.

14. A detergent comprising at least one isolated protein of Claim 10.

15. A composition for the tenderizing of meat comprising at least one isolated protein of Claim 10.

16. A composition for the processing of cheese comprising at least one isolated protein of Claim 10.

17. A composition for increasing bread volume comprising at least one isolated protein of Claim 10.

18. A composition for increasing the protein yield in the production of rice bran protein comprising at least one isolated protein of Claim 10.

19. A composition for the reduction of acrylamide in food products comprising at least one isolated protein of Claim 10.

20. A composition for the processing of proteins comprising at least one isolated protein of Claim 10.

21. A pharmaceutical composition for the treatment of ischemic stroke comprising at least one isolated protein of Claim 10.

22. A pharmaceutical composition for the debridement of wounds comprising at least one isolated protein of Claim 10.

23. A pharmaceutical composition for the treatment inflammation comprising at least one isolated protein of Claim 10.

24. A pharmaceutical composition for the treatment of sepsis comprising at least one isolated protein of Claim 10.

25. A pharmaceutical composition for the reduction of fine wrinkles of the skin comprising at least one isolated protein of Claim 10.

26. A recombinant nucleic acid sequence comprising the isolated nucleic acid sequence of any one of Claims 1 to 8, operatively linked to at least one expression control sequence.

27. The recombinant nucleic acid sequence of Claim 26, wherein the recombinant nucleic acid sequence comprises an expression vector.

28. The recombinant nucleic acid sequence of Claim 26, wherein the recombinant nucleic acid sequence comprises a targeting vector.

29. An isolated host cell transfected with the nucleic acid sequence of any one of Claims 1 to 9.

30. The isolated host cell of Claim 29, wherein the host cell is selected from the group consisting of: a fungal cell, a plant cell, an algal cell, and a bacterium.

31. The isolated host cell of Claim 29, wherein the host cell is selected from the group consisting of: yeast, mushroom, or a filamentous fungus.

32. The isolated host cell of Claim 29, wherein the filamentous fungus is from a genus selected from the group consisting of: Chrysosporium, Thielavia, Thermomyces,

Thermoascus, Neurospora, Aureobasidium, Filibasidhim, Piromyces, Corynascus, Ciyplococcics, Acremonium, Tolypocladhim, Scytalidium, Schizophyllum, Sporotrichum, Penicillium, Gibberella, Myceliophthora, Mucor, Aspergillus, Fusariwn, Humicola, Talaromyce and Trichoderma, and anamorphs and teleomorphs thereof.

33. The isolated host cell of Claim 29, wherein the host cell is a bacterium.

34. An oligonucleotide consisting essentially of at least 12 consecutive nucleotides of a nucleic acid sequence selected from the group consisting of the nucleic acid sequence of Sequences PR1- PR 430, or the complement thereof.

35. A kit comprising at least one oligonucleotide of claim 34.

36. A method for producing the protein of Claim 10, comprising culturing a cell that has been transfected with a nucleic acid sequence comprising a nucleic acid sequence encoding the protein, and expressing the protein with the transfected cell.

37. The method of Claim 36, further comprising recovering the protein from the cell or from a culture comprising the cell.

38. A genetically modified organism comprising components suitable for degrading proteins, wherein the organism has been genetically modified to express at least one protein of Claim 10.

39. The genetically modified organism of Claim 38, wherein the genetically modified organism is selected from the group consisting of: plants, algae, fungi, and bacteria.

40. The genetically modified organism of Claim 39, wherein the fungus is selected from the group consisting of: yeast, mushroom and filamentous fungus.

41. The genetically modified organism of Claim 40, wherein the filamentous fungus is from a genus selected from the group consisting of: Chrysosporhim, Thielavia, Thermomyces, Thermoascus, Neurospora, Aureobasidium, Filibasidium, Piromyces, Corynascus, Cryptococcus, Acremonium, Tolypocladium, Scytalidium, Schizophyllum, Sporotrichum, Penicillium, Talaromyces, Gibberella, Myceliophthora, Mucor,

Aspergillus, Fusarhim, Humicola, and Trichoderma.

42. The genetically modified organism of Claim 40, wherein the filamentous fungus is selected from the group consisting of: Trichoderma reesei, Chrysosporium lucknowense, Aspergillus japonicus, Penicillium canescens, Penicillium solitum, Penicillium funiculosum, and Talaromyces flavus.

43. The genetically modified organism of Claim 38, wherein the organism has been genetically modified to express at least one additional enzyme.

44. The genetically modified organism of Claim 43, wherein the additional enzyme is an enzyme selected from the group consisting of: cellulase, glucosidase, xylanase, xylosidase, ligninase, glucuronidase, arabinofiiranosidase, arabinase, arabinogalactanase, ferulic acid esterase, lipase, pectinase, (gluco)mannanase, amylase, laminarinase, xyloglucanase, galactanase, galactosidase, glucoamylase, pectate or pectin lyase, chitosanases, exo-P-D-glucosaminidase, cellobiose dehydrogenase, glucuronyl esterase and acetylxylan esterase.

45. The genetically modified organism of Claim 38, wherein the genetically modified organism is a plant.

46. A recombinant enzyme isolated from the genetically modified microorganism of any one of claims 38 to 45.

47. The recombinant enzyme of claim 46, wherein the enzyme has been subjected to a purification step.

48. A crude fermentation product produced by culturing the cells from the genetically modified organism of any one of claims 38 to 45, wherein the crude fermentation product contains the at least one protein of Claim 10.

49. A multi-enzyme composition comprising enzymes produced by the genetically modified organism of any one of Claims 38 to 45, and recovered therefrom.

50. A multi-enzyme composition comprising at least one protein of Claim 10, and at least one additional protein for processing food or animal feed or a fragment thereof that has biological activity.

51. The multi-enzyme composition of any one of Claims 49 to 50, wherein the composition is a crude fermentation product that has been subjected to a purification step.

52. A method for degrading a protein into lower molecular proteins or amino acids, comprising contacting protein with at least one isolated protein of Claim 10.

53. A method for metabolizing a protein into lower molecular proteins or amino acids, comprising contacting protein with at least one isolated protein of Claim 10.

54. The method of Claims 52 or 53, further comprising contacting protein with at least one additional isolated protein comprising an amino acid sequence that is at least about 95% identical to an amino acid sequence selected from the group consisting of the amino acid sequences of a nucleic acid sequence encoding a protein comprising an amino acid sequence selected from the amino acid sequences of SEQ ID NO: 2, SEQ ID No: 4, SEQ ID No: 6, SEQ ID No: 8, SEQ ID No: 10, SEQ ID No: 12, SEQ ID No: 14, SEQ ID No: 16, SEQ ID No: 18, SEQ ID No: 20, SEQ ID No: 22, SEQ ID No: 24, SEQ ID No: 26, SEQ ID NO: 28, SEQ ID No: 30, SEQ ID No: 32, SEQ ID No: 34, SEQ ED No: 36, SEQ ID No: 38,^! SEQ ID No: 40, SEQ ID No: 42, SEQ ED No: 44, SEQ ID No: 46, SEQ ED No: 48, SEQ ED No: 50, SEQ ED No: 52, SEQ ED No: 54, SEQ ED No: 56, SEQ ED No: 58, SEQ ID No: 60, SEQ ED No: 62, SEQ ID No: 64, SEQ ID No: 66, SEQ ID No: 68, SEQ ED No: 70, SEQ ED No: 72, SEQ ID No: 74, SEQ ED No: 76, SEQ ED No: 78, SEQ ID No: 80, SEQ ID No: 82, SEQ ED No: 84, SEQ ID No: 86, SEQ ED No: 88, SEQ ED No: 90, SEQ ID No: 92, SEQ ID No: 94, SEQ ID No: 96, SEQ ID No: 98, SEQ ID No: 100, SEQ ID No: 102, SEQ ED No: 104, SEQ ID No: 106, SEQ ID No: 108, SEQ ID No: 110, SEQ ID No: 112, SEQ ID No: 114, SEQ ID No: 116, SEQ ID No: 118, SEQ ID No: 120, SEQ ID No: 122, SEQ ED No: 124, SEQ ID No: 126, SEQ ID No: 128, SEQ ID No: 130, SEQ ED No: 132, SEQ ED No: 134, SEQ ID No: 136, SEQ ID No: 138, SEQ ED No: 140, SEQ ID No: 142, SEQ ID No: 144, SEQ ID No: 146, SEQ ID No: 148, SEQ ID No: 150, SEQ ID No: 152, SEQ ED No: 154, SEQ ID No: 156, SEQ ID No: 158, SEQ ED No: 160, SEQ ID No: 162, SEQ ED No: 164, SEQ ID No: 166, SEQ ID No: 168, SEQ ID No: 170, SEQ ID No: 172, SEQ ED No: 174, SEQ ED No: 176, SEQ ID No: 178, SEQ ID No: 180, SEQ ID No: 182, SEQ ID No: 184, SEQ ED No: 186, SEQ ID No: 188, SEQ ID No: 190, SEQ ED No: 192, SEQ ED No: 194, SEQ ID No: 196, SEQ ID No: 198, SEQ ID No: 200, SEQ ID No: 202, SEQ ID No: 204, SEQ ID No: 206, SEQ ED No: 208, SEQ ED No: 210, SEQ ED No: 212, SEQ ED No: 214, SEQ ID No: 216, SEQ ID No: 218, SEQ ID No: 220, SEQ ID No: 222, SEQ ID No: 224, SEQ ID No: 226, SEQ ED No: 228, SEQ ID No: 230, SEQ ID No: 232, SEQ ID No: 234, SEQ ID No: 236, SEQ ID No: 238, SEQ ID No: 240, SEQ ID No: 242, SEQ ID No: 244, SEQ ED No: 246, SEQ ID No: 248, SEQ ID No: 250, SEQ ID No: 252, SEQ ID No: 254, SEQ ID No: 256, SEQ ID No: 258, SEQ ID No: 260, SEQ ID No: 262, SEQ ID No: 264, SEQ ID No: 266, SEQ ID No: 268, SEQ ED No: 270, SEQ ID No: 272, SEQ ID No: 274, SEQ ID No: 276, SEQ ID No: 278, SEQ ID No: 280, SEQ ID No: 282, SEQ ED No: 284, SEQ ID No: 286, SEQ ED No: 288, SEQ ID No: 290, SEQ ED No: 292, SEQ ID No: 294, SEQ ID No: 296, SEQ ID No: 298, SEQ ID No:300, SEQ ID No: 302, SEQ ID No: 304, SEQ ID No: 306, SEQ ID No: 308, SEQ ID No: 310, SEQ ID No: 312, SEQ ID No: 314, SEQ ID No: 316, SEQ ID No: 318, SEQ ID No: 320, SEQ ID No: 322, SEQ ID No: 324, SEQ ID No: 326, SEQ ID No: 328, SEQ ID No: 330, SEQ ID No: 332, SEQ ID No: 334, SEQ ID No: 336, SEQ ID No: 338, SEQ ID No: 340, SEQ ID No: 342, SEQ ID No: 344, SEQ ID No: 346, SEQ ID No: 348, SEQ ID No: 350, SEQ ID No: 352, SEQ ID No: 354, SEQ ID No: 356, SEQ ID No: 358, SEQ ID No: 360, SEQ ID No: 362, SEQ ID No: 364, SEQ ID No: 366, SEQ ID No: 368, SEQ ID No: 370, SEQ ID Nor 372, SEQ ID No: 374, SEQ ID No: 376, SEQ ID No: 378, SEQ ID No: 380, SEQ ID No: 382, SEQ ID No: 384, SEQ ID No: 386, SEQ ID No: 388, SEQ ID No: 390, SEQ ID No: 392, SEQ ID No: 394, SEQ ID No: 396, SEQ ID No: 398, 400, SEQ ID No: 402, SEQ ID No: 404, SEQ ID No: 406, SEQ ID No: 408, SEQ ID No: 410, SEQ ID No: 412, SEQ ID No: 414, SEQ ID No: 416, SEQ ID No: 418, SEQ ID No: 420, SEQ ID No: 422, SEQ ID No: 424, SEQ ID No: 426, SEQ ID No: 428, SEQ ID No: 430, SEQ ID No: 432, SEQ ID No: 434, SEQ ID No: 436, SEQ ID No: 438, SEQ ID No: 440, SEQ ID No: 442, SEQ ID No: 444, SEQ ID No: 446, SEQ ID No: 448, SEQ ID No: 450, SEQ ID No: 452, SEQ ID.No: 454, SEQ ID No: 456, SEQ ID No: 458, SEQ ID No: 460, SEQ ID No: 462, SEQ ID No: 464, SEQ ID No: 466, SEQ ID No: 468, SEQ ID No: 470, SEQ ID No: 472, SEQ ID No: 474, SEQ ID No: 476, SEQ ID No: 478, SEQ ID No: 480, SEQ ID No: 482, SEQ ID No: 484, SEQ ID No: 486, SEQ ED No: 488, SEQ ID No: 490, SEQ ED No: 492, SEQ ED No: ,4.94, SEQ ED No: 496, SEQ ED No: 498, SEQ ED No: 500, SEQ ID No: 502, SEQ ID No: 504, SEQ ID No: 506, SEQ ID No: 508, SEQ ED No: 510, SEQ ED No: 512, SEQ ID No: 514, SEQ ED No: 516, SEQ ID No: 518, SEQ ID No: 520, SEQ ID No: 522, SEQ ID No: 524, SEQ ED No: 526, SEQ ED No: 528, SEQ ID No: 530, SEQ ED No: 532, SEQ ID No: 534, SEQ ED No: 536, SEQ ED No: 538, SEQ ED No: 540, SEQ ED No: 542, SEQ ID No: 544, SEQ ID No: 546, SEQ ED No: 548, SEQ ED No: 550, SEQ ID No: 552, SEQ ID No: 554, SEQ ID No: 556, SEQ ED No: 558, SEQ ED No: 560, SEQ ED No: 562, SEQ ID No: 564, SEQ ID No: 566, SEQ ED No: 568, SEQ ID No: 570, SEQ ED No: 572, SEQ ID No: 574, SEQ ID No: 576, SEQ ID No: 578, SEQ ID No: 580, SEQ ED No: 582, SEQ ID No: 584, SEQ ID No: 586, SEQ ED No: 588, SEQ ED No: 590, SEQ ID No: 592, SEQ ID No: 594, SEQ ID No: 596, SEQ ED No: 598, SEQ ED No:600, SEQ ED No: 602, SEQ ID No: 604, SEQ ID No: 606, SEQ ED No: 608, SEQ ED No: 610, SEQ ED No: 612, SEQ ID No: 614, SEQ ID No: 616, SEQ ED No: 618, SEQ ED No: 620, SEQ ED No: 622, SEQ ID No: 624, SEQ ID No: 626, SEQ ED No: 628, SEQ ED No: 630, SEQ ED No: 632, SEQ ID No: 634, SEQ ID No: 636, SEQ ID No: 638, SEQ ID No: 640, SEQ ED No: 642, SEQ ID No: 644, SEQ ID No: 646, SEQ ED No: 648, SEQ ED No: 650, SEQ ED No: 652, SEQ ID No: 654, SEQ ID No: 656, SEQ ED No: 658, SEQ ED No: 660, SEQ ED No: 662, SEQ ID No: 664, SEQ ID No: 666, SEQ ED No: 668, SEQ ED No: 670, SEQ ED No: 672, SEQ ID No: 674, SEQ ID No: 676, SEQ ED No: 678, SEQ ID No: 680, SEQ ID No: 682, SEQ ID No: 684,-SEQ ID No: 686, SEQ ED No: 688, SEQ ED No: 690, SEQ ED No: 692, SEQ ID No: 694, SEQ ID No: 696, SEQ ED No: 698, SEQ ED No: 700, SEQ ED No: 702, SEQ ID No: 704, SEQ ID No: 706, SEQ ED No: 708, SEQ ED No: 710, SEQ ED No: 712, SEQ ID No: 714, SEQ ID No: 716, SEQ ED No: 718, SEQ ED No: 720, SEQ ED No: 722, SEQ ID No: 724, SEQ ID No: 726, SEQ ED No: 728, SEQ ED No: 730, SEQ ED No: 732, SEQ ID No: 734, SEQ ID No: 736, SEQ ED No: 738, SEQ ED No: 740, SEQ ED No: 742, SEQ ID No: 744, SEQ ID No: 746, SEQ ED No: 748, SEQ ED No: 750, SEQ ED No: 752, SEQ ID No: 754, SEQ ED No: 756, SEQ ED No: 758, SEQ ED No: 760, SEQ ED No: 762, SEQ ED No: 764, SEQ ED No: 766, SEQ ED No: 768, SEQ ED No: 770, SEQ ED No: 772, SEQ ID No: 774, SEQ ED No: 776, SEQ ID No: 778, SEQ ED No: 780, SEQ ID No: 782, SEQ ID No: 784, SEQ ID No: 786, SEQ ID No: 788, SEQ ID No: 790, SEQ ID No: 792, SEQ ID No: 794, SEQ ID No: 796, SEQ ID No: 798, SEQ ID No: 800, SEQ ED No: 802, SEQ ID No: 804, SEQ ED No: 806, SEQ ED No: 808, SEQ ED No: 810, SEQ ED No: 812, SEQ ED No: 814, SEQ ED No: 816, SEQ ED No: 818, SEQ ED No: 820, SEQ ED No: 822, SEQ ID No: 824, SEQ ED No: 826, SEQ ED No: 828, SEQ ED No: 830, SEQ ID No: 832, SEQ ID No: 834, SEQ ED No: 836, SEQ ED No: 838, SEQ ED No: 840, SEQ ID No: 842, SEQ ID No: 844, SEQ ED No: 846, SEQ ID No: 848, SEQ ID No: 850, SEQ ED No: 852, SEQ ED No: 854, SEQ ID No: 856, SEQ ED No: 858, SEQ ED No: 860.

55. The method of Claim 54, wherein the isolated protein is part of a multi-enzyme composition.

56. A method for degrading a protein into lower molecular weight proteins or amino acids, comprising contacting the protein with at least one multi-enzyme composition of any one of Claims 49-51.

57. A method for metabolizing a protein into lower molecular weight proteins or amino acids, comprising contacting the protein with at least one multi-enzyme composition of any one of Claims 49-51.

58. A feed additive comprising at least one protein of Claim 10.

59. The feed additive of Claim 58, wherein the utilizable protein content is higher than that of the feed material without the feed additive.

60. A method of improving the performance of an animal which comprises administering to the animal the feed additive of Claims 58 or 59.

61. A method for improving the nutritional quality of an animal feed comprising adding the feed additive of Claims 58 or 59 to an animal feed.

62. A method for removing stains from a fabric, comprising contacting the stained material with at least one isolated protein of Claim 10.

63. The method of Claim 62, wherein the fabric is carpet or clothing.

64. A method for washing fabric, comprising contacting the fabric with at least one isolated protein of Claim 10.

65. A method for enhancing the cleaning ability of a detergent composition, comprising adding at least one isolated protein of Claim 10 to the detergent composition.

66. A method for enhancing the cleaning ability of a detergent composition, comprising adding at least one multi-enzyme composition of any one of Claims 49-51 to the detergent composition.

67. A detergent composition, comprising at least one isolated protein of Claim 10 and at least one surfactant.

68. A detergent composition, comprising at least one multi-enzyme composition of any one of Claims 49-51 and at least one surfactant.

69. A method for improving the nutritional quality of food comprising adding to the food at least one isolated protein of Claim 10.

70. A method for improving the nutritional quality of food comprising pretreating the food with at least one isolated protein of Claim 10.

71. A method for improving the nutritional quality of animal feed comprising adding to the animal feed at least one isolated protein of Claim 10.

72. A method for improving the nutritional quality of animal feed comprising pretreating the feed with at least one isolated protein of Claim 10.

73. A genetically modified organism comprising at least one nucleic acid sequence encoding al least one protein of Claim 10, in which the activity of one or more of the proteins of claim 10 is upregulated, the activity of one or more of the proteins of claim 10 downregulated, or the activity of one or more of the proteins of claim 10 is upregulated and the activity of one or more of the proteins of claim 10 is downregulated.